New and Exciting in PLoS ONE

I know, I know, I’ve been traveling so I’ve been remiss at highlighting the best new articles over the past few days. In the meantime, we published 25 new articles on Friday night, 29 new articles last night, and 30 new articles tonight in PLoS ONE. So, there is a whole lot of them to check out, and as always, I will showcase below some of the stunningly good ones and some I personally am interested in. 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, 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:
Clickstream Data Yields High-Resolution Maps of Science:

Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams) that are issued by a variety of users across many different domains. Given these advantages of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science. Over the course of 2007 and 2008, we collected nearly 1 billion user interactions recorded by the scholarly web portals of some of the most significant publishers, aggregators and institutional consortia. The resulting reference data set covers a significant part of world-wide use of scholarly web portals in 2006, and provides a balanced coverage of the humanities, social sciences, and natural sciences. A journal clickstream model, i.e. a first-order Markov chain, was extracted from the sequences of user interactions in the logs. The clickstream model was validated by comparing it to the Getty Research Institute’s Architecture and Art Thesaurus. The resulting model was visualized as a journal network that outlines the relationships between various scientific domains and clarifies the connection of the social sciences and humanities to the natural sciences. Maps of science resulting from large-scale clickstream data provide a detailed, contemporary view of scientific activity and correct the underrepresentation of the social sciences and humanities that is commonly found in citation data.

Mystery Solved: The Identification of the Two Missing Romanov Children Using DNA Analysis:

One of the greatest mysteries for most of the twentieth century was the fate of the Romanov family, the last Russian monarchy. Following the abdication of Tsar Nicholas II, he and his wife, Alexandra, and their five children were eventually exiled to the city of Yekaterinburg. The family, along with four loyal members of their staff, was held captive by members of the Ural Soviet. According to historical reports, in the early morning hours of July 17, 1918 the entire family along with four loyal members of their staff was executed by a firing squad. After a failed attempt to dispose of the remains in an abandoned mine shaft, the bodies were transported to an open field only a few kilometers from the mine shaft. Nine members of the group were buried in one mass grave while two of the children were buried in a separate grave. With the official discovery of the larger mass grave in 1991, and subsequent DNA testing to confirm the identities of the Tsar, the Tsarina, and three of their daughters – doubt persisted that these remains were in fact those of the Romanov family. In the summer of 2007, a group of amateur archeologists discovered a collection of remains from the second grave approximately 70 meters from the larger grave. We report forensic DNA testing on the remains discovered in 2007 using mitochondrial DNA (mtDNA), autosomal STR, and Y- STR testing. Combined with additional DNA testing of material from the 1991 grave, we have virtually irrefutable evidence that the two individuals recovered from the 2007 grave are the two missing children of the Romanov family: the Tsarevich Alexei and one of his sisters.

Universality of Rank-Ordering Distributions in the Arts and Sciences:

Searching for generic behaviors has been one of the driving forces leading to a deep understanding and classification of diverse phenomena. Usually a starting point is the development of a phenomenology based on observations. Such is the case for power law distributions encountered in a wealth of situations coming from physics, geophysics, biology, lexicography as well as social and financial networks. This finding is however restricted to a range of values outside of which finite size corrections are often invoked. Here we uncover a universal behavior of the way in which elements of a system are distributed according to their rank with respect to a given property, valid for the full range of values, regardless of whether or not a power law has previously been suggested. We propose a two parameter functional form for these rank-ordered distributions that gives excellent fits to an impressive amount of very diverse phenomena, coming from the arts, social and natural sciences. It is a discrete version of a generalized beta distribution, given by f(r) = A(N+1-r)b/ra, where r is the rank, N its maximum value, A the normalization constant and (a, b) two fitting exponents. Prompted by our genetic sequence observations we present a growth probabilistic model incorporating mutation-duplication features that generates data complying with this distribution. The competition between permanence and change appears to be a relevant, though not necessary feature. Additionally, our observations mainly of social phenomena suggest that a multifactorial quality resulting from the convergence of several heterogeneous underlying processes is an important feature. We also explore the significance of the distribution parameters and their classifying potential. The ubiquity of our findings suggests that there must be a fundamental underlying explanation, most probably of a statistical nature, such as an appropriate central limit theorem formulation.

