title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2016-03 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Sushi barcoding in the UK: another kettle of fish link: https://peerj.com/articles/1891 last-modified: 2016-03-31 description: Although the spread of sushi restaurants in the European Union and United States is a relatively new phenomenon, they have rapidly become among the most popular food services globally. Recent studies indicate that they can be associated with very high levels (>70%) of fish species substitution. Based on indications that the European seafood retail sector may currently be under better control than its North American counterpart, here we investigated levels of seafood labelling accuracy in sushi bars and restaurants across England. We used the COI barcoding gene to screen samples of tuna, eel, and a variety of other products characterised by less visually distinctive ‘white flesh’. Moderate levels of substitution were found (10%), significantly lower than observed in North America, which lends support to the argument that public awareness, policy and governance of seafood labels is more effective in the European Union. Nevertheless, the results highlight that current labelling practice in UK restaurants lags behind the level of detail implemented in the retail sector, which hinders consumer choice, with potentially damaging economic, health and environmental consequences. Specifically, critically endangered species of tuna and eel continue to be sold without adequate information to consumers. creator: Sara G. Vandamme creator: Andrew M. Griffiths creator: Sasha-Ann Taylor creator: Cristina Di Muri creator: Elizabeth A. Hankard creator: Jessica A. Towne creator: Mhairi Watson creator: Stefano Mariani uri: https://doi.org/10.7717/peerj.1891 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Vandamme et al. title: Soft tissue artifact evaluation of the cervical spine in motion patterns of flexion and lateral bending: a preliminary study link: https://peerj.com/articles/1893 last-modified: 2016-03-31 description: Background. Soft tissue artifact (STA) is increasingly becoming a focus of research as the skin marker method is widely employed in motion capture technique. At present, medical imaging methods provide reliable ways to investigate the cervical STA. Among these approaches, magnetic resonance imaging (MRI) is a highly preferred tool because of its low radiation.Methods. In the study, the 3D spatial location of vertebral landmarks and corresponding skin markers of the spinous processes of the second (C2), fifth (C5), and sixth (C6) cervical levels during flexion and lateral bending were investigated. A series of static postures were scanned using MRI. Skin deformation was obtained by the Mimics software.Results. Results shows that during flexion, the maximum skin deformation occurs at C6, in the superior–inferior (Z) direction. Upon lateral bending, the maximum skin displacement occurs at C2 level, in the left–right (Y) direction. The result presents variability of soft tissue in the terms of direction and magnitude, which is consistent with the prevailing opinion.Discussion. The results testified variability of cervical STA. Future studies involving large ranges of subject classification, such as age, sex, height, gravity, and etc. should be performed to completely verify the existing hypothesis on human cervical skin deformation. creator: Jiajia Wang creator: Zhongwen Lui creator: Zhihui Qian creator: Luquan Ren uri: https://doi.org/10.7717/peerj.1893 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Integrative microRNA-gene expression network analysis in genetic hypercalciuric stone-forming rat kidney link: https://peerj.com/articles/1884 last-modified: 2016-03-31 description: Background. MicroRNAs (miRNAs) influence a variety of biological functions by regulating gene expression post-transcriptionally. Aberrant miRNA expression has been associated with many human diseases. Urolithiasis is a common disease, and idiopathic hypercalciuria (IH) is an important risk factor for calcium urolithiasis. However, miRNA expression patterns and their biological functions in urolithiasis remain unknown.Methods and Results. A multi-step approach combining microarray miRNA and mRNA expression profile and bioinformatics analysis was adopted to analyze dysregulated miRNAs and genes in genetic hypercalciuric stone-forming (GHS) rat kidneys, using normal Sprague-Dawley (SD) rats as controls. We identified 2418 mRNAs and 19 miRNAs as significantly differentially expressed, over 700 gene ontology (GO) terms and 83 KEGG pathways that were significantly enriched in GHS rats. In addition, we constructed an miRNA-gene network that suggested that rno-miR-674-5p, rno-miR-672-5p, rno-miR-138-5p and rno-miR-21-3p may play important roles in the regulatory network. Furthermore, signal-net analysis suggested that NF-kappa B likely plays a crucial role in hypercalciuria urolithiasis.Conclusions. This study presents a global view of mRNA and miRNA expression in GHS rat kidneys, and suggests that miRNAs may be important in the regulation of hypercalciuria. The data provide valuable insights for future research, which should aim at validating the role of the genes featured here in the pathophysiology of hypercalciuria. creator: Yuchao Lu creator: Baolong Qin creator: Henglong Hu creator: Jiaqiao Zhang creator: Yufeng Wang creator: Qing Wang creator: Shaogang Wang uri: https://doi.org/10.7717/peerj.1884 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lu et al. title: People with gambling disorder and risky alcohol habits benefit more from motivational interviewing than from cognitive behavioral group therapy link: https://peerj.com/articles/1899 last-modified: 2016-03-31 description: Background. Effective psychological treatment, including cognitive behavioral therapy and motivational interviewing (MI), is available for people with problematic gambling behaviors. To advance the development of treatment for gambling disorder, it is critical to further investigate how comorbidity impacts different types of treatments. The purpose of this study was to investigate whether screening for risky alcohol habits can provide guidance on whether people with gambling disorder should be recommended cognitive behavioral group therapy (CBGT) or MI.Methods. The present study is a secondary analysis of a previous randomized controlled trial that compared the effects of CBGT, MI and a waitlist control group in the treatment of disordered gambling. Assessment and treatment was conducted at an outpatient dependency clinic in Stockholm, Sweden, where 53 trial participants with gambling disorder began treatment. A modified version of the National Opinion Research Centre DSM-IV Screen for gambling problems was used to assess gambling disorder. The Alcohol Use Disorders Identification Test (AUDIT) was used to screen for risky alcohol habits.Results. The interaction between treatment and alcohol habits was significant and suggests that patients with gambling disorder and risky alcohol habits were better helped by MI, while those without risky alcohol habits were better helped by CBGT.Conclusions. The results support a screening procedure including the AUDIT prior to starting treatment for gambling disorder because the result of the screening can provide guidance in the choice of treatment. Patients with gambling disorder and risky alcohol habits are likely to be best helped if they are referred to MI, while those without risky alcohol habits are likely to be best helped if they are referred to CBGT. creator: Henrik Josephson creator: Per Carlbring creator: Lars Forsberg creator: Ingvar Rosendahl uri: https://doi.org/10.7717/peerj.1899 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Josephson et al. title: Resveratrol ameliorates 2,4-dinitrofluorobenzene-induced atopic dermatitis-like lesions through effects on the epithelium link: https://peerj.com/articles/1889 last-modified: 2016-03-31 description: Background. Resveratrol is a natural polyphenol that exhibits anti-inflammatory effects. The aim of this study was to investigate the effects of resveratrol treatment on epithelium-derived cytokines and epithelial apoptosis in a murine model of atopic dermatitis-like lesions.Material and Methods. Atopic dermatitis-like lesions were induced in BALB/c mice by repeated application of 2,4-dinitrofluorobenzene to shaved dorsal skin. Twenty-one BALB/c mice were divided into three groups: group I (control), group II (vehicle control), and group III (resveratrol). Systemic resveratrol (30 mg/kg/day) was administered repeatedly during the 6th week of the experiment. After the mice had been sacrificed, skin tissues were examined histologically for epithelial thickness. Epithelial apoptosis (caspase-3) and epithelium-derived cytokines [interleukin (IL)-25, IL-33, and thymic stromal lymphopoietin (TSLP)] were evaluated immunohistochemically.Results. Epithelial thickness and the numbers of IL-25, IL-33, TSLP and caspase-3-positive cells were significantly higher in group II compared to group I mice. There was significant improvement in epithelial thickness in group III compared with group II mice (p < 0.05). The numbers of IL-25, IL-33, and TSLP-positive cells in the epithelium were lower in group III than in group II mice (p < 0.05). The number of caspase-3-positive cells, as an indicator of apoptosis, in the epithelium was significantly lower in group III than in group II mice (p < 0.05).Conclusion. Treatment with resveratrol was effective at ameliorating histological changes and inflammation by acting on epithelium-derived cytokines and epithelial apoptosis. creator: Sule Caglayan Sozmen creator: Meral Karaman creator: Serap Cilaker Micili creator: Sakine Isik creator: Zeynep Arikan Ayyildiz creator: Alper Bagriyanik creator: Nevin Uzuner creator: Ozkan Karaman uri: https://doi.org/10.7717/peerj.1889 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Caglayan Sozmen et al. title: Auto-correlation of journal impact factor for consensus research reporting statements: a cohort study link: https://peerj.com/articles/1887 last-modified: 2016-03-31 description: Background. The Journal Citation Reports journal impact factors (JIFs) are widely used to rank and evaluate journals, standing as a proxy for the relative importance of a journal within its field. However, numerous criticisms have been made of use of a JIF to evaluate importance. This problem is exacerbated when the use of JIFs is extended to evaluate not only the journals, but the papers therein. The purpose of this study was therefore to investigate the relationship between the number of citations and journal IF for identical articles published simultaneously in multiple journals.Methods. Eligible articles were consensus research reporting statements listed on the EQUATOR Network website that were published simultaneously in three or more journals. The correlation between the citation count for each article and the median journal JIF over the published period, and between the citation count and number of article accesses was calculated for each reporting statement.Results. Nine research reporting statements were included in this analysis, representing 85 articles published across 58 journals in biomedicine. The number of citations was strongly correlated to the JIF for six of the nine reporting guidelines, with moderate correlation shown for the remaining three guidelines (median r = 0.66, 95% CI [0.45–0.90]). There was also a strong positive correlation between the number of citations and the number of article accesses (median r = 0.71, 95% CI [0.5–0.8]), although the number of data points for this analysis were limited. When adjusted for the individual reporting guidelines, each logarithm unit of JIF predicted a median increase of 0.8 logarithm units of citation counts (95% CI [−0.4–5.2]), and each logarithm unit of article accesses predicted a median increase of 0.1 logarithm units of citation counts (95% CI [−0.9–1.4]). This model explained 26% of the variance in citations (median adjusted r2 = 0.26, range 0.18–1.0).Conclusion. The impact factor of the journal in which a reporting statement was published was shown to influence the number of citations that statement will gather over time. Similarly, the number of article accesses also influenced the number of citations, although to a lesser extent than the impact factor. This demonstrates that citation counts are not purely a reflection of scientific merit and the impact factor is, in fact, auto-correlated. creator: Daniel R. Shanahan uri: https://doi.org/10.7717/peerj.1887 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shanahan title: Spillover of a biological control agent (Chrysolina quadrigemina) onto native St. Johnswort (Hypericum punctatum) link: https://peerj.com/articles/1886 last-modified: 2016-03-31 description: Biological control agents may have unintended effects on native biota, particularly species that are closely related to the target invader. Here, we explored how Chrysolina quadrigemina, a beetle introduced to control the invasive weed Hypericum perforatum, impacts native H. punctatum in Tompkins County, New York, USA. Using a suite of complementary field surveys and experimental manipulations, we examined beetle preference for native and exotic Hypericum species and whether beetle herbivory influences the spatial distribution of H. punctatum. We found that the introduced beetle readily consumes native H. punctatum in addition to its intended target, and that H. punctatum at our field sites generally occurs along forest edges despite higher performance of experimental plants in more open habitats. However, we found no evidence that the beetle limits H. punctatum to forest edge habitats. creator: Jessica L. Tingle creator: Susan C. Cook-Patton creator: Anurag A. Agrawal uri: https://doi.org/10.7717/peerj.1886 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tingle et al. title: Sub-milliSievert ultralow-dose CT colonography with iterative model reconstruction technique link: https://peerj.com/articles/1883 last-modified: 2016-03-31 description: Purpose. The purpose of this study was to evaluate the technical and diagnostic performance of sub-milliSievert ultralow-dose (ULD) CT colonograpy (CTC) in the detection of colonic and extracolonic lesions.Materials and Methods. CTC with standard dose (SD) and ULD acquisitions of 64 matched patients, half of them with colonic findings, were reconstructed with filtered back projection (FBP), hybrid (HIR) and iterative model reconstruction techniques (IMR). Image noise in six colonic segments, in the left psoas muscle and aorta were measured. Image quality of the left adrenal gland and of the colon in the endoscopic and 2D view was rated on a five point Likert scale by two observers, who also completed the reading of CTC for colonic and extracolonic findings.Results. The mean radiation dose estimate was 4.1 ± 1.4 mSv for SD and 0.86 ± 0.17 mSv for ULD for both positions (p < 0.0001). In ULD-IMR, SD-IMR and SD-HIR, the endoluminal noise was decreased in all colonic segments compared to SD-FBP (p < 0.001). There were 27 small (6–9 mm) and 17 large (≥10 mm) colonic lesions that were classified as sessile polyps (n = 38), flat lesions (n = 3), or as a mass (n = 3). Per patient sensitivity and specificity were 0.82 and 0.93 for ULD-FBP, 0.97 and 0.97 for ULD-HIR, 0.97 and 1.0 for ULD-IMR. Per polyp sensitivity was 0.84 for ULD-FBP, 0.98 for ULD-HIR, 0.98 for ULD-IMR. Significantly less extracolonic findings were detected in ULD-FBP and ULD-HIR, but in the E4 category by C-RADS (potentially important findings), the detection was similar.Conclusion. Both HIR and IMR are suitable for sub-milliSievert ULD CTC without sacrificing diagnostic performance of the study. creator: Lukas Lambert creator: Petr Ourednicek creator: Jan Briza creator: Walter Giepmans creator: Jiri Jahoda creator: Lukas Hruska creator: Jan Danes uri: https://doi.org/10.7717/peerj.1883 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lambert et al. title: Test–re-test reliability and inter-rater reliability of a digital pelvic inclinometer in young, healthy males and females link: https://peerj.com/articles/1881 last-modified: 2016-03-31 description: Objective. The purpose of this study was to investigate the reliability of a digital pelvic inclinometer (DPI) for measuring sagittal plane pelvic tilt in 18 young, healthy males and females.Method. The inter-rater reliability and test–re-test reliabilities of the DPI for measuring pelvic tilt in standing on both the right and left sides of the pelvis were measured by two raters carrying out two rating sessions of the same subjects, three weeks apart.Results. For measuring pelvic tilt, inter-rater reliability was designated as good on both sides (ICC = 0.81–0.88), test–re-test reliability within a single rating session was designated as good on both sides (ICC = 0.88–0.95), and test–re-test reliability between two rating sessions was designated as moderate on the left side (ICC = 0.65) and good on the right side (ICC = 0.85).Conclusion. Inter-rater reliability and test–re-test reliability within a single rating session of the DPI in measuring pelvic tilt were both good, while test–re-test reliability between rating sessions was moderate-to-good. Caution is required regarding the interpretation of the test–re-test reliability within a single rating session, as the raters were not blinded. Further research is required to establish validity. creator: Chris Beardsley creator: Tim Egerton creator: Brendon Skinner uri: https://doi.org/10.7717/peerj.1881 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Beardsley et al. title: Investigation of the effects of estrogen on skeletal gene expression during zebrafish larval head development link: https://peerj.com/articles/1878 last-modified: 2016-03-31 description: The development of craniofacial skeletal structures requires well-orchestrated tissue interactions controlled by distinct molecular signals. Disruptions in normal function of these molecular signals have been associated with a wide range of craniofacial malformations. A pathway mediated by estrogens is one of those molecular signals that plays role in formation of bone and cartilage including craniofacial skeletogenesis. Studies in zebrafish have shown that while higher concentrations of 17-β estradiol (E2) cause severe craniofacial defects, treatment with lower concentrations result in subtle changes in head morphology characterized with shorter snouts and flatter faces. The molecular basis for these morphological changes, particularly the subtle skeletal effects mediated by lower E2 concentrations, remains unexplored. In the present study we address these effects at a molecular level by quantitative expression analysis of sets of candidate genes in developing heads of zebrafish larvae treated with two different E2 concentrations. To this end, we first validated three suitable reference genes, ppia2, rpl8 and tbp, to permit sensitive quantitative real-time PCR analysis. Next, we profiled the expression of 28 skeletogenesis-associated genes that potentially respond to estrogen signals and play role in craniofacial development. We found E2 mediated differential expression of genes involved in extracellular matrix (ECM) remodelling, mmp2/9/13, sparc and timp2a, as well as components of skeletogenic pathways, bmp2a, erf, ptch1/2, rankl, rarab and sfrp1a. Furthermore, we identified a co-expressed network of genes, including cpn1, dnajc3, esr1, lman1, rrbp1a, ssr1 and tram1 with a stronger inductive response to a lower dose of E2 during larval head development. creator: Ehsan Pashay Ahi creator: Benjamin S. Walker creator: Christopher S. Lassiter creator: Zophonías O. Jónsson uri: https://doi.org/10.7717/peerj.1878 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pashay Ahi et al. title: Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon link: https://peerj.com/articles/1865 last-modified: 2016-03-31 description: The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow. creator: András Tartally creator: Andreas Kelager creator: Matthias A. Fürst creator: David R. Nash uri: https://doi.org/10.7717/peerj.1865 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tartally et al. title: Improved ultrastructure of marine invertebrates using non-toxic buffers link: https://peerj.com/articles/1860 last-modified: 2016-03-31 description: Many marine biology studies depend on field work on ships or remote sampling locations where sophisticated sample preservation techniques (e.g., high-pressure freezing) are often limited or unavailable. Our aim was to optimize the ultrastructural preservation of marine invertebrates, especially when working in the field. To achieve chemically-fixed material of the highest quality, we compared the resulting ultrastructure of gill tissue of the mussel Mytilus edulis when fixed with differently buffered EM fixatives for marine specimens (seawater, cacodylate and phosphate buffer) and a new fixative formulation with the non-toxic PHEM buffer (PIPES, HEPES, EGTA and MgCl2). All buffers were adapted for immersion fixation to form an isotonic fixative in combination with 2.5% glutaraldehyde. We showed that PHEM buffer based fixatives resulted in equal or better ultrastructure preservation when directly compared to routine standard fixatives. These results were also reproducible when extending the PHEM buffered fixative to the fixation of additional different marine invertebrate species, which also displayed excellent ultrastructural detail. We highly recommend the usage of PHEM-buffered fixation for the fixation of marine invertebrates. creator: Jacqueline Montanaro creator: Daniela Gruber creator: Nikolaus Leisch uri: https://doi.org/10.7717/peerj.1860 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Montanaro et al. title: Aging and serum MCP-1 are associated with gut microbiome composition in a murine model link: https://peerj.com/articles/1854 last-modified: 2016-03-31 description: Introduction. Age is the primary risk factor for major human chronic diseases, including cardiovascular disorders, cancer, type 2 diabetes, and neurodegenerative diseases. Chronic, low-grade, systemic inflammation is associated with aging and the progression of immunosenescence. Immunosenescence may play an important role in the development of age-related chronic disease and the widely observed phenomenon of increased production of inflammatory mediators that accompany this process, referred to as “inflammaging.” While it has been demonstrated that the gut microbiome and immune system interact, the relationship between the gut microbiome and age remains to be clearly defined, particularly in the context of inflammation. The aim of our study was to clarify the associations between age, the gut microbiome, and pro-inflammatory marker serum MCP-1 in a C57BL/6 murine model.Results. We used 16S rRNA gene sequencing to profile the composition of fecal microbiota associated with young and aged mice. Our analysis identified an association between microbiome structure and mouse age and revealed specific groups of taxa whose abundances stratify young and aged mice. This includes the Ruminococcaceae, Clostridiaceae, and Enterobacteriaceae. We also profiled pro-inflammatory serum MCP-1 levels of each mouse and found that aged mice exhibited elevated serum MCP-1, a phenotype consistent with inflammaging. Robust correlation tests identified several taxa whose abundance in the microbiome associates with serum MCP-1 status, indicating that they may interact with the mouse immune system. We find that taxonomically similar organisms can exhibit differing, even opposite, patterns of association with the host immune system. We also find that many of the OTUs that associate with serum MCP-1 stratify individuals by age.Discussion. Our results demonstrate that gut microbiome composition is associated with age and the pro-inflammatory marker, serum MCP-1. The correlation between age, relative abundance of specific taxa in the gut microbiome, and serum MCP-1 status in mice indicates that the gut microbiome may play a modulating role in age-related inflammatory processes. These findings warrant further investigation of taxa associated with the inflammaging phenotype and the role of gut microbiome in the health status and immune function of aged individuals. creator: Melissa N. Conley creator: Carmen P. Wong creator: Kyle M. Duyck creator: Norman Hord creator: Emily Ho creator: Thomas J. Sharpton uri: https://doi.org/10.7717/peerj.1854 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Conley et al. title: Association of NOD1, CXCL16, STAT6 and TLR4 gene polymorphisms with Malaysian patients with Crohn’s disease link: https://peerj.com/articles/1843 last-modified: 2016-03-31 description: Crohn’s disease (CD) is a prominent type of inflammatory bowel disease (IBD) that can affect any part of the gastrointestinal tract. CD is known to have higher prevalence in the Western countries, but the number of cases has been increasing in the past decades in Asia, including Malaysia. Therefore, there is a need to investigate the underlining causes of CD that may shed light on its prevention and treatment. In this study, genetic polymorphisms in NOD1 (rs2075820), CXCL16 (rs2277680), STAT6 (rs324015) and TLR4 (rs4986791) genes were examined in a total of 335 individuals (85 CD patients and 250 healthy controls) with PCR-RFLP approach. There was no significant association observed between NOD1 rs2075820 and STAT6 rs324015 with the onset of CD in the studied cohort. However, the G allele of CXCL16 rs2277680 was found to have a weak association with CD patients (P = 0.0482; OR = 1.4310). The TLR4 rs4986791 was also significantly associated to CD. Both the homozygous C genotype (P = 0.0029; OR = 0.3611) and C allele (P = 0.0069; OR = 0.4369) were observed to confer protection against CD. On the other hand, the heterozygous C/T genotype was a risk genotype (P = 0.0015; OR = 3.1392). Further ethnic-stratified analysis showed that the significant associations in CXCL16 rs2277680 and TLR4 rs4986791 were accounted by the Malay cohort. In conclusion, the present study reported two CD-predisposing loci in the Malay CD patients. However, these loci were not associated to the onset of CD in Chinese and Indian patients. creator: Kek Heng Chua creator: Jin Guan Ng creator: Ching Ching Ng creator: Ida Hilmi creator: Khean Lee Goh creator: Boon Pin Kee uri: https://doi.org/10.7717/peerj.1843 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chua et al. title: Impact of paid work on the academic performance of nursing students link: https://peerj.com/articles/1838 last-modified: 2016-03-31 description: Background. Little research exists on the impact of paid work on academic performance of students of health sciences. No research exists on this subject for students in Colombia.Objectives. This paper seeks to analyze the impact of paid work on academic performance among nursing students. Design, settings and participants: cross-sectional research, involving 430 of nursing students from the National University of Colombia (N = 566).Methods. Variables analyzed: sex, age, work activity, attendance, current semester, degree subjects studied and unavailable, lost credits, grades during the second semester of 2013, and delayed semesters. Subgroups analyzed: (i) according to labor activity: do not work, work up to 20 h and work more than 20 h per week; (ii) Grade point average: failing is considered as less than 3.0 and passing 3.0 or above out of 5.0. Percentage of delayed semesters were calculated. Qualitative and quantitative variables were analyzed for groups by work activity. The percentage and probability of students getting a grade point average less than 3.0 and delaying semesters were calculated by multivariate logistic regression.Results. A total of 219 of the students work (50.9%), the main reason is socioeconomic, of which 99 (45.2%) work more than 20 h per week and have an increased risk of failing, which is higher in the first semester. They also get lower grades, lose more credits and take longer to finish the degree. The logistic bivariate regressions of success (grade point average, credits gained, courses gained and not having delayed semesters) reduce with work, above all in those who work more than 20 h per week and increase as the number of semesters completed increases, independent of sex.Conclusion. A high percentage of nursing students work more than 20 h per week. The compatibility of paid work with studies in university nursing students has a negative impact on academic performance, more so when they work more than 20 h per