title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2014-08 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Davanloo’s Intensive Short-Term Dynamic Psychotherapy in a tertiary psychotherapy service: overall effectiveness and association between unlocking the unconscious and outcome link: https://peerj.com/articles/548 last-modified: 2014-08-28 description: Background. Intensive Short-Term Dynamic Psychotherapy (ISTDP), as developed by Habib Davanloo, is an intensive emotion-focused psychodynamic therapy with an explicit focus on handling resistance in treatment. A core assumption in ISTDP is that psychotherapeutic effects are dependent on in-session emotional processing in the form of rise in complex transference feelings that occurs when treatment resistance is challenged. Recent research indicates that an unlocking of the unconscious, a powerful emotional breakthrough achieved at a high rise in complex transference feelings, can potentially enhance ISTDP’s effectiveness. While ISTDP has a growing evidence base, most of the research conducted has used small samples and has tested therapy delivered by expert therapists. The aims of this study were to evaluate the overall effectiveness of ISTDP when delivered in a tertiary psychotherapy service, and to investigate if having an unlocking of the unconscious during therapy predicted enhanced treatment effectiveness.Methods. A total of 412 patients were included in the analyses. The average length of treatment was 10.2 sessions (SD 13.3). Multilevel growth curve modeling was used to evaluate treatment effectiveness and the association between unlocking the unconscious and outcome. A number of control predictors including type of treatment resistance were selected and included in the analyses. Outcome measures were the Brief Symptom Inventory (BSI) and the Inventory of Interpersonal Problems (IIP). About half of the patients in the study were treated by therapists in training and the other half by more experienced therapists.Results. Growth curve analyses using the full intention-to-treat sample revealed significant within-group effects of ISTDP on both the BSI and the IIP. Effect sizes were large (>0.80). Unlocking the unconscious during therapy was associated with significantly larger treatment outcome. The relationship was further moderated by type of treatment resistance.Conclusion. This study adds to the empirical base of Davanloo’s ISTDP with confirmed treatment effectiveness in a large-scale patient sample when ISTDP was delivered by therapists with a range of experience. Furthermore, emotional mobilization in the form of unlocking the unconscious was confirmed as a process factor enhancing the effectiveness of ISTDP. creator: Robert Johansson creator: Joel M. Town creator: Allan Abbass uri: https://doi.org/10.7717/peerj.548 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Johansson et al. title: New craniodental remains of Thylacinus potens (Dasyuromorphia: Thylacinidae), a carnivorous marsupial from the late Miocene Alcoota Local Fauna of central Australia link: https://peerj.com/articles/547 last-modified: 2014-08-28 description: New craniodental specimens that are referrable to the thylacinid marsupial, Thylacinus potens, are described from the late Miocene Alcoota Local Fauna of the Northern Territory, Australia. The remains include a largely complete maxilla and dentary, showing for the first time the anterior dentition of the dentary. The new remains indicate that Th. potens was a more variable species than previously recognised. The dentary, in particular, is more gracile, than other specimens referred to this species. A revised apomorphy-based diagnosis of Th. potens that takes this variability into account is presented. A cladistic analysis supports previous analyses that placed Th. potens in a derived position within Thylacinidae, close to the modern Th. cynocephalus. New estimations of body size are made using published regressions of dental measurements of dasyuromorphians as well as by assuming geometric similitude with Th. cynocephalus. All methods produce body mass estimates in excess of 35 kg. creator: Adam M. Yates uri: https://doi.org/10.7717/peerj.547 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Yates title: Disease dynamics and potential mitigation among restored and wild staghorn coral, Acropora cervicornis link: https://peerj.com/articles/541 last-modified: 2014-08-28 description: The threatened status (both ecologically and legally) of Caribbean staghorn coral, Acropora cervicornis, has prompted rapidly expanding efforts in culture and restocking, although tissue loss diseases continue to affect populations. In this study, disease surveillance and histopathological characterization were used to compare disease dynamics and conditions in both restored and extant wild populations. Disease had devastating effects on both wild and restored populations, but dynamics were highly variable and appeared to be site-specific with no significant differences in disease prevalence between wild versus restored sites. A subset of 20 haphazardly selected colonies at each site observed over a four-month period revealed widely varying disease incidence, although not between restored and wild sites, and a case fatality rate of 8%. A tropical storm was the only discernable environmental trigger associated with a consistent spike in incidence across all sites. Lastly, two field mitigation techniques, (1) excision of apparently healthy branch tips from a diseased colony, and (2) placement of a band of epoxy fully enclosing the diseased margin, gave equivocal results with no significant benefit detected for either treatment compared to controls. Tissue condition of associated samples was fair to very poor; unsuccessful mitigation treatment samples had severe degeneration of mesenterial filament cnidoglandular bands. Polyp mucocytes in all samples were infected with suspect rickettsia-like organisms; however, no bacterial aggregates were found. No histological differences were found between disease lesions with gross signs fitting literature descriptions of white-band disease (WBD) and rapid tissue loss (RTL). Overall, our results do not support differing disease quality, quantity, dynamics, nor health management strategies between restored and wild colonies of A. cervicornis in the Florida Keys. creator: Margaret W. Miller creator: Kathryn E. Lohr creator: Caitlin M. Cameron creator: Dana E. Williams creator: Esther C. Peters uri: https://doi.org/10.7717/peerj.541 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: © 2014 Miller et al. title: Recommended survey designs for occupancy modelling using motion-activated cameras: insights from empirical wildlife data link: https://peerj.com/articles/532 last-modified: 2014-08-28 description: Motion-activated cameras are a versatile tool that wildlife biologists can use for sampling wild animal populations to estimate species occurrence. Occupancy modelling provides a flexible framework for the analysis of these data; explicitly recognizing that given a species occupies an area the probability of detecting it is often less than one. Despite the number of studies using camera data in an occupancy framework, there is only limited guidance from the scientific literature about survey design trade-offs when using motion-activated cameras. A fuller understanding of these trade-offs will allow researchers to maximise available resources and determine whether the objectives of a monitoring program or research study are achievable. We use an empirical dataset collected from 40 cameras deployed across 160 km2 of the Western Slope of Colorado, USA to explore how survey effort (number of cameras deployed and the length of sampling period) affects the accuracy and precision (i.e., error) of the occupancy estimate for ten mammal and three virtual species. We do this using a simulation approach where species occupancy and detection parameters were informed by empirical data from motion-activated cameras. A total of 54 survey designs were considered by varying combinations of sites (10–120 cameras) and occasions (20–120 survey days). Our findings demonstrate that increasing total sampling effort generally decreases error associated with the occupancy estimate, but changing the number of sites or sampling duration can have very different results, depending on whether a species is spatially common or rare (occupancy = ψ) and easy or hard to detect when available (detection probability = p). For rare species with a low probability of detection (i.e., raccoon and spotted skunk) the required survey effort includes maximizing the number of sites and the number of survey days, often to a level that may be logistically unrealistic for many studies. For common species with low detection (i.e., bobcat and coyote) the most efficient sampling approach was to increase the number of occasions (survey days). However, for common species that are moderately detectable (i.e., cottontail rabbit and mule deer), occupancy could reliably be estimated with comparatively low numbers of cameras over a short sampling period. We provide general guidelines for reliably estimating occupancy across a range of terrestrial species (rare to common: ψ = 0.175–0.970, and low to moderate detectability: p = 0.003–0.200) using motion-activated cameras. Wildlife researchers/managers with limited knowledge of the relative abundance and likelihood of detection of a particular species can apply these guidelines regardless of location. We emphasize the importance of prior biological knowledge, defined objectives and detailed planning (e.g., simulating different study-design scenarios) for designing effective monitoring programs and research studies. creator: Graeme Shannon creator: Jesse S. Lewis creator: Brian D. Gerber uri: https://doi.org/10.7717/peerj.532 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Shannon et al. title: Obesity increases operating room times in patients undergoing primary hip arthroplasty: a retrospective cohort analysis link: https://peerj.com/articles/530 last-modified: 2014-08-28 description: Background. Obesity impacts utilization of healthcare resources. The goal of this study was to measure the relationship between increasing body mass index (BMI) in patients undergoing total hip arthroplasty (THA) with different components of operating room (OR) time.Methods. The Stanford Translational Research Integrated Database Environment (STRIDE) was utilized to identify all ASA PS 2 or 3 patients who underwent primary THA at Stanford Medical Center from February 1, 2008 through January 1, 2013. Patients were divided into five groups based on the BMI weight classification. Regression analysis was used to quantify relationships between BMI and the different components of total OR time.Results. 