The Architecture of the Golfer’s Brain:

Several recent studies have shown practice-dependent structural alterations in humans. Cross-sectional studies of intensive practice of specific tasks suggest associated long-term structural adaptations. Playing golf at a high level of performance is one of the most demanding sporting activities. In this study, we report the relationship between a particular level of proficiency in playing golf (indicated by golf handicap level) and specific neuroanatomical features. Using voxel-based morphometry (VBM) of grey (GM) and white matter (WM) volumes and fractional anisotropy (FA) measures of the fibre tracts, we identified differences between skilled (professional golfers and golfers with an handicap from 1-14) and less-skilled golfers (golfers with an handicap from 15-36 and non-golfer). Larger GM volumes were found in skilled golfers in a fronto-parietal network including premotor and parietal areas. Skilled golfers revealed smaller WM volume and FA values in the vicinity of the corticospinal tract at the level of the internal and external capsule and in the parietal operculum. However, there was no structural difference within the skilled and less-skilled golfer group. There is no linear relationship between the anatomical findings and handicap level, amount of practice, and practice hours per year. There was however a strong difference between highly-practiced golfers (at least 800-3,000 hours) and those who have practised less or non-golfers without any golfing practise, thus indicating a step-wise structural and not a linear change.

Reality = Relevance? Insights from Spontaneous Modulations of the Brain’s Default Network when Telling Apart Reality from Fiction:

Although human beings regularly experience fictional worlds through activities such as reading novels and watching movies, little is known about what mechanisms underlie our implicit knowledge of the distinction between reality and fiction. The first neuroimaging study to address this issue revealed that the mere exposure to contexts involving real entities compared to fictional characters led to engagement of regions in the anterior medial prefrontal and posterior cingulate cortices (amPFC, PCC). As these core regions of the brain’s default network are involved during self-referential processing and autobiographical memory retrieval, it was hypothesized that real entities may be conceptually coded as being more personally relevant to us than fictional characters. In the present functional magnetic resonance imaging (fMRI) study, we directly test the hypothesis that entity-associated personal relevance is the critical factor underlying the differential engagement of these brain regions by comparing the brain’s response when processing contexts involving family or friends (high relevance), famous people (medium relevance), or fictional characters (low relevance). In line with predictions, a gradient pattern of activation was observed such that higher entity-associated personal relevance was associated with stronger activation in the amPFC and the PCC. The results of the study have several important implications. Firstly, they provide informed grounds for characterizing the dynamics of reality-fiction distinction. Secondly, they provide further insights into the functions of the amPFC and the PCC. Thirdly, in view of the current debate related to the functional relevance and specificity of brain’s default network, they reveal a novel approach by which the functions of this network can be further explored.

Desiccation of Rock Pool Habitats and Its Influence on Population Persistence in a Daphnia Metacommunity:

Habitat instability has an important influence on species’ occurrence and community composition. For freshwater arthropods that occur in ephemeral rock pools, the most drastic habitat instabilities are droughts and the intermittent availability of water. However, although the desiccation of a rock pool is detrimental for planktonic populations, it may also bring certain benefits: the exclusion of predators or parasites, for example, or the coexistence of otherwise competitively exclusive species. The commonness of drought resistant resting stages in many aquatic organisms shows the ecological significance of droughts. We measured daily evaporation in 50 rock pools inhabited by three Daphnia species D. magna, D. longispina and D. pulex over one summer. Daily evaporation and ultimately desiccation showed significantly seasonally influenced correlation with pool surface area, presence of vegetation, ambient temperature, wind and standardized evaporation measures. We used the estimates from this analysis to develop a simulation model to predict changes in the water level in 530 individual pools on a daily basis over a 25-year period. Eventually, hydroperiod lengths and desiccation events could be predicted for all of these rock pools. We independently confirmed the validity of this simulation by surveying desiccation events in the 530 rock pools over a whole season in 2006. In the same 530 rock pools, Daphnia communities had been recorded over the 25 years the simulation model considered. We correlated pool-specific occupation lengths of the three species with pool-specific measures of desiccation risk. Occupation lengths of all three Daphnia species were positively correlated with maximum hydroperiod length and negatively correlated with the number of desiccation events. Surprisingly, these effects were not species-specific.

