title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-01 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Evidence for a sexual dimorphism in gene expression noise in metazoan species link: https://peerj.com/articles/750 last-modified: 2015-01-29 description: Many biological processes depend on very few copies of intervening elements, which makes such processes particularly susceptible to the stochastic fluctuations of these elements. The intrinsic stochasticity of certain processes is propagated across biological levels, causing genotype- and environment-independent biological variation which might permit populations to better cope with variable environments. Biological variations of stochastic nature might also allow the accumulation of variations at the genetic level that are hidden from natural selection, which might have a great potential for population diversification. The study of any mechanism that resulted in the modulation of stochastic variation is, therefore, of potentially wide interest. I propose that sex might be an important modulator of the stochastic variation in gene expression, i.e., gene expression noise. Based on known associations between different patterns of gene expression variation, I hypothesize that in metazoans the gene expression noise might be generally larger in heterogametic than in homogametic individuals. I directly tested this hypothesis by comparing putative genotype- and environment-independent variations in gene expression between females and males of Drosophila melanogaster strains. Also, considering the potential effect of the propagation of gene expression noise across biological levels, I indirectly tested the existence of a metazoan sexual dimorphism in gene expression noise by analyzing putative genotype- and environment-independent variation in phenotypes related to interaction with the environment in D. melanogaster strains and metazoan species. The results of these analyses are consistent with the hypothesis that gene expression is generally noisier in heterogametic than in homogametic individuals. Further analyses and discussion of existing literature permits the speculation that the sexual dimorphism in gene expression noise is ultimately based on the nuclear dynamics in gametogenesis and very early embryogenesis of sex-specific chromosomes, i.e., Y and W chromosomes. creator: Carlos Díaz-Castillo uri: https://doi.org/10.7717/peerj.750 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Díaz-Castillo title: More coral, more fish? Contrasting snapshots from a remote Pacific atoll link: https://peerj.com/articles/745 last-modified: 2015-01-29 description: Coral reefs are in decline across the globe as a result of overexploitation, pollution, disease and, more recently, climate change. The impacts of changes in coral cover on associated fish communities can be difficult to predict because of the uneven dependence of reef fish species on corals for food, shelter or the three-dimensional structure they provide. We compared live coral cover, reef fish community metrics, and their associations in two surveys of the lagoon of the remote atoll of Mataiva (French Polynesia) carried out 31 years apart. In contrast to the general pattern of decreasing coral cover reported for many parts of the Indo-Pacific region, live coral cover increased 6–7 fold at Mataiva between 1981 and 2012, and fish density nearly doubled. The stable overall reef fish species richness belied a significant shift in community structure. There was little overlap in community composition across years, and fish assemblages in 2012 were more homogeneous in composition than they were in 1981. Changes in species abundance were not clearly related to species-specific reliance on corals. The strong positive relationships between live coral cover and fish diversity and abundance noted in 1981, when coral cover rarely exceeded 10%, were no longer present in 2012, when coral cover rarely fell below this value. The most parsimonious explanation for these contrasting relationships is that, over the combined range of coral cover observed in the 1981 and 2012 snapshots, there is a rapidly asymptotic relationship between coral and fish. Our results, and other data from the south and west Pacific, suggest that fish diversity and abundance might accumulate rapidly up to a threshold of approximately 10% live coral cover. Such a relationship would have implications for our expectations of resistance and recovery of reef fish communities facing an increasingly severe regime of coral reef disturbances. creator: Ricardo Beldade creator: Suzanne C. Mills creator: Joachim Claudet creator: Isabelle M. Côté uri: https://doi.org/10.7717/peerj.745 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Beldade et al. title: Rangeland dynamics: investigating vegetation composition and structure of urban and exurban prairie dog habitat link: https://peerj.com/articles/736 last-modified: 2015-01-29 description: Rapid human population growth and habitat modification in the western United States has led to the formation of urban and exurban rangelands. Many of these rangelands are also home to populations of black-tailed prairie dogs (Cynomys ludovicianus). Our study aimed to compare the vegetation composition of an urban and exurban rangeland, and explore the role that prairie dogs play in these systems. The percent absolute canopy cover of graminoids (grasses and grass-likes), forbs, shrubs, litter, and bare ground were estimated at sampling areas located on and off prairie dog colonies at an urban and an exurban site. Herbaceous forage quality and quantity were determined on plant material collected from exclosure cages located on the colony during the entire growing season, while a relative estimate of prairie dog density was calculated using maximum counts. The exurban site had more litter and plant cover and less bare ground than the urban site. Graminoids were the dominant vegetation at the exurban plots. In contrast, mostly introduced forbs were found on the urban prairie dog colony. However, the forage quality and quantity tests demonstrated no difference between the two colonies. The relative prairie dog density was greater at the urban colony, which has the potential to drive greater vegetation utilization and reduced cover. Exurban rangeland showed lower levels of impact and retained all of the plant functional groups both on- and off-colony. These results suggest that activities of prairie dogs might further exacerbate the impacts of humans in fragmented urban rangeland habitats. Greater understanding of the drivers of these impacts and the spatial scales at which they occur are likely to prove valuable in the management and conservation of rangelands in and around urban areas. creator: Rebecca Hopson creator: Paul Meiman creator: Graeme Shannon uri: https://doi.org/10.7717/peerj.736 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hopson et al. title: First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking link: https://peerj.com/articles/740 last-modified: 2015-01-27 description: Filamentous cells belonging to the candidate bacterial phylum KSB3 were previously identified as the causative agent of fatal filament overgrowth (bulking) in a high-rate industrial anaerobic wastewater treatment bioreactor. Here, we obtained near complete genomes from two KSB3 populations in the bioreactor, including the dominant bulking filament, using differential coverage binning of metagenomic data. Fluorescence in situ hybridization with 16S rRNA-targeted probes specific for the two populations confirmed that both are filamentous organisms. Genome-based metabolic reconstruction and microscopic observation of the KSB3 filaments in the presence of sugar gradients indicate that both filament types are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility, and have a strikingly large number of sensory and response regulator genes. We propose that the KSB3 filaments