title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-06
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Histopathology of crustose coralline algae affected by white band and white patch diseases
link: https://peerj.com/articles/1034
last-modified: 2015-06-30
description: Crustose coralline algae (CCA) are major benthic calcifiers that play crucial roles in marine ecosystems, particularly coral reefs. Over the past two decades, epizootics have been reported for several CCA species on coral reefs worldwide. However, their causes remain often unknown in part because few studies have investigated CCA pathologies at a microscopic scale. We studied the cellular changes associated with two syndromes: Coralline White Band Syndrome (CWBS) and Coralline White Patch Disease (CWPD) from samples collected in Curaçao, southern Caribbean. Healthy-looking tissue of diseased CCA did not differ from healthy tissue of healthy CCA. In diseased tissues of both pathologies, the three characteristic cell layers of CCA revealed cells completely depleted of protoplasmic content, but presenting an intact cell wall. In addition, CWBS showed a transition area between healthy and diseased tissues consisting of cells partially deprived of protoplasmic material, most likely corresponding to the white band characterizing the disease at the macroscopic level. This transition area was absent in CWPD. Regrowth at the lesion boundary were sometimes observed in both syndromes. Tissues of both healthy and diseased CCA were colonised by diverse boring organisms. Fungal infections associated with the diseased cells were not seen. However, other bioeroders were more abundant in diseased vs healthy CCA and in diseased vs healthy-looking tissues of diseased CCA. Although their role in the pathogenesis is unclear, this suggests that disease increases CCA susceptibility to bioerosion. Further investigations using an integrated approach are needed to carry out the complete diagnosis of these diseases.
creator: Gaëlle Quéré
creator: Anne-Leila Meistertzheim
creator: Robert S. Steneck
creator: Maggy M. Nugues
uri: https://doi.org/10.7717/peerj.1034
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Quéré et al.

title: The destructive effect of botulinum neurotoxins on the SNARE protein: SNAP-25 and synaptic membrane fusion
link: https://peerj.com/articles/1065
last-modified: 2015-06-30
description: Synaptic exocytosis requires the assembly of syntaxin 1A and SNAP-25 on the plasma membrane and synaptobrevin 2 (VAMP2) on the vesicular membrane to bridge the two opposite membranes. It is believed that the three SNARE proteins assemble in steps along the dynamic assembly pathway. The C-terminus of SNAP-25 is known to be the target of botulinum neurotoxins (BoNT/A and BoNT/E) that block neurotransmitters release in vivo. In this study, we employed electron paramagnetic resonance (EPR) spectroscopy to investigate the conformation of the SNAP-25 C-terminus in binary and ternary SNARE complexes. The fluorescence lipid mixing assay shows that the C-terminal of SNAP-25 is essential for membrane fusion, and that the truncated SNAP-25 mutants cleaved by BoNT/A and BoNT/E display different inhibition effects on membrane fusion: SNAP-25E (Δ26) abolishes the fusion activity of the SNARE complex, while SNAP-25A (Δ9) loses most of its function, although it can still form a SDS-resistant SNARE complex as the wild-type SNAP-25. CW-EPR spectra validate the unstable structures of the SNARE complex formed by SNAP-25 mutants. We propose that the truncated SNAP-25 mutants will disrupt the assembly of the SNARE core complex, and then inhibit the synaptic membrane fusion accordingly.
creator: Bin Lu
uri: https://doi.org/10.7717/peerj.1065
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Lu

title: Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae)
link: https://peerj.com/articles/1064
last-modified: 2015-06-30
description: The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.
creator: Cristina Frías-López
creator: Francisca C. Almeida
creator: Sara Guirao-Rico
creator: Joel Vizueta
creator: Alejandro Sánchez-Gracia
creator: Miquel A. Arnedo
creator: Julio Rozas
uri: https://doi.org/10.7717/peerj.1064
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Frías-López et al

title: The last marine pelomedusoids (Testudines: Pleurodira): a new species of Bairdemys and the paleoecology of Stereogenyina
link: https://peerj.com/articles/1063
last-modified: 2015-06-30
description: The extinct Stereogenyina turtles form a relatively diverse Podocnemididae lineage, with twelve described and phylogenetically positioned species. They are characterized by a wide geographic and temporal range, from the Eocene of Africa to the Pleistocene of Southeast Asia, and a peculiar palate morphology, with a secondary palate that is unique among side-necked turtles. Here, we describe a new Stereogenyina species, based on an almost complete skull from the middle Miocene Capadare Formation, of Venezuela. A new phylogenetic analysis supports the assignment of the new species to the genus Bairdemys. Based on geometric morphometrics analyses, we related the development of the stereogenyin secondary palate with the acquisition of a durophagous diet. Based on a review of the sedimentary environments where their fossils are found, we also propose that stereogenyins were a marine radiation of podocnemidid turtles, as corroborated by previous studies of fossil eggs and limb morphology. These two inferences allowed us to hypothesize that stereogenyins occupied an ecological niche similar to that of the extant Carettini sea turtles, and that the rise of the latter group may be related to the Stereogenyina diversity fall in the end of the Miocene.
creator: Gabriel S. Ferreira
creator: Ascanio D. Rincón
creator: Andrés Solórzano
creator: Max C. Langer
uri: https://doi.org/10.7717/peerj.1063
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ferreira et al.

title: Photosynthetic response of Persian Gulf acroporid corals to summer versus winter temperature deviations
link: https://peerj.com/articles/1062
last-modified: 2015-06-30
description: With on-going climate change, coral susceptibility to thermal stress constitutes a central concern in reefconservation. In the Persian Gulf, coral reefs are confronted with a high seasonal variability in water temperature, and both hot and cold extremes have been associated with episodes of coral bleaching and mortality. Using physiological performance as a measure of coral health, we investigated the thermal susceptibility of the common acroporid, Acropora downingi, near Hengam Island where the temperature oscillates seasonally in the range 20.2–34.2 °C. In a series of two short-term experiments comparing coral response in summer versus winter conditions, we exposed corals during each season (1) to the corresponding seasonal average and extreme temperature levels in a static thermal environment, and (2) to a progressive temperature deviation from the annual mean toward the corresponding extreme seasonal value and beyond in a dynamic thermal environment. We monitored four indictors of coral physiological performance: net photosynthesis (Pn), dark respiration (R), autotrophic capability (Pn/R), and survival. Corals exposed to warming during summer showed a decrease in net photosynthesis and ultimately died, while corals exposed to cooling during winter were not affected in their photosynthetic performance and survival. Coral autotrophic capability Pn/R was lower at the warmer thermal level within eachseason, and during summer compared to winter. Corals exposed to the maximum temperature of summer displayed Pn/R < 1, inferring that photosynthetic performance could not support basal metabolic needs under this environment. Our results suggest that the autotrophic performance of the Persian Gulf A. downingi is sensitive to the extreme temperatures endured in summer, and therefore its populations may be impacted by future increases in water temperature.
creator: Jahangir Vajed Samiei
creator: Abolfazl Saleh
creator: Ali Mehdinia
creator: Arash Shirvani
creator: Mohsen Kayal
uri: https://doi.org/10.7717/peerj.1062
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Vajed Samiei et al.

title: HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases
link: https://peerj.com/articles/1057
last-modified: 2015-06-30
description: Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded.
creator: Albert Palleja
creator: Lars J. Jensen
uri: https://doi.org/10.7717/peerj.1057
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2015 Palleja and Jensen

title: Influence of rimonabant treatment on peripheral blood mononuclear cells; flow cytometry analysis and gene expression profiling
link: https://peerj.com/articles/1056
last-modified: 2015-06-30
description: The cannabinoid receptor type 1 (CB1) antagonist rimonabant has been used as treatment for obesity. In addition, anti-proliferative effects on mitogen-activated leukocytes have been demonstrated in vitro. We have previously shown that rimonabant (SR141716A) induces cell death in ex vivo isolated malignant lymphomas with high expression of CB1 receptors. Since CB1 targeting may be part of a future lymphoma therapy, it was of interest to investigate possible effects on peripheral blood mononuclear cells (PBMC) in patients treated with rimonabant. We therefore evaluated leukocyte subsets by 6 color flow cytometry in eight patients before and at treatment with rimonabant for 4 weeks. Whole-transcript gene expression profiling in PBMC before and at 4 weeks of rimonabant treatment was done using Affymetrix Human Gene 1.0 ST Arrays. Our data show no significant changes of monocytes, B cells, total T cells or T cell subsets in PBMC during treatment with rimonabant. There was a small but significant increase in CD3–, CD16+ and/or CD56+ cells after rimonabant therapy. Gene expression analysis detected significant changes in expression of genes associated with innate immunity, cell death and metabolism. The present study shows that normal monocytes and leukocyte subsets in blood remain rather constant during rimonabant treatment. This is in contrast to the induction of cell death previously observed in CB1 expressing lymphoma cells in response to treatment with rimonabant in vitro. These differential effects observed on normal and malignant lymphoid cells warrant investigation of CB1 targeting as a potential lymphoma treatment.
creator: Stefan Almestrand
creator: Xiao Wang
creator: Åsa Jeppsson-Ahlberg
creator: Marcus Nordgren
creator: Jenny Flygare
creator: Birger Christensson
creator: Stephan Rössner
creator: Birgitta Sander
uri: https://doi.org/10.7717/peerj.1056
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Almestrand et al.

title: Comprehensive comparison of large-scale tissue expression datasets
link: https://peerj.com/articles/1054
last-modified: 2015-06-30
description: For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression. By developing comparable confidence scores for all types of evidence, we show that it is possible to improve both quality and coverage by combining the datasets. To facilitate use and visualization of our work, we have developed the TISSUES resource (http://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface.
creator: Alberto Santos
creator: Kalliopi Tsafou
creator: Christian Stolte
creator: Sune Pletscher-Frankild
creator: Seán I. O’Donoghue
creator: Lars Juhl Jensen
uri: https://doi.org/10.7717/peerj.1054
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Santos et al.

title: US adolescents’ friendship networks and health risk behaviors: a systematic review of studies using social network analysis and Add Health data
link: https://peerj.com/articles/1052
last-modified: 2015-06-30
description: Background. Documented trends in health-related risk behaviors among US adolescents have remained high over time. Studies indicate relationships among mutual friends are a major influence on adolescents’ risky behaviors. Social Network Analysis (SNA) can help understand friendship ties affecting individual adolescents’ engagement in these behaviors. Moreover, a systematic literature review can synthesize findings from a range of studies using SNA, as well as assess these studies’ methodological quality. Review findings also can help health educators and promoters develop more effective programs.Objective. This review systematically examined studies of the influence of friendship networks on adolescents’ risk behaviors, which utilized SNA and the Add Health data (a nationally representative sample).Methods. We employed the Matrix Method to synthesize and evaluate 15 published studies that met our inclusion and exclusion criteria, retrieved from the Add Health website and 3 major databases (Medline, Eric, and PsycINFO). Moreover, we assigned each study a methodological quality score (MQS).Results. In all studies, friendship networks among adolescents promoted their risky behaviors, including drinking alcohol, smoking, sexual intercourse, and marijuana use. The average MQS was 4.6, an indicator of methodological rigor (scale: 1–9).Conclusion. Better understanding of risky behaviors influenced by friends can be useful for health educators and promoters, as programs targeting friendships might be more effective. Additionally, the overall MQ of these reviewed studies was good, as average scores fell above the scale’s mid-point.
creator: Kwon Chan Jeon
creator: Patricia Goodson
uri: https://doi.org/10.7717/peerj.1052
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Jeon and Goodson

title: Attitudes of medical students in Lahore, Pakistan towards the doctor–patient relationship
link: https://peerj.com/articles/1050
last-modified: 2015-06-30
description: Background. A good doctor–patient relationship is the centre stone of modern medicine. Patients are getting increasingly aware about exercising their autonomy and thus modern medicine cannot deliver all its advances to the patients if a good doctor–patient relationship is not established. We initiated this study with the aim to assess the leaning of medical students, who are the future physicians, towards either a doctor-centered or a patient-centered care, and to explore the effects of personal attributes on care such as gender, academic year, etc.Materials & Methods. A cross-sectional study was conducted between July and Sep 2013. CMH Lahore Medical and Dental College Ethical Review Committee approved the study questionnaire. The study population consisted of 1,181 medical students in years 1–5 from two medical colleges. The English version of Patient Practitioner Orientation Scale (PPOS) was used to assess attitudes of medical students towards doctor–patient relationship. PPOS yields a mean score range of 1–6, where 1 signifies tendency towards a doctor centered relationship and 6 signifies patient-centered relationship. The relationship between PPOS scores and individual characteristics like gender, academic year etc. were examined by multiple regression.Results. A total of 783 students formed the final sample (response rate = 92%). Mean PPOS score of the entire sample was 3.40 (± .49 S.D.). Mean sharing sub-scale score was 3.18 (± 0.62 S.D. Mean caring sub-scale score was 3.63 (± 0.56 S.D.). Characteristics associated with most patient-centered attitudes were advanced academic year, having a clinical rotation, foreign background and studying in a private college. Gender, having doctor parents, relationship and residence status had no bearing on the attitudes (p > 0.05).Conclusion. Despite ongoing debate and the emphasis on a patient-centered curriculum, our study suggests that the current curriculum and its teachings are not producing the results they are designed to achieve. Students should be adequately exposed to the patients from the beginning of their medical education in clinical settings which are more sympathetic to a patient-centered care.
creator: Waqas Ahmad
creator: Edward Krupat
creator: Yumna Asma
creator: Noor-E- Fatima
creator: Rayan Attique
creator: Umar Mahmood
creator: Ahmed Waqas
uri: https://doi.org/10.7717/peerj.1050
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ahmad et al.

title: Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids
link: https://peerj.com/articles/1040
last-modified: 2015-06-30
description: FadD catalyses the first step in E. coli beta-oxidation, the activation of free fatty acids into acyl-CoA thioesters. This activation makes fatty acids competent for catabolism and reduction into derivatives like alcohols and alkanes. Alcohols and alkanes derived from medium chain fatty acids (MCFAs, 6–12 carbons) are potential biofuels; however, FadD has low activity on MCFAs. Herein, we generate mutations in fadD that enhance its acyl-CoA synthetase activity on MCFAs. Homology modeling reveals that these mutations cluster on a face of FadD from which the co-product, AMP, is expected to exit. Using FadD homology models, we design additional FadD mutations that enhance E. coli growth rate on octanoate and provide evidence for a model wherein FadD activity on octanoate can be enhanced by aiding product exit. These studies provide FadD mutants useful for producing MCFA derivatives and a rationale to alter the substrate specificity of adenylating enzymes.
creator: Tyler J. Ford
creator: Jeffrey C. Way
uri: https://doi.org/10.7717/peerj.1040
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ford and Way

title: Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas
link: https://peerj.com/articles/1019
last-modified: 2015-06-30
description: Patterns of dispersal and connectivity of the Caribbean gorgonian Antillogorgia elisabethae in The Bahamas were assessed in both adults and recently settled recruits from 13 sites using microsatellite loci. Adult populations along the Little Bahama Bank (LBB) exhibited a clear pattern of isolation by distance (IBD) which described 86% of the variance in pairwise genetic distances. Estimates of dispersal based on the IBD model suggested dispersal distances along the LBB on the order of 100 m. Increasing the spatial scale to include sites separated by open ocean generated an apparent IBD signal but the relationship had a greater slope and explained less of the variance. This relationship with distance reflected both stepping stone based IBD and regional differentiation probably created by ocean currents and barriers to dispersal that are correlated with geographic distance. Analysis of recruits from 4 sites on the LBB from up to 6 years did not detect differences between years nor differences with adult populations. The result suggests that neither selection on recruits nor inter-annual variation in dispersal affected adult population structure. Assignment tests of recruits indicated the most likely sources of the recruits were the local or adjacent populations. Most of the patterning in population structure in the northern Bahamas can be explained by geographic distance and oceanographic connectivity. Recognition of these complex patterns is important in developing management plans for A. elisabethae and in understanding the effects of disturbance to adult populations of A. elisabethae and similar species with limited dispersal.
creator: Howard R. Lasker
creator: Isabel Porto-Hannes
uri: https://doi.org/10.7717/peerj.1019
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Lasker and Porto-Hannes

title: HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors
link: https://peerj.com/articles/1060
last-modified: 2015-06-25
description: The production of recombinant proteins such as the fibroblast growth factors (FGFs) is the key to establishing their function in cell communication. The production of recombinant FGFs in E. coli is limited, however, due to expression and solubility problems. HaloTag has been used as a fusion protein to introduce a genetically-encoded means for chemical conjugation of probes. We have expressed 11 FGF proteins with an N-terminal HaloTag, followed by a tobacco etch virus (TEV) protease cleavage site to allow release of the FGF protein. These were purified by heparin-affinity chromatography, and in some instances by further ion-exchange chromatography. It was found that HaloTag did not adversely affect the expression of FGF1 and FGF10, both of which expressed well as soluble proteins. The N-terminal HaloTag fusion was found to enhance the expression and yield of FGF2, FGF3 and FGF7. Moreover, whereas FGF6, FGF8, FGF16, FGF17, FGF20 and FGF22 were only expressed as insoluble proteins, their N-terminal HaloTag fusion counterparts (Halo-FGFs) were soluble, and could be successfully purified. However, cleavage of Halo-FGF6, -FGF8 and -FGF22 with TEV resulted in aggregation of the FGF protein. Measurement of phosphorylation of p42/44 mitogen-activated protein kinase and of cell growth demonstrated that the HaloTag fusion proteins were biologically active. Thus, HaloTag provides a means to enhance the expression of soluble recombinant proteins, in addition to providing a chemical genetics route for covalent tagging of proteins.
creator: Changye Sun
creator: Yong Li
creator: Sarah E. Taylor
creator: Xianqing Mao
creator: Mark C. Wilkinson
creator: David G. Fernig
uri: https://doi.org/10.7717/peerj.1060
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sun et al.

title: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
link: https://peerj.com/articles/1047
last-modified: 2015-06-25
description: Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators’ diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction.
creator: Matthieu Leray
creator: Christopher P. Meyer
creator: Suzanne C. Mills
uri: https://doi.org/10.7717/peerj.1047
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Leray et al.

title: FDAAA legislation is working, but methodological flaws undermine the reliability of clinical trials: a cross-sectional study
link: https://peerj.com/articles/1015
last-modified: 2015-06-25
description: The relationship between clinical research and the pharmaceutical industry has placed clinical trials in jeopardy. According to the medical literature, more than 70% of clinical trials are industry-funded. Many of these trials remain unpublished or have methodological flaws that distort their results. In 2007, it was signed into law the Food and Drug Administration Amendments Act (FDAAA), aiming to provide publicly access to a broad range of biomedical information to be made available on the platform ClinicalTrials (available at https://www.clinicaltrials.gov). We accessed ClinicalTrials.gov and evaluated the compliance of researchers and sponsors with the FDAAA. Our sample comprised 243 protocols of clinical trials of biological monoclonal antibodies (mAb) adalimumab, bevacizumab, infliximab, rituximab, and trastuzumab. We demonstrate that the new legislation has positively affected transparency patterns in clinical research, through a significant increase in publication and online reporting rates after the enactment of the law. Poorly designed trials, however, remain a challenge to be overcome, due to a high prevalence of methodological flaws. These flaws affect the quality of clinical information available, breaching ethical duties of sponsors and researchers, as well as the human right to health.
creator: Douglas H. Marin dos Santos
creator: Álvaro N. Atallah
uri: https://doi.org/10.7717/peerj.1015
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2015 Marin dos Santos and Atallah

title: Imbalance in the blood antioxidant system in growth hormone-deficient children before and after 1 year of recombinant growth hormone therapy
link: https://peerj.com/articles/1055
last-modified: 2015-06-25
description: The aim of our study was to examine the effects of 12-month therapy with recombinant growth hormone (rGH) on the blood antioxidant system in children with growth hormone deficiency (GHD). Total antioxidant capacity (TAC) of plasma was measured by FRAP (ferric reducing antioxidant power or ferric reducing ability of plasma); activities of superoxide dismutase (SOD) and catalase (CAT) in erythrocytes were assessed; non-protein thiols (NT) and ceruloplasmin (CP) levels were also measured. These parameters were determined before and after 12 month of rGH treatment. Eleven treatment-naive prepubertal children with growth hormone deficiency were included in the study. Another 11 prepubertal children comprised a control group. Before rGH treatment, TAC of plasma and NT level in the control group were significantly lower (726 ± 196 vs. 525 ± 166 µmol/L, P = 0.0182 and 0.92 ± 0.18 vs. 0.70 ± 0.22 µmol/ml, P = 0.0319, before and after the therapy, respectively). The only parameter that significantly (19.6 ± 4.7 vs. 14.5 ± 3.4 Units/g Hb, P = 0.0396) exceeded the same in the control group after rGH therapy was SOD activity. However, none of the measured parameters of antioxidant system in GHD children, except for TAC (525 ± 166 vs. 658 ± 115 µmol/L, P = 0.0205), exhibited significant improvement toward the end of the 12-month treatment period, although non-significant changes in CAT activity and CP level were also observed. This work has demonstrated that some parameters of the blood antioxidant system are out of balance and even impaired in GHD children. A 12-month treatment with rGH resulted in a partial improvement of the antioxidant system.
creator: Maria S. Pankratova
creator: Adil A. Baizhumanov
creator: Alexander I. Yusipovich
creator: Maria Faassen
creator: Tatyana Yu. Shiryaeva
creator: Valentina A. Peterkova
creator: Svetlana S. Kovalenko
creator: Tatiana A. Kazakova
creator: Georgy V. Maksimov
uri: https://doi.org/10.7717/peerj.1055
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Pankratova et al.

title: Staphylococcus Aureus carriage and long-term Rituximab treatment for Granulomatosis with polyangiitis
link: https://peerj.com/articles/1051
last-modified: 2015-06-25
description: Objective. Chronic nasal carriage of Staphylococcus aureus (SA) increases the risk of relapse while Rituximab (RTX) is an effective agent for inducing and maintaining remission in patients with Granulomatosis with polyangiitis (GPA). We investigated whether B cell depletion and hypogammaglobulinemia that occur during RTX treatment increase the risk of chronic SA nasal carriage and subsequent disease flares, in GPA patients on long-term RTX maintenance therapy.Methods. Retrospective cohort study from a disease registry involving 29 GPA patients receiving RTX maintenance (median RTX dose of 9 g) during a median period of 49 months. Nasal swabs were collected prior and during RTX for a median of 3 and 9 swabs respectively. Persistent SA nasal carriage was defined with the presence of SA in more than 75% of nasal swabs.Results. SA nasal carriage did not change during RTX (p = 0.297). However, the rate of positive nasal swabs in GPA patients with transient SA nasal carriage during RTX maintenance increased from 0 prior RTX to 0.42 during RTX (p = 0.017). Persistent SA nasal carriage did not increase the risk of relapses (p = 0.844), of hypogammaglobulinemia (p = 0.122) and of severe infections (p = 0.144), but reduced the risk of chronic infections (p = 0.044). Change in SA carriage status during RTX did not influence the risk of relapses (p = 0.756), hypogammaglobulinamia (p = 0.474) and infections, either severe (p = 0.913) or chronic (p = 0.121).Conclusion. Long-term RTX maintenance therapy in GPA patients did not significantly influence SA nasal carriage status. Persistent SA carriage during long-term RTX treatment did not seem to increase the risk of relapses, but seemed to decrease the risk of hypogammaglobulinemia associated chronic infections.
creator: Emilio Besada
creator: Wenche Koldingsnes
creator: Johannes C. Nossent
uri: https://doi.org/10.7717/peerj.1051
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Besada et al.

title: Parents’ evaluation of support in Australian hospitals following stillbirth
link: https://peerj.com/articles/1049
last-modified: 2015-06-25
description: The present study evaluated the level of support and satisfaction among parents of stillborn babies in Australian hospitals. One-hundred and eighty-nine mothers and fathers completed an online survey designed by the researcher based on the guidelines designed by the Perinatal Society of Australia and New Zealand. Support was inconsistent with guidelines implemented on average only 55% of the time. Areas of support regarding creating memories, birth options and autopsy were most problematic. A significant positive correlation was found between support and satisfaction and there is indication that there has been some increase in support and satisfaction over time. There has been a significant increase in both support and satisfaction since the release of the guidelines in 2009. Creating memories was regarded by parents as the most influential to their grief. It is recommended that health professionals review guidelines and seek feedback from parents as to how they can improve the support they provide.
creator: Melanie L. Basile
creator: Einar B. Thorsteinsson
uri: https://doi.org/10.7717/peerj.1049
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Basile and Thorsteinsson

title: Family structure as a predictor of screen time among youth
link: https://peerj.com/articles/1048
last-modified: 2015-06-25
description: The family plays a central role in the development of health-related behaviors among youth. The objective of this study was to determine whether non-traditional parental structure and shared custody arrangements predict how much time youth spend watching television, using a computer recreationally, and playing video games. Participants were a nationally representative sample of Canadian youth (N = 26,068) in grades 6–10 who participated in the 2009/10 Health Behaviour in School-aged Children Survey. Screen time in youth from single parent and reconstituted families, with or without regular visitation with their non-residential parent, was compared to that of youth from traditional dual-parent families. Multiple imputation was used to account for missing data. After multiple imputation, the relative odds of being in the highest television, computer use, video game, and total screen time quartiles were not different in boys and girls from non-traditional families by comparison to boys and girls from traditional dual-parent families. In conclusion, parental structure and child custody arrangements did not have a meaningful impact on screen time among youth.
creator: Rachel McMillan
creator: Michael McIsaac
creator: Ian Janssen
uri: https://doi.org/10.7717/peerj.1048
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McMillan et al.

title: A Bayesian approach to optimizing cryopreservation protocols
link: https://peerj.com/articles/1039
last-modified: 2015-06-25
description: Cryopreservation is beset with the challenge of protocol alignment across a wide range of cell types and process variables. By taking a cross-sectional assessment of previously published cryopreservation data (sample means and standard errors) as preliminary meta-data, a decision tree learning analysis (DTLA) was performed to develop an understanding of target survival using optimized pruning methods based on different approaches. Briefly, a clear direction on the decision process for selection of methods was developed with key choices being the cooling rate, plunge temperature on the one hand and biomaterial choice, use of composites (sugars and proteins as additional constituents), loading procedure and cell location in 3D scaffolding on the other. Secondly, using machine learning and generalized approaches via the Naïve Bayes Classification (NBC) method, these metadata were used to develop posterior probabilities for combinatorial approaches that were implicitly recorded in the metadata. These latter results showed that newer protocol choices developed using probability elicitation techniques can unearth improved protocols consistent with multiple unidimensionally-optimized physical protocols. In conclusion, this article proposes the use of DTLA models and subsequently NBC for the improvement of modern cryopreservation techniques through an integrative approach.
creator: Sammy Sambu
uri: https://doi.org/10.7717/peerj.1039
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sambu

title: Beliefs in being unlucky and deficits in executive functioning: an ERP study
link: https://peerj.com/articles/1007
last-modified: 2015-06-25
description: There has been initial evidence to support the Dysexecutive Luck hypothesis, which proposes that beliefs in being unlucky are associated with deficits in executive functioning (Maltby et al., 2013). The present study tested the Dysexecutive Luck hypothesis by examining whether deficits in the early stage of top down attentional control led to an increase of neural activity in later stages of response related selection process among those who thought themselves to be unlucky. Individuals with these beliefs were compared to a control group using an Event-Related Potential (ERP) measure assessing underlying neural activity of semantic inhibition while completing a Stroop test. Results showed stronger main interference effects in the former group, via greater reaction times and a more negative distributed scalp late ERP component during incongruent trials in the time window of 450–780 ms post stimulus onset. Further, less efficient maintenance of task set among the former group was associated with greater late ERP response-related activation to compensate for the lack of top-down attentional control. These findings provide electrophysiological evidence to support the Dysexecutive Luck hypothesis.
creator: Jaime Martín del Campo Ríos
creator: Giorgio Fuggetta
creator: John Maltby
uri: https://doi.org/10.7717/peerj.1007
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Martín del Campo et al.

