Category Archives: Science News

There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Improvements of Sound Localization Abilities by the Facial Ruff of the Barn Owl (Tyto alba) as Demonstrated by Virtual Ruff Removal:

When sound arrives at the eardrum it has already been filtered by the body, head, and outer ear. This process is mathematically described by the head-related transfer functions (HRTFs), which are characteristic for the spatial position of a sound source and for the individual ear. HRTFs in the barn owl (Tyto alba) are also shaped by the facial ruff, a specialization that alters interaural time differences (ITD), interaural intensity differences (ILD), and the frequency spectrum of the incoming sound to improve sound localization. Here we created novel stimuli to simulate the removal of the barn owl’s ruff in a virtual acoustic environment, thus creating a situation similar to passive listening in other animals, and used these stimuli in behavioral tests. HRTFs were recorded from an owl before and after removal of the ruff feathers. Normal and ruff-removed conditions were created by filtering broadband noise with the HRTFs. Under normal virtual conditions, no differences in azimuthal head-turning behavior between individualized and non-individualized HRTFs were observed. The owls were able to respond differently to stimuli from the back than to stimuli from the front having the same ITD. By contrast, such a discrimination was not possible after the virtual removal of the ruff. Elevational head-turn angles were (slightly) smaller with non-individualized than with individualized HRTFs. The removal of the ruff resulted in a large decrease in elevational head-turning amplitudes. The facial ruff a) improves azimuthal sound localization by increasing the ITD range and b) improves elevational sound localization in the frontal field by introducing a shift of iso-ILD lines out of the midsagittal plane, which causes ILDs to increase with increasing stimulus elevation. The changes at the behavioral level could be related to the changes in the binaural physical parameters that occurred after the virtual removal of the ruff. These data provide new insights into the function of external hearing structures and open up the possibility to apply the results on autonomous agents, creation of virtual auditory environments for humans, or in hearing aids.

Correlating Molecular Phylogeny with Venom Apparatus Occurrence in Panamic Auger Snails (Terebridae):

Central to the discovery of neuroactive compounds produced by predatory marine snails of the superfamily Conoidea (cone snails, terebrids, and turrids) is identifying those species with a venom apparatus. Previous analyses of western Pacific terebrid specimens has shown that some Terebridae groups have secondarily lost their venom apparatus. In order to efficiently characterize terebrid toxins, it is essential to devise a key for identifying which species have a venom apparatus. The findings presented here integrate molecular phylogeny and the evolution of character traits to infer the presence or absence of the venom apparatus in the Terebridae. Using a combined dataset of 156 western and 33 eastern Pacific terebrid samples, a phylogenetic tree was constructed based on analyses of 16S, COI and 12S mitochondrial genes. The 33 eastern Pacific specimens analyzed represent four different species: Acus strigatus, Terebra argyosia, T. ornata, and T. cf. formosa. Anatomical analysis was congruent with molecular characters, confirming that species included in the clade Acus do not have a venom apparatus, while those in the clade Terebra do. Discovery of the association between terebrid molecular phylogeny and the occurrence of a venom apparatus provides a useful tool for effectively identifying the terebrid lineages that may be investigated for novel pharmacological active neurotoxins, enhancing conservation of this important resource, while providing supplementary information towards understanding terebrid evolutionary diversification.

Effect before Cause: Supramodal Recalibration of Sensorimotor Timing:

Our motor actions normally generate sensory events, but how do we know which events were self generated and which have external causes? Here we use temporal adaptation to investigate the processing stage and generality of our sensorimotor timing estimates. Adaptation to artificially-induced delays between action and event can produce a startling percept–upon removal of the delay it feels as if the sensory event precedes its causative action. This temporal recalibration of action and event occurs in a quantitatively similar manner across the sensory modalities. Critically, it is robust to the replacement of one sense during the adaptation phase with another sense during the test judgment. Our findings suggest a high-level, supramodal recalibration mechanism. The effects are well described by a simple model which attempts to preserve the expected synchrony between action and event, but only when causality indicates it is reasonable to do so. We further demonstrate that this model successfully characterises related adaptation data from outside the sensorimotor domain.

Visual Properties of Transgenic Rats Harboring the Channelrhodopsin-2 Gene Regulated by the Thy-1.2 Promoter:

Channelrhodopsin-2 (ChR2), one of the archea-type rhodopsins from green algae, is a potentially useful optogenetic tool for restoring vision in patients with photoreceptor degeneration, such as retinitis pigmentosa. If the ChR2 gene is transferred to retinal ganglion cells (RGCs), which send visual information to the brain, the RGCs may be repurposed to act as photoreceptors. In this study, by using a transgenic rat expressing ChR2 specifically in the RGCs under the regulation of a Thy-1.2 promoter, we tested the possibility that direct photoactivation of RGCs could restore effective vision. Although the contrast sensitivities of the optomotor responses of transgenic rats were similar to those observed in the wild-type rats, they were enhanced for visual stimuli of low-spatial frequency after the degeneration of native photoreceptors. This result suggests that the visual signals derived from the ChR2-expressing RGCs were reinterpreted by the brain to form behavior-related vision.

A Decade Later, How Much of Rwanda’s Musculoskeletal Impairment Is Caused by the War in 1994 and by Related Violence?:

In 1994 there was a horrific genocide in Rwanda following years of tension, resulting in the murder of at least 800,000 people. Although many people were injured in addition to those killed, no attempt has been made to assess the lasting burden of physical injuries related to these events. The aim of this study was to estimate the current burden of musculoskeletal impairment (MSI) attributable to the 1994 war and related violence. A national cross-sectional survey of MSI was conducted in Rwanda. 105 clusters of 80 people were selected through probability proportionate to size sampling. Households within clusters were selected through compact segment sampling. Enumerated people answered a seven-question screening test to assess whether they might have an MSI. Those who were classed as potential cases in the screening test were examined and interviewed by a physiotherapist, using a standard protocol that recorded the site, nature, cause, and severity of the MSI. People with MSI due to trauma were asked whether this trauma occurred during the 1990-1994 war or during the episodes that preceded or followed this war. Out of 8,368 people enumerated, 6,757 were available for screening and examination (80.8%). 352 people were diagnosed with an MSI (prevalence = 5.2%, 95% CI = 4.5-5.9%). 106 cases of MSI (30.6%) were classified as resulting from trauma, based on self-report and the physiotherapist’s assessment. Of these, 14 people (13.2%) reported that their trauma-related MSI occurred during the 1990-1994 war, and a further 7 (6.6%) that their trauma-related MSI occurred during the violent episodes that preceded and followed the war, giving an overall prevalence of trauma-related MSI related to the 1990-1994 war of 0.3% (95% CI = 0.2-0.4%). A decade on, the overall prevalence of MSI was relatively high in Rwanda but few cases appeared to be the result of the 1994 war or related violence.

There are 14 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Experience Matters: Females Use Smell to Select Experienced Males for Paternal Care:

Mate choice and mating preferences often rely on the information content of signals exchanged between potential partners. In species where a female’s reproduction is the terminal event in life it is to be expected that females choose high quality males and assess males using some honest indicator of male quality. The Nereidid polychaete, Neanthes acuminata, exhibits monogamous pairing and the release of eggs by females terminates her life and larval success relies entirely on a male’s ability to provide paternal care. As such females should have developed reliable, condition-dependent criteria to choose mates to guarantee survival and care for offspring. We show that females actively chose males experienced in fatherhood over others. In the absence of experienced males dominance, as evident from male-male fights, is utilized for mate selection. The preference for experienced males is not affected by previous social interactions between the individuals. We show that the choice of the partner is based on chemical signals demonstrating a ‘scent of experience’ to females providing evidence for the role of chemical signals in sexual selection for paternal care adding to our understanding of the mechanisms regulating condition-dependent mate choice.

Why Amphibians Are More Sensitive than Mammals to Xenobiotics:

Dramatic declines in amphibian populations have been described all over the world since the 1980s. The evidence that the sensitivity to environmental threats is greater in amphibians than in mammals has been generally linked to the observation that amphibians are characterized by a rather permeable skin. Nevertheless, a numerical comparison of data of percutaneous (through the skin) passage between amphibians and mammals is lacking. Therefore, in this investigation we have measured the percutaneous passage of two test molecules (mannitol and antipyrine) and three heavily used herbicides (atrazine, paraquat and glyphosate) in the skin of the frog Rana esculenta (amphibians) and of the pig ear (mammals), by using the same experimental protocol and a simple apparatus which minimizes the edge effect, occurring when the tissue is clamped in the usually used experimental device.
The percutaneous passage (P) of each substance is much greater in frog than in pig. LogP is linearly related to logKow (logarithm of the octanol-water partition coefficient). The measured P value of atrazine was about 134 times larger than that of glyphosate in frog skin, but only 12 times in pig ear skin. The FoD value (Pfrog/Ppig) was 302 for atrazine, 120 for antipyrine, 66 for mannitol, 29 for paraquat, and 26 for glyphosate.
The differences in structure and composition of the skin between amphibians and mammals are discussed.

Chimerism in Wild Adult Populations of the Broadcast Spawning Coral Acropora millepora on the Great Barrier Reef:

Chimeras are organisms containing tissues or cells of two or more genetically distinct individuals, and are known to exist in at least nine phyla of protists, plants, and animals. Although widespread and common in marine invertebrates, the extent of chimerism in wild populations of reef corals is unknown. The extent of chimerism was explored within two populations of a common coral, Acropora millepora, on the Great Barrier Reef, Australia, by using up to 12 polymorphic DNA microsatellite loci. At least 2% and 5% of Magnetic Island and Pelorus Island populations of A. millepora, respectively, were found to be chimeras (3% overall), based on conservative estimates. A slightly less conservative estimate indicated that 5% of colonies in each population were chimeras. These values are likely to be vast underestimates of the true extent of chimerism, as our sampling protocol was restricted to a maximum of eight branches per colony, while most colonies consist of hundreds of branches. Genotypes within chimeric corals showed high relatedness, indicating that genetic similarity is a prerequisite for long-term acceptance of non-self genotypes within coral colonies. While some brooding corals have been shown to form genetic chimeras in their early life history stages under experimental conditions, this study provides the first genetic evidence of the occurrence of coral chimeras in the wild and of chimerism in a broadcast spawning species. We hypothesize that chimerism is more widespread in corals than previously thought, and suggest that this has important implications for their resilience, potentially enhancing their capacity to compete for space and respond to stressors such as pathogen infection.

New this morning in PLoS ONE, PLoS Biology and PLoS Medicine. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers:
Mandatory Disclosure of Pharmaceutical Industry-Funded Events for Health Professionals:

We are in a period of unprecedented scrutiny of the relationships between the pharmaceutical industry and doctors [1]-[4]. Legislators are now considering how they might become involved in the regulation of these practices. This is a telling comment on the perceived failure of the medical profession to regulate itself and of self-regulation by industry. But reliable and comprehensive data on the nature and extent of industry sponsorship are rare. Several states in the US have mandatory disclosure laws for physician payments, but these data have proved difficult to access and analyse [5]. The US Congress is considering new mechanisms for revealing industry-professional interactions (the so-called “Sunshine” Acts) [6],[7]…

Somatosensory Cortices Are Required for the Acquisition of Morphine-Induced Conditioned Place Preference:

Sensory system information is thought to play an important role in drug addiction related responses. However, how somatic sensory information participates in the drug related behaviors is still unclear. Many studies demonstrated that drug addiction represents a pathological usurpation of neural mechanisms of learning and memory that normally relate to the pursuit of rewards. Thus, elucidate the role of somatic sensory in drug related learning and memory is of particular importance to understand the neurobiological mechanisms of drug addiction. In the present study, we investigated the role of somatosensory system in reward-related associative learning using the conditioned place preference model. Lesions were made in somatosensory cortices either before or after conditioning training. We found that lesion of somatosensory cortices before, rather than after morphine conditioning impaired the acquisition of place preference. These results demonstrate that somatosensory cortices are necessary for the acquisition but not retention of morphine induced place preference.

Evolutionary History of the HAP2/GCS1 Gene and Sexual Reproduction in Metazoans:

The HAP2/GCS1 gene first appeared in the common ancestor of plants, animals, and protists, and is required in the male gamete for fusion to the female gamete in the unicellular organisms Chlamydomonas and Plasmodium. We have identified a HAP2/GCS1 gene in the genome sequence of the sponge Amphimedon queenslandica. This finding provides a continuous evolutionary history of HAP2/GCS1 from unicellular organisms into the metazoan lineage. Divergent versions of the HAP2/GCS1 gene are also present in the genomes of some but not all arthropods. By examining the expression of the HAP2/GCS1 gene in the cnidarian Hydra, we have found the first evidence supporting the hypothesis that HAP2/GCS1 was used for male gamete fusion in the ancestor of extant metazoans and that it retains that function in modern cnidarians.

A Simple Rule for Proteins to Follow:

Proteins are the workhorses of cells, acting as enzymes, structural elements, and signal transducers. The tremendous variability in proteins’ chemical and physical properties is achieved through the manner in which they are made–by the mixing and matching of a set of basic building blocks known as amino acids. Each amino acid consists of a carbon atom attached to an amine group, a carboxyl group, a hydrogen atom, and one of 22 structurally and chemically distinct side groups. When a cell builds a protein, it uses the instructions encoded in a corresponding gene to tell it which amino acids to use, and in what order. A new protein is assembled front-to-back, with each new amino acid added to the growing chain by hooking its amine group to the carboxyl group of the previous amino acid…

An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum:

Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to acclimate their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0-0.5 h), an intermediate acclimation phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiance have been identified.

There are 21 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Extreme Cranial Ontogeny in the Upper Cretaceous Dinosaur Pachycephalosaurus:

Extended neoteny and late stage allometric growth increase morphological disparity between growth stages in at least some dinosaurs. Coupled with relatively low dinosaur density in the Upper Cretaceous of North America, ontogenetic transformational representatives are often difficult to distinguish. For example, many hadrosaurids previously reported to represent relatively small lambeosaurine species were demonstrated to be juveniles of the larger taxa. Marginocephalians (pachycephalosaurids + ceratopsids) undergo comparable and extreme cranial morphological change during ontogeny. Cranial histology, morphology and computer tomography reveal patterns of internal skull development that show the purported diagnostic characters for the pachycephalosaurids Dracorex hogwartsia and Stygimoloch spinifer are ontogenetically derived features. Coronal histological sections of the frontoparietal dome of an adult Pachycephalosaurus wyomingensis reveal a dense structure composed of metaplastic bone with a variety of extremely fibrous and acellular tissue. Coronal histological sections and computer tomography of a skull and frontoparietal dome of Stygimoloch spinifer reveal an open intrafrontal suture indicative of a subadult stage of development. These dinosaurs employed metaplasia to rapidly grow and change the size and shape of their horns, cranial ornaments and frontoparietal domes, resulting in extreme cranial alterations during late stages of growth. We propose that Dracorex hogwartsia, Stygimoloch spinifer and Pachycephalosaurus wyomingensis are the same taxon and represent an ontogenetic series united by shared morphology and increasing skull length. Dracorex hogwartsia (juvenile) and Stygimoloch spinifer (subadult) are reinterpreted as younger growth stages of Pachycephalosaurus wyomingensis (adult). This synonymy reduces the number of pachycephalosaurid taxa from the Upper Cretaceous of North America and demonstrates the importance of cranial ontogeny in evaluating dinosaur diversity and taxonomy. These growth stages reflect a continuum rather than specific developmental steps defined by “known” terminal morphologies.

Timing of Locomotor Activity Circadian Rhythms in Caenorhabditis elegans:

Circadian rhythms are driven by endogenous biological clocks and are synchronized to environmental cues. The chronobiological study of Caenorhabditis elegans, an extensively used animal model for developmental and genetic research, might provide fundamental information about the basis of circadian rhythmicity in eukaryotes, due to its ease of use and manipulations, as well as availability of genetic data and mutant strains. The aim of this study is to fully characterize the circadian rhythm of locomotor activity in C. elegans, as well as a means for genetic screening in this nematode and the identification of circadian mutants. We have developed an infrared method to measure locomotor activity in C. elegans and found that, under constant conditions, although inter-individual variability is present, circadian periodicity shows a population distribution of periods centered at 23.9±0.4 h and is temperature-compensated. Locomotor activity is entrainable by light-dark cycles and by low-amplitude temperature cycles, peaking around the night-day transition and day, respectively. In addition, lin-42(mg152) or lin-42(n1089) mutants (bearing a mutation in the lin-42 gene, homolog to the per gene) exhibit a significantly longer circadian period of 25.2±0.4 h or 25.6±0.5 h, respectively. Our results represent a complete description of the locomotor activity rhythm in C. elegans, with a methodology that allowed us to uncover three of the key features of circadian systems: entrainment, free-running and temperature compensation. In addition, abnormal circadian periods in clock mutants suggest a common molecular machinery responsible for circadian rhythmicity. Our analysis of circadian rhythmicity in C. elegans opens the possibility for further screening for circadian mutations in this species.

A Validated Methodology for Genetic Identification of Tuna Species (Genus Thunnus):

Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue. After testing several genetic markers, a complete discrimination of the eight tuna species was achieved using Forensically Informative Nucleotide Sequencing based primarily on the sequence variability of the hypervariable genetic marker mitochondrial DNA control region (mtDNA CR), followed, in some specific cases, by a second validation by a nuclear marker rDNA first internal transcribed spacer (ITS1). This methodology was able to distinguish all tuna species, including those belonging to the subgenus Neothunnus that are very closely related, and in consequence can not be differentiated with other genetic markers of lower variability. This methodology also took into consideration the presence of introgression that has been reported in past studies between T. thynnus, T. orientalis and T. alalunga. Finally, we applied the methodology to cross-check the species identity of 26 processed tuna samples. Using the combination of two genetic markers, one mitochondrial and another nuclear, allows a full discrimination between all eight tuna species. Unexpectedly, the genetic marker traditionally used for DNA barcoding, cytochrome oxidase 1, could not differentiate all species, thus its use as a genetic marker for tuna species identification is questioned.

There are 18 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Experimental Infection of a North American Raptor, American Kestrel (Falco sparverius), with Highly Pathogenic Avian Influenza Virus (H5N1):

Several species of wild raptors have been found in Eurasia infected with highly pathogenic avian influenza virus (HPAIV) subtype H5N1. Should HPAIV (H5N1) reach North America in migratory birds, species of raptors are at risk not only from environmental exposure, but also from consuming infected birds and carcasses. In this study we used American kestrels as a representative species of a North American raptor to examine the effects of HPAIV (H5N1) infection in terms of dose response, viral shedding, pathology, and survival. Our data showed that kestrels are highly susceptible to HPAIV (H5N1). All birds typically died or were euthanized due to severe neurologic disease within 4-5 days of inoculation and shed significant amounts of virus both orally and cloacally, regardless of dose administered. The most consistent microscopic lesions were necrosis in the brain and pancreas. This is the first experimental study of HPAIV infection in a North American raptor and highlights the potential risks to birds of prey if HPAIV (H5N1) is introduced into North America.

Fast and Flexible Selection with a Single Switch:

Selection methods that require only a single-switch input, such as a button click or blink, are potentially useful for individuals with motor impairments, mobile technology users, and individuals wishing to transmit information securely. We present a single-switch selection method, “Nomon,” that is general and efficient. Existing single-switch selection methods require selectable options to be arranged in ways that limit potential applications. By contrast, traditional operating systems, web browsers, and free-form applications (such as drawing) place options at arbitrary points on the screen. Nomon, however, has the flexibility to select any point on a screen. Nomon adapts automatically to an individual’s clicking ability; it allows a person who clicks precisely to make a selection quickly and allows a person who clicks imprecisely more time to make a selection without error. Nomon reaps gains in information rate by allowing the specification of beliefs (priors) about option selection probabilities and by avoiding tree-based selection schemes in favor of direct (posterior) inference. We have developed both a Nomon-based writing application and a drawing application. To evaluate Nomon’s performance, we compared the writing application with a popular existing method for single-switch writing (row-column scanning). Novice users wrote 35% faster with the Nomon interface than with the scanning interface. An experienced user (author TB, with 10 hours practice) wrote at speeds of 9.3 words per minute with Nomon, using 1.2 clicks per character and making no errors in the final text.

Parallel Explicit and Implicit Control of Reaching:

Human movement can be guided automatically (implicit control) or attentively (explicit control). Explicit control may be engaged when learning a new movement, while implicit control enables simultaneous execution of multiple actions. Explicit and implicit control can often be assigned arbitrarily: we can simultaneously drive a car and tune the radio, seamlessly allocating implicit or explicit control to either action. This flexibility suggests that sensorimotor signals, including those that encode spatially overlapping perception and behavior, can be accurately segregated to explicit and implicit control processes. We tested human subjects’ ability to segregate sensorimotor signals to parallel control processes by requiring dual (explicit and implicit) control of the same reaching movement and testing for interference between these processes. Healthy control subjects were able to engage dual explicit and implicit motor control without degradation of performance compared to explicit or implicit control alone. We then asked whether segregation of explicit and implicit motor control can be selectively disrupted by studying dual-control performance in subjects with no clinically manifest neurologic deficits in the presymptomatic stage of Huntington’s disease (HD). These subjects performed successfully under either explicit or implicit control alone, but were impaired in the dual-control condition. The human nervous system can exert dual control on a single action, and is therefore able to accurately segregate sensorimotor signals to explicit and implicit control. The impairment observed in the presymptomatic stage of HD points to a possible crucial contribution of the striatum to the segregation of sensorimotor signals to multiple control processes.

There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Dominance, Politics, and Physiology: Voters’ Testosterone Changes on the Night of the 2008 United States Presidential Election:

Background
Political elections are dominance competitions. When men win a dominance competition, their testosterone levels rise or remain stable to resist a circadian decline; and when they lose, their testosterone levels fall. However, it is unknown whether this pattern of testosterone change extends beyond interpersonal competitions to the vicarious experience of winning or losing in the context of political elections. Women’s testosterone responses to dominance competition outcomes are understudied, and to date, a clear pattern of testosterone changes in response to winning and losing dominance competitions has not emerged. The present study investigated voters’ testosterone responses to the outcome of the 2008 United States Presidential election. 183 participants provided multiple saliva samples before and after the winner was announced on Election Night. The results show that male Barack Obama voters (winners) had stable post-outcome testosterone levels, whereas testosterone levels dropped in male John McCain and Robert Barr voters (losers). There were no significant effects in female voters. The findings indicate that male voters exhibit biological responses to the realignment of a country’s dominance hierarchy as if they participated in an interpersonal dominance contest.