1,332 patients were included in the study. There were no statistically significant differences in age, gender, height, and ASA PS classification between the BMI groups. Normal-weight patients had a total OR time of 138.9 min compared 167.9 min (P < 0.001) for morbidly obese patients. At a BMI > 35 kg/m2 each incremental BMI unit increase was associated with greater incremental total OR time increases.Conclusion. Morbidly obese patients required significantly more total OR time than normal-weight patients undergoing a THA procedure. This increase in time is relevant when scheduling obese patients for surgery and has an important impact on health resource utilization. creator: Bassam Kadry creator: Christopher D. Press creator: Hassan Alosh creator: Isaac M. Opper creator: Joe Orsini creator: Igor A. Popov creator: Jay B. Brodsky creator: Alex Macario uri: https://doi.org/10.7717/peerj.530 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Kadry et al. title: Rice koji reduced body weight gain, fat accumulation, and blood glucose level in high-fat diet-induced obese mice link: https://peerj.com/articles/540 last-modified: 2014-08-26 description: Rice koji is considered a readily accessible functional food that may have health-promoting effects. We investigated whether white, yellow, and red koji have the anti-obesity effect in C57BL/6J mice fed a high-fat diet (HFD), which is a model for obesity. Mice were fed HFD containing 10% (w/w) of rice koji powder or steamed rice for 4 weeks. Weight gain, epididymal white adipose tissue, and total adipose tissue weight were significantly lower in all rice koji groups than in the HFD-rice group after 4 weeks. Feed efficiency was significantly reduced in the yellow koji group. Blood glucose levels were significantly lower in the white and red koji groups with HOMA-R and leptin levels being reduced in the white koji group. White and red koji increased glucose uptake and GLUT4 protein expression in L6 myotube cells. These results showed that all rice koji have the anti-obesity or anti-diabetes effects although the mechanisms may differ depending on the type of rice koji consumed. creator: Yumiko Yoshizaki creator: Chihiro Kawasaki creator: Kai-Chun Cheng creator: Miharu Ushikai creator: Haruka Amitani creator: Akihiro Asakawa creator: Kayu Okutsu creator: Yoshihiro Sameshima creator: Kazunori Takamine creator: Akio Inui uri: https://doi.org/10.7717/peerj.540 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2014 Yoshizaki et al. title: Evaluation of a semiquantitative SNAP test for measurement of bile acids in dogs link: https://peerj.com/articles/539 last-modified: 2014-08-26 description: Background. Serum bile acids (SBA) are used as a routine screening tool of liver function in dogs. Serum samples are usually shipped to a referral laboratory for quantitative analysis with an enzymatic chemistry analyzer. The canine SNAP Bile Acids Test (SNAP-BAT) provides an immediate, semi-quantitative measurement of bile acid concentrations in-house. With the SNAP-BAT, bile acids concentrations of 5–30 µmol/L are quantified, and results outside of that range are classified as <5 or >30 µmol/L. Agreement of the SNAP-BAT with the enzymatic method has not been extensively investigated.Objectives. The purposes of this prospective clinical study were to assess the precision of the SNAP-BAT and determine agreement of SNAP-BAT with results from an in-house chemistry analyzer.Methods. After verifying intra-assay precision of the SNAP-BAT, a prospective analysis was performed using blood samples collected from 56 dogs suspected to have liver disease. Each sample was analyzed with an enzymatic, in-house chemistry analyzer and the SNAP-BAT. Agreement between the two methods was statistically assessed using the κ index of agreement.Results. Intra-assay variability was minimal. The κ index for agreement between the SNAP-BAT and routine chemistry analyzer was between 0.752 and 0.819, indicating substantial to near perfect agreement.Conclusions. The SNAP-BAT is a highly accurate, semi-quantitative test that yields immediate results, and has very little intra-assay variability, particularly for results >30 µmol/L. creator: Rachel L. Seibert creator: Karen M. Tobias creator: Ann Reed creator: Karl R. Snyder uri: https://doi.org/10.7717/peerj.539 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Seibert et al. title: Sexually transmitted infections in HIV-infected people in Switzerland: cross-sectional study link: https://peerj.com/articles/537 last-modified: 2014-08-26 description: Sexually transmitted infections (STI) in HIV-infected people are of increasing concern. We estimated STI prevalence and sexual healthcare seeking behaviour in 224 sexually active HIV-infected people, including men who have sex with men (MSM, n = 112), heterosexual men (n = 65) and women (n = 47). Laboratory-diagnosed bacterial STI were more common in MSM (Chlamydia trachomatis 10.7%; 95% CI 6.2, 18.0%, lymphogranuloma venereum 0.9%; 95% CI 0.1, 6.2%, Neisseria gonorrhoeae 2.7%; 95% CI 0.9, 8.0%, syphilis seroconversion 5.4%; 95% CI 2.0, 11.3%) than heterosexual men (gonorrhoea 1.5%; 95% CI 0.2, 10.3%) or women (no acute infections). Combined rates of laboratory-diagnosed and self-reported bacterial STI in the year before the study were: MSM (27.7%; 95% CI 21.1, 36.7%); heterosexual men (1.5%; 95% CI 0.2, 10.3%); and women (6.4%; 95% CI 2.1, 21.0%). Antibodies to hepatitis C virus were least common in MSM. Antibodies to herpes simplex type 2 virus were least common in heterosexual men. Most MSM, but not heterosexual men or women, agreed that STI testing should be offered every year. In this study, combined rates of bacterial STI in MSM were high; a regular assessment of sexual health would allow those at risk of STI to be offered testing, treatment and partner management. creator: Katharina Sprenger creator: John Marc Evison creator: Marcel Zwahlen creator: Cedric M. Vogt creator: Maria Verena Elzi creator: Christoph Hauser creator: Hansjakob Furrer creator: Nicola Low uri: https://doi.org/10.7717/peerj.537 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Sprenger et al. title: Psychometric properties of the Children’s Revised Impact of Events Scale (CRIES) with Bangladeshi children and adolescents link: https://peerj.com/articles/536 last-modified: 2014-08-26 description: Identification of possible cases suffering post-traumatic stress disorder (PTSD) is important, especially in developing countries where traumatic events are typically prevalent. The Children’s Revised Impact of Events Scale is a reliable and valid measure that has two brief versions (13 items and 8 items) to assess reactions to traumatic events among young people. The current study evaluated the psychometric properties of both versions of the CRIES in a sample of 1,342 children and adolescents aged 9–17 years (M = 12.3 years, SD = 2.12) recruited from six districts of Bangladesh. A sub-group of 120 children from four schools was re-tested on the measures within 3.5 weeks. Confirmatory factor analysis supported factor structures similar to those found in other studies for both versions of the CRIES. Multiple group confirmatory factor analysis showed gender and age-group differences within the sample, supporting established age and gender differences in prevalence of PTSD symptoms. Analyses also indicated moderate to excellent internal consistency and test-retest reliability and clear discriminant and convergent validity. These data support use of both the CRIES-13 and CRIES-8 to provide quick and psychometrically sound assessment of symptoms of PTSD among children and adolescents from Bangla-speaking communities. creator: Farah Deeba creator: Ronald M. Rapee creator: Tania Prvan uri: https://doi.org/10.7717/peerj.536 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Deeba et al. title: Rat sightings in New York City are associated with neighborhood sociodemographics, housing characteristics, and proximity to open public space link: https://peerj.com/articles/533 last-modified: 2014-08-26 description: Rats are ubiquitous in urban environments and, as established reservoirs for infectious pathogens, present a control priority for public health agencies. New York City (NYC) harbors one