Free-Ranging Macaque Mothers Exaggerate Tool-Using Behavior when Observed by Offspring:

The population-level use of tools has been reported in various animals. Nonetheless, how tool use might spread throughout a population is still an open question. In order to answer that, we observed the behavior of inserting human hair or human-hair-like material between their teeth as if they were using dental floss in a group of long-tailed macaques (Macaca fascicularis) in Thailand. The observation was undertaken by video-recording the tool-use of 7 adult females who were rearing 1-year-old infants, using the focal-animal-sampling method. When the data recorded were analyzed separately according to the presence/absence of the infant of the target animal in the target animal’s proximity, the pattern of the tool-using action of long-tailed adult female macaques under our observation changed in the presence of the infant as compared with that in the absence of the infant so that the stream of tool-using action was punctuated by more pauses, repeated more often, and performed for a longer period during each bout in the presence of the infant. We interpret this as evidence for the possibility that they exaggerate their action in tool-using so as to facilitate the learning of the action by their own infants.

Use of Number by Fish:

Research on human infants, mammals, birds and fish has demonstrated that rudimentary numerical abilities pre-date the evolution of human language. Yet there is controversy as to whether animals represent numbers mentally or rather base their judgments on non-numerical perceptual variables that co-vary with numerosity. To date, mental representation of number has been convincingly documented only for a few mammals. Here we used a training procedure to investigate whether mosquitofish could learn to discriminate between two and three objects even when denied access to non-numerical information. In the first experiment, fish were trained to discriminate between two sets of geometric figures. These varied in shape, size, brightness and distance, but no control for non-numerical variables was made. Subjects were then re-tested while controlling for one non-numerical variable at a time. Total luminance of the stimuli and the sum of perimeter of figures appeared irrelevant, but performance dropped to chance level when stimuli were matched for the cumulative surface area or for the overall space occupied by the arrays, indicating that these latter cues had been spontaneously used by the fish during the learning process. In a second experiment, where the task consisted of discriminating 2 vs 3 elements with all non-numerical variables simultaneously controlled for, all subjects proved able to learn the discrimination, and interestingly they did not make more errors than the fish in Experiment 1 that could access non-numerical information in order to accomplish the task. Mosquitofish can learn to discriminate small quantities, even when non-numerical indicators of quantity are unavailable, hence providing the first evidence that fish, like primates, can use numbers. As in humans and non-human primates, genuine counting appears to be a ‘last resort’ strategy in fish, when no other perceptual mechanism may suggest the quantity of the elements. However, our data suggest that, at least in fish, the priority of perceptual over numerical information is not related to a greater cognitive load imposed by direct numerical computation.

Self-Medication as Adaptive Plasticity: Increased Ingestion of Plant Toxins by Parasitized Caterpillars:

Self-medication is a specific therapeutic behavioral change in response to disease or parasitism. The empirical literature on self-medication has so far focused entirely on identifying cases of self-medication in which particular behaviors are linked to therapeutic outcomes. In this study, we frame self-medication in the broader realm of adaptive plasticity, which provides several testable predictions for verifying self-medication and advancing its conceptual significance. First, self-medication behavior should improve the fitness of animals infected by parasites or pathogens. Second, self-medication behavior in the absence of infection should decrease fitness. Third, infection should induce self-medication behavior. The few rigorous studies of self-medication in non-human animals have not used this theoretical framework and thus have not tested fitness costs of self-medication in the absence of disease or parasitism. Here we use manipulative experiments to test these predictions with the foraging behavior of woolly bear caterpillars (Grammia incorrupta; Lepidoptera: Arctiidae) in response to their lethal endoparasites (tachinid flies). Our experiments show that the ingestion of plant toxins called pyrrolizidine alkaloids improves the survival of parasitized caterpillars by conferring resistance against tachinid flies. Consistent with theoretical prediction, excessive ingestion of these toxins reduces the survival of unparasitized caterpillars. Parasitized caterpillars are more likely than unparasitized caterpillars to specifically ingest large amounts of pyrrolizidine alkaloids. This case challenges the conventional view that self-medication behavior is restricted to animals with advanced cognitive abilities, such as primates, and empowers the science of self-medication by placing it in the domain of adaptive plasticity theory.

Morphological Diversity and the Roles of Contingency, Chance and Determinism in African Cichlid Radiations:

Deterministic evolution, phylogenetic contingency and evolutionary chance each can influence patterns of morphological diversification during adaptive radiation. In comparative studies of replicate radiations, convergence in a common morphospace implicates determinism, whereas non-convergence suggests the importance of contingency or chance. The endemic cichlid fish assemblages of the three African great lakes have evolved similar sets of ecomorphs but show evidence of non-convergence when compared in a common morphospace, suggesting the importance of contingency and/or chance. We then analyzed the morphological diversity of each assemblage independently and compared their axes of diversification in the unconstrained global morphospace. We find that despite differences in phylogenetic composition, invasion history, and ecological setting, the three assemblages are diversifying along parallel axes through morphospace and have nearly identical variance-covariance structures among morphological elements. By demonstrating that replicate adaptive radiations are diverging along parallel axes, we have shown that non-convergence in the common morphospace is associated with convergence in the global morphospace. Applying these complimentary analyses to future comparative studies will improve our understanding of the relationship between morphological convergence and non-convergence, and the roles of contingency, chance and determinism in driving morphological diversification.

Physically Active Lifestyle Does Not Decrease the Risk of Fattening:

Increasing age is associated with declining physical activity and a gain in fat mass. The objective was to observe the consequence of the age-associated reduction in physical activity for the maintenance of energy balance as reflected in the fat store of the body. Young adults were observed over an average time interval of more than 10 years. Physical activity was measured over two-week periods with doubly labeled water and doubly labeled water validated triaxial accelerometers, and body fat gain was measured with isotope dilution. There was a significant association between the change in physical activity and the change in body fat, where a high initial activity level was predictive for a higher fat gain. The change from a physically active to a more sedentary routine does not induce an equivalent reduction of energy intake and requires cognitive restriction to maintain energy balance.

Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus):

The Iberian lynx (Lynx pardinus) is considered the most endangered felid species in the world. In order to save this species, the Spanish authorities implemented a captive breeding program recruiting lynxes from the wild. In this context, a retrospective survey on prevalence of selected feline pathogens in free-ranging lynxes was initiated. We systematically analyzed the prevalence and importance of seven viral, one protozoan (Cytauxzoon felis), and several bacterial (e.g., hemotropic mycoplasma) infections in 77 of approximately 200 remaining free-ranging Iberian lynxes of the Doñana and Sierra Morena areas, in Southern Spain, between 2003 and 2007. With the exception of feline immunodeficiency virus (FIV), evidence of infection by all tested feline pathogens was found in Iberian lynxes. Fourteen lynxes were feline leukemia virus (FeLV) provirus-positive; eleven of these were antigenemic (FeLV p27 positive). All 14 animals tested negative for other viral infections. During a six-month period in 2007, six of the provirus-positive antigenemic lynxes died. Infection with FeLV but not with other infectious agents was associated with mortality (p<0.001). Sequencing of the FeLV surface glycoprotein gene revealed a common origin for ten of the eleven samples. The ten sequences were closely related to FeLV-A/61E, originally isolated from cats in the USA. Endogenous FeLV sequences were not detected. It was concluded that the FeLV infection most likely originated from domestic cats invading the lynx's habitats. Data available regarding the time frame, co-infections, and outcome of FeLV-infections suggest that, in contrast to the domestic cat, the FeLV strain affecting the lynxes in 2007 is highly virulent to this species. Our data argue strongly for vaccination of lynxes and domestic cats in and around lynx's habitats in order to prevent further spread of the virus as well as reduction the domestic cat population if the lynx population is to be maintained.

A Large Scale shRNA Barcode Screen Identifies the Circadian Clock Component ARNTL as Putative Regulator of the p53 Tumor Suppressor Pathway:

The p53 tumor suppressor gene is mutated in about half of human cancers, but the p53 pathway is thought to be functionally inactivated in the vast majority of cancer. Understanding how tumor cells can become insensitive to p53 activation is therefore of major importance. Using an RNAi-based genetic screen, we have identified three novel genes that regulate p53 function. We have screened the NKI shRNA library targeting 8,000 human genes to identify modulators of p53 function. Using the shRNA barcode technique we were able to quickly identify active shRNA vectors from a complex mixture. Validation of the screening results indicates that the shRNA barcode technique can reliable identify active shRNA vectors from a complex pool. Using this approach we have identified three genes, ARNTL, RBCK1 and TNIP1, previously unknown to regulate p53 function. Importantly, ARNTL (BMAL1) is an established component of the circadian regulatory network. The latter finding adds to recent observations that link circadian rhythm to the cell cycle and cancer. We show that cells having suppressed ARNTL are unable to arrest upon p53 activation associated with an inability to activate the p53 target gene p21CIP1. We identified three new regulators of the p53 pathway through a functional genetic screen. The identification of the circadian core component ARNTL strengthens the link between circadian rhythm and cancer.

One response to “New and Exciting in PLoS ONE

  1. The clickstream paper is the tops. I’ve just started digging into the possibilities here, thanks!