title: Decreasing seagrass density negatively influences associated fauna
link: https://peerj.com/articles/1053
last-modified: 2015-06-23
description: Seagrass meadows globally are disappearing at a rapid rate with physical disturbances being one of the major drivers of this habitat loss. Disturbance of seagrass can lead to fragmentation, a reduction in shoot density, canopy height and coverage, and potentially permanent loss of habitat. Despite being such a widespread issue, knowledge of how such small scale change affects the spatial distribution and abundances of motile fauna remains limited. The present study investigated fish and macro faunal community response patterns to a range of habitat variables (shoot length, cover and density), including individual species habitat preferences within a disturbed and patchy intertidal seagrass meadow. Multivariate analysis showed a measurable effect of variable seagrass cover on the abundance and distribution of the fauna, with species specific preferences to both high and low seagrass cover seagrass. The faunal community composition varied significantly with increasing/decreasing cover. The faunal species composition of low cover seagrass was more similar to sandy control plots than to higher cover seagrass. Shannon Wiener Diversity (H′) and species richness was significantly higher in high cover seagrass than in low cover seagrass, indicating increasing habitat value as density increases. The results of this study underline how the impacts of small scale disturbances from factors such as anchor damage, boat moorings and intertidal vehicle use on seagrass meadows that reduce shoot density and cover can impact upon associated fauna. These impacts have negative consequences for the delivery of ecosystem services such as the provision of nursery habitat.
creator: Rosemary M. McCloskey
creator: Richard K.F. Unsworth
uri: https://doi.org/10.7717/peerj.1053
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McCloskey and Unsworth

title: The invasive land planarian Platydemus manokwari (Platyhelminthes, Geoplanidae): records from six new localities, including the first in the USA
link: https://peerj.com/articles/1037
last-modified: 2015-06-23
description: The land planarian Platydemus manokwari de Beauchamp, 1963 or “New Guinea flatworm” is a highly invasive species, mainly in the Pacific area, and recently in Europe (France). We report specimens from six additional countries and territories: New Caledonia (including mainland and two of the Loyalty Islands, Lifou and Maré), Wallis and Futuna Islands, Singapore, Solomon Islands, Puerto Rico, and Florida, USA. We analysed the COI gene (barcoding) in these specimens with two sets of primers and obtained 909 bp long sequences. In addition, specimens collected in Townsville (Australia) were also sequenced. Two haplotypes of the COI sequence, differing by 3.7%, were detected: the “World haplotype” found in France, New Caledonia, French Polynesia, Singapore, Florida and Puerto Rico; and the “Australian haplotype” found in Australia. The only locality with both haplotypes was in the Solomon Islands. The country of origin of Platydemus manokwari is New Guinea, and Australia and the Solomon Islands are the countries closest to New Guinea from which we had specimens. These results suggest that two haplotypes exist in the area of origin of the species, but that only one of the two haplotypes (the “World haplotype”) has, through human agency, been widely dispersed. However, since P. manokwari is now recorded from 22 countries in the world and we have genetic information from only 8 of these, with none from New Guinea, this analysis provides only partial knowledge of the genetic structure of the invasive species. Morphological analysis of specimens from both haplotypes has shown some differences in ratio of the genital structures but did not allow us to interpret the haplotypes as different species. The new reports from Florida and Puerto Rico are firsts for the USA, for the American continent, and the Caribbean. P. manokwari is a known threat for endemic terrestrial molluscs and its presence is a matter of concern. While most of the infected territories reported until now were islands, the newly reported presence of the species in mainland US in Florida should be considered a potential major threat to the whole US and even the Americas.
creator: Jean-Lou Justine
creator: Leigh Winsor
creator: Patrick Barrière
creator: Crispus Fanai
creator: Delphine Gey
creator: Andrew Wee Kien Han
creator: Giomara La Quay-Velázquez
creator: Benjamin Paul Yi-Hann Lee
creator: Jean-Marc Lefevre
creator: Jean-Yves Meyer
creator: David Philippart
creator: David G. Robinson
creator: Jessica Thévenot
creator: Francis Tsatsia
uri: https://doi.org/10.7717/peerj.1037
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Justine et al.

title: Delivery by caesarean section and risk of childhood obesity: analysis of a Peruvian prospective cohort
link: https://peerj.com/articles/1046
last-modified: 2015-06-23
description: Objectives. We aimed to assess if Caesarean section is a risk factor for overnutrition in early- and late-childhood, and to assess the magnitude of the effect of child- versus family-related variables in these risk estimates.Methods. Longitudinal data from Peruvian children from the Young Lives Study was used. Outcomes assessed were overweight, obesity, overnutrition (overweight plus obesity), and central obesity (waist circumference) at the age 5 (first follow-up) and 7 (second follow-up) years. The exposure of interests was delivery by Caesarean section. Relative risks (RR) and 95% confidence intervals (95% CI) were calculated using multivariable models adjusted for child-related (e.g., birth weight) and family-related (e.g., maternal nutritional status) variables.Results. At baseline, mean age was 11.7 (± 3.5) months and 50.1% were boys. Children born by Caesarean section were 15.6%. The 10.5% of the children were overweight and 2.4% were obese. For the obesity outcome, data from 6,038 and 9,625 children-years was included from baseline to the first and second follow-up, respectively. Compared to those who did not experience Caesarean delivery, the risk of having obesity was higher in the group born by Caesarean: RRs were higher at early-childhood (first follow-up: 2.25; 95% CI [1.36–3.74]) than later in life (second follow-up: 1.57; 95% CI [1.02–2.41]). Family-related variables had a greater effect in attenuating the risk estimates for obesity at the first, than at the second follow-up.Conclusion. Our results suggest a higher probability of developing obesity, but not overweight, among children born by Caesarean section delivery. The magnitude of risk estimates decreased over time, and family-related variables had a stronger effect on the risk estimates at early-childhood.
creator: Rodrigo M. Carrillo-Larco
creator: J. Jaime Miranda
creator: Antonio Bernabé-Ortiz
uri: https://doi.org/10.7717/peerj.1046
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Carrillo-Larco et al.

title: Weather conditions associated with autumn migration by mule deer in Wyoming
link: https://peerj.com/articles/1045
last-modified: 2015-06-23
description: Maintaining ecological integrity necessitates a proactive approach of identifying and acquiring lands to conserve unfragmented landscapes, as well as evaluating existing mitigation strategies to increase connectivity in fragmented landscapes. The increased use of highway underpasses and overpasses to restore connectivity for wildlife species offers clear conservation benefits, yet also presents a unique opportunity to understand how weather conditions may impact movement of wildlife species. We used remote camera observations (19,480) from an existing wildlife highway underpass in Wyoming and daily meteorological observations to quantify weather conditions associated with autumn migration of mule deer in 2009 and 2010. We identified minimal daily temperature and snow depth as proximate cues associated with mule deer migration to winter range. These weather cues were consistent across does and bucks, but differed slightly by year. Additionally, extreme early season snow depth or cold temperature events appear to be associated with onset of migration. This information will assist wildlife managers and transportation officials as they plan future projects to maintain and enhance migration routes for mule deer.
creator: Chadwick D. Rittenhouse
creator: Tony W. Mong
creator: Thomas Hart
uri: https://doi.org/10.7717/peerj.1045
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Rittenhouse et al.

title: A reappraisal of the Middle Triassic chirotheriid Chirotherium ibericus Navás, 1906 (Iberian Range NE Spain), with comments on the Triassic tetrapod track biochronology of the Iberian Peninsula
link: https://peerj.com/articles/1044
last-modified: 2015-06-23
description: Triassic vertebrate tracks are known from the beginning of the 19th century and have a worldwide distribution. Several Triassic track ichnoassemblages and ichnotaxa have a restricted stratigraphic range and are useful in biochronology and biostratigraphy. The record of Triassic tracks in the Iberian Peninsula has gone almost unnoticed although more than 25 localities have been described since 1897. In one of these localities, the naturalist Longinos Navás described the ichnotaxon Chirotherium ibericus in 1906.The vertebrate tracks are in two sandy slabs from the Anisian (Middle Triassic) of the Moncayo massif (Zaragoza, Spain). In a recent revision, new, previously undescribed vertebrate tracks have been identified. The tracks considered to be C. ibericus as well as other tracks with the same morphology from both slabs have been classified as Chirotherium barthii. The rest of the tracks have been assigned to Chirotheriidae indet., Rhynchosauroides isp. and undetermined material. This new identification of C. barthii at the Navás site adds new data to the Iberian record of this ichnotaxon, which is characterized by the small size of the tracks when compared with the main occurrences of this ichnotaxon elsewhere. As at the Navás tracksite, the Anisian C. barthii-Rhynchosauroides ichnoassemblage has been found in other coeval localities in Iberia and worldwide. This ichnoassemblage belongs to the upper Olenekian-lower Anisian interval according to previous biochronological proposals. Analysis of the Triassic Iberian record of tetrapod tracks is uneven in terms of abundance over time. From the earliest Triassic to the latest Lower Triassic the record is very scarce, with Rhynchosauroides being the only known ichnotaxon. Rhynchosauroides covers a wide temporal range and gives poor information for biochronology. The record from the uppermost Lower Triassic to the Middle Triassic is abundant. The highest ichnodiversity has been reported for the Anisian with an assemblage composed of Dicynodontipus, Procolophonichnium, Rhynchosauroides, Rotodactylus, Chirotherium, Isochirotherium, Coelurosaurichnus and Paratrisauropus. The Iberian track record from the Anisian is coherent with the global biochronology proposed for Triassic tetrapod tracks. Nevertheless, the scarcity of track occurrences during the late Olenekian and Ladinian prevents analysis of the corresponding biochrons. Finally, although the Iberian record for the Upper Triassic is not abundant, the presence of Eubrontes, Anchisauripus and probably Brachychirotherium is coherent with the global track biochronology as well. Thus, the Triassic track record in the Iberian Peninsula matches the expected record for this age on the basis of a global biochronological approach, supporting the idea that vertebrate Triassic tracks are a useful tool in biochronology.
creator: Ignacio Díaz-Martínez
creator: Diego Castanera
creator: José Manuel Gasca
creator: José Ignacio Canudo
uri: https://doi.org/10.7717/peerj.1044
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Díaz-Martínez et al.

title: Life as a bachelor: quantifying the success of an alternative reproductive tactic in male blue monkeys
link: https://peerj.com/articles/1043
last-modified: 2015-06-23
description: In species that live in one-male groups, resident males monopolize access to a group of females and are assumed to have higher reproductive success than bachelors. We tested this assumption using genetic, demographic, and behavioral data from 8 groups of wild blue monkeys observed over 10 years to quantify reproduction by residents and bachelors and compare the success of the two tactics. We used maximum-likelihood methods to assign sires to 104 offspring born in the study groups, 36 of which were sired by extra-group males, i.e., residents of neighboring groups and bachelors. Among these extra-group males, high-ranking males (many of whom were neighboring residents) were more likely to sire offspring than low-ranking males, but the time these visiting males spent in the mother’s group when she conceived (male presence) did not predict their relative success. When bachelors competed for reproduction with other bachelors, neither rank nor male presence during the mother’s conceptive period affected the probability of siring an offspring, suggesting that highly opportunistic mating with conceptive females is important in bachelor reproduction. In a second analysis, we used long-term data to estimate resident and bachelor reproductive success over the long term, and particularly to determine if there are any circumstances in which a typical bachelor may sire as many offspring as a typical resident during one or two periods of residency. Our findings generally support the assumption of a resident reproductive advantage because in most circumstances, a lifelong bachelor would be unable to sire as many offspring as a resident. However, a bachelor who performs at the average rate in the average number of groups for several years may have similar lifetime reproductive success as a male whose reproduction is limited to one short period of residency, especially in a small group. Our findings suggest that one should not assume a resident reproductive advantage for males in one-male groups in all circumstances.
creator: Su-Jen Roberts
creator: Marina Cords
uri: https://doi.org/10.7717/peerj.1043
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Roberts and Cords

title: Sensitivity to the visual field origin of natural image patches in human low-level visual cortex
link: https://peerj.com/articles/1038
last-modified: 2015-06-23
description: Asymmetries in the response to visual patterns in the upper and lower visual fields (above and below the centre of gaze) have been associated with ecological factors relating to the structure of typical visual environments. Here, we investigated whether the content of the upper and lower visual field representations in low-level regions of human visual cortex are specialised for visual patterns that arise from the upper and lower visual fields in natural images. We presented image patches, drawn from above or below the centre of gaze of an observer navigating a natural environment, to either the upper or lower visual fields of human participants (n = 7) while we used functional magnetic resonance imaging (fMRI) to measure the magnitude of evoked activity in the visual areas V1, V2, and V3. We found a significant interaction between the presentation location (upper or lower visual field) and the image patch source location (above or below fixation); the responses to lower visual field presentation were significantly greater for image patches sourced from below than above fixation, while the responses in the upper visual field were not significantly different for image patches sourced from above and below fixation. This finding demonstrates an association between the representation of the lower visual field in human visual cortex and the structure of the visual input that is likely to be encountered below the centre of gaze.
creator: Damien J. Mannion
uri: https://doi.org/10.7717/peerj.1038
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Mannion

title: Primate tarsal bones from Egerkingen, Switzerland, attributable to the middle Eocene adapiform Caenopithecus lemuroides
link: https://peerj.com/articles/1036
last-modified: 2015-06-23
description: The middle Eocene species Caenopithecus lemuroides, known solely from the Egerkingen fissure fillings in Switzerland, was the first Paleogene fossil primate to be correctly identified as such (by Ludwig Rütimeyer in 1862), but has long been represented only by fragmentary mandibular and maxillary remains. More recent discoveries of adapiform fossils in other parts of the world have revealed Caenopithecus to be a biogeographic enigma, as it is potentially more closely related to Eocene adapiforms from Africa, Asia, and North America than it is to any known European forms. More anatomical evidence is needed, however, to provide robust tests of such phylogenetic hypotheses. Here we describe and analyze the first postcranial remains that can be attributed to C. lemuroides—an astragalus and three calcanei held in the collections of the Naturhistorisches Museum Basel that were likely recovered from Egerkingen over a century ago. Qualitative and multivariate morphometric analyses of these elements suggest that C. lemuroides was even more loris-like than European adapines such as Adapis and Leptadapis, and was not simply an adapine with an aberrant dentition. The astragalus of Caenopithecus is similar to that of younger Afradapis from the late Eocene of Egypt, and parsimony and Bayesian phylogenetic analyses that include the new tarsal data strongly support the placement of Afradapis and Caenopithecus as sister taxa to the exclusion of all other known adapiforms, thus implying that dispersal between Europe and Africa occurred during the middle Eocene. The new tarsal evidence, combined with previously known craniodental fossils, allows us to reconstruct C. lemuroides as having been an arboreal and highly folivorous 1.5–2.5 kg primate that likely moved slowly and deliberately with little or no capacity for acrobatic leaping, presumably maintaining consistent powerful grasps on branches in both above-branch and inverted postures.
creator: Erik R. Seiffert
creator: Loïc Costeur
creator: Doug M. Boyer
uri: https://doi.org/10.7717/peerj.1036
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Seiffert et al.

