New and Exciting in PLoS ONE

There are 63 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.
Note: you may have noticed that today’s papers were not published last night as you are used to seeing them. Starting today, PLOS ONE papers are published online on the same date as the official publication date (at or close to 2pm Pacific, 5pm Eastern, I believe). That same date/time is when embrago lifts and that same date/time is the moment when article-level metrics start to get collected. Thus all four important dates/times are now one and the same – easy to remember that way, right? For those of you on the press list, the same old rule applies – before hitting the “Post” button on your blog (or Twitter, Facebook, anywhere online), first check if the paper itself is online on the PLoS site. If it is, you are free to publish your blog post. If it is not, hold off for a minute, re-check the embargo date/time, come back later and check again, or e-mail me to ask (there may be a technical problem delaying publication). By doing this, you are safe not to to break the embargo (no blogger has broken it in the past three years, so you are doing something right!).
Here are my own picks for the week – you go and look for your own favourites:

Differences in Ultrasonic Vocalizations between Wild and Laboratory California Mice (Peromyscus californicus):

Ultrasonic vocalizations (USVs) emitted by muroid rodents, including laboratory mice and rats, are used as phenotypic markers in behavioral assays and biomedical research. Interpretation of these USVs depends on understanding the significance of USV production by rodents in the wild. However, there has never been a study of muroid rodent ultrasound function in the wild and comparisons of USVs produced by wild and laboratory rodents are lacking to date. Here, we report the first comparison of wild and captive rodent USVs recorded from the same species, Peromyscus californicus. We used standard ultrasound recording techniques to measure USVs from California mice in the laboratory (Peromyscus Genetic Stock Center, SC, USA) and the wild (Hastings Natural History Reserve, CA, USA). To determine which California mouse in the wild was vocalizing, we used a remote sensing method that used a 12-microphone acoustic localization array coupled with automated radio telemetry of all resident Peromyscus californicus in the area of the acoustic localization array. California mice in the laboratory and the wild produced the same types of USV motifs. However, wild California mice produced USVs that were 2-8 kHz higher in median frequency and significantly more variable in frequency than laboratory California mice. The similarity in overall form of USVs from wild and laboratory California mice demonstrates that production of USVs by captive Peromyscus is not an artifact of captivity. Our study validates the widespread use of USVs in laboratory rodents as behavioral indicators but highlights that particular characteristics of laboratory USVs may not reflect natural conditions.

A New Auditory Multi-Class Brain-Computer Interface Paradigm: Spatial Hearing as an Informative Cue:

Most P300-based brain-computer interface (BCI) approaches use the visual modality for stimulation. For use with patients suffering from amyotrophic lateral sclerosis (ALS) this might not be the preferable choice because of sight deterioration. Moreover, using a modality different from the visual one minimizes interference with possible visual feedback. Therefore, a multi-class BCI paradigm is proposed that uses spatially distributed, auditory cues. Ten healthy subjects participated in an offline oddball task with the spatial location of the stimuli being a discriminating cue. Experiments were done in free field, with an individual speaker for each location. Different inter-stimulus intervals of 1000 ms, 300 ms and 175 ms were tested. With averaging over multiple repetitions, selection scores went over 90% for most conditions, i.e., in over 90% of the trials the correct location was selected. One subject reached a 100% correct score. Corresponding information transfer rates were high, up to an average score of 17.39 bits/minute for the 175 ms condition (best subject 25.20 bits/minute). When presenting the stimuli through a single speaker, thus effectively canceling the spatial properties of the cue, selection scores went down below 70% for most subjects. We conclude that the proposed spatial auditory paradigm is successful for healthy subjects and shows promising results that may lead to a fast BCI that solely relies on the auditory sense.

Efficient Estimation of the Robustness Region of Biological Models with Oscillatory Behavior:

Robustness is an essential feature of biological systems, and any mathematical model that describes such a system should reflect this feature. Especially, persistence of oscillatory behavior is an important issue. A benchmark model for this phenomenon is the Laub-Loomis model, a nonlinear model for cAMP oscillations in Dictyostelium discoideum. This model captures the most important features of biomolecular networks oscillating at constant frequencies. Nevertheless, the robustness of its oscillatory behavior is not yet fully understood. Given a system that exhibits oscillating behavior for some set of parameters, the central question of robustness is how far the parameters may be changed, such that the qualitative behavior does not change. The determination of such a “robustness region” in parameter space is an intricate task. If the number of parameters is high, it may be also time consuming. In the literature, several methods are proposed that partially tackle this problem. For example, some methods only detect particular bifurcations, or only find a relatively small box-shaped estimate for an irregularly shaped robustness region. Here, we present an approach that is much more general, and is especially designed to be efficient for systems with a large number of parameters. As an illustration, we apply the method first to a well understood low-dimensional system, the Rosenzweig-MacArthur model. This is a predator-prey model featuring satiation of the predator. It has only two parameters and its bifurcation diagram is available in the literature. We find a good agreement with the existing knowledge about this model. When we apply the new method to the high dimensional Laub-Loomis model, we obtain a much larger robustness region than reported earlier in the literature. This clearly demonstrates the power of our method. From the results, we conclude that the biological system underlying is much more robust than was realized until now.