of the largest rat populations in the United States, but surprising little study has been undertaken to define rat ecology across varied features of this urban landscape. More importantly, factors that may contribute to increased encounters between rats and humans have rarely been explored. Using city-wide records of rat sightings reported to the NYC Department of Health and Mental Hygiene, this investigation sought to identify sociodemographic, housing, and physical landscape characteristics that are associated with increased rat sightings across NYC census tracts. A hierarchical Bayesian conditional autoregressive Poisson model was used to assess these associations while accounting for spatial heterogeneity in the variance. Closer proximity to both subway lines and recreational public spaces was associated with a higher concentration of rat sightings, as was a greater presence of older housing, vacant housing units, and low education among the population. Moreover, these aspects of the physical and social landscape accurately predicted rat sightings across the city. These findings have identified specific features of the NYC urban environment that may help to provide direct control targets for reducing human–rat encounters. creator: Michael G. Walsh uri: https://doi.org/10.7717/peerj.533 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Walsh title: Restoration of MPTP-induced deficits by exercise and Milmed® co-treatment link: https://peerj.com/articles/531 last-modified: 2014-08-26 description: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induces permanent neurochemical and functional deficits. Following the administration of either two or four injections of the dopamine neurotoxin, MPTP, at a dose of 40 mg/kg, C57/BL6 mice were given access to running-wheels (30-min sessions, four times/week, Monday–Thursday) and treatment with the treated yeast, Milmed® (four times/week, Monday–Thursday), or simply running-wheel exercise by itself, over ten weeks. It was observed that the combination of physical exercise and Milmed® treatment, the MPTP + Exercise + Yeast (MC) group [MPTP + Exercise + Milmed® (MC)], restored spontaneous motor activity markedly by test day 10, restored completely subthreshold L-Dopa-induced activity, and dopamine concentration to 76% of control values, in the condition wherein two administrations of MPTP (2 × 40 mg/kg) were given prior to initiation of exercise and/or Milmed® treatment. Physical exercise by itself, MPTP + Exercise (MC) group, attenuated these deficits only partially. Administration of MPTP four times (i.e., 40 mg/kg, s.c., once weekly over four weeks for a total of 160 mg/kg, MPTP + Exercise + Yeast (MC) group [MPTP + Exercise + Milmed® (SC)] and MPTP + Exercise (SC), induced a lesioning effect that was far too severe for either exercise alone or the exercise + Milmed® combination to ameliorate. Nevertheless, these findings indicate a powerful effect of physical exercise reinforced by Milmed® treatment in restoring MPTP-induced deficits of motor function and dopamine neurochemistry in mice. creator: Trevor Archer creator: Danilo Garcia creator: Anders Fredriksson uri: https://doi.org/10.7717/peerj.531 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Archer et al. title: Metabolic fingerprinting of gilthead seabream (Sparus aurata) liver to track interactions between dietary factors and seasonal temperature variations link: https://peerj.com/articles/527 last-modified: 2014-08-26 description: Farmed gilthead seabream is sometimes affected by a metabolic syndrome, known as the “winter disease”, which has a significant economic impact in the Mediterranean region. It is caused, among other factors, by the thermal variations that occur during colder months and there are signs that an improved nutritional status can mitigate the effects of this thermal stress. For this reason, a trial was undertaken where we assessed the effect of two different diets on gilthead seabream physiology and nutritional state, through metabolic fingerprinting of hepatic tissue. For this trial, four groups of 25 adult gilthead seabream were reared for 8 months, being fed either with a control diet (CTRL, low-cost commercial formulation) or with a diet called “Winter Feed” (WF, high-cost improved formulation). Fish were sampled at two time-points (at the end of winter and at the end of spring), with liver tissue being taken for FT-IR spectroscopy. Results have shown that seasonal temperature variations constitute a metabolic challenge for gilthead seabream, with hepatic carbohydrate stores being consumed over the course of the inter-sampling period. Regarding the WF diet, results point towards a positive effect in terms of performance and improved nutritional status. This diet seems to have a mitigating effect on the deleterious impact of thermal shifts, confirming the hypothesis that nutritional factors can affect the capacity of gilthead seabream to cope with seasonal thermal variations and possibly contribute to prevent the onset of “winter disease”. creator: Tomé S. Silva creator: Ana M.R. da Costa creator: Luís E.C. Conceição creator: Jorge P. Dias creator: Pedro M.L. Rodrigues creator: Nadège Richard uri: https://doi.org/10.7717/peerj.527 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Silva et al. title: A survey on cultivable heterotrophic bacteria inhabiting a thermally unstratified water column in an Atlantic Rainforest lake link: https://peerj.com/articles/478 last-modified: 2014-08-26 description: Due to the importance of heterotrophic bacteria in biogeochemical cycles and their influence on water quality, many studies have assessed the composition of the bacterial community. Most of these were made in temperate freshwaters. Eighteen heterotrophic bacteria communities distributed over time and space in the water column of Carioca Lake, not exposed to anthropogenic activities, were analyzed to characterize their composition. A polyphasic approach was used, including 16S rDNA restriction analysis, 16S rRNA gene sequence analysis, BIOLOG Ecoplates and statistical methods. The physiological profiles among the 18 microbial communities were diverse. Clustering analysis and the metabolic fingerprint of the Biolog EcoplateTM system data separated the communities based on temporal scale. A set of 673 isolates were recovered on high nutrient medium. The 673 isolates obtained yielded 360 Amplified Ribosomal DNA Restriction Analysis (ARDRA) Operational Taxonomic Units (OTUs). Most (313) of the ARDRA patterns, OTUs, were from isolates obtained in a single sampling point, in temporal and spatial scales, indicating changes in the bacterial community. A subset of representative isolates for each ARDRA OTU was identified by 16S rRNA gene fragment sequencing and categorized into five phyla, Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Deinococcus-Thermus, represented by 38 genera. The results of this work contribute to a better understanding about the phylogeny of tropical freshwater heterotrophic bacteria. creator: Cláudia I. Lima-Bittencourt creator: Patrícia S. Costa creator: Mariana P. Reis creator: Alexandre B. Santos creator: Francisco A.R. Barbosa creator: Jean L. Valentin creator: Fabiano L. Thompson creator: Edmar Chartone-Souza creator: Andréa M.A. Nascimento uri: https://doi.org/10.7717/peerj.478 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Lima-Bittencourt et al. title: Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences link: https://peerj.com/articles/545 last-modified: 2014-08-21 description: We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to “classic” open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, “classic” open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of “classic” open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “classic” open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME’s uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME’s OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME. creator: Jai Ram Rideout creator: Yan He creator: Jose A. Navas-Molina creator: William A. Walters creator: Luke K. Ursell creator: Sean M. Gibbons creator: John Chase creator: Daniel McDonald creator: Antonio Gonzalez creator: Adam Robbins-Pianka creator: Jose C. Clemente creator: Jack A. Gilbert creator: Susan M. Huse creator: Hong-Wei Zhou creator: Rob Knight creator: J. Gregory Caporaso uri: https://doi.org/10.7717/peerj.545 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Rideout et al. title: Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management link: https://peerj.com/articles/542 last-modified: 2014-08-21 description: Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership (i.e., Associate Editors and Editors-in-Chief) from 1985 to 2013. We found that during this time period only 16% of subject editors were women, with more pronounced disparities in positions of editorial leadership. Although the trend was towards improvement over time, there was surprising variation between journals, including those with similar disciplinary foci. While demographic changes in academia may reduce these disparities over time, we argue journals should proactively strive for gender parity on their editorial boards. This will both increase the number of women afforded the opportunities and benefits that accompany board membership and increase the number of role models and potential mentors for early-career scientists and students. creator: Alyssa H. Cho creator: Shelly A. Johnson creator: Carrie E. Schuman creator: Jennifer