title: Responses to simulated nitrogen deposition by the neotropical epiphytic orchid Laelia speciosa
link: https://peerj.com/articles/1021
last-modified: 2015-06-23
description: Potential ecophysiological responses to nitrogen deposition, which is considered to be one of the leading causes for global biodiversity loss, were studied for the endangered endemic Mexican epiphytic orchid, Laelia speciosa, via a shadehouse dose-response experiment (doses were 2.5, 5, 10, 20, 40, and 80 kg N ha−1 yr−1) in order to assess the potential risk facing this orchid given impending scenarios of nitrogen deposition. Lower doses of nitrogen of up to 20 kg N ha yr−1, the dose that led to optimal plant performance, acted as fertilizer. For instance, the production of leaves and pseudobulbs were respectively 35% and 36% greater for plants receiving 20 kg N ha yr−1 than under any other dose. Also, the chlorophyll content and quantum yield peaked at 0.66 ± 0.03 g m−2 and 0.85 ± 0.01, respectively, for plants growing under the optimum dose. In contrast, toxic effects were observed at the higher doses of 40 and 80 kg N ha yr−1. The δ13C for leaves averaged −14.7 ± 0.2‰ regardless of the nitrogen dose. In turn, δ15N decreased as the nitrogen dose increased from 0.9 ± 0.1‰ under 2.5 kg N ha−1yr−1 to −3.1 ± 0.2‰ under 80 kg N ha−1yr−1, indicating that orchids preferentially assimilate NH4+ rather than NO3− of the solution under higher doses of nitrogen. Laelia speciosa showed a clear response to inputs of nitrogen, thus, increasing rates of atmospheric nitrogen deposition can pose an important threat for this species.
creator: Edison A. Díaz-Álvarez
creator: Roberto Lindig-Cisneros
creator: Erick de la Barrera
uri: https://doi.org/10.7717/peerj.1021
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Díaz-Álvarez et al.

title: Once bitten, twice shy: experienced regret and non-adaptive choice switching
link: https://peerj.com/articles/1035
last-modified: 2015-06-18
description: When a good decision leads to a bad outcome, the experience of regret can bias subsequent choices: people are less likely to select the regret-producing alternative a second time, even when it is still objectively the best alternative (non-adaptive choice switching). The first study presented herein showed that nearly half of participants experiencing regret rejected a previous alternative they had recognized as the best one, and chose a non-optimal alternative instead. The second study investigated the mechanism underlying this bias, and results supported the hypothesis that this non-adaptive choice switching is caused by inhibition of the previous decision (direct effect of experienced regret), rather than by increased sensitivity to anticipated regret in subsequent choices (indirect effect of experienced regret mediated by anticipated regret).
creator: Francesco Marcatto
creator: Anna Cosulich
creator: Donatella Ferrante
uri: https://doi.org/10.7717/peerj.1035
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Marcatto et al.

title: The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird?
link: https://peerj.com/articles/1032
last-modified: 2015-06-18
description: The exceptionally well-preserved Romanian dinosaur Balaur bondoc is the most complete theropod known to date from the Upper Cretaceous of Europe. Previous studies of this remarkable taxon have included its phylogenetic interpretation as an aberrant dromaeosaurid with velociraptorine affinities. However, Balaur displays a combination of both apparently plesiomorphic and derived bird-like characters. Here, we analyse those features in a phylogenetic revision and show how they challenge its referral to Dromaeosauridae. Our reanalysis of two distinct phylogenetic datasets focusing on basal paravian taxa supports the reinterpretation of Balaur as an avialan more crownward than Archaeopteryx but outside of Pygostylia, and as a flightless taxon within a paraphyletic assemblage of long-tailed birds. Our placement of Balaur within Avialae is not biased by character weighting. The placement among dromaeosaurids resulted in a suboptimal alternative that cannot be rejected based on the data to hand. Interpreted as a dromaeosaurid, Balaur has been assumed to be hypercarnivorous and predatory, exhibiting a peculiar morphology influenced by island endemism. However, a dromaeosaurid-like ecology is contradicted by several details of Balaur’s morphology, including the loss of a third functional manual digit, the non-ginglymoid distal end of metatarsal II, and a non-falciform ungual on the second pedal digit that lacks a prominent flexor tubercle. Conversely, an omnivorous ecology is better supported by Balaur’s morphology and is consistent with its phylogenetic placement within Avialae. Our reinterpretation of Balaur implies that a superficially dromaeosaurid-like taxon represents the enlarged, terrestrialised descendant of smaller and probably volant ancestors.
creator: Andrea Cau
creator: Sienna A Birch
creator: Darren Naish
uri: https://doi.org/10.7717/peerj.1032
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Cau et al.

title: Exploring the attitudes of medical faculty members and students in Pakistan towards plagiarism: a cross sectional survey
link: https://peerj.com/articles/1031
last-modified: 2015-06-18
description: Objective. The objective of this survey was to explore the attitudes towards plagiarism of faculty members and medical students in Pakistan.Methods. The Attitudes Toward Plagiarism questionnaire (ATP) was modified and distributed among 550 medical students and 130 faculty members in 7 medical colleges of Lahore and Rawalpindi. Data was entered in the SPSS v.20 and descriptive statistics were analyzed. The questionnaire was validated by principal axis factoring analysis.Results. Response rate was 93% and 73%, respectively. Principal axis factoring analysis confirmed one factor structure of ATP in the present sample. It had an acceptable Cronbach’s alpha value of 0.73. There were 421 medical students (218 (52%) female, 46% 3rd year MBBS students, mean age of 20.93 ± 1.4 years) and 95 faculty members (54.7% female, mean age 34.5 ± 8.9 years). One fifth of the students (19.7%) trained in medical writing (19.7%), research ethics (25.2%) or were currently involved in medical writing (17.6%). Most of the faculty members were demonstrators (66) or assistant professors (20) with work experience between 1 and 10 years. Most of them had trained in medical writing (68), research ethics (64) and were currently involved in medical writing (64). Medical students and faculty members had a mean score of 43.21 (7.1) and 48.4 (5.9) respectively on ATP. Most of the respondents did not consider that they worked in a plagiarism free environment and reported that self-plagiarism should not be punishable in the same way as plagiarism. Opinion regarding leniency in punishment of younger researchers who were just learning medical writing was divided.Conclusions. The general attitudes of Pakistani medical faculty members and medical students as assessed by ATP were positive. We propose training in medical writing and research ethics as part of the under and post graduate medical curriculum.
creator: Farooq Azam Rathore
creator: Ahmed Waqas
creator: Ahmad Marjan Zia
creator: Martina Mavrinac
creator: Fareeha Farooq
uri: https://doi.org/10.7717/peerj.1031
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Rathore et al.

title: Compact graphical representation of phylogenetic data and metadata with GraPhlAn
link: https://peerj.com/articles/1029
last-modified: 2015-06-18
description: The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn’s potential for modern microbial and community genomics.
creator: Francesco Asnicar
creator: George Weingart
creator: Timothy L. Tickle
creator: Curtis Huttenhower
creator: Nicola Segata
uri: https://doi.org/10.7717/peerj.1029
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Asnicar et al.

title: Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae)
link: https://peerj.com/articles/1028
last-modified: 2015-06-18
description: Adaptation to pollinators is a key factor of diversification in angiosperms. The Caribbean sister genera Rhytidophyllum and Gesneria present an important diversification of floral characters. Most of their species can be divided in two major pollination syndromes. Large-open flowers with pale colours and great amount of nectar represent the generalist syndrome, while the hummingbird-specialist syndrome corresponds to red tubular flowers with a less important nectar volume. Repeated convergent evolution toward the generalist syndrome in this group suggests that such transitions rely on few genes of moderate to large effect. To test this hypothesis, we built a linkage map and performed a QTL detection for divergent pollination syndrome traits by crossing one specimen of the generalist species Rhytidophyllum auriculatum with one specimen of the hummingbird pollinated R. rupincola. Using geometric morphometrics and univariate traits measurements, we found that floral shape among the second-generation hybrids is correlated with morphological variation observed between generalist and hummingbird-specialist species at the genus level. The QTL analysis showed that colour and nectar volume variation between syndromes involve each one major QTL while floral shape has a more complex genetic basis and rely on few genes of moderate effect. Finally, we did not detect any genetic linkage between the QTLs underlying those traits. This genetic independence of traits could have facilitated evolution toward optimal syndromes.
creator: Hermine Alexandre
creator: Justine Vrignaud
creator: Brigitte Mangin
creator: Simon Joly
uri: https://doi.org/10.7717/peerj.1028
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Alexandre et al.

title: How reproducible are the measurements of leaf fluctuating asymmetry?
link: https://peerj.com/articles/1027
last-modified: 2015-06-18
description: Fluctuating asymmetry (FA) represents small, non-directional deviations from perfect symmetry in morphological characters. FA is generally assumed to increase in response to stress; therefore, FA is frequently used in ecological studies as an index of environmental or genetic stress experienced by an organism. The values of FA are usually small, and therefore the reliable detection of FA requires precise measurements. The reproducibility of fluctuating asymmetry (FA) was explored by comparing the results of measurements of scanned images of 100 leaves of downy birch (Betula pubescens) conducted by 31 volunteer scientists experienced in studying plant FA. The median values of FA varied significantly among the participants, from 0.000 to 0.074, and the coefficients of variation in FA for individual leaves ranged from 25% to 179%. The overall reproducibility of the results among the participants was rather low (0.074). Variation in instruments and methods used by the participants had little effect on the reported FA values, but the reproducibility of the measurements increased by 30% following exclusion of data provided by seven participants who had modified the suggested protocol for leaf measurements. The scientists working with plant FA are advised to pay utmost attention to adequate and detailed description of their data acquisition protocols in their forthcoming publications, because all characteristics of instruments and methods need to be controlled to increase the quality and reproducibility of the data. Whenever possible, the images of all measured objects and the results of primary measurements should be published as electronic appendices to scientific papers.
creator: Mikhail V. Kozlov
uri: https://doi.org/10.7717/peerj.1027
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kozlov

title: Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos
link: https://peerj.com/articles/1022
last-modified: 2015-06-18
description: It is well known that gene regulation is a tightly controlled process in early organismal development. However, the roles of key processes involved in this regulation, such as transcription and translation, are less well understood, and mathematical modeling approaches in this field are still in their infancy. In recent studies, biologists have taken precise measurements of protein and mRNA abundance to determine the relative contributions of key factors involved in regulating protein levels in mammalian cells. We now approach this question from a mathematical modeling perspective. In this study, we use a simple dynamic mathematical model that incorporates terms representing transcription, translation, mRNA and protein decay, and diffusion in an early Drosophila embryo. We perform global sensitivity analyses on this model using various different initial conditions and spatial and temporal outputs. Our results indicate that transcription and translation are often the key parameters to determine protein abundance. This observation is in close agreement with the experimental results from mammalian cells for various initial conditions at particular time points, suggesting that a simple dynamic model can capture the qualitative behavior of a gene. Additionally, we find that parameter sensitivites are temporally dynamic, illustrating the importance of conducting a thorough global sensitivity analysis across multiple time points when analyzing mathematical models of gene regulation.
creator: Gregory D. McCarthy
creator: Robert A. Drewell
creator: Jacqueline M. Dresch
uri: https://doi.org/10.7717/peerj.1022
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McCarthy et al.

title: Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium
link: https://peerj.com/articles/1017
last-modified: 2015-06-18
description: Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs) and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element) in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.
creator: Marie-Mathilde Perrineau
creator: Dana C. Price
creator: Georg Mohr
creator: Debashish Bhattacharya
uri: https://doi.org/10.7717/peerj.1017
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Perrineau et al.

title: Leadership and management influences the outcome of wildlife reintroduction programs: findings from the Sea Eagle Recovery Project
link: https://peerj.com/articles/1012
last-modified: 2015-06-18
description: Wildlife reintroductions and translocations are statistically unlikely to succeed. Nevertheless, they remain a critical part of conservation because they are the only way to actively restore a species into a habitat from which it has been extirpated. Past efforts to improve these practices have attributed the low success rate to failures in the biological knowledge (e.g., ignorance of social behavior, poor release site selection), or to the inherent challenges of reinstating a species into an area where threats have already driven it to local extinction. Such research presumes that the only way to improve reintroduction outcomes is through improved biological knowledge. This emphasis on biological solutions may have caused researchers to overlook the potential influence of other factors on reintroduction outcomes. I employed a grounded theory approach to study the leadership and management of a successful reintroduction program (the Sea Eagle Recovery Project in Scotland, UK) and identify four critical managerial elements that I theorize may have contributed to the successful outcome of this 50-year reintroduction. These elements are: 1. Leadership & Management: Small, dedicated team of accessible experts who provide strong political and scientific advocacy (“champions”) for the project. 2. Hierarchy & Autonomy: Hierarchical management structure that nevertheless permits high individual autonomy. 3. Goals & Evaluation: Formalized goal-setting and regular, critical evaluation of the project’s progress toward those goals. 4. Adaptive Public Relations: Adaptive outreach campaigns that are open, transparent, inclusive (esp. linguistically), and culturally relevant.
creator: Alexandra E. Sutton
uri: https://doi.org/10.7717/peerj.1012
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sutton

title: A new perspective on how humans assess their surroundings; derivation of head orientation and its role in ‘framing’ the environment
link: https://peerj.com/articles/908
last-modified: 2015-06-18
description: Understanding the way humans inform themselves about their environment is pivotal in helping explain our susceptibility to stimuli and how this modulates behaviour and movement patterns. We present a new device, the Human Interfaced Personal Observation Platform (HIPOP), which is a head-mounted (typically on a hat) unit that logs magnetometry and accelerometry data at high rates and, following appropriate calibration, can be used to determine the heading and pitch of the wearer’s head. We used this device on participants visiting a botanical garden and noted that although head pitch ranged between −80° and 60°, 25% confidence limits were restricted to an arc of about 25° with a tendency for the head to be pitched down (mean head pitch ranged between −43° and 0°). Mean rates of change of head pitch varied between −0.00187°/0.1 s and 0.00187°/0.1 s, markedly slower than rates of change of head heading which varied between −0.3141°/0.1 s and 0.01263°/0.1 s although frequency distributions of both parameters showed them to be symmetrical and monomodal. Overall, there was considerable variation in both head pitch and head heading, which highlighted the role that head orientation might play in exposing people to certain features of the environment. Thus, when used in tandem with accurate position-determining systems, the HIPOP can be used to determine how the head is orientated relative to gravity and geographic North and in relation to geographic position, presenting data on how the environment is being ‘framed’ by people in relation to environmental content.
creator: Gwendoline Ixia Wilson
creator: Mark D. Holton
creator: James Walker
creator: Mark W. Jones
creator: Ed Grundy
creator: Ian M. Davies
creator: David Clarke
creator: Adrian Luckman
creator: Nick Russill
creator: Vianney Wilson
creator: Rosie Plummer
creator: Rory P. Wilson
uri: https://doi.org/10.7717/peerj.908
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wilson et al.

title: Were early pterosaurs inept terrestrial locomotors?
link: https://peerj.com/articles/1018
last-modified: 2015-06-16
description: Pterodactyloid pterosaurs are widely interpreted as terrestrially competent, erect-limbed quadrupeds, but the terrestrial capabilities of non-pterodactyloids are largely thought to have been poor. This is commonly justified by the absence of a non-pterodactyloid footprint record, suggestions that the expansive uropatagia common to early pterosaurs would restrict hindlimb motion in walking or running, and the presence of sprawling forelimbs in some species. Here, these arguments are re-visited and mostly found problematic. Restriction of limb mobility is not a problem faced by extant animals with extensive fight membranes, including species which routinely utilise terrestrial locomotion. The absence of non-pterodactyloid footprints is not necessarily tied to functional or biomechanical constraints. As with other fully terrestrial clades with poor ichnological records, biases in behaviour, preservation, sampling and interpretation likely contribute to the deficit of early pterosaur ichnites. Suggestions that non-pterodactyloids have slender, mechanically weak limbs are demonstrably countered by the proportionally long and robust limbs of many Triassic and Jurassic species. Novel assessments of pterosaur forelimb anatomies conflict with notions that all non-pterodactyloids were obligated to sprawling forelimb postures. Sprawling forelimbs seem appropriate for species with ventrally-restricted glenoid articulations (seemingly occurring in rhamphorhynchines and campylognathoidids). However, some early pterosaurs, such as Dimorphodon macronyx and wukongopterids, have glenoid arthrologies which are not ventrally restricted, and their distal humeri resemble those of pterodactyloids. It seems fully erect forelimb stances were possible in these pterosaurs, and may be probable given proposed correlation between pterodactyloid-like distal humeral morphology and forces incurred through erect forelimb postures. Further indications of terrestrial habits include antungual sesamoids, which occur in the manus and pes anatomy of many early pterosaur species, and only occur elsewhere in terrestrial reptiles, possibly developing through frequent interactions of large claws with firm substrates. It is argued that characteristics possibly associated with terrestriality are deeply nested within Pterosauria and not restricted to Pterodactyloidea as previously thought, and that pterodactyloid-like levels of terrestrial competency may have been possible in at least some early pterosaurs.
creator: Mark P. Witton
uri: https://doi.org/10.7717/peerj.1018
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Witton

title: Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY
link: https://peerj.com/articles/1026
last-modified: 2015-06-16
description: The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6), based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited.
creator: Abhishek Kumar
uri: https://doi.org/10.7717/peerj.1026
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kumar

title: GenomePeek—an online tool for prokaryotic genome and metagenome analysis
link: https://peerj.com/articles/1025
last-modified: 2015-06-16
description: As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.
creator: Katelyn McNair
creator: Robert A. Edwards
uri: https://doi.org/10.7717/peerj.1025
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McNair and Edwards

title: Is grazing exclusion effective in restoring vegetation in degraded alpine grasslands in Tibet, China?
link: https://peerj.com/articles/1020
last-modified: 2015-06-16
description: Overgrazing is considered one of the key disturbance factors that results in alpine grassland degradation in Tibet. Grazing exclusion by fencing has been widely used as an approach to restore degraded grasslands in Tibet since 2004. Is the grazing exclusion management strategy effective for the vegetation restoration of degraded alpine grasslands? Three alpine grassland types were selected in Tibet to investigate the effect of grazing exclusion on plant community structure and biomass. Our results showed that species biodiversity indicators, including the Pielou evenness index, the Shannon–Wiener diversity index, and the Simpson dominance index, did not significantly change under grazing exclusion conditions. In contrast, the total vegetation cover, the mean vegetation height of the community, and the aboveground biomass were significantly higher in the grazing exclusion grasslands than in the free grazed grasslands. These results indicated that grazing exclusion is an effective measure for maintaining community stability and improving aboveground vegetation growth in alpine grasslands. However, the statistical analysis showed that the growing season precipitation (GSP) plays a more important role than grazing exclusion in which influence on vegetation in alpine grasslands. In addition, because the results of the present study come from short term (6–8 years) grazing exclusion, it is still uncertain whether these improvements will be continuable if grazing exclusion is continuously implemented. Therefore, the assessments of the ecological effects of the grazing exclusion management strategy on degraded alpine grasslands in Tibet still need long term continued research.
creator: Yan Yan
creator: Xuyang Lu
uri: https://doi.org/10.7717/peerj.1020
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yan and Lu

title: Influence of sediment characteristics on the composition of soft-sediment intertidal communities in the northern Gulf of Mexico
link: https://peerj.com/articles/1014
last-modified: 2015-06-16
description: Benthic infaunal communities are important components of coastal ecosystems. Understanding the relationships between the structure of these communities and characteristics of the habitat in which they live is becoming progressively more important as coastal systems face increasing stress from anthropogenic impacts and changes in climate. To examine how sediment characteristics and infaunal community composition were related along the northern Gulf of Mexico coast, we sampled intertidal infaunal communities at seven sites covering common habitat types at a regional scale. Across 69 samples, the communities clustered into four distinct groups on the basis of faunal composition. Nearly 70% of the variation in the composition of the communities was explained by salinity, median grain size, and total organic content. Our results suggest that at a regional level coarse habitat characteristics are able to explain a large amount of the variation among sites in infaunal community structure. By examining the relationships between infaunal communities and their sedimentary habitats, we take a necessary first step that will allow the exploration of how changes in habitat and community composition influence higher trophic levels and ecosystem scale processes.
creator: Kyle E. Coblentz
creator: Jessica R. Henkel
creator: Bryan J. Sigel
creator: Caz M. Taylor
uri: https://doi.org/10.7717/peerj.1014
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Coblentz et al.

title: Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review
link: https://peerj.com/articles/1008
last-modified: 2015-06-16
description: Associations between microorganisms occur extensively throughout Earth’s oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually.
creator: Felipe H. Coutinho
creator: Pedro M. Meirelles
creator: Ana Paula B. Moreira
creator: Rodolfo P. Paranhos
creator: Bas E. Dutilh
creator: Fabiano L. Thompson
uri: https://doi.org/10.7717/peerj.1008
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Coutinho et al.

title: Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea
link: https://peerj.com/articles/997
last-modified: 2015-06-16
description: Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years.
creator: Dawn B. Goldsmith
creator: Rachel J. Parsons
creator: Damitu Beyene
creator: Peter Salamon
creator: Mya Breitbart
uri: https://doi.org/10.7717/peerj.997
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Goldsmith et al.

title: Modelling Tradescantia fluminensis to assess long term survival
link: https://peerj.com/articles/1013
last-modified: 2015-06-11
description: We present a simple Poisson process model for the growth of Tradescantia fluminensis, an invasive plant species that inhibits the regeneration of native forest remnants in New Zealand. The model was parameterised with data derived from field experiments in New Zealand and then verified with independent data. The model gave good predictions which showed that its underlying assumptions are sound. However, this simple model had less predictive power for outputs based on variance suggesting that some assumptions were lacking. Therefore, we extended the model to include higher variability between plants thereby improving its predictions. This high variance model suggests that control measures that promote node death at the base of the plant or restrict the main stem growth rate will be more effective than those that reduce the number of branching events. The extended model forms a good basis for assessing the efficacy of various forms of control of this weed, including the recently-released leaf-feeding tradescantia leaf beetle (Neolema ogloblini).
creator: Alex James
creator: Sue M. Molloy
creator: Agate Ponder-Sutton
creator: Michael J. Plank
creator: Shona L. Lamoureaux
creator: Graeme W. Bourdôt
creator: Dave Kelly
uri: https://doi.org/10.7717/peerj.1013
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 James et al.

title: Non-lethal approach identifies variability of δ15N values in the fin rays of Atlantic Goliath Grouper, Epinephelus itajara
link: https://peerj.com/articles/1010
last-modified: 2015-06-11
description: The Atlantic Goliath Grouper, Epinephelus itajara, is critically endangered throughout its range but has begun to show initial signs of recovery in Florida state waters. As the population continues to rebound, researchers face a pressing need to fill the knowledge gaps about this iconic species. Here, we examined the δ15N isotopic records in fin rays collected from Atlantic Goliath Grouper, and related changes of isotopic ratios over time to life history characteristics. Fin-ray analysis was used as a non-lethal technique to sample individuals from two locations at similar latitudes from the west and east coasts of Florida, USA. δ15N data were acquired by mechanically separating the annuli of each fin ray and then analyzing the material in an Irradiance Elemental Analyzer Mass Spectrometer. The δ15N values were consistent among individuals within populations from each coast of Florida, and mirrored the expected changes over the lives of the fish. Overall, differences were found between δ15N values at juvenile life history phases versus adult phases, but the patterns associated with these differences were unique to each coastal group. We demonstrated, for the first time, that δ15N values from fin rays can be used to assess the life histories of Atlantic Goliath Grouper. The non-lethal strategies outlined here can be used to acquire information essential to the management of species of concern, such as those that are threatened or endangered.
creator: Orian E. Tzadik
creator: Ethan A. Goddard
creator: David J. Hollander
creator: Christopher C. Koenig
creator: Christopher D. Stallings
uri: https://doi.org/10.7717/peerj.1010
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Tzadik et al.

title: Rotation survival forest for right censored data
link: https://peerj.com/articles/1009
last-modified: 2015-06-11
description: Recently, survival ensembles have found more and more applications in biological and medical research when censored time-to-event data are often confronted. In this research, we investigate the plausibility of extending a rotation forest, originally proposed for classification purpose, to survival analysis. Supported by the proper statistical analysis, we show that rotation survival forests are able to outperform the state-of-art survival ensembles on right censored data. We also provide a C-index based variable importance measure for evaluating covariates in censored survival data.
creator: Lifeng Zhou
creator: Qingsong Xu
creator: Hong Wang
uri: https://doi.org/10.7717/peerj.1009
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhou et al.