Oldest Evidence of Toolmaking Hominins in a Grassland-Dominated Ecosystem:

Major biological and cultural innovations in late Pliocene hominin evolution are frequently linked to the spread or fluctuating presence of C4 grass in African ecosystems. Whereas the deep sea record of global climatic change provides indirect evidence for an increase in C4 vegetation with a shift towards a cooler, drier and more variable global climatic regime beginning approximately 3 million years ago (Ma), evidence for grassland-dominated ecosystems in continental Africa and hominin activities within such ecosystems have been lacking. We report stable isotopic analyses of pedogenic carbonates and ungulate enamel, as well as faunal data from ~2.0 Ma archeological occurrences at Kanjera South, Kenya. These document repeated hominin activities within a grassland-dominated ecosystem. These data demonstrate what hitherto had been speculated based on indirect evidence: that grassland-dominated ecosystems did in fact exist during the Plio-Pleistocene, and that early Homo was active in open settings. Comparison with other Oldowan occurrences indicates that by 2.0 Ma hominins, almost certainly of the genus Homo, used a broad spectrum of habitats in East Africa, from open grassland to riparian forest. This strongly contrasts with the habitat usage of Australopithecus, and may signal an important shift in hominin landscape usage.

Discovery of the Largest Orbweaving Spider Species: The Evolution of Gigantism in Nephila:

More than 41,000 spider species are known with about 400-500 added each year, but for some well-known groups, such as the giant golden orbweavers, Nephila, the last valid described species dates from the 19th century. Nephila are renowned for being the largest web-spinning spiders, making the largest orb webs, and are model organisms for the study of extreme sexual size dimorphism (SSD) and sexual biology. Here, we report on the discovery of a new, giant Nephila species from Africa and Madagascar, and review size evolution and SSD in Nephilidae. We formally describe N. komaci sp. nov., the largest web spinning species known, and place the species in phylogenetic context to reconstruct the evolution of mean size (via squared change parsimony). We then test female and male mean size correlation using phylogenetically independent contrasts, and simulate nephilid body size evolution using Monte Carlo statistics. Nephila females increased in size almost monotonically to establish a mostly African clade of true giants. In contrast, Nephila male size is effectively decoupled and hovers around values roughly one fifth of female size. Although N. komaci females are the largest Nephila yet discovered, the males are also large and thus their SSD is not exceptional.

Evidence for Repeated Independent Evolution of Migration in the Largest Family of Bats:

How migration evolved represents one of the most poignant questions in evolutionary biology. While studies on the evolution of migration in birds are well represented in the literature, migration in bats has received relatively little attention. Yet, more than 30 species of bats are known to migrate annually from breeding to non-breeding locations. Our study is the first to test hypotheses on the evolutionary history of migration in bats using a phylogenetic framework. In addition to providing a review of bat migration in relation to existing hypotheses on the evolution of migration in birds, we use a previously published supertree to formulate and test hypotheses on the evolutionary history of migration in bats. Our results suggest that migration in bats has evolved independently in several lineages potentially as the need arises to track resources (food, roosting site) but not through a series of steps from short- to long-distance migrants, as has been suggested for birds. Moreover, our analyses do not indicate that migration is an ancestral state but has relatively recently evolved in bats. Our results also show that migration is significantly less likely to evolve in cave roosting bats than in tree roosting species. This is the first study to provide evidence that migration has evolved independently in bat lineages that are not closely related. If migration evolved as a need to track seasonal resources or seek adequate roosting sites, climate change may have a pivotal impact on bat migratory habits. Our study provides a strong framework for future research on the evolution of migration in chiropterans.

New Episodic Learning Interferes with the Reconsolidation of Autobiographical Memories:

It is commonly assumed that, with time, an initially labile memory is transformed into a permanent one via a process of consolidation. Yet, recent evidence indicates that memories can return to a fragile state again when reactivated, requiring a period of reconsolidation. In the study described here, we found that participants who memorized a story immediately after they had recalled neutral and emotional experiences from their past were impaired in their memory for the neutral (but not for the emotional) experiences one week later. The effect of learning the story depended critically on the preceding reactivation of the autobiographical memories since learning without reactivation had no effect. These results suggest that new learning impedes the reconsolidation of neutral autobiographical memories.

Five Years of Access and Activism:

In April 2009, we marked the five year anniversary of PLoS Medicine’s first call for papers with an editorial titled “A Medical Journal for the World’s Health Priorities” [1]. The editorial was a renewed and revitalized call for papers, announcing a “refocusing of the journal’s priorities.” Going forward, we said, we would prioritize papers addressing those diseases with the greatest global burden. We would also aim to be as broad a journal as possible, publishing papers that explored not just biological causes of illness, but also social, environmental, and political determinants of health. Six months later, as we now mark the journal’s official five-year anniversary (our launch issue was October 19, 2004), has our refocused scope had any impact on what we publish?

Male or Female? For Honeybees, a Single Gene Makes All the Difference:

Male or female? How genes send a developing embryo down one path or the other varies substantially among species. In honeybees, it boils down to whether a particular chromosomal location has the same version of a gene (called homozygous) or two different versions (heterozygous). Honeybees that have two different versions of the sex determination locus (SDL) develop female traits. Those that have two of the same version–or, more commonly, have only one version as a result of developing from an unfertilized egg–become male. This approach, known as complementary sex determination, is found in a number of social insects, yet is still poorly understood.

Sex Determination in Honeybees: Two Separate Mechanisms Induce and Maintain the Female Pathway:

Sexual differentiation is a fundamental process in the animal kingdom, and different species have evolved a bewildering diversity of mechanisms to generate the two sexes in the proper proportions. Sex determination in honeybees (Apis mellifera) provides an interesting and unusual system to study, as it is governed by heterozygosity of a single locus harbouring the complementary sex determiner gene (csd), in contrast to the well-studied sex chromosome system of Drosophila melanogaster. We show that the female sex determination pathway is exclusively induced by the csd gene in early embryogenesis. Later on and throughout development this inductive signal is maintained via a positive feedback loop of the feminizer (fem) gene, in which the Fem protein mediates its own synthesis. The findings reveal how the sex determination process in honeybees is realized by the regulation and function of two genes differing from Drosophila.

There are 19 new articles in PLoS ONE today.
But first, you need to look at the new Collection of articles – Structural Biology and Human Health: Medically Relevant Proteins from the SGC – in which you can see the protein structures in 3D, turn them around, zoom in and out, and do other manipulations of the embedded object, right there inside the articles. Read more about it in: A New Method for Publishing Three-Dimensional Content:

A new method for electronic publishing of articles with text linked to its interactive three dimensional content is described. The method is based on a single document containing a variety of objects such as formatted text, multiple three dimensional molecular objects, textured shapes and surfaces, data tables and graphs, chemical spreadsheets, alignments, etc. The 3D article can then be published for an online web delivery using the activeICM/active X components as well as be downloaded as a single file to be browsed with all its attached objects locally with the ICM browser. Both activeICM and ICM browser are freely available for the public. This method eliminates the need for multiple methods for the web and the local off-line delivery; it offers the dramatically enhanced, customizable and interactive delivery of article’s three dimensional content and data attachments in a single compact file.

See the explanation on everyONE blog and the first reactions by Dave Bath, Jean-Claude Bradley and Nick Anthis.

Also today – and as always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers – here are my own picks for the week:
Influenza A Gradual and Epochal Evolution: Insights from Simple Models:

The recurrence of influenza A epidemics has originally been explained by a “continuous antigenic drift” scenario. Recently, it has been shown that if genetic drift is gradual, the evolution of influenza A main antigen, the haemagglutinin, is punctuated. As a consequence, it has been suggested that influenza A dynamics at the population level should be approximated by a serial model. Here, simple models are used to test whether a serial model requires gradual antigenic drift within groups of strains with the same antigenic properties (antigenic clusters). We compare the effect of status based and history based frameworks and the influence of reduced susceptibility and infectivity assumptions on the transient dynamics of antigenic clusters. Our results reveal that the replacement of a resident antigenic cluster by a mutant cluster, as observed in data, is reproduced only by the status based model integrating the reduced infectivity assumption. This combination of assumptions is useful to overcome the otherwise extremely high model dimensionality of models incorporating many strains, but relies on a biological hypothesis not obviously satisfied. Our findings finally suggest the dynamical importance of gradual antigenic drift even in the presence of punctuated immune escape. A more regular renewal of susceptible pool than the one implemented in a serial model should be part of a minimal theory for influenza at the population level.

Temporal-Difference Reinforcement Learning with Distributed Representations:

Temporal-difference (TD) algorithms have been proposed as models of reinforcement learning (RL). We examine two issues of distributed representation in these TD algorithms: distributed representations of belief and distributed discounting factors. Distributed representation of belief allows the believed state of the world to distribute across sets of equivalent states. Distributed exponential discounting factors produce hyperbolic discounting in the behavior of the agent itself. We examine these issues in the context of a TD RL model in which state-belief is distributed over a set of exponentially-discounting “micro-Agents”, each of which has a separate discounting factor (γ). Each µAgent maintains an independent hypothesis about the state of the world, and a separate value-estimate of taking actions within that hypothesized state. The overall agent thus instantiates a flexible representation of an evolving world-state. As with other TD models, the value-error (δ) signal within the model matches dopamine signals recorded from animals in standard conditioning reward-paradigms. The distributed representation of belief provides an explanation for the decrease in dopamine at the conditioned stimulus seen in overtrained animals, for the differences between trace and delay conditioning, and for transient bursts of dopamine seen at movement initiation. Because each µAgent also includes its own exponential discounting factor, the overall agent shows hyperbolic discounting, consistent with behavioral experiments.

Balancing with Vibration: A Prelude for ‘Drift and Act’ Balance Control:

Stick balancing at the fingertip is a powerful paradigm for the study of the control of human balance. Here we show that the mean stick balancing time is increased by about two-fold when a subject stands on a vibrating platform that produces vertical vibrations at the fingertip (0.001 m, 15-50 Hz). High speed motion capture measurements in three dimensions demonstrate that vibration does not shorten the neural latency for stick balancing or change the distribution of the changes in speed made by the fingertip during stick balancing, but does decrease the amplitude of the fluctuations in the relative positions of the fingertip and the tip of the stick in the horizontal plane, A(x,y). The findings are interpreted in terms of a time-delayed “drift and act” control mechanism in which controlling movements are made only when controlled variables exceed a threshold, i.e. the stick survival time measures the time to cross a threshold. The amplitude of the oscillations produced by this mechanism can be decreased by parametric excitation. It is shown that a plot of the logarithm of the vibration-induced increase in stick balancing skill, a measure of the mean first passage time, versus the standard deviation of the A(x,y) fluctuations, a measure of the distance to the threshold, is linear as expected for the times to cross a threshold in a stochastic dynamical system. These observations suggest that the balanced state represents a complex time-dependent state which is situated in a basin of attraction that is of the same order of size. The fact that vibration amplitude can benefit balance control raises the possibility of minimizing risk of falling through appropriate changes in the design of footwear and roughness of the walking surfaces.

Some cool papers tonight in 4 out of 7 PLoS journals. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Short Telomeres in Hatchling Snakes: Erythrocyte Telomere Dynamics and Longevity in Tropical Pythons:

Telomere length (TL) has been found to be associated with life span in birds and humans. However, other studies have demonstrated that TL does not affect survival among old humans. Furthermore, replicative senescence has been shown to be induced by changes in the protected status of the telomeres rather than the loss of TL. In the present study we explore whether age- and sex-specific telomere dynamics affect life span in a long-lived snake, the water python (Liasis fuscus). Erythrocyte TL was measured using the Telo TAGGG TL Assay Kit (Roche). In contrast to other vertebrates, TL of hatchling pythons was significantly shorter than that of older snakes. However, during their first year of life hatchling TL increased substantially. While TL of older snakes decreased with age, we did not observe any correlation between TL and age in cross-sectional sampling. In older snakes, female TL was longer than that of males. When using recapture as a proxy for survival, our results do not support that longer telomeres resulted in an increased water python survival/longevity. In fish high telomerase activity has been observed in somatic cells exhibiting high proliferation rates. Hatchling pythons show similar high somatic cell proliferation rates. Thus, the increase in TL of this group may have been caused by increased telomerase activity. In older humans female TL is longer than that of males. This has been suggested to be caused by high estrogen levels that stimulate increased telomerase activity. Thus, high estrogen levels may also have caused the longer telomeres in female pythons. The lack of correlation between TL and age among old snakes and the fact that longer telomeres did not appear to affect python survival do not support that erythrocyte telomere dynamics has a major impact on water python longevity.

‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators:

Robustness is an intrinsic property of many biological systems. To quantify the robustness of a model that represents such a system, two approaches exist: global methods assess the volume in parameter space that is compliant with the proper functioning of the system; and local methods, in contrast, study the model for a given parameter set and determine its robustness. Local methods are fundamentally biased due to the a priori choice of a particular parameter set. Our ‘glocal’ analysis combines the two complementary approaches and provides an objective measure of robustness. We apply this method to two prominent, recent models of the cyanobacterial circadian oscillator. Our results allow discriminating the two models based on this analysis: both global and local measures of robustness favor one of the two models. The ‘glocal’ method also identifies key factors that influence robustness. For instance, we find that in both models the most fragile reactions are the ones that affect the concentration of the feedback component.

The Rewarding Aspects of Music Listening Are Related to Degree of Emotional Arousal:

Listening to music is amongst the most rewarding experiences for humans. Music has no functional resemblance to other rewarding stimuli, and has no demonstrated biological value, yet individuals continue listening to music for pleasure. It has been suggested that the pleasurable aspects of music listening are related to a change in emotional arousal, although this link has not been directly investigated. In this study, using methods of high temporal sensitivity we investigated whether there is a systematic relationship between dynamic increases in pleasure states and physiological indicators of emotional arousal, including changes in heart rate, respiration, electrodermal activity, body temperature, and blood volume pulse. Twenty-six participants listened to self-selected intensely pleasurable music and “neutral” music that was individually selected for them based on low pleasure ratings they provided on other participants’ music. The “chills” phenomenon was used to index intensely pleasurable responses to music. During music listening, continuous real-time recordings of subjective pleasure states and simultaneous recordings of sympathetic nervous system activity, an objective measure of emotional arousal, were obtained. Results revealed a strong positive correlation between ratings of pleasure and emotional arousal. Importantly, a dissociation was revealed as individuals who did not experience pleasure also showed no significant increases in emotional arousal. These results have broader implications by demonstrating that strongly felt emotions could be rewarding in themselves in the absence of a physically tangible reward or a specific functional goal.

Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization:

The origin of life has ever been attracting scientific inquiries. The RNA world hypothesis suggests that, before the evolution of DNA and protein, primordial life was based on RNA-like molecules both for information storage and chemical catalysis. In the simplest form, an RNA world consists of RNA molecules that can catalyze the replication of their own copies. Thus, an interesting question is whether a system of RNA-like replicators can increase its complexity through Darwinian evolution and approach the modern form of life. It is, however, known that simple natural selection acting on individual replicators is insufficient to account for the evolution of complexity due to the evolution of parasite-like templates. Two solutions have been suggested: compartmentalization of replicators by membranes (i.e., protocells) and spatial self-organization of a replicator population. Here, we make a direct comparison of the two suggestions by computer simulations. Our results show that the two suggestions can lead to unanticipated and contrasting consequences in the long-term evolution of replicating molecules. The results also imply a novel advantage in the spatial self-organization for the evolution of complexity in RNA-like replicator systems.

On the Track of DNA Methylation: An Interview with Adrian Bird:

The day school let out for the summer, my daughter and I packed our bags for Britain, where we had lived for a few months in 2006. Annie was eager to reconnect with her friends there, and I had arranged to conduct three interviews. In desperation and with the clock ticking, I struggled to fit my bulky recorder into my wheelie when it dawned on me that the “talk app” on my daughter’s iphone should be up to the job. You can imagine the reluctance and skepticism on the part of my 15-year-old, but she managed to get into the spirit and acquiesced.
First up on my schedule was Adrian Bird (Image 1), who holds the Buchanan Chair of Genetics at the University of Edinburgh and is also Director of the Wellcome Trust Centre for Cell Biology. Long before the word “epigenome” was coined, Bird began mapping the distribution of DNA methylation (occurring at the cytosine of CpG dinucleotides) in the genomes of a variety of species. His work emerged just as agarose gels, restriction enzymes, and Southern blots were being developed. Bird later spawned the idea of CpG islands, pockets of DNA rich in unmethylated CpGs and frequently found in conjunction with the promoter regions of mammalian genes. Bird’s observation provided a roadmap for disease gene discovery for about 15 years, until human genome draft sequences began to emerge.

There are 17 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Circadian Modulation of Gene Expression, but not Glutamate Uptake, in Mouse and Rat Cortical Astrocytes:

Circadian clocks control daily rhythms including sleep-wake, hormone secretion, and metabolism. These clocks are based on intracellular transcription-translation feedback loops that sustain daily oscillations of gene expression in many cell types. Mammalian astrocytes display circadian rhythms in the expression of the clock genes Period1 (Per1) and Period2 (Per2). However, a functional role for circadian oscillations in astrocytes is unknown. Because uptake of extrasynaptic glutamate depends on the presence of Per2 in astrocytes, we asked whether glutamate uptake by glia is circadian. We measured glutamate uptake, transcript and protein levels of the astrocyte-specific glutamate transporter, Glast, and the expression of Per1 and Per2 from cultured cortical astrocytes and from explants of somatosensory cortex. We found that glutamate uptake and Glast mRNA and protein expression were significantly reduced in Clock/Clock, Per2- or NPAS2-deficient glia. Uptake was augmented when the medium was supplemented with dibutyryl-cAMP or B27. Critically, glutamate uptake was not circadian in cortical astrocytes cultured from rats or mice or in cortical slices from mice. We conclude that glutamate uptake levels are modulated by CLOCK, PER2, NPAS2, and the composition of the culture medium, and that uptake does not show circadian variations.

Social Structure Predicts Genital Morphology in African Mole-Rats:

African mole-rats (Bathyergidae, Rodentia) exhibit a wide range of social structures, from solitary to eusocial. We previously found a lack of sex differences in the external genitalia and morphology of the perineal muscles associated with the phallus in the eusocial naked mole-rat. This was quite surprising, as the external genitalia and perineal muscles are sexually dimorphic in all other mammals examined. We hypothesized that the lack of sex differences in naked mole-rats might be related to their unusual social structure. We compared the genitalia and perineal muscles in three African mole-rat species: the naked mole-rat, the solitary silvery mole-rat, and the Damaraland mole-rat, a species considered to be eusocial, but with less reproductive skew than naked mole-rats. Our findings support a relationship between social structure, mating system, and sexual differentiation. Naked mole-rats lack sex differences in genitalia and perineal morphology, silvery mole-rats exhibit sex differences, and Damaraland mole-rats are intermediate. The lack of sex differences in naked mole-rats is not an attribute of all African mole-rats, but appears to have evolved in relation to their unusual social structure and reproductive biology.

Nutrient Enrichment and Food Web Composition Affect Ecosystem Metabolism in an Experimental Seagrass Habitat:

Food web composition and resource levels can influence ecosystem properties such as productivity and elemental cycles. In particular, herbivores occupy a central place in food webs as the species richness and composition of this trophic level may simultaneously influence the transmission of resource and predator effects to higher and lower trophic levels, respectively. Yet, these interactions are poorly understood. Using an experimental seagrass mesocosm system, we factorially manipulated water column nutrient concentrations, food chain length, and diversity of crustacean grazers to address two questions: (1) Does food web composition modulate the effects of nutrient enrichment on plant and grazer biomasses and stoichiometry? (2) Do ecosystem fluxes of dissolved oxygen and nutrients more closely reflect above-ground biomass and community structure or sediment processes? Nutrient enrichment and grazer presence generally had strong effects on biomass accumulation, stoichiometry, and ecosystem fluxes, whereas predator effects were weaker or absent. Nutrient enrichment had little effect on producer biomass or net ecosystem production but strongly increased seagrass nutrient content, ecosystem flux rates, and grazer secondary production, suggesting that enhanced production was efficiently transferred from producers to herbivores. Gross ecosystem production (oxygen evolution) correlated positively with above-ground plant biomass, whereas inorganic nutrient fluxes were unrelated to plant or grazer biomasses, suggesting dominance by sediment microbial processes. Finally, grazer richness significantly stabilized ecosystem processes, as predators decreased ecosystem production and respiration only in the zero- and one- species grazer treatments. Overall, our results indicate that consumer presence and species composition strongly influence ecosystem responses to nutrient enrichment, and that increasing herbivore diversity can stabilize ecosystem flux rates in the face of perturbations.

There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Chimpanzees Help Each Other upon Request:

The evolution of altruism has been explained mainly from ultimate perspectives. However, it remains to be investigated from a proximate point of view how and in which situations such social propensity is achieved. We investigated chimpanzees’ targeted helping in a tool transfer paradigm, and discuss the similarities and differences in altruism between humans and chimpanzees. Previously it has been suggested that chimpanzees help human experimenters by retrieving an object which the experimenter is trying to reach. In the present study, we investigated the importance of communicative interactions between chimpanzees themselves and the influence of conspecific partner’s request on chimpanzees’ targeted helping. We presented two tool-use situations (a stick-use situation and a straw-use situation) in two adjacent booths, and supplied non-corresponding tools to paired chimpanzees in the two booths. For example, a chimpanzee in the stick-use situation was supplied with a straw, and the partner in the straw-use situation possessed a stick. Spontaneous tool transfer was observed between paired chimpanzees. The tool transfer events occurred predominantly following recipients’ request. Even without any hope of reciprocation from the partner, the chimpanzees continued to help the partner as long as the partner required help. These results provide further evidence for altruistic helping in chimpanzees in the absence of direct personal gain or even immediate reciprocation. Our findings additionally highlight the importance of request as a proximate mechanism motivating prosocial behavior in chimpanzees whether between kin or non-kin individuals and the possible confounding effect of dominance on the symmetry of such interactions. Finally, in contrast to humans, our study suggests that chimpanzees rarely perform acts of voluntary altruism. Voluntary altruism in chimpanzees is not necessarily prompted by simple observation of another’s struggle to attain a goal and therefore an accurate understanding of others’ desires in the absence of communicative signals.