M. Adler creator: Oscar Gonzalez creator: Sarah J. Graves creator: Jana R. Huebner creator: D. Blaine Marchant creator: Sami W. Rifai creator: Irina Skinner creator: Emilio M. Bruna uri: https://doi.org/10.7717/peerj.542 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Cho et al. title: Stream grazers determine their crawling direction on the basis of chemical and particulate microalgal cues link: https://peerj.com/articles/503 last-modified: 2014-08-21 description: This study aimed to determine the association between herbivore behavior and cues from producers. We used stream grazer Glossosoma larvae and determined their crawling direction in relation to chemical and visual cues from microalgae. The experimental treatments included control (no cue), particulate (chemical and particulate cues), and dissolved (chemical cue) cues from microalgae. The experimental water samples were randomly placed into either arm of a Y-shaped channel, and the crawling direction of the grazers was determined. Although the grazers crawled toward the arm containing either particulate or dissolved cues, they preferred the arm with particulate cues. This suggested that grazers responded well to both particulate (i.e., drifting algal cells) and chemical (algal smell) cues, and that particulate cues were more important for foraging. In natural habitats, grazers detect cues from producers and change their behaviors to maintain a balance between top-down and bottom-up cues. creator: Izumi Katano creator: Hideyuki Doi uri: https://doi.org/10.7717/peerj.503 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Katano and Doi title: Scaling of olfactory antennae of the terrestrial hermit crabs Coenobita rugosus and Coenobita perlatus during ontogeny link: https://peerj.com/articles/535 last-modified: 2014-08-19 description: Although many lineages of terrestrial crustaceans have poor olfactory capabilities, crabs in the family Coenobitidae, including the terrestrial hermit crabs in the genus Coenobita, are able to locate food and water using olfactory antennae (antennules) to capture odors from the surrounding air. Terrestrial hermit crabs begin their lives as small marine larvae and must find a suitable place to undergo metamorphosis into a juvenile form, which initiates their transition to land. Juveniles increase in size by more than an order of magnitude to reach adult size. Since odor capture is a process heavily dependent on the size and speed of the antennules and physical properties of the fluid, both the transition from water to air and the large increase in size during ontogeny could impact odor capture. In this study, we examine two species of terrestrial hermit crabs, Coenobita perlatus H. Milne-Edwards and Coenobita rugosus H. Milne-Edwards, to determine how the antennule morphometrics and kinematics of flicking change in comparison to body size during ontogeny, and how this scaling relationship could impact odor capture by using a simple model of mass transport in flow. Many features of the antennules, including the chemosensory sensilla, scaled allometrically with carapace width and increased slower than expected by isometry, resulting in relatively larger antennules on juvenile animals. Flicking speed scaled as expected with isometry. Our mass-transport model showed that allometric scaling of antennule morphometrics and kinematics leads to thinner boundary layers of attached fluid around the antennule during flicking and higher odorant capture rates as compared to antennules which scaled isometrically. There were no significant differences in morphometric or kinematic measurements between the two species. creator: Lindsay D. Waldrop creator: Roxanne M. Bantay creator: Quang V. Nguyen uri: https://doi.org/10.7717/peerj.535 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Waldrop et al. title: Applying a reservoir functional-zone paradigm to littoral bluegills: differences in length and catch frequency? link: https://peerj.com/articles/528 last-modified: 2014-08-19 description: Reservoirs exhibit gradients in conditions and resources along the transition from lotic to lentic habitat that may be important to bluegill ecology. The lotic–lentic gradient can be partitioned into three functional zones: the riverine, transitional, and lacustrine zones. We measured catch frequency and length of bluegills (Lepomis macrochirus) captured along the periphery of these areas (i.e., in the littoral zone of each functional zone) for four small reservoirs in Southeastern Ohio during the summer months of three years. Catch frequency differed between zones for two reservoirs, but these differences were not observed in other years. There was no relationship between reservoir zone and either standard length or catch frequency when the data for all reservoirs were pooled, but we did observe a bimodal length distribution in all reservoirs. A combination of ecological factors including inter and intraspecific competition, predation intensity, management practices, limnology, and assemblage complexity may be mitigating bluegill distribution and abundance in reservoirs. Therefore, a functional zone (categorical) approach to understanding bluegill ecology in reservoirs may not be appropriate. creator: Nathan Ruhl creator: Holly DeAngelis creator: Abigale M. Crosby creator: Willem M. Roosenburg uri: https://doi.org/10.7717/peerj.528 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Ruhl et al. title: Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition link: https://peerj.com/articles/520 last-modified: 2014-08-19 description: Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines. creator: Yan Wei Lim creator: Daniel A. Cuevas creator: Genivaldo Gueiros Z. Silva creator: Kristen Aguinaldo creator: Elizabeth A. Dinsdale creator: Andreas F. Haas creator: Mark Hatay creator: Savannah E. Sanchez creator: Linda Wegley-Kelly creator: Bas E. Dutilh creator: Timothy T. Harkins creator: Clarence C. Lee creator: Warren Tom creator: Stuart A. Sandin creator: Jennifer E. Smith creator: Brian Zgliczynski creator: Mark J.A. Vermeij creator: Forest Rohwer creator: Robert A. Edwards uri: https://doi.org/10.7717/peerj.520 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Lim et al. title: Motivational interviewing may facilitate professional interactions with inspectees during environmental inspections and enforcement conversations link: https://peerj.com/articles/508 last-modified: 2014-08-19 description: In the present work inspectors used Motivational Interviewing (MI) to promote environmentally sustainable behaviour in inspectees. MI is a counselling method with scientific support for various health behaviour changes. Inspectors (n = 32) in four Swedish municipalities received training in MI over a yearlong period. Their MI competency as well as their experience of using MI in routine inspections was monitored over the year. The results showed that inspectors significantly increased their competence in the Empathy variable, defined as accurate listening to inspectees. Inspectors judged MI to be useful in inspections, approximately 5 on the 6-point scale. There were indications that MI may be easier or more appropriate to use in certain inspections than in others. creator: Lars Forsberg creator: Hans Wickström creator: Håkan Källmén uri: https://doi.org/10.7717/peerj.508 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Forsberg et al. title: Data-driven discovery of the spatial scales of habitat choice by elephants link: https://peerj.com/articles/504 last-modified: 2014-08-19 description: Setting conservation goals and management objectives relies on understanding animal habitat preferences. Models that predict preferences combine location data from tracked animals with environmental information, usually at a spatial resolution determined by the available data. This resolution may be biologically irrelevant for the species in question. Individuals likely integrate environmental characteristics over varying distances when evaluating their surroundings; we call this the scale of selection. Even a single characteristic might be viewed differently at different scales; for example, a preference for sheltering under trees does not necessarily imply a fondness for continuous forest. Multi-scale preference is likely to be particularly evident for animals that occupy coarsely heterogeneous landscapes like savannahs. We designed a method to identify scales at which species respond to resources and used these scales to build preference models. We represented different scales of selection by locally averaging, or smoothing, the environmental data using kernels of increasing radii. First, we examined each environmental variable separately across a spectrum of selection scales and found peaks of fit. These ‘candidate’ scales then determined the environmental data layers entering a multivariable conditional logistic model. We used model selection via AIC to determine the important predictors out of this set. We demonstrate this method using savannah elephants (Loxodonta africana) inhabiting two parks in southern Africa. The multi-scale models were more parsimonious than models using environmental data at only the source resolution. Maps describing habitat preferences also improved when multiple scales were included, as elephants were more often in places predicted to have high neighborhood quality. We conclude that elephants select habitat based on environmental qualities at multiple scales. For them, and likely many other species, biologists should include