title: Uneven distribution of enamel in the tooth crown of a Plains Zebra (Equus quagga)
link: https://peerj.com/articles/1002
last-modified: 2015-06-11
description: Unworn teeth of herbivorous mammals are not immediately functional. They have to be partially worn to expose enamel ridges which can then act as shear-cutting blades to break the food down. We use the Plains Zebra (Equus quagga) as a hypsodont, herbivorous model organism to investigate how initial wear of the tooth crown is controlled by underlying structures. We find that the enamel proportion is smaller at the apical half of the tooth crown in all upper tooth positions and suggest that lower enamel content here could promote early wear. Besides this uneven enamel distribution, we note that the third molar has a higher overall enamel content than any other tooth position. The M3 is thus likely to have a slightly different functional trait in mastication, resisting highest bite forces along the tooth row and maintaining functionality when anterior teeth are already worn down.
creator: Daniela E. Winkler
creator: Thomas M. Kaiser
uri: https://doi.org/10.7717/peerj.1002
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Winkler and Kaiser

title: Musculoskeletal modelling of an ostrich (Struthio camelus) pelvic limb: influence of limb orientation on muscular capacity during locomotion
link: https://peerj.com/articles/1001
last-modified: 2015-06-11
description: We developed a three-dimensional, biomechanical computer model of the 36 major pelvic limb muscle groups in an ostrich (Struthio camelus) to investigate muscle function in this, the largest of extant birds and model organism for many studies of locomotor mechanics, body size, anatomy and evolution. Combined with experimental data, we use this model to test two main hypotheses. We first query whether ostriches use limb orientations (joint angles) that optimize the moment-generating capacities of their muscles during walking or running. Next, we test whether ostriches use limb orientations at mid-stance that keep their extensor muscles near maximal, and flexor muscles near minimal, moment arms. Our two hypotheses relate to the control priorities that a large bipedal animal might evolve under biomechanical constraints to achieve more effective static weight support. We find that ostriches do not use limb orientations to optimize the moment-generating capacities or moment arms of their muscles. We infer that dynamic properties of muscles or tendons might be better candidates for locomotor optimization. Regardless, general principles explaining why species choose particular joint orientations during locomotion are lacking, raising the question of whether such general principles exist or if clades evolve different patterns (e.g., weighting of muscle force–length or force–velocity properties in selecting postures). This leaves theoretical studies of muscle moment arms estimated for extinct animals at an impasse until studies of extant taxa answer these questions. Finally, we compare our model’s results against those of two prior studies of ostrich limb muscle moment arms, finding general agreement for many muscles. Some flexor and extensor muscles exhibit self-stabilization patterns (posture-dependent switches between flexor/extensor action) that ostriches may use to coordinate their locomotion. However, some conspicuous areas of disagreement in our results illustrate some cautionary principles. Importantly, tendon-travel empirical measurements of muscle moment arms must be carefully designed to preserve 3D muscle geometry lest their accuracy suffer relative to that of anatomically realistic models. The dearth of accurate experimental measurements of 3D moment arms of muscles in birds leaves uncertainty regarding the relative accuracy of different modelling or experimental datasets such as in ostriches. Our model, however, provides a comprehensive set of 3D estimates of muscle actions in ostriches for the first time, emphasizing that avian limb mechanics are highly three-dimensional and complex, and how no muscles act purely in the sagittal plane. A comparative synthesis of experiments and models such as ours could provide powerful synthesis into how anatomy, mechanics and control interact during locomotion and how these interactions evolve. Such a framework could remove obstacles impeding the analysis of muscle function in extinct taxa.
creator: John R. Hutchinson
creator: Jeffery W. Rankin
creator: Jonas Rubenson
creator: Kate H. Rosenbluth
creator: Robert A. Siston
creator: Scott L. Delp
uri: https://doi.org/10.7717/peerj.1001
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hutchinson et al.

title: Can endocranial volume be estimated accurately from external skull measurements in great-tailed grackles (Quiscalus mexicanus)?
link: https://peerj.com/articles/1000
last-modified: 2015-06-11
description: There is an increasing need to validate and collect data approximating brain size on individuals in the field to understand what evolutionary factors drive brain size variation within and across species. We investigated whether we could accurately estimate endocranial volume (a proxy for brain size), as measured by computerized tomography (CT) scans, using external skull measurements and/or by filling skulls with beads and pouring them out into a graduated cylinder for male and female great-tailed grackles. We found that while females had higher correlations than males, estimations of endocranial volume from external skull measurements or beads did not tightly correlate with CT volumes. We found no accuracy in the ability of external skull measures to predict CT volumes because the prediction intervals for most data points overlapped extensively. We conclude that we are unable to detect individual differences in endocranial volume using external skull measurements. These results emphasize the importance of validating and explicitly quantifying the predictive accuracy of brain size proxies for each species and each sex.
creator: Corina J. Logan
creator: Christin R. Palmstrom
uri: https://doi.org/10.7717/peerj.1000
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Logan et al.

title: Development of a cognitive bias methodology for measuring low mood in chimpanzees
link: https://peerj.com/articles/998
last-modified: 2015-06-11
description: There is an ethical and scientific need for objective, well-validated measures of low mood in captive chimpanzees. We describe the development of a novel cognitive task designed to measure ‘pessimistic’ bias in judgments of expectation of reward, a cognitive marker of low mood previously validated in a wide range of species, and report training and test data from three common chimpanzees (Pan troglodytes). The chimpanzees were trained on an arbitrary visual discrimination in which lifting a pale grey paper cone was associated with reinforcement with a peanut, whereas lifting a dark grey cone was associated with no reward. The discrimination was trained by sequentially presenting the two cone types until significant differences in latency to touch the cone types emerged, and was confirmed by simultaneously presenting both cone types in choice trials. Subjects were subsequently tested on their latency to touch unrewarded cones of three intermediate shades of grey not previously seen. Pessimism was indicated by the similarity between the latency to touch intermediate cones and the latency to touch the trained, unreinforced, dark grey cones. Three subjects completed training and testing, two adult males and one adult female. All subjects learnt the discrimination (107–240 trials), and retained it during five sessions of testing. There was no evidence that latencies to lift intermediate cones increased over testing, as would have occurred if subjects learnt that these were never rewarded, suggesting that the task could be used for repeated testing of individual animals. There was a significant difference between subjects in their relative latencies to touch intermediate cones (pessimism index) that emerged following the second test session, and was not changed by the addition of further data. The most dominant male subject was least pessimistic, and the female most pessimistic. We argue that the task has the potential to be used to assess longitudinal changes in sub-clinical levels of low mood in chimpanzees, however further work with a larger sample of animals is required to validate this claim.
creator: Melissa Bateson
creator: Daniel Nettle
uri: https://doi.org/10.7717/peerj.998
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bateson and Nettle

title: A rapid assessment of post-disclosure experiences of urban HIV-positive and HIV-negative school-aged children in Kenya
link: https://peerj.com/articles/956
last-modified: 2015-06-11
description: There has been limited involvement of HIV-negative children in HIV disclosure studies; most studies conducted on the effects of disclosure on children have been with HIV-positive children and HIV-positive mother-child dyads. Seven HIV-positive and five HIV-negative children participated in a larger study conducted to understand the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. In this study, the experiences of these 12 children after receiving disclosure of their own and their parents’ illnesses respectively are presented. Each child underwent an in-depth qualitative semi-structured digitally recorded interview. The recorded interviews were transcribed and loaded into NVivo8 for phenomenological data analysis. Five themes emerged from the data, indicating that HIV-positive and negative children appear to have differing post-disclosure experiences revolving around acceptance of illness, stigma and discrimination, medication consumption, sexual awareness, and use of coping mechanisms. Following disclosure, HIV-negative children accepted their parents’ illnesses within a few hours to a few weeks; HIV-positive children took weeks to months to accept their own illnesses. HIV-negative children knew of high levels of stigma and discrimination within the community; HIV-positive children reported experiencing indirect incidences of stigma and discrimination. HIV-negative children wanted their parents to take their medications, stay healthy, and pay their school fees so they could have a better life in the future; HIV-positive children viewed medication consumption as an ordeal necessary to keep them healthy. HIV-negative children wanted their parents to speak to them about sexual-related matters; HIV-positive children had lingering questions about relationships, use of condoms, marriage, and childbearing options. All but one preadolescent HIV-positive child had self-identified a person to speak with for social support. When feeling overwhelmed by their circumstances, the children self-withdrew and performed positive activities (e.g., praying, watching TV, listening to the radio, singing, dancing) to help themselves feel better. Many HIV-affected families have a combination of HIV-positive and negative siblings within the household. Pending further studies conducted with larger sample sizes, the results of this study should assist healthcare professionals to better facilitate disclosure between HIV-positive parents and their children of mixed HIV statuses.
creator: Grace Gachanja
uri: https://doi.org/10.7717/peerj.956
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gachanja

title: Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora
link: https://peerj.com/articles/890
last-modified: 2015-06-11
description: Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study.
creator: Zhao-Ming Gao
creator: Yong Wang
creator: Ren-Mao Tian
creator: On On Lee
creator: Yue Him Wong
creator: Zenon B. Batang
creator: Abdulaziz Al-Suwailem
creator: Feras F. Lafi
creator: Vladimir B. Bajic
creator: Pei-Yuan Qian
uri: https://doi.org/10.7717/peerj.890
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gao et al.

title: Can sea urchins beat the heat? Sea urchins, thermal tolerance and climate change
link: https://peerj.com/articles/1006
last-modified: 2015-06-09
description: The massive die-off of the long-spined sea urchin, Diadema antillarum, a significant reef grazer, in the mid 1980s was followed by phase shifts from coral dominated to macroalgae dominated reefs in the Caribbean. While Diadema populations have recovered in some reefs with concomitant increases in coral cover, the additional threat of increasing temperatures due to global climate change has not been investigated in adult sea urchins. In this study, I measured acute thermal tolerance of D. antillarum and that of a sympatric sea urchin not associated with coral cover, Echinometra lucunter, over winter, spring, and summer, thus exposing them to substantial natural thermal variation. Animals were taken from the wild and placed in laboratory tanks in room temperature water (∼22 °C) that was then heated at 0.16–0.3 °C min−1 and the righting behavior of individual sea urchins was recorded. I measured both the temperature at which the animal could no longer right itself (TLoR) and the righting time at temperatures below the TLoR. In all seasons, D. antillarum exhibited a higher mean TLoR than E. lucunter. The mean TLoR of each species increased with increasing environmental temperature revealing that both species acclimatize to seasonal changes in temperatures. The righting times of D. antillarum were much shorter than those of E. lucunter. The longer relative spine length of Diadema compared to that of Echinometra may contribute to their shorter righting times, but does not explain their higher TLoR. The thermal safety margin (the difference between the mean collection temperature and the mean TLoR) was between 3.07–3.66 °C for Echinometra and 3.79–5.67 °C for Diadema. While these thermal safety margins exceed present day temperatures, they are modest compared to those of temperate marine invertebrates. If sea temperatures increase more rapidly than can be accommodated by the sea urchins (either by genetic adaptation, phenotypic plasticity, or both), this will have important consequences for the structure of coral reefs.
creator: Elizabeth Sherman
uri: https://doi.org/10.7717/peerj.1006
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sherman

title: A mathematical model for predicting glucose levels in critically-ill patients: the PIGnOLI model
link: https://peerj.com/articles/1005
last-modified: 2015-06-09
description: Background and Objectives. Glycemic control is of paramount importance in the intensive care unit. Presently, several BG control algorithms have been developed for clinical trials, but they are mostly based on experts’ opinion and consensus. There are no validated models predicting how glucose levels will change after initiating of insulin infusion in critically ill patients. The study aimed to develop an equation for initial insulin dose setting.Methods. A large critical care database was employed for the study. Linear regression model fitting was employed. Retested blood glucose was used as the independent variable. Insulin rate was forced into the model. Multivariable fractional polynomials and interaction terms were used to explore the complex relationships among covariates. The overall fit of the model was examined by using residuals and adjusted R-squared values. Regression diagnostics were used to explore the influence of outliers on the model.Main Results. A total of 6,487 ICU admissions requiring insulin pump therapy were identified. The dataset was randomly split into two subsets at 7 to 3 ratio. The initial model comprised fractional polynomials and interactions terms. However, this model was not stable by excluding several outliers. I fitted a simple linear model without interaction. The selected prediction model (Predicting Glucose Levels in ICU, PIGnOLI) included variables of initial blood glucose, insulin rate, PO volume, total parental nutrition, body mass index (BMI), lactate, congestive heart failure, renal failure, liver disease, time interval of BS recheck, dextrose rate. Insulin rate was significantly associated with blood glucose reduction (coefficient: −0.52, 95% CI [−1.03, −0.01]). The parsimonious model was well validated with the validation subset, with an adjusted R-squared value of 0.8259.Conclusion. The study developed the PIGnOLI model for the initial insulin dose setting. Furthermore, experimental study is mandatory to examine whether adjustment of the insulin infusion rate based on PIGnOLI will benefit patients’ outcomes.
creator: Zhongheng Zhang
uri: https://doi.org/10.7717/peerj.1005
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhang

title: Beliefs and attitudes towards mental illness: an examination of the sex differences in mental health literacy in a community sample
link: https://peerj.com/articles/1004
last-modified: 2015-06-09
description: Objectives. The current study investigated mental health literacy in an Australian sample to examine sex differences in the identification of and attitudes towards various aspects of mental illness.Method. An online questionnaire was completed by 373 participants (M = 34.87 years). Participants were randomly assigned either a male or female version of a vignette depicting an individual exhibiting the symptoms of one of three types of mental illness (depression, anxiety, or psychosis) and asked to answer questions relating to aspects of mental health literacy.Results. Males exhibited poorer mental health literacy skills compared to females. Males were less likely to correctly identify the type of mental illness, more likely to rate symptoms as less serious, to perceive the individual as having greater personal control over such symptoms, and less likely to endorse the need for treatment for anxiety or psychosis.Conclusion. Generally, the sample was relatively proficient at correctly identifying mental illness but overall males displayed poorer mental health literacy skills than females.
creator: Raymond J. Gibbons
creator: Einar B. Thorsteinsson
creator: Natasha M. Loi
uri: https://doi.org/10.7717/peerj.1004
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gibbons et al.

title: Catch, bycatch and discards of the Galapagos Marine Reserve small-scale handline fishery
link: https://peerj.com/articles/995
last-modified: 2015-06-09
description: Fisheries bycatch is a significant marine conservation issue as valuable fish are wasted and protected species harmed with potential negative ecological and socio-economic consequences. Even though there are indications that the small-scale handline fishery of the Galapagos Marine Reserve has a low selectivity, information on its bycatch has never been published. We used onboard monitoring and interview data to assess the bycatch of the Galapagos handline fishery by estimating the bycatch ratio, determining species compositions of landings and bycatch, identifying fishers’ reasons for discarding certain individuals, and revealing historical trends in the bycatch ratio. The estimated bycatch ratio as a function of biomass of 0.40 and a diverse species composition of target catch and bycatch confirmed the low selectivity of this fishery. Most individuals were not landed for economic motivations, either because species (77.4%) or sizes (17.7%) are unmarketable or for regulatory reasons (5.9%). We found that bycatch contributes to growth overfishing of some target species because they are discarded or used as bait before reaching their first maturity. Moreover, over half of interviewees perceived a historical decrease in bycatch ratios that was explained by a diversification of the target catch due to the reduction in abundance of the traditionally most important target species. As some target species show signs of overfishing and to date there are no specific regulations for the finfish fishery species in place, we recommend the implementation of a series of management measures to protect critical life stages of overexploited species and to improve the selectivity of the Galapagos handline fishery.
creator: Johanna S. Zimmerhackel
creator: Anna C. Schuhbauer
creator: Paolo Usseglio
creator: Lena C. Heel
creator: Pelayo Salinas-de-León
uri: https://doi.org/10.7717/peerj.995
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zimmerhackel et al.