Updating Systematic Reviews: An International Survey:

Systematic reviews (SRs) should be up to date to maintain their importance in informing healthcare policy and practice. However, little guidance is available about when and how to update SRs. Moreover, the updating policies and practices of organizations that commission or produce SRs are unclear. The objective was to describe the updating practices and policies of agencies that sponsor or conduct SRs. An Internet-based survey was administered to a purposive non-random sample of 195 healthcare organizations within the international SR community. Survey results were analyzed using descriptive statistics. The completed response rate was 58% (n = 114) from across 26 countries with 70% (75/107) of participants identified as producers of SRs. Among responders, 79% (84/107) characterized the importance of updating as high or very-high and 57% (60/106) of organizations reported to have a formal policy for updating. However, only 29% (35/106) of organizations made reference to a written policy document. Several groups (62/105; 59%) reported updating practices as irregular, and over half (53/103) of organizational respondents estimated that more than 50% of their respective SRs were likely out of date. Authors of the original SR (42/106; 40%) were most often deemed responsible for ensuring SRs were current. Barriers to updating included resource constraints, reviewer motivation, lack of academic credit, and limited publishing formats. Most respondents (70/100; 70%) indicated that they supported centralization of updating efforts across institutions or agencies. Furthermore, 84% (83/99) of respondents indicated they favoured the development of a central registry of SRs, analogous to efforts within the clinical trials community. Most organizations that sponsor and/or carry out SRs consider updating important. Despite this recognition, updating practices are not regular, and many organizations lack a formal written policy for updating SRs. This research marks the first baseline data available on updating from an organizational perspective.

Hydrologic Response and Watershed Sensitivity to Climate Warming in California’s Sierra Nevada:

This study focuses on the differential hydrologic response of individual watersheds to climate warming within the Sierra Nevada mountain region of California. We describe climate warming models for 15 west-slope Sierra Nevada watersheds in California under unimpaired conditions using WEAP21, a weekly one-dimensional rainfall-runoff model. Incremental climate warming alternatives increase air temperature uniformly by 2°, 4°, and 6°C, but leave other climatic variables unchanged from observed values. Results are analyzed for changes in mean annual flow, peak runoff timing, and duration of low flow conditions to highlight which watersheds are most resilient to climate warming within a region, and how individual watersheds may be affected by changes to runoff quantity and timing. Results are compared with current water resources development and ecosystem services in each watershed to gain insight into how regional climate warming may affect water supply, hydropower generation, and montane ecosystems. Overall, watersheds in the northern Sierra Nevada are most vulnerable to decreased mean annual flow, southern-central watersheds are most susceptible to runoff timing changes, and the central portion of the range is most affected by longer periods with low flow conditions. Modeling results suggest the American and Mokelumne Rivers are most vulnerable to all three metrics, and the Kern River is the most resilient, in part from the high elevations of the watershed. Our research seeks to bridge information gaps between climate change modeling and regional management planning, helping to incorporate climate change into the development of regional adaptation strategies for Sierra Nevada watersheds.

Parental and Grandparental Ages in the Autistic Spectrum Disorders: A Birth Cohort Study:

A number of studies have assessed ages of parents of children with autistic spectrum disorders (ASD), and reported both maternal and paternal age effects. Here we assess relationships with grandparental ages. We compared the parental and grandparental ages of children in the population-based Avon Longitudinal Study of Parents and Children (ALSPAC), according to their scores in regard to 4 autistic trait measures and whether they had been given a diagnosis of ASD. Mean maternal and paternal ages of ASD cases were raised, but this appears to be secondary to a maternal grandmother age effect (P = 0.006): OR = 1.66[95%CI 1.16, 2.37] for each 10-year increase in the grandmother’s age at the birth of the mother. Trait measures also revealed an association between the maternal grandmother’s age and the major autistic trait-the Coherence Scale (regression coefficient b = 0.142, [95%CI = 0.057, 0.228]P = 0.001). After allowing for confounders the effect size increased to b = 0.217[95%CI 0.125, 0.308](P<0.001) for each 10 year increase in age. Although the relationship between maternal grandmother's age and ASD and a major autistic trait was unexpected, there is some biological plausibility, for the maternal side at least, given that the timing of female meiosis I permits direct effects on the grandchild's genome during the grandmother's pregnancy. An alternative explanation is the meiotic mismatch methylation (3 M) hypothesis, presented here for the first time. Nevertheless the findings should be treated as hypothesis generating pending corroborative results from other studies.

Barcoding of Arrow Worms (Phylum Chaetognatha) from Three Oceans: Genetic Diversity and Evolution within an Enigmatic Phylum:

Arrow worms (Phylum Chaetognatha) are abundant planktonic organisms and important predators in many food webs; yet, the classification and evolutionary relationships among chaetognath species remain poorly understood. A seemingly simple body plan is underlain by subtle variation in morphological details, obscuring the affinities of species within the phylum. Many species achieve near global distributions, spanning the same latitudinal bands in all ocean basins, while others present disjunct ranges, in some cases with the same species apparently found at both poles. To better understand how these complex evolutionary and geographic variables are reflected in the species makeup of chaetognaths, we analyze DNA barcodes of the mitochondrial cytochrome oxidase c subunit I (COI) gene, from 52 specimens of 14 species of chaetognaths collected mainly from the Atlantic Ocean. Barcoding analysis was highly successful at discriminating described species of chaetognaths across the phylum, and revealed little geographical structure. This barcode analysis reveals hitherto unseen genetic variation among species of arrow worms, and provides insight into some species relationships of this enigmatic group.

CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges of the Family Irciniidae (Demospongiae: Dictyoceratida):

DNA barcoding is a promising tool to facilitate a rapid and unambiguous identification of sponge species. Demosponges of the order Dictyoceratida are particularly challenging to identify, but are of ecological as well as biochemical importance. Here we apply DNA barcoding with the standard CO1-barcoding marker on selected Indo-Pacific specimens of two genera, Ircinia and Psammocinia of the family Irciniidae. We show that the CO1 marker identifies several species new to science, reveals separate radiation patterns of deep-sea Ircinia sponges and indicates dispersal patterns of Psammocinia species. However, some species cannot be unambiguously barcoded by solely this marker due to low evolutionary rates. We support previous suggestions for a combination of the standard CO1 fragment with an additional fragment for sponge DNA barcoding.

Vesicomyidae (Bivalvia): Current Taxonomy and Distribution:

Vesicomyid bivalves are a consistent component of communities of sulphide-rich reducing environments distributed worldwide from 77° N to 70°S at depths from 100 to 9050 m. Up-to-now the taxonomy of the family has been uncertain. In this paper, the current state of vesicomyid taxonomy and distribution at the generic rank are considered. This survey is founded on a database including information both from literature sources and also unpublished data of the authors on all recent species of vesicomyids. We suggest that the Vesicomyidae is not a synonym of Kelliellidae, and is therefore a valid family name. We propose to divide the family Vesicomyidae into two subfamilies: Vesicomyinae and Pliocardiinae. The Vesicomyinae includes one genus, Vesicomya, which comprises small-sized bivalves characterized by non-reduced gut and the absence of subfilamental tissue in gills. Symbiosis with chemoautotrophic bacteria has, so far, not been proved for Vesicomya and the genus is not restricted to sulphide-rich reducing habitats. The subfamily Pliocardiinae currently contains about 15 genera with mostly medium or large body size, characterized by the presence of subfilamental tissue in the gills. The Pliocardiinae are highly specialized for sulphide-rich reducing environments, harbouring chemoautrophic bacteria in their gills. This is the first summary of the generic structure of the family Vesicomyidae that allow us to analyze the distribution of vesicomyids at the generic level. We recognize here five different distribution patterns that are related to the specific environmental demands. The general trends in the distribution patterns of the vesicomyids are an occurrence of the majority of genera in broad geographical ranges and the prevalence of near continental type of distribution.

Growing Season Temperatures in Europe and Climate Forcings Over the Past 1400 Years:

The lack of instrumental data before the mid-19th-century limits our understanding of present warming trends. In the absence of direct measurements, we used proxies that are natural or historical archives recording past climatic changes. A gridded reconstruction of spring-summer temperature was produced for Europe based on tree-rings, documentaries, pollen assemblages and ice cores. The majority of proxy series have an annual resolution. For a better inference of long-term climate variation, they were completed by low-resolution data (decadal or more), mostly on pollen and ice-core data. An original spectral analog method was devised to deal with this heterogeneous dataset, and to preserve long-term variations and the variability of temperature series. So we can replace the recent climate changes in a broader context of the past 1400 years. This preservation is possible because the method is not based on a calibration (regression) but on similarities between assemblages of proxies. The reconstruction of the April-September temperatures was validated with a Jack-knife technique. It was also compared to other spatially gridded temperature reconstructions, literature data, and glacier advance and retreat curves. We also attempted to relate the spatial distribution of European temperature anomalies to known solar and volcanic forcings. We found that our results were accurate back to 750. Cold periods prior to the 20th century can be explained partly by low solar activity and/or high volcanic activity. The Medieval Warm Period (MWP) could be correlated to higher solar activity. During the 20th century, however only anthropogenic forcing can explain the exceptionally high temperature rise. Warm periods of the Middle Age were spatially more heterogeneous than last decades, and then locally it could have been warmer. However, at the continental scale, the last decades were clearly warmer than any period of the last 1400 years. The heterogeneity of MWP versus the homogeneity of the last decades is likely an argument that different forcings could have operated. These results support the fact that we are living a climate change in Europe never seen in the past 1400 years.

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