are highly sensitive to their surroundings and that cellular processes, including those causing bulking, are controlled by external stimuli. The obtained genomes lay the foundation for a more detailed understanding of environmental cues used by KSB3 filaments, which may lead to more robust treatment options to prevent bulking. creator: Yuji Sekiguchi creator: Akiko Ohashi creator: Donovan H. Parks creator: Toshihiro Yamauchi creator: Gene W. Tyson creator: Philip Hugenholtz uri: https://doi.org/10.7717/peerj.740 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sekiguchi et al. title: Loss of wwox expression in zebrafish embryos causes edema and alters Ca2+ dynamics link: https://peerj.com/articles/727 last-modified: 2015-01-27 description: We investigated the role of the WW domain-containing oxidoreductase (wwox) gene in the embryonic development of zebrafish, with particular emphasis on intracellular Ca2+ dynamics because Ca2+ is an important intracellular messenger. Comparisons between zebrafish wwox and human WWOX sequences identified highly conserved domain structures. wwox was expressed in developing heart tissues in the zebrafish embryo. Moreover, wwox knockdown induced pericardial edema with similarities to conditions observed in human breast cancer. The wwox knockdown embryos with the edema died within a week. High Ca2+ levels were observed at the boundary between the edema and yolk in wwox knockdown embryos. creator: Yusuke Tsuruwaka creator: Masataka Konishi creator: Eriko Shimada uri: https://doi.org/10.7717/peerj.727 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Tsuruwaka et al. title: Temporal variability predicts the magnitude of between-group attentional blink differences in developmental dyslexia: a meta-analysis link: https://peerj.com/articles/746 last-modified: 2015-01-22 description: Background. Here we report on a meta-analysis of the between-group main effect (Group Difference) noted in the attentional blink (AB) research focused on specific reading impairment, commonly referred to as developmental dyslexia. The AB effect relates to a limitation in the allocation of attention over time and is examined in a dual-target rapid serial visual presentation (RSVP) paradigm. When the second target appears in close temporal proximity to the first target, the second target is reported less accurately.Method. A Web of Science search with terms “attentional blink” & dyslexia returned 13 AB experiments (11 papers) conducted with developmental dyslexia. After exclusions, 12 experiments were included in the meta-analysis. The main pattern of performance from those experiments was lower overall accuracy in groups of individuals with dyslexia relative to typically reading peers; that is, a between-group main effect. This meta-analysis examined the size of the Group Difference in relation to temporal and task-set related features, which differed between and within experiments.Results. Random effects modelling indicated a significant Group Difference of −0.74 standard deviation units, 95% CI [−.96, −.52], p < .001 (excluding one anomalous result): implicating significantly poorer overall dual-target performance in dyslexic readers. Meta-regression analyses indicated two variables related to the Group Difference; pre-RSVP time and temporal variability of the second target relative to the first target within the RSVP.Discussion. It is suggested that the endogenous engagement of the temporal features of task-set is slower or disrupted in developmental dyslexia. creator: Nicholas A. Badcock creator: Joanna C. Kidd uri: https://doi.org/10.7717/peerj.746 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Badcock and Kidd title: Chronologically sampled flight feathers permits recognition of individual molt-migrants due to varying protein sources link: https://peerj.com/articles/743 last-modified: 2015-01-22 description: This is a proof of concept paper based on chronological samples of growing feathers from geese thought to be molt-migrants. When molt-migrant birds initiate molt shortly after migrating to a new isoscape, isotope values measured along the length of their feathers should change continuously. To assess long-term changes and daily cycling in δ15N and δ13C values, we serially sampled a growing primary from three presumed molt-migrant geese. Two showed changing δ15N signatures along the length of their growing primary, indicating they were molt-migrants, while the third, presumably a resident, showed no change. We then resampled these feathers at closer intervals for evidence of the predicted diel cycle in the use of exogenous and endogenous protein for feather growth, generated by the diel feeding cycle of these geese. As predicted, a periodicity of ca. 24 h in δ15N values was found along the primary of the two equilibrating geese, but not in the other goose that was probably a resident. Our results demonstrate that chronological sampling along the length of individual primaries holds great potential for identifying individuals that are molt-migrants. creator: Sievert Rohwer creator: Anthony D. Fox creator: Thomas Daniel creator: Jeffrey F. Kelly uri: https://doi.org/10.7717/peerj.743 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Rohwer et al. title: First photographic records of the giant manta ray Manta birostris off eastern Australia link: https://peerj.com/articles/742 last-modified: 2015-01-22 description: We present the first photographic evidence of the presence of the giant manta ray Manta birostris in east Australian waters. Two individuals were photographed off Montague Island in New South Wales and off the north east coast of Tasmania, during summer 2012 and 2014, respectively. These sightings confirm previous unverified reports on the species occurrence and extend the known distribution range of M. birostris to 40°S. We discuss these findings in the context of the species’ migratory behaviour, the regional oceanography along the south east Australian coastline and local productivity events. creator: Lydie I.E. Couturier creator: Fabrice R.A. Jaine creator: Tom Kashiwagi uri: https://doi.org/10.7717/peerj.742 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Couturier et al. title: The association between shame and substance use in young people: a systematic review link: https://peerj.com/articles/737 last-modified: 2015-01-22 description: Background. Shame has been associated with a range of maladaptive behaviours, including substance use. Young people may be particularly vulnerable to heightened shame sensitivity, and substance use is a significant problem amongst UK adolescents. Although there appears to be a relationship between shame and substance use, the direction of the relationship remains unclear.Aim. The purpose of this study was to undertake a systematic review of the literature relating to shame and substance use in young people.Method. Five electronic databases were searched for articles containing terms related to ‘adolescence,’ ‘shame’ and ‘substance use.’ Six articles were included in the final analyses.Results. Adverse early experiences, particularly sexual abuse, predict shame-proneness, and substance use is a mechanism by which some individuals cope with negative feelings. In general, there is a dearth of literature investigating the shame-substance use relationship in adolescent samples. The available literature associates shame-proneness with poorer functioning and suggests that it may potentially lead to psychopathology and early-onset substance use. Scant attention has been paid to the cognitive and emotional processes implicated. Further research is required to ascertain the strength of the shame-substance use relationship in young people and to develop appropriate interventions for this population. creator: Masuma Rahim creator: Robert Patton uri: https://doi.org/10.7717/peerj.737 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Rahim and Patton title: A surge of p-values between 0.041 and 0.049 in recent decades (but negative results are increasing rapidly too) link: https://peerj.com/articles/733 last-modified: 2015-01-22 description: It is known that statistically significant (positive) results are more likely to be published than non-significant (negative) results. However, it has been unclear whether any increasing prevalence of positive results is stronger in the “softer” disciplines (social sciences) than in the “harder” disciplines (physical sciences), and whether the prevalence of negative results is decreasing over time. Using Scopus, we searched the abstracts of papers published between 1990 and 2013, and measured longitudinal trends of multiple expressions of positive versus negative results, including p-values between 0.041 and 0.049 versus p-values between 0.051 and 0.059, textual reporting of “significant difference” versus “no significant difference,” and the reporting of p < 0.05 versus p > 0.05. We found no support for a “hierarchy of sciences” with physical sciences at the top and social sciences at the bottom. However, we found large differences in reporting practices between disciplines, with p-values between 0.041 and 0.049 over 1990–2013 being 65.7 times more prevalent in the biological sciences than in the physical sciences. The p-values near the significance threshold of 0.05 on either side have both increased but with those p-values between 0.041 and 0.049 having increased to a greater extent (2013-to-1990 ratio of the percentage of papers = 10.3) than those between 0.051 and 0.059 (ratio = 3.6). Contradictorily, p < 0.05 has increased more slowly than p > 0.05 (ratios = 1.4 and 4.8, respectively), while the use of “significant difference” has shown only a modest increase compared to “no significant difference” (ratios = 1.5 and 1.1, respectively). We also compared reporting of significance in the United States, Asia, and Europe and found that the results are too inconsistent to draw conclusions on cross-cultural differences in significance reporting. We argue that the observed longitudinal trends are caused by negative factors, such as an increase of questionable research practices, but also by positive factors, such as an increase of quantitative research and structured reporting. creator: Joost CF de Winter creator: Dimitra Dodou uri: https://doi.org/10.7717/peerj.733 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 de Winter and Dodou title: From a word to a world: the current situation in the interdisciplinary field of synthetic biology link: https://peerj.com/articles/728 last-modified: 2015-01-22 description: Using a carefully designed search query, we describe the field of synthetic biology in terms of leading countries, organizations and funding sources. Besides articles we also paid some attention to patents. The USA is the leading country in this field, followed by China. There is a clear exponential growth in the field of synthetic biology over the latest 14 years. Keywords were analyzed using the notion of year-based h-indices, core gap and relative core gap. We conclude that the term “synthetic biology” hides a large world ready to be explored by interdisciplinary research. creator: Xiaojun Hu creator: Ronald Rousseau uri: https://doi.org/10.7717/peerj.728 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hu and Rousseau title: Health-related quality of life and emotional and behavioral difficulties after extreme preterm birth: developmental trajectories link: https://peerj.com/articles/738 last-modified: 2015-01-20 description: Background. Knowledge of long-term health related outcomes in contemporary populations born extremely preterm (EP) is scarce. We aimed to explore developmental trajectories of health-related quality of life (HRQoL) and behavior from mid-childhood to early adulthood in extremely preterm and term-born individuals.Methods. Subjects born at gestational age ≤28 weeks or with birth weight ≤1,000 g within a region of Norway in 1991–92 and matched term-born control subjects were assessed at 10 and 18 years. HRQoL was measured with the Child Health Questionnaire (CHQ) and behavior with the Child Behavior Checklist (CBCL), using parent assessment at both ages and self-assessment at 18 years.Results. All eligible EP (n = 35) and control children participated at 10 years, and 31 (89%) and 29 (83%) at 18 years. At 10 years, the EP born boys were given significantly poorer scores by their parents than term-born controls on most CHQ and CBCL scales, but the differences were minor at 18 years; i.e., significant improvements had occurred in several CHQ (self-esteem, general health and parental impact-time) and CBCL (total problem, internalizing and anxious/depressed) scales. For the girls, the differences were smaller at 10 years and remained unchanged by 18 years. Emotional/behavioral difficulties at 10 years similarly predicted poorer improvement on CHQ-scales for both EP and term-born subjects at 18 years. Self-assessment of HRQoL and behavior at 18 years was similar in the EP and term-born groups on most scales.Conclusions. HRQoL and behavior improved towards adulthood for EP born boys, while the girls remained relatively similar, and early emotional and behavioral difficulties predicted poorer development in HRQoL through adolescence. These data indicate that gender and a longitudinal perspective should be considered when addressing health and wellbeing after extremely preterm birth. creator: Bente Johanne Vederhus creator: Geir Egil Eide creator: Gerd Karin Natvig creator: Trond Markestad creator: Marit Graue creator: Thomas Halvorsen uri: https://doi.org/10.7717/peerj.738 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Vederhus et al. title: The landscape configuration of zoonotic transmission of Ebola virus disease in West and Central Africa: interaction between population density and vegetation cover link: https://peerj.com/articles/735 last-modified: 2015-01-20 description: Ebola virus disease (EVD) is an emerging infectious disease of zoonotic origin that has been responsible for high mortality and significant social disruption in West and Central Africa. Zoonotic transmission of EVD requires contact between susceptible human hosts and the reservoir species for Ebolaviruses, which are believed to be fruit bats. Nevertheless, features of the landscape that may facilitate such points of contact have not yet been adequately identified. Nor have spatial dependencies between zoonotic EVD transmission and landscape structures been delineated. This investigation sought to describe the spatial relationship between zoonotic EVD transmission events, or spillovers, and population density and vegetation cover. An inhomogeneous Poisson process model was fitted to all precisely geolocated zoonotic transmissions of EVD in West and Central Africa. Population density was strongly associated with spillover; however, there was significant interaction between population density and green vegetation cover. In areas of very low population density, increasing vegetation cover was associated with a decrease in risk of zoonotic transmission, but as population density increased in a given area, increasing vegetation cover was associated with increased risk of zoonotic transmission. This study showed that the spatial dependencies of Ebolavirus spillover were associated with the distribution of population density and vegetation cover in the landscape, even after controlling for climate and altitude. While this is an observational study, and thus precludes direct causal inference, the findings do highlight areas that may be at risk for zoonotic EVD transmission based on the spatial configuration of important features of the landscape. creator: Michael G. Walsh creator: MA Haseeb uri: https://doi.org/10.7717/peerj.735 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Walsh and Haseeb title: Captive rearing of the deep-sea coral Eguchipsammia fistula from the Red Sea demonstrates remarkable