week. This negative impact diminishes as the student completes semesters, irrespective of the sex of the students. creator: Mery Constanza García-Vargas creator: Mercedes Rizo-Baeza creator: Ernesto Cortés-Castell uri: https://doi.org/10.7717/peerj.1838 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 García-Vargas et al. title: Transgenerational effects enhance specific immune response in a wild passerine link: https://peerj.com/articles/1766 last-modified: 2016-03-31 description: Vertebrate mothers transfer diverse compounds to developing embryos that can affect their development and final phenotype (i.e., maternal effects). However, the way such effects modulate offspring phenotype, in particular their immunity, remains unclear. To test the impact of maternal effects on offspring development, we treated wild breeding house sparrows (Passer domesticus) in Sevilla, SE Spain with Newcastle disease virus (NDV) vaccine. Female parents were vaccinated when caring for first broods, eliciting a specific immune response to NDV. The immune response to the same vaccine, and to the PHA inflammatory test were measured in 11-day-old chicks from their following brood. Vaccinated chicks from vaccinated mothers developed a stronger specific response that was related to maternal NDV antibody concentration while rearing their chicks. The chicks’ carotenoid concentration and total antioxidant capacity in blood were negatively related to NDV antibody concentration, whereas no relation with PHA response was found. Specific NDV antibodies could not be detected in 11-day-old control chicks from vaccinated mothers, implying that maternally transmitted antibodies are not directly involved but may promote offspring specific immunity through a priming effect, while other immunity components remain unaffected. Maternally transmitted antibodies in the house sparrow are short-lived, depend on maternal circulation levels and enhance pre-fledging chick specific immunity when exposed to the same pathogens as the mothers. creator: Juli Broggi creator: Ramon C. Soriguer creator: Jordi Figuerola uri: https://doi.org/10.7717/peerj.1766 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Broggi et al. title: Caribbean Bulimulus revisited: physical moves and molecular traces (Mollusca, Gastropoda, Bulimulidae) link: https://peerj.com/articles/1836 last-modified: 2016-03-29 description: Twenty-five samples of Bulimulus species are studied, partly from localities within their known distribution range, partly based on interceptions where the material originates from localities where the species seem to be recently introduced and non-native. Molecular study of cytochrome oxidase 1 (CO1) reveals the origin of some of these introductions, but is less conclusive for others. Four different methods for species delimitation were applied, which did not result in unambiguous species hypotheses. For a rapid identification of morphologically indistinct species, a more comprehensive database of sequences is needed. creator: Abraham S.H. Breure uri: https://doi.org/10.7717/peerj.1836 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Breure title: Specializations of the mandibular anatomy and dentition of Segnosaurus galbinensis (Theropoda: Therizinosauria) link: https://peerj.com/articles/1885 last-modified: 2016-03-29 description: Definitive therizinosaurid cranial materials are exceptionally rare, represented solely by an isolated braincase and tooth in the North American taxon Nothronychus mckinleyi, the remarkably complete skull of the Asian taxon Erlikosaurus andrewsi, and the lower hemimandibles of Segnosaurus galbinensis. To date, comprehensive descriptions of the former taxa are published; however, the mandibular materials of S. galbinensis have remained largely understudied since their initial description in 1979. Here we provide a comprehensive description of the well-preserved hemimandibles and dentition of S. galbinensis (MPC-D 100/80), from the Upper Cretaceous Bayanshiree Formation, Gobi Desert, Mongolia. The subrectangular and ventrally displaced caudal hemimandible, extreme ventral deflection of the rostral dentary, and edentulism of the caudal dentary of S. galbinensis are currently apomorphic among therizinosaurians. Unique, unreported dental traits including lingually folded mesial carinae, development of a denticulated triangular facet on the distal carinae near the cervix, and extracarinal accessory denticles, suggest a highly specialized feeding strategy in S. galbinensis. The presence of triple carinae on the distalmost lateral tooth crowns is also unique, although may represent an abnormality. Contrasted with the simplistic dentition of the contemporaneous therizinosaurid E. andrewsi, the dentition of S. galbinensis is indicative of niche partitioning in food acquisition, processing, or resources among known therizinosaurids inhabiting Asian ecosystems in the Late Cretaceous. Although not quantitatively correlated with diet, this suite of specializations is otherwise unique among theropod dinosaurs and supports derived inferences of facultative or obligate herbivory in therizinosaurids, ultimately adding novel information to our understanding of ecomorphology in theropods. creator: Lindsay E. Zanno creator: Khishigjav Tsogtbaatar creator: Tsogtbaatar Chinzorig creator: Terry A. Gates uri: https://doi.org/10.7717/peerj.1885 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zanno et al. title: What doesn’t kill them makes them stronger: an association between elongation factor 1-α overdominance in the sea star Pisaster ochraceus and “sea star wasting disease” link: https://peerj.com/articles/1876 last-modified: 2016-03-29 description: In recent years, a massive mortality event has killed millions of sea stars, of many different species, along the Pacific coast of North America. This disease event, known as ‘sea star wasting disease’ (SSWD), is linked to viral infection. In one affected sea star (Pisaster ochraceus), previous work had identified that the elongation factor 1-α locus (EF1A) harbored an intronic insertion allele that is lethal when homozygous yet appears to be maintained at moderate frequency in populations through increased fitness for heterozygotes. The environmental conditions supporting this increased fitness are unknown, but overdominance is often associated with disease. Here, we evaluate populations of P. ochraceus to identify the relationship between SSWD and EF1A genotype. Our data suggest that there may be significantly decreased occurrence of SSWD in individuals that are heterozygous at this locus. These results suggest further studies are warranted to understand the functional relationship between diversity at EF1A and survival in P. ochraceus. creator: John P. Wares creator: Lauren M. Schiebelhut uri: https://doi.org/10.7717/peerj.1876 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wares and Schiebelhut title: Intersexual chemo-sensation in a “visually-oriented” lizard, Anolis sagrei link: https://peerj.com/articles/1874 last-modified: 2016-03-29 description: While the conspicuous visual displays of anoles have been studied in great depth, the possibility that these lizards may also interact through chemical signalling has received hardly any consideration. In this study, we observed the behaviour of male brown anoles (Anolis sagrei) when introduced into an environment previously inhabited by female conspecifics, and compared it to when they were introduced into an untreated environment. The males in our tests exhibited significantly more elaborate display behaviour (i.e., greater number of dewlap extensions and head-nods) and a significantly greater number of tongue extrusions while in the cage formerly occupied by females than when placed in the untreated, control cage. The absolute numbers of tongue extrusions, however, were relatively low in comparison to average tongue-flick rates of ‘true’ chemically-oriented lizards. Our results strongly suggest that the males were capable of detecting chemical cues left behind by the females. These observations provide the first evidence of intersexual chemo-sensation in an anole lizard. creator: Simon Baeckens creator: Tess Driessens creator: Raoul Van Damme uri: https://doi.org/10.7717/peerj.1874 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baeckens et al. title: The impact of serum uric acid on the natural history of glomerular filtration rate: a retrospective study in the general population link: https://peerj.com/articles/1859 last-modified: 2016-03-29 description: Serum uric acid (SUA) level has been proposed to have important connections with chronic kidney disease (CKD), while the impact of SUA level on the natural history of glomerular filtration rate (GFR) decline remains unknown. The present study aims to study the association of the SUA level with the GFR decline in a general population. Two thousand, seven hundred and eighty-nine subjects who visited the Health Checkup Clinic both at 2008 and 2013 were identified. A significant inverse correlation was observed between change in SUA from 2008–2013 (ΔSUA) and change in eGFR (ΔeGFR) during the same period. Multivariate regression analysis of ΔeGFR indicated that the increase in SUA over time were a negative predictor of the change in eGFR. Our result indicates that the decline of eGFR over years is larger in subjects with an increased SUA level, which helps to underline the importance of SUA level management in the context of kidney function preservation. creator: Ying Xu creator: Xiang Liu creator: Xiaohe Sun creator: Yibing Wang uri: https://doi.org/10.7717/peerj.1859 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Xu et al. title: The effect of the dispersal kernel on isolation-by-distance in a continuous population link: https://peerj.com/articles/1848 last-modified: 2016-03-29 description: Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population which represents a standardized measure of gene flow. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional landscape using seven dispersal kernels: Rayleigh, exponential, half-normal, triangular, gamma, Lomax and Pareto. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform over the neighborhood area which suggests that the common description of neighborhood size as a measure of an effective, local panmictic population is valid for popular families of dispersal distributions. We further show how to draw random variables from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important. creator: Tara N. Furstenau creator: Reed A. Cartwright uri: https://doi.org/10.7717/peerj.1848 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Furstenau and Cartwright title: Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies link: https://peerj.com/articles/1839 last-modified: 2016-03-29 description: High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes. creator: Tom O. Delmont creator: A. Murat Eren uri: https://doi.org/10.7717/peerj.1839 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Delmont and Eren title: Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater link: https://peerj.com/articles/1829 last-modified: 2016-03-29 description: Mussel biofiltration is a widely used approach for the mitigation of aquaculture water. In this study, we investigated the effect of mussel biofiltration on the communities of particle-associated bacteria and unicellular eukaryotes in a sea bass aquaculture in southern North Sea. We assessed the planktonic community changes before and after biofiltration based on the diversity of the 16S and 18S rRNA genes by using next generation sequencing technologies. Although there was no overall reduction in the operational taxonomic units (OTU) numbers between the control (no mussels) and the test (with mussels) tanks, a clear reduction in the relative abundance of the top three most dominant OTUs in every sampling time was observed, ranging between 2–28% and 16–82% for Bacteria and Eukarya, respectively. The bacterial community was dominated by OTUs related to phytoplankton blooms and/or high concentrations of detritus. Among the eukaryotes, several fungal and parasitic groups were found. Their relative abundance in most cases was also reduced from the control to the test tanks; a similar decreasing pattern was also observed for both major higher taxa and functional (trophic) groups. Overall, this study showed the effectiveness of mussel biofiltration on the decrease of microbiota abundance and diversity in seawater fueling fish farms. creator: Eleni Voudanta creator: Konstantinos Ar Kormas creator: Sebastién Monchy creator: Alice Delegrange creator: Dorothée Vincent creator: Savvas Genitsaris creator: Urania Christaki uri: https://doi.org/10.7717/peerj.1829 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Voudanta et al. title: Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system link: https://peerj.com/articles/1869 last-modified: 2016-03-28 description: Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina’s MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT) DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3–V5, V1–V3, V1–V5, V1–V6, and V1–V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1–V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina’s MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting. creator: Patrick D. Schloss creator: Matthew L. Jenior creator: Charles C. Koumpouras creator: Sarah L. Westcott creator: Sarah K. Highlander uri: https://doi.org/10.7717/peerj.1869 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Schloss et al. title: Characterisation of Schizosaccharomyces pombe α-actinin link: https://peerj.com/articles/1858 last-modified: 2016-03-28 description: The actin cytoskeleton plays a fundamental role in eukaryotic cells. Its reorganization is regulated by a plethora of actin-modulating proteins, such as a-actinin. In higher organisms, α-actinin is characterized by the presence of three distinct structural domains: an N-terminal actin-binding domain and a C-terminal region with EF-hand motif separated by a central rod domain with four spectrin repeats. Sequence analysis has revealed that the central rod domain of α-actinin from the fission yeast Schizosaccharomyces pombe consists of only two spectrin repeats. To obtain a firmer understanding of the structure and function of this unconventional α-actinin, we have cloned and characterized each structural domain. Our results show that this a-actinin isoform is capable of forming dimers and that the rod domain is required for this. However, its actin-binding and cross-linking activity appears less efficient compared to conventional α-actinins. The solved crystal structure of the actin-binding domain indicates that the closed state is stabilised by hydrogen bonds and a salt bridge not present in other α-actinins, which may reduce the affinity for actin. creator: Barbara Addario creator: Linda Sandblad creator: Karina Persson creator: Lars Backman uri: https://doi.org/10.7717/peerj.1858 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Addario et al. title: Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome link: https://peerj.com/articles/1847 last-modified: 2016-03-28 description: Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized.Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized.Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. creator: Pin Cui creator: Ulrike Löber creator: David E. Alquezar-Planas creator: Yasuko Ishida creator: Alexandre Courtiol creator: Peter Timms creator: Rebecca N. Johnson creator: Dorina Lenz creator: Kristofer M. Helgen creator: Alfred L. Roca creator: Stefanie Hartman creator: Alex D. Greenwood uri: https://doi.org/10.7717/peerj.1847 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cui et al. title: The comparison of cold-water immersion and cold air therapy on maximal cycling performance and recovery markers following strength exercises link: https://peerj.com/articles/1841 last-modified: 2016-03-28 description: This study examined the effects of cold-water immersion (CWI) and cold air therapy (CAT) on maximal cycling performance (i.e. anaerobic power) and markers of muscle damage following a strength training session. Twenty endurance-trained but strength-untrained male (n = 10) and female (n = 10) participants were randomised into either: CWI (15 min in 14 °C water to iliac crest) or CAT (15 min in 14 °C air) immediately following strength training (i.e. 3 sets of leg press, leg extensions and leg curls at 6 repetition maximum, respectively). Creatine kinase, muscle soreness and fatigue, isometric knee extensor and flexor torque and cycling anaerobic power were measured prior to, immediately after and at 24 (T24), 48 (T48) and 72 (T72) h post-strength exercises. No significant differences were found between treatments for any of the measured variables (p > 0.05). However, trends suggested recovery was greater in CWI than CAT for cycling anaerobic power at T24 (10% ± 2%, ES = 0.90), T48 (8% ± 2%, ES = 0.64) and T72 (8% ± 7%, ES = 0.76). The findings suggest the combination of hydrostatic pressure and cold temperature may be favourable for recovery from strength training rather than cold temperature alone. creator: Kane J. Hayter creator: Kenji Doma creator: Moritz Schumann creator: Glen B. Deakin uri: https://doi.org/10.7717/peerj.1841 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hayter et al. title: Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts link: https://peerj.com/articles/1840 last-modified: 2016-03-28 description: Wolbachia is an alpha-proteobacterial symbiont widely distributed in arthropods. Since the identification of Wolbachia in certain animal-parasitic nematodes (the Onchocercidae or filariae), the relationship between arthropod and nematode Wolbachia has attracted great interest. The obligate symbiosis in filariae, which renders infected species susceptible to antibiotic chemotherapy, was held to be distinct from the Wolbachia-arthropod relationship, typified by reproductive parasitism. While co-evolutionary signatures in Wolbachia-arthropod symbioses are generally weak, reflecting horizontal transmission events, strict co-evolution between filariae and Wolbachia has been reported previously. However, the absence of close outgroups for phylogenetic studies prevented the determination of which host group originally acquired Wolbachia. Here, we present the largest co-phylogenetic analysis of Wolbachia in filariae performed to date including: (i) a screening and an updated phylogeny of Wolbachia; (ii) a co-phylogenetic analysis; and (iii) a hypothesis on the acquisition of Wolbachia infection. First, our results show a general overestimation of Wolbachia occurrence and support the hypothesis of an ancestral absence of infection in the nematode phylum. The accuracy of supergroup J is also underlined. Second, although a global pattern of coevolution remains, the signal is derived predominantly from filarial clades associated with Wolbachia in supergroups C and J. In other filarial clades, harbouring Wolbachia supergroups D and F, horizontal acquisitions and secondary losses are common. Finally, our results suggest that supergroup C is the basal Wolbachia clade within the Ecdysozoa. This hypothesis on the origin of Wolbachia would change drastically our understanding of Wolbachia evolution. creator: Emilie Lefoulon creator: Odile Bain creator: Benjamin L. Makepeace creator: Cyrille d’Haese creator: Shigehiko Uni creator: Coralie Martin creator: Laurent Gavotte uri: https://doi.org/10.7717/peerj.1840 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lefoulon et al. title: When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensis and M. paradoxus) link: https://peerj.com/articles/1827 last-modified: 2016-03-28 description: In the marine environment, an increasing number of studies have documented introgression and hybridization using genetic markers. Hybridization appears to occur preferentially between sister-species, with the probability of introgression decreasing with an increase in evolutionary divergence. Exceptions to this pattern were reported for the Cape hakes (Merluccius capensis and M. paradoxus), two distantly related Merluciidae species that diverged 3–4.2 million years ago. Yet, it is expected that contemporary hybridization between such divergent species would result in reduced hybrid fitness. We analysed 1,137 hake individuals using nine microsatellite markers and control region mtDNA data to assess the validity of the described hybridization event. To distinguish between interbreeding, ancestral polymorphism and homplasy we sequenced the flanking region of the most divergent microsatellite marker. Simulation and empirical analyses showed that hybrid identification significantly varied with the number of markers, model and approach used. Phylogenetic analyses based on the sequences of the flanking region of Mmerhk-3b, combined with the absence of mito-nuclear discordance, suggest that previously reported hybridization between M. paradoxus and M. capensis cannot be substantiated. Our findings highlight the need to conduct a priori simulation studies to establish the suitability of a particular set of microsatellite loci for detecting multiple hybridization events. In our example, the identification of hybrids was severely influenced by the number of loci and their variability, as well as the different models employed. More importantly, we provide quantifiable evidence showing that homoplasy mimics the effects of heterospecific crossings which can lead to the incorrect identification of hybridization. creator: Romina Henriques creator: Sophie von der Heyden creator: Conrad A. Matthee uri: https://doi.org/10.7717/peerj.1827 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Henriques et al. title: A citizen science approach to monitoring bleaching in the zoantharian Palythoa tuberculosa link: https://peerj.com/articles/1815 last-modified: 2016-03-28 description: Coral reef bleaching events are expected to become more frequent and severe in the near future as climate changes. The zoantharian Palythoa tuberculosa bleaches earlier than many scleractinian corals and may serve as an indicator species. Basic monitoring of such species could help to detect and even anticipate bleaching events, especially in areas where more sophisticated approaches that rely on buoy or satellite measurements of sea surface temperature are unavailable or too coarse. One simple and inexpensive monitoring method involves training volunteers to record observations of host color as a proxy for symbiosis quality. Here, we trained university students to take the ‘color fingerprint’ of a reef by assessing the color of multiple randomly selected colonies of P. tuberculosa at one time point in Okinawa Island, Japan. We tested the reliability of the students’ color scores and whether they matched expectations based on previous monthly monitoring of tagged colonies at the same locations. We also measured three traditional metrics of symbiosis quality for comparison: symbiont morphological condition, cell density, and chlorophyll a content. We found that P. tuberculosa color score, although highly correlated among observers, provided little predictive power for the other variables. This was likely due to inherent variation in colony color among generally healthy zoantharians in midwinter, as well as low sample size and brief training owing to the course structure. Despite certain limitations of P. tuberculosa as a focal organism, the citizen science approach to color monitoring has promise, and we outline steps that could improve similar efforts in the future. creator: John Everett Parkinson creator: Sung-Yin Yang creator: Iori Kawamura creator: Gordon Byron creator: Peter Alan Todd creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.1815 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Parkinson et al. title: Gene expression profiles during short-term heat stress; branching vs. massive Scleractinian corals of the Red Sea link: https://peerj.com/articles/1814 last-modified: 2016-03-28 description: It is well-established that there is a hierarchy of susceptibilities amongst coral genera during heat-stress. However, molecular mechanisms governing these differences are still poorly understood. Here we explored if specific corals possessing different morphologies and different susceptibilities to heat stress may manifest varied gene expression patterns. We examined expression patterns of seven genes in the branching corals Stylophora pistillata and Acropora eurystoma and additionally in the massive robust coral, Porites sp. The tested genes are representatives of key cellular processes occurring during heat-stress in Cnidaria: oxidative stress, ER stress, energy metabolism, DNA repair and apoptosis. Varied response to the heat-stress, in terms of visual coral paling, algal maximum quantum yield and host gene expression was evident in the different growth forms. The two branching corals exhibited similar overall responses that differed from that of the massive coral. A. eurystoma that is considered as a susceptible species did not bleach in our experiment, but tissue sloughing was evident at 34 °C. Interestingly, in this species redox regulation genes were up-regulated at the very onset of the thermal challenge. In S. pistillata, bleaching was evident at 34 °C and most of the stress markers were already up-regulated at 32 °C, either remaining highly expressed or decreasing when temperatures reached 34 °C. The massive Porites species displayed severe bleaching at 32 °C but stress marker genes were only significantly elevated at 34 °C. We postulate that by expelling the algal symbionts from Porites tissues, oxidation damages are reduced and stress genes are activated only at a progressed stage. The differential gene expression responses exhibited here can be correlated with the literature well-documented hierarchy of susceptibilities amongst coral morphologies and genera in Eilat’s coral reef. creator: Keren Maor-Landaw creator: Oren Levy uri: https://doi.org/10.7717/peerj.1814 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Maor-Landaw and Levy title: Are patients who call a primary care office referred to the emergency department by non-healthcare personnel without the input of a physician? link: https://peerj.com/articles/1507 last-modified: 2016-03-28 description: Objective. We hypothesized that a significant percentage of patients who are referred to the Emergency Department (ED) after calling their primary care physician’s (PCP) office receive such instructions without the input of a physician.Methods. We enrolled a convenience sample of stable adults at an inner-city ED. Patients provided written answers to structured questions regarding PCP contact prior to the ED visit. Continuous data are presented as means ± standard deviation; categorical data as frequency of occurrence. 