multiple scales in models of habitat selection. Species environmental preferences and their geospatial projections will be more accurately represented, improving management decisions and conservation planning. creator: Andrew F. Mashintonio creator: Stuart L. Pimm creator: Grant M. Harris creator: Rudi J. van Aarde creator: Gareth J. Russell uri: https://doi.org/10.7717/peerj.504 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Mashintonio et al. title: Physical activity and pre-diabetes—an unacknowledged mid-life crisis: findings from NHANES 2003–2006 link: https://peerj.com/articles/499 last-modified: 2014-08-19 description: The prevalence of pre-diabetes (PD) among US adults has increased substantially over the past two decades. By current estimates, over 34% of US adults fall in the PD category, 84% of whom meet the American Diabetes Association’s criteria for impaired fasting glucose (IFG). Low physical activity (PA) and/or sedentary behavior are key drivers of hyperglycemia. We examined the relationship between PD and objectively measured PA in NHANES 2003–2006 of 20,470 individuals, including 7,501 individuals between 20 and 65 yrs.We excluded all participants without IFG measures or adequate accelerometry data (final N = 1,317). Participants were identified as PD if FPG was 100–125 mg/dL (5.6–6.9 mmol/L). Moderate and vigorous PA in minutes/day individuals were summed to create the exposure variable “moderate-vigorous PA” (MVPA). The analysis sample included 884 normoglycemic persons and 433 with PD. There were significantly fewer PD subjects in the middle (30.3%) and highest (24.6%) tertiles of PA compared to the lowest tertile (35.5%). After adjusting for BMI, participants were 0.77 times as likely to be PD if they were in the highest tertile compared to the lowest PA tertile (p < 0.001). However, these results were no longer significant when age and BMI were held constant. Univariate analysis revealed that physical activity was associated with decreased fasting glucose of 0.5 mg/dL per minute of MVPA, but multivariate analysis adjusting for age and BMI was not significant. Overall, our data suggest a negative association between measures of PA and the prevalence of PD in middle-aged US adults independent of adiposity, but with significant confounding influence from measures of BMI and age. creator: Kathryn Farni creator: David A. Shoham creator: Guichan Cao creator: Amy H. Luke creator: Jennifer Layden creator: Richard S. Cooper creator: Lara R. Dugas uri: https://doi.org/10.7717/peerj.499 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2014 Farni et al. title: Recent genome reduction of Wolbachia in Drosophila recens targets phage WO and narrows candidates for reproductive parasitism link: https://peerj.com/articles/529 last-modified: 2014-08-14 description: Wolbachia are maternally transmitted endosymbionts that often alter their arthropod hosts’ biology to favor the success of infected females, and they may also serve as a speciation microbe driving reproductive isolation. Two of these host manipulations include killing males outright and reducing offspring survival when infected males mate with uninfected females, a phenomenon known as cytoplasmic incompatibility. Little is known about the mechanisms behind these phenotypes, but interestingly either effect can be caused by the same Wolbachia strain when infecting different hosts. For instance, wRec causes cytoplasmic incompatibility in its native host Drosophila recens and male killing in D. subquinaria. The discovery of prophage WO elements in most arthropod Wolbachia has generated the hypothesis that WO may encode genes involved in these reproductive manipulations. However, PCR screens for the WO minor capsid gene indicated that wRec lacks phage WO. Thus, wRec seemed to provide an example where phage WO is not needed for Wolbachia-induced reproductive manipulation. To enable investigation of the mechanism of phenotype switching in different host backgrounds, and to examine the unexpected absence of phage WO, we sequenced the genome of wRec. Analyses reveal that wRec diverged from wMel approximately 350,000 years ago, mainly by genome reduction in the phage regions. While it lost the minor capsid gene used in standard PCR screens for phage WO, it retained two regions encompassing 33 genes, several of which have previously been associated with reproductive parasitism. Thus, WO gene involvement in reproductive manipulation cannot be excluded and reliance on single gene PCR should not be used to rule out the presence of phage WO in Wolbachia. Additionally, the genome sequence for wRec will enable transcriptomic and proteomic studies that may help elucidate the Wolbachia mechanisms of altered reproductive manipulations associated with host switching, perhaps among the 33 remaining phage genes. creator: Jason A. Metcalf creator: Minhee Jo creator: Sarah R. Bordenstein creator: John Jaenike creator: Seth R. Bordenstein uri: https://doi.org/10.7717/peerj.529 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Metcalf et al. title: Demographic effects on fruit set in the dioecious shrub Canada buffaloberry (Shepherdia canadensis) link: https://peerj.com/articles/526 last-modified: 2014-08-14 description: The effects of pollen limitation on reproductive success in plants have been well-documented using pollen supplementation experiments. However, the role of local demographics in determining pollen limitation, particularly in terms of the additive and interactive effects of pollen availability and competition are not well known. We measured fruit set in the dioecious shrub Canada buffaloberry (Shepherdia canadensis) in Central Alberta, Canada to evaluate whether local demographics measured at three spatial scales (25, 50, and 100 m2) affect fruit set in buffaloberry. We test whether density-dependence (population density), pollen donor (measured as male density, distance to nearest male plant and size of nearest male plant), female competitor (measured as female density and distance to nearest female plant), or the combined pollen donor and competitor hypotheses best explain natural variations in fruit set for a population of Canada buffaloberry. Support was highest for the combined pollen donor and competitor hypothesis at an intermediate spatial scale of 50 m2. Proportion fruit set increased with male shrub density (pollen donors) and decreased with female shrub density (pollen competitors), but was more affected by the presence of males than females. This illustrates that access to male shrubs within a 3.99 m radius affects pollen availability, while nearby females compete intra-specifically for pollen. creator: Kate M. Johnson creator: Scott E. Nielsen uri: https://doi.org/10.7717/peerj.526 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Johnson and Nielsen title: Divergence by depth in an oceanic fish link: https://peerj.com/articles/525 last-modified: 2014-08-14 description: Despite the striking physical and environmental gradients associated with depth variation in the oceans, relatively little is known about their impact on population diversification, adaptation and speciation. Changes in light associated with increasing depth are likely to alter the visual environment of organisms, and adaptive changes in visual systems may be expected. The pelagic beaked redfish, Sebastes mentella, exhibits depth-associated patterns of substructure in the central North Atlantic, with a widely distributed shallow-pelagic population inhabiting waters between 250 and 550 m depth and a deep-pelagic population dwelling between 550 and 800 m. Here we performed a molecular genetic investigation of samples from fish collected from ‘shallow’ and ‘deep’ populations, using the mitochondrial control region and the gene coding for the visual-pigment rhodopsin. We identify patterns suggestive of potential adaptation to different depths, by detecting a specific amino acid replacement at the rhodopsin gene. Mitochondrial DNA results reflect a scenario of long-term demographic independence between the two S. mentella groups, and raise the possibility that these ‘stocks’ may in fact be two incipient species. creator: Peter Shum creator: Christophe Pampoulie creator: Carlotta Sacchi creator: Stefano Mariani uri: https://doi.org/10.7717/peerj.525 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2014 Shum et al. title: Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation link: https://peerj.com/articles/524 last-modified: 2014-08-14 description: Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO) project, using a hybrid of machine learning based on natural language processing, and a simplified user interface designed to help scientists curate their data with minimum effort. We have carried out this work based on the premise that pure machine learning is insufficiently accurate, and that expecting scientists to find the time to annotate their protocols manually is unrealistic. By combining these approaches, we have created an effective prototype for which annotation of bioassay text within the domain of the training set can be accomplished very quickly. Well-trained annotations require single-click user approval, while annotations from outside the training set domain can be identified using the search feature of a well-designed user interface, and subsequently used to improve the underlying models. By drastically reducing the time required for scientists to annotate their assays, we can realistically advocate for semantic annotation to become a standard