Understanding Ancient Hominin Dispersals Using Artefactual Data: A Phylogeographic Analysis of Acheulean Handaxes:

Reconstructing the dispersal patterns of extinct hominins remains a challenging but essential goal. One means of supplementing fossil evidence is to utilize archaeological evidence in the form of stone tools. Based on broad dating patterns, it has long been thought that the appearance of Acheulean handaxe technologies outside of Africa was the result of hominin dispersals, yet independent tests of this hypothesis remain rare. Cultural transmission theory leads to a prediction of a strong African versus non-African phylogeographic pattern in handaxe datasets, if the African Acheulean hypothesis is to be supported. Here, this prediction is tested using an intercontinental dataset of Acheulean handaxes and a biological phylogenetic method (maximum parsimony). The analyses produce a tree consistent with the phylogeographic prediction. Moreover, a bootstrap analysis provides evidence that this pattern is robust, and the maximum parsimony tree is also shown to be statistically different from a tree constrained by stone raw materials. These results demonstrate that nested analyses of behavioural data, utilizing methods drawn from biology, have the potential to shed light on ancient hominin dispersals. This is an encouraging prospect for human palaeobiology since sample sizes for lithic artefacts are many orders of magnitude higher than those of fossil data. These analyses also suggest that the sustained occurrence of Acheulean handaxe technologies in regions such as Europe and the Indian subcontinent resulted from dispersals by African hominin populations.

Understanding Others’ Regret: A fMRI Study:

Previous studies showed that the understanding of others’ basic emotional experiences is based on a “resonant” mechanism, i.e., on the reactivation, in the observer’s brain, of the cerebral areas associated with those experiences. The present study aimed to investigate whether the same neural mechanism is activated both when experiencing and attending complex, cognitively-generated, emotions. A gambling task and functional-Magnetic-Resonance-Imaging (fMRI) were used to test this hypothesis using regret, the negative cognitively-based emotion resulting from an unfavorable counterfactual comparison between the outcomes of chosen and discarded options. Do the same brain structures that mediate the experience of regret become active in the observation of situations eliciting regret in another individual? Here we show that observing the regretful outcomes of someone else’s choices activates the same regions that are activated during a first-person experience of regret, i.e. the ventromedial prefrontal cortex, anterior cingulate cortex and hippocampus. These results extend the possible role of a mirror-like mechanism beyond basic emotions.

Mapping Oil and Gas Development Potential in the US Intermountain West and Estimating Impacts to Species:

Many studies have quantified the indirect effect of hydrocarbon-based economies on climate change and biodiversity, concluding that a significant proportion of species will be threatened with extinction. However, few studies have measured the direct effect of new energy production infrastructure on species persistence. We propose a systematic way to forecast patterns of future energy development and calculate impacts to species using spatially-explicit predictive modeling techniques to estimate oil and gas potential and create development build-out scenarios by seeding the landscape with oil and gas wells based on underlying potential. We illustrate our approach for the greater sage-grouse (Centrocercus urophasianus) in the western US and translate the build-out scenarios into estimated impacts on sage-grouse. We project that future oil and gas development will cause a 7-19 percent decline from 2007 sage-grouse lek population counts and impact 3.7 million ha of sagebrush shrublands and 1.1 million ha of grasslands in the study area. Maps of where oil and gas development is anticipated in the US Intermountain West can be used by decision-makers intent on minimizing impacts to sage-grouse. This analysis also provides a general framework for using predictive models and build-out scenarios to anticipate impacts to species. These predictive models and build-out scenarios allow tradeoffs to be considered between species conservation and energy development prior to implementation.

Species-Specific Traits Rather Than Resource Partitioning Mediate Diversity Effects on Resource Use:

The link between biodiversity and ecosystem processes has firmly been established, but the mechanisms underpinning this relationship are poorly documented. Most studies have focused on terrestrial plant systems where resource use can be difficult to quantify as species rely on a limited number of common resources. Investigating resource use at the bulk level may not always be of sufficient resolution to detect subtle differences in resource use, as species-specific nutritional niches at the biochemical level may also moderate diversity effects on resource use. Here we use three co-occurring marine benthic echinoderms (Brissopsis lyrifera, Mesothuria intestinalis, Parastichopus tremulus) that feed on the same phytodetrital food source, to determine whether resource partitioning is the principal mechanism underpinning diversity effects on resource use. Specifically we investigate the use of phytodetrital pigments (chlorophylls and carotenoids) because many of these are essential for biological functions, including reproduction. Pigments were identified and quantified using reverse-phase high performance liquid Chromatography (HPLC) and data were analysed using a combination of extended linear regression with generalised least squares (GLS) estimation and standard multivariate techniques. Our analyses reveal no species-specific selectivity for particular algal pigments, confirming that these three species do not partition food resources at the biochemical level. Nevertheless, we demonstrate increased total resource use in diverse treatments as a result of selection effects and the dominance of one species (B. lyrifera). Overall, we found no evidence for resource partitioning at the biochemical level, as pigment composition was similar between individuals, which is likely due to plentiful food availability. Reduced intra-specific competition in the species mixture combined with greater adsorption efficiency and differences in feeding behaviour likely explain the dominant use of resources by B. lyrifera.

Ecological Equivalence: A Realistic Assumption for Niche Theory as a Testable Alternative to Neutral Theory:

Hubbell’s 2001 neutral theory unifies biodiversity and biogeography by modelling steady-state distributions of species richness and abundances across spatio-temporal scales. Accurate predictions have issued from its core premise that all species have identical vital rates. Yet no ecologist believes that species are identical in reality. Here I explain this paradox in terms of the ecological equivalence that species must achieve at their coexistence equilibrium, defined by zero net fitness for all regardless of intrinsic differences between them. I show that the distinction of realised from intrinsic vital rates is crucial to evaluating community resilience. An analysis of competitive interactions reveals how zero-sum patterns of abundance emerge for species with contrasting life-history traits as for identical species. I develop a stochastic model to simulate community assembly from a random drift of invasions sustaining the dynamics of recruitment following deaths and extinctions. Species are allocated identical intrinsic vital rates for neutral dynamics, or random intrinsic vital rates and competitive abilities for niche dynamics either on a continuous scale or between dominant-fugitive extremes. Resulting communities have steady-state distributions of the same type for more or less extremely differentiated species as for identical species. All produce negatively skewed log-normal distributions of species abundance, zero-sum relationships of total abundance to area, and Arrhenius relationships of species to area. Intrinsically identical species nevertheless support fewer total individuals, because their densities impact as strongly on each other as on themselves. Truly neutral communities have measurably lower abundance/area and higher species/abundance ratios. Neutral scenarios can be parameterized as null hypotheses for testing competitive release, which is a sure signal of niche dynamics. Ignoring the true strength of interactions between and within species risks a substantial misrepresentation of community resilience to habitat loss.

Lots of interesting articles in PLoS Biology, PLoS Medicine, PLoS Neglected Tropical Diseases and PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Perfect Family: Decision Making in Biparental Care:

Previous theoretical work on parental decisions in biparental care has emphasized the role of the conflict between evolutionary interests of parents in these decisions. A prominent prediction from this work is that parents should compensate for decreases in each other’s effort, but only partially so. However, experimental tests that manipulate parents and measure their responses fail to confirm this prediction. At the same time, the process of parental decision making has remained unexplored theoretically. We develop a model to address the discrepancy between experiments and the theoretical prediction, and explore how assuming different decision making processes changes the prediction from the theory. We assume that parents make decisions in behavioral time. They have a fixed time budget, and allocate it between two parental tasks: provisioning the offspring and defending the nest. The proximate determinant of the allocation decisions are parents’ behavioral objectives. We assume both parents aim to maximize the offspring production from the nest. Experimental manipulations change the shape of the nest production function. We consider two different scenarios for how parents make decisions: one where parents communicate with each other and act together (the perfect family), and one where they do not communicate, and act independently (the almost perfect family). The perfect family model is able to generate all the types of responses seen in experimental studies. The kind of response predicted depends on the nest production function, i.e. how parents’ allocations affect offspring production, and the type of experimental manipulation. In particular, we find that complementarity of parents’ allocations promotes matching responses. In contrast, the relative responses do not depend on the type of manipulation in the almost perfect family model. These results highlight the importance of the interaction between nest production function and how parents make decisions, factors that have largely been overlooked in previous models.

Bayesian Estimation of Animal Movement from Archival and Satellite Tags:

The reliable estimation of animal location, and its associated error is fundamental to animal ecology. There are many existing techniques for handling location error, but these are often ad hoc or are used in isolation from each other. In this study we present a Bayesian framework for determining location that uses all the data available, is flexible to all tagging techniques, and provides location estimates with built-in measures of uncertainty. Bayesian methods allow the contributions of multiple data sources to be decomposed into manageable components. We illustrate with two examples for two different location methods: satellite tracking and light level geo-location. We show that many of the problems with uncertainty involved are reduced and quantified by our approach. This approach can use any available information, such as existing knowledge of the animal’s potential range, light levels or direct location estimates, auxiliary data, and movement models. The approach provides a substantial contribution to the handling uncertainty in archival tag and satellite tracking data using readily available tools.

Dynamic Coupling of Pattern Formation and Morphogenesis in the Developing Vertebrate Retina:

The vertebrate brain contains a point-to-point representation of sensory input from the eye. This visual map forms during embryonic development, by neuronal cells of the retina sending targeted axon projections to the brain. Since the projection needs to wire up neighboring cell positions in the retina to neighboring target areas in the brain, all retinal cells must harbor a defined spatial coordinate as prerequisite for map formation. How such a retinal coordinate system is established and maintained in the dynamically evolving embryo is a fundamental, but unresolved, question. By combining genetic analysis and in vivo imaging in zebrafish embryos, we have tracked the developmental origin of cell coordinates in the retina. We find that three related Fgf signals emanating from outside the eye define relative cell positions in the retina very early, already at the onset of its formation. But the absolute position of retinal cells relative to the body axes is greatly rearranged during subsequent development. In this phase, surprisingly, the same Fgf signals that at first defined retinal cell positions now balance asymmetric cell movements and cell shape changes, which are required for harmonic retinal growth and the final alignment of cell coordinates in the eye.

The Comparative Oncology Trials Consortium: Using Spontaneously Occurring Cancers in Dogs to Inform the Cancer Drug Development Pathway:

Despite evidence of drug efficacy in mouse models of cancer, many novel anti-cancer agents fail in human cancer patients because of unacceptable toxicity or poor efficacy [1]. Naturally occurring tumors in dogs and other animals have clinical and biological similarities to human cancers that are difficult to replicate in other model systems. A recently launched cooperative effort, the National Cancer Institute’s (NCI’s) Comparative Oncology Trials Consortium (COTC; http://ccr.cancer.gov/resources/cop/COTC​.asp ), now provides infrastructure and resources needed to integrate these naturally occurring cancer models into the development of new human cancer drugs, devices, and imaging techniques.

Let’s look back at the week and see what’s cool. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
ECG Response of Koalas to Tourists Proximity: A Preliminary Study:

Koalas operate on a tight energy budget and, thus, may not always display behavioral avoidance reaction when placed in a stressful condition. We investigated the physiological response of captive koalas Phascolarctos cinereus in a conservation centre to the presence of tourists walking through their habitat. We compared, using animal-attached data-recorders, the electrocardiogram activity of female koalas in contact with tourists and in a human-free area. One of the koalas in the tourist zone presented elevated heart rate values and variability throughout the recording period. The remaining female in the exhibit area showed a higher field resting heart rates during the daytime than that in the isolated area. In the evening, heart rate profiles changed drastically and both the koalas in the exhibit and in the tourist-free zones displayed similar field resting heart rates, which were lower than those during the day. In parallel, the autonomic nervous systems of these two individuals evolved from sympathetic-dominant during the day to parasympathetic-dominant in the evening. Our results report ECG of free-living koalas for the first time. Although they are preliminary due to the difficulty of having sufficient samples of animals of the same sex and age, our results stress out the importance of studies investigating the physiological reaction of animals to tourists.

Packages of Care for Mental, Neurological, and Substance Use Disorders in Low- and Middle-Income Countries: PLoS Medicine Series:

This Perspective introduces a new series in PLoS Medicine on mental health disorders in low- and middle-income countries that reviews the evidence for packages of care for ADHD, alcohol misuse disorders, dementia, depression, epilepsy, and schizophrenia.

Identification of Plasmodium malariae, a Human Malaria Parasite, in Imported Chimpanzees:

It is widely believed that human malaria parasites infect only man as a natural host. However, earlier morphological observations suggest that great apes are likely to be natural reservoirs as well. To identify malaria parasites in great apes, we screened 60 chimpanzees imported into Japan. Using the sequences of small subunit rRNA and the mitochondrial genome, we identified infection of Plasmodium malariae, a human malaria parasite, in two chimpanzees that were imported about thirty years ago. The chimpanzees have been asymptomatic to the present. In Japan, indigenous malaria disappeared more than fifty years ago; and thus, it is most likely inferred that the chimpanzees were infected in Africa, and P. malariae isolates were brought into Japan from Africa with their hosts, suggesting persistence of parasites at low level for thirty years. Such a long term latent infection is a unique feature of P. malariae infection in humans. To our knowledge, this is the first to report P. malariae infection in chimpanzees and a human malaria parasite from nonhuman primates imported to a nonendemic country.

Plasticity of the Chemoreceptor Repertoire in Drosophila melanogaster:

Rapid adaptation and phenotypic plasticity to the chemical environment are essential prerequisites for survival; and, consequently, large families of genes that mediate the recognition of olfactory and gustatory cues have evolved. We asked how flexible the expression of these genes is in the face of rapidly changing conditions encountered during an individual’s lifetime. We used the fruit fly, Drosophila melanogaster, to address this question, since both the genetic composition and environmental rearing conditions can be controlled precisely in this experimentally amenable model organism. By measuring expression levels of all chemosensory genes simultaneously, we identified genes that show altered expression at different developmental stages, during aging, in males and females, following mating, and in different social conditions. We asked whether chemosensory genes are regulated independently or whether their regulation is structured. We found that chemosensory genes that are located in close proximity to one another on the chromosome are often regulated independently. However, statistical analysis showed that groups of chemosensory genes are coordinately expressed in response to a range of environmental conditions, revealing an underlying modular organization of the phenotypic plasticity of the chemosensory receptor repertoire.

Long-Term GPS Tracking of Ocean Sunfish Mola mola Offers a New Direction in Fish Monitoring:

Satellite tracking of large pelagic fish provides insights on free-ranging behaviour, distributions and population structuring. Up to now, such fish have been tracked remotely using two principal methods: direct positioning of transmitters by Argos polar-orbiting satellites, and satellite relay of tag-derived light-level data for post hoc track reconstruction. Error fields associated with positions determined by these methods range from hundreds of metres to hundreds of kilometres. However, low spatial accuracy of tracks masks important details, such as foraging patterns. Here we use a fast-acquisition global positioning system (Fastloc GPS) tag with remote data retrieval to track long-term movements, in near real time and position accuracy of <70 m, of the world's largest bony fish, the ocean sunfish Mola mola. Search-like movements occurred over at least three distinct spatial scales. At fine scales, sunfish spent longer in highly localised areas with faster, straighter excursions between them. These 'stopovers' during long-distance movement appear consistent with finding and exploiting food patches. This demonstrates the feasibility of GPS tagging to provide tracks of unparalleled accuracy for monitoring movements of large pelagic fish, and with nearly four times as many locations obtained by the GPS tag than by a conventional Argos transmitter. The results signal the potential of GPS-tagged pelagic fish that surface regularly to be detectors of resource 'hotspots' in the blue ocean and provides a new capability for understanding large pelagic fish behaviour and habitat use that is relevant to ocean management and species conservation.

There are 17 new articles in PLoS ONE published last night. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Was Dinosaurian Physiology Inherited by Birds? Reconciling Slow Growth in Archaeopteryx

Background
Archaeopteryx is the oldest and most primitive known bird (Avialae). It is believed that the growth and energetic physiology of basalmost birds such as Archaeopteryx were inherited in their entirety from non-avialan dinosaurs. This hypothesis predicts that the long bones in these birds formed using rapidly growing, well-vascularized woven tissue typical of non-avialan dinosaurs.
Methodology/Principal Findings
We report that Archaeopteryx long bones are composed of nearly avascular parallel-fibered bone. This is among the slowest growing osseous tissues and is common in ectothermic reptiles. These findings dispute the hypothesis that non-avialan dinosaur growth and physiology were inherited in totality by the first birds. Examining these findings in a phylogenetic context required intensive sampling of outgroup dinosaurs and basalmost birds. Our results demonstrate the presence of a scale-dependent maniraptoran histological continuum that Archaeopteryx and other basalmost birds follow. Growth analysis for Archaeopteryx suggests that these animals showed exponential growth rates like non-avialan dinosaurs, three times slower than living precocial birds, but still within the lowermost range for all endothermic vertebrates.
Conclusions/Significance
The unexpected histology of Archaeopteryx and other basalmost birds is actually consistent with retention of the phylogenetically earlier paravian dinosaur condition when size is considered. The first birds were simply feathered dinosaurs with respect to growth and energetic physiology. The evolution of the novel pattern in modern forms occurred later in the group’s history.

Molecular Signatures Reveal Circadian Clocks May Orchestrate the Homeorhetic Response to Lactation:

Genes associated with lactation evolved more slowly than other genes in the mammalian genome. Higher conservation of milk and mammary genes suggest that species variation in milk composition is due in part to the environment and that we must look deeper into the genome for regulation of lactation. At the onset of lactation, metabolic changes are coordinated among multiple tissues through the endocrine system to accommodate the increased demand for nutrients and energy while allowing the animal to remain in homeostasis. This process is known as homeorhesis. Homeorhetic adaptation to lactation has been extensively described; however how these adaptations are orchestrated among multiple tissues remains elusive. To develop a clearer picture of how gene expression is coordinated across multiple tissues during the pregnancy to lactation transition, total RNA was isolated from mammary, liver and adipose tissues collected from rat dams (n = 5) on day 20 of pregnancy and day 1 of lactation, and gene expression was measured using Affymetrix GeneChips. Two types of gene expression analysis were performed. Genes that were differentially expressed between days within a tissue were identified with linear regression, and univariate regression was used to identify genes commonly up-regulated and down-regulated across all tissues. Gene set enrichment analysis showed genes commonly up regulated among the three tissues enriched gene ontologies primary metabolic processes, macromolecular complex assembly and negative regulation of apoptosis ontologies. Genes enriched in transcription regulator activity showed the common up regulation of 2 core molecular clock genes, ARNTL and CLOCK. Commonly down regulated genes enriched Rhythmic process and included: NR1D1, DBP, BHLHB2, OPN4, and HTR7, which regulate intracellular circadian rhythms. Changes in mammary, liver and adipose transcriptomes at the onset of lactation illustrate the complexity of homeorhetic adaptations and suggest that these changes are coordinated through molecular clocks.

Evolution with Stochastic Fitness and Stochastic Migration:

Migration between local populations plays an important role in evolution – influencing local adaptation, speciation, extinction, and the maintenance of genetic variation. Like other evolutionary mechanisms, migration is a stochastic process, involving both random and deterministic elements. Many models of evolution have incorporated migration, but these have all been based on simplifying assumptions, such as low migration rate, weak selection, or large population size. We thus have no truly general and1 exact mathematical description of evolution that incorporates migration. We derive an exact equation for directional evolution, essentially a stochastic Price equation with migration, that encompasses all processes, both deterministic and stochastic, contributing to directional change in an open population. Using this result, we show that increasing the variance in migration rates reduces the impact of migration relative to selection. This means that models that treat migration as a single parameter tend to be biassed – overestimating the relative impact of immigration. We further show that selection and migration interact in complex ways, one result being that a strategy for which fitness is negatively correlated with migration rates (high fitness when migration is low) will tend to increase in frequency, even if it has lower mean fitness than do other strategies. Finally, we derive an equation for the effective migration rate, which allows some of the complex stochastic processes that we identify to be incorporated into models with a single migration parameter. As has previously been shown with selection, the role of migration in evolution is determined by the entire distributions of immigration and emigration rates, not just by the mean values. The interactions of stochastic migration with stochastic selection produce evolutionary processes that are invisible to deterministic evolutionary theory.

There are 21 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
From the Eye of the Albatrosses: A Bird-Borne Camera Shows an Association between Albatrosses and a Killer Whale in the Southern Ocean:

Albatrosses fly many hundreds of kilometers across the open ocean to find and feed upon their prey. Despite the growing number of studies concerning their foraging behaviour, relatively little is known about how albatrosses actually locate their prey. Here, we present our results from the first deployments of a combined animal-borne camera and depth data logger on free-ranging black-browed albatrosses (Thalassarche melanophrys). The still images recorded from these cameras showed that some albatrosses actively followed a killer whale (Orcinus orca), possibly to feed on food scraps left by this diving predator. The camera images together with the depth profiles showed that the birds dived only occasionally, but that they actively dived when other birds or the killer whale were present. This association with diving predators or other birds may partially explain how albatrosses find their prey more efficiently in the apparently ‘featureless’ ocean, with a minimal requirement for energetically costly diving or landing activities.