physiological plasticity link: https://peerj.com/articles/734 last-modified: 2015-01-20 description: The presence of the cosmopolitan deep-sea coral Eguchipsammia fistula has recently been documented in the Red Sea, occurring in warm (>20 °C), oxygen- and nutrient-limited habitats. We collected colonies of this species from the central Red Sea that successfully resided in aquaria for more than one year. During this period the corals were exposed to increased oxygen levels and nutrition ad libitum unlike in their natural habitat. Specimens of long-term reared E. fistula colonies were incubated for 24 h and calcification (G) as well as respiration rates (R) were measured. In comparison to on-board measurements of G and R rates on freshly collected specimens, we found that G was increased while R was decreased. E. fistula shows extensive tissue growth and polyp proliferation in aquaculture and can be kept at conditions that notably differ from its natural habitat. Its ability to cope with rapid and prolonged changes in regard to prevailing environmental conditions indicates a wide physiological plasticity. This may explain in part the cosmopolitan distribution of this species and emphasizes its value as a deep-sea coral model to study mechanisms of acclimation and adaptation. creator: Anna Roik creator: Till Röthig creator: Cornelia Roder creator: Paul J. Müller creator: Christian R. Voolstra uri: https://doi.org/10.7717/peerj.734 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Roik et al. title: Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus link: https://peerj.com/articles/731 last-modified: 2015-01-20 description: The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy–Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species. creator: Carla Sousa-Santos creator: Paulo J. Fonseca creator: Maria Clara P. Amorim uri: https://doi.org/10.7717/peerj.731 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sousa-Santos et al. title: A quantitative approach for integrating multiple lines of evidence for the evaluation of environmental health risks link: https://peerj.com/articles/730 last-modified: 2015-01-15 description: Decision analysis often considers multiple lines of evidence during the decision making process. Researchers and government agencies have advocated for quantitative weight-of-evidence approaches in which multiple lines of evidence can be considered when estimating risk. Therefore, we utilized Bayesian Markov Chain Monte Carlo to integrate several human-health risk assessment, biomonitoring, and epidemiology studies that have been conducted for two common insecticides (malathion and permethrin) used for adult mosquito management to generate an overall estimate of risk quotient (RQ). The utility of the Bayesian inference for risk management is that the estimated risk represents a probability distribution from which the probability of exceeding a threshold can be estimated. The mean RQs after all studies were incorporated were 0.4386, with a variance of 0.0163 for malathion and 0.3281 with a variance of 0.0083 for permethrin. After taking into account all of the evidence available on the risks of ULV insecticides, the probability that malathion or permethrin would exceed a level of concern was less than 0.0001. Bayesian estimates can substantially improve decisions by allowing decision makers to estimate the probability that a risk will exceed a level of concern by considering seemingly disparate lines of evidence. creator: Jerome J. Schleier III creator: Lucy A. Marshall creator: Ryan S. Davis creator: Robert K.D. Peterson uri: https://doi.org/10.7717/peerj.730 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Schleier III et al. title: The socio-matrix reloaded: from hierarchy to dominance profile in wild lemurs link: https://peerj.com/articles/729 last-modified: 2015-01-15 description: Dominance hierarchy influences the life quality of social animals, and its definition should in principle be based on the outcome of agonistic interactions. However, defining and comparing the dominance profile of social groups is difficult due to the different dominance measures used and because no one measure explains it all. We applied different analytical methods to winner-loser sociomatrices to determine the dominance profile of five groups of wild lemurs (species: Lemur catta, Propithecus verreauxi, and Eulemur rufus x collaris) from the Berenty forest (Madagascar). They are an excellent study model because they share the same habitat and an apparently similar dominance profile: linear hierarchy and female dominance. Data were collected over more than 1200 h of observation. Our approach included four steps: (1) by applying the binary dyadic dominance relationship method (I&SI) on either aggressions or supplant sociomatrices we verified whether hierarchy was aggression or submission based; (2) by calculating normalized David’s scores and measuring steepness from aggression sociomatrices we evaluated whether hierarchy was shallow or steep; (3) by comparing the ranking orders obtained with methods 1 and 2 we assessed whether hierarchy was consistent or not; and (4) by assessing triangle transitivity and comparing it with the linearity index and the level of group cohesion we determined if hierarchy was more or less cohesive. Our results show that L. catta groups have got a steep, consistent, highly transitive and cohesive hierarchy. P. verreauxi groups are characterized by a moderately steep and consistent hierarchy, with variable levels of triangle transitivity and cohesion. E. rufus x collaris group possesses a shallow and inconsistent hierarchy, with lower (but not lowest) levels of transitivity and cohesion. A multiple analytical approach on winner-loser sociomatrices other than leading to an in-depth description of the dominance profile, allows intergroup and cross-species comparisons. creator: Ivan Norscia creator: Elisabetta Palagi uri: https://doi.org/10.7717/peerj.729 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Norscia and Palagi title: Changes in the timing of departure and arrival of Irish migrant waterbirds link: https://peerj.com/articles/726 last-modified: 2015-01-15 description: There have been many recent reports across Europe and North America of a change in the timing of arrival and departure of a range of migrant bird species to their breeding grounds. These studies have focused primarily on passerine birds and climate warming has been found to be one of the main drivers of earlier arrival and departure in spring. In Ireland, rising spring temperature has been shown to result in the earlier arrival of sub-Saharan passerine species and the early departure of the Whooper Swan. In order to investigate changes in spring arrival and departure dates of waterbirds to Ireland, we extracted latest dates as an indicator of the timing of departure of winter visitors (24 species) and earliest dates as an indicator of the timing of arrival of spring/summer migrants (2 species) from BirdWatch Ireland’s East Coast Bird reports (1980–2003). Three of the winter visitors showed evidence of later departure and one of earlier departure whereas one of the spring/summer visitors showed evidence of earlier arrival. In order to determine any influence of local temperature on these trends, we analysed data from two synoptic weather stations within the study area and found that spring (average February, March and April) air temperature significantly (P < 0.05) increased at a rate of 0.03 °C per year, which was strongly correlated with changes in latest and earliest records. We also tested the sensitivity of bird departure/arrival to temperature and found that Northern Pintail would leave 10 days earlier in response to a 1 °C increase in spring temperature. In addition, we investigated the impact of a large-scale circulation pattern, the North Atlantic Oscillation (NAO), on the timing of arrival and departure which correlated with both