part of the publication process. Once even a small proportion of the public body of bioassay data is marked up, bioinformatics researchers can begin to construct sophisticated and useful searching and analysis algorithms that will provide a diverse and powerful set of tools for drug discovery researchers. creator: Alex M. Clark creator: Barry A. Bunin creator: Nadia K. Litterman creator: Stephan C. Schürer creator: Ubbo Visser uri: https://doi.org/10.7717/peerj.524 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Clark et al. title: Three dimensional digital reconstruction of the jaw adductor musculature of the extinct marsupial giant Diprotodon optatum link: https://peerj.com/articles/514 last-modified: 2014-08-14 description: The morphology and arrangement of the jaw adductor muscles in vertebrates reflects masticatory style and feeding processes, diet and ecology. However, gross muscle anatomy is rarely preserved in fossils and is, therefore, heavily dependent on reconstructions. An undeformed skull of the extinct marsupial, Diprotodon optatum, recovered from Pleistocene sediments at Bacchus Marsh in Victoria, represents the most complete and best preserved specimen of the species offering a unique opportunity to investigate functional anatomy. Computed tomography (CT) scans and digital reconstructions make it possible to visualise internal cranial anatomy and predict location and morphology of soft tissues, including muscles. This study resulted in a 3D digital reconstruction of the jaw adductor musculature of Diprotodon, revealing that the arrangement of muscles is similar to that of kangaroos and that the muscle actions were predominantly vertical. 3D digital muscle reconstructions provide considerable advantages over 2D reconstructions for the visualisation of the spatial arrangement of the individual muscles and the measurement of muscle properties (length, force vectors and volume). Such digital models can further be used to estimate muscle loads and attachment sites for biomechanical analyses. creator: Alana C. Sharp uri: https://doi.org/10.7717/peerj.514 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Sharp title: The relationship between managed bees and the prevalence of parasites in bumblebees link: https://peerj.com/articles/522 last-modified: 2014-08-12 description: Honey bees and, more recently, bumblebees have been domesticated and are now managed commercially primarily for crop pollination, mixing with wild pollinators during foraging on shared flower resources. There is mounting evidence that managed honey bees or commercially produced bumblebees may affect the health of wild pollinators such as bumblebees by increasing competition for resources and the prevalence of parasites in wild bees. Here we screened 764 bumblebees from around five greenhouses that either used commercially produced bumblebees or did not, as well as bumblebees from 10 colonies placed at two sites either close to or far from a honey bee apiary, for the parasites Apicystis bombi, Crithidia bombi, Nosema bombi, N. ceranae, N. apis and deformed wing virus. We found that A. bombi and C. bombi were more prevalent around greenhouses using commercially produced bumblebees, while C. bombi was 18% more prevalent in bumblebees at the site near to the honey bee apiary than those at the site far from the apiary. Whilst these results are from only a limited number of sites, they support previous reports of parasite spillover from commercially produced bumblebees to wild bumblebees, and suggest that the impact of stress from competing with managed bees or the vectoring of parasites by them on parasite prevalence in wild bees needs further investigation. It appears increasingly likely that the use of managed bees comes at a cost of increased parasites in wild bumblebees, which is not only a concern for bumblebee conservation, but which may impact other pollinators as well. creator: Peter Graystock creator: Dave Goulson creator: William O.H. Hughes uri: https://doi.org/10.7717/peerj.522 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Graystock et al. title: Feeding behaviour of Caenorhabditis elegans is an indicator of Pseudomonas aeruginosa PAO1 virulence link: https://peerj.com/articles/521 last-modified: 2014-08-12 description: Caenorhabditis elegans is commonly used as an infection model for pathogenesis studies in Pseudomonas aeruginosa. The standard virulence assays rely on the slow and fast killing or paralysis of nematodes but here we developed a behaviour assay to monitor the preferred bacterial food sources of C. elegans. We monitored the food preferences of nematodes fed the wild type PAO1 and mutants in the type III secretion (T3S) system, which is a conserved mechanism to inject secreted effectors into the host cell cytosol. A ΔexsEΔpscD mutant defective for type III secretion served as a preferred food source, while an ΔexsE mutant that overexpresses the T3S effectors was avoided. Both food sources were ingested and observed in the gastrointestinal tract. Using the slow killing assay, we showed that the ΔexsEΔpscD had reduced virulence and thus confirmed that preferred food sources are less virulent than the wild type. Next we developed a high throughput feeding behaviour assay with 48 possible food colonies in order to screen a transposon mutant library and identify potential virulence genes. C. elegans identified and consumed preferred food colonies from a grid of 48 choices. The mutants identified as preferred food sources included known virulence genes, as well as novel genes not identified in previous C. elegans infection studies. Slow killing assays were performed and confirmed that several preferred food sources also showed reduced virulence. We propose that C. elegans feeding behaviour can be used as a sensitive indicator of virulence for P. aeruginosa PAO1. creator: Shawn Lewenza creator: Laetitia Charron-Mazenod creator: Lauriane Giroux creator: Alexandra D. Zamponi uri: https://doi.org/10.7717/peerj.521 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Lewenza et al. title: Yawn contagion in humans and bonobos: emotional affinity matters more than species link: https://peerj.com/articles/519 last-modified: 2014-08-12 description: In humans and apes, yawn contagion echoes emotional contagion, the basal layer of empathy. Hence, yawn contagion is a unique tool to compare empathy across species. If humans are the most empathic animal species, they should show the highest empathic response also at the level of emotional contagion. We gathered data on yawn contagion in humans (Homo sapiens) and bonobos (Pan paniscus) by applying the same observational paradigm and identical operational definitions. We selected a naturalistic approach because experimental management practices can produce different psychological and behavioural biases in the two species, and differential attention to artificial stimuli. Within species, yawn contagion was highest between strongly bonded subjects. Between species, sensitivity to others’ yawns was higher in humans than in bonobos when involving kin and friends but was similar when considering weakly-bonded subjects. Thus, emotional contagion is not always highest in humans. The cognitive components concur in empowering emotional affinity between individuals. Yet, when they are not in play, humans climb down from the empathic podium to return to the “understory”, which our species shares with apes. creator: Elisabetta Palagi creator: Ivan Norscia creator: Elisa Demuru uri: https://doi.org/10.7717/peerj.519 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Palagi et al. title: Whale shark economics: a valuation of wildlife tourism in South Ari Atoll, Maldives link: https://peerj.com/articles/515 last-modified: 2014-08-12 description: Whale sharks attract large numbers of tourists, divers and snorkelers each year to South Ari Atoll in the Republic of Maldives. Yet without information regarding the use and economic extent of the attraction, it is difficult to prioritize conservation or implement effective management plans. We used empirical recreational data and generalized mixed statistical models to conduct the first economic valuation (with direct spend as the primary proxy) of whale shark tourism in Maldives. We estimated that direct expenditures for whale shark focused tourism in the South Ari Marine Protected Area for 2012 and 2013 accounted for US$7.6 and $9.4 million respectively. These expenditures are based on an estimate of 72,000–78,000 tourists who are involved in whale shark excursions annually. That substantial amount of income to resort owners and operators, and tourism businesses in a relatively small area highlights the need to implement regulations and management that safeguard the sustainability of the industry through ensuring guest satisfaction and whale shark conservation. creator: Edgar Fernando Cagua creator: Neal Collins creator: James Hancock creator: Richard Rees uri: https://doi.org/10.7717/peerj.515 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Cagua et al. title: Intergenerational conflicts may help explain parental absence effects on reproductive timing: a model of age at first birth in humans link: https://peerj.com/articles/512 last-modified: 2014-08-12 description: Background. Parental absences in childhood are often associated with accelerated reproductive maturity in humans. These results are counterintuitive for evolutionary social scientists because reductions in parental investment should be detrimental for offspring, but earlier