Edge Detection in Landing Budgerigars (Melopsittacus undulatus):

While considerable scientific effort has been devoted to studying how birds navigate over long distances, relatively little is known about how targets are detected, obstacles are avoided and smooth landings are orchestrated. Here we examine how visual features in the environment, such as contrasting edges, determine where a bird will land. Landing in budgerigars (Melopsittacus undulatus) was investigated by training them to fly from a perch to a feeder, and video-filming their landings. The feeder was placed on a grey disc that produced a contrasting edge against a uniformly blue background. We found that the birds tended to land primarily at the edge of the disc and walk to the feeder, even though the feeder was in the middle of the disc. This suggests that the birds were using the visual contrast at the boundary of the disc to target their landings. When the grey level of the disc was varied systematically, whilst keeping the blue background constant, there was one intermediate grey level at which the budgerigar’s preference for the disc boundary disappeared. The budgerigars then landed randomly all over the test surface. Even though this disc is (for humans) clearly distinguishable from the blue background, it offers very little contrast against the background, in the red and green regions of the spectrum. We conclude that budgerigars use visual edges to target and guide landings. Calculations of photoreceptor excitation reveal that edge detection in landing budgerigars is performed by a color-blind luminance channel that sums the signals from the red and green photoreceptors, or, alternatively, receives input from the red double-cones. This finding has close parallels to vision in honeybees and primates, where edge detection and motion perception are also largely color-blind.

The Impact of Nature Experience on Willingness to Support Conservation:

We hypothesized that willingness to financially support conservation depends on one’s experience with nature. In order to test this hypothesis, we used a novel time-lagged correlation analysis to look at times series data concerning nature participation, and evaluate its relationship with future conservation support (measured as contributions to conservation NGOs). Our results suggest that the type and timing of nature experience may determine future conservation investment. Time spent hiking or backpacking is correlated with increased conservation contributions 11-12 years later. On the other hand, contributions are negatively correlated with past time spent on activities such as public lands visitation or fishing. Our results suggest that each hiker or backpacker translates to $200-$300 annually in future NGO contributions. We project that the recent decline in popularity of hiking and backpacking will negatively impact conservation NGO contributions from approximately 2010-2011 through at least 2018.

Reassortment Patterns in Swine Influenza Viruses:

Three human influenza pandemics occurred in the twentieth century, in 1918, 1957, and 1968. Influenza pandemic strains are the results of emerging viruses from non-human reservoirs to which humans have little or no immunity. At least two of these pandemic strains, in 1957 and in 1968, were the results of reassortments between human and avian viruses. Also, many cases of swine influenza viruses have reportedly infected humans, in particular, the recent H1N1 influenza virus of swine origin, isolated in Mexico and the United States. Pigs are documented to allow productive replication of human, avian, and swine influenza viruses. Thus it has been conjectured that pigs are the “mixing vessel” that create the avian-human reassortant strains, causing the human pandemics. Hence, studying the process and patterns of viral reassortment, especially in pigs, is a key to better understanding of human influenza pandemics. In the last few years, databases containing sequences of influenza A viruses, including swine viruses, collected since 1918 from diverse geographical locations, have been developed and made publicly available. In this paper, we study an ensemble of swine influenza viruses to analyze the reassortment phenomena through several statistical techniques. The reassortment patterns in swine viruses prove to be similar to the previous results found in human viruses, both in vitro and in vivo, that the surface glycoprotein coding segments reassort most often. Moreover, we find that one of the polymerase segments (PB1), reassorted in the strains responsible for the last two human pandemics, also reassorts frequently.

There are 32 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Dynamic Locomotor Capabilities Revealed by Early Dinosaur Trackmakers from Southern Africa:

A new investigation of the sedimentology and ichnology of the Early Jurassic Moyeni tracksite in Lesotho, southern Africa has yielded new insights into the behavior and locomotor dynamics of early dinosaurs. The tracksite is an ancient point bar preserving a heterogeneous substrate of varied consistency and inclination that includes a ripple-marked riverbed, a bar slope, and a stable algal-matted bar top surface. Several basal ornithischian dinosaurs and a single theropod dinosaur crossed its surface within days or perhaps weeks of one another, but responded to substrate heterogeneity differently. Whereas the theropod trackmaker accommodated sloping and slippery surfaces by gripping the substrate with its pedal claws, the basal ornithischian trackmakers adjusted to the terrain by changing between quadrupedal and bipedal stance, wide and narrow gauge limb support (abduction range = 31°), and plantigrade and digitigrade foot posture. The locomotor adjustments coincide with changes in substrate consistency along the trackway and appear to reflect ‘real time’ responses to a complex terrain. It is proposed that these responses foreshadow important locomotor transformations characterizing the later evolution of the two main dinosaur lineages. Ornithischians, which shifted from bipedal to quadrupedal posture at least three times in their evolutionary history, are shown to have been capable of adopting both postures early in their evolutionary history. The substrate-gripping behavior demonstrated by the early theropod, in turn, is consistent with the hypothesized function of pedal claws in bird ancestors.

High Resolution MEMS Accelerometers to Estimate VO2 and Compare Running Mechanics between Highly Trained Inter-Collegiate and Untrained Runners:

The purposes of this study were to determine the validity and reliability of high resolution accelerometers (HRA) relative to VO2 and speed, and compare putative differences in HRA signal between trained (T) and untrained (UT) runners during treadmill locomotion. Runners performed 2 incremental VO2max trials while wearing HRA. RMS of high frequency signal from three axes (VT, ML, AP) and the Euclidean resultant (RES) were compared to VO2 to determine validity and reliability. Additionally, axial rms relative to speed, and ratio of axial accelerations to RES were compared between T and UT to determine if differences in running mechanics could be identified between the two groups. Regression of RES was strongly related to VO2, but T was different than UT (r = 0.96 vs 0.92; p<.001) for walking and running. During walking, only the ratio of ML and AP to RES were different between groups. For running, nearly all acceleration parameters were lower for T than UT, the exception being ratio of VT to RES, which was higher in T than UT. All of these differences during running were despite higher VO2, O2 cost, and lower RER in T vs UT, which resulted in no significant difference in energy expenditure between groups. These results indicate that HRA can accurately and reliably estimate VO2 during treadmill locomotion, but differences exist between T and UT that should be considered when estimating energy expenditure. Differences in running mechanics between T and UT were identified, yet the importance of these differences remains to be determined.

Coral Fluorescent Proteins as Antioxidants:

A wide array of fluorescent proteins (FP) is present in anthozoans, although their biochemical characteristics and function in host tissue remain to be determined. Upregulation of FP’s frequently occurs in injured or compromised coral tissue, suggesting a potential role of coral FPs in host stress responses. The presence of FPs was determined and quantified for a subsample of seven healthy Caribbean coral species using spectral emission analysis of tissue extracts. FP concentration was correlated with the in vivo antioxidant potential of the tissue extracts by quantifying the hydrogen peroxide (H2O2) scavenging rates. FPs of the seven species varied in both type and abundance and demonstrated a positive correlation between H2O2 scavenging rate and FP concentration. To validate this data, the H2O2 scavenging rates of four pure scleractinian FPs, cyan (CFP), green (GFP), red (RFP) and chromoprotein (CP), and their mutant counterparts (without chromophores), were investigated. In vitro, each FP scavenged H2O2 with the most efficient being CP followed by equivalent activity of CFP and RFP. Scavenging was significantly higher in all mutant counterparts. Both naturally occurring and pure coral FPs have significant H2O2 scavenging activity. The higher scavenging rate of RFP and the CP in vitro is consistent with observed increases of these specific FPs in areas of compromised coral tissue. However, the greater scavenging ability of the mutant counterparts suggests additional roles of scleractinian FPs, potentially pertaining to their color. This study documents H2O2 scavenging of scleractinian FPs, a novel biochemical characteristic, both in vivo across multiple species and in vitro with purified proteins. These data support a role for FPs in coral stress and immune responses and highlights the multi-functionality of these conspicuous proteins.

Resilience of Coral-Associated Bacterial Communities Exposed to Fish Farm Effluent:

The coral holobiont includes the coral animal, algal symbionts, and associated microbial community. These microbes help maintain the holobiont homeostasis; thus, sustaining robust mutualistic microbial communities is a fundamental part of long-term coral reef survival. Coastal pollution is one major threat to reefs, and intensive fish farming is a rapidly growing source of this pollution. We investigated the susceptibility and resilience of the bacterial communities associated with a common reef-building coral, Porites cylindrica, to coastal pollution by performing a clonally replicated transplantation experiment in Bolinao, Philippines adjacent to intensive fish farming. Ten fragments from each of four colonies (total of 40 fragments) were followed for 22 days across five sites: a well-flushed reference site (the original fragment source); two sites with low exposure to milkfish (Chanos chanos) aquaculture effluent; and two sites with high exposure. Elevated levels of dissolved organic carbon (DOC), chlorophyll a, total heterotrophic and autotrophic bacteria abundance, virus like particle (VLP) abundances, and culturable Vibrio abundance characterized the high effluent sites. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed rapid, dramatic changes in the coral-associated bacterial communities within five days of high effluent exposure. The community composition on fragments at these high effluent sites shifted towards known human and coral pathogens (i.e. Arcobacter, Fusobacterium, and Desulfovibrio) without the host corals showing signs of disease. The communities shifted back towards their original composition by day 22 without reduction in effluent levels. This study reveals fish farms as a likely source of pathogens with the potential to proliferate on corals and an unexpected short-term resilience of coral-associated bacterial communities to eutrophication pressure. These data highlight a need for improved aquaculture practices that can achieve both sustainable industry goals and long-term coral reef survival.

Adenotonsillectomy and Neurocognitive Deficits in Children with Sleep Disordered Breathing:

Sleep Disordered Breathing (SDB) is a common childhood disorder that encompasses a range of sleep-related upper airway obstruction. Children with SDB demonstrate significant neurocognitive deficits. Adenotonsillectomy is the first line of treatment for SDB and whilst this improves respiratory disturbance, it remains to be established whether neurocognitive gains also result. A total of 44 healthy snoring children aged 3-12 years awaiting adenotonsillectomy (SDB group), and 48 age and gender matched non-snoring controls from the general community, completed the study. All children underwent polysomnography and neurocognitive assessment at baseline and after a 6-month follow-up (after surgery in the snoring group). Our primary aim was to determine whether neurocognitive deficits in snoring children were significantly improved following adenotonsillectomy. Wide ranging neurocognitive deficits were found at baseline in SDB children compared to controls, most notably a 10 point IQ difference (P<.001) and similar deficits in language and executive function. Whilst adenotonsillectomy improved respiratory parameters and snoring frequency at 6 months post surgery, neurocognitive performance did not improve relative to controls. Adenotonsillectomy successfully treated the respiratory effects of SDB in children. However, neurocognitive deficits did not improve 6-months post-operatively.

Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Areceaceae) Identifies Syagrus as Sister Group of the Coconut:

The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the “abominable mysteries” of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut. We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree. This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family.

Let’s check all seven PLoS journals today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Circadian and Social Cues Regulate Ion Channel Trafficking:

Excitable cells, such as neurons and muscle cells, control behavior by generating action potentials, electrical signals that propagate along the cell membrane. Action potentials are generated when the cell allows charged molecules (ions) such as sodium and potassium to move across the membrane through specialized proteins called ion channels. By changing the number of ion channels in the plasma membrane, excitable cells can rapidly remodel their functional characteristics, potentially causing changes in behavior. To gain an understanding of how environmental events cause the remodeling of excitable cell membranes and the resulting behavioral adaptations, we studied the electric communication/navigation signals of an electric fish, Sternopygus macrurus. High amplitude signals facilitate communication and electrolocation, but are energetically costly and more detectable by those predators that can detect electrical signals. We found that Sternopygus increase signal amplitude at night, when they are active, and increase signal amplitude rapidly during social encounters. Electrocytes, the cells that produce the signal, rapidly boost the signal amplitude when they allow more sodium to cross the cell membrane, thereby generating larger action potentials. To increase sodium currents during the action potential, electrocytes rapidly insert additional sodium channels into the cell membrane in response to hormones released into circulation by the pituitary. By adding new ion channels to the electrocyte membrane only during periods of activity or social encounters and removing these channels during inactive periods, these animals can save energy and reduce predation risks associated with communication.

It’s not too Late for the Harpy Eagle (Harpia harpyja): High Levels Of Genetic Diversity and Differentiation Can Fuel Conservation Programs:

The harpy eagle (Harpia harpyja) is the largest Neotropical bird of prey and is threatened by human persecution and habitat loss and fragmentation. Current conservation strategies include local education, captive rearing and reintroduction, and protection or creation of trans-national habitat blocks and corridors. Baseline genetic data prior to reintroduction of captive-bred stock is essential for guiding such efforts but has not been gathered previously. We assessed levels of genetic diversity, population structure and demographic history for harpy eagles using samples collected throughout a large portion of their geographic distribution in Central America (n = 32) and South America (n = 31). Based on 417 bp of mitochondrial control region sequence data, relatively high levels of haplotype and nucleotide diversity were estimated for both Central and South America, although haplotype diversity was significantly higher for South America. Historical restriction of gene flow across the Andes (i.e. between our Central and South American subgroups) is supported by coalescent analyses, the haplotype network and significant FST values, however reciprocally monophyletic lineages do not correspond to geographical locations in maximum likelihood analyses. A sudden population expansion for South America is indicated by a mismatch distribution analysis, and further supported by significant (p<0.05) negative values of Fu and Li's DF and F, and Fu's FS. This expansion, estimated at approximately 60 000 years BP (99 000-36 000 years BP 95% CI), encompasses a transition from a warm and dry time period prior to 50 000 years BP to an interval of maximum precipitation (50 000-36 000 years BP). Notably, this time period precedes the climatic and habitat changes associated with the last glacial maximum. In contrast, a multimodal distribution of haplotypes was observed for Central America suggesting either population equilibrium or a recent decline. High levels of mitochondrial genetic diversity in combination with genetic differentiation among subgroups within regions and between regions highlight the importance of local population conservation in order to preserve maximal levels of genetic diversity in this species. Evidence of historically restricted female-mediated gene flow is an important consideration for captive-breeding programs.

Spread of Avian Influenza Viruses by Common Teal (Anas crecca) in Europe:

Since the recent spread of highly pathogenic (HP) H5N1 subtypes, avian influenza virus (AIV) dispersal has become an increasing focus of research. As for any other bird-borne pathogen, dispersal of these viruses is related to local and migratory movements of their hosts. In this study, we investigated potential AIV spread by Common Teal (Anas crecca) from the Camargue area, in the South of France, across Europe. Based on bird-ring recoveries, local duck population sizes and prevalence of infection with these viruses, we built an individual-based spatially explicit model describing bird movements, both locally (between wintering areas) and at the flyway scale. We investigated the effects of viral excretion duration and inactivation rate in water by simulating AIV spread with varying values for these two parameters. The results indicate that an efficient AIV dispersal in space is possible only for excretion durations longer than 7 days. Virus inactivation rate in the environment appears as a key parameter in the model because it allows local persistence of AIV over several months, the interval between two migratory periods. Virus persistence in water thus represents an important component of contamination risk as ducks migrate along their flyway. Based on the present modelling exercise, we also argue that HP H5N1 AIV is unlikely to be efficiently spread by Common Teal dispersal only.

Novel Vaccines to Human Rabies:

Rabies, the most fatal of all infectious diseases, remains a major public health problem in developing countries, claiming the lives of an estimated 55,000 people each year. Most fatal rabies cases, with more than half of them in children, result from dog bites and occur among low-income families in Southeast Asia and Africa. Safe and efficacious vaccines are available to prevent rabies. However, they have to be given repeatedly, three times for pre-exposure vaccination and four to five times for post-exposure prophylaxis (PEP). In cases of severe exposure, a regimen of vaccine combined with a rabies immunoglobulin (RIG) preparation is required. The high incidence of fatal rabies is linked to a lack of knowledge on the appropriate treatment of bite wounds, lack of access to costly PEP, and failure to follow up with repeat immunizations. New, more immunogenic but less costly rabies virus vaccines are needed to reduce the toll of rabies on human lives. A preventative vaccine used for the immunization of children, especially those in high incidence countries, would be expected to lower fatality rates. Such a vaccine would have to be inexpensive, safe, and provide sustained protection, preferably after a single dose. Novel regimens are also needed for PEP to reduce the need for the already scarce and costly RIG and to reduce the number of vaccine doses to one or two. In this review, the pipeline of new rabies vaccines that are in pre-clinical testing is provided and an opinion on those that might be best suited as potential replacements for the currently used vaccines is offered.

Drugs Associated with More Suicidal Ideations Are also Associated with More Suicide Attempts:

In randomized controlled trials (RCTs), some drugs, including CB1 antagonists for obesity treatment, have been shown to cause increased suicidal ideation. A key question is whether drugs that increase or are associated with increased suicidal ideations are also associated with suicidal behavior, or whether drug-induced suicidal ideations are unlinked epiphenomena that do not presage the more troubling and potentially irrevocable outcome of suicidal behavior. This is difficult to determine in RCTs because of the rarity of suicidal attempts and completions. To determine whether drugs associated with more suicidal ideations are also associated with more suicide attempts in large spontaneous adverse event (AE) report databases. Generalized linear models with negative binomial distribution were fitted to Food and Drug Administration (FDA) Adverse Event (AE) Reporting System (AERS) data from 2004 to 2008. A total of 1,404,470 AEs from 832 drugs were analyzed as a function of reports of suicidal ideations; other non-suicidal adverse reactions; drug class; proportion of reports from males; and average age of subject for which AE was filed. Drug was treated as the unit of analysis, thus the statistical models effectively had 832 observations. Reported suicide attempts and completed suicides per drug. 832 drugs, ranging from abacavir to zopiclone, were evaluated. The 832 drugs, as primary suspect drugs in a given adverse event, accounted for over 99.9% of recorded AERS. Suicidal ideations had a significant positive association with suicide attempts (p<.0001) and had an approximately 131-fold stronger magnitude of association than non-suicidal AERs, after adjusting for drug class, gender, and age. In AE reports, drugs that are associated with increased suicidal ideations are also associated with increased suicidal attempts or completions. This association suggests that drug-induced suicidal ideations observed in RCTs plausibly represent harbingers that presage the more serious suicide attempts and completions and should be a cause for concern.

Ensuring Integrity in Comparative Effectiveness Research: Accentuate the Negative:

In recent weeks, PLoS Medicine has published several research papers that challenge current health care practices.
One study found that a campaign to promote solar drinking water disinfection did not substantially decrease rates of childhood diarrhea [1]. Another found more than a doubled risk of hospitalization for bradycardia in older people taking cholinesterase inhibitors used to treat cognitive impairment [2]. A systematic review failed to find any randomized trials that support the internationally recommended retreatment regimen for tuberculosis [3]. Finally, a study of one of the main international registries for clinical trials, ClinicalTrials.gov, found that requirements to register clinical trials have not resulted in high publication rates [4].
A study that questions the accepted or desired way of doing things can be at least as important as one that supports a new approach. Physicians mindful of Hippocrates’ vow to “first do no harm” should take a keen interest in such studies, for while a new intervention that proves efficacious in clinical trials may pass slowly, if at all, through practical barriers to effective implementation, the demonstration that an existing practice is ineffective or potentially harmful can (or should) prompt a rapid change in research agendas, policy, and clinical care. Knowing what doesn’t work is particularly useful in efforts to control medical spending, where redirecting limited resources away from ineffective interventions is of obvious benefit.

Public Access to Genome-Wide Data: Five Views on Balancing Research with Privacy and Protection:

Just over twelve months ago, PLoS Genetics published a paper [1] demonstrating that, given genome-wide genotype data from an individual, it is, in principle, possible to ascertain whether that individual is a member of a larger group defined solely by aggregate genotype frequencies, such as a forensic sample or a cohort of participants in a genome-wide association study (GWAS). As a consequence, the National Institutes of Health (NIH) and Wellcome Trust agreed to shut down public access not just to individual genotype data but even to aggregate genotype frequency data from each study published using their funding. Reactions to this decision span the full breadth of opinion, from “too little, too late–the public trust has been breached” to “a heavy-handed bureaucratic response to a practically minimal risk that will unnecessarily inhibit scientific research.” Scientific concerns have also been raised over the conditions under which individual identity can truly be accurately determined from GWAS data. These concerns are addressed in two papers published in this month’s issue of PLoS Genetics [2],[3]. We received several submissions on this topic and decided to assemble these viewpoints as a contribution to the debate and ask readers to contribute their thoughts through the PLoS online commentary features.

Needles in the Haystack: Identifying Individuals Present in Pooled Genomic Data:

In this report, we evaluate a recently-published method for resolving whether individuals are present in a complex genomic DNA mixture. Based on the intuition that an individual will be genetically “closer” to a sample containing him than to a sample not, the method investigated here uses a distance metric to quantify the similarity of an individual relative to two population samples. Although initial applications of this approach showed a promising false-negative rate, the accuracy of the assumed null distribution (and hence the true false-positive rate) remained uninvestigated; here, we explore this question analytically and describe tests of this method to assess the likelihood that an individual who is not in the mixture is mistakenly classified as being a member. Our results show that the method has a high false-positive rate in practice due to its sensitivity to underlying assumptions, limiting its utility for inferring the presence of an individual in a population. By revealing both the strengths and limitations of the proposed method, we elucidate situations in which this distance metric may be used in an appropriate manner in forensics and medical privacy policy.

There are 32 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Common Avian Infection Plagued the Tyrant Dinosaurs:

Tyrannosaurus rex and other tyrannosaurid fossils often display multiple, smooth-edged full-thickness erosive lesions on the mandible, either unilaterally or bilaterally. The cause of these lesions in the Tyrannosaurus rex specimen FMNH PR2081 (known informally by the name ‘Sue’) has previously been attributed to actinomycosis, a bacterial bone infection, or bite wounds from other tyrannosaurids. We conducted an extensive survey of tyrannosaurid specimens and identified ten individuals with full-thickness erosive lesions. These lesions were described, measured and photographed for comparison with one another. We also conducted an extensive survey of related archosaurs for similar lesions. We show here that these lesions are consistent with those caused by an avian parasitic infection called trichomonosis, which causes similar abnormalities on the mandible of modern birds, in particular raptors. This finding represents the first evidence for the ancient evolutionary origin of an avian transmissible disease in non-avian theropod dinosaurs. It also provides a valuable insight into the palaeobiology of these now extinct animals. Based on the frequency with which these lesions occur, we hypothesize that tyrannosaurids were commonly infected by a Trichomonas gallinae-like protozoan. For tyrannosaurid populations, the only non-avian dinosaur group that show trichomonosis-type lesions, it is likely that the disease became endemic and spread as a result of antagonistic intraspecific behavior, consumption of prey infected by a Trichomonas gallinae-like protozoan and possibly even cannibalism. The severity of trichomonosis-related lesions in specimens such as Tyrannosaurus rex FMNH PR2081 and Tyrannosaurus rex MOR 980, strongly suggests that these animals died as a direct result of this disease, mostly likely through starvation.