advances and delays in departure and arrival. We conclude that the impact of climate change on earliest and latest records of these birds is, as expected, species specific and that local temperature had less of an influence than large-scale circulation patterns. creator: Alison Donnelly creator: Heather Geyer creator: Rong Yu uri: https://doi.org/10.7717/peerj.726 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Donnelly et al. title: Using citizen-science data to identify local hotspots of seabird occurrence link: https://peerj.com/articles/704 last-modified: 2015-01-15 description: Seabirds have been identified and used as indicators of ecosystem processes such as climate change and human activity in nearshore ecosystems around the globe. Temporal and spatial trends have been documented at large spatial scales, but few studies have examined more localized patterns of spatiotemporal variation, by species or functional group. In this paper, we apply spatial occupancy models to assess the spatial patchiness and interannual trends of 18 seabird species in the Puget Sound region (Washington State, USA). Our dataset, the Puget Sound Seabird Survey of the Seattle Audubon Society, is unique in that it represents a seven-year study, collected with a focus on winter months (October–April). Despite historic declines of seabirds in the region over the last 50 years, results from our study are optimistic, suggesting increases in probabilities of occurrence for 14 of the 18 species included. We found support for declines in occurrence for white-winged scoters, brants, and 2 species of grebes. The decline of Western grebes in particular is troubling, but in agreement with other recent studies that have shown support for a range shift south in recent years, to the southern end of California Current. creator: Eric J. Ward creator: Kristin N. Marshall creator: Toby Ross creator: Adam Sedgley creator: Todd Hass creator: Scott F. Pearson creator: Gerald Joyce creator: Nathalie J. Hamel creator: Peter J. Hodum creator: Rob Faucett uri: https://doi.org/10.7717/peerj.704 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ward et al. title: Tandem-repeat protein domains across the tree of life link: https://peerj.com/articles/732 last-modified: 2015-01-13 description: Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. creator: Kristin K. Jernigan creator: Seth R. Bordenstein uri: https://doi.org/10.7717/peerj.732 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Jernigan and Bordenstein title: DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit link: https://peerj.com/articles/725 last-modified: 2015-01-13 description: During the past few years, pharmacophore modeling has become one of the key components in computer-aided drug design and in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design) to perform pharmacophore modeling through an efficient combination of the PharmACOphore, Gromacs, Ligbuilder and PDB2PQR suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process. For the pharmacophore modeling we are focusing on either the characteristics of the receptor or the full molecular system, including a set of selected ligands. DrugOn can be freely downloaded from our dedicated server system at www.bioacademy.gr/bioinformatics/drugon/. creator: Dimitrios Vlachakis creator: Paraskevas Fakourelis creator: Vasileios Megalooikonomou creator: Christos Makris creator: Sophia Kossida uri: https://doi.org/10.7717/peerj.725 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Vlachakis et al. title: Sizing ocean giants: patterns of intraspecific size variation in marine megafauna link: https://peerj.com/articles/715 last-modified: 2015-01-13 description: What are the greatest sizes that the largest marine megafauna obtain? This is a simple question with a difficult and complex answer. Many of the largest-sized species occur in the world’s oceans. For many of these, rarity, remoteness, and quite simply the logistics of measuring these giants has made obtaining accurate size measurements difficult. Inaccurate reports of maximum sizes run rampant through the scientific literature and popular media. Moreover, how intraspecific variation in the body sizes of these animals relates to sex, population structure, the environment, and interactions with humans remains underappreciated. Here, we review and analyze body size for 25 ocean giants ranging across the animal kingdom. For each taxon we document body size for the largest known marine species of several clades. We also analyze intraspecific variation and identify the largest known individuals for each species. Where data allows, we analyze spatial and temporal intraspecific size variation. We also provide allometric scaling equations between different size measurements as resources to other researchers. In some cases, the lack of data prevents us from fully examining these topics and instead we specifically highlight these deficiencies and the barriers that exist for data collection. Overall, we found considerable variability in intraspecific size distributions from strongly left- to strongly right-skewed. We provide several allometric equations that allow for estimation of total lengths and weights from more easily obtained measurements. In several cases, we also quantify considerable geographic variation and decreases in size likely attributed to humans. creator: Craig R. McClain creator: Meghan A. Balk creator: Mark C. Benfield creator: Trevor A. Branch creator: Catherine Chen creator: James Cosgrove creator: Alistair D.M. Dove creator: Leo Gaskins creator: Rebecca R. Helm creator: Frederick G. Hochberg creator: Frank B. Lee creator: Andrea Marshall creator: Steven E. McMurray creator: Caroline Schanche creator: Shane N. Stone creator: Andrew D. Thaler uri: https://doi.org/10.7717/peerj.715 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McClain et al. title: Is the Neutrophil-to-Lymphocyte Ratio more correlated than C-reactive protein with postoperative complications after major abdominal surgery? link: https://peerj.com/articles/713 last-modified: 2015-01-13 description: Background. The Neutrophil-to-Lymphocyte Ratio (NLR) is an inflammatory marker that has proven usefulness for predicting late complications. Whether it is associated with immediate postoperative complications after abdominal surgery is not known. In this study, we attempted to correlate the NLR and the C-reactive protein (CRP) with postoperative complications rate.Methods. We performed a post-hoc analysis of previously collected data concerning 82 consecutive patients (median age: 62 years, range: 27–80, female/male 32/50) undergoing major abdominal surgeries. For each patient, we recorded preoperative characteristics, the NLR and CRP values, and postoperative complications (between D + 8 and D + 30) such as infections (N = 29), cardiovascular complications (N = 12) and other complications (N = 28). We performed uni- and multivariate analyses using logistic/linear regression models.Results. Patients with complications did not present a higher preoperative NLR than those without, but a higher ratio at D + 7 (10.73 ± 9.86 vs. 4.73 ± 3.38 without complication) (P < 0.001). In the univariate analysis, the NLR at D + 7 was associated with postoperative complications (P < 0.001). At D + 7, in the multivariate analysis, an increased NLR was associated with more complications (P < 0.001), whereas none of the other factors, including CRP, showed any correlation.Conclusion. Postoperative NLR at day 7 after major abdominal surgery is associated with complications during the first postsurgical month, in contrast with the CRP level. The NLR is a simple and interesting parameter in the perioperative period. creator: Patrice Forget creator: Valérie Dinant creator: Marc De Kock uri: https://doi.org/10.7717/peerj.713 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Forget et al. title: Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen link: https://peerj.com/articles/705 last-modified: 2015-01-13 description: The level of atmospheric oxygen, a driver of free radical damage and tumorigenesis, decreases sharply with rising elevation. To understand whether ambient oxygen plays a role in human carcinogenesis, we characterized age-adjusted cancer incidence (compiled by the National Cancer Institute from 2005 to 2009) across counties of the elevation-varying Western United States and compared trends displayed by respiratory cancer (lung) and non-respiratory cancers (breast, colorectal, and prostate). To adjust for important demographic and cancer-risk factors, 8–12 covariates were considered for each cancer. We produced regression models that captured known risks. Models demonstrated that elevation is strongly, negatively associated with lung cancer incidence (p < 10−16), but not with the incidence of non-respiratory cancers. For every 1,000 m rise in elevation, lung cancer incidence decreased by 7.23 99% CI [5.18–9.29] cases per 100,000 individuals, equivalent to 12.7% of the mean incidence, 56.8. As a predictor of lung cancer incidence, elevation was second only to smoking prevalence in terms of significance and effect size. Furthermore, no evidence of ecological fallacy or of confounding arising from evaluated factors was detected: the lung cancer association was robust to varying regression models, county stratification, and population subgrouping; additionally seven environmental correlates of elevation, such as exposure to sunlight and fine particulate matter, could not capture the association. Overall, our findings suggest the presence of an inhaled carcinogen inherently and inversely tied to elevation, offering epidemiological support for oxygen-driven tumorigenesis. Finally, highlighting the need to consider elevation in studies of lung cancer, we demonstrated that previously reported inverse lung cancer associations with radon and UVB became insignificant after accounting for elevation. creator: Kamen P. Simeonov creator: Daniel S. Himmelstein uri: https://doi.org/10.7717/peerj.705 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Simeonov and Himmelstein title: Association between intrinsic disorder and serine/threonine phosphorylation in Mycobacterium tuberculosis link: https://peerj.com/articles/724 last-modified: 2015-01-08 description: Serine/threonine phosphorylation is an important mechanism that is involved in the regulation of protein function. In eukaryotes, phosphorylation occurs predominantly in intrinsically disordered regions of proteins. Though serine/threonine phosphorylation and protein disorder are much less prevalent in prokaryotes, some bacteria have high levels of serine/threonine phosphorylation and disorder, including the medically important M. tuberculosis. Here I show that serine/threonine phosphorylation sites in M. tuberculosis are highly enriched in intrinsically disordered regions, indicating similarity in the substrate recognition mechanisms of eukaryotic and M. tuberculosis kinases. Serine/threonine phosphorylation has been linked to the pathogenicity and survival of M. tuberculosis. Thus, a better understanding of how its kinases recognize their substrates could have important implications in understanding and controlling the biology of this deadly pathogen. These results also indicate that the association between serine/threonine phosphorylation and disorder is not a feature restricted to eukaryotes. creator: Gajinder Pal Singh uri: https://doi.org/10.7717/peerj.724 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Singh title: Piecing together the biogeographic history of Chenopodium vulvaria L. using botanical literature and collections link: https://peerj.com/articles/723 last-modified: 2015-01-08 description: This study demonstrates the value of legacy literature and historic collections as a source of data on environmental history. Chenopodium vulvaria L. has declined in northern Europe and is of conservation concern in several countries, whereas in other countries outside Europe it has naturalised and is considered an alien weed. In its European range it is considered native in the south, but the northern boundary of its native range is unknown. It is hypothesised that much of its former distribution in northern Europe was the result of repeated introductions from southern Europe and that its decline in northern Europe is the result of habitat change and a reduction in the number of propagules imported to the north. A historical analysis of its ecology and distribution was conducted by mining legacy literature and historical botanical collections. Text analysis of habitat descriptions written on specimens and published in botanical literature covering a period of more than 200 years indicate that the habitat and introduction pathways of C. vulvaria have changed with time. Using the non-European naturalised range in a climate niche model, it is possible to project the range in Europe. By comparing this predicted model with a similar model created from all observations, it is clear that there is a large discrepancy between the realized and predicted distributions. This is discussed together with the social, technological and economic changes that have occurred in northern Europe, with respect to their influence on C. vulvaria. creator: Quentin J. Groom uri: https://doi.org/10.7717/peerj.723 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Groom title: Modeling functional changes to Escherichia coli thymidylate synthase upon single residue replacements: a structure-based approach link: https://peerj.com/articles/721 last-modified: 2015-01-08 description: Escherichia coli thymidylate synthase (TS) is an enzyme that is indispensable to DNA synthesis and cell division, as it provides the only de novo source of dTMP by catalyzing the reductive methylation of dUMP, thus making it a key target for chemotherapeutic agents. High resolution X-ray crystallographic structures are available for TS and, owing to its relatively small size, successful experimental mutagenesis studies have been conducted on the enzyme. In this study, an in silico mutagenesis technique is used to investigate the effects of single amino acid substitutions in TS on enzymatic activity, one that employs the TS protein structure as well as a knowledge-based, four-body statistical potential. For every single residue TS variant, this approach yields both a global structural perturbation score and a set of local environmental perturbation scores that characterize the mutated position as well as all structurally neighboring residues. Global scores for the TS variants are capable of uniquely characterizing groups of residue positions in the enzyme according to their physicochemical, functional, or structural properties. Additionally, these global scores elucidate a statistically significant structure–function relationship among a collection of 372 single residue TS variants whose activity levels have been experimentally determined. Predictive models of TS variant activity are subsequently trained on this dataset of experimental mutants, whose respective feature vectors encode information regarding the mutated position as well as its six nearest residue neighbors in the TS structure, including their environmental perturbation scores. creator: Majid Masso uri: https://doi.org/10.7717/peerj.721 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Masso title: Comparing two models that reduce the number of nephrology fellowship positions in the United States link: https://peerj.com/articles/720 last-modified: 2015-01-08 description: There has been a steady decline in the number of applications to nephrology training programs. One solution is to decrease the number of available fellowship positions. Proponents believe that training programs have grown too big but the method for reduction has not been established. This investigation analyzes two models that decrease the number of available training