reproduction is generally associated with higher fitness. In this paper we discuss a neglected hypothesis that early reproduction is often associated with parental absence because it decreases the average relatedness of a developing child to her future siblings. Family members often help each other reproduce, meaning that parents and offspring may find themselves in competition over reproductive opportunities. In these intergenerational negotiations offspring will have less incentive to help the remaining parent rear future half-siblings relative to beginning reproduction themselves.Method. We illustrate this “intergenerational conflict hypothesis” with a formal game-theoretic model.Results. We show that when resources constrain reproductive opportunities within the family, parents will generally win reproductive conflicts with their offspring, i.e., they will produce more children of their own and therefore delay existing offsprings’ reproduction. This is due to the asymmetric relatedness between grandparents and grandchildren (r = .25), compared to siblings (r = 0.5), resulting in greater incentives for older siblings to help rear younger siblings than for grandparents to help rear grandchildren. However, if a parent loses or replaces their partner, the conflict between the parent and offspring becomes symmetric since half siblings are as related to one another as grandparents are to grandchildren. This means that the offspring stand to gain more from earlier reproduction when their remaining parent would produce half, rather than full, siblings. We further show that if parents senesce in a way that decreases the quality of their infant relative to their offspring’s infant, the intergenerational conflict can shift to favor the younger generation. creator: Cristina Moya creator: Rebecca Sear uri: https://doi.org/10.7717/peerj.512 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Moya and Sear title: A comparison of success rates of introduced passeriform birds in New Zealand, Australia and the United States link: https://peerj.com/articles/509 last-modified: 2014-08-12 description: In this study, we compiled lists of successful and unsuccessful passeriform introductions to nine sites in New Zealand, Australia and the United States. We limited our analysis to introductions during the 19th century to minimize potential variation in transport modes and habitat quality changes, such as those due to increasing urbanization. We compared introduction success rates at three levels. First we included all passeriforms introduced to any of the sites in the three locations, then we compared the fates of just those species with a European origin and finally we compared success rates of just the 13 species released into all three locations. We found that the pattern of success or failure differed significantly across the three locations: Passeriforms introduced by acclimatization organizations to the United States were significantly more likely to fail than those introduced to New Zealand or Australia. Several species that succeeded in either New Zealand or Australia failed in the United States, even after the introduction of seemingly sufficient numbers. creator: Michael P. Moulton creator: Wendell P. Cropper uri: https://doi.org/10.7717/peerj.509 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Moulton and Cropper Jr title: The mitochondrial genome of Paragonimus westermani (Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda) link: https://peerj.com/articles/484 last-modified: 2014-08-12 description: Among helminth parasites, Paragonimus (zoonotic lung fluke) gains considerable importance from veterinary and medical points of view because of its diversified effect on its host. Nearly fifty species of Paragonimus have been described across the globe. It is estimated that more than 20 million people are infected worldwide and the best known species is Paragonimus westermani, whose type locality is probably India and which infects millions of people in Asia causing disease symptoms that mimic tuberculosis. Human infections occur through eating raw crustaceans containing metacercarie or ingestion of uncooked meat of paratenic hosts such as pigs. Though the fluke is known to parasitize a wide range of mammalian hosts representing as many as eleven families, the status of its prevalence, host range, pathogenic manifestations and its possible survivors in nature from where the human beings contract the infection is not well documented in India. We took advantage of the whole genome sequence data for P. westermani, generated by Next Generation Sequencing, and its comparison with the existing data for the P. westermani for comparative mt DNA phylogenomic analyses. Specific primers were designed for the 12 protein coding genes with the aid of existing P. westermani mtDNA as the reference. The Ion torrent next generation sequencing platform was harnessed to completely sequence the mitochondrial genome, and applied innovative approaches to bioinformatically assemble and annotate it. A strategic PCR primer design utilizing the whole genome sequence data from P. westermani enabled us to design specific primers capable of amplifying all regions of the mitochondrial genome from P. westermani. Assembly of NGS data from libraries enriched in mtDNA sequence by PCR gave rise to a total of 11 contigs spanning the entire 14.7 kb mt DNA sequence of P. westermani available at NCBI. We conducted gap-filling by traditional Sanger sequencing to fill in the gaps. Annotation of non-protein coding genes successfully identified tRNA regions for the 24 tRNAs coded in mtDNA and 12 protein coding genes. Bayesian phylogenetic analyses of the concatenated protein coding genes placed P. westermani within the family Opisthorchida. The complete mtDNA sequence of P. westermani is 15,004 base pairs long; the lung fluke is the major etiological agent of paragonimiasis and the first Indian representative for the family Paragonimidae to be fully sequenced that provides important genetic markers for ecological, population and biogeographical studies and molecular diagnostic of digeneans that cause trematodiases. creator: Devendra K. Biswal creator: Anupam Chatterjee creator: Alok Bhattacharya creator: Veena Tandon uri: https://doi.org/10.7717/peerj.484 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Biswal et al. title: Asymmetric connectivity of spawning aggregations of a commercially important marine fish using a multidisciplinary approach link: https://peerj.com/articles/511 last-modified: 2014-08-07 description: Understanding patterns of larval dispersal is key in determining whether no-take marine reserves are self-sustaining, what will be protected inside reserves and where the benefits of reserves will be observed. We followed a multidisciplinary approach that merged detailed descriptions of fishing zones and spawning time at 17 sites distributed in the Midriff Island region of the Gulf of California with a biophysical oceanographic model that simulated larval transport at Pelagic Larval Duration (PLD) 14, 21 and 28 days for the most common and targeted predatory reef fish, (leopard grouper Mycteroperca rosacea). We tested the hypothesis that source–sink larval metapopulation dynamics describing the direction and frequency of larval dispersal according to an oceanographic model can help to explain empirical genetic data. We described modeled metapopulation dynamics using graph theory and employed empirical sequence data from a subset of 11 sites at two mitochondrial genes to verify the model predictions based on patterns of genetic diversity within sites and genetic structure between sites. We employed a population graph describing a network of genetic relationships among sites and contrasted it against modeled networks. While our results failed to explain genetic diversity within sites, they confirmed that ocean models summarized via graph and adjacency distances over modeled networks can explain seemingly chaotic patterns of genetic structure between sites. Empirical and modeled networks showed significant similarities in the clustering coefficients of each site and adjacency matrices between sites. Most of the connectivity patterns observed towards downstream sites (Sonora coast) were strictly asymmetric, while those between upstream sites (Baja and the Midriffs) were symmetric. The best-supported gene flow model and analyses of modularity of the modeled networks confirmed a pulse of larvae from the Baja Peninsula, across the Midriff Island region and towards the Sonoran coastline that acts like a larval sink, in agreement with the cyclonic gyre (anti-clockwise) present at the peak of spawning (May–June). Our approach provided a mechanistic explanation of the location of fishing zones: most of the largest areas where fishing takes place seem to be sustained simultaneously by high levels of local retention, contribution of larvae from upstream sites and oceanographic patterns that concentrate larval density from all over the region. The general asymmetry in marine connectivity observed highlights that benefits from reserves are biased towards particular directions, that no-take areas need to be located upstream of targeted fishing zones, and that some fishing localities might not directly benefit from avoiding fishing within reserves located adjacent to their communities. We discuss the implications of marine connectivity for the current network of marine protected areas and no-take zones, and identify ways of improving it. creator: Adrian