Dragon’s Paradise Lost: Palaeobiogeography, Evolution and Extinction of the Largest-Ever Terrestrial Lizards (Varanidae):

The largest living lizard species, Varanus komodoensis Ouwens 1912, is vulnerable to extinction, being restricted to a few isolated islands in eastern Indonesia, between Java and Australia, where it is the dominant terrestrial carnivore. Understanding how large-bodied varanids responded to past environmental change underpins long-term management of V. komodoensis populations. We reconstruct the palaeobiogeography of Neogene giant varanids and identify a new (unnamed) species from the island of Timor. Our data reject the long-held perception that V. komodoensis became a giant because of insular evolution or as a specialist hunter of pygmy Stegodon. Phyletic giantism, coupled with a westward dispersal from mainland Australia, provides the most parsimonious explanation for the palaeodistribution of V. komodoensis and the newly identified species of giant varanid from Timor. Pliocene giant varanid fossils from Australia are morphologically referable to V. komodoensis suggesting an ultimate origin for V. komodoensis on mainland Australia (>3.8 million years ago). Varanus komodoensis body size has remained stable over the last 900,000 years (ka) on Flores, a time marked by major faunal turnovers, extinction of the island’s megafauna, the arrival of early hominids by 880 ka, co-existence with Homo floresiensis, and the arrival of modern humans by 10 ka. Within the last 2000 years their populations have contracted severely. Giant varanids were once a ubiquitous part of Subcontinental Eurasian and Australasian faunas during the Neogene. Extinction played a pivotal role in the reduction of their ranges and diversity throughout the late Quaternary, leaving only V. komodoensis as an isolated long-term survivor. The events over the last two millennia now threaten its future survival.

The Origin and Initial Rise of Pelagic Cephalopods in the Ordovician:

During the Ordovician the global diversity increased dramatically at family, genus and species levels. Partially the diversification is explained by an increased nutrient, and phytoplankton availability in the open water. Cephalopods are among the top predators of todays open oceans. Their Ordovician occurrences, diversity evolution and abundance pattern potentially provides information on the evolution of the pelagic food chain. We reconstructed the cephalopod departure from originally exclusively neritic habitats into the pelagic zone by the compilation of occurrence data in offshore paleoenvironments from the Paleobiology Database, and from own data, by evidence of the functional morphology, and the taphonomy of selected cephalopod faunas. The occurrence data show, that cephalopod associations in offshore depositional settings and black shales are characterized by a specific composition, often dominated by orthocerids and lituitids. The siphuncle and conch form of these cephalopods indicate a dominant lifestyle as pelagic, vertical migrants. The frequency distribution of conch sizes and the pattern of epibionts indicate an autochthonous origin of the majority of orthocerid and lituitid shells. The consistent concentration of these cephalopods in deep subtidal sediments, starting from the middle Tremadocian indicates the occupation of the pelagic zone early in the Early Ordovician and a subsequent diversification which peaked during the Darriwilian. The exploitation of the pelagic realm started synchronously in several independent invertebrate clades during the latest Cambrian to Middle Ordovician. The initial rise and diversification of pelagic cephalopods during the Early and Middle Ordovician indicates the establishment of a pelagic food chain sustainable enough for the development of a diverse fauna of large predators. The earliest pelagic cephalopods were slowly swimming vertical migrants. The appearance and early diversification of pelagic cephalopods is interpreted as a consequence of the increased food availability in the open water since the latest Cambrian.

The Cultural Dynamics of Copycat Suicide:

The observation that suicides sometimes cluster in space and/or time has led to suggestions that these clusters are caused by the social learning of suicide-related behaviours, or “copycat suicides”. Point clusters are clusters of suicides localised in both time and space, and have been attributed to direct social learning from nearby individuals. Mass clusters are clusters of suicides localised in time but not space, and have been attributed to the dissemination of information concerning celebrity suicides via the mass media. Here, agent-based simulations, in combination with scan statistic methods for detecting clusters of rare events, were used to clarify the social learning processes underlying point and mass clusters. It was found that social learning between neighbouring agents did generate point clusters as predicted, although this effect was partially mimicked by homophily (individuals preferentially assorting with similar others). The one-to-many transmission dynamics characterised by the mass media were shown to generate mass clusters, but only where social learning was weak, perhaps due to prestige bias (only copying prestigious celebrities) and similarity bias (only copying similar models) acting to reduce the subset of available models. These findings can help to clarify and formalise existing hypotheses and to guide future empirical work relating to real-life copycat suicides.

Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups:

Understanding the genetic contribution to phenotype variation of human groups is necessary to elucidate differences in disease predisposition and response to pharmaceutical treatments in different human populations. We have investigated the genome-wide profile of structural variation on pooled samples from the three populations studied in the HapMap project by comparative genome hybridization (CGH) in different array platforms. We have identified and experimentally validated 33 genomic loci that show significant copy number differences from one population to the other. Interestingly, we found an enrichment of genes related to environment adaptation (immune response, lipid metabolism and extracellular space) within these regions and the study of expression data revealed that more than half of the copy number variants (CNVs) translate into gene-expression differences among populations, suggesting that they could have functional consequences. In addition, the identification of single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium with the copy number alleles allowed us to detect evidences of population differentiation and recent selection at the nucleotide variation level. Overall, our results provide a comprehensive view of relevant copy number changes that might play a role in phenotypic differences among major human populations, and generate a list of interesting candidates for future studies.

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There are 30 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Neuroanatomical Variability of Religiosity:

We hypothesized that religiosity, a set of traits variably expressed in the population, is modulated by neuroanatomical variability. We tested this idea by determining whether aspects of religiosity were predicted by variability in regional cortical volume. We performed structural magnetic resonance imaging of the brain in 40 healthy adult participants who reported different degrees and patterns of religiosity on a survey. We identified four Principal Components of religiosity by Factor Analysis of the survey items and associated them with regional cortical volumes measured by voxel-based morphometry. Experiencing an intimate relationship with God and engaging in religious behavior was associated with increased volume of R middle temporal cortex, BA 21. Experiencing fear of God was associated with decreased volume of L precuneus and L orbitofrontal cortex BA 11. A cluster of traits related with pragmatism and doubting God’s existence was associated with increased volume of the R precuneus. Variability in religiosity of upbringing was not associated with variability in cortical volume of any region. Therefore, key aspects of religiosity are associated with cortical volume differences. This conclusion complements our prior functional neuroimaging findings in elucidating the proximate causes of religion in the brain.

Evolutionary Descent of Prion Genes from the ZIP Family of Metal Ion Transporters:

In the more than twenty years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into a possible function of PrP may be obtained through the characterization of its molecular neighborhood in cells. Quantitative interactome data demonstrated the spatial proximity of two metal ion transporters of the ZIP family, ZIP6 and ZIP10, to mammalian prion proteins in vivo. A subsequent bioinformatic analysis revealed the unexpected presence of a PrP-like amino acid sequence within the N-terminal, extracellular domain of a distinct sub-branch of the ZIP protein family that includes ZIP5, ZIP6 and ZIP10. Additional structural threading and orthologous sequence alignment analyses argued that the prion gene family is phylogenetically derived from a ZIP-like ancestral molecule. The level of sequence homology and the presence of prion protein genes in most chordate species place the split from the ZIP-like ancestor gene at the base of the chordate lineage. This relationship explains structural and functional features found within mammalian prion proteins as elements of an ancient involvement in the transmembrane transport of divalent cations. The phylogenetic and spatial connection to ZIP proteins is expected to open new avenues of research to elucidate the biology of the prion protein in health and disease.

Home Educating in an Extended Family Culture and Aging Society May Fare Best during a Pandemic:

Large cities can contain populations that move rapidly from one section to another in an efficient transportation network. An emerging air-borne or contact based pathogen could use these transportation routes to rapidly spread an infection throughout an entire population in a short time. Further, in many developed countries, the aging population is increasing. The family structure in these societies may also affect the course of a disease. To help understand the impact of an epidemic on family structure in a networked population, an individual based computer model that randomly generates networked cities with a specified range of population and disease characteristics and individual schedules, infectivity, transmission and hygiene factors was developed. Several salient issues emerged. First, a city of highly active individuals may in fact diminish the number of fatalities because the average duration of the interactions between agents is reduced. Second, home schooling can significantly improve survival because the institutional clustering of weak individuals is minimized. Third, the worst scenario for an aging population is the nuclear family where the aged population is confined to large housing facilities. Naturally, hygiene is the first barrier to infection. The results suggest that societies where extended families and small groups manage most of their own affairs may also be the most suitable for defense against a pandemic. This may prove applicable in city planning and policy making.

Let’s check all seven PLoS journals tonight…. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 21 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution:

Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, †Creodonta, Lipotyphla, and the †raoellid artiodactylan †Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to †Indohyus, with †Mesonychia outside of Artiodactyla. The relationships of †Mesonychia and †Indohyus are highly unstable, however – in trees only two steps longer than minimum length, †Mesonychia falls inside Artiodactyla and displaces †Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. Integration of new fossil material of †Indohyus impacts placement of another extinct clade †Mesonychia, pushing it much farther down the tree. The phylogenetic position of †Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales + hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.

How to Achieve Fast Entrainment? The Timescale to Synchronization:

Entrainment, where oscillators synchronize to an external signal, is ubiquitous in nature. The transient time leading to entrainment plays a major role in many biological processes. Our goal is to unveil the specific dynamics that leads to fast entrainment. By studying a generic model, we characterize the transient time to entrainment and show how it is governed by two basic properties of an oscillator: the radial relaxation time and the phase velocity distribution around the limit cycle. Those two basic properties are inherent in every oscillator. This concept can be applied to many biological systems to predict the average transient time to entrainment or to infer properties of the underlying oscillator from the observed transients. We found that both a sinusoidal oscillator with fast radial relaxation and a spike-like oscillator with slow radial relaxation give rise to fast entrainment. As an example, we discuss the jet-lag experiments in the mammalian circadian pacemaker.

How Are ‘Barack Obama’ and ‘President Elect’ Differentially Stored in the Brain? An ERP Investigation on the Processing of Proper and Common Noun Pairs:

One of the most debated issues in the cognitive neuroscience of language is whether distinct semantic domains are differentially represented in the brain. Clinical studies described several anomic dissociations with no clear neuroanatomical correlate. Neuroimaging studies have shown that memory retrieval is more demanding for proper than common nouns in that the former are purely arbitrary referential expressions. In this study a semantic relatedness paradigm was devised to investigate neural processing of proper and common nouns. 780 words (arranged in pairs of Italian nouns/adjectives and the first/last names of well known persons) were presented. Half pairs were semantically related (“Woody Allen” or “social security”), while the others were not (“Sigmund Parodi” or “judicial cream”). All items were balanced for length, frequency, familiarity and semantic relatedness. Participants were to decide about the semantic relatedness of the two items in a pair. RTs and N400 data suggest that the task was more demanding for common nouns. The LORETA neural generators for the related-unrelated contrast (for proper names) included the left fusiform gyrus, right medial temporal gyrus, limbic and parahippocampal regions, inferior parietal and inferior frontal areas, which are thought to be involved in the conjoined processing a familiar face with the relevant episodic information. Person name was more emotional and sensory vivid than common noun semantic access. When memory retrieval is not required, proper name access (conspecifics knowledge) is not more demanding. The neural generators of N400 to unrelated items (unknown persons and things) did not differ as a function of lexical class, thus suggesting that proper and common nouns are not treated differently as belonging to different grammatical classes.

Early In-Hospital Mortality following Trainee Doctors’ First Day at Work:

There is a commonly held assumption that early August is an unsafe period to be admitted to hospital in England, as newly qualified doctors start work in NHS hospitals on the first Wednesday of August. We investigate whether in-hospital mortality is higher in the week following the first Wednesday in August than in the previous week. A retrospective study in England using administrative hospital admissions data. Two retrospective cohorts of all emergency patients admitted on the last Wednesday in July and the first Wednesday in August for 2000 to 2008, each followed up for one week. The odds of death for patients admitted on the first Wednesday in August was 6% higher (OR 1.06, 95% CI 1.00 to 1.15, p = 0.05) after controlling for year, gender, age, socio-economic deprivation and co-morbidity. When subdivided into medical, surgical and neoplasm admissions, medical admissions admitted on the first Wednesday in August had an 8% (OR 1.08, 95% CI 1.01 to 1.16, p = 0.03) higher odds of death. In 2007 and 2008, when the system for junior doctors’ job applications changed, patients admitted on Wednesday August 1st had 8% higher adjusted odds of death than those admitted the previous Wednesday, but this was not statistically significant (OR 1.08, 95% CI 0.95 to 1.23, p = 0.24). We found evidence that patients admitted on the first Wednesday in August have a higher early death rate in English hospitals compared with patients admitted on the previous Wednesday. This was higher for patients admitted with a medical primary diagnosis.

A Mammalian Lost World in Southwest Europe during the Late Pliocene:

Over the last decades, there has been an increasing interest on the chronology, distribution and mammal taxonomy (including hominins) related with the faunal turnovers that took place around the Pliocene-Pleistocene transition [ca. 1.8 mega-annum (Ma)] in Europe. However, these turnovers are not fully understood due to: the precarious nature of the period’s fossil record; the “non-coexistence” in this record of many of the species involved; and the enormous geographical area encompassed. This palaeontological information gap can now be in part bridged with data from the Fonelas P-1 site (Granada, Spain), whose faunal composition and late Upper Pliocene date shed light on some of the problems concerning the timing and geography of the dispersals. This rich fossil site yielded 32 species of mammals, among which autochthonous species of the European Upper Villafranchian coexist with canids (Canis), ovibovines (Praeovibos) and giraffids (Mitilanotherium) from Asia. Typical African species, such as the brown hyena (Hyaena brunnea) and the bush pig (Potamochoerus) are also present. This assemblage is taxonomically and palaeobiogeographically unique, and suggests that fewer dispersal events than was previously thought (possibly only one close to 2.0 Ma) are responsible for the changes seen around 1.9-1.7 Ma ago in the fauna of the two continents.

There are 15 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov:

Photosynthetic eukaryotes with a secondary plastid of red algal origin (cryptophytes, haptophytes, stramenopiles, dinoflagellates, and apicomplexans) are hypothesized to share a single origin of plastid acquisition according to Chromalveolate hypothesis. Recent phylogenomic analyses suggest that photosynthetic “chromalveolates” form a large clade with inclusion of several non-photosynthetic protist lineages. Katablepharids are one such non-photosynthetic lineage closely related to cryptophytes. Despite their evolutionary and ecological importance, katablepharids are poorly investigated. Here, we report a newly discovered flagellate, Roombia truncata gen. et sp. nov., that is related to katablepharids, but is morphologically distinct from othermembers of the group in the following ways: (1) two flagella emerge from a papilla-like subapical protrusion, (2) conspicuous ejectisomes are aligned in multiple (5-11) rows, (3) each ejectisome increases in size towards the posterior end of the rows, and (4) upon feeding, a part of cytoplasm elastically stretch to engulf whole prey cell. Molecular phylogenies inferred from Hsp90, SSU rDNA, and LSU rDNA sequences consistently and strongly show R. truncata as the sister lineage to all other katablepharids, including lineages known only from environmental sequence surveys. A close association between katablepharids and cryptophytes was also recovered in most analyses. Katablepharids and cryptophytes are together part of a larger, more inclusive, group that also contains haptophytes, telonemids, centrohelids and perhaps biliphytes. The monophyly of this group is supported by several different molecular phylogenetic datasets and one shared lateral gene transfer; therefore, we formally establish this diverse clade as the “Hacrobia.” Our discovery of R. truncata not only expands our knowledge in the less studied flagellate group, but provide a better understanding of phylogenetic relationship and evolutionary view of plastid acquisition/losses of Hacrobia. Being an ancestral to all katablepharids, and readily cultivable, R. truncata is a good candidate for multiple gene analyses that will contribute to future phylogenetic studies of Hacrobia.

Dopamine in Motor Cortex Is Necessary for Skill Learning and Synaptic Plasticity:

Preliminary evidence indicates that dopamine given by mouth facilitates the learning of motor skills and improves the recovery of movement after stroke. The mechanism of these phenomena is unknown. Here, we describe a mechanism by demonstrating in rat that dopaminergic terminals and receptors in primary motor cortex (M1) enable motor skill learning and enhance M1 synaptic plasticity. Elimination of dopaminergic terminals in M1 specifically impaired motor skill acquisition, which was restored upon DA substitution. Execution of a previously acquired skill was unaffected. Reversible blockade of M1 D1 and D2 receptors temporarily impaired skill acquisition but not execution, and reduced long-term potentiation (LTP) within M1, a form of synaptic plasticity critically involved in skill learning. These findings identify a behavioral and functional role of dopaminergic signaling in M1. DA in M1 optimizes the learning of a novel motor skill.

There are 23 awesome new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Something Old, Something New, Something Borrowed; How the Thermoacidophilic Archaeon Sulfolobus solfataricus Responds to Oxidative Stress:

To avoid molecular damage of biomolecules due to oxidation, all cells have evolved constitutive and responsive systems to mitigate and repair chemical modifications. Archaea have adapted to some of the most extreme environments known to support life, including highly oxidizing conditions. However, in comparison to bacteria and eukaryotes, relatively little is known about the biology and biochemistry of archaea in response to changing conditions and repair of oxidative damage. In this study transcriptome, proteome, and chemical reactivity analyses of hydrogen peroxide (H2O2) induced oxidative stress in Sulfolobus solfataricus (P2) were conducted. Microarray analysis of mRNA expression showed that 102 transcripts were regulated by at least 1.5 fold, 30 minutes after exposure to 30 µM H2O2. Parallel proteomic analyses using two-dimensional differential gel electrophoresis (2D-DIGE), monitored more than 800 proteins 30 and 105 minutes after exposure and found that 18 had significant changes in abundance. A recently characterized ferritin-like antioxidant protein, DPSL, was the most highly regulated species of mRNA and protein, in addition to being post-translationally modified. As expected, a number of antioxidant related mRNAs and proteins were differentially regulated. Three of these, DPSL, superoxide dismutase, and peroxiredoxin were shown to interact and likely form a novel supramolecular complex for mitigating oxidative damage. A scheme for the ability of this complex to perform multi-step reactions is presented. Despite the central role played by DPSL, cells maintained a lower level of protection after disruption of the dpsl gene, indicating a level of redundancy in the oxidative stress pathways of S. solfataricus. This work provides the first “omics” scale assessment of the oxidative stress response for an archeal organism and together with a network analysis using data from previous studies on bacteria and eukaryotes reveals evolutionarily conserved pathways where complex and overlapping defense mechanisms protect against oxygen toxicity.

Climate Change and the Potential Spreading of Marine Mucilage and Microbial Pathogens in the Mediterranean Sea:

Marine snow (small amorphous aggregates with colloidal properties) is present in all oceans of the world. Surface water warming and the consequent increase of water column stability can favour the coalescence of marine snow into marine mucilage, large marine aggregates representing an ephemeral and extreme habitat. Marine mucilage characterize aquatic systems with altered environmental conditions. We investigated, by means of molecular techniques, viruses and prokaryotes within the mucilage and in surrounding seawater to examine the potential of mucilage to host new microbial diversity and/or spread marine diseases. We found that marine mucilage contained a large and unexpectedly exclusive microbial biodiversity and hosted pathogenic species that were absent in surrounding seawater. We also investigated the relationship between climate change and the frequency of mucilage in the Mediterranean Sea over the last 200 years and found that the number of mucilage outbreaks increased almost exponentially in the last 20 years. The increasing frequency of mucilage outbreaks is closely associated with the temperature anomalies. We conclude that the spreading of mucilage in the Mediterranean Sea is linked to climate-driven sea surface warming. The mucilage can act as a controlling factor of microbial diversity across wide oceanic regions and could have the potential to act as a carrier of specific microorganisms, thereby increasing the spread of pathogenic bacteria.

A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community:

Gray wolves (Canis lupus) were reintroduced into Yellowstone National Park (YNP) after a >70 year absence, and as part of recovery efforts, the population has been closely monitored. In 1999 and 2005, pup survival was significantly reduced, suggestive of disease outbreaks. We analyzed sympatric wolf, coyote (Canis latrans), and red fox (Vulpes vulpes) serologic data from YNP, spanning 1991-2007, to identify long-term patterns of pathogen exposure, identify associated risk factors, and examine evidence for disease-induced mortality among wolves for which there were survival data. We found high, constant exposure to canine parvovirus (wolf seroprevalence: 100%; coyote: 94%), canine adenovirus-1 (wolf pups [0.5-0.9 yr]: 91%, adults [≥1 yr]: 96%; coyote juveniles [0.5-1.5 yrs]: 18%, adults [≥1.6 yrs]: 83%), and canine herpesvirus (wolf: 87%; coyote juveniles: 23%, young adults [1.6-4.9 yrs]: 51%, old adults [≥5 yrs]: 87%) suggesting that these pathogens were enzootic within YNP wolves and coyotes. An average of 50% of wolves exhibited exposure to the protozoan parasite, Neospora caninum, although individuals’ odds of exposure tended to increase with age and was temporally variable. Wolf, coyote, and fox exposure to canine distemper virus (CDV) was temporally variable, with evidence for distinct multi-host outbreaks in 1999 and 2005, and perhaps a smaller, isolated outbreak among wolves in the interior of YNP in 2002. The years of high wolf-pup mortality in 1999 and 2005 in the northern region of the park were correlated with peaks in CDV seroprevalence, suggesting that CDV contributed to the observed mortality. Of the pathogens we examined, none appear to jeopardize the long-term population of canids in YNP. However, CDV appears capable of causing short-term population declines. Additional information on how and where CDV is maintained and the frequency with which future epizootics might be expected might be useful for future management of the Northern Rocky Mountain wolf population.

EpiCollect: Linking Smartphones to Web Applications for Epidemiology, Ecology and Community Data Collection:

Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases. Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within http://www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field workers or, for example, those data within certain values of a measured variable or a time period. Data collection frameworks utilising mobile phones with data submission to and from central databases are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting ‘citizen scientists’ to contribute data easily to central databases through their mobile phone.

A Non-Humanoid Robot in the ‘Uncanny Valley’: Experimental Analysis of the Reaction to Behavioral Contingency in 2-3 Year Old Children:

Infants’ sensitivity to social or behavioral contingency has been examined in the field of developmental psychology and behavioral sciences, mainly using a double video paradigm or a still face paradigm. These studies have shown that infants distinguish other individuals’ contingent behaviors from non-contingent ones. The present experiment systematically examined if this ability extends to the detection of non-humanoids’ contingent actions in a communicative context. We examined two- to three-year-olds’ understanding of contingent actions produced by a non-humanoid robot. The robot either responded contingently to the actions of the participants (contingent condition) or programmatically reproduced the same sequence of actions to another participant (non-contingent condition). The results revealed that the participants exhibited different patterns of response depending on whether or not the robot responded contingently. It was also found that the participants did not respond positively to the contingent actions of the robot in the earlier periods of the experimental sessions. This might reflect the conflict between the non-humanlike appearance of the robot and its humanlike contingent actions, which presumably led the children to experience the uncanny valley effect.

Monday, Monday – let’s see what’s new. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Real Lives and White Lies in the Funding of Scientific Research:

It is a summer day in 2009 in Cambridge, England, and K. (39) looks out of his lab window, wondering why he chose the life of a scientist [1]. Yet it had all begun so well! His undergraduate studies in Prague had excited him about biomedical research, and he went on to a PhD at an international laboratory in Heidelberg. There, he had every advantage, technical and intellectual, and his work had gone swimmingly. He had moved to a Wellcome-funded research institute in England in 1999. And although his postdoc grant, as is typical, was for only two years, he won a rare career development award that gave him some independence for four more years. A six-year postdoc was an unusual opportunity, and it allowed him to define his own research field. By 2004, he had published six experimental papers in good journals, and on four of these, he was first author. It was the high point in his career, and when he applied for posts in Cambridge, London, Stanford, and Tubingen, he was short-listed for them all. He chose Cambridge University and a Royal Society Research Fellowship that offered him up to ten years’ salary. This should have brought the peace of mind to plan projects that would take five years, or even longer. So, what went wrong?

Silent Springs: Why Are All the Frogs ‘Croaking’?:

Amphibians became the most ancient class of land-dwelling vertebrates when, 360 million years ago, primitive amphibia such as Ichthyostega first hauled themselves out of their aquatic environment. Since that ancient event, the amphibia have ramified into over 6,300 species of breathtaking diversity: they inhabit all continents (excepting Antarctica), from deserts to altitudes of over 5,300 metres, manufacture an astoundingly complex arsenal of chemicals, and undergo complex metamorphic transitions that bridge aquatic and terrestrial ecosystems….

Grading Quality of Evidence and Strength of Recommendations: A Perspective:

Evidence-based practice requires translating research findings into clinical and policy decision making. Clinical practice guidelines (CPGs) serve this purpose by evaluating evidence and making recommendations about therapeutic and diagnostic interventions and clinical management strategies. Systematic reviews are considered the best available evidence and are often used in the development of CPGs [1],[2]. Since guideline development involves an assessment of the overall quality of evidence and complex balancing of trade-offs between the important benefits and harms of any given intervention, arbitrariness, value judgements, and subjectivity ultimately come into play in the guideline development process and associated recommendations [3]. In order to minimize cognitive bias in interpreting evidence and make the inherently subjective process more transparent and consistent, CPGs have traditionally employed formal systems or frameworks to understand and grade the quality of the body of evidence and strength of recommendations [4],[5].

Oxygen Consumption Can Regulate the Growth of Tumors, a New Perspective on the Warburg Effect:

The unique metabolism of tumors was described many years ago by Otto Warburg, who identified tumor cells with increased glycolysis and decreased mitochondrial activity. However, “aerobic glycolysis” generates fewer ATP per glucose molecule than mitochondrial oxidative phosphorylation, so in terms of energy production, it is unclear how increasing a less efficient process provides tumors with a growth advantage. We carried out a screen for loss of genetic elements in pancreatic tumor cells that accelerated their growth as tumors, and identified mitochondrial ribosomal protein L28 (MRPL28). Knockdown of MRPL28 in these cells decreased mitochondrial activity, and increased glycolysis, but paradoxically, decreased cellular growth in vitro. Following Warburg’s observations, this mutation causes decreased mitochondrial function, compensatory increase in glycolysis and accelerated growth in vivo. Likewise, knockdown of either mitochondrial ribosomal protein L12 (MRPL12) or cytochrome oxidase had a similar effect. Conversely, expression of the mitochondrial uncoupling protein 1 (UCP1) increased oxygen consumption and decreased tumor growth. Finally, treatment of tumor bearing animals with dichloroacetate (DCA) increased pyruvate consumption in the mitochondria, increased total oxygen consumption, increased tumor hypoxia and slowed tumor growth. We interpret these findings to show that non-oncogenic genetic changes that alter mitochondrial metabolism can regulate tumor growth through modulation of the consumption of oxygen, which appears to be a rate limiting substrate for tumor proliferation.

Characterization of an Enantioselective Odorant Receptor in the Yellow Fever Mosquito Aedes aegypti:

Enantiomers differ only in the left or right handedness (chirality) of their orientations and exhibit identical chemical and physical properties. In chemical communication systems, enantiomers can be differentially active at the physiological and behavioral levels. Only recently were enantioselective odorant receptors demonstrated in mammals while their existence in insects has remained hypothetical. Using the two-microelectrode voltage clamp of Xenopus oocytes, we show that the yellow fever mosquito, Aedes aegypti, odorant receptor 8 (AaOR8) acts as a chiral selective receptor for the (R)-(–)-enantiomer of 1-octen-3-ol, which in the presence of other kairomones is an attractant used by blood-sucking insects to locate their hosts. In addition to steric constraints, chain length and degree of unsaturation play important roles in this recognition process. This is the first characterization of an enantioselective odorant receptor in insects and the results demonstrate that an OR alone, without helper proteins, can account for chiral specificity exhibited by olfactory sensory neurons (OSNs).

Eye-Hand Coordination during Dynamic Visuomotor Rotations:

For many technology-driven visuomotor tasks such as tele-surgery, human operators face situations in which the frames of reference for vision and action are misaligned and need to be compensated in order to perform the tasks with the necessary precision. The cognitive mechanisms for the selection of appropriate frames of reference are still not fully understood. This study investigated the effect of changing visual and kinesthetic frames of reference during wrist pointing, simulating activities typical for tele-operations. Using a robotic manipulandum, subjects had to perform center-out pointing movements to visual targets presented on a computer screen, by coordinating wrist flexion/extension with abduction/adduction. We compared movements in which the frames of reference were aligned (unperturbed condition) with movements performed under different combinations of visual/kinesthetic dynamic perturbations. The visual frame of reference was centered to the computer screen, while the kinesthetic frame was centered around the wrist joint. Both frames changed their orientation dynamically (angular velocity = 36°/s) with respect to the head-centered frame of reference (the eyes). Perturbations were either unimodal (visual or kinesthetic), or bimodal (visual+kinesthetic). As expected, pointing performance was best in the unperturbed condition. The spatial pointing error dramatically worsened during both unimodal and most bimodal conditions. However, in the bimodal condition, in which both disturbances were in phase, adaptation was very fast and kinematic performance indicators approached the values of the unperturbed condition. This result suggests that subjects learned to exploit an “affordance” made available by the invariant phase relation between the visual and kinesthetic frames. It seems that after detecting such invariance, subjects used the kinesthetic input as an informative signal rather than a disturbance, in order to compensate the visual rotation without going through the lengthy process of building an internal adaptation model. Practical implications are discussed as regards the design of advanced, high-performance man-machine interfaces.

There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Major Role of Microbes in Carbon Fluxes during Austral Winter in the Southern Drake Passage:

Carbon cycling in Southern Ocean is a major issue in climate change, hence the need to understand the role of biota in the regulation of carbon fixation and cycling. Southern Ocean is a heterogeneous system, characterized by a strong seasonality, due to long dark winter. Yet, currently little is known about biogeochemical dynamics during this season, particularly in the deeper part of the ocean. We studied bacterial communities and processes in summer and winter cruises in the southern Drake Passage. Here we show that in winter, when the primary production is greatly reduced, Bacteria and Archaea become the major producers of biogenic particles, at the expense of dissolved organic carbon drawdown. Heterotrophic production and chemoautotrophic CO2 fixation rates were substantial, also in deep water, and bacterial populations were controlled by protists and viruses. A dynamic food web is also consistent with the observed temporal and spatial variations in archaeal and bacterial communities that might exploit various niches. Thus, Southern Ocean microbial loop may substantially maintain a wintertime food web and system respiration at the expense of summer produced DOC as well as regenerate nutrients and iron. Our findings have important implications for Southern Ocean ecosystem functioning and carbon cycle and its manipulation by iron enrichment to achieve net sequestration of atmospheric CO2.

Does the Order of Invasive Species Removal Matter? The Case of the Eagle and the Pig:

Invasive species are recognized as a primary driver of native species endangerment and their removal is often a key component of a conservation strategy. Removing invasive species is not always a straightforward task, however, especially when they interact with other species in complex ways to negatively influence native species. Because unintended consequences may arise if all invasive species cannot be removed simultaneously, the order of their removal is of paramount importance to ecological restoration. In the mid-1990s, three subspecies of the island fox Urocyon littoralis were driven to near extinction on the northern California Channel Islands owing to heightened predation by golden eagles Aquila chrysaetos. Eagles were lured to the islands by an abundant supply of feral pigs Sus scrofa and through the process of apparent competition pigs indirectly facilitated the decline in foxes. As a consequence, both pigs and eagles had to be removed to recover the critically endangered fox. Complete removal of pigs was problematic: removing pigs first could force eagles to concentrate on the remaining foxes, increasing their probability of extinction. Removing eagles first was difficult: eagles are not easily captured and lethal removal was politically distasteful. Using prey remains collected from eagle nests both before and after the eradication of pigs, we show that one pair of eagles that eluded capture did indeed focus more on foxes. These results support the premise that if the threat of eagle predation had not been mitigated prior to pig removal, fox extinction would have been a more likely outcome. If complete eradication of all interacting invasive species is not possible, the order in which they are removed requires careful consideration. If overlooked, unexpected consequences may result that could impede restoration.

I have been remiss this week….so here’s a sampling from all seven PLoS journals over the course of this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Continue reading →

There are 15 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Continue reading →

It’s almost Friday, so let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Googling Food Webs: Can an Eigenvector Measure Species’ Importance for Coextinctions?:

Predicting the consequences of species’ extinction is a crucial problem in ecology. Species are not isolated, but connected to each others in tangled networks of relationships known as food webs. In this work we want to determine which species are critical as they support many other species. The fact that species are not independent, however, makes the problem difficult to solve. Moreover, the number of possible “importance'” rankings for species is too high to allow a solution by enumeration. Here we take a “reverse engineering” approach: we study how we can make biodiversity collapse in the most efficient way in order to investigate which species cause the most damage if removed. We show that adapting the algorithm Google uses for ranking web pages always solves this seemingly intractable problem, finding the most efficient route to collapse. The algorithm works in this sense better than all the others previously proposed and lays the foundation for a complete analysis of extinction risk in ecosystems.

Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals:

Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin’s theory of descent with modification.

A Structured Model of Video Reproduces Primary Visual Cortical Organisation:

When we look at a visual scene, neurons in our eyes “fire” short, electrical pulses in a pattern that encodes information about the visual world. This pattern passes through a series of processing stages within the brain, eventually leading to cells whose firing encodes high-level aspects of the scene, such as the identity of a visible object regardless of its position, apparent size or angle. Remarkably, features of these firing patterns, at least at the earlier stages of the pathway, can be predicted by building “efficient” codes for natural images: that is, codes based on models of the statistical properties of the environment. In this study, we have taken a first step towards extending this theoretical success to describe later stages of processing, building a model that extracts a structured representation in much the same way as does the visual system. The model describes discrete, persistent visual elements, whose appearance varies over time–a simplified version of a world built of objects that move and rotate. We show that when fit to natural image sequences, features of the “code” implied by this model match many aspects of processing in the first cortical stage of the visual system, including: the individual firing patterns of types of cells known as “simple” and “complex”; the distribution of coding properties over these cells; and even how these properties depend on the cells’ physical proximity. The model thus brings us closer to understanding the functional principles behind the organisation of the visual system.

Cortical Contributions to Saccadic Suppression:

The stability of visual perception is partly maintained by saccadic suppression: the selective reduction of visual sensitivity that accompanies rapid eye movements. The neural mechanisms responsible for this reduced perisaccadic visibility remain unknown, but the Lateral Geniculate Nucleus (LGN) has been proposed as a likely site. Our data show, however, that the saccadic suppression of a target flashed in the right visual hemifield increased with an increase in background luminance in the left visual hemifield. Because each LGN only receives retinal input from a single hemifield, this hemifield interaction cannot be explained solely on the basis of neural mechanisms operating in the LGN. Instead, this suggests that saccadic suppression must involve processing in higher level cortical areas that have access to a considerable part of the ipsilateral hemifield.

There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Direct and Indirect Effects of Climate Change on a Prairie Plant Community:

Climate change directly affects species by altering their physical environment and indirectly affects species by altering interspecific interactions such as predation and competition. Recent studies have shown that the indirect effects of climate change may amplify or counteract the direct effects. However, little is known about the the relative strength of direct and indirect effects or their potential to impact population persistence. We studied the effects of altered precipitation and interspecific interactions on the low-density tiller growth rates and biomass production of three perennial grass species in a Kansas, USA mixed prairie. We transplanted plugs of each species into local neighborhoods of heterospecific competitors and then exposed the plugs to a factorial manipulation of growing season precipitation and neighbor removal. Precipitation treatments had significant direct effects on two of the three species. Interspecific competition also had strong effects, reducing low-density tiller growth rates and aboveground biomass production for all three species. In fact, in the presence of competitors, (log) tiller growth rates were close to or below zero for all three species. However, we found no convincing evidence that per capita competitive effects changed with precipitation, as shown by a lack of significant precipitation × competition interactions. We found little evidence that altered precipitation will influence per capita competitive effects. However, based on species’ very low growth rates in the presence of competitors in some precipitation treatments, interspecific interactions appear strong enough to affect the balance between population persistence and local extinction. Therefore, ecological forecasting models should include the effect of interspecific interactions on population growth, even if such interaction coefficients are treated as constants.

Cowpox Virus Outbreak in Banded Mongooses (Mungos mungo) and Jaguarundis (Herpailurus yagouaroundi) with a Time-Delayed Infection to Humans:

Often described as an extremely rare zoonosis, cowpox virus (CPXV) infections are on the increase in Germany. CPXV is rodent-borne with a broad host range and contains the largest and most complete genome of all poxviruses, including parts with high homology to variola virus (smallpox). So far, most CPXV cases have occurred individually in unvaccinated animals and humans and were caused by genetically distinguishable virus strains. Generalized CPXV infections in banded mongooses (Mungos mungo) and jaguarundis (Herpailurus yagouaroundi) at a Zoological Garden were observed with a prevalence of the affected animal group of 100% and a mortality of 30%. A subsequent serological investigation of other exotic animal species provided evidence of subclinical cases before the onset of the outbreak. Moreover, a time-delayed human cowpox virus infection caused by the identical virus strain occurred in a different geographical area indicating that handling/feeding food rats might be the common source of infection. Reports on the increased zoonotic transmission of orthopoxviruses have renewed interest in understanding interactions between these viruses and their hosts. The list of animals known to be susceptible to CPXV is still growing. Thus, the likely existence of unknown CPXV hosts and their distribution may present a risk for other exotic animals but also for the general public, as was shown in this outbreak. Animal breeders and suppliers of food rats represent potential multipliers and distributors of CPXV, in the context of increasingly pan-European trading. Taking the cessation of vaccination against smallpox into account, this situation contributes to the increased incidence of CPXV infections in man, particularly in younger age groups, with more complicated courses of clinical infections.

Influenza Outbreak during Sydney World Youth Day 2008: The Utility of Laboratory Testing and Case Definitions on Mass Gathering Outbreak Containment:

Influenza causes annual epidemics and often results in extensive outbreaks in closed communities. To minimize transmission, a range of interventions have been suggested. For these to be effective, an accurate and timely diagnosis of influenza is required. This is confirmed by a positive laboratory test result in an individual whose symptoms are consistent with a predefined clinical case definition. However, the utility of these clinical case definitions and laboratory testing in mass gathering outbreaks remains unknown. An influenza outbreak was identified during World Youth Day 2008 in Sydney. From the data collected on pilgrims presenting to a single clinic, a Markov model was developed and validated against the actual epidemic curve. Simulations were performed to examine the utility of different clinical case definitions and laboratory testing strategies for containment of influenza outbreaks. Clinical case definitions were found to have the greatest impact on averting further cases with no added benefit when combined with any laboratory test. Although nucleic acid testing (NAT) demonstrated higher utility than indirect immunofluorescence antigen or on-site point-of-care testing, this effect was lost when laboratory NAT turnaround times was included. The main benefit of laboratory confirmation was limited to identification of true influenza cases amenable to interventions such as antiviral therapy. Continuous re-evaluation of case definitions and laboratory testing strategies are essential for effective management of influenza outbreaks during mass gatherings.

There are 7 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Re-Shuffling of Species with Climate Disruption: A No-Analog Future for California Birds?:

By facilitating independent shifts in species’ distributions, climate disruption may result in the rapid development of novel species assemblages that challenge the capacity of species to co-exist and adapt. We used a multivariate approach borrowed from paleoecology to quantify the potential change in California terrestrial breeding bird communities based on current and future species-distribution models for 60 focal species. Projections of future no-analog communities based on two climate models and two species-distribution-model algorithms indicate that by 2070 over half of California could be occupied by novel assemblages of bird species, implying the potential for dramatic community reshuffling and altered patterns of species interactions. The expected percentage of no-analog bird communities was dependent on the community scale examined, but consistent geographic patterns indicated several locations that are particularly likely to host novel bird communities in the future. These no-analog areas did not always coincide with areas of greatest projected species turnover. Efforts to conserve and manage biodiversity could be substantially improved by considering not just future changes in the distribution of individual species, but including the potential for unprecedented changes in community composition and unanticipated consequences of novel species assemblages.

Sources and Coverage of Medical News on Front Pages of US Newspapers:

Medical news that appears on newspaper front pages is intended to reach a wide audience, but how this type of medical news is prepared and distributed has not been systematically researched. We thus quantified the level of visibility achieved by front-page medical stories in the United States and analyzed their news sources. Using the online resource Newseum, we investigated front-page newspaper coverage of four prominent medical stories, and a high-profile non-medical news story as a control, reported in the US in 2007. Two characteristics were quantified by two raters: which newspaper titles carried each target front-page story (interrater agreement, >96%; kappa, >0.92) and the news sources of each target story (interrater agreement, >94%; kappa, >0.91). National rankings of the top 200 US newspapers by audited circulation were used to quantify the extent of coverage as the proportion of the total circulation of ranked newspapers in Newseum. In total, 1630 front pages were searched. Each medical story appeared on the front pages of 85 to 117 (67.5%-78.7%) ranked newspaper titles that had a cumulative daily circulation of 23.1 to 33.4 million, or 61.8% to 88.4% of all newspapers. In contrast, the non-medical story achieved front-page coverage in 152 (99.3%) newspaper titles with a total circulation of 41.0 million, or 99.8% of all newspapers. Front-page medical stories varied in their sources, but the Washington Post, Los Angeles Times, New York Times and the Associated Press together supplied 61.7% of the total coverage of target front-page medical stories. Front-page coverage of medical news from different sources is more accurately revealed by analysis of circulation counts rather than of newspaper titles. Journals wishing to widen knowledge of research news and organizations with important health announcements should target at least the four dominant media organizations identified in this study.

More than Mere Numbers: The Impact of Lethal Control on the Social Stability of a Top-Order Predator:

Population control of socially complex species may have profound ecological implications that remain largely invisible if only their abundance is considered. Here we discuss the effects of control on a socially complex top-order predator, the dingo (Canis lupus dingo). Since European occupation of Australia, dingoes have been controlled over much of the continent. Our aim was to investigate the effects of control on their abundance and social stability. We hypothesized that dingo abundance and social stability are not linearly related, and proposed a theoretical model in which dingo populations may fluctuate between three main states: (A) below carrying capacity and socially fractured, (B) above carrying capacity and socially fractured, or (C) at carrying capacity and socially stable. We predicted that lethal control would drive dingoes into the unstable states A or B, and that relaxation of control would allow recovery towards C. We tested our predictions by surveying relative abundance (track density) and indicators of social stability (scent-marking and howling) at seven sites in the arid zone subject to differing degrees of control. We also monitored changes in dingo abundance and social stability following relaxation and intensification of control. Sites where dingoes had been controlled within the previous two years were characterized by low scent-marking activity, but abundance was similar at sites with and without control. Signs of social stability steadily increased the longer an area was allowed to recover from control, but change in abundance did not follow a consistent path. Comparison of abundance and stability among all sites and years demonstrated that control severely fractures social groups, but that the effect of control on abundance was neither consistent nor predictable. Management decisions involving large social predators must therefore consider social stability to ensure their conservation and ecological functioning.

Monday – and new articles in PLoS Biology, PLoS Medicine, PLoS Neglected Tropical Diseases and PLoS ONE. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Skeeter Buster: A Stochastic, Spatially Explicit Modeling Tool for Studying Aedes aegypti Population Replacement and Population Suppression Strategies:

Dengue is a viral disease that affects approximately 50 million people annually, and is estimated to result in 12,500 fatalities. Dengue viruses are vectored by mosquitoes, predominantly by the species Aedes aegypti. Because there is currently no vaccine or specific treatment, the only available strategy to reduce dengue transmission is to control the populations of these mosquitoes. This can be achieved by traditional approaches such as insecticides, or by recently developed genetic methods that propose the release of mosquitoes genetically engineered to be unable to transmit dengue viruses. The expected outcome of different control strategies can be compared by simulating the population dynamics and genetics of mosquitoes at a given location. Development of optimal control strategies can then be guided by the modeling approach. To that end, we introduce a new modeling tool called Skeeter Buster. This model describes the dynamics and the genetics of Ae. aegypti populations at a very fine scale, simulating the contents of individual houses, and even the individual water-holding containers in which mosquito larvae reside. Skeeter Buster can be used to compare the predicted outcomes of multiple control strategies, traditional or genetic, making it an important tool in the fight against dengue.

REV-ERBα Participates in Circadian SREBP Signaling and Bile Acid Homeostasis:

The mammalian circadian timing system has a hierarchical architecture: a central pacemaker in the brain’s suprachiasmatic nucleus (SCN) synchronizes subsidiary oscillators present in most peripheral cell types. In both SCN neurons and peripheral cells, circadian oscillators are thought to rely on two negative feedback loops. A major feedback loop involves the two cryptochromes CRY1 and CRY2 and the two period proteins PER1 and PER2, which serve as transcriptional repressors for their own genes. An accessory feedback loop couples the expression and activity of the transcriptional activators CLOCK and BMAL1 to the expression of cryptochrome and period proteins. The orphan nuclear receptor REV-ERBα is a key player in this accessory feedback loop, in that it periodically represses Bmal1 transcription. In liver, molecular clocks mediate the temporal gating of metabolic processes. Here we demonstrate that hepatocyte clocks participate in the control of cholesterol and bile acid homeostasis. According to this scenario, REV-ERBα shapes the circadian expression pattern of insulin-induced gene 2 (INSIG2), a resident protein of the endoplasmic reticulum that interferes with the proteolytic activation of sterol response element binding proteins (SREBPs). In turn SREBPs govern the rhythmic expression of enzymes with key functions in sterol and fatty acid synthesis. The circadian production of sterols (in particular oxysterols) may engender the cyclic activation of LXR nuclear receptors, which serve as critical activators of Cyp7a1 transcription. CYP7A1, also known as cholesterol 7α-hydroxylase, catalyzes the rate-limiting step in bile acid synthesis.

How Humans Differ from Other Animals in Their Levels of Morphological Variation:

Animal species come in many shapes and sizes, as do the individuals and populations that make up each species. To us, humans might seem to show particularly high levels of morphological variation, but perhaps this perception is simply based on enhanced recognition of individual conspecifics relative to individual heterospecifics. We here more objectively ask how humans compare to other animals in terms of body size variation. We quantitatively compare levels of variation in body length (height) and mass within and among 99 human populations and 848 animal populations (210 species). We find that humans show low levels of within-population body height variation in comparison to body length variation in other animals. Humans do not, however, show distinctive levels of within-population body mass variation, nor of among-population body height or mass variation. These results are consistent with the idea that natural and sexual selection have reduced human height variation within populations, while maintaining it among populations. We therefore hypothesize that humans have evolved on a rugged adaptive landscape with strong selection for body height optima that differ among locations.

A Many-Body Field Theory Approach to Stochastic Models in Population Biology:

Many models used in theoretical ecology, or mathematical epidemiology are stochastic, and may also be spatially-explicit. Techniques from quantum field theory have been used before in reaction-diffusion systems, principally to investigate their critical behavior. Here we argue that they make many calculations easier and are a possible starting point for new approximations. We review the many-body field formalism for Markov processes and illustrate how to apply it to a ‘Brownian bug’ population model, and to an epidemic model. We show how the master equation and the moment hierarchy can both be written in particularly compact forms. The introduction of functional methods allows the systematic computation of the effective action, which gives the dynamics of mean quantities. We obtain the 1-loop approximation to the effective action for general (space-) translation invariant systems, and thus approximations to the non-equilibrium dynamics of the mean fields. The master equations for spatial stochastic systems normally take a neater form in the many-body field formalism. One can write down the dynamics for generating functional of physically-relevant moments, equivalent to the whole moment hierarchy. The 1-loop dynamics of the mean fields are the same as those of a particular moment-closure.

The Effects of Governmental Protected Areas and Social Initiatives for Land Protection on the Conservation of Mexican Amphibians:

Traditionally, biodiversity conservation gap analyses have been focused on governmental protected areas (PAs). However, an increasing number of social initiatives in conservation (SICs) are promoting a new perspective for analysis. SICs include all of the efforts that society implements to conserve biodiversity, such as land protection, from private reserves to community zoning plans some of which have generated community-protected areas. This is the first attempt to analyze the status of conservation in Latin America when some of these social initiatives are included. The analyses were focused on amphibians because they are one of the most threatened groups worldwide. Mexico is not an exception, where more than 60% of its amphibians are endemic. We used a niche model approach to map the potential and real geographical distribution (extracting the transformed areas) of the endemic amphibians. Based on remnant distribution, all the species have suffered some degree of loss, but 36 species have lost more than 50% of their potential distribution. For 50 micro-endemic species we could not model their potential distribution range due to the small number of records per species, therefore the analyses were performed using these records directly. We then evaluated the efficiency of the existing set of governmental protected areas and established the contribution of social initiatives (private and community) for land protection for amphibian conservation. We found that most of the species have some proportion of their potential ecological niche distribution protected, but 20% are not protected at all within governmental PAs. 73% of endemic and 26% of micro-endemic amphibians are represented within SICs. However, 30 micro-endemic species are not represented within either governmental PAs or SICs. This study shows how the role of land conservation through social initiatives is therefore becoming a crucial element for an important number of species not protected by governmental PAs.

There are 30 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Circadian Dysregulation Disrupts Bile Acid Homeostasis:

Bile acids are potentially toxic compounds and their levels of hepatic production, uptake and export are tightly regulated by many inputs, including circadian rhythm. We tested the impact of disrupting the peripheral circadian clock on integral steps of bile acid homeostasis. Both restricted feeding, which phase shifts peripheral clocks, and genetic ablation in Per1−/−/Per2−/− (PERDKO) mice disrupted normal bile acid control and resulted in hepatic cholestasis. Restricted feeding caused a dramatic, transient elevation in hepatic bile acid levels that was associated with activation of the xenobiotic receptors CAR and PXR and elevated serum aspartate aminotransferase (AST), indicative of liver damage. In the PERDKO mice, serum bile acid levels were elevated and the circadian expression of key bile acid synthesis and transport genes, including Cyp7A1 and NTCP, was lost. This was associated with blunted expression of a primary clock output, the transcription factor DBP, which transactivates the promoters of both genes. We conclude that disruption of the circadian clock results in dysregulation of bile acid homeostasis that mimics cholestatic disease.

Infant Motor Development Predicts Sports Participation at Age 14 Years: Northern Finland Birth Cohort of 1966:

Motor proficiency is positively associated with physical activity levels. The aim of this study is to investigate associations between the timing of infant motor development and subsequent sports participation during adolescence. Prospective observational study. The study population consisted of 9,009 individuals from the Northern Finland Birth Cohort 1966. Motor development was assessed by parental report at age 1 year, using age at walking with support and age at standing unaided. At follow up aged 14 years, data were collected on the school grade awarded for physical education (PE). Self report was used to collect information on the frequency of sports participation and number of different sports reported. Earlier infant motor development was associated with improved school PE grade, for age at walking supported (p<0.001) and standing unaided (p = <0.001). Earlier infant motor development, in terms of age at walking supported, was positively associated with the number of different sports reported (p = 0.003) and with a greater frequency of sports participation (p = 0.043). These associations were independent of gestational age and birth weight, as well as father's social class and body mass index at age 14 years. Earlier infant motor development may predict higher levels of physical activity as indicated by higher school PE grade, participation in a greater number of different types of sports and increased frequency of sports participation. Identification of young children with slower motor development may allow early targeted interventions to improve motor skills and thereby increase physical activity in later life.

So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Explaining Dog Wolf Differences in Utilizing Human Pointing Gestures: Selection for Synergistic Shifts in the Development of Some Social Skills:

The comparison of human related communication skills of socialized canids may help to understand the evolution and the epigenesis of gesture comprehension in humans. To reconcile previously contradicting views on the origin of dogs’ outstanding performance in utilizing human gestures, we suggest that dog-wolf differences should be studied in a more complex way. We present data both on the performance and the behaviour of dogs and wolves of different ages in a two-way object choice test. Characteristic behavioural differences showed that for wolves it took longer to establish eye contact with the pointing experimenter, they struggled more with the handler, and pups also bit her more before focusing on the human’s signal. The performance of similarly hand-reared 8-week-old dogs and wolves did not differ in utilizing the simpler proximal momentary pointing. However, when tested with the distal momentary pointing, 4-month-old pet dogs outperformed the same aged hand reared wolves. Thus early and intensive socialisation does not diminish differences between young dogs and wolves in behaviour and performance. Socialised adult wolves performed similarly well as dogs in this task without pretraining. The success of adult wolves was accompanied with increased willingness to cooperate. Thus, we provide evidence for the first time that socialised adult wolves are as successful in relying on distal momentary pointing as adult pet dogs. However, the delayed emergence of utilising human distal momentary pointing in wolves shows that these wild canines react to a lesser degree to intensive socialisation in contrast to dogs, which are able to control agonistic behaviours and inhibition of actions in a food related task early in development. We suggest a “synergistic” hypothesis, claiming that positive feedback processes (both evolutionary and epigenetic) have increased the readiness of dogs to attend to humans, providing the basis for dog-human communication.

The Origins of Lactase Persistence in Europe:

Most adults worldwide do not produce the enzyme lactase and so are unable to digest the milk sugar lactose. However, most people in Europe and many from other populations continue to produce lactase throughout their life (lactase persistence). In Europe, a single genetic variant, −13,910*T, is strongly associated with lactase persistence and appears to have been favoured by natural selection in the last 10,000 years. Since adult consumption of fresh milk was only possible after the domestication of animals, it is likely that lactase persistence coevolved with the cultural practice of dairying, although it is not known when lactase persistence first arose in Europe or what factors drove its rapid spread. To address these questions, we have developed a simulation model of the spread of lactase persistence, dairying, and farmers in Europe, and have integrated genetic and archaeological data using newly developed statistical approaches. We infer that lactase persistence/dairying coevolution began around 7,500 years ago between the central Balkans and central Europe, probably among people of the Linearbandkeramik culture. We also find that lactase persistence was not more favoured in northern latitudes through an increased requirement for dietary vitamin D. Our results illustrate the possibility of integrating genetic and archaeological data to address important questions on human evolution.

There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Playing Charades in the fMRI: Are Mirror and/or Mentalizing Areas Involved in Gestural Communication?:

Communication is an important aspect of human life, allowing us to powerfully coordinate our behaviour with that of others. Boiled down to its mere essentials, communication entails transferring a mental content from one brain to another. Spoken language obviously plays an important role in communication between human individuals. Manual gestures however often aid the semantic interpretation of the spoken message, and gestures may have played a central role in the earlier evolution of communication. Here we used the social game of charades to investigate the neural basis of gestural communication by having participants produce and interpret meaningful gestures while their brain activity was measured using functional magnetic resonance imaging. While participants decoded observed gestures, the putative mirror neuron system (pMNS: premotor, parietal and posterior mid-temporal cortex), associated with motor simulation, and the temporo-parietal junction (TPJ), associated with mentalizing and agency attribution, were significantly recruited. Of these areas only the pMNS was recruited during the production of gestures. This suggests that gestural communication relies on a combination of simulation and, during decoding, mentalizing/agency attribution brain areas. Comparing the decoding of gestures with a condition in which participants viewed the same gestures with an instruction not to interpret the gestures showed that although parts of the pMNS responded more strongly during active decoding, most of the pMNS and the TPJ did not show such significant task effects. This suggests that the mere observation of gestures recruits most of the system involved in voluntary interpretation.

Integrating Economic Costs and Biological Traits into Global Conservation Priorities for Carnivores:

Prioritization schemes usually highlight species-rich areas, where many species are at imminent risk of extinction. To be ecologically relevant these schemes should also include species biological traits into area-setting methods. Furthermore, in a world of limited funds for conservation, conservation action is constrained by land acquisition costs. Hence, including economic costs into conservation priorities can substantially improve their conservation cost-effectiveness. We examined four global conservation scenarios for carnivores based on the joint mapping of economic costs and species biological traits. These scenarios identify the most cost-effective priority sets of ecoregions, indicating best investment opportunities for safeguarding every carnivore species, and also establish priority sets that can maximize species representation in areas harboring highly vulnerable species. We compared these results with a scenario that minimizes the total number of ecoregions required for conserving all species, irrespective of other factors. We found that cost-effective conservation investments should focus on 41 ecoregions highlighted in the scenario that consider simultaneously both ecoregion vulnerability and economic costs of land acquisition. Ecoregions included in priority sets under these criteria should yield best returns of investments since they harbor species with high extinction risk and have lower mean land cost. Our study highlights ecoregions of particular importance for the conservation of the world’s carnivores defining global conservation priorities in analyses that encompass socioeconomic and life-history factors. We consider the identification of a comprehensive priority-set of areas as a first step towards an in-situ biodiversity maintenance strategy.

Social Transmission of Avoidance Behavior under Situational Change in Learned and Unlearned Rats:

Rats receive information from other conspecifics by observation or other types of social interaction. Such social interaction may contribute to the effective adaptation to changes of environment such as situational switching. Learning to avoid dangerous places or objects rapidly occurs with even a single conditioning session, and the conditioned memory tends to be sustained over long periods. The avoidance is important for adaptation, but the details of the conditions under which the social transmission of avoidance is formed are unknown. We demonstrate that the previous experience of avoidance learning is important for the formation of behaviors for social transmission of avoidance and that the experienced rats adapt to a change of situation determined by the presence or absence of aversive stimuli. We systematically investigated social influence on avoidance behavior using a passive avoidance test in a light/dark two-compartment apparatus. Rats were divided into two groups, one receiving foot shocks and another with no aversive experience in a dark compartment. Experienced and inexperienced rats were further divided into subjects and partners. In Experiment 1, each subject experienced (1) interaction with an experienced partner, (2) interaction with an inexperienced partner, or (3) no interaction. In Experiment 2, each subject experienced interaction with a partner that received a shock. The entering latency to a light compartment was measured. The avoidance behavior of experienced rats was inhibited by interaction with inexperienced or experienced partners in a safely-changed situation. The avoidance of experienced rats was reinstated in a dangerously-changed situation by interaction with shocked rats. In contrast, the inexperienced rats were not affected by any social circumstances. These results suggest that transmitted information among rats can be updated under a situational change and that the previous experience is crucial for social enhancement and inhibition of avoidance behavior in rats.

There are 33 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are many interesting articles published in PLoS ONE, PLoS Medicine, PLoS Biology and PLoS Neglected Tropical Diseases today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 15 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Hippocampal Sharp Wave/Ripples during Sleep for Consolidation of Associative Memory:

The beneficial effect of sleep on memory has been well-established by extensive research on humans, but the neurophysiological mechanisms remain a matter of speculation. This study addresses the hypothesis that the fast oscillations known as ripples recorded in the CA1 region of the hippocampus during slow wave sleep (SWS) may provide a physiological substrate for long term memory consolidation. We trained rats in a spatial discrimination task to retrieve palatable reward in three fixed locations. Hippocampal local field potentials and cortical EEG were recorded for 2 h after each daily training session. There was an increase in ripple density during SWS after early training sessions, in both trained rats and in rats randomly rewarded for exploring the maze. In rats learning the place -reward association, there was a striking further significant increase in ripple density correlated with subsequent improvements in behavioral performance as the rat learned the spatial discrimination aspect of the task. The results corroborate others showing an experience-dependent increase in ripple activity and associated ensemble replay after exploratory activity, but in addition, for the first time, reveal a clear further increase in ripple activity related to associative learning based on spatial discrimination.

Modulatory Communication Signal Performance Is Associated with a Distinct Neurogenomic State in Honey Bees:

Studies of animal communication systems have revealed that the perception of a salient signal can cause large-scale changes in brain gene expression, but little is known about how communication affects the neurogenomic state of the sender. We explored this issue by studying honey bees that produce a vibratory modulatory signal. We chose this system because it represents an extreme case of animal communication; some bees perform this behavior intensively, effectively acting as communication specialists. We show large differences in patterns of brain gene expression between individuals producing vibratory signal as compared with carefully matched non-senders. Some of the differentially regulated genes have previously been implicated in the performance of other motor activities, including courtship behavior in Drosophila melanogaster and Parkinson’s Disease in humans. Our results demonstrate for the first time a neurogenomic brain state associated with sending a communication signal and provide suggestive glimpses of molecular roots for motor control.

Monday – let’s see what’s up in PLoS Biology, PLoS Medicine, PLoS ONE and PLoS Neglected Tropical Diseases. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 29 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Apollo Number: Space Suits, Self-Support, and the Walk-Run Transition:

How space suits affect the preferred walk-run transition is an open question with relevance to human biomechanics and planetary extravehicular activity. Walking and running energetics differ; in reduced gravity (<0.5 g), running, unlike on Earth, uses less energy per distance than walking. The walk-run transition (denoted *) correlates with the Froude Number (Fr = v2/gL, velocity v, gravitational acceleration g, leg length L). Human unsuited Fr* is relatively constant (~0.5) with gravity but increases substantially with decreasing gravity below ~0.4 g, rising to 0.9 in 1/6 g; space suits appear to lower Fr*. Because of pressure forces, space suits partially (1 g) or completely (lunar-g) support their own weight. We define the Apollo Number (Ap = Fr/M) as an expected invariant of locomotion under manipulations of M, the ratio of human-supported to total transported mass. We hypothesize that for lunar suited conditions Ap* but not Fr* will be near 0.9, because the Apollo Number captures the effect of space suit self-support. We used the Apollo Lunar Surface Journal and other sources to identify 38 gait events during lunar exploration for which we could determine gait type (walk/lope/run) and calculate Ap. We estimated the binary transition between walk/lope (0) and run (1), yielding Fr* (0.36±0.11, mean±95% CI) and Ap* (0.68±0.20). The Apollo Number explains 60% of the difference between suited and unsuited Fr*, appears to capture in large part the effects of space suits on the walk-run transition, and provides several testable predictions for space suit locomotion and, of increasing relevance here on Earth, exoskeleton locomotion. The knowledge of how space suits affect gait transitions can be used to optimize space suits for use on the Moon and Mars.

Ants, Cataglyphis cursor, Use Precisely Directed Rescue Behavior to Free Entrapped Relatives:

Although helping behavior is ubiquitous throughout the animal kingdom, actual rescue activity is particularly rare. Nonetheless, here we report the first experimental evidence that ants, Cataglyphis cursor, use precisely directed rescue behavior to free entrapped victims; equally important, they carefully discriminate between individuals in distress, offering aid only to nestmates. Our experiments simulate a natural situation, which we often observed in the field when collecting Catagyphis ants, causing sand to collapse in the process. Using a novel experimental technique that binds victims experimentally, we observed the behavior of separate, randomly chosen groups of 5 C. cursor nestmates under one of six conditions. In five of these conditions, a test stimulus (the “victim”) was ensnared with nylon thread and held partially beneath the sand. The test stimulus was either (1) an individual from the same colony; (2) an individual from a different colony of C cursor; (3) an ant from a different ant species; (4) a common prey item; or, (5) a motionless (chilled) nestmate. In the final condition, the test stimulus (6) consisted of the empty snare apparatus. Our results demonstrate that ants are able to recognize what, exactly, holds their relative in place and direct their behavior to that object, the snare, in particular. They begin by excavating sand, which exposes the nylon snare, transporting sand away from it, and then biting at the snare itself. Snare biting, a behavior never before reported in the literature, demonstrates that rescue behavior is far more sophisticated, exact and complexly organized than the simple forms of helping behavior already known, namely limb pulling and sand digging. That is, limb pulling and sand digging could be released directly by a chemical call for help and thus result from a very simple mechanism. However, it’s difficult to see how this same releasing mechanism could guide rescuers to the precise location of the nylon thread, and enable them to target their bites to the thread itself.

Illusionary Self-Motion Perception in Zebrafish:

Zebrafish mutant belladonna (bel) carries a mutation in the lhx2 gene (encoding a Lim domain homeobox transcription factor) that results in a defect in retinotectal axon pathfinding, which can lead to uncrossed optic nerves failing to form an optic chiasm. Here, we report on a novel swimming behavior of the bel mutants, best described as looping. Together with two previously reported oculomotor instabilities that have been related to achiasmatic bel mutants, reversed optokinetic response (OKR) and congenital nystagmus (CN, involuntary conjugate oscillations of both eyes), looping opens a door to study the influence of visual input and eye movements on postural balance. Our result shows that looping correlates perfectly with reversed OKR and CN and is vision-dependent and contrast sensitive. CN precedes looping and the direction of the CN slow phase is predictive of the looping direction, but is absent during looping. Therefore, looping may be triggered by CN in bel. Moreover, looping in wild-type fish can also be evoked by whole-field motion, suggesting that looping in a bel mutant larvae is a result of self-motion perception. In contrary to previous hypotheses, our findings indicate that postural control in vertebrates relies on both direct visual input (afference signal) and eye-movement-related signals (efference copy or reafference signal).

Neural Correlates of Appetite and Hunger-Related Evaluative Judgments:

How much we desire a meal depends on both the constituent foods and how hungry we are, though not every meal becomes more desirable with increasing hunger. The brain therefore needs to be able to integrate hunger and meal properties to compute the correct incentive value of a meal. The present study investigated the functional role of the amygdala and the orbitofrontal cortex in mediating hunger and dish attractiveness. Furthermore, it explored neural responses to dish descriptions particularly susceptible to value-increase following fasting. We instructed participants to rate how much they wanted food menu items while they were either hungry or sated, and compared the rating differences in these states. Our results point to the representation of food value in the amygdala, and to an integration of attractiveness with hunger level in the orbitofrontal cortex. Dishes particularly desirable during hunger activated the thalamus and the insula. Our results specify the functions of evaluative structures in the context of food attractiveness, and point to a complex neural representation of dish qualities which contribute to state-dependent value.

Do Genetic Diversity Effects Drive the Benefits Associated with Multiple Mating? A Test in a Marine Invertebrate:

Mothers that mate with multiple males often produce higher quality offspring than mothers that mate with a single male. By engaging in polyandry, mothers may increase their chances of mating with a compatible male or promote sperm competition – both of which act to increase maternal fitness via the biasing of the paternity of offspring. Surprisingly, mating with multiple males, can carry benefits without biasing paternity and may be due simply to differences in genetic diversity between monandrous and polyandrous clutches but role of genetic diversity effects in driving the benefits of polyandry remains poorly tested. Disentangling indirect, genetic benefits from genetic diversity effects is challenging but crucial if we are to understand the selection pressures acting to promote polyandry. Here, we examine the post-fertilisation benefits of accessing the sperm of multiple males in an externally fertilising polychaete worm. Accessing the sperm of multiple males increases offspring performance but this benefit was driven entirely by genetic diversity effects and not by the biasing of paternity at fertilisation. Previous studies on polyandry should be interpreted cautiously as genetic diversity effects alone can explain the benefits of polyandry yet these diversity effects may be difficult to disentangle from other mechanisms. We suggest that future studies use a modified experimental design in order to discriminate between genetic diversity effects and indirect, genetic benefits.

Brain Potentials of Conflict and Error-Likelihood Following Errorful and Errorless Learning in Obsessive-Compulsive Disorder:

The anterior cingulate cortex (ACC) is thought to be overacting in patients with Obsessive Compulsive Disorder (OCD) reflecting an enhanced action monitoring system. However, influences of conflict and error-likelihood have not been explored. Here, the error-related negativity (ERN) originating in ACC served as a measure of conflict and error-likelihood during memory recognition following different learning modes. Errorless learning prevents the generation of false memory candidates and has been shown to be superior to trial-and-error-learning. The latter, errorful learning, introduces false memory candidates which interfere with correct information in later recognition leading to enhanced conflict processing. Sixteen OCD patients according to DSM-IV criteria and 16 closely matched healthy controls participated voluntarily in the event-related potential study. Both, OCD- and control group showed enhanced memory performance following errorless compared to errorful learning. Nevertheless, response-locked data showed clear modulations of the ERN amplitude. OCD patients compared to controls showed an increased error-likelihood effect after errorless learning. However, with increased conflict after errorful learning, OCD patients showed a reduced error-likelihood effect in contrast to controls who showed an increase. The increase of the errorlikelihood effect for OCD patients within low conflict situations (recognition after errorless learning) might be conceptualized as a hyperactive monitoring system. However, within high conflict situations (recognition after EF-learning) the opposite effect was observed: whereas the control group showed an increased error-likelihood effect, the OCD group showed a reduction of the error-likelihood effect based on altered ACC learning rates in response to errors. These findings support theoretical frameworks explaining differences in ACC activity on the basis of conflict and perceived error-likelihood as influenced by individual error learning rate.

The Genome Response to Artificial Selection: A Case Study in Dairy Cattle:

Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated FST within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing FST values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the FST value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.

Let’s see what’s new in PLoS ONE, PLoS Biology, PLoS Medicine and PLoS Neglected Tropical Diseases today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Long-Term Functional Side-Effects of Stimulants and Sedatives in Drosophila melanogaster:

Small invertebrate animals, such as nematodes and fruit flies, are increasingly being used to test candidate drugs both for specific therapeutic purposes and for long-term health effects. Some of the protocols used in these experiments feature such experimental design features as lifelong virginity and very low densities. By contrast, the ability of both fruit flies and nematodes to resist stress is frequently correlated with their longevity and other functional measures, suggesting that low-stress assays are not necessarily the only useful protocol for testing the long-term effects of drugs. Here we report an alternative protocol for fruit fly drug-testing that maximizes reproductive opportunities and other types of interaction, with moderately high population densities. We validate this protocol using two types of experimental tests: 1. We show that this protocol detects previously well-established genetic differences between outbred fruit fly populations. 2. We show that this protocol is able to distinguish among the long-term effects of similar types of drugs within two broad categories, stimulants and tranquilizers. Large-scale fly drug testing can be conducted using mixed-sex high-density cage assays. We find that the commonly-used stimulants caffeine and theobromine differ dramatically in their chronic functional effects, theobromine being more benign. Likewise, we find that two generic pharmaceutical tranquilizers, lithium carbonate and valproic acid, differ dramatically in their chronic effects, lithium being more benign. However, these findings do not necessarily apply to human subjects, and we thus do not recommend the use of any one substance over any other.

Distinct Parietal and Temporal Pathways to the Homologues of Broca’s Area in the Monkey:

Two distinct cortical areas in the frontal lobe of the human brain, known as Broca’s region, are involved with language production. This region has also been shown to exist in nonhuman primates. In this study, we explored the precise neural connectivity of Broca’s region in macaque monkeys using the autoradiographic method to achieve a level of detail impossible in the human brain. We identified two major streams of connections feeding into Broca’s area: a ventral stream from the temporal region, which includes areas processing auditory, multisensory, and visual information and a dorsal stream originating from the inferior parietal lobule and the adjacent superior temporal sulcus. Our detailed connectivity analysis illuminates the pathways via which posterior cortical areas can interact functionally with Broca’s region, in addition to contributing to an understanding of the evolution of language. We suggest that a fundamental function of Broca’s region is to retrieve information in a controlled strategic way from posterior cortical regions and to translate this information into action. This fundamental function was adapted during evolution of the left hemisphere of the human brain to serve language.

Motor Properties of Peripersonal Space in Humans:

A stimulus approaching the body requires fast processing and appropriate motor reactions. In monkeys, fronto-parietal networks are involved both in integrating multisensory information within a limited space surrounding the body (i.e. peripersonal space, PPS) and in action planning and execution, suggesting an overlap between sensory representations of space and motor representations of action. In the present study we investigate whether these overlapping representations also exist in the human brain. We recorded from hand muscles motor-evoked potentials (MEPs) induced by single-pulse of transcranial magnetic stimulation (TMS) after presenting an auditory stimulus either near the hand or in far space. MEPs recorded 50 ms after the near-sound onset were enhanced compared to MEPs evoked after far sounds. This near-far modulation faded at longer inter-stimulus intervals, and reversed completely for MEPs recorded 300 ms after the sound onset. At that time point, higher motor excitability was associated with far sounds. Such auditory modulation of hand motor representation was specific to a hand-centred, and not a body-centred reference frame. This pattern of corticospinal modulation highlights the relation between space and time in the PPS representation: an early facilitation for near stimuli may reflect immediate motor preparation, whereas, at later time intervals, motor preparation relates to distant stimuli potentially approaching the body.

Adaptive Lévy Walks in Foraging Fallow Deer:

Lévy flights are random walks, the step lengths of which come from probability distributions with heavy power-law tails, such that clusters of short steps are connected by rare long steps. Lévy walks maximise search efficiency of mobile foragers. Recently, several studies raised some concerns about the reliability of the statistical analysis used in previous analyses. Further, it is unclear whether Lévy walks represent adaptive strategies or emergent properties determined by the interaction between foragers and resource distribution. Thus two fundamental questions still need to be addressed: the presence of Lévy walks in the wild and whether or not they represent a form of adaptive behaviour. We studied 235 paths of solitary and clustered (i.e. foraging in group) fallow deer (Dama dama), exploiting the same pasture. We used maximum likelihood estimation for discriminating between a power-tailed distribution and the exponential alternative and rank/frequency plots to discriminate between Lévy walks and composite Brownian walks. We showed that solitary deer perform Lévy searches, while clustered animals did not adopt that strategy. Our demonstration of the presence of Lévy walks is, at our knowledge, the first available which adopts up-to-date statistical methodologies in a terrestrial mammal. Comparing solitary and clustered deer, we concluded that the Lévy walks of solitary deer represent an adaptation maximising encounter rates with forage resources and not an epiphenomenon induced by a peculiar food distribution.

Can We Systematically Review Studies That Evaluate Complex Interventions?:

The UK Medical Research Council defines complex interventions as those comprising “a number of separate elements which seem essential to the proper functioning of the interventions although the ‘active ingredient’ of the intervention that is effective is difficult to specify.” A typical example is specialist care on a stroke unit, which involves a wide range of health professionals delivering a variety of treatments. Michelle Campbell and colleagues have argued that there are “specific difficulties in defining, developing, documenting, and reproducing complex interventions that are subject to more variation than a drug” [10]. These difficulties are one of the reasons why it is challenging for researchers to systematically review complex interventions and synthesize data from separate studies. This PLoS Medicine Debate considers the challenges facing systematic reviewers and suggests several ways of addressing them.

Schizophrenia and Violence: Systematic Review and Meta-Analysis:

Schizophrenia is a lifelong, severe psychotic condition. One in 100 people will have at least one episode of schizophrenia during their lifetime. Symptoms include delusions (for example, patients believe that someone is plotting against them) and hallucinations (hearing or seeing things that are not there). In men, schizophrenia usually starts in the late teens or early 20s; women tend to develop schizophrenia a little later. The causes of schizophrenia include genetic predisposition, obstetric complications, illegal drug use (substance abuse), and experiencing traumatic life events. The condition can be treated with a combination of antipsychotic drugs and supportive therapy; hospitalization may be necessary in very serious cases to prevent self harm. Many people with schizophrenia improve sufficiently after treatment to lead satisfying lives although some patients need lifelong support and supervision.

Cross-National Analysis of the Associations among Mental Disorders and Suicidal Behavior: Findings from the WHO World Mental Health Surveys:

Suicide is a leading cause of death worldwide. Every 40 seconds, someone somewhere commits suicide. Over a year, this adds up to about 1 million self-inflicted deaths. In the USA, for example, where suicide is the 11th leading cause of death, more than 30,000 people commit suicide every year. The figures for nonfatal suicidal behavior (suicidal thoughts or ideation, suicide planning, and suicide attempts) are even more shocking. Globally, suicide attempts, for example, are estimated to be 20 times as frequent as completed suicides. Risk factors for nonfatal suicidal behaviors and for suicide include depression and other mental disorders, alcohol or drug abuse, stressful life events, a family history of suicide, and having a friend or relative commit suicide. Importantly, nonfatal suicidal behaviors are powerful predictors of subsequent suicide deaths so individuals who talk about killing themselves must always be taken seriously and given as much help as possible by friends, relatives, and mental-health professionals.

There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
What You See Is What You Get? Exclusion Performances in Ravens and Keas:

Among birds, corvids and parrots are prime candidates for advanced cognitive abilities. Still, hardly anything is known about cognitive similarities and dissimilarities between them. Recently, exclusion has gained increasing interest in comparative cognition. To select the correct option in an exclusion task, one option has to be rejected (or excluded) and the correct option may be inferred, which raises the possibility that causal understanding is involved. However, little is yet known about its evolutionary history, as only few species, and mainly mammals, have been studied. We tested ravens and keas in a choice task requiring the search for food in two differently shaped tubes. We provided the birds with partial information about the content of one of the two tubes and asked whether they could use this information to infer the location of the hidden food and adjust their searching behaviour accordingly. Additionally, this setup allowed us to investigate whether the birds would appreciate the impact of the shape of the tubes on the visibility of food. The keas chose the baited tube more often than the ravens. However, the ravens applied the more efficient strategy, choosing by exclusion more frequently than the keas. An additional experiment confirmed this, indicating that ravens and keas either differ in their cognitive skills or that they apply them differently. To our knowledge, this is the first study to demonstrate that corvids and parrots may perform differently in cognitive tasks, highlighting the potential impact of different selection pressures on the cognitive evolution of these large-brained birds.

Cognitive Processes Associated with Sequential Tool Use in New Caledonian Crows:

Using tools to act on non-food objects–for example, to make other tools–is considered to be a hallmark of human intelligence, and may have been a crucial step in our evolution. One form of this behaviour, ‘sequential tool use’, has been observed in a number of non-human primates and even in one bird, the New Caledonian crow (Corvus moneduloides). While sequential tool use has often been interpreted as evidence for advanced cognitive abilities, such as planning and analogical reasoning, the behaviour itself can be underpinned by a range of different cognitive mechanisms, which have never been explicitly examined. Here, we present experiments that not only demonstrate new tool-using capabilities in New Caledonian crows, but allow examination of the extent to which crows understand the physical interactions involved. In two experiments, we tested seven captive New Caledonian crows in six tasks requiring the use of up to three different tools in a sequence to retrieve food. Our study incorporated several novel features: (i) we tested crows on a three-tool problem (subjects were required to use a tool to retrieve a second tool, then use the second tool to retrieve a third one, and finally use the third one to reach for food); (ii) we presented tasks of different complexity in random rather than progressive order; (iii) we included a number of control conditions to test whether tool retrieval was goal-directed; and (iv) we manipulated the subjects’ pre-testing experience. Five subjects successfully used tools in a sequence (four from their first trial), and four subjects repeatedly solved the three-tool condition. Sequential tool use did not require, but was enhanced by, pre-training on each element in the sequence (‘chaining’), an explanation that could not be ruled out in earlier studies. By analyzing tool choice, tool swapping and improvement over time, we show that successful subjects did not use a random probing strategy. However, we find no firm evidence to support previous claims that sequential tool use demonstrates analogical reasoning or human-like planning. While the ability of subjects to use three tools in sequence reveals a competence beyond that observed in any other species, our study also emphasises the importance of parsimony in comparative cognitive science: seemingly intelligent behaviour can be achieved without the involvement of high-level mental faculties, and detailed analyses are necessary before accepting claims for complex cognitive abilities.

Keeping in Touch with One’s Self: Multisensory Mechanisms of Self-Consciousness:

The spatial unity between self and body can be disrupted by employing conflicting visual-somatosensory bodily input, thereby bringing neurological observations on bodily self-consciousness under scientific scrutiny. Here we designed a novel paradigm linking the study of bodily self-consciousness to the spatial representation of visuo-tactile stimuli by measuring crossmodal congruency effects (CCEs) for the full body. We measured full body CCEs by attaching four vibrator-light pairs to the trunks (backs) of subjects who viewed their bodies from behind via a camera and a head mounted display (HMD). Subjects made speeded elevation (up/down) judgments of the tactile stimuli while ignoring light stimuli. To modulate self-identification for the seen body subjects were stroked on their backs with a stick and the felt stroking was either synchronous or asynchronous with the stroking that could be seen via the HMD. We found that (1) tactile stimuli were mislocalized towards the seen body (2) CCEs were modulated systematically during visual-somatosensory conflict when subjects viewed their body but not when they viewed a body-sized object, i.e. CCEs were larger during synchronous than during asynchronous stroking of the body and (3) these changes in the mapping of tactile stimuli were induced in the same experimental condition in which predictable changes in bodily self-consciousness occurred. These data reveal that systematic alterations in the mapping of tactile stimuli occur in a full body illusion and thus establish CCE magnitude as an online performance proxy for subjective changes in global bodily self-consciousness.

Monday – time to check out PLoS Biology, PLoS Medicine and PLoS Neglected Tropical Diseases, as well as, of course, PLoS ONE.
As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Equity for Open-Access Journal Publishing by Stuart M. Shieber:

Scholars write articles to be read–the more access to their articles the better–so one might think that the open-access approach to publishing, in which articles are freely available online to all without interposition of an access fee, would be an attractive competitor to traditional subscription-based journal publishing.
But open-access journal publishing is currently at a systematic disadvantage relative to the traditional model.
I propose a simple, cost-effective remedy to this inequity that would put open-access publishing on a path to become a sustainable, efficient system, allowing the two journal publishing systems to compete on a more level playing field. The issue is important, first, because academic institutions shouldn’t perpetuate barriers to an open-access business model on principle and, second, because the subscription-fee business model has manifested systemic dysfunctionalities in practice. After describing the problem with the subscription-fee model, I turn to the proposal for providing equity for open-access journal publishing–the open-access compact.

Prolonged Grief Disorder: A Problem for the Past, the Present, and the Future:

In systematically, and to me at least, persuasively establishing prolonged grief disorder (PGD) as a uniquely identifiable illness that requires specific treatments, Holly Prigerson and colleagues have separated PGD from normal grief and from other forms of pathologic grief responses [2]. Is it useful to include it in the DSM (Diagnostic and Statistical Manual of Mental Disorders)? I believe it is for several reasons. First, treatment for PGD is effective and substantially different from treatment for other forms of psychiatric illnesses that can be triggered by or arise with grief and loss.

The Validation and Assessment of Machine Learning: A Game of Prediction from High-Dimensional Data:

In applied statistics, tools from machine learning are popular for analyzing complex and high-dimensional data. However, few theoretical results are available that could guide to the appropriate machine learning tool in a new application. Initial development of an overall strategy thus often implies that multiple methods are tested and compared on the same set of data. This is particularly difficult in situations that are prone to over-fitting where the number of subjects is low compared to the number of potential predictors. The article presents a game which provides some grounds for conducting a fair model comparison. Each player selects a modeling strategy for predicting individual response from potential predictors. A strictly proper scoring rule, bootstrap cross-validation, and a set of rules are used to make the results obtained with different strategies comparable. To illustrate the ideas, the game is applied to data from the Nugenob Study where the aim is to predict the fat oxidation capacity based on conventional factors and high-dimensional metabolomics data. Three players have chosen to use support vector machines, LASSO, and random forests, respectively.

There are 14 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are new articles in PLoS ONE, PLoS Genetics and PLoS Computational Biology today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Does the Clock Make the Poison? Circadian Variation in Response to Pesticides:

Circadian clocks govern daily physiological and molecular rhythms, and putative rhythms in expression of xenobiotic metabolizing (XM) genes have been described in both insects and mammals. Such rhythms could have important consequences for outcomes of chemical exposures at different times of day. To determine whether reported XM gene expression rhythms result in functional rhythms, we examined daily profiles of enzyme activity and dose responses to the pesticides propoxur, deltamethrin, fipronil, and malathion. Published microarray expression data were examined for temporal patterns. Male Drosophila were collected for ethoxycoumarin-O-deethylase (ECOD), esterase, glutathione-S-transferase (GST), and, and uridine 5′-diphosphoglucosyltransferase (UGT) enzyme activity assays, or subjected to dose-response tests at four hour intervals throughout the day in both light/dark and constant light conditions. Peak expression of several XM genes cluster in late afternoon. Significant diurnal variation was observed in ECOD and UGT enzyme activity, however, no significant daily variation was observed in esterase or GST activity. Daily profiles of susceptibility to lethality after acute exposure to propoxur and fipronil showed significantly increased resistance in midday, while susceptibility to deltamethrin and malathion varied little. In constant light, which interferes with clock function, the daily variation in susceptibility to propoxur and in ECOD and UGT enzyme activity was depressed. Expression and activities of specific XM enzymes fluctuate during the day, and for specific insecticides, the concentration resulting in 50% mortality varies significantly during the day. Time of day of chemical exposure should be an important consideration in experimental design, use of pesticides, and human risk assessment.

Recent and Widespread Rapid Morphological Change in Rodents:

In general, rapid morphological change in mammals has been infrequently documented. Examples that do exist are almost exclusively of rodents on islands. Such changes are usually attributed to selective release or founder events related to restricted gene flow in island settings. Here we document rapid morphological changes in rodents in 20 of 28 museum series collected on four continents, including 15 of 23 mainland sites. Approximately 17,000 measurements were taken of 1302 rodents. Trends included both increases and decreases in the 15 morphological traits measured, but slightly more trends were towards larger size. Generalized linear models indicated that changes in several of the individual morphological traits were associated with changes in human population density, current temperature gradients, and/or trends in temperature and precipitation. When we restricted these analyses to samples taken in the US (where data on human population trends were presumed to be more accurate), we found changes in two additional traits to be positively correlated with changes in human population density. Principle component analysis revealed general trends in cranial and external size, but these general trends were uncorrelated with climate or human population density. Our results indicate that over the last 100+ years, rapid morphological change in rodents has occurred quite frequently, and that these changes have taken place on the mainland as well as on islands. Our results also suggest that these changes may be driven, at least in part, by human population growth and climate change.

Scientists←Editors←Scientists: The Past, Present, and Future of PLoS Genetics:

PLoS Genetics is different: different not only because of the PLoS-wide vision for open access and new ways of communicating science, but also in terms of administration and leadership. We are, first and foremost, a community journal, where editorial decisions and direction are made by consensus. This model, where responsibility is distributed among a team of more than 80 working scientists in a way that promotes and encourages discussion, has been nourished and developed fully by Wayne Frankel, who has been with the journal since its inception, and first introduced us to PLoS Genetics exactly four years ago. As the founding Editor-in-Chief, Wayne brought us to where we are today–with nearly 150 new submissions per month, a scope that covers the entire tree of life (and occasionally synthetic biology), and a focus on scientific substance together with a goal of serving the interests of both readers and authors. In making the transition from scientist to Editor-in-Chief, and again to scientist earlier this year, Wayne’s contributions have shown how one role can strengthen the other. Happily, he remains an active member of the Editorial Board, shepherding and consulting on manuscripts in the areas of mammalian genetics and neurobiology.

Evolution of a Novel Appendage Ground Plan in Water Striders Is Driven by Changes in the Hox Gene Ultrabithorax:

Water striders are derived semi-aquatic bugs that possess a remarkable diversity of leg lengths and shapes among species and between sexes, and the selective forces shaping this diversity are well studied. The transition to living on the water surface was accompanied by dramatic changes in the size and function of their legs. The mid-legs are disproportionately long and function as oars, whereas the hind-legs are shorter and function as rudders. We present evidence demonstrating that changes in the pattern of expression and function of the Hox gene Ultrabithorax are responsible for establishing the relative size differences between mid- and hind-legs in the water strider Gerris buenoi. These changes in Ubx expression and function may have been a key event in the evolution of the distinct appendage ground plan in water striders.

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There are 21 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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