95% confidence intervals were calculated.Results. The study group of 660 patients had a mean age of 41.7 ± 14.7 years and 72.6% had income below $20,000/year. 472 patients (71.51%; 67.9%–74.8%) indicated that they had a PCP. A total of 155 patients (23.0%; 19.9%–26.4%) called to contact their PCP prior to ED visit. For patients who called their PCP office and were directed by phone to the ED, the referral pattern was observed as follows: 31/98 (31.63%; 23.2%–41.4%) by a non-health care provider without physician input, 11/98 (11.2%; 6.2%–19.1%) by a non-healthcare provider after consultation with a physician, 12/98 (12.3%; 7.7%–20.3%) by a nurse without physician input, and 14/98 (14.3%; 8.6%–22.7%) by a nurse after consultation with physician. An additional 11/98, 11.2%; 6.2–19.1%) only listened to a recorded message and felt the message was directing them to the ED.Conclusion. A relatively small percentage of patients were referred to the ED without the consultation of a physician in our overall population. However, over half of those that contacted their PCP’s office felt directed to the ED by non-health care staff. creator: Russell Hill creator: Albert Gest creator: Cynthia Smith creator: Jose H. Guardiola creator: Michael Apolinario creator: Joann Ha creator: Jose R. Gonzalez creator: Peter B. Richman uri: https://doi.org/10.7717/peerj.1507 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hill et al. title: Non-adaptive territory selection by a bird with exceptionally long parental care link: https://peerj.com/articles/1852 last-modified: 2016-03-24 description: High-quality territories are expected to provide greater fitness return for breeding individuals and, thus, are likely to have higher long-term occupation rate in comparison to low-quality territories. However, if environmental and ecological cues used for territory selection cannot reliably predict true territory quality, a mismatch between preferences and fitness may occur. We suggest that this kind of non-adaptive territory selection is more likely in species with long reproductive cycles, as a long time interval between territory establishment and young fledgling should reduce predictability of conditions during the critical stages of brood care. In this study, we investigated adaptiveness of territory selection in a migratory bird with exceptionally long parental care, the mute swan Cygnus olor, which requires over four months to complete the entire reproductive cycle from egg laying to young fledging. For this purpose, we collected information on the long-term (10–19 years) occupancy of 222 swan breeding territories and correlated it with reproductive performance (n = 1,345 breeding attempts) and body condition of breeding adults. We found that long-term occupancy positively correlated with the timing of breeding, suggesting that individuals settled earlier in the attractive, frequently occupied territories. By contrast, we found no relationship between territory occupancy and reproductive output (hatching and fledging success) or adult body condition. The results indicate that at the time of territory selection swans might not be able to reliably assess territory quality, likely due to: (1) exceptionally long period of parental care, which reduces temporal correlation between the conditions at the time of territory selection and conditions during chick rearing; and (2) unpredictability of human-related activities that had a major impact on reproductive output of swan pairs in our population. creator: Radosław Włodarczyk creator: Piotr Minias uri: https://doi.org/10.7717/peerj.1852 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Włodarczyk & Minias title: Dramatyping: a generic algorithm for detecting reasonable temporal correlations between drug administration and lab value alterations link: https://peerj.com/articles/1851 last-modified: 2016-03-24 description: According to the World Health Organization, one of the criteria for the standardized assessment of case causality in adverse drug reactions is the temporal relationship between the intake of a drug and the occurrence of a reaction or a laboratory test abnormality. This article presents and describes an algorithm for the detection of a reasonable temporal correlation between the administration of a drug and the alteration of a laboratory value course. The algorithm is designed to process normalized lab values and is therefore universally applicable. It has a sensitivity of 0.932 for the detection of lab value courses that show changes in temporal correlation with the administration of a drug and it has a specificity of 0.967 for the detection of lab value courses that show no changes. Therefore, the algorithm is appropriate to screen the data of electronic health records and to support human experts in revealing adverse drug reactions. A reference implementation in Python programming language is available. creator: Axel Newe uri: https://doi.org/10.7717/peerj.1851 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Newe title: The sex lives of ctenophores: the influence of light, body size, and self-fertilization on the reproductive output of the sea walnut, Mnemiopsis leidyi link: https://peerj.com/articles/1846 last-modified: 2016-03-24 description: Ctenophores (comb jellies) are emerging as important animals for investigating fundamental questions across numerous branches of biology (e.g., evodevo, neuroscience and biogeography). A few ctenophore species including, most notably, Mnemiopsis leidyi, are considered as invasive species, adding to the significance of studying ctenophore ecology. Despite the growing interest in ctenophore biology, relatively little is known about their reproduction. Like most ctenophores, M. leidyi is a simultaneous hermaphrodite capable of self-fertilization. In this study, we assess the influence of light on spawning, the effect of body size on spawning likelihood and reproductive output, and the cost of self-fertilization on egg viability in M. leidyi. Our results suggest that M. leidyi spawning is more strongly influenced by circadian rhythms than specific light cues and that body size significantly impacts spawning and reproductive output. Mnemiopsis leidyi adults that spawned alone produced a lower percentage of viable embryos versus those that spawned in pairs, suggesting that self-fertilization may be costly in this species. These results provide insight into the reproductive ecology of M. leidyi and provide a fundamental resource for researchers working with them in the laboratory. creator: Daniel A. Sasson creator: Joseph F. Ryan uri: https://doi.org/10.7717/peerj.1846 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sasson & Ryan title: A molecular classification of human mesenchymal stromal cells link: https://peerj.com/articles/1845 last-modified: 2016-03-24 description: Mesenchymal stromal cells (MSC) are widely used for the study of mesenchymal tissue repair, and increasingly adopted for cell therapy, despite the lack of consensus on the identity of these cells. In part this is due to the lack of specificity of MSC markers. Distinguishing MSC from other stromal cells such as fibroblasts is particularly difficult using standard analysis of surface proteins, and there is an urgent need for improved classification approaches. Transcriptome profiling is commonly used to describe and compare different cell types; however, efforts to identify specific markers of rare cellular subsets may be confounded by the small sample sizes of most studies. Consequently, it is difficult to derive reproducible, and therefore useful markers. We addressed the question of MSC classification with a large integrative analysis of many public MSC datasets. We derived a sparse classifier (The Rohart MSC test) that accurately distinguished MSC from non-MSC samples with >97% accuracy on an internal training set of 635 samples from 41 studies derived on 10 different microarray platforms. The classifier was validated on an external test set of 1,291 samples from 65 studies derived on 15 different platforms, with >95% accuracy. The genes that contribute to the MSC classifier formed a protein-interaction network that included known MSC markers. Further evidence of the relevance of this new MSC panel came from the high number of Mendelian disorders associated with mutations in more than 65% of the network. These result in mesenchymal defects, particularly impacting on skeletal growth and function. The Rohart MSC test is a simple in silico test that accurately discriminates MSC from fibroblasts, other adult stem/progenitor cell types or differentiated stromal cells. It has been implemented in the www.stemformatics.org resource, to assist researchers wishing to benchmark their own MSC datasets or data from the public domain. The code is available from the CRAN repository and all data used to generate the MSC test is available to download via the Gene Expression Omnibus or the Stemformatics resource. creator: Florian Rohart creator: Elizabeth A. Mason creator: Nicholas Matigian creator: Rowland Mosbergen creator: Othmar Korn creator: Tyrone Chen creator: Suzanne Butcher creator: Jatin Patel creator: Kerry Atkinson creator: Kiarash Khosrotehrani creator: Nicholas M. Fisk creator: Kim-Anh Lê Cao creator: Christine A. Wells uri: https://doi.org/10.7717/peerj.1845 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rohart et al. title: Anti-apoptotic response during anoxia and recovery in a freeze-tolerant wood frog (Rana sylvatica) link: https://peerj.com/articles/1834 last-modified: 2016-03-24 description: The common wood frog, Rana sylvatica, utilizes freeze tolerance as a means of winter survival. Concealed beneath a layer of leaf litter and blanketed by snow, these frogs withstand subzero temperatures by allowing approximately 65–70% of total body water to freeze. Freezing is generally considered to be an ischemic event in which the blood oxygen supply is impeded and may lead to low levels of ATP production and exposure to oxidative stress. Therefore, it is as important to selectively upregulate cytoprotective mechanisms such as the heat shock protein (HSP) response and expression of antioxidants as it is to shut down majority of ATP consuming processes in the cell. The objective of this study was to investigate another probable cytoprotective mechanism, anti-apoptosis during oxygen deprivation and recovery in the anoxia tolerant wood frog. In particular, relative protein expression levels of two important apoptotic regulator proteins, Bax and p-p53 (S46), and five anti-apoptotic/pro-survival proteins, Bcl-2, p-Bcl-2 (S70), Bcl-xL, x-IAP, and c-IAP in response to normoxic, 24 Hr anoxic exposure, and 4 Hr recovery stages were assessed in the liver and skeletal muscle using western immunoblotting. The results suggest a tissue-specific regulation of the anti-apoptotic pathway in the wood frog, where both liver and skeletal muscle shows an overall decrease in apoptosis and an increase in cell survival. This type of cytoprotective mechanism could be aimed at preserving the existing cellular components during long-term anoxia and oxygen recovery phases in the wood frog. creator: Victoria E.M. Gerber creator: Sanoji Wijenayake creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.1834 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gerber et al. title: Factor structure of the Positive and Negative Affect Schedule (PANAS) in adult women with fibromyalgia from Southern Spain: the al-Ándalus project link: https://peerj.com/articles/1822 last-modified: 2016-03-24 description: Background: Fibromyalgia is a syndrome characterized by the presence of widespread chronic pain. People with fibromyalgia report lower levels of Positive Affect and higher levels of Negative Affect than non-fibromyalgia peers. The Positive and Negative Affect Schedule (PANAS)–a widely used questionnaire to assess two core domains of affect; namely ‘Positive Affect’ and ‘Negative Affect’ –has a controversial factor structure varying across studies. The internal structure of a measurement instrument has an impact on the meaning and validity of its score. Therefore, the aim of the present study was to assess the structural construct validity of the PANAS in adult women with fibromyalgia. Methods: This population-based cross-sectional study included 442 adult women with fibromyalgia (age: 51.3 ± 7.4 years old) from Andalusia (Southern Spain). Confirmatory factor analyses were conducted to test the factor structure of the PANAS. Results: A structure with two correlated factors (Positive Affect and Negative Affect) obtained the best fit; S-B χ2 = 288.49, df = 155, p < .001; RMSEA = .04; 90% CI of RMSEA = (.036, .052); the best fit SRMR = .05; CFI = .96; CAIC = −810.66, respectively. Conclusions: The present study demonstrates that both Positive Affect and Negative Affect are core dimensions of affect in adult women with fibromyalgia. A structure with two correlated factors of the PANAS emerged from our sample of women with fibromyalgia from Andalusia (Southern Spain). In this model, the amount of variance shared by Positive Affect and Negative Affect was small. Therefore, our findings support to use and interpret the Positive Affect and Negative Affect subscales of the PANAS as separate factors that are associated but distinctive as well. creator: Fernando Estévez-López creator: Manuel Pulido-Martos creator: Christopher J. Armitage creator: Alison Wearden creator: Inmaculada C. Álvarez-Gallardo creator: Manuel Javier Arrayás-Grajera creator: María J. Girela-Rejón creator: Ana Carbonell-Baeza creator: Virginia A. Aparicio creator: Rinie Geenen creator: Manuel Delgado-Fernández creator: Víctor Segura-Jiménez uri: https://doi.org/10.7717/peerj.1822 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Estévez-López et al. title: Development and characterization of 26 novel microsatellite loci for the trochid gastropod Gibbula divaricata (Linnaeus, 1758), using Illumina MiSeq next generation sequencing technology link: https://peerj.com/articles/1789 last-modified: 2016-03-24 description: In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snail Gibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genus Gibbula, as G. rarilineata and G. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found. creator: Violeta López-Márquez creator: Ricardo García-Jiménez creator: José Templado creator: Annie Machordom uri: https://doi.org/10.7717/peerj.1789 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 López-Márquez et al title: Spatiotemporal distribution of caudal-type homeobox proteins during development of the hindgut and anorectum in human embryos link: https://peerj.com/articles/1771 last-modified: 2016-03-24 description: Background. The objectives of this study were to determine the spatiotemporal distribution of human caudal-type homeobox proteins CDX1, CDX2 and CDX4 during development of the hindgut and anorectum in the embryo and to explore the possible roles of CDX genes during morphogenesis of the hindgut and anorectum.Methods. Embryos (89) were cut into sections serially and sagittally. From gestation weeks 4–9, CDX1, CDX2 and CDX4 proteins were detected on the caudal midline by immunohistochemical staining.Results. During week 4, extensive immunoreactivity of CDX1, CDX2 and CDX4 was detected in the dorsal urorectal septum, urogenital sinus and hindgut. From weeks 5–7, CDX1-, CDX2- and CDX4- positive cells were detected mainly in the mesenchyme of the urorectal septum and hindgut. The levels of CDX2 and CDX4 immunoreactivity were lower compared to CDX1. During weeks 8 and 9, the anorectal epithelium stained positive for CDX1 and CDX4, and the anal epithelium was positive for CDX2.Conclusions. The CDX proteins are constantly distributed during development of the hindgut and anorectum and exhibit overlapping distribution patterns in the cloaca/hindgut, suggesting they are important in the morphogenesis of the human hindgut and anorectum. CDX genes might be involved in development of the anorectal epithelium after the rectum has separated from the urorectal septum. creator: Xiao Bing Tang creator: Tao Zhang creator: Wei Lin Wang creator: Zheng Wei Yuan creator: Yu Zuo Bai uri: https://doi.org/10.7717/peerj.1771 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tang et al. title: Evolution of Philodendron (Araceae) species in Neotropical biomes link: https://peerj.com/articles/1744 last-modified: 2016-03-24 description: Philodendron is the second most diverse genus of the Araceae, a tropical monocot family with significant morphological diversity along its wide geographic distribution in the Neotropics. Although evolutionary studies of Philodendron were conducted in recent years, the phylogenetic relationship among its species remains unclear. Additionally, analyses conducted to date suggested the inclusion of all American representatives of a closely-related genus, Homalomena, within the Philodendron clade. A thorough evaluation of the phylogeny and timescale of these lineages is thus necessary to elucidate the tempo and mode of evolution of this large Neotropical genus and to unveil the biogeographic history of Philodendron evolution along the Amazonian and Atlantic rainforests as well as open dry forests of South America. To this end, we have estimated the molecular phylogeny for 68 Philodendron species, which consists of the largest sampling assembled to date aiming the study of the evolutionary affinities. We have also performed ancestral reconstruction of species distribution along biomes. Finally, we contrasted these results with the inferred timescale of Philodendron and Homalomena lineage diversification. Our estimates indicate that American Homalomena is the sister clade to Philodendron. The early diversification of Philodendron took place in the Amazon forest from Early to Middle Miocene, followed by colonization of the Atlantic forest and the savanna-like landscapes, respectively. Based on the age of the last common ancestor of Philodendron, the species of this genus diversified by rapid radiations, leading to its wide extant distribution in the Neotropical region. creator: Leticia Loss-Oliveira creator: Cassia Sakuragui creator: Maria de Lourdes Soares creator: Carlos G. Schrago uri: https://doi.org/10.7717/peerj.1744 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Loss-Oliveira et al. title: Cost-effectiveness of antiviral therapy during late pregnancy to prevent perinatal transmission of hepatitis B virus link: https://peerj.com/articles/1709 last-modified: 2016-03-24 description: Background. Hepatitis B virus (HBV) infections are perinatally transmitted from chronically infected mothers. Supplemental antiviral therapy during late pregnancy with lamivudine (LAM), telbivudine (LdT), or tenofovir (TDF) can substantially reduce perinatal HBV transmission compared to postnatal immunoprophylaxis (IP) alone. However, the cost-effectiveness of these measures is not clear.Aim. This study evaluated the cost-effectiveness from a societal perspective of supplemental antiviral agents for preventing perinatal HBV transmission in mothers with high viral load (>6 log10 copies/mL).Methods. A systematic review and network meta-analysis were performed for the risk of perinatal HBV transmission with antiviral therapies. A decision analysis was conducted to evaluate the clinical and economic outcomes in China of four competing strategies: postnatal IP alone (strategy IP), or in combination with perinatal LAM (strategy LAM + IP), LdT (strategy LdT + IP), or TDF (strategy TDF + IP). Antiviral treatments were administered from week 28 of gestation to 4 weeks after birth. Outcomes included treatment-related costs, number of infections, and quality-adjusted life years (QALYs). One- and two-way sensitivity analyses were performed to identify influential clinical and cost-related variables. Probabilistic sensitivity analyses were used to estimate the probabilities of being cost-effective for each strategy.Results. LdT + IP and TDF + IP averted the most infections and HBV-related deaths, and gained the most QALYs. IP and TDF + IP were dominated as they resulted in less or equal QALYs with higher associated costs. LdT + IP had an incremental $2,891 per QALY gained (95% CI [$932–$20,372]) compared to LAM + IP (GDP per capita for China in 2013 was $6,800). One-way sensitivity analyses showed that the cost-effectiveness of LdT + IP was only sensitive to the relative risk of HBV transmission comparing LdT + IP with LAM + IP. Probabilistic sensitivity analyses demonstrated that LdT + IP was cost-effective in most cases across willingness-to-pay range of $6,800 ∼ $20,400 per QALY gained.Conclusions. For pregnant HBV-infected women with high levels of viremia, supplemental use of LdT during late pregnancy combined with postnatal IP for infants is cost-effective in China. creator: Wenjun Wang creator: Jingjing Wang creator: Shuangsuo Dang creator: Guihua Zhuang uri: https://doi.org/10.7717/peerj.1709 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) link: https://peerj.com/articles/1842 last-modified: 2016-03-22 description: Background. While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, the non-pathogenic microbes in these habitats have received less consideration. Preliminary work has demonstrated that the interior of the International Space Station (ISS) has a microbial community resembling those of built environments on Earth. Here we report the results of sending 48 bacterial strains, collected from built environments on Earth, for a growth experiment on the ISS. This project was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS).Results. Of the 48 strains sent to the ISS, 45 of them showed similar growth in space and on Earth using a relative growth measurement adapted for microgravity. The vast majority of species tested in this experiment have also been found in culture-independent surveys of the ISS. Only one bacterial strain showed significantly different growth in space. Bacillus safensis JPL-MERTA-8-2 grew 60% better in space than on Earth.Conclusions. The majority of bacteria tested were not affected by conditions aboard the ISS in this experiment (e.g., microgravity, cosmic radiation). Further work on Bacillus safensis could lead to interesting insights on why this strain grew so much better in space. creator: David A. Coil creator: Russell Y. Neches creator: Jenna M. Lang creator: Wendy E. Brown creator: Mark Severance creator: Darlene Cavalier creator: Jonathan A. Eisen uri: https://doi.org/10.7717/peerj.1842 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Coil et al. title: Lizard movement tracks: variation in path re-use behaviour is consistent with a scent-marking function link: https://peerj.com/articles/1844 last-modified: 2016-03-22 description: Individual movement influences the spatial and social structuring of a population. Animals regularly use the same paths to move efficiently to familiar places, or to patrol and mark home ranges. We found that Australian sleepy lizards (Tiliqua rugosa), a monogamous species with stable pair-bonds, repeatedly used the same paths within their home ranges and investigated whether path re-use functions as a scent-marking behaviour, or whether it is influenced by site familiarity. Lizards can leave scent trails on the substrate when moving through the environment and have a well-developed vomeronasal system to detect and respond to those scents. Path re-use would allow sleepy lizards to concentrate scent marks along these well-used trails, advertising their presence. Hypotheses of mate attraction and mating competition predict that sleepy lizard males, which experience greater intra-sexual competition, mark more strongly. Consistent with those hypotheses, males re-used their paths more than females, and lizards that showed pairing behaviour with individuals of the opposite sex re-used paths more than unpaired lizards, particularly among females. Hinterland marking is most economic when home ranges are large and mobility is low, as is the case in the sleepy lizard. Consistent with this strategy, re-used paths were predominantly located in the inner 50% home range areas. Together, our detailed movement analyses suggest that path re-use is a scent marking behaviour in the sleepy lizard. We also investigated but found less support for alternative explanations of path re-use behaviour, such as site familiarity and spatial knowledge. Lizards established the same number of paths, and used them as often, whether they had occupied their home ranges for one or for more years. We discuss our findings in relation to maintenance of the monogamous mating system of this species, and the spatial and social structuring of the population. creator: Stephan T. Leu creator: Grant Jackson creator: John F. Roddick creator: C. Michael Bull uri: https://doi.org/10.7717/peerj.1844 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Leu et al. title: Psychometric properties of the Greek TCI-R and its clinical correlates: schizotypy and the self-regulation of affective and cognitive functioning link: https://peerj.com/articles/1830 last-modified: 2016-03-22 description: Background. The revised Temperament and Character Inventory (TCI-R) measures Cloninger’s psychobiological model of personality. The average effects of individual temperament and character traits have been associated with schizotypy and with impaired regulation of affect and cognition. We extended prior research by testing predictions about the association of specific multidimensional configurations of temperament and character traits on schizotypy, affect balance, and self-perceived cognitive functioning.Method. A well-educated sample of native Greeks (N = 483), completed a new Greek translation of the TCI-R, as well as the Schizotypal Personality Questionnaire (SPQ), the Positive/Negative Affect Schedule (PANAS) and the Cognitive Failures Questionnaire (CFQ). The factor structure of the TCI-R was examined with exploratory and confirmatory tests. Associations between reported measures were examined with correlational and regression analyses.Results. The TCI-R had good psychometric properties as expected from studies in other countries. As predicted, specific configurations of temperament and character were associated with schizotypy, negative affect balance, and cognitive lapses. The “Borderline/Explosive temperament” (high Novelty Seeking, high Harm Avoidance, low Reward Dependence), “Schizotypal/Disorganized character” (low Self-directedness, low Cooperativeness, high Self-transcendence), and “Low Ego Strength/Fragile” profile (high Harm Avoidance, low Persistence, low Self-Directedness) were each strongly associated with higher stereotypy, negative affect balance (low positive affect and high negative affect), and subjective cognitive lapses compared to their contrast groups.Discussion. Multidimensional TCI profiles are strongly related to individual differences in schizotypy and self-reported regulation of affect and cognition. The Greek translation of the TCI-R is psychometrically sound and useful for clinical assessment and research. creator: Stella G. Giakoumaki creator: Leda Karagiannopoulou creator: Sándor Rózsa creator: Chrysoula Zouraraki creator: Penny Karamaouna creator: C. Robert Cloninger uri: https://doi.org/10.7717/peerj.1830 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Giakoumaki et al. title: Questions of time and affect: a person’s affectivity profile, time perspective, and well-being link: https://peerj.com/articles/1826 last-modified: 2016-03-22 description: Background. A “balanced” time perspective has been suggested to have a positive influence on well-being: a sentimental and positive view of the past (high Past Positive), a less pessimistic attitude toward the past (low Past Negative), the desire of experiencing pleasure with slight concern for future consequences (high Present Hedonistic), a less fatalistic and hopeless view of the future (low Present Fatalistic), and the ability to find reward in achieving specific long-term goals (high Future). We used the affective profiles model (i.e., combinations of individuals’ experience of high/low positive/negative affectivity) to investigate differences between individuals in time perspective dimensions and to investigate if the influence of time perspective dimensions on well-being was moderated by the individual’s type of profile.Method. Participants (N = 720) answered to the Positive Affect Negative Affect Schedule, the Zimbardo Time Perspective Inventory and two measures of well-being: the Temporal Satisfaction with Life Scale and Ryff’s Scales of Psychological Well-Being-short version. A Multivariate Analysis of Variance (MANOVA) was conducted to identify differences in time perspective dimensions and well-being among individuals with distinct affective profiles. Four structural equation models (SEM) were used to investigate which time perspective dimensions predicted well-being for individuals in each profile.Results. Comparisons between individuals at the extreme of the affective profiles model suggested that individuals with a self-fulfilling profile (high positive/low negative affect) were characterized by a “balanced” time perspective and higher well-being compared to individuals with a self-destructive profile (low positive/high negative affect). However, a different pattern emerged when individuals who differed in one affect dimension but matched in the other were compared to each other. For instance, decreases in the past negative time perspective dimension lead to high positive affect when negative affect is high (i.e., self-destructive vs. high affective) but to low negative affect when positive affect was high (i.e., high affective vs. self-fulfilling). The moderation analyses showed, for example, that for individuals with a self-destructive profile, psychological well-being was significantly predicted by the past negative, present fatalistic and future time perspectives. Among individuals with a high affective or a self-fulfilling profile, psychological well-being was significantly predicted by the present fatalistic dimension.Conclusions. The interactions found here go beyond the postulation of a “balanced” time perspective being the only way to promote well-being. Instead, we present a more person-centered approach to achieve higher levels of emotional, cognitive, and psychological well-being. creator: Danilo Garcia creator: Uta Sailer creator: Ali Al Nima creator: Trevor Archer uri: https://doi.org/10.7717/peerj.1826 