Munguia-Vega creator: Alexis Jackson creator: Silvio Guido Marinone creator: Brad Erisman creator: Marcia Moreno-Baez creator: Alfredo Girón-Nava creator: Tad Pfister creator: Octavio Aburto-Oropeza creator: Jorge Torre uri: https://doi.org/10.7717/peerj.511 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2014 Munguia-Vega et al. title: No population bias to left-hemisphere language in 4-year-olds with language impairment link: https://peerj.com/articles/507 last-modified: 2014-08-07 description: Background. An apparent paradox in the field of neuropsychology is that people with atypical cerebral lateralization do not appear to suffer any cognitive disadvantage, yet atypical cerebral lateralization is more common in children and adults with developmental language disorders. This study was designed to explore possible reasons for this puzzling pattern of results.Methods. We used functional transcranial Doppler ultrasound (fTCD) to assess cerebral blood flow during language production in 57 four-year-olds, including 15 children who had been late-talkers when first seen at 20 months of age. We categorized cerebral lateralization as left, right or bilateral, and compared proportions with each type of laterality with those seen in a previously tested sample of children aged 6–16 years. We also compared language scores at 4 years for those with typical and atypical lateralization, and then looked at the association the opposite way: comparing those with typical or impaired language in terms of their cerebral lateralization.Results. The distribution of types of cerebral lateralization was similar for 4-year-olds to that seen in older children. Overall, cerebral lateralization was not predictive of language level. However, for children who had language difficulties at 20 months and/or 4 years (N = 21), there was no population bias to left-hemisphere language activation, whereas children without language problems at either age showed a pronounced bias to left-sided language lateralization. Nevertheless, many children with right hemisphere language had no indications of language difficulties, confirming that atypical cerebral asymmetry is not a direct cause of problems.Conclusions. We suggest that atypical lateralization at the individual level is not associated with language impairment. However, lack of lateralization at the population level is a marker of risk for language impairment, which could be due to genetic or non-genetic causes. creator: Dorothy V.M. Bishop creator: Georgina Holt creator: Andrew J.O. Whitehouse creator: Margriet Groen uri: https://doi.org/10.7717/peerj.507 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Bishop et al. title: Factors and associations for physical activity in severely obese adults during a two-year lifestyle intervention link: https://peerj.com/articles/505 last-modified: 2014-08-07 description: Objective. This study of severely obese adults participating in a two-year lifestyle intervention investigates associations between the independent variables: change in self-efficacy for physical activity (PA) in the face of psychological barriers, perceived behavioural control over PA, and PA self-identity and the dependent variable of change in objectively assessed PA. The intervention comprised four residential periods in a rehabilitation centre and combined diet, physical activity, and cognitive behavioural therapy.Materials and Methods. Forty-nine severely obese adults (37 women, mean body mass index 42.1 kg/m2) were included in the study. Assessment was done four times using questionnaires and an accelerometer. A linear mixed model based on restricted maximum likelihood was used in analyses for change over time. Associations were studied using linear regression analyses. Age, gender, and change in body mass index were used as control variables.Results. In the adjusted analyses, change in perceived behavioural control over PA was associated with change in PA (Stand. coeff. = 0.32, p = .005). Change in PA was not associated with either change in self-efficacy over PA in the face of psychological barriers (Stand. coeff. = 0.13, p = .259) or PA self-identity (Stand. coeff. = −0.07, p = .538).Conclusion. Perceived behavioural control may be a valid target to increase and maintain PA in severely obese adults participating in lifestyle interventions. More research is needed to investigate the process of behaviour change in this population. creator: Randi Jepsen creator: Eivind Aadland creator: Lesley Robertson creator: Merete Kristiansen creator: John Roger Andersen creator: Gerd Karin Natvig uri: https://doi.org/10.7717/peerj.505 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Jepsen et al. title: Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis link: https://peerj.com/articles/506 last-modified: 2014-08-05 description: Hair from different individuals can be distinguished by physical properties. Although some data exist on other species, examination of the individual molecular differences within the human hair shaft has not been thoroughly investigated. Shotgun proteomic analysis revealed considerable variation in profile among samples from Caucasian, African–American, Kenyan and Korean subjects. Within these ethnic groups, prominent keratin proteins served to distinguish individual profiles. Differences between ethnic groups, less marked, relied to a large extent on levels of keratin associated proteins. In samples from Caucasian subjects, hair shafts from axillary, beard, pubic and scalp regions exhibited distinguishable profiles, with the last being most different from the others. Finally, the profile of isolated hair cuticle cells was distinguished from that of total hair shaft by levels of more than 20 proteins, the majority of which were prominent keratins. The cuticle also exhibited relatively high levels of epidermal transglutaminase (TGM3), accounting for its observed low degree of protein extraction by denaturants. In addition to providing insight into hair structure, present findings may lead to improvements in differentiating hair from various ethnic origins and offer an approach to extending use of hair in crime scene evidence for distinguishing among individuals. creator: Chelsea N. Laatsch creator: Blythe P. Durbin-Johnson creator: David M. Rocke creator: Sophie Mukwana creator: Abby B. Newland creator: Michael J. Flagler creator: Michael G. Davis creator: Richard A. Eigenheer creator: Brett S. Phinney creator: Robert H. Rice uri: https://doi.org/10.7717/peerj.506 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Laatsch et al. title: RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments link: https://peerj.com/articles/494 last-modified: 2014-08-05 description: Methane is formed by methanogenic archaea in the rumen as one of the end products of feed fermentation in the ruminant digestive tract. To develop strategies to mitigate anthropogenic methane emissions due to ruminant farming, and to understand rumen microbial differences in animal feed conversion efficiency, it is essential that methanogens can be identified and taxonomically classified with high accuracy. Currently available taxonomic frameworks offer only limited resolution beyond the genus level for taxonomic assignments of sequence data stemming from high throughput sequencing technologies. Therefore, we have developed a QIIME-compatible database (DB) designed for species-level taxonomic assignment of 16S rRNA gene amplicon data targeting methanogenic archaea from the rumen, and from animal and human intestinal tracts. Called RIM-DB (Rumen and Intestinal Methanogen-DB), it contains a set of 2,379 almost full-length chimera-checked 16S rRNA gene sequences, including 20 previously unpublished sequences from isolates from three different orders. The taxonomy encompasses the recently-proposed seventh order of methanogens, the Methanomassiliicoccales, and allows differentiation between defined groups within this order. Sequence reads from rumen contents from a range of ruminant-diet combinations were taxonomically assigned using RIM-DB, Greengenes and SILVA. This comparison clearly showed that taxonomic assignments with RIM-DB resulted in the most detailed assignment, and only RIM-DB taxonomic assignments allowed methanogens to be distinguished taxonomically at the species level. RIM-DB complements the use of comprehensive databases such as Greengenes and SILVA for community structure analysis of methanogens from the rumen and other intestinal environments, and allows identification of target species for methane mitigation strategies. creator: Henning Seedorf creator: Sandra Kittelmann creator: Gemma Henderson creator: Peter H. Janssen uri: https://doi.org/10.7717/peerj.494 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Seedorf et al. title: Insights on the structure and stability of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans link: https://peerj.com/articles/457 last-modified: 2014-08-05 description: Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery from bioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can form stable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm “Rosetta Fold-and-Dock”. To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic’s secondary and tertiary structure. creator: Fernando Abarca creator: Sebastian E. Gutierrez-Maldonado creator: Pilar Parada creator: Patricio Martinez creator: Alejandro Maass creator: Tomas Perez-Acle uri: https://doi.org/10.7717/peerj.457 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2014 Abarca et al.