positions and compares them head-to-head to identify the least burdensome method by which this reduction should occur. In the survival of the fittest model (SotFM) fellowship positions are eliminated if they were unfilled in the National Residency Match Program’s (NRMP) 2013 Specialty Match. In the equal proportions model (EPM) a formula is used to calculate a priority score using ESRD prevalence data from the 2013 USRDS Report and the geometric mean between a given jurisdiction’s current apportionment (n) and its next position (n + 1). The least burdensome model is that which results in the (1) least number of jurisdictions losing fellow positions and (2) lowest percent reduction for any single jurisdiction. There were 416 nephrology positions offered and 47 unfilled in 2013. In the SotFM, 23 jurisdictions would sacrifice these 47 positions. In the EPM, 369 positions were apportioned (=416–47); only 9 jurisdictions would experience a reduction. The largest single-jurisdiction reduction in fellow positions was 67% (SotFM) and 50% (EPM). The EPM results in a less burdensome reduction of fellow positions nationwide. The EPM is a time-tested model that injects fairness into the painful process of reducing the total number of fellow positions across America. creator: Tejas Desai uri: https://doi.org/10.7717/peerj.720 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Desai title: Effects of five southern California macroalgal diets on consumption, growth, and gonad weight, in the purple sea urchin Strongylocentrotus purpuratus link: https://peerj.com/articles/719 last-modified: 2015-01-08 description: Consumer growth and reproductive capacity are direct functions of diet. Strongylocentrotid sea urchins, the dominant herbivores in California kelp forests, strongly prefer giant kelp (Macrocystis pyrifera), but are highly catholic in their ability to consume other species. The biomass of Macrocystis fluctuates greatly in space and time, and the extent to which urchins can use alternate species of algae or a mixed diet of multiple algal species to maintain fitness when giant kelp is unavailable is unknown. We experimentally examined the effects of single and mixed species diets on consumption, growth and gonad weight in the purple sea urchin Strongylocentrotus purpuratus. Urchins were fed single species diets consisting of one of four common species of macroalgae (the kelps Macrocystis pyrifera and Pterygophora californica, and the red algae Chondracanthus corymbiferus and Rhodymenia californica (hereafter referred to by genus)) or a mixed diet containing all four species ad libitum over a 13-week period in a controlled laboratory setting. Urchins fed Chondracanthus, Macrocystis and a mixed diet showed the highest growth (in terms of test diameter, wet weight and jaw length) and gonad weight, while urchins fed Pterygophora and Rhodymenia showed the lowest. Urchins consumed their preferred food, Macrocystis, at the highest rate when offered a mixture, but consumed Chondracanthus or Macrocystis at similar rates when the two algae were offered alone. The differences in urchin feeding behavior and growth observed between these diet types suggest the relative availability of the algae tested here could affect urchin populations and their interactions with the algal assemblage. The fact that the performance of urchins fed Chondracanthus was similar or higher than those fed the preferred Macrocystis suggests that the availability of the former could could sustain growth and reproduction of purple sea urchins during times of low Macrocystis abundance as is common following large wave events. creator: Matthew C. Foster creator: Jarrett E.K. Byrnes creator: Daniel C. Reed uri: https://doi.org/10.7717/peerj.719 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Foster et al. title: Under-five mortality among mothers employed in agriculture: findings from a nationally representative sample link: https://peerj.com/articles/710 last-modified: 2015-01-08 description: Background. India accounts for 24% to all under-five mortality in the world. Residence in rural area, poverty and low levels of mother’s education are known confounders of under-five mortality. Since two-thirds of India’s population lives in rural areas, mothers employed in agriculture present a particularly vulnerable population in the Indian context and it is imperative that concerns of this sizeable population are addressed in order to achieve MDG4 targets of reducing U5MR to fewer than 41 per 1,000 by 2015. This study was conducted to examine factors associated with under-five mortality among mothers employed in agriculture.Methods. Data was retrieved from National Family Household Survey-3 in India (2008). The study population is comprised of a national representative sample of single children aged 0 to 59 months and born to mothers aged 15 to 49 years employed in agriculture from all 29 states of India. Univariate and Multivariate Cox PH regression analysis was used to analyse the Hazard Rates of mortality. The predictive power of child mortality among mothers employed in agriculture was assessed by calculating the area under the receiver operating characteristic (ROC) curve.Results. An increase in mothers’ ages corresponds with a decrease in child mortality. Breastfeeding reduces child mortality by 70% (HR 0.30, 0.25–0.35, p = 0.001). Standard of Living reduces child mortality by 32% with high standard of living (HR 0.68, 0.52–0.89, 0.001) in comparison to low standard of living. Prenatal care (HR 0.40, 0.34–0.48, p = 0.001) and breastfeeding health nutrition education (HR 0.45, 0.31–0.66, p = 0.001) are associated significant factors for child mortality. Birth Order five is a risk factor for mortality (HR 1.49, 1.05–2.10, p = 0.04) in comparison to Birth Order one among women engaged in agriculture while the household size (6–10 members and ≥ 11 members) is significant in reducing child mortality in comparison to ≤5 members in the house. Under-five mortality among mothers employed in agriculture in India discriminated well between death and survival (Area Under ROC was 0.75, 95% CI [0.73–0.77]) indicating that the model is good for appropriate prediction of child mortality.Conclusion. In a nationally representative sample of households in India, mother’s age, breastfeeding, standard of living, prenatal care and breastfeeding health nutrition education are associated with reduction in child mortality. creator: Rajvir Singh creator: Vrijesh Tripathi uri: https://doi.org/10.7717/peerj.710 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Singh et al. title: Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae) link: https://peerj.com/articles/718 last-modified: 2015-01-06 description: Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming). creator: Kevin Weitemier creator: Shannon C.K. Straub creator: Mark Fishbein creator: Aaron Liston uri: https://doi.org/10.7717/peerj.718 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Weitemier et al. title: SATRAT: Staphylococcus aureus transcript regulatory network analysis tool link: https://peerj.com/articles/717 last-modified: 2015-01-06 description: Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel exploratory tool—SATRAT—the S. aureus transcript regulatory network analysis tool, based on the updated database. This tool is capable of performing deep searches using a query and generating an interactive regulatory network based on associations among the regulators of any query gene. We believe this integrated regulatory network analysis tool would help researchers explore the missing links and identify novel pathways that regulate virulence in S. aureus. Also, the data model and the network generation code used to build this resource is open sourced, enabling researchers to build similar resources for other bacterial systems. creator: Tamilselvi Gopal creator: Vijayaraj Nagarajan creator: Mohamed O. Elasri uri: https://doi.org/10.7717/peerj.717 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gopal et al. title: Fish mislabelling in France: substitution rates and retail types link: https://peerj.com/articles/714 last-modified: 2015-01-06 description: Market policies have profound implications for consumers as well as for the management of resources. One of the major concerns in fish trading is species mislabelling: the commercial name used does not correspond to the product, most often because the product is in fact a cheaper or a more easily available species. Substitution rates depend heavily on species, some often being sold mislabelled while others rarely or never mislabelled. Rates also vary largely depending on countries. In this study, we analyse the first market-wide dataset collected for France, the largest sea food market in Europe, for fish species substitution. We sequenced and analysed 371 samples bearing 55 commercial species names, collected in fishmonger shops, supermarkets and restaurants; the largest dataset assembled to date in an European country. Sampling included fish fillets, both fresh and frozen, and prepared meals. We found a total of 14 cases of mislabelling in five species: bluefin tuna, cod, yellowfin tuna, sole and seabream, setting the overall substitution rate at 3.7% CI [2.2–6.4], one of the lowest observed for comparable surveys with large sampling. We detected no case of species mislabelling among the frozen fillets or in industrially prepared meals, and all the substitutions were observed in products sold in fishmongers shops or restaurants. The rate of mislabelling does not differ between species, except for bluefin tuna. Despite a very small sample size (n = 6), the rate observed for this species (83.3% CI [36–99]) stands in sharp contrast with the low substitution rate observed for the other substituted species. In agreement with studies from other countries, this work shows that fish mislabelling can vary greatly within a country depending on the species. It further suggests that more efforts should be directed to the control of high value species like bluefin tuna. creator: Julien Bénard-Capelle creator: Victoire Guillonneau creator: Claire Nouvian creator: Nicolas Fournier creator: Karine Le Loët creator: Agnès Dettai uri: https://doi.org/10.7717/peerj.714 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Bénard-Capelle et al. title: Effects of load on good morning kinematics and EMG activity link: https://peerj.com/articles/708 last-modified: 2015-01-06 description: Many strength and conditioning coaches utilize the good morning (GM) to strengthen the hamstrings and spinal erectors. However, little research exists on its electromyography (EMG) activity and kinematics, and how these variables change as a function of load. The purpose of this investigation was to examine how estimated hamstring length, integrated EMG (IEMG) activity of the hamstrings and spinal erectors, and kinematics of the lumbar spine, hip, knee, and ankle are affected by changes in load. Fifteen trained male participants (age = 24.6 ± 5.3 years; body mass = 84.7 ± 11.3 kg; height = 180.9 ± 6.8 cm) were recruited for this study. Participants performed five sets of the GM, utilizing 50, 60, 70, 80, and 90% of one-repetition maximum (1RM) in a randomized fashion. IEMG activity of hamstrings and spinal erectors tended to increase with load. Knee flexion increased with load on all trials. Estimated hamstring length decreased with load. However, lumbar flexion, hip flexion, and plantar flexion experienced no remarkable changes between trials. These data provide insight as to how changing the load of the GM affects EMG activity, kinematic variables, and estimated hamstring length. Implications for hamstring injury prevention are discussed. More research is needed for further insight as to how load affects EMG activity and kinematics of other exercises. creator: Andrew David Vigotsky creator: Erin Nicole Harper creator: David Russell Ryan creator: Bret Contreras uri: https://doi.org/10.7717/peerj.708 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Vigotsky et al. title: Male emergence schedule and dispersal behaviour are modified by mate availability in heterogeneous landscapes: evidence from the orange-tip butterfly link: https://peerj.com/articles/707 last-modified: 2015-01-06 description: Protandry (prior emergence of males) in insect populations is usually considered to be the result of natural selection acting directly on eclosion timing. When females are monandrous (mate once), males in high density populations benefit from early emergence in the intense scramble competition for mates. In low density populations, however, scramble competition is reduced or absent, and theoretical models predict that protandry will be less favoured. This raises the question of how males behave in heterogeneous landscapes characterized by high density core populations in a low density continuum. We hypothesized that disadvantaged late emerging males in a core population would disperse to the continuum to find mates. We tested this idea using the protandrous, monandrous, pierid butterfly Anthocharis cardamines (the orange-tip) in a core population in Cheshire, northwest England. Over a six-year period, predicted male fitness (the number of matings a male can expect during his residence time, determined by the daily ratio of virgin females to competing males) consistently declined to <1 in late season. This decline affected a large proportion (∼44%) of males in the population and was strongly associated with decreased male recapture-rates, which we attribute to dispersal to the surrounding continuum. In contrast, reanalysis of mark-release-recapture data from an isolated population in Durham, northeast England, showed that in the absence of a continuum very few males (∼3%) emerged when fitness declined to <1 in late season. Hence the existence of a low density continuum may lead to the evolution of plastic dispersal behaviour in high density core populations, maintaining late emerging males which would otherwise be eliminated by selection. This has important theoretical consequences, since a truncated male emergence curve is a key prediction in game theoretic models of emergence timing which has so far received limited support. Our results have implications for conservation, since plastic dispersal behaviour in response to imperfect emergence timing in core (source) populations could help to maintain sink populations in heterogeneous landscapes which would otherwise be driven to extinction by low mate encounter-rates (Allee effects). creator: W James Davies creator: Ilik J. Saccheri uri: https://doi.org/10.7717/peerj.707 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Davies and Saccheri title: The physiologic and therapeutic role of heparin in implantation and placentation link: https://peerj.com/articles/691 last-modified: 2015-01-06 description: Implantation, trophoblast development and placentation are crucial processes in the establishment and development of normal pregnancy. Abnormalities of these processes can lead to pregnancy complications known as the great obstetrical syndromes: preeclampsia, intrauterine growth restriction, fetal demise, premature prelabor rupture of membranes, preterm labor, and recurrent pregnancy loss. There is mounting evidence regarding the physiological and therapeutic role of heparins in the establishment of normal gestation and as a modality for treatment and prevention of pregnancy complications. In this review, we will summarize the properties and the physiological contributions of heparins to the success of implantation, placentation and normal pregnancy. creator: Michela Quaranta creator: Offer Erez creator: Salvatore Andrea Mastrolia creator: Arie Koifman creator: Elad Leron creator: Tamar Eshkoli creator: Moshe Mazor creator: Gershon Holcberg uri: https://doi.org/10.7717/peerj.691 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Quaranta et al.