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Garcia et al. title: No effect of low-level chronic neonicotinoid exposure on bumblebee learning and fecundity link: https://peerj.com/articles/1808 last-modified: 2016-03-22 description: In recent years, many pollinators have declined in abundance and diversity worldwide, presenting a potential threat to agricultural productivity, biodiversity and the functioning of natural ecosystems. One of the most debated factors proposed to be contributing to pollinator declines is exposure to pesticides, particularly neonicotinoids, a widely used class of systemic insecticide. Also, newly emerging parasites and diseases, thought to be spread via contact with managed honeybees, may pose threats to other pollinators such as bumblebees. Compared to honeybees, bumblebees could be particularly vulnerable to the effects of stressors due to their smaller and more short-lived colonies. Here, we studied the effect of field-realistic, chronic clothianidin exposure and inoculation with the parasite Nosema ceranae on survival, fecundity, sugar water collection and learning using queenless Bombus terrestris audax microcolonies in the laboratory. Chronic exposure to 1 ppb clothianidin had no significant effects on the traits studied. Interestingly, pesticide exposure in combination with additional stress caused by harnessing bees for Proboscis Extension Response (PER) learning assays, led to an increase in mortality. In contrast to previous findings, the bees did not become infected by N. ceranae after experimental inoculation with the parasite spores, suggesting variability in host resistance or parasite virulence. However, this treatment induced a slight, short-term reduction in sugar water collection, potentially through stimulation of the immune system of the bees. Our results suggest that chronic exposure to 1 ppb clothianidin does not have adverse effects on bumblebee fecundity or learning ability. creator: Saija Piiroinen creator: Cristina Botías creator: Elizabeth Nicholls creator: Dave Goulson uri: https://doi.org/10.7717/peerj.1808 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Piiroinen et al. title: Evaluation of transport conditions for autologous bone marrow-derived mesenchymal stromal cells for therapeutic application in horses link: https://peerj.com/articles/1773 last-modified: 2016-03-22 description: Background. Mesenchymal stromal cells (MSCs) are increasingly used for clinical applications in equine patients. For MSC isolation and expansion, a laboratory step is mandatory, after which the cells are sent back to the attending veterinarian. Preserving the biological properties of MSCs during this transport is paramount. The goal of the study was to compare transport-related parameters (transport container, media, temperature, time, cell concentration) that potentially influence characteristics of culture expanded equine MSCs.Methods. The study was arranged in three parts comparing (I) five different transport containers (cryotube, two types of plastic syringes, glass syringe, CellSeal), (II) seven different transport media, four temperatures (4 °C vs. room temperature; −20 °C vs. −80 °C), four time frames (24 h vs. 48 h; 48 h vs. 72 h), and (III) three MSC concentrations (5 × 106, 10 × 106, 20 × 106 MSC/ml). Cell viability (Trypan Blue exclusion; percent and total number viable cell), proliferation and trilineage differentiation capacity were assessed for each test condition. Further, the recovered volume of the suspension was determined in part I. Each condition was evaluated using samples of six horses (n = 6) and differentiation protocols were performed in duplicates.Results. In part I of the study, no significant differences in any of the parameters were found when comparing transport containers at room temperature. The glass syringe was selected for all subsequent evaluations (highest recoverable volume of cell suspension and cell viability). In part II, media, temperatures, or time frames had also no significant influence on cell viability, likely due to the large number of comparisons and small sample size. Highest cell viability was observed using autologous bone marrow supernatant as transport medium, and “transport” at 4 °C for 24 h (70.6% vs. control group 75.3%); this was not significant. Contrary, viability was unacceptably low (<40%) for all freezing protocols at −20 °C or −80 °C, particularly with bone marrow supernatant or plasma and DMSO. In part III, various cell concentrations also had no significant influence on any of the evaluated parameters. Chondrogenic differentiation showed a trend towards being decreased for all transport conditions, compared to control cells.Discussion. In this study, transport conditions were not found to impact viability, proliferation or ability for trilineage differentiation of MSCs, most likely due to the small sample size and large number of comparisons. The unusual low viability after all freezing protocols is in contrast to previous equine studies. Potential causes are differences in the freezing, but also in thawing method. Also, the selected container (glass syringe) may have impacted viability. Future research may be warranted into the possibly negative effect of transport on chondrogenic differentiation. creator: Miguel Espina creator: Henriette Jülke creator: Walter Brehm creator: Iris Ribitsch creator: Karsten Winter creator: Uta Delling uri: https://doi.org/10.7717/peerj.1773 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Espina et al. title: Consumer-grade EEG devices: are they usable for control tasks? link: https://peerj.com/articles/1746 last-modified: 2016-03-22 description: We present the evaluation of two well-known, low-cost consumer-grade EEG devices: the Emotiv EPOC and the Neurosky MindWave. Problems with using the consumer-grade EEG devices (BCI illiteracy, poor technical characteristics, and adverse EEG artefacts) are discussed. The experimental evaluation of the devices, performed with 10 subjects asked to perform concentration/relaxation and blinking recognition tasks, is given. The results of statistical analysis show that both devices exhibit high variability and non-normality of attention and meditation data, which makes each of them difficult to use as an input to control tasks. BCI illiteracy may be a significant problem, as well as setting up of the proper environment of the experiment. The results of blinking recognition show that using the Neurosky device means recognition accuracy is less than 50%, while the Emotiv device has achieved a recognition accuracy of more than 75%; for tasks that require concentration and relaxation of subjects, the Emotiv EPOC device has performed better (as measured by the recognition accuracy) by ∼9%. Therefore, the Emotiv EPOC device may be more suitable for control tasks using the attention/meditation level or eye blinking than the Neurosky MindWave device. creator: Rytis Maskeliunas creator: Robertas Damasevicius creator: Ignas Martisius creator: Mindaugas Vasiljevas uri: https://doi.org/10.7717/peerj.1746 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Maskeliunas et al. title: Evaluation of putative reference genes for quantitative real-time PCR normalization in Lilium regale during development and under stress link: https://peerj.com/articles/1837 last-modified: 2016-03-21 description: Normalization to reference genes is the most common method to avoid bias in real-time quantitative PCR (qPCR), which has been widely used for quantification of gene expression. Despite several studies on gene expression, Lilium, and particularly L. regale, has not been fully investigated regarding the evaluation of reference genes suitable for normalization. In this study, nine putative reference genes, namely 18S rRNA, ACT, BHLH, CLA, CYP, EF1, GAPDH, SAND and TIP41, were analyzed for accurate quantitative PCR normalization at different developmental stages and under different stress conditions, including biotic (Botrytis elliptica), drought, salinity, cold and heat stress. All these genes showed a wide variation in their Cq (quantification Cycle) values, and their stabilities were calculated by geNorm, NormFinder and BestKeeper. In a combination of the results from the three algorithms, BHLH was superior to the other candidates when all the experimental treatments were analyzed together; CLA and EF1 were also recommended by two of the three algorithms. As for specific conditions, EF1 under various developmental stages, SAND under biotic stress, CYP/GAPDH under drought stress, and TIP41 under salinity stress were generally considered suitable. All the algorithms agreed on the stability of SAND and GAPDH under cold stress, while only CYP was selected under heat stress by all of them. Additionally, the selection of optimal reference genes under biotic stress was further verified by analyzing the expression level of LrLOX in leaves inoculated with B. elliptica. Our study would be beneficial for future studies on gene expression and molecular breeding of Lilium. creator: Qiang Liu creator: Chi Wei creator: Ming-Fang Zhang creator: Gui-Xia Jia uri: https://doi.org/10.7717/peerj.1837 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Liu et al. title: GPR18 undergoes a high degree of constitutive trafficking but is unresponsive to N-Arachidonoyl Glycine link: https://peerj.com/articles/1835 last-modified: 2016-03-21 description: The orphan receptor GPR18 has become a research target following the discovery of a putative endogenous agonist, N-arachidonoyl glycine (NAGly). Chemical similarity between NAGly and the endocannabinoid anandamide suggested the hypothesis that GPR18 is a third cannabinoid receptor. GPR18-mediated cellular signalling through inhibition of cyclic adenosine monophosphate (cAMP) and phosphorylation of extracellular signal-regulated kinase (ERK), in addition to physiological consequences such as regulation of cellular migration and proliferation/apoptosis have been described in response to both NAGly and anandamide. However, discordant findings have also been reported. Here we sought to describe the functional consequences of GPR18 activation in heterologously-expressing HEK cells. GPR18 expression was predominantly intracellular in stably transfected cell lines, but moderate cell surface expression could be achieved in transiently transfected cells which also had higher overall expression. Assays were employed to characterise the ability of NAGly or anandamide to inhibit cAMP or induce ERK phosphorylation through GPR18, or induce receptor trafficking. Positive control experiments, which utilised cells expressing hCB1 receptors (hCB1R), were performed to validate assay design and performance. While these functional pathways in GPR18-expressing cells were not modified on treatment with a panel of putative GPR18 ligands, a constitutive phenotype was discovered for this receptor. Our data reveal that GPR18 undergoes rapid constitutive receptor membrane trafficking—several-fold faster than hCB1R, a highly constitutively active receptor. To enhance the likelihood of detecting agonist-mediated receptor signalling responses, we increased GPR18 protein expression (by tagging with a preprolactin signal sequence) and generated a putative constitutively inactive receptor by mutating the hGPR18 gene at amino acid site 108 (alanine to asparagine). This A108N mutant did cause an increase in surface receptor expression (which may argue for reduced constitutive activity), but no ligand-mediated effects were detected. Two glioblastoma multiforme cell lines (which endogenously express GPR18) were assayed for NAGly-induced pERK phosphorylation, with negative results. Despite a lack of ligand-mediated responses in all assays, the constitutive trafficking of GPR18 remains an interesting facet of receptor function and will have consequences for understanding the role of GPR18 in physiology. creator: David B. Finlay creator: Wayne R. Joseph creator: Natasha L. Grimsey creator: Michelle Glass uri: https://doi.org/10.7717/peerj.1835 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Finlay et al. title: Distribution and regulation of gonadotropin-releasing hormone, kisspeptin, RF-amide related peptide-3, and dynorphin in the bovine hypothalamus link: https://peerj.com/articles/1833 last-modified: 2016-03-21 description: Recent work has led to the hypothesis that kisspeptin/neurokinin B/dynorphin (KNDy) neurons in the arcuate nucleus (ARC) play a key role in gonadotropin-releasing hormone (GnRH) pulse generation and gonadal steroid feedback, with kisspeptin driving GnRH release and neurokinin B and dynorphin acting as pulse start and stop signals, respectively. A separate cell group, expressing RFamide-related peptide-3 (RFRP-3) has been shown to be a primary inhibitor of GnRH release. Very little is known regarding these cell groups in the bovine. In this study, we examined the relative immunoreactivity of kisspeptin, dynorphin, and RFRP-3 and their possible connectivity to GnRH neurons in the hypothalami of periestrus and diestrus bovine. While GnRH and RFRP-3 immunoreactivity were unchanged, kisspeptin and dynorphin immunoreactivity levels varied in relation to plasma progesterone concentrations and estrous status. Animals with higher plasma progesterone concentrations in diestrus had lower kisspeptin and increased dynorphin immunoreactivity in the ARC. The percentage of GnRH cells with kisspeptin or RFRP-3 fibers in close apposition did not differ between estrous stages. However, the proportions of GnRH cells with kisspeptin or RFRP-3 contacts (∼49.8% and ∼31.3%, respectively) suggest direct communication between kisspeptin and RFRP-3 cells to GnRH cells in the bovine. The data produced in this work support roles for kisspeptin and dynorphin, within the KNDy neural network, in controlling GnRH release over the ovarian cycle and conveying progesterone-negative feedback onto GnRH neurons in the bovine. creator: Valeria M. Tanco creator: Brian K. Whitlock creator: Melaney A. Jones creator: Robyn R. Wilborn creator: Terry D. Brandebourg creator: Chad D. Foradori uri: https://doi.org/10.7717/peerj.1833 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tanco et al. title: Comparative analysis of different survey methods for monitoring fish assemblages in coastal habitats link: https://peerj.com/articles/1832 last-modified: 2016-03-21 description: Coastal ecosystems are among the most productive yet increasingly threatened marine ecosystems worldwide. Particularly vegetated habitats, such as eelgrass (Zostera marina) beds, play important roles in providing key spawning, nursery and foraging habitats for a wide range of fauna. To properly assess changes in coastal ecosystems and manage these critical habitats, it is essential to develop sound monitoring programs for foundation species and associated assemblages. Several survey methods exist, thus understanding how different methods perform is important for survey selection. We compared two common methods for surveying macrofaunal assemblages: beach seine netting and underwater visual census (UVC). We also tested whether assemblages in shallow nearshore habitats commonly sampled by beach seines are similar to those of nearby eelgrass beds often sampled by UVC. Among five estuaries along the Southern Gulf of St. Lawrence, Canada, our results suggest that the two survey methods yield comparable results for species richness, diversity and evenness, yet beach seines yield significantly higher abundance and different species composition. However, sampling nearshore assemblages does not represent those in eelgrass beds despite considerable overlap and close proximity. These results have important implications for how and where macrofaunal assemblages are monitored in coastal ecosystems. Ideally, multiple survey methods and locations should be combined to complement each other in assessing the entire assemblage and full range of changes in coastal ecosystems, thereby better informing coastal zone management. creator: Duncan G.L. Baker creator: Tyler D. Eddy creator: Reba McIver creator: Allison L. Schmidt creator: Marie-Hélène Thériault creator: Monica Boudreau creator: Simon C. Courtenay creator: Heike K. Lotze uri: https://doi.org/10.7717/peerj.1832 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baker et al. title: Evaluation of unmanned aerial vehicle shape, flight path and camera type for waterfowl surveys: disturbance effects and species recognition link: https://peerj.com/articles/1831 last-modified: 2016-03-21 description: The use of unmanned aerial vehicles (UAVs) for ecological research has grown rapidly in recent years, but few studies have assessed the disturbance impacts of these tools on focal subjects, particularly when observing easily disturbed species such as waterfowl. In this study we assessed the level of disturbance that a range of UAV shapes and sizes had on free-living, non-breeding waterfowl surveyed in two sites in eastern Australia between March and May 2015, as well as the capability of airborne digital imaging systems to provide adequate resolution for unambiguous species identification of these taxa. We found little or no obvious disturbance effects on wild, mixed-species flocks of waterfowl when UAVs were flown at least 60m above the water level (fixed wing models) or 40m above individuals (multirotor models). Disturbance in the form of swimming away from the UAV through to leaving the water surface and flying away from the UAV was visible at lower altitudes and when fixed-wing UAVs either approached subjects directly or rapidly changed altitude and/or direction near animals. Using tangential approach flight paths that did not cause disturbance, commercially available onboard optical equipment was able to capture images of sufficient quality to identify waterfowl and even much smaller taxa such as swallows. Our results show that with proper planning of take-off and landing sites, flight paths and careful UAV model selection, UAVs can provide an excellent tool for accurately surveying wild waterfowl populations and provide archival data with fewer logistical issues than traditional methods such as manned aerial surveys. creator: John F. McEvoy creator: Graham P. Hall creator: Paul G. McDonald uri: https://doi.org/10.7717/peerj.1831 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 McEvoy et al. title: Angiosperms and the Linnean shortfall: three new species from three lineages of Melastomataceae at one spot at the Atlantic Forest link: https://peerj.com/articles/1824 last-modified: 2016-03-21 description: Three new species of Angiosperms have been found in four short collection trips to the same protected reserve—“Estação Ecológica Estadual de Wenceslau Guimarães”—and neighboring areas in the Atlantic Forest in the south of the Brazilian state of Bahia. These new species belong to three genera from three distinct lineages in the family Melastomataceae: Huberia, Meriania and Physeterostemon. The description of these species represent a good example of a Linnean shortfall, i.e., the absence of basic knowledge about the biodiversity in the area, as well as in tropical forests as a whole. The description of these probably endemic species per se is a signal that this area deserves more attention regarding research and policies, but its consequences go farther: this area has a relevant role as a phylogenetic (both genetic and morphological) stock, and thus is also valuable as a phylogenetic conservation priority. creator: Renato Goldenberg creator: Fabián A. Michelangeli creator: Lidyanne Y.S. Aona creator: André M. Amorim uri: https://doi.org/10.7717/peerj.1824 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Goldenberg et al. title: Adaptation prevents the extinction of Chlamydomonas reinhardtii under toxic beryllium link: https://peerj.com/articles/1823 last-modified: 2016-03-21 description: The current biodiversity crisis represents a historic challenge for natural communities: the environmental rate of change exceeds the population’s adaptation capability. Integrating both ecological and evolutionary responses is necessary to make reliable predictions regarding the loss of biodiversity. The race against extinction from an eco-evolutionary perspective is gaining importance in ecological risk assessment. Here, we performed a classical study of population dynamics—a fluctuation analysis—and evaluated the results from an adaption perspective. Fluctuation analysis, widely used with microorganisms, is an effective empirical procedure to study adaptation under strong selective pressure because it incorporates the factors that influence demographic, genetic and environmental changes. The adaptation of phytoplankton to beryllium (Be) is of interest because human activities are increasing the concentration of Be in freshwater reserves; therefore, predicting the effects of human-induced pollutants is necessary for proper risk assessment. The fluctuation analysis was performed with phytoplankton, specifically, the freshwater microalgae Chlamydomonas reinhardtii, under acute Be exposure. High doses of Be led to massive microalgae death; however, by conducting a fluctuation analysis experiment, we found that C. reinhardtii was able to adapt to 33 mg/l of Be due to pre-existing genetic variability. The rescuing adapting genotype presented a mutation rate of 9.61 × 10−6 and a frequency of 10.42 resistant cells per million wild-type cells. The genetic adaptation pathway that was experimentally obtained agreed with the theoretical models of evolutionary rescue (ER). Furthermore, the rescuing genotype presented phenotypic and physiologic differences from the wild-type genotype, was 25% smaller than the Be-resistant genotype and presented a lower fitness and quantum yield performance. The abrupt distinctions between the wild-type and the Be-resistant genotype suggest a pleiotropic effect mediated by an advantageous mutation; however, no sequencing confirmation was performed. creator: Beatriz Baselga-Cervera creator: Eduardo Costas creator: Estéfano Bustillo-Avendaño creator: Camino García-Balboa uri: https://doi.org/10.7717/peerj.1823 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baselga-Cervera et al. title: An integrated text mining framework for metabolic interaction network reconstruction link: https://peerj.com/articles/1811 last-modified: 2016-03-21 description: Text mining (TM) in the field of biology is fast becoming a routine analysis for the extraction and curation of biological entities (e.g., genes, proteins, simple chemicals) as well as their relationships. Due to the wide applicability of TM in situations involving complex relationships, it is valuable to apply TM to the extraction of metabolic interactions (i.e., enzyme and metabolite interactions) through metabolic events. Here we present an integrated TM framework containing two modules for the extraction of metabolic events (Metabolic Event Extraction module—MEE) and for the construction of a metabolic interaction network (Metabolic Interaction Network Reconstruction module—MINR). The proposed integrated TM framework performed well based on standard measures of recall, precision and F-score. Evaluation of the MEE module using the constructed Metabolic Entities (ME) corpus yielded F-scores of 59.15% and 48.59% for the detection of metabolic events for production and consumption, respectively. As for the testing of the entity tagger for Gene and Protein (GP) and metabolite with the test corpus, the obtained F-score was greater than 80% for the Superpathway of leucine, valine, and isoleucine biosynthesis. Mapping of enzyme and metabolite interactions through network reconstruction showed a fair performance for the MINR module on the test corpus with F-score >70%. Finally, an application of our integrated TM framework on a big-scale data (i.e., EcoCyc extraction data) for reconstructing a metabolic interaction network showed reasonable precisions at 69.93%, 70.63% and 46.71% for enzyme, metabolite and enzyme–metabolite interaction, respectively. This study presents the first open-source integrated TM framework for reconstructing a metabolic interaction network. This framework can be a powerful tool that helps biologists to extract metabolic events for further reconstruction of a metabolic interaction network. The ME corpus, test corpus, source code, and virtual machine image with pre-configured software are available at www.sbi.kmutt.ac.th/ preecha/metrecon. creator: Preecha Patumcharoenpol creator: Narumol Doungpan creator: Asawin Meechai creator: Bairong Shen creator: Jonathan H. Chan creator: Wanwipa Vongsangnak uri: https://doi.org/10.7717/peerj.1811 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Patumcharoenpol et al. title: The effects of an invasive seaweed on native communities vary along a gradient of land-based human impacts link: https://peerj.com/articles/1795 last-modified: 2016-03-21 description: The difficulty in teasing apart the effects of biological invasions from those of other anthropogenic perturbations has hampered our understanding of the mechanisms underpinning the global biodiversity crisis. The recent elaboration of global-scale maps of cumulative human impacts provides a unique opportunity to assess how the impact of invaders varies among areas exposed to different anthropogenic activities. A recent meta-analysis has shown that the effects of invasive seaweeds on native biota tend to be more negative in relatively pristine than in human-impacted environments. Here, we tested this hypothesis through the experimental removal of the invasive green seaweed, Caulerpa cylindracea, from rocky reefs across the Mediterranean Sea. More specifically, we assessed which out of land-based and sea-based cumulative impact scores was a better predictor of the direction and magnitude of the effects of this seaweed on extant and recovering native assemblages. Approximately 15 months after the start of the experiment, the removal of C. cylindracea from extant assemblages enhanced the cover of canopy-forming macroalgae at relatively pristine sites. This did not, however, result in major changes in total cover or species richness of native assemblages. Preventing C. cylindracea re-invasion of cleared plots at pristine sites promoted the recovery of canopy-forming and encrusting macroalgae and hampered that of algal turfs, ultimately resulting in increased species richness. These effects weakened progressively with increasing levels of land-based human impacts and, indeed, shifted in sign at the upper end of the gradient investigated. Thus, at sites exposed to intense disturbance from land-based human activities, the removal of C. cylindracea fostered the cover of algal turfs and decreased that of encrusting algae, with no net effect on species richness. Our results suggests that competition from C. cylindracea is an important determinant of benthic assemblage diversity in pristine environments, but less so in species-poor assemblages found at sites exposed to intense disturbance from land-based human activities, where either adverse physical factors or lack of propagules may constrain the number of potential native colonizers. Implementing measures to reduce the establishment and spread of C. cylindracea in areas little impacted by land-based human activities should be considered a priority for preserving the biodiversity of Mediterranean shallow rocky reefs. creator: Fabio Bulleri creator: Fabio Badalamenti creator: Ljiljana Iveša creator: Barbara Mikac creator: Luigi Musco creator: Andrej Jaklin creator: Alex Rattray creator: Tomás Vega Fernández creator: Lisandro Benedetti-Cecchi uri: https://doi.org/10.7717/peerj.1795 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bulleri et al. title: Origin and evolution of GATA2a and GATA2b in teleosts: insights from tongue sole, Cynoglossus semilaevis link: https://peerj.com/articles/1790 last-modified: 2016-03-21 description: Background. Following the two rounds of whole-genome duplication that occurred during deuterostome evolution, a third genome duplication occurred in the lineage of teleost fish and is considered to be responsible for much of the biological diversification within the lineage. GATA2, a member of GATA family of transcription factors, is an important regulator of gene expression in hematopoietic cell in mammals, yet the role of this gene or its putative paralogs in ray-finned fishes remains relatively unknown.Methods. In this study, we attempted to identify GATA2 sequences from the transcriptomes and genomes of multiple teleosts using the bioinformatic tools MrBayes, MEME, and PAML. Following identification, comparative analysis of genome structure, molecular evolution rate, and expression by real-time qPCR were used to predict