title: Personality psychopathology, drug use and psychological symptoms in adolescents with substance use disorders and community controls
link: https://peerj.com/articles/992
last-modified: 2015-06-09
description: Substance use is a risk behavior that tends to increase during adolescence, a time when part of the personality is still in development. Traditionally, personality psychopathology has been measured in terms of categories, although dimensional models have demonstrated better consistency. This study aimed to analyze differences in personality profiles between adolescents with substance use disorders (SUD n = 74) and matched community controls (MCC n = 74) using the Personality Psychopathology Five (PSY-5) dimensional model. Additionally, we compared age at first drug use, level of drug use and internalizing and externalizing symptoms between the groups. In this study, the PSY-5 model has proved to be useful for differentiating specific personality disturbances in adolescents with SUD and community adolescents. The Disconstraint scale was particularly useful for discriminating adolescents with substance use problems and the Delinquent Attitudes facet offered the best differentiation.
creator: Ernesto Magallón-Neri
creator: Rosa Díaz
creator: Maria Forns
creator: Javier Goti
creator: Josefina Castro-Fornieles
uri: https://doi.org/10.7717/peerj.992
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Magallón-Neri et al.

title: Research groups: How big should they be?
link: https://peerj.com/articles/989
last-modified: 2015-06-09
description: Understanding the relationship between scientific productivity and research group size is important for deciding how science should be funded. We have investigated the relationship between these variables in the life sciences in the United Kingdom using data from 398 principle investigators (PIs). We show that three measures of productivity, the number of publications, the impact factor of the journals in which papers are published and the number of citations, are all positively correlated to group size, although they all show a pattern of diminishing returns—doubling group size leads to less than a doubling in productivity. The relationships for the impact factor and the number of citations are extremely weak. Our analyses suggest that an increase in productivity will be achieved by funding more PIs with small research groups, unless the cost of employing post-docs and PhD students is less than 20% the cost of a PI. We also provide evidence that post-docs are more productive than PhD students both in terms of the number of papers they produce and where those papers are published.
creator: Isabelle Cook
creator: Sam Grange
creator: Adam Eyre-Walker
uri: https://doi.org/10.7717/peerj.989
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Cook et al.

title: The taxonomy of a new parvicursorine alvarezsauroid specimen IVPP V20341 (Dinosauria: Theropoda) from the Upper Cretaceous Wulansuhai Formation of Bayan Mandahu, Inner Mongolia, China
link: https://peerj.com/articles/986
last-modified: 2015-06-09
description: A new parvicursorine alvarezsauroid theropod specimen IVPP V20341 from the Upper Cretaceous Wulansuhai Formation of Bayan Mandahu, Inner Mongolia, China is described. IVPP V20341 appears to be distinguishable amongst alvarezsauroids by possible cervical procoely and relatively larger semi-circular caudal neural canals, but these features are not proposed as autapomorphies because current knowledge of alvarezsauroid necks and tails remains sparse. IVPP V20341 is distinguishable from Linhenykus—the sole parvicursorine at Bayan Mandahu—by the location of the origination points of the anterior caudal transverse processes; in IVPP V20341 this is the anterodorsal corner of the centra, whereas in Linhenykus it is the posterior end of the prezygapophyses. A number of additional tentative differences between IVPP V20341 and Linhenykus are also identified, but cannot be confirmed until further details of anatomical variation along the neck and tail are revealed by future finds. Thus, following the study of IVPP V20341 there are still seven parvicursorine species from the Upper Cretaceous Gobi Basin, but future finds could increase this to eight species.
creator: Michael Pittman
creator: Xing Xu
creator: Josef B. Stiegler
uri: https://doi.org/10.7717/peerj.986
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Pittman et al.

title: Local villagers’ perceptions of wolves in Jiuzhaigou County, western China
link: https://peerj.com/articles/982
last-modified: 2015-06-09
description: While there have been increasing numbers of reports of human-wolf conflict in China during recent years, little is known about the nature of this conflict. In this study, we used questionnaires and semi-structured interviews to investigate local villagers’ perceptions of wolves in Jiuzhaigou County, western China. We sampled nine villages with more frequent reports of wolf depredation to the local government, but included three villages near alpine pastures in which reports of depredation were less frequent. We sampled 100 residents, a subset of the local population who were more likely to have had experience with wolves. During the preceding three years, most families of the respondents grazed livestock on alpine pastures, and most of them reported that their livestock suffered from depredation by wolves. The mean value of the reported annual livestock loss rates was considerably higher in villages that reported depredation more frequently than in those with less frequent reports of depredation. Most respondents in the more frequently depredated villages perceived an increase in wolf populations, whereas many in the less frequently depredated villages perceived a decrease in wolf populations in their areas. People’s attitudes towards wolves did not differ significantly between these two village categories. The majority of the respondents were negative in their attitude to wolves, despite a prevalent Tibetan culture that favors the protection of wildlife. People’s negative attitude was directly related to the number of livestock owned by their family. Those with a larger number of livestock were more likely to have a negative attitude towards wolves. Factors such as village category, ethnicity, age and education level did not influence people’s attitudes to wolves. We suggest that improved guarding of livestock and provision of monetary support on human resources and infrastructure may mitigate human-wolf conflicts in this region.
creator: Yu Xu
creator: Biao Yang
creator: Liang Dou
uri: https://doi.org/10.7717/peerj.982
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Xu et al.

title: Options for modulating intra-specific competition in colonial pinnipeds: the case of harbour seals (Phoca vitulina) in the Wadden Sea
link: https://peerj.com/articles/957
last-modified: 2015-06-09
description: Colonial pinnipeds may be subject to substantial consumptive competition because they are large, slow-moving central place foragers. We examined possible mechanisms for reducing this competition by examining the diving behaviour of harbour seals (Phoca vitulina) after equipping 34 seals (11 females, 23 males) foraging from three locations; Rømø, Denmark and Lorenzenplate and Helgoland, Germany, in the Wadden Sea area with time-depth recorders. Analysis of 319,021 dives revealed little between-colony variation but appreciable inter-sex differences, with males diving deeper than females, but for shorter periods. Males also had higher vertical descent rates. This result suggests that males may have higher overall swim speeds, which would increase higher oxygen consumption, and may explain the shorter dive durations compared to females. Intersex variation in swim speed alone is predicted to lead to fundamental differences in the time use of three-dimensional space, which may help reduce consumptive competition in harbour seals and other colonial pinnipeds.
creator: Rory P. Wilson
creator: Nikolai Liebsch
creator: Agustina Gómez-Laich
creator: William P. Kay
creator: Andrew Bone
creator: Victoria J. Hobson
creator: Ursula Siebert
uri: https://doi.org/10.7717/peerj.957
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wilson et al.

title: Properties evaluation of silorane, low-shrinkage, non-flowable and flowable resin-based composites in dentistry
link: https://peerj.com/articles/864
last-modified: 2015-06-09
description: Purpose. This study tested the null hypothesis that different classes of direct restorative dental materials: silorane-based resin, low-shrinkage and conventional (non-flowable and flowable) resin-based composite (RBC) do not differ from each other with regard to polymerization shrinkage, depth of cure or microhardness.Methods. 140 RBC samples were fabricated and tested by one calibrated operator. Polymerization shrinkage was measured using a gas pycnometer both before and immediately after curing with 36 J/cm2 light energy density. Depth of cure was determined, using a penetrometer and the Knoop microhardness was tested from the top surface to a depth of 5 mm.Results. Considering polymerization shrinkage, the authors found significant differences (p < 0.05) between different materials: non-flowable RBCs showed lower values compared to flowable RBCs, with the silorane-based resin presenting the smallest shrinkage. The low shrinkage flowable composite performed similarly to non-flowable with significant statistical differences compared to the two other flowable RBCs. Regarding to depth of cure, low-shrinkage flowable RBC, were most effective compared to other groups. Microhardness was generally higher for the non-flowable vs. flowable RBCs (p < 0.05). However, the values for low-shrinkage flowable did not differ significantly from those of non-flowable, but were significantly higher than those of the other flowable RBCs.Clinical Significance. RBCs have undergone many modifications as they have evolved and represent the most relevant restorative materials in today’s dental practice. This study of low-shrinkage RBCs, conventional RBCs (non-flowable and flowable) and silorane-based composite—by in vitro evaluation of volumetric shrinkage, depth of cure and microhardness—reveals that although filler content is an important determinant of polymerization shrinkage, it is not the only variable that affects properties of materials that were tested in this study.
creator: Rodrigo R. Maia
creator: Rodrigo S. Reis
creator: André F.V. Moro
creator: Cesar R. Perez
creator: Bárbara M. Pessôa
creator: Katia R.H.C. Dias
uri: https://doi.org/10.7717/peerj.864
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Maia et al.

title: Seven new microendemic species of Brachycephalus (Anura: Brachycephalidae) from southern Brazil
link: https://peerj.com/articles/1011
last-modified: 2015-06-04
description: Brachycephalus (Anura: Brachycephalidae) is a remarkable genus of miniaturized frogs of the Brazilian Atlantic Rainforest. Many of its species are highly endemic to cloud forests, being found only on one or a few mountaintops. Such level of microendemism might be caused by their climatic tolerance to a narrow set of environmental conditions found only in montane regions. This restriction severely limits the chance of discovery of new species, given the difficulty of exploring these inaccessible habitats. Following extensive fieldwork in montane areas of the southern portion of the Atlantic Rainforest, in this study we describe seven new species of Brachycephalus from the states of Paraná and Santa Catarina, southern Brazil. These species can be distinguished from one another based on coloration and the level of rugosity of the skin in different parts of their body. These discoveries increase considerably the number of described species of Brachycephalus in southern Brazil.
creator: Luiz F. Ribeiro
creator: Marcos R. Bornschein
creator: Ricardo Belmonte-Lopes
creator: Carina R. Firkowski
creator: Sergio A.A. Morato
creator: Marcio R. Pie
uri: https://doi.org/10.7717/peerj.1011
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ribeiro et al.

title: Assessment of water pollution in the Brazilian Pampa biome by means of stress biomarkers in tadpoles of the leaf frog Phyllomedusa iheringii (Anura: Hylidae)
link: https://peerj.com/articles/1016
last-modified: 2015-06-04
description: The Brazilian Pampa biome is currently under constant threat due to increase of agriculture and improper management of urban effluents. Studies with a focus on the assessment of impacts caused by human activities in this biome are scarce. In the present study, we measured stress-related biomarkers in tadpoles of the leaf frog Phyllomedusa iheringii, an endemic species to the Pampa biome, and tested its suitability as a bioindicator for the assessment of potential aquatic contamination in selected ponds (S1 and S2) nearby agricultural areas in comparison to a reference site. A significant decrease in acetylcholinesterase activity was observed in S2 when compared to S1 and reference. The levels of total-hydroperoxides were increased in S2 site. In parallel, increased activity of the antioxidant enzymes catalase, superoxide dismutase and glutathione S-transferase were observed in S2 when compared to S1 and reference. Further studies are necessary in order to correlate the changes observed here with different chemical stressors in water, as well as to elucidate mechanisms of toxicity induced by pesticides in amphibian species endemic to the Pampa biome. Nevertheless, our study validates Phyllomedusa iheringii as a valuable bioindicator in environmental studies.
creator: TG Santos
creator: R Melo
creator: DG Costa-Silva
creator: MEM Nunes
creator: NR Rodrigues
creator: JL Franco
uri: https://doi.org/10.7717/peerj.1016
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Santos et al.

title: Cryopreservation of lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt
link: https://peerj.com/articles/1003
last-modified: 2015-06-04
description: This study has established a successful protocol to cryopreserve lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt. Three cryosolutions were tested based on Mounib’s medium; the original medium including reduced l-glutathione (GSH), the basic sucrose and potassium bicarbonate medium without GSH, or with hen’s egg yolk (EY). Dimethyl sulphoxide (DMSO) was used as the cryoprotectant along with all three diluents in a 1–2 dilution. Cryopreservation was performed with the mentioned cryosolutions at two freezing rates. Motility percentages of spermatozoa were evaluated using ImageJ with a computer assisted sperm analyzer (CASA) plug-in. Findings revealed that spermatozoa cryopreserved in Mounib’s medium without GSH had a post-thaw motility score of 6.4 percentage points (pp) higher than those in the original Mounib’s medium, and an addition of EY to the modified Mounib’s medium lowered the post-thaw motility score by 19.3 pp. The difference in motility between both freezing rates was 13.0 pp, and samples cryopreserved on a 4.8 cm high tray resulted in a better post-thaw motility score. On average, cryopreserved milt had a 24.1 pp lower post-thaw motility score than fresh milt. There was no significant difference in fertilisation success between cryopreserved and fresh milt. Cryopreservation of lumpfish milt has, to our knowledge, never been successfully carried out before. The established protocol will be a main contributing factor in a stable production of lumpfish juveniles in future.
creator: Gunnvør Norðberg
creator: Asa Johannesen
creator: Regin Arge
uri: https://doi.org/10.7717/peerj.1003
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Norðberg et al.

title: Soundscape manipulation enhances larval recruitment of a reef-building mollusk
link: https://peerj.com/articles/999
last-modified: 2015-06-04
description: Marine seafloor ecosystems, and efforts to restore them, depend critically on the influx and settlement of larvae following their pelagic dispersal period. Larval dispersal and settlement patterns are driven by a combination of physical oceanography and behavioral responses of larvae to a suite of sensory cues both in the water column and at settlement sites. There is growing evidence that the biological and physical sounds associated with adult habitats (i.e., the “soundscape”) influence larval settlement and habitat selection; however, the significance of acoustic cues is rarely tested. Here we show in a field experiment that the free-swimming larvae of an estuarine invertebrate, the eastern oyster, respond to the addition of replayed habitat-related sounds. Oyster larval recruitment was significantly higher on larval collectors exposed to oyster reef sounds compared to no-sound controls. These results provide the first field evidence that soundscape cues may attract the larval settlers of a reef-building estuarine invertebrate.
creator: Ashlee Lillis
creator: DelWayne R. Bohnenstiehl
creator: David B. Eggleston
uri: https://doi.org/10.7717/peerj.999
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Lillis et al.

title: Population structure of three Psammodromus species in the Iberian Peninsula
link: https://peerj.com/articles/994
last-modified: 2015-06-04
description: The knowledge of a species’ population structure is essential for the development of adequate conservation actions as well as for the understanding of its evolution. The population structure is unknown in all species of the Genus Psammodromus, including the Western Sand Racer (Psammodromus occidentalis; a recently described species), the Edward’s Sand Racer (P. edwardsianus) and the Spanish Sand Racer (P. hispanicus). In this article, the genetic variability and population structure of Psammodromus edwardsianus, P. hispanicus, and P. occidentalis were studied in the Iberian Peninsula covering their natural geographic distribution. Mitochondrial DNA showed genetically different units in all species with higher genetic variability in their southern populations (latitudinal variation). Genetic differentiation was different among species and contrasted to those of species with similar characteristics. Our results therefore highlight the importance of species-specific studies analysing population structure.
creator: Jose L. Horreo
creator: Patrick Fitze
uri: https://doi.org/10.7717/peerj.994
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Horreo and Fitze

title: NxRepair: error correction in de novo sequence assembly using Nextera mate pairs
link: https://peerj.com/articles/996
last-modified: 2015-06-02
description: Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.
creator: Rebecca R. Murphy
creator: Jared O’Connell
creator: Anthony J. Cox
creator: Ole Schulz-Trieglaff
uri: https://doi.org/10.7717/peerj.996
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Murphy et al.

title: Profiling and initial validation of urinary microRNAs as biomarkers in IgA nephropathy
link: https://peerj.com/articles/990
last-modified: 2015-06-02
description: Background. MicroRNAs (miRNAs) have been found in virtually all body fluids and used successfully as biomarkers for various diseases. Evidence indicates that miRNAs have important roles in IgA nephropathy (IgAN), a major cause of renal failure. In this study, we looked for differentially expressed miRNAs in IgAN and further evaluated the correlations between candidate miRNAs and the severity of IgAN.Methods. Microarray and RT-qRCR (real-time quantitative polymerase chain reaction) were sequentially used to screen and further verify miRNA expression profiles in urinary sediments of IgAN patients in two independent cohorts. The screening cohort consisted of 32 urine samples from 18 patients with IgAN, 4 patients with MN (membranous nephropathy), 4 patients with MCD (minimal changes disease) and 6 healthy subjects; the validation cohort consisted of 102 IgAN patients, 41 MN patients, 27 MCD patients and 34 healthy subjects. The renal pathological lesions of patients with IgAN were evaluated according to Lee’s grading system and Oxford classification.Results. At the screening phase, significance analysis of microarrays analysis showed that no miRNA was differentially expressed in the IgAN group compared to all control groups. But IgAN grade I–II and III subgroups (according to Lee’s grading system) shared dysregulation of two miRNAs (miR-3613-3p and miR-4668-5p). At the validation phase, RT-qPCR results showed that urinary level of miR-3613-3p was significantly lower in IgAN than that in MN, MCD and healthy controls (0.47, 0.44 and 0.24 folds, respectively, all P < 0.01 by Mann–Whitney U test); urinary level of miR-4668-5p was also significantly lower in IgAN than that in healthy controls (0.49 fold, P < 0.01). Significant correlations were found between urinary levels of miR-3613-3p with 24-hour urinary protein excretion (Spearman r = 0.50, P = 0.034), eGFR (estimated glomerular filtration rate) (r = − 0.48, P = 0.043) and Lee’s grades (r = 0.57, P = 0.014). Similarly, miR-4668-5p was significantly correlated with eGFR (r = − 0.50, P = 0.034) and Lee’s grades (r = 0.57, P = 0.013). For segmental glomerulosclerosis according to Oxford classification, patients scored as S0 had significantly lower levels of urinary miR-3613-3p and miR-4668-5p than those scored as S1 (0.41 and 0.43 folds, respectively, all P < 0.05).Conclusions. The expression profile of miRNAs was significantly altered in urinary sediments from patients with IgAN. Urinary expression of miR-3613-3p was down-regulated in patients with IgAN. Moreover, urinary levels of both miR-3613-3p and miR-4668-5p were correlated with disease severity. Further studies are needed to explore the roles of miR-3613-3p and miR-4668-5p in the pathogenesis and progression of IgA nephropathy.
creator: Nannan Wang
creator: Ru Bu
creator: Zhiyu Duan
creator: Xueguang Zhang
creator: Pu Chen
creator: Zuoxiang Li
creator: Jie Wu
creator: Guangyan Cai
creator: Xiangmei Chen
uri: https://doi.org/10.7717/peerj.990
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wang et al.

title: The sensitivity of biological finite element models to the resolution of surface geometry: a case study of crocodilian crania
link: https://peerj.com/articles/988
last-modified: 2015-06-02
description: The reliability of finite element analysis (FEA) in biomechanical investigations depends upon understanding the influence of model assumptions. In producing finite element models, surface mesh resolution is influenced by the resolution of input geometry, and influences the resolution of the ensuing solid mesh used for numerical analysis. Despite a large number of studies incorporating sensitivity studies of the effects of solid mesh resolution there has not yet been any investigation into the effect of surface mesh resolution upon results in a comparative context. Here we use a dataset of crocodile crania to examine the effects of surface resolution on FEA results in a comparative context. Seven high-resolution surface meshes were each down-sampled to varying degrees while keeping the resulting number of solid elements constant. These models were then subjected to bite and shake load cases using finite element analysis. The results show that incremental decreases in surface resolution can result in fluctuations in strain magnitudes, but that it is possible to obtain stable results using lower resolution surface in a comparative FEA study. As surface mesh resolution links input geometry with the resulting solid mesh, the implication of these results is that low resolution input geometry and solid meshes may provide valid results in a comparative context.
creator: Matthew R. McCurry
creator: Alistair R. Evans
creator: Colin R. McHenry
uri: https://doi.org/10.7717/peerj.988
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McCurry et al.

title: The metabolic cost of walking on an incline in the Peacock (Pavo cristatus)
link: https://peerj.com/articles/987
last-modified: 2015-06-02
description: Altering speed and moving on a gradient can affect an animal’s posture and gait, which in turn can change the energetic requirements of terrestrial locomotion. Here, the energetic and kinematic effects of locomoting on an incline were investigated in the Indian peacock, Pavo cristatus. The mass-specific metabolic rate of the Indian peacock was elevated on an incline, but this change was not dependent on the angle ascended and the cost of lifting remained similar between the two inclines (+5 and +7°). Interestingly, the Indian peacock had the highest efficiency when compared to any other previously studied avian biped, despite the presence of a large train. Duty factors were higher for birds moving on an incline, but there was no difference between +5 and +7°. Our results highlight the importance of investigating kinematic responses during energetic studies, as these may enable explanation of what is driving the underlying metabolic differences when moving on inclines. Further investigations are required to elucidate the underlying mechanical processes occurring during incline movement.
creator: Holly Wilkinson
creator: Nathan Thavarajah
creator: Jonathan Codd
uri: https://doi.org/10.7717/peerj.987
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wilkinson et al.

title: A four-year cardiovascular risk score for type 2 diabetic inpatients
link: https://peerj.com/articles/984
last-modified: 2015-06-02
description: As cardiovascular risk tables currently in use were constructed using data from the general population, the cardiovascular risk of patients admitted via the hospital emergency department may be underestimated. Accordingly, we constructed a predictive model for the appearance of cardiovascular diseases in patients with type 2 diabetes admitted via the emergency department. We undertook a four-year follow-up of a cohort of 112 adult patients with type 2 diabetes admitted via the emergency department for any cause except patients admitted with acute myocardial infarction, stroke, cancer, or a palliative status. The sample was selected randomly between 2010 and 2012. The primary outcome was time to cardiovascular disease. Other variables (at baseline) were gender, age, heart failure, renal failure, depression, asthma/chronic obstructive pulmonary disease, hypertension, dyslipidaemia, insulin, smoking, admission for cardiovascular causes, pills per day, walking habit, fasting blood glucose and creatinine. A cardiovascular risk table was constructed based on the score to estimate the likelihood of cardiovascular disease. Risk groups were established and the c-statistic was calculated. Over a mean follow-up of 2.31 years, 39 patients had cardiovascular disease (34.8%, 95% CI [26.0–43.6%]). Predictive factors were gender, age, hypertension, renal failure, insulin, admission due to cardiovascular reasons and walking habit. The c-statistic was 0.734 (standard error: 0.049). After validation, this study will provide a tool for the primary health care services to enable the short-term prediction of cardiovascular disease after hospital discharge in patients with type 2 diabetes admitted via the emergency department.
creator: Dolores Ramírez-Prado
creator: Antonio Palazón-Bru
creator: David Manuel Folgado-de la Rosa
creator: María Ángeles Carbonell-Torregrosa
creator: Ana María Martínez-Díaz
creator: Damian Robert James Martínez-St. John
creator: Vicente Francisco Gil-Guillén
uri: https://doi.org/10.7717/peerj.984
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ramírez-Prado et al.

title: Elevational gradient of Hemiptera (Heteroptera, Auchenorrhyncha) on a tropical mountain in Papua New Guinea
link: https://peerj.com/articles/978
last-modified: 2015-06-02
description: Malaise trap sampling of Hemiptera (Heteroptera; Auchenorrhyncha) was conducted at 500 m intervals along an elevational gradient from 200 m to 3,700 m on the east slope of Mount Wilhelm, Madang Province, Papua New Guinea. Hemiptera had a decrease in morphospecies richness and overall abundance with increasing elevation, however, the Heteroptera did not exhibit either pattern. A few species were relatively abundant at each elevation, whereas the majority of species were represented by ≤5 specimens. Morphospecies richness of Auchenorrhyncha, Cicadomorpha, Fulgoromorpha, Cicadellidae, Cixiidae, and Derbidae also decreased with increasing elevation but abundance decline was not significant due to the large number of specimens captured at 200 m relative to those captured at higher elevations. The percentage of Cicadomorpha specimens decreased with increasing elevation relative to that of the Fulgoromorpha which increased with increasing elevation. Environmental factors that may influence patterns of species richness along the elevational gradient are discussed.
creator: Maxime Le Cesne
creator: Stephen W. Wilson
creator: Adeline Soulier-Perkins
uri: https://doi.org/10.7717/peerj.978
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Le Cesne et al.

title: Prior CT imaging history for patients who undergo PAN CT for acute traumatic injury
link: https://peerj.com/articles/963
last-modified: 2015-06-02
description: Objective. A single PAN scan may provide more radiation to a patient than is felt to be safe within a one-year period. Our objective was to determine how many patients admitted to the trauma service following a PAN scan had prior CT imaging within our six-hospital system.Methods. We performed a secondary analysis of a prospectively collected trauma registry. The study was based at a level-two trauma center and five affiliated hospitals, which comprise 70.6% of all Emergency Department visits within a twelve county region of southern Texas. Electronic medical records were reviewed dating from the point of trauma evaluation back to December 5, 2005 to determine evidence of prior CT imaging.Results. There were 867 patients were admitted to the trauma service between January 1, 2012 and December 31, 2012. 460 (53%) received a PAN scan and were included in the study group. The mean age of the study group was 37.7 ± 1.54 years old, 24.8% were female, and the mean ISS score was 13.4 ± 1.07. The most common mechanism of injury was motor vehicle collision (47%). 65 (14%; 95% CI [11–18]%) of the patients had at least one prior CT. The most common prior studies performed were: CT head (29%; 19–42%), CT Face (29%; 19–42%) and CT Abdomen and Pelvis (18%; 11–30%).Conclusion. Within our trauma registry, 14% of patients had prior CT imaging within our hospital system before their traumatic event and PAN scan.
creator: Jeremy Kenter
creator: Osbert Blow
creator: Scott P. Krall
creator: Albert Gest
creator: Cynthia Smith
creator: Peter B. Richman
uri: https://doi.org/10.7717/peerj.963
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kenter et al.

title: The role of multiple negative social relationships in inflammatory cytokine responses to a laboratory stressor
link: https://peerj.com/articles/959
last-modified: 2015-06-02
description: The present study examined the unique impact of perceived negativity in multiple social relationships on endocrine and inflammatory responses to a laboratory stressor. Via hierarchical cluster analysis, those who reported negative social exchanges across relationships with a romantic partner, family, and their closest friend had higher mean IL-6 across time and a greater increase in TNF-α from 15 min to 75 min post stress. Those who reported negative social exchanges across relationships with roommates, family, and their closest friend showed greater IL-6 responses to stress. Differences in mean IL-6 were accounted for by either depressed mood or hostility, whereas differences in the cytokine stress responses remained significant after controlling for those factors. Overall, this research provides preliminary evidence to suggest that having multiple negative relationships may exacerbate acute inflammatory responses to a laboratory stressor independent of hostility and depressed mood.
creator: Sunmi Song
creator: Jennifer E. Graham-Engeland
creator: Elizabeth J. Corwin
creator: Rachel M. Ceballos
creator: Shelley E. Taylor
creator: Teresa Seeman
creator: Laura Cousino Klein
uri: https://doi.org/10.7717/peerj.959
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Song et al.