functional divergence of GATA2 paralogs and their relative transcription in organs of female and male tongue soles (Cynoglossus semilaevis).Results. Two teleost GATA2 genes were identified in the transcriptomes of tongue sole and Japanese flounder (Paralichthysolivaceus). Synteny and phylogenetic analysis confirmed that the two genes likely originated from the teleost-specific genome duplication . Additionally, selection pressure analysis predicted these gene duplicates to have undergone purifying selection and possible divergent new functions. This was supported by differential expression pattern of GATA2a and GATA2b observed in organs of female and male tongue soles.Discussion. Our results indicate that two GATA2 genes originating from the first teleost-specific genome duplication have remained transcriptionally active in some fish species and have likely undergone neofunctionalization. This knowledge provides novel insights into the evolution of the teleost GATA2 genes and constituted important groundwork for further research on the GATA gene family. creator: Jinxiang Liu creator: Jiajun Jiang creator: Zhongkai Wang creator: Yan He creator: Quanqi Zhang uri: https://doi.org/10.7717/peerj.1790 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liu et al. title: Facial width-to-height ratio relates to dominance style in the genus Macaca link: https://peerj.com/articles/1775 last-modified: 2016-03-21 description: Background. Physical, visual, chemical, and auditory cues signalling fighting ability have independently evolved in many animal taxa as a means to resolve conflicts without escalating to physical aggression. Facial width-to-height ratio (fWHR, i.e., the relative width to height of the face) has been associated with dominance-related phenotypes both in humans and in other primates. In humans, faces with a larger fWHR are perceived as more aggressive.Methods. We examined fWHR variation among 11 species of the genus Macaca. Macaques have been grouped into four distinct categories, from despotic to tolerant, based on their female dominance style. Female dominance style is related to intra- and inter-sexual competition in both males and females and is the result of different evolutionary pressure across species. We used female dominance style as a proxy of intra-/inter-sexual competition to test the occurrence of correlated evolution between competitive regimes and dominance-related phenotypes. fWHR was calculated from 145 2D photographs of male and female adult macaques.Results. We found no phylogenetic signal on the differences in fWHR across species in the two sexes. However, fWHR was greater, in females and males, in species characterised by despotic female dominance style than in tolerant species.Discussion. Our results suggest that dominance-related phenotypes are related to differences in competitive regimes and intensity of inter- and intra-sexual selection across species. creator: Marta Borgi creator: Bonaventura Majolo uri: https://doi.org/10.7717/peerj.1775 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Borgi and Majolo title: French validation of the Barcelona Music Reward Questionnaire link: https://peerj.com/articles/1760 last-modified: 2016-03-21 description: Background. The Barcelona Music Reward Questionnaire (BMRQ) questionnaire investigates the main facets of music experience that could explain the variance observed in how people experience reward associated with music. Currently, only English and Spanish versions of this questionnaire are available. The objective of this study is to validate a French version of the BMRQ.Methods. The original BMRQ was translated and adapted into an international French version. The questionnaire was then administered through an online survey aimed at adults aged over 18 years who were fluent in French. Statistical analyses were performed and compared to the original English and Spanish version for validation purposes.Results. A total of 1,027 participants completed the questionnaire. Most responses were obtained from France (89.4%). Analyses revealed that congruence values between the rotated loading matrix and the ideal loading matrix ranged between 0.88 and 0.96. Factor reliabilities of subscales (i.e., Musical Seeking, Emotion Evocation, Mood Regulation, Social Reward and Sensory-Motor) also ranged between 0.88 and 0.96. In addition, reliability of the overall factor score (i.e., Music reward) was 0.91. Finally, the internal consistency of the overall scale was 0.85. The factorial structure obtained in the French translation was similar to that of the original Spanish and English samples.Conclusion. The French version of the BMRQ appears valid and reliable. Potential applications of the BMRQ include its use as a valuable tool in music reward and emotion research, whether in healthy individuals or in patients suffering from a wide variety of cognitive, neurologic and auditory disorders. creator: Joe Saliba creator: Urbano Lorenzo-Seva creator: Josep Marco-Pallares creator: Barbara Tillmann creator: Anthony Zeitouni creator: Alexandre Lehmann uri: https://doi.org/10.7717/peerj.1760 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Saliba et al. title: Simulation of potential habitat overlap between red deer (Cervus elaphus) and roe deer (Capreolus capreolus) in northeastern China link: https://peerj.com/articles/1756 last-modified: 2016-03-21 description: Background. Understanding species distribution, especially areas of overlapping habitat between sympatric species, is essential for informing conservation through natural habitat protection. New protection strategies should simultaneously consider conservation efforts for multiple species that exist within the same landscape, which requires studies that include habitat overlap analysis.Methods. We estimated the potential habitat of cervids, which are typical ungulates in northern China, using the present locations of red deer (Cervus elaphus; N = 90) and roe deer (Capreolus capreolus; N = 106) in a Maximum Entropy (MaxEnt) model. Our study area was a human-dominated landscape in the Tieli Forestry Bureau located at the southern slope of the Lesser Xing’an Mountains. We grouped 17 environmental predictor variables into five predictor classes (terrain, habitat accessibility, land cover, vegetation feature, and interference), which were used to build habitat suitability models.Results. Habitat accessibility and human interferences were found to have the strongest influence on habitat suitability among the five variable classes. Among the environmental factors, distance to farmland (26.8%), distance to bush-grass land (14.6%), elevation (13.5%), and distance to water source (12.2%) were most important for red deer, distance to farmland (22.9%), distance to settlement (21.4%), elevation (11.6%), and coverage of shrub-grass (8%) were most important for roe deer. Model accuracy was high for both species (mean area under the curve (AUC) = 0.936 for red deer and 0.924 for roe deer). The overlapping habitat comprised 89.93 km2 within the study area, which occupied 94% of potentially suitable habitat for red deer and 27% for roe deer.Conclusions. In terms of habitat suitability, roe deer showed greater selectivity than red deer. The overlapping habitat was mostly located in the eastern mountains. The southwestern plain was not a suitable habitat for deer because it was close to Tieli City. Regarding management measures, we suggest that priority protection should be given to the potential areas of overlapping deer habitats found in this study. creator: Wen Wu creator: Yuehui Li creator: Yuanman Hu uri: https://doi.org/10.7717/peerj.1756 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wu et al. title: Changes in pigment, spectral transmission and element content of pink chicken eggshells with different pigment intensity during incubation link: https://peerj.com/articles/1825 last-modified: 2016-03-17 description: Objective. The objective of this study was to investigate changes in pigment, spectral transmission and element content of chicken eggshells with different intensities of pink pigment during the incubation period. We also investigated the effects of the region (small pole, equator and large pole) and pink pigment intensity of the chicken eggshell on the percent transmission of light passing through the chicken eggshells.Method. Eggs of comparable weight from a meat-type breeder (Meihuang) were used, and divided based on three levels of pink pigment (light, medium and dark) in the eggshells. During the incubation (0–21 d), the values of the eggshell pigment (ΔE, L∗, a∗, b∗) were measured. The percent transmission of light for different regions and intensities of eggshell pigmentation was measured by using the visible wavelength range of 380–780 nm.Result. Three measured indicators of eggshell color, ΔE, L∗ and a∗, did not change significantly during incubation. Compared with other regions and pigment intensities, eggshell at the small pole and with light pigmentation intensity showed the highest percent transmission of light. The transmission value varied significantly (P < 0.001) with incubation time. The element analysis of eggshells with different levels of pink pigment showed that the potassium content of the eggshells for all pigment levels decreased significantly during incubation.Conclusion. In summary, pigment intensity and the region of the eggshell influenced the percent transmission of light of eggshell. Differences in the spectral characteristics of different eggshells may influence the effects of photostimulation during the incubation of eggs. All of these results will be applicable for perfecting the design of light intensity for lighted incubation to improve productivity. creator: Yue Yu creator: Zhanming Li creator: Jinming Pan uri: https://doi.org/10.7717/peerj.1825 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yu et al. title: Sponge distribution and the presence of photosymbionts in Moorea, French Polynesia link: https://peerj.com/articles/1816 last-modified: 2016-03-17 description: Photosymbionts play an important role in the ecology and evolution of diverse host species within the marine environment. Although sponge-photosymbiont interactions have been well described from geographically disparate sites worldwide, our understanding of these interactions from shallow water systems within French Polynesia is limited. We surveyed diverse habitats around the north coast of Moorea, French Polynesia and screened sponges for the presence of photosymbionts. Overall sponge abundance and diversity were low, with <1% cover and only eight putative species identified by 28S barcoding from surveys at 21 sites. Of these eight species, seven were found predominately in shaded or semi-cryptic habitats under overhangs or within caverns. Lendenfeldia chondrodes was the only species that supported a high abundance of photosymbionts and was also the only species found in exposed, illuminated habitats. Interestingly, L. chondrodes was found at three distinct sites, with a massive, fan-shaped growth form at two of the lagoon sites and a thin, encrusting growth form within a bay site. These two growth forms differed in their photosymbiont abundance, with massive individuals of L. chondrodes having higher photosymbiont abundance than encrusting individuals from the bay. We present evidence that some sponges from French Polynesia support abundant photosymbiont communities and provide initial support for the role of these communities in host ecology. creator: Christopher J. Freeman creator: Cole G. Easson uri: https://doi.org/10.7717/peerj.1816 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Freeman and Easson title: Microphytoplankton variations during coral spawning at Los Roques, Southern Caribbean link: https://peerj.com/articles/1747 last-modified: 2016-03-17 description: Phytoplankton drives primary productivity in marine pelagic systems. This is also true for the oligotrophic waters in coral reefs, where natural and anthropogenic sources of nutrients can alter pelagic trophic webs. In this study, microphytoplankton assemblages were characterized for the first time in relation to expected coral spawning dates in the Caribbean. A hierarchical experimental design was used to examine these assemblages in Los Roques archipelago, Venezuela, at various temporal and spatial scales for spawning events in both 2007 and 2008. At four reefs, superficial water samples were taken daily for 9 days after the full moon of August, including days before, during and after the expected days of coral spawning. Microphytoplankton assemblages comprised 100 microalgae taxa at up to 50 cells per mL (mean ± 8 SD) and showed temporal and spatial variations related to the coral spawning only in 2007. However, chlorophyll a concentrations increased during and after the spawning events in both years, and this was better matched with analyses of higher taxonomical groups (diatoms, cyanophytes and dinoflagellates), that also varied in relation to spawning times in 2007 and 2008, but asynchronously among reefs. Heterotrophic and mixotrophic dinoflagellates increased in abundance, correlating with a decrease of the diatom Cerataulina pelagica and an increase of the diatom Rhizosolenia imbricata. These variations occurred during and after the coral spawning event for some reefs in 2007. For the first time, a fresh-water cyanobacteria species of Anabaena was ephemerally found (only 3 days) in the archipelago, at reefs closest to human settlements. Variability among reefs in relation to spawning times indicated that reef-specific processes such as water residence time, re-mineralization rates, and benthic-pelagic coupling can be relevant to the observed patterns. These results suggest an important role of microheterotrophic grazers in re-mineralization of organic matter in coral reef waters and highlight the importance of assessing compositional changes of larger size fractions of the phytoplankton when evaluating primary productivity and nutrient fluxes. creator: Francoise Cavada-Blanco creator: Ainhoa L. Zubillaga creator: Carolina Bastidas uri: https://doi.org/10.7717/peerj.1747 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cavada-Blanco et al. title: NeisseriaBase: a specialised Neisseria genomic resource and analysis platform link: https://peerj.com/articles/1698 last-modified: 2016-03-17 description: Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species.Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages.Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains.Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. creator: Wenning Zheng creator: Naresh V.R. Mutha creator: Hamed Heydari creator: Avirup Dutta creator: Cheuk Chuen Siow creator: Nicholas S. Jakubovics creator: Wei Yee Wee creator: Shi Yang Tan creator: Mia Yang Ang creator: Guat Jah Wong creator: Siew Woh Choo uri: https://doi.org/10.7717/peerj.1698 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zheng et al. title: Mechanism of action of novel piperazine containing a toxicant against human liver cancer cells link: https://peerj.com/articles/1588 last-modified: 2016-03-17 description: The purpose of this study was to assess the cytotoxic potential of a novel piperazine derivative (PCC) against human liver cancer cells. SNU-475 and 423 human liver cancer cell lines were used to determine the IC50 of PCC using the standard MTT assay. PCC displayed a strong suppressive effect on liver cancer cells with an IC50 value of 6.98 ± 0.11 µM and 7.76 ± 0.45 µM against SNU-475 and SNU-423 respectively after 24 h of treatment. Significant dipping in the mitochondrial membrane potential and elevation in the released of cytochrome c from the mitochondria indicated the induction of the intrinsic apoptosis pathway by PCC. Activation of this pathway was further evidenced by significant activation of caspase 3/7 and 9. PCC was also shown to activate the extrinsic pathways of apoptosis via activation of caspase-8 which is linked to the suppression of NF-κB translocation to the nucleus. Cell cycle arrest in the G1 phase was confirmed by flow cytometry and up-regulation of glutathione reductase expression was quantified by qPCR. Results of this study suggest that PCC is a potent anti-cancer agent inducing both intrinsic and extrinsic pathways of apoptosis in liver cancer cell lines. creator: Nima Samie creator: Sekaran Muniandy creator: MS Kanthimathi creator: Batoul Sadat Haerian uri: https://doi.org/10.7717/peerj.1588 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Samie et al. title: Functional assessment of chronic illness therapy—the fatigue scale exhibits stronger associations with clinical parameters in chronic dialysis patients compared to other fatigue-assessing instruments link: https://peerj.com/articles/1818 last-modified: 2016-03-15 description: Background. Patients with end-stage renal disease (ESRD) have a high symptom burden, among which fatigue is highly prevalent. Many fatigue-assessing instruments exist, but comparisons among instruments in this patient population have yet to be investigated.Methods. ESRD patients under chronic hemodialysis were prospectively enrolled and seven types of fatigue instruments were administered: Brief Fatigue Inventory (BFI), Functional Assessment of Chronic Illness Therapy–Fatigue (FACIT-F), Fatigue Severity Scale (FSS), Lee Fatigue Scale (LFS), Fatigue Questionnaire (FQ), Fatigue Symptom Inventory (FSI), and Short-Form 36-Vitality (SF36-V). Using these instruments, we investigated the correlation between fatigue severity and clinical/biochemical parameters, including demographic/comorbidity profile, dialysis-related complications, and frailty severity. We used regression analysis with serum albumin and frailty severity as the dependent variables to investigate the independent correlations.Results. A total of 46 ESRD patients were enrolled (average age of 67 ± 11.6 years), and 50% of them had type 2 diabetes mellitus. Results from the seven tested instruments showed high correlation with each other. We found that the fatigue severity by FACIT-F was significantly associated with age (p = 0.03), serum albumin (p = 0.003) and creatinine (p = 0.02) levels, while SF36-V scores were also significantly associated with age (p = 0.02) and serum creatinine levels (p = 0.04). However, the fatigue severity measured by the FSS, FSI, FQ, BFI, and LFS did not exhibit these associations. Moreover, regression analysis showed that only FACIT-F scores were independently associated with serum albumin levels and frailty severity in ESRD patients.Conclusion. Among the seven fatigue-assessing instruments, only the FACIT-F yielded results that demonstrated significant and independent associations with important outcome-related features in ESRD patients. creator: Chia-Ter Chao creator: Jenq-Wen Huang creator: Chih-Kang Chiang uri: https://doi.org/10.7717/peerj.1818 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chao et al. title: Movement, demographics, and occupancy dynamics of a federally-threatened salamander: evaluating the adequacy of critical habitat link: https://peerj.com/articles/1817 last-modified: 2016-03-15 description: Critical habitat for many species is often limited to occupied localities. For rare and cryptic species, or those lacking sufficient data, occupied habitats may go unrecognized, potentially hindering species recovery. Proposed critical habitat for the aquatic Jollyville Plateau salamander (Eurycea tonkawae) and two sister species were delineated based on the assumption that surface habitat is restricted to springs and excludes intervening stream reaches. To test this assumption, we performed two studies to understand aspects of individual, population, and metapopulation ecology of E. tonkawae. First, we examined movement and population demographics using capture-recapture along a spring-influenced stream reach. We then extended our investigation of stream habitat use with a study of occupancy and habitat dynamics in multiple headwater streams. Indications of extensive stream channel use based on capture-recapture results included frequent movements of >15 m, and high juvenile abundance downstream of the spring. Initial occupancy of E. tonkawae was associated with shallow depths, maidenhair fern presence and low temperature variation (indicative of groundwater influence), although many occupied sites were far from known springs. Additionally, previously dry sites were three times more likely to be colonized than wet sites. Our results indicate extensive use of stream habitats, including intermittent ones, by E. tonkawae. These areas may be important for maintaining population connectivity or even as primary habitat patches. Restricting critical habitat to occupied sites will result in a mismatch with actual habitat use, particularly when assumptions of habitat use are untested, thus limiting the potential for recovery. creator: Nathan F. Bendik creator: Kira D. McEntire creator: Blake N. Sissel uri: https://doi.org/10.7717/peerj.1817 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bendik et al. title: Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism link: https://peerj.com/articles/1812 last-modified: 2016-03-15 description: Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals.Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation.Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated “social relationships” and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated.Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions. creator: Marco Campennì creator: Gabriele Schino uri: https://doi.org/10.7717/peerj.1812 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Campennì and Schino title: Selection of reference genes for RT-qPCR studies in blood of beluga whales (Delphinapterus leucas) link: https://peerj.com/articles/1810 last-modified: 2016-03-15 description: Reverse transcription quantitative PCR (RT-qPCR) is used for research in gene expression, and it is vital to choose appropriate housekeeping genes (HKGs) as reference genes to obtain correct results. The purpose of this study is to determine stably expressed HKGs in blood of beluga whales (Delphinapterus leucas) that can be the appropriate reference genes in relative quantification in gene expression research. Sixty blood samples were taken from four beluga whales. Thirteen candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ) were tested using RT-qPCR. The stability values of the HKGs were determined by four different algorithms. Comprehensive analysis of the results revealed that RPL4, PGK1 and ACTB are strongly recommended for use in future RT-qPCR studies in beluga blood samples. This research provides recommendation of reference gene selection, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans. The gene expression assessment of the immune components in blood have the potential to serve as an important approach to evaluating cetacean health influenced by environmental insults. creator: I-Hua Chen creator: Jiann-Hsiung Wang creator: Shih-Jen Chou creator: Yeong-Huey Wu creator: Tsung-Hsien Li creator: Ming-Yih Leu creator: Wen-Been Chang creator: Wei Cheng Yang uri: https://doi.org/10.7717/peerj.1810 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chen et al. title: Pre- and post-experimental manipulation assessments confirm the increase in number of birds due to the addition of nest boxes link: https://peerj.com/articles/1806 last-modified: 2016-03-15 description: Secondary cavity nesting (SCN) birds breed in holes that they do not excavate themselves. This is possible where there are large trees whose size and age permit the digging of holes by primary excavators and only rarely happens in forest plantations, where we expected a deficit of both breeding holes and SCN species. We assessed whether the availability of tree cavities influenced the number of SCNs in two temperate forest types, and evaluated the change in number of SCNs after adding nest boxes. First, we counted all cavities within each of our 25-m radius sampling points in mature and young forest plots during 2009. We then added nest boxes at standardised locations during 2010 and 2011 and conducted fortnightly bird counts (January–October 2009–2011). In 2011 we added two extra plots of each forest type, where we also conducted bird counts. Prior to adding nest boxes, counts revealed more SCNs in mature than in young forest. Following the addition of nest boxes, the number of SCNs increased significantly in the points with nest boxes in both types of forest. Counts in 2011 confirmed the increase in number of birds due to the addition of nest boxes. Given the likely benefits associated with a richer bird community we propose that, as is routinely done in some countries, forest management programs preserve old tree stumps and add nest boxes to forest plantations in order to increase bird numbers and bird community diversity. creator: Cecilia Cuatianquiz Lima creator: Constantino Macías Garcia uri: https://doi.org/10.7717/peerj.1806 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cuatianquiz Lima and Macías Garcia title: Species presence frequency and diversity in different patch types along an altitudinal gradient: Larix chinensis Beissn in Qinling Mountains (China) link: https://peerj.com/articles/1803 last-modified: 2016-03-15 description: Forest communities are mosaic systems composed of patches classified into four different developmental patch types: gap patch (G), building patch (B), mature patch (M) and degenerate patch (D). To study the mechanisms maintaining diversity in subalpine coniferous forests, species presence frequency and diversity in the four distinct patch types (G, B, M and D) of Larix chinensis conifer forests at three altitudinal gradients in the Qinling Mountains were analyzed. Our results were as follows: (1) Different species (or functional groups) had distinct presence frequencies in the four different patch types along the altitudinal gradient; (2) Some species or functional groups (species groups sharing similar traits and responses to the environment) only occurred in some specific patches. For seed dispersal, species using wind mainly occurred in G and D, while species using small animals mainly occurred in B and M; (3) Species composition of adjacent patch types was more similar than non-adjacent patch types, based on the lower β diversity index of the former; (4) The maximum numbers of species and two diversity indices (D′ and H′) were found in the middle altitudes. Various gap-forming processes and dispersal limitation may be the two major mechanisms determining species diversity in Larix chinensis coniferous forests at the patch scale. creator: Minyi Huang creator: Renyan Duan creator: Shixiong Wang creator: Zhigao Wang creator: Weiyi Fan uri: https://doi.org/10.7717/peerj.1803 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Huang et al. title: Molecular evidence of Burkholderia pseudomallei genotypes based on geographical distribution link: https://peerj.com/articles/1802 last-modified: 2016-03-15 description: Background. Central intermediary metabolism (CIM) in bacteria is defined as a set of metabolic biochemical reactions within a cell, which is essential for the cell to survive in response to environmental perturbations. The genes associated with CIM are commonly found in both pathogenic and non-pathogenic strains. As these genes are involved in vital metabolic processes of bacteria, we explored the efficiency of the genes in genotypic characterization of Burkholderia pseudomallei isolates, compared with the established pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) schemes.Methods. Nine previously sequenced B. pseudomallei isolates from Malaysia were characterized by PFGE, MLST and CIM genes. The isolates were later compared to the other 39 B. pseudomallei strains, retrieved from GenBank using both MLST and sequence analysis of CIM genes. UniFrac and hierachical clustering analyses were performed using the results generated by both MLST and sequence analysis of CIM genes.Results. Genetic relatedness of nine Malaysian B. pseudomallei isolates and the other 39 strains was investigated. The nine Malaysian isolates were subtyped into six PFGE profiles, four MLST profiles and five sequence types based on CIM genes alignment. All methods demonstrated the clonality of OB and CB as well as CMS and THE. However, PFGE showed less than 70% similarity between a pair of morphology variants, OS and OB. In contrast, OS was identical to the soil isolate, MARAN. To have a better understanding of the genetic diversity of B. pseudomallei worldwide, we further aligned the sequences of genes used in MLST and genes associated with CIM for the nine Malaysian isolates and 39 B. pseudomallei strains from NCBI database. Overall, based on the CIM genes, the strains were subtyped into 33 profiles where majority of the strains from Asian countries were clustered together. On the other hand, MLST resolved the isolates into 31 profiles which formed three clusters. Hierarchical clustering using UniFrac distance suggested that the isolates from Australia were genetically distinct from the Asian isolates. Nevertheless, statistical significant differences were detected between isolates from Malaysia, Thailand and Australia.Discussion. Overall, PFGE showed higher discriminative power in clustering the nine Malaysian B. pseudomallei isolates and indicated its suitability for localized epidemiological study. Compared to MLST, CIM genes showed higher resolution in distinguishing those non-related strains and better clustering of strains from different geographical regions. A closer genetic relatedness of Malaysian isolates with all Asian strains in comparison to Australian strains was observed. This finding was supported by UniFrac analysis which resulted in geographical segregation between Australia and the Asian countries. creator: Noorfatin Jihan Zulkefli creator: Vanitha Mariappan creator: Kumutha Malar Vellasamy creator: Chun Wie Chong creator: Kwai Lin Thong creator: Sasheela Ponnampalavanar creator: Jamuna Vadivelu creator: Cindy Shuan Ju Teh uri: https://doi.org/10.7717/peerj.1802 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zulkefli et al. title: The risk of smoking on multiple sclerosis: a meta-analysis based on 20,626 cases from case-control and cohort studies link: https://peerj.com/articles/1797 last-modified: 2016-03-15 description: Background. Multiple sclerosis (MS) has become a disease that represents a tremendous burden on patients, families, and societies. The exact etiology of MS is still unclear, but it is believed that a combination of genetic and environmental factors contribute to this disease. Although some meta-analyses on the association between smoking and MS have been previously published, a number of new studies with larger population data have published since then. Consequently, these additional critical articles need to be taken into consideration.Method. We reviewed articles by searching in PubMed and EMBASE. Both conservative and non-conservative models were used to investigate the association between smoking and the susceptibility to MS. We also explored the effect of smoking on the susceptibility to MS in strata of different genders and smoking habits. The association between passive smoking and MS was also explored.Results.The results of this study suggest that smoking is a risk factor for MS (conservative model: odds ratio (OR) 1.55, 95% CI [1.48–1.62], p < 0.001; non-conservative model: 1.57, 95% CI [1.50–1.64], p < 0.001). Smoking appears to increase the risk of MS more in men than in women and in current smokers more than in past smokers. People who exposed to passive smoking have higher risk of MS than those unexposed.Conclusion.This study demonstrated that exposure to smoking is an important risk factor for MS. People will benefit from smoking cessation, and policymakers should pay attention to the association between smoking and MS. creator: Peng Zhang creator: Rui Wang creator: Zhijun Li creator: Yuhan Wang creator: Chunshi Gao creator: Xin Lv creator: Yuanyuan Song creator: Bo Li uri: https://doi.org/10.7717/peerj.1797 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhang et al. title: Taxonomic reassessment of Hydralmosaurus as Styxosaurus: new insights on the elasmosaurid neck evolution throughout the Cretaceous link: https://peerj.com/articles/1777 last-modified: 2016-03-15 description: Two extremely-long necked elasmosaurids, AMNH 1495, holotype of Hydralmosaurus serpentinus, and AMNH 5835, previously referred to H. serpentinus, are here reviewed in detail. Unique features of the cervical vertebrae, which are only present on elasmosaurids from the Western Interior Seaway, are recognized based on these specimens and by comparison with penecontemporaneous taxa with biogeographic affinities. Phylogenetic analysis, bivariate graphic analysis of cervical vertebrae proportions, comparisons of different cervical vertebral types, paleobiogeographic distribution and study of the elasmosaurid axial evolution throughout the Cretaceous are here integrated. As a result, at least two separate lineages within the Elasmosauridae are identified by independently acquired extremely-long necks (over 60 cervical vertebrae). First, a still scarcely known lineage is so far represented by the lower Cenomanian Thalassomedon haningtoni, the Turonian Libonectes morgani and close relatives. A second lineage is here defined as a new clade, the Styxosaurinae, which groups the Campanian genera Terminonatator, Styxosaurus (=‘Hydralmosaurus’), Albertonectes and Elasmosaurus, the two latter forming a derived branch that includes the most extreme amniote necks known to date (more than 70 cervical vertebrae). Phylogenetic analysis supports AMNH 1495 and AMNH 5835 as being closely related to Styxosaurus snowii. Therefore, the species Styxosaurus browni is re-validated, while AMNH 1495 is here referred to Styxosaurus sp. This research also recognizes the ‘Cimoliasauridae’ (nomen dubium) as a paraphyletic group but informative of a plesiomorphic cervical vertebral morphology of elasmosaurids which was persistent throughout the whole Cretaceous and from whom aristonectines, styxosaurines and Thalassomedon and close relatives are derived. The genus Hydralmosaurus is recommended for being abandoned. creator: Rodrigo A. Otero uri: https://doi.org/10.7717/peerj.1777 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Otero title: Evaluation of thyroid antibodies and benign disease prevalence among young adults exposed to 131I more than 25 years after the accident at the Chernobyl Nuclear Power Plant link: https://peerj.com/articles/1774 last-modified: 2016-03-15 description: Background. The Chernobyl Nuclear Power Plant (CNPP) accident exposed a large number of inhabitants to internal 131I radiation. The associations between internal 131I exposure and thyroid autoimmunity and benign thyroid diseases remain controversial in the population living in the contaminated area around the CNNP. In this study, we evaluate the association of 131I with benign thyroid diseases. Methods. We compared the prevalence of Anti-Thyroid Autoantibodies (ATAs), thyroid function, and prevalence of thyroid ultrasound finding outcomes in 300 residents of the contaminated area of Ukraine who were 0–5 years of age at the time of the CNPP accident (group 1) and 300 sex-matched residents who were born after the accident (group 2). Results. We did not find any differences of the prevalence of Antithyroglobulin Antibodies (TGAb) positive, Antithyroid Peroxidase Antibodies (TPOAb) positive, and TGAb and/or TPOAb positive between the study groups. (11.7% vs 10.3%; p = 0.602, 17.3% vs 13.0%; p = 0.136, 21.0% vs 17.3%; p = 0.254, respectively); after adjusting for age and sex, the prevalence was not associated with the 131I exposure status in the study groups. The prevalence of subclinical and overt hypothyroidism cases was not significantly different (p = 0.093 and p = 0.320) in the two groups, nor was the prevalence of goiter (p = 0.482). On the other hand, the prevalence of nodules was significantly higher in group 1 (p = 0.003), though not significantly so after adjustment for age and sex. Discussion. Working 26–27 years after the CNNP accident, we found no increased prevalence of ATAs or benign thyroid diseases in young adults exposed to 131I fallout during early childhood in the contaminated area of Ukraine. Long-term follow-up is needed to clarify the effects of radiation exposure on autoimmunity reaction in the thyroid. creator: Yuko Kimura creator: Naomi Hayashida creator: Jumpei Takahashi creator: Ruslan Rafalsky creator: Alexsey Saiko creator: Alexander Gutevich creator: Sergiy Chorniy creator: Takashi Kudo creator: Noboru Takamura uri: https://doi.org/10.7717/peerj.1774 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kimura et al. title: Evaluation of the validity of the Psychology Experiment Building Language tests of vigilance, auditory memory, and decision making link: https://peerj.com/articles/1772 last-modified: 2016-03-15 description: Background. The Psychology Experimental Building Language (PEBL) test battery (http://pebl.sourceforge.net/) is a popular application for neurobehavioral investigations. This study evaluated the correspondence between the PEBL and the non-PEBL versions of four executive function tests.Methods. In one cohort, young-adults (N = 44) completed both the Conner’s Continuous Performance Test (CCPT) and the PEBL CPT (PCPT) with the order counter-balanced. In a second cohort, participants (N = 47) completed a non-computerized (Wechsler) and a computerized (PEBL) Digit Span (WDS or PDS) both Forward and Backward. Participants also completed the Psychological Assessment Resources or the PEBL versions of the Iowa Gambling Task (PARIGT or PEBLIGT).Results. The between-test correlations were moderately high (reaction time r = 0.78, omission errors r = 0.65, commission errors r = 0.66) on the CPT. DS Forward was significantly greater than DS Backward on the WDS (p < .0005) and the PDS (p < .0005). The total WDS score was moderately correlated with the PDS (r = 0.56). The PARIGT and the PEBLIGTs showed a very similar pattern for response times across blocks, development of preference for Advantageous over Disadvantageous Decks, and Deck selections. However, the amount of money earned (score–loan) was significantly higher in the PEBLIGT during the last Block.Conclusions. These findings are broadly supportive of the criterion validity of the PEBL measures of sustained attention, short-term memory, and decision making. Select differences between workalike versions of the same test highlight how detailed aspects of implementation may have more important consequences for computerized testing than has been previously acknowledged. creator: Brian Piper creator: Shane T. Mueller creator: Sara Talebzadeh creator: Min Jung Ki uri: https://doi.org/10.7717/peerj.1772 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Piper et al. title: A new ornithurine from the Early Cretaceous of China sheds light on the evolution of early ecological and cranial diversity in birds link: https://peerj.com/articles/1765 last-modified: 2016-03-15 description: Despite the increasing number of exceptional feathered fossils discovered in the Late Jurassic and Cretaceous of northeastern China, representatives of Ornithurae, a clade that includes comparatively-close relatives of crown clade Aves (extant birds) and that clade, are still comparatively rare. Here, we report a new ornithurine species Changzuiornis ahgmi from the Early Cretaceous Jiufotang Formation. The new species shows an extremely elongate rostrum so far unknown in basal ornithurines and changes our understanding of the evolution of aspects of extant avian ecology and cranial evolution. Most of this elongate rostrum in Changzuiornis ahgmi is made up of maxilla, a characteristic not present in the avian crown clade in which most of the rostrum and nearly the entire facial margin is made up by premaxilla. The only other avialans known to exhibit an elongate rostrum with the facial margin comprised primarily of maxilla are derived ornithurines previously placed phylogenetically as among the closest outgroups to the avian crown clade as well as one derived enantiornithine clade. We find that, consistent with a proposed developmental shift in cranial ontogeny late in avialan evolution, this elongate rostrum is achieved through elongation of the maxilla while the premaxilla remains only a small part of rostral length. Thus, only in Late Cretaceous ornithurine taxa does the premaxilla begin to play a larger role. The rostral and postcranial proportions of Changzuiornis suggest an ecology not previously reported in Ornithurae; the only other species with an elongate rostrum are two marine Late Cretacous taxa interpreted as showing a derived picivorous diet. creator: Jiandong Huang creator: Xia Wang creator: Yuanchao Hu creator: Jia Liu creator: Jennifer A. Peteya creator: Julia A. Clarke uri: https://doi.org/10.7717/peerj.1765 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Huang et al. title: Occurrence of Terranova larval types (Nematoda: Anisakidae) in Australian marine fish with comments on their specific identities link: https://peerj.com/articles/1722 last-modified: 2016-03-15 description: Pseudoterranovosis is a well-known human disease caused by anisakid larvae belonging to the genus Pseudoterranova. Human infection occurs after consuming infected fish. Hence the presence of Pseudoterranova larvae in the flesh of the fish can cause serious losses and problems for the seafood, fishing and fisheries industries. The accurate identification of Pseudoterranova larvae in fish is important, but challenging because the larval stages of a number of different genera, including Pseudoterranova, Terranova and Pulchrascaris, look similar and cannot be differentiated from each other using morphological criteria, hence they are all referred to as Terranova larval type. Given that Terranova larval types in seafood are not necessarily Pseudoterranova and may not be dangerous, the aim of the present study was to investigate the occurrence of Terranova larval types in Australian marine fish and to determine their specific identity. A total of 137 fish belonging to 45 species were examined. Terranova larval types were found in 13 species, some of which were popular edible fish in Australia. The sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2 respectively) of the Terranova larvae in the present study showed a high degree of similarity suggesting that they all belong to the same species. Due to the lack of a comparable sequence data of a well identified adult in the GenBank database the specific identity of Terranova larval type in the present study remains unknown. The sequence of the ITS regions of the Terranova larval type in the present study and those of Pseudoterranova spp. available in GenBank are significantly different, suggesting that larvae found in the present study do not belong to the genus Pseudoterranova, which is zoonotic. This study does not rule out the presence of Pseudoterranova larvae in Australian fish as Pseudoterranova decipiens E has been reported in adult form from seals in Antarctica and it is known that they have seasonal presence in Australian southern coasts. The genetic distinction of Terranova larval type in the present study from Pseudoterranova spp. along with the presence of more species of elasmobranchs in Australian waters (definitive hosts of Terranova spp. and Pulchrascaris spp.) than seals (definitive hosts of Pseudoterranova spp.) suggest that Terranova larval type in the present study belong to either genus Terranova or Pulchrascaris, which are not known to cause disease in humans. The present study provides essential information that could be helpful to identify Australian Terranova larval types in future studies. Examination and characterisation of further specimens, especially adults of Terranova and Pulchrascaris, is necessary to fully elucidate the identity of these larvae. creator: Shokoofeh Shamsi creator: Jaydipbhai Suthar uri: https://doi.org/10.7717/peerj.1722 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shamsi and Suthar title: Flower color preferences of insects and livestock: effects on Gentiana lutea reproductive success link: https://peerj.com/articles/1685 last-modified: 2016-03-15 description: Angiosperms diversification was primarily driven by pollinator agents, but non-pollinator agents also promoted floral evolution. Gentiana lutea shows pollinator driven flower color variation in NW Spain. We test whether insect herbivores and livestock, which frequently feed in G.lutea, play a role in G. lutea flower color variation, by answering the following questions: (i) Do insect herbivores and grazing livestock show flower color preferences when feeding on G. lutea? (ii) Do mutualists (pollinators) and antagonists (seed predators, insect herbivores and livestock) jointly affect G. lutea reproductive success? Insect herbivores fed more often on yellow flowering individuals but they did not affect seed production, whereas livestock affected seed production but did not show clear color preferences. Our data indicate that flower color variation of G. lutea is not affected by insect herbivores or grazing livestock. creator: Mar Sobral creator: María Losada creator: Tania Veiga creator: Javier Guitián creator: José Guitián creator: Pablo Guitián uri: https://doi.org/10.7717/peerj.1685 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sobral et al. title: Reproductive biology of the biofuel plant Jatropha curcas in its center of origin link: https://peerj.com/articles/1819 last-modified: 2016-03-14 description: In this work, we studied the main characteristics of flowering, reproductive system and diversity of pollinators for the biofuel plant Jatropha curcas (L.) in a site of tropical southeastern Mexico, within its center of origin. The plants were monoecious with inflorescences of unisexual flowers. The male flowers produced from 3062–5016 pollen grains (266–647 per anther). The plants produced fruits with both geitonogamy and xenogamy, although insect pollination significantly increased the number and quality of fruits. A high diversity of flower visiting insects (36 species) was found, of which nine were classified as efficient pollinators. The native stingless bees Scaptotrigona mexicana (Guérin-Meneville) and Trigona (Tetragonisca) angustula (Latreille) were the most frequent visitors and their presence coincided with the hours when the stigma was receptive. It is noteworthy that the female flowers open before the male flowers, favoring xenogamy, which may explain the high genetic variability reported in J. curcas for this region of the world. creator: Manuel Rincón-Rabanales creator: Laura I. Vargas-López creator: Lourdes Adriano-Anaya creator: Alfredo Vázquez-Ovando creator: Miguel Salvador-Figueroa creator: Isidro Ovando-Medina uri: https://doi.org/10.7717/peerj.1819 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Rincón-Rabanales et al. title: Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages link: https://peerj.com/articles/1813 last-modified: 2016-03-14 description: In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FST and DC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using DC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis. creator: William Peterman creator: Emily R. Brocato creator: Raymond D. Semlitsch creator: Lori S. Eggert uri: https://doi.org/10.7717/peerj.1813 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Peterman et al. title: The role of sex and age in the architecture of intrapopulation howler monkey-plant networks in continuous and fragmented rain forests link: https://peerj.com/articles/1809 last-modified: 2016-03-14 description: We evaluated the structure of intrapopulation howler monkey-plant interactions by focusing on the plant species consumed by different sex and age classes in continuous and fragmented forests in southern Mexico. For this we used network analysis to evaluate the impact of fragmentation on howler population traits and on resource availability and food choice. A total of 37 tree and liana species and seven plant items (bark, immature fruits, flowers, mature fruits, immature leaves, mature leaves and petioles) were consumed, but their relative consumption varied according to sex and age classes and habitat type. Overall, adult females consumed the greatest number of plant species and items while infants and juveniles the lowest. For both continuous and fragmented forests, we found a nested diet for howler monkey-plant networks: diets of more selective monkeys represent subsets of the diets of other individuals. Nestedness was likely due to the high selectivity of early life stages in specific food plants and items, which contrasts with the generalized foraging behaviour of adults. Information on the extent to which different plant species and primate populations depend on such interactions in different habitats will help to make accurate predictions about the potential impact of disturbances on plant-animal interaction networks. creator: Julieta Benitez-Malvido creator: Ana Paola Martínez-Falcón creator: Wesley Dattilo creator: Ana María González-DiPierro creator: Rafael Lombera Estrada creator: Anna Traveset uri: https://doi.org/10.7717/peerj.1809 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Benitez-Malvido et al. title: A new species of Psychrophrynella (Amphibia, Anura, Craugastoridae) from the humid montane forests of Cusco, eastern slopes of the Peruvian Andes link: https://peerj.com/articles/1807 last-modified: 2016-03-14 description: We describe a new species of Psychrophrynella from the humid montane forest of the Department Cusco in Peru. Specimens were collected at 2,670–3,165 m elevation in the Área de Conservación Privada Ukumari Llakta, Japumayo valley, near Comunidad Campesina de Japu, in the province of Paucartambo. The new species is readily distinguished from all other species of Psychrophrynella but P. bagrecito and P. usurpator by possessing a tubercle on the inner edge of the tarsus, and from these two species by its yellow ventral coloration on abdomen and limbs. Furthermore, the new species is like P. bagrecito and P. usurpator in having an advertisement call composed of multiple notes, whereas other species of Psychrophrynella whose calls are known have a pulsed call (P. teqta) or a short, tonal call composed of a single note. The new species has a snout-vent length of 16.1–24.1 mm in males and 23.3–27.7 mm in females. Like other recently described species in the genus, this new Psychrophrynella inhabits high-elevation forests in the tropical Andes and likely has a restricted geographic distribution. creator: Alessandro Catenazzi creator: Alex Ttito uri: https://doi.org/10.7717/peerj.1807 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Catenazzi and Ttito title: ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients link: https://peerj.com/articles/1804 last-modified: 2016-03-14 description: Colorectal cancer (CRC) is a heterogeneous disease with a high mortality rate and is still lacking an effective treatment. Our goal is to develop a robust prognosis model for predicting the prognosis in CRC patients. In this study, 871 stage II and III CRC samples were collected from six gene expression profilings. ColoFinder was developed using a 9-gene signature based Random Survival Forest (RSF) prognosis model. The 9-gene signature recurrence score was derived with a 5-fold cross validation to test the association with relapse-free survival, and the value of AUC was gained with 0.87 in GSE39582(95% CI [0.83–0.91]). The low-risk group had a significantly better relapse-free survival (HR, 14.8; 95% CI [8.17–26.8]; P < 0.001) than the high-risk group. We also found that the 9-gene signature recurrence score contributed more information about recurrence than standard clinical and pathological variables in univariate and multivariate Cox analyses when applied to GSE17536(p = 0.03 and p = 0.01 respectively). Furthermore, ColoFinder improved the predictive ability and better stratified the risk subgroups when applied to CRC gene expression datasets GSE14333, GSE17537, GSE12945and GSE24551. In summary, ColoFinder significantly improves the risk assessment in stage II and III CRC patients. The 9-gene prognostic classifier informs patient prognosis and treatment response. creator: Mingguang Shi creator: Jianmin He uri: https://doi.org/10.7717/peerj.1804 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shi and He title: Palatability and pharmacokinetics of flunixin when administered to sheep through feed link: https://peerj.com/articles/1800 last-modified: 2016-03-14 description: Applying analgesics to feed is a potentially easy method of providing pain-relief to sheep and lambs that undergo painful husbandry procedures. To be effective, the medicated feed needs to be readily accepted by sheep and its consumption needs to result in therapeutic concentrations of the drug. In the present experiment, pelleted feed was supplemented with flunixin (4.0 mg/kg live weight) and offered to eight sheep. To test the palatability of flunixin, the individually penned sheep were offered normal feed and feed supplemented with flunixin in separate troughs for two consecutive days. A trend for a day by feed-type (control versus flunixin supplemented) interaction suggested that sheep may have had an initial mild aversion to pellets supplemented with flunixin on the first day of exposure, however, by on the second day there was no difference in consumption of normal feed and feed supplemented with flunixin. To test pharmacokinetics, sheep were offered 800 g of flunixin supplemented feed for a 12 h period. Blood samples were taken over 48 h and plasma drug concentrations were determined using ultra-high-pressure liquid chromatography, negative electrospray ionisation and tandem mass spectrometry. The mean ± S.D. time required to reach maximum concentration was 6.00 ± 4.14 h and ranged from 1 to 12 h. Average maximum plasma concentration was 1.78 ± 0.48 µg/mL and ranged from 1.61 to 2.80 µg/mL. The average half-life of flunixin was 7.95 ± 0.77 h and there was a mean residence time of 13.62 ± 1.17 h. Free access to flunixin supplemented feed enabled all sheep to obtain inferred therapeutic concentrations of flunixin in plasma within 6 h of starting to consume the feed. Provision of an analgesic in feed may be an alternative practical method for providing pain relief to sheep. creator: Danila Marini creator: Joe Pippia creator: Ian G. Colditz creator: Geoff N. Hinch creator: Carol J. Petherick creator: Caroline Lee uri: https://doi.org/10.7717/peerj.1800 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Marini et al. title: Serum uric acid levels during leprosy reaction episodes link: https://peerj.com/articles/1799 last-modified: 2016-03-14 description: Background. Leprosy reactions are acute inflammatory episodes that occur mainly in the multibacillary forms of the disease. The reactions are classified as type 1 (reverse reaction) or type 2 (erythema nodosum leprosum). Leprosy-associated oxidative stress has been widely demonstrated. Several recent studies have shown uric acid (UA) to have antioxidative effects under pathologic conditions. The objective of this study was to assess serum levels of UA in patients with leprosy reactions, with the aim of monitoring their levels before and after treatment, compared with levels in leprosy patients without reactions.Methods. The study included patients aged 18–69 years assisted at a leprosy treatment reference center in the Central Region of Brazil. Patients who were pregnant; were using immunosuppressant drugs or immunobiologicals; or had an autoimmune disease, human immunodeficiency virus infection, acquired immune deficiency syndrome, or tuberculosis were excluded. Upon recruitment, all individuals were clinically assessed for skin lesions and neural or systemic impairment. Some patients had already completed treatment for leprosy, while others were still undergoing treatment or had initiated treatment after being admitted. The treatment of the reactional episode was started only after the initial evaluation. Laboratory assessments were performed upon admission (baseline) and at approximately 30 and 60 days (time points 1 and 2, respectively).Results. A total of 123 leprosy patients were recruited between June 2012 and June 2015; among them, 56, 42, and 25 presented with type 1, type 2, and no reactions, respectively. Serum UA levels were significantly reduced in patients with type 2 leprosy reactions compared with patients in the control group and remained lower in the two subsequent assessments, after initiation of anti-reaction treatments, with similar values to those recorded before the treatment.Discussion. The decreased serum UA levels in patients with type 2 leprosy reactions might be due to the consumption of UA to neutralize the enhanced production of oxygen- and nitrogen-reactive species that occurs during type 2 reactions. The maintenance of the reduced levels in the follow-up assessments may indicate persistence of oxidative stress in the initial post-treatment stages, despite improved clinical conditions. The results of this study suggest that serum UA may play an antioxidative role during type 2 leprosy reactions. creator: Yvelise T. Morato-Conceicao creator: Eduardo R. Alves-Junior creator: Talita A. Arruda creator: Jose C. Lopes creator: Cor J.F. Fontes uri: https://doi.org/10.7717/peerj.1799 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Morato-Conceicao et al. title: Scientific publications in nursing journals from Mainland China, Taiwan, and Hong Kong: a 10-year survey of the literature link: https://peerj.com/articles/1798 last-modified: 2016-03-14 description: Background: China has witnessed remarkable progress in scientific performance in recent years. However, the quantity and quality of nursing publications from three major regions (Mainland China, Taiwan, and Hong Kong) have not been reported. This study aimed to investigate the characteristics of scientific research productivity from Mainland China, Taiwan, and Hong Kong in the field of nursing. Methods: Articles published in the 110 nursing journals originating from Mainland China, Taiwan, and Hong Kong between 2005 and 2014 were retrieved from the Web of Science. The total number of articles published, the impact factor, and the citation count were analyzed. Results: There were 2,439 publications between 2005 and 2014 from China, including 438 from Mainland China, 1,506 from Taiwan, and 495 from Hong Kong. There was a significant increase in publications for these three regions (p < 0.05), especially for Mainland China, with a 59.50-fold increase experienced. From 2011, the number of publications from Mainland China exceeded that from Hong Kong. Taiwan had the highest total journal impact factor (2,142.81), followed by Hong Kong (720.39) and Mainland China (583.94). The mean journal impact factor from Hong Kong (1.46) was higher than that from Taiwan (1.42) and Mainland China (1.33). Taiwan had the highest total citation count (8,392), followed by Hong Kong (3,785) and Mainland China (1,493). The mean citation count from Hong Kong (7.65) was higher than that from Taiwan (5.57) and Mainland China (3.41). The Journal of Clinical Nursing was the most popular journal in the three regions. Discussion: Chinese contributions to the field of nursing have significantly increased in the past ten years, particularly from Mainland China. Taiwan is the most productive region in China. Hong Kong had the highest-quality research output, according to mean journal impact factor and mean citation count. creator: Di Zhang creator: Xiaming Wang creator: Xueru Yuan creator: Li Yang creator: Yu Xue creator: Qian Xie uri: https://doi.org/10.7717/peerj.1798 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang et al. title: The effect of ribosomal protein S15a in lung adenocarcinoma link: https://peerj.com/articles/1792 last-modified: 2016-03-14 description: Background: RPS15A (Ribosomal Protein S15A) promotes mRNA/ribosome interactions in translation. It is critical for the process of eukaryotic protein biosynthesis. Recently, aberrantly expressed RPS15A was found in the hepatitis virus and in malignant tumors. However, the role of RPS15A has not been fully revealed on the development of lung cancer. Method: In this study, a Tissue Microarray (TMA) of primary lung adenocarcinoma tissue specimens was carried out. Furthermore, to further investigate the function of RPS15A in lung cancer, RPS15A-specific short hairpin RNA (shRNA) expressing lentivirus (Lv-shRPS15A) was constructed and used to infect H1299 and A549 cells. Result: Our data showed that RPS15A expression was increased in tumor tissues. Furthermore, the knockdown of RSP15A inhibited cancer cell growth and induced apoptosis in the cancer cells. Gene expression profile microarray also revealed that the P53 signaling pathway was activated in Lv-shRPS15A-infected cancer cells. Conclusion: Taken together, our results demonstrate that RPS15A is a novel oncogene in non-small cell lung cancer and may be a potential therapeutic target in lung cancer. creator: Yifan Zhang creator: Guangxin Zhang creator: Xin Li creator: Bingjin Li creator: Xingyi Zhang uri: https://doi.org/10.7717/peerj.1792 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang et al. title: Computational inference of H3K4me3 and H3K27ac domain length link: https://peerj.com/articles/1750 last-modified: 2016-03-14 description: Background. Recent epigenomic studies have shown that the length of a DNA region covered by an epigenetic mark is not just a byproduct of the assaying technologies and has functional implications for that locus. For example, expanded regions of DNA sequences that are marked by enhancer-specific histone modifications, such as acetylation of histone H3 lysine 27 (H3K27ac) domains coincide with cell-specific enhancers, known as super or stretch enhancers. Similarly, promoters of genes critical for cell-specific functions are marked by expanded H3K4me3 domains in the cognate cell type, and these can span DNA regions from 4–5kb up to 40–50kb in length. These expanded H3K4me3 domains are known as buffer domains or super promoters.Methods. To ask what correlates with—and potentially regulates—the length of loci marked with these two important histone marks, H3K4me3 and H3K27ac, we built Random Forest regression models. With these models, we computationally identified genomic and epigenomic patterns that are predictive for the length of these marks in seven ENCODE cell lines.Results. We found that certain epigenetic marks and transcription factors explain the variability of the length of H3K4me3 and H3K27ac marks across different cell types, which implies that the lengths of these two epigenetic marks are tightly regulated in a given cell type. Our source code for the regression models and data can be found at our GitHub page: https://github.com/zubekj/broad_peaks.Discussion. Our Random Forest based regression models enabled us to estimate the individual contribution of different epigenetic marks and protein binding patterns to the length of H3K4me3 and H3K27ac deposition patterns, therefore potentially revealing genomic signatures at cell specific regulatory elements. creator: Julian Zubek creator: Michael L. Stitzel creator: Duygu Ucar creator: Dariusz M. Plewczynski uri: https://doi.org/10.7717/peerj.1750 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zubek et al. title: Genetic variants in the MicroRNA biosynthetic pathway Gemin3 and Gemin4 are associated with a risk of cancer: a meta-analysis link: https://peerj.com/articles/1724 last-modified: 2016-03-15 description: The effects of the microRNA (miRNA) processing genes Gemin3 and Gemin4 on cellular signaling pathways could have a major impact on the risk of cancer. Several studies concerning the association between the Gemin3 rs197412, Gemin4 rs7813 and Gemin4 rs2740348 polymorphisms with cancer susceptibility have been published. The present meta-analysis summarized this evidence and evaluated the precision of these relationships. Relevant studies (published prior to December 16th, 2015) without language restriction were identified using the PubMed, Web of Science and China National Knowledge Infrastructure (CNKI) on-line databases. The data were extracted from the eligible studies and were processed using Stata 12.0 software. Seven studies (2,588 cases and 2,549 controls) indicated that the rs7813 polymorphism was significantly associated with increased cancer risk (TT vs TC + CC, OR = 1.18 95% CI [1.05–1.32]). Six studies (1,314 cases and 1,244 controls) indicated that rs2740348 was associated with an increased cancer risk (GG vs. GC + CC, OR = 1.41 95% CI [1.00–1.83]). However the rs197412 polymorphism was not associated with an increased cancer risk (OR = 0.97 95% CI [0.80–1.19]). Our results suggest that the Gemin4 rs7813 T > C and rs2740348 G > C polymorphisms are associated with cancer susceptibility. creator: Wenbo Zhu creator: Jun Zhao creator: Jieyu He creator: Daxun Qi creator: Lina Wang creator: Xu Ma creator: Pei Liu uri: https://doi.org/10.7717/peerj.1724 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhu et al. title: Prevalence of asymptomatic urinary tract infections in morbidly obese dogs link: https://peerj.com/articles/1711 last-modified: 2016-03-14 description: Background. Obesity has reached epidemic proportions in dogs and, as in humans, cost of care has increased due to associated comorbidities. In humans, asymptomatic urinary tract infections (UTI) may be more prevalent in the obese. Asymptomatic bacteriuria (AB) is the term used when UTI are asymptomatic. We hypothesized that morbidly obese dogs are similarly more likely to have asymptomatic bacteriuria than lean, overweight, and moderately obese dogs.Methods. A retrospective study was undertaken to explore a possible association between obesity and asymptomatic bacteriuria. Records from lean, overweight, and obese dogs receiving both a dual energy absorptiometry (DXA) scan and urine culture were included.Results. Six positive urine cultures were identified among 46 dogs fulfilling search criteria. All six positive cultures were found in dogs with body fat percentage of >45%. In dogs with body fat percentage of <45%, there were no positive urine cultures.Discussion. There was an increased prevalence of asymptomatic bacteriuria in the morbidly obese dogs in this study compared to those that were lean, overweight, or moderately obese. Whether antibiotic therapy is necessary in such cases is still being debated, but because asymptomatic bacteriuria may be associated with ascending infections, uroliths, or other complications, the data reported herein support the screening of obese patients for bacteriuria. creator: Susan G. Wynn creator: Angela L. Witzel creator: Joseph W. Bartges creator: Tamberlyn S. Moyers creator: Claudia A. Kirk uri: https://doi.org/10.7717/peerj.1711 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wynn et al. title: Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata link: https://peerj.com/articles/1793 last-modified: 2016-03-10 description: The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. creator: Andrea C. Aplasca creator: John B. Iverson creator: Mark E. Welch creator: Giuliano Colosimo creator: Evon R. Hekkala uri: https://doi.org/10.7717/peerj.1793 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Aplasca et al. title: A de novo transcriptome of the Malpighian tubules in non-blood-fed and blood-fed Asian tiger mosquitoes Aedes albopictus: insights into diuresis, detoxification, and blood meal processing link: https://peerj.com/articles/1784 last-modified: 2016-03-10 description: Background. In adult female mosquitoes, the renal (Malpighian) tubules play an important role in the post-prandial diuresis, which removes excess ions and water from the hemolymph of mosquitoes following a blood meal. After the post-prandial diuresis, the roles that Malpighian tubules play in the processing of blood meals are not well described.Methods. We used a combination of next-generation sequencing (paired-end RNA sequencing) and physiological/biochemical assays in adult female Asian tiger mosquitoes (Aedes albopictus) to generate molecular and functional insights into the Malpighian tubules and how they may contribute to blood meal processing (3–24 h after blood ingestion).Results/Discussion. Using RNA sequencing, we sequenced and assembled the first de novo transcriptome of Malpighian tubules from non-blood-fed (NBF) and blood-fed (BF) mosquitoes. We identified a total of 8,232 non-redundant transcripts. The Malpighian tubules of NBF mosquitoes were characterized by the expression of transcripts associated with active transepithelial fluid secretion/diuresis (e.g., ion transporters, water channels, V-type H+-ATPase subunits), xenobiotic detoxification (e.g., cytochrome P450 monoxygenases, glutathione S-transferases, ATP-binding cassette transporters), and purine metabolism (e.g., xanthine dehydrogenase). We also detected the expression of transcripts encoding sodium calcium exchangers, G protein coupled-receptors, and septate junctional proteins not previously described in mosquito Malpighian tubules. Within 24 h after a blood meal, transcripts associated with active transepithelial fluid secretion/diuresis exhibited a general downregulation, whereas those associated with xenobiotic detoxification and purine catabolism exhibited a general upregulation, suggesting a reinvestment of the Malpighian tubules’ molecular resources from diuresis to detoxification. Physiological and biochemical assays were conducted in mosquitoes and isolated Malpighian tubules, respectively, to confirm that the transcriptomic changes were associated with functional consequences. In particular, in vivo diuresis assays demonstrated that adult female mosquitoes have a reduced diuretic capacity within 24 h after a blood meal. Moreover, biochemical assays in isolated Malpighian tubules showed an increase in glutathione S-transferase activity and the accumulation of uric acid (an end product of purine catabolism) within 24 h after a blood meal. Our data provide new insights into the molecular physiology of Malpighian tubules in culicine mosquitoes and reveal potentially important molecular targets for the development of chemical and/or gene-silencing insecticides that would disrupt renal function in mosquitoes. creator: Carlos J. Esquivel creator: Bryan J. Cassone creator: Peter M. Piermarini uri: https://doi.org/10.7717/peerj.1784 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Esquivel et al. title: Molecular phylogeny of porcelain crabs (Porcellanidae: Petrolisthes and allies) from the south eastern Pacific: the genera Allopetrolisthes and Liopetrolisthes are not natural entities link: https://peerj.com/articles/1805 last-modified: 2016-03-10 description: Porcelain crabs from the closely related genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes are known for their diversity of lifestyles, habitats, and coloration. The evolutionary relationships among the species belonging to these three genera is not fully resolved. A molecular phylogeny of the group may help to resolve the long-standing taxonomic question about the validity of the genera Allopetrolisthes and Liopetrolisthes. Using both ‘total evidence’ and single-marker analyses based on a 362-bp alignment of the 16S rRNA mitochondrial DNA and a 328-bp alignment of the Histone 3 nuclear DNA, the phylogenetic relationships among 11 species from Petrolisthes (6 species), Liopetrolisthes (2 species), and Allopetrolisthes (3 species), all native to the south eastern Pacific, were examined. The analyses supported three pairs of sister species: L. mitra + L. patagonicus, P. tuberculatus + P. tuberculosus, and A. angulosus + A. punctatus. No complete segregation of species, according to genera, was evident from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of an alternative tree in which monophyly of the three genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes. Taking into account the above and other recent molecular phylogenetic analyses focused on other representatives from the family Porcellanidae, it is tentatively proposed to eliminate the genera Liopetrolisthes and Allopetrolisthes, and to transfer their members to the genus Petrolisthes. creator: J. Antonio Baeza uri: https://doi.org/10.7717/peerj.1805 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baeza title: Within-person variability in men’s facial width-to-height ratio link: https://peerj.com/articles/1801 last-modified: 2016-03-10 description: Background. In recent years, researchers have investigated the relationship between facial width-to-height ratio (FWHR) and a variety of threat and dominance behaviours. The majority of methods involved measuring FWHR from 2D photographs of faces. However, individuals can vary dramatically in their appearance across images, which poses an obvious problem for reliable FWHR measurement.Methods. I compared the effect sizes due to the differences between images taken with unconstrained camera parameters (Studies 1 and 2) or varied facial expressions (Study 3) to the effect size due to identity, i.e., the differences between people. In Study 1, images of Hollywood actors were collected from film screenshots, providing the least amount of experimental control. In Study 2, controlled photographs, which only varied in focal length and distance to camera, were analysed. In Study 3, images of different facial expressions, taken in controlled conditions, were measured.Results. Analyses revealed that simply varying the focal length and distance between the camera and face had a relatively small effect on FWHR, and therefore may prove less of a problem if uncontrolled in study designs. In contrast, when all camera parameters (including the camera itself) are allowed to vary, the effect size due to identity was greater than the effect of image selection, but the ranking of the identities was significantly altered by the particular image used. Finally, I found significant changes to FWHR when people posed with four of seven emotional expressions in comparison with neutral, and the effect size due to expression was larger than differences due to identity.Discussion. The results of these three studies demonstrate that even when head pose is limited to forward facing, changes to the camera parameters and a person’s facial expression have sizable effects on FWHR measurement. Therefore, analysing images that fail to constrain some of these variables can lead to noisy and unreliable results, but also relationships caused by previously unconsidered confounds. creator: Robin S.S. Kramer uri: https://doi.org/10.7717/peerj.1801 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kramer title: Taxonomic revision of the Malagasy members of the Nesomyrmex angulatus species group using the automated morphological species delineation protocol NC-PART-clustering link: https://peerj.com/articles/1796 last-modified: 2016-03-10 description: Background. Applying quantitative morphological approaches in systematics research is a promising way to discover cryptic biological diversity. Information obtained through twenty-first century science poses new challenges to taxonomy by offering the possibility of increased objectivity in independent and automated hypothesis formation. In recent years a number of promising new algorithmic approaches have been developed to recognize morphological diversity among insects based on multivariate morphometric analyses. These algorithms objectively delimit components in the data by automatically assigning objects into clusters.Method. In this paper, hypotheses on the diversity of the Malagasy Nesomyrmex angulatus group are formulated via a highly automated protocol involving a fusion of two algorithms, (1) Nest Centroid clustering (NC clustering) and (2) Partitioning Algorithm based on Recursive Thresholding (PART). Both algorithms assign samples into clusters, making the class assignment results of different algorithms readily inferable. The results were tested by confirmatory cross-validated Linear Discriminant Analysis (LOOCV-LDA).Results. Here we reveal the diversity of a unique and largely unexplored fragment of the Malagasy ant fauna using NC-PART-clustering on continuous morphological data, an approach that brings increased objectivity to taxonomy. We describe eight morphologically distinct species, including seven new species: Nesomyrmex angulatus (Mayr, 1862), N. bidentatussp. n., N. clypeatussp. n., N. deviussp. n., N. exiguussp. n., N. fragilissp. n., N. gracilissp. n., and N. hirtellussp. n.. An identification key for their worker castes using morphometric data is provided.Conclusions. Combining the dimensionality reduction feature of NC clustering with the assignment of samples into clusters by PART advances the automatization of morphometry-based alpha taxonomy. creator: Sándor Csősz creator: Brian L. Fisher uri: https://doi.org/10.7717/peerj.1796 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Csősz and Fisher title: Occurrence patterns of coral-dwelling gall crabs (Cryptochiridae) over depth intervals in the Caribbean link: https://peerj.com/articles/1794 last-modified: 2016-03-10 description: Coral-associated invertebrates form a major part of the diversity on reefs, but their distribution and occurrence patterns are virtually unstudied. For associated taxa data are lacking on their distribution across shelves and environmental gradients, but also over various depths. Off Curaçao we studied the prevalence and density of coral-dwelling gall crabs (Cryptochiridae), obligate symbionts of stony corals. Belt transects (10 × 0.5m2) were laid out at 6, 12 and 18 m depth intervals at 27 localities. Twenty-one known host coral species were surveyed, measured, and the number of crab dwellings was recorded to study the influence of host occurrence, depth distribution, and colony size on the occurrence rates of three Atlantic gall crab species: Opecarcinus hypostegus, Troglocarcinus corallicola and Kroppcarcinus siderastreicola. The overall gall crab prevalence rate was 20.3% across all available host corals at all depths. The agariciid-associated species O. hypostegus was found to mostly inhabit Agaricia lamarcki and its prevalence was highest at deeper depths, following the depth distribution of its host. Kroppcarcinus siderastreicola, associated with Siderastrea and Stephanocoenia, inhabited shallower depths despite higher host availability at deeper depths. The generalist species T. corallicola showed no clear host or depth specialisation. These results show that the primary factors affecting the distribution and occurrence rates over depth intervals differed between each of the three Atlantic cryptochirid species, which in turn influences their vulnerability to reef degradation. creator: Kaj M. van Tienderen creator: Sancia E.T. van der Meij uri: https://doi.org/10.7717/peerj.1794 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 van Tienderen and van der Meij title: Proteome-wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin link: https://peerj.com/articles/1791 last-modified: 2016-03-10 description: Besides its anti-inflammatory, analgesic and anti-pyretic properties, aspirin is used for the prevention of cardiovascular disease and various types of cancer. The multiple activities of aspirin likely involve several molecular targets and pathways rather than a single target. Therefore, systematic identification of these targets of aspirin can help us understand the underlying mechanisms of the activities. In this study, we identified 23 putative targets of aspirin in the human proteome by using binding pocket similarity detecting tool combination with molecular docking, free energy calculation and pathway analysis. These targets have diverse folds and are derived from different protein family. However, they have similar aspirin-binding pockets. The binding free energy with aspirin for newly identified targets is comparable to that for the primary targets. Pathway analysis revealed that the targets were enriched in several pathways such as vascular endothelial growth factor (VEGF) signaling, Fc epsilon RI signaling and arachidonic acid metabolism, which are strongly involved in inflammation, cardiovascular disease and cancer. Therefore, the predicted target profile of aspirin suggests a new explanation for the disease prevention ability of aspirin. Our findings provide a new insight of aspirin and its efficacy of disease prevention in a systematic and global view. creator: Shao-Xing Dai creator: Wen-Xing Li creator: Gong-Hua Li creator: Jing-Fei Huang uri: https://doi.org/10.7717/peerj.1791 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dai et al. title: Direct dating of Pleistocene stegodon from Timor Island, East Nusa Tenggara link: https://peerj.com/articles/1788 last-modified: 2016-03-10 description: Stegodons are a commonly recovered extinct proboscidean (elephants and allies) from the Pleistocene record of Southeast Asian oceanic islands. Estimates on when stegodons arrived on individual islands and the timings of their extinctions are poorly constrained due to few reported direct geochronological analyses of their remains. Here we report on uranium-series dating of a stegodon tusk recovered from the Ainaro Gravels of Timor. The six dates obtained indicate the local presence of stegodons in Timor at or before 130 ka, significantly pre-dating the earliest evidence of humans on the island. On the basis of current data, we find no evidence for significant environmental changes or the presence of modern humans in the region during that time. Thus, we do not consider either of these factors to have contributed significantly to their extinction. In the absence of these, we propose that their extinction was possibly the result of long-term demographic and genetic declines associated with an isolated island population. creator: Julien Louys creator: Gilbert J. Price creator: Sue O’Connor uri: https://doi.org/10.7717/peerj.1788 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Louys et al. title: Updating movement estimates for American black ducks (Anas rubripes) link: https://peerj.com/articles/1787 last-modified: 2016-03-10 description: Understanding migratory connectivity for species of concern is of great importance if we are to implement management aimed at conserving them. New methods are improving our understanding of migration; however, banding (ringing) data is by far the most widely available and accessible movement data for researchers. Here, we use band recovery data for American black ducks (Anas rubripes) from 1951–2011 and analyze their movement among seven management regions using a hierarchical Bayesian framework. We showed that black ducks generally exhibit flyway fidelity, and that many black ducks, regardless of breeding region, stopover or overwinter on the Atlantic coast of the United States. We also show that a non-trivial portion of the continental black duck population either does not move at all or moves to the north during the fall migration (they typically move to the south). The results of this analysis will be used in a projection modeling context to evaluate how habitat or harvest management actions in one region would propagate throughout the continental population of black ducks. This analysis may provide a guide for future research and help inform management efforts for black ducks as well as other migratory species. creator: Orin J. Robinson creator: Conor P. McGowan creator: Patrick K. Devers uri: https://doi.org/10.7717/peerj.1787 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Robinson et al. title: From commensalism to parasitism in Carapidae (Ophidiiformes): heterochronic modes of development? link: https://peerj.com/articles/1786 last-modified: 2016-03-10 description: Phenotypic variations allow a lineage to move into new regions of the adaptive landscape. The purpose of this study is to analyse the life history of the pearlfishes (Carapinae) in a phylogenetic framework and particularly to highlight the evolution of parasite and commensal ways of life. Furthermore, we investigate the skull anatomy of parasites and commensals and discuss the developmental process that would explain the passage from one form to the other. The genus Carapus forms a paraphyletic grouping in contrast to the genus Encheliophis, which forms a monophyletic cluster. The combination of phylogenetic, morphologic and ontogenetic data clearly indicates that parasitic species derive from commensal species and do not constitute an iterative evolution from free-living forms. Although the head morphology of Carapus species differs completely from Encheliophis, C. homei is the sister group of the parasites. Interestingly, morphological characteristics allowing the establishment of the relation between Carapus homei and Encheliophis spp. concern the sound-producing mechanism, which can explain the diversification of the taxon but not the acquisition of the parasite morphotype. Carapus homei already has the sound-producing mechanism typically found in the parasite form but still has a commensal way of life and the corresponding head structure. Moreover, comparisons between the larval and adult Carapini highlight that the adult morphotype “Encheliophis” is obtained by going beyond the adult stage reached by Carapus. The entrance into the new adaptive landscape could have been realised by at least two processes: paedomorphosis and allometric repatterning. creator: Eric Parmentier creator: Déborah Lanterbecq creator: Igor Eeckhaut uri: https://doi.org/10.7717/peerj.1786 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Parmentier et al. title: An exploration of key issues and potential solutions that impact physician wellbeing and professional fulfillment at an academic center link: https://peerj.com/articles/1783 last-modified: 2016-03-10 description: Background. Physician wellness is a vital element of a well-functioning health care system. Not only is physician wellness empirically associated with quality and patient outcomes, but its ramifications span individual, interpersonal, organizational, and societal levels. The purpose of this study was to explore academic physicians’ perceptions about their work-related wellness, including the following questions: (a) What are the workplace barriers and facilitators to their wellness? (b) What workplace solutions do theythinkwouldimprove their wellness? (c)What motivates their work? and (d) What existing wellness programs are they aware of?Methods. A multi-method design was applied to conduct a total of 19 focus group sessions in 17 clinical departments. All academic faculty ranks and career lines were represented in the 64 participating physicians, who began the sessions with five open-ended survey questions pertaining to physician wellness in their work environment. Participants entered their answers into a web-based survey program that enabled anonymous data collection. The initial survey component was followed by semi-structured focus group discussion. Data analysis of this qualitative study was informed by the general inductive approach as well as a review of extant literature through September 2015 on physician wellness, professional fulfillment, satisfaction, dissatisfaction, burnout and work-life.Results. Factors intrinsic to the work of physicians dominated the expressed reasons for work motivation. These factors all related to the theme of overall contribution, with categories of meaningful work, patient care, teaching, scientific discovery, self-motivation and matching of career interests. Extrinsic factors such as perceptions of suboptimal goal alignment, inadequate support, restricted autonomy, lack of appreciation, and suboptimal compensation and benefits dominated the risk of professional dissatisfaction.Discussion. Our findings indicate that the factors that enhance professional fulfillment and those that precipitate burnout are distinct: motivation and quality of work performed were supported by domains intrinsic to the work itself, whereas external dysfunctional work aspects resulted in frustration. Thus, it can be anticipated that optimization of physician wellness would require tailored approaches in each of these dimensions with sustained funding and support for wellness initiatives. Physicians identified the availability of resources to enable them to thrive and provide excellent patient care as their most important wellness-enhancing factor. creator: Iris Schrijver creator: Keri J.S. Brady creator: Mickey Trockel uri: https://doi.org/10.7717/peerj.1783 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Schrijver et al. title: H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups link: https://peerj.com/articles/1782 last-modified: 2016-03-10 description: Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities. creator: Sarah Piché-Choquette creator: Julien Tremblay creator: Susannah G. Tringe creator: Philippe Constant uri: https://doi.org/10.7717/peerj.1782 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Piché-Choquette et al. title: Microgeographic variation in locomotor traits among lizards in a human-built environment link: https://peerj.com/articles/1776 last-modified: 2016-03-10 description: Microgeographic variation in fitness-relevant traits may be more common than previously appreciated. The fitness of many vertebrates is directly related to their locomotor capacity, a whole-organism trait integrating behavior, morphology, and physiology. Because locomotion is inextricably related to context, I hypothesized that it might vary with habitat structure in a wide-ranging lizard, Podarcis erhardii, found in the Greek Cyclade Islands. I compared lizard populations living on human-built rock walls, a novel habitat with complex vertical structure, with nearby lizard populations that are naive to human-built infrastructure and live in flat, loose-substrate habitat. I tested for differences in morphology, behavior, and performance. Lizards from built sites were larger and had significantly (and relatively) longer forelimbs and hindlimbs. The differences in hindlimb morphology were especially pronounced for distal components—the foot and longest toe. These morphologies facilitated a significant behavioral shift in jumping propensity across a rocky experimental substrate. I found no difference in maximum velocity between these populations; however, females originating from wall sites potentially accelerated faster over the rocky experimental substrate. The variation between these closely neighboring populations suggests that the lizards inhabiting walls have experienced a suite of trait changes enabling them to take advantage of the novel habitat structure created by humans. creator: Colin Donihue uri: https://doi.org/10.7717/peerj.1776 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Donihue title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose link: https://peerj.com/articles/1768 last-modified: 2016-03-10 description: A better understanding of the control of lipogenesis is of critical importance for both human and animal physiology. This requires a better knowledge of the changes of gene expression during the process of adipose tissue development. Thus, the objective of the current study was to determine the effects of development on subcutaneous adipose tissue gene expression in growing and adult pigs. Here, we present a comprehensive investigation of mRNA transcriptomes in porcine subcutaneous adipose tissue across four developmental stages using digital gene expression profiling. We identified 3,274 differential expressed genes associated with oxidative stress, immune processes, apoptosis, energy metabolism, insulin stimulus, cell cycle, angiogenesis and translation. A set of universally abundant genes (ATP8, COX2, COX3, ND1, ND2, SCD and TUBA1B) was found across all four developmental stages. This set of genes may play important roles in lipogenesis and development. We also identified development-related gene expression patterns that are linked to the different adipose phenotypes. We showed that genes enriched in significantly up-regulated profiles were associated with phosphorylation and angiogenesis. In contrast, genes enriched in significantly down-regulated profiles were related to cell cycle and cytoskeleton organization, suggesting an important role for these biological processes in adipose growth and development. These results provide a resource for studying adipose development and promote the pig as a model organism for researching the development of human obesity, as well as being used in the pig industry. creator: Jie Zhang creator: Jideng Ma creator: Keren Long creator: Long Jin creator: Yihui Liu creator: Chaowei Zhou creator: Shilin Tian creator: Lei Chen creator: Zonggang Luo creator: Qianzi Tang creator: An’an Jiang creator: Xun Wang creator: Dawei Wang creator: Zhi Jiang creator: Jinyong Wang creator: Xuewei Li creator: Mingzhou Li uri: https://doi.org/10.7717/peerj.1768 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang et al. title: Effects of glucose, ethanol and acetic acid on regulation of ADH2 gene from Lachancea fermentati link: https://peerj.com/articles/1751 last-modified: 2016-03-10 description: Background. Not all yeast alcohol dehydrogenase 2 (ADH2) are repressed by glucose, as reported in Saccharomyces cerevisiae. Pichia stipitis ADH2 is regulated by oxygen instead of glucose, whereas Kluyveromyces marxianus ADH2 is regulated by neither glucose nor ethanol. For this reason, ADH2 regulation of yeasts may be species dependent, leading to a different type of expression and fermentation efficiency. Lachancea fermentati is a highly efficient ethanol producer, fast-growing cells and adapted to fermentation-related stresses such as ethanol and organic acid, but the metabolic information regarding the regulation of glucose and ethanol production is still lacking.Methods. Our investigation started with the stimulation of ADH2 activity from S. cerevisiae and L. fermentati by glucose and ethanol induction in a glucose-repressed medium. The study also embarked on the retrospective analysis of ADH2 genomic and protein level through direct sequencing and sites identification. Based on the sequence generated, we demonstrated ADH2 gene expression highlighting the conserved NAD(P)-binding domain in the context of glucose fermentation and ethanol production.Results. An increase of ADH2 activity was observed in starved L. fermentati (LfeADH2) and S. cerevisiae (SceADH2) in response to 2% (w/v) glucose induction. These suggest that in the presence of glucose, ADH2 activity was activated instead of being repressed. An induction of 0.5% (v/v) ethanol also increased LfeADH2 activity, promoting ethanol resistance, whereas accumulating acetic acid at a later stage of fermentation stimulated ADH2 activity and enhanced glucose consumption rates. The lack in upper stream activating sequence (UAS) and TATA elements hindered the possibility of Adr1 binding to LfeADH2. Transcription factors such as SP1 and RAP1 observed in LfeADH2 sequence have been implicated in the regulation of many genes including ADH2. In glucose fermentation, L. fermentati exhibited a bell-shaped ADH2 expression, showing the highest expression when glucose was depleted and ethanol-acetic acid was increased. Meanwhile, S. cerevisiae showed a constitutive ADH2 expression throughout the fermentation process.Discussion. ADH2 expression in L. fermentati may be subjected to changes in the presence of non-fermentative carbon source. The nucleotide sequence showed that ADH2 transcription could be influenced by other transcription genes of glycolysis oriented due to the lack of specific activation sites for Adr1. Our study suggests that if Adr1 is not capable of promoting LfeADH2 activation, the transcription can be controlled by Rap1 and Sp1 due to their inherent roles. Therefore in future, it is interesting to observe ADH2 gene being highly regulated by these potential transcription factors and functioned as a promoter for yeast under high volume of ethanol and organic acids. creator: Norhayati Yaacob creator: Mohd Shukuri Mohamad Ali creator: Abu Bakar Salleh creator: Nor Aini Abdul Rahman uri: https://doi.org/10.7717/peerj.1751 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yaacob et al. title: Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues link: https://peerj.com/articles/1762 last-modified: 2016-03-08 description: Background. Ruminants are successful herbivorous mammals, in part due to their specialized forestomachs, the rumen complex, which facilitates the conversion of feed to soluble nutrients by micro-organisms. Is the rumen complex a modified stomach expressing new epithelial (cornification) and metabolic programs, or a specialised stratified epithelium that has acquired new metabolic activities, potentially similar to those of the colon? How has the presence of the rumen affected other sections of the gastrointestinal tract (GIT) of ruminants compared to non-ruminants?Methods. Transcriptome data from 11 tissues covering the sheep GIT, two stratified epithelial and two control tissues, was analysed using principal components to cluster tissues based on gene expression profile similarity. Expression profiles of genes along the sheep GIT were used to generate a network to identify genes enriched for expression in different compartments of the GIT. The data from sheep was compared to similar data sets from two non-ruminants, pigs (closely related) and humans (more distantly related).Results. The rumen transcriptome clustered with the skin and tonsil, but not the GIT transcriptomes, driven by genes from the epidermal differentiation complex, and genes encoding stratified epithelium keratins and innate immunity proteins. By analysing all of the gene expression profiles across tissues together 16 major clusters were identified. The strongest of these, and consistent with the high turnover rate of the GIT, showed a marked enrichment of cell cycle process genes (P = 1.4 E−46), across the whole GIT, relative to liver and muscle, with highest expression in the caecum followed by colon and rumen. The expression patterns of several membrane transporters (chloride, zinc, nucleosides, amino acids, fatty acids, cholesterol and bile acids) along the GIT was very similar in sheep, pig and humans. In contrast, short chain fatty acid uptake and metabolism appeared to be different between the species and different between the rumen and colon in sheep. The importance of nitrogen and iodine recycling in sheep was highlighted by the highly preferential expression of SLC14A1-urea (rumen), RHBG-ammonia (intestines) and SLC5A5-iodine (abomasum). The gene encoding a poorly characterized member of the maltase-glucoamylase family (MGAM2), predicted to play a role in the degradation of starch or glycogen, was highly expressed in the small and large intestines.Discussion. The rumen appears to be a specialised stratified cornified epithelium, probably derived from the oesophagus, which has gained some liver-like and other specialized metabolic functions, but probably not by expression of pre-existing colon metabolic programs. Changes in gene transcription downstream of the rumen also appear have occurred as a consequence of the evolution of the rumen and its effect on nutrient composition flowing down the GIT. creator: Ruidong Xiang creator: Victor Hutton Oddy creator: Alan L. Archibald creator: Phillip E. Vercoe creator: Brian P. Dalrymple uri: https://doi.org/10.7717/peerj.1762 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Xiang et al. title: Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon link: https://peerj.com/articles/1758 last-modified: 2016-03-08 description: Diuron is a herbicide commonly used in agricultural areas where excess application causes it to leach into rivers, reach sensitive marine environments like the Great Barrier Reef (GBR) lagoon and pose risks to marine life. To investigate the impact of diuron on whole prokaryotic communities that underpin the marine food web and are integral to coral reef health, GBR lagoon water was incubated with diuron at environmentally-relevant concentration (8 µg/L), and sequenced at specific time points over the following year. 16S rRNA gene amplicon profiling revealed no significant short- or long-term effect of diuron on microbiome structure. The relative abundance of prokaryotic phototrophs was not significantly altered by diuron, which suggests that they were largely tolerant at this concentration. Assembly of a metagenome derived from waters sampled at a similar location in the GBR lagoon did not reveal the presence of mutations in the cyanobacterial photosystem that could explain diuron tolerance. However, resident phages displayed several variants of this gene and could potentially play a role in tolerance acquisition. Slow biodegradation of diuron was reported in the incubation flasks, but no correlation with the relative abundance of heterotrophs was evident. Analysis of metagenomic reads supports the hypothesis that previously uncharacterized hydrolases carried by low-abundance species may mediate herbicide degradation in the GBR lagoon. Overall, this study offers evidence that pelagic phototrophs of the GBR lagoon may be more tolerant of diuron than other tropical organisms, and that heterotrophs in the microbial seed bank may have the potential to degrade diuron and alleviate local anthropogenic stresses to inshore GBR ecosystems. creator: Florent E. Angly creator: Olga Pantos creator: Thomas C. Morgan creator: Virginia Rich creator: Hemerson Tonin creator: David G. Bourne creator: Philip Mercurio creator: Andrew P. Negri creator: Gene W. Tyson uri: https://doi.org/10.7717/peerj.1758 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Angly et al. title: A quantitative look on northwestern Tethyan foraminiferal assemblages, Campanian Nierental Formation, Austria link: https://peerj.com/articles/1757 last-modified: 2016-03-08 description: Deposits spanning the Radotruncana calcarata Taxon Range Zone at the Postalm section, Northern Calcareous Alps (Austria) are examined quantitatively for foraminiferal assemblages, especially the planktonic group. This study focuses on establishing a high resolution record spanning an 800 ka long stratigraphic interval from the active continental margin of the Penninic Ocean. The Postalm section displays reddish limestone- marl alternations representing precession cycles. For this study, 26 samples were taken bed by bed to allow a “per-precession-cycle” resolution (i.e., a minimum sample distance of ∼20 ka). Samples from limestones as well as from marls were examined for foraminiferal assemblages. Data suggest a typical, open marine Campanian foraminiferal community. The >63 µm fraction is dominated by opportunist taxa, i.e., members of Muricohedbergella and biserial planktic foraminifera. Archaeoglobigerina and “Globigerinelloides” appear frequently and benthic foraminifera are very sparsely found. The share of globotruncanids, representing more complex morphotypes amongst planktonic foraminifera, is recorded with 5–10%. The state of preservation of foraminifera from the Postalm section is moderate to poor. Differences between samples from marls and samples from limestone are evident, but do not reveal evidence that there was an influence on the postdepositional microfossil communities. However, data from microfossils showing moderate to bad preservation can still offer valuable insight into the palaeoenvironment and biostratigraphy. Information gathered on the composition of the planktonic foraminiferal assemblage confirms a low-to-mid-latitude setting for the Postalm section. As well resolved records of Late Cretaceous foraminifera assemblages are rare, the examination of the Radotruncana calcarata Taxon Range Zone provides some insights into variations and short term changes during the very short period of 800 ka. creator: Erik Wolfgring creator: Michael Wagreich uri: https://doi.org/10.7717/peerj.1757 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wolfgring and Wagreich title: Adverse events associated with incretin-based drugs in Japanese spontaneous reports: a mixed effects logistic regression model link: https://peerj.com/articles/1753 last-modified: 2016-03-08 description: Background: Spontaneous Reporting Systems (SRSs) are passive systems composed of reports of suspected Adverse Drug Events (ADEs), and are used for Pharmacovigilance (PhV), namely, drug safety surveillance. Exploration of analytical methodologies to enhance SRS-based discovery will contribute to more effective PhV. In this study, we proposed a statistical modeling approach for SRS data to address heterogeneity by a reporting time point. Furthermore, we applied this approach to analyze ADEs of incretin-based drugs such as DPP-4 inhibitors and GLP-1 receptor agonists, which are widely used to treat type 2 diabetes. Methods: SRS data were obtained from the Japanese Adverse Drug Event Report (JADER) database. Reported adverse events were classified according to the MedDRA High Level Terms (HLTs). A mixed effects logistic regression model was used to analyze the occurrence of each HLT. The model treated DPP-4 inhibitors, GLP-1 receptor agonists, hypoglycemic drugs, concomitant suspected drugs, age, and sex as fixed effects, while the quarterly period of reporting was treated as a random effect. Before application of the model, Fisher’s exact tests were performed for all drug-HLT combinations. Mixed effects logistic regressions were performed for the HLTs that were found to be associated with incretin-based drugs. Statistical significance was determined by a two-sided p-value <0.01 or a 99% two-sided confidence interval. Finally, the models with and without the random effect were compared based on Akaike’s Information Criteria (AIC), in which a model with a smaller AIC was considered satisfactory. Results: The analysis included 187,181 cases reported from January 2010 to March 2015. It showed that 33 HLTs, including pancreatic, gastrointestinal, and cholecystic events, were significantly associated with DPP-4 inhibitors or GLP-1 receptor agonists. In the AIC comparison, half of the HLTs reported with incretin-based drugs favored the random effect, whereas HLTs reported frequently tended to favor the mixed model. Conclusion: The model with the random effect was appropriate for analyzing frequently reported ADEs; however, further exploration is required to improve the model. The core concept of the model is to introduce a random effect of time. Modeling the random effect of time is widely applicable to various SRS data and will improve future SRS data analyses. creator: Daichi Narushima creator: Yohei Kawasaki creator: Shoji Takamatsu creator: Hiroshi Yamada uri: https://doi.org/10.7717/peerj.1753 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Narushima et al. title: Response diversity of free-floating plants to nutrient stoichiometry and temperature: growth and resting body formation link: https://peerj.com/articles/1781 last-modified: 2016-03-07 description: Free-floating plants, like most groups of aquatic primary producers, can become nuisance vegetation under certain conditions. On the other hand, there is substantial optimism for the applied uses of free-floating plants, such as wastewater treatment, biofuel production, and aquaculture. Therefore, understanding the species-specific responses of floating plants to abiotic conditions will inform both management decisions and the beneficial applications of these plants. I measured the responses of three floating plant species common in the northeast United States (Lemna minor, Spirodela polyrhiza, and Wolffia brasiliensis) to nutrient stoichiometry (nitrogen and phosphorus) and temperature in the laboratory. I also used survey data to determine the pattern of species richness of floating plants in the field and its relationship with the dominance of this group. Floating plant species exhibited unique responses to nutrient stoichiometry and temperature in the laboratory, especially under low temperatures (18 °C) and low nutrient conditions (0.5 mg N L−1, 0.083 mg P L−1). The three species displayed an apparent tradeoff with different strategies of growth or dormancy. In the field, water bodies with three or more species of floating plants were not more frequently dominated by this group. The response diversity observed in the lab may not be associated with the dominance of this group in the field because it is masked by environmental variability, has a weak effect, or is only important during transient circumstances. Future research to develop applied uses of floating plants should examine response diversity across a greater range of species or clones and environmental conditions. creator: Michael J. McCann uri: https://doi.org/10.7717/peerj.1781 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 McCann title: Growth and fatty acid characterization of microalgae isolated from municipal waste-treatment systems and the potential role of algal-associated bacteria in feedstock production link: https://peerj.com/articles/1780 last-modified: 2016-03-07 description: Much research has focused on growing microalgae for biofuel feedstock, yet there remain concerns about the feasibility of freshwater feedstock systems. To reduce cost and improve environmental sustainability, an ideal microalgal feedstock system would be fed by municipal, agricultural or industrial wastewater as a main source of water and nutrients. Nonetheless, the microalgae must also be tolerant of fluctuating wastewater quality, while still producing adequate biomass and lipid yields. To address this problem, our study focused on isolating and characterizing microalgal strains from three municipal wastewater treatment systems (two activated sludge and one aerated-stabilization basin systems) for their potential use in biofuel feedstock production. Most of the 19 isolates from wastewater grew faster than two culture collection strains under mixotrophic conditions, particularly with glucose. The fastest growing wastewater strains included the genera Chlorella and Dictyochloris. The fastest growing microalgal strains were not necessarily the best lipid producers. Under photoautotrophic and mixotrophic growth conditions, single strains of Chlorella and Scenedesmus each produced the highest lipid yields, including those most relevant to biodiesel production. A comparison of axenic and non-axenic versions of wastewater strains showed a notable effect of commensal bacteria on fatty acid composition. Strains grown with bacteria tended to produce relatively equal proportions of saturated and unsaturated fatty acids, which is an ideal lipid blend for biodiesel production. These results not only show the potential for using microalgae isolated from wastewater for growth in wastewater-fed feedstock systems, but also the important role that commensal bacteria may have in impacting the fatty acid profiles of microalgal feedstock. creator: Kevin Stemmler creator: Rebecca Massimi creator: Andrea E. Kirkwood uri: https://doi.org/10.7717/peerj.1780 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Stemmler et al. title: Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus link: https://peerj.com/articles/1779 last-modified: 2016-03-07 description: Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber. creator: Xiaoxu Zhou creator: Jun Cui creator: Shikai Liu creator: Derong Kong creator: He Sun creator: Chenlei Gu creator: Hongdi Wang creator: Xuemei Qiu creator: Yaqing Chang creator: Zhanjiang Liu creator: Xiuli Wang uri: https://doi.org/10.7717/peerj.1779 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhou et al. title: Analyzing the proximity to cover in a landscape of fear: a new approach applied to fine-scale habitat use by rabbits facing feral cat predation on Kerguelen archipelago link: https://peerj.com/articles/1769 last-modified: 2016-03-07 description: Although proximity to cover has been routinely considered as an explanatory variable in studies investigating prey behavioral adjustments to predation pressure, the way it shapes risk perception still remains equivocal. This paradox arises from both the ambivalent nature of cover as potentially both obstructive and protective, making its impact on risk perception complex and context-dependent, and from the choice of the proxy used to measure proximity to cover in the field, which leads to an incomplete picture of the landscape of fear experienced by the prey. Here, we study a simple predator-prey-habitat system, i.e., rabbits Oryctolagus cuniculus facing feral cat Felis catus predation on Kerguelen archipelago. We assess how cover shapes risk perception in prey and develop an easily implementable field method to improve the estimation of proximity to cover. In contrast to protocols considering the “distance to nearest cover”, we focus on the overall “area to cover”. We show that fine-scale habitat use by rabbits is clearly related to our measure, in accordance with our hypothesis of higher risk in patches with smaller area to cover in this predator-prey-habitat system. In contrast, classical measures of proximity to cover are not retained in the best predictive models of habitat use. The use of this new approach, together with a more in-depth consideration of contrasting properties of cover, could help to better understand the role of this complex yet decisive parameter for predator-prey ecology. creator: Pierrick Blanchard creator: Christine Lauzeral creator: Simon Chamaillé-Jammes creator: Nigel G. Yoccoz creator: Dominique Pontier uri: https://doi.org/10.7717/peerj.1769 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Blanchard et al. title: The miRNA biogenesis in marine bivalves link: https://peerj.com/articles/1763 last-modified: 2016-03-07 description: Small non-coding RNAs include powerful regulators of gene expression, transposon mobility and virus activity. Among the various categories, mature microRNAs (miRNAs) guide the translational repression and decay of several targeted mRNAs. The biogenesis of miRNAs depends on few gene products, essentially conserved from basal to higher metazoans, whose protein domains allow specific interactions with dsRNA. Here, we report the identification of key genes responsible of the miRNA biogenesis in 32 bivalves, with particular attention to the aquaculture species Mytilus galloprovincialis and Crassostrea gigas. In detail, we have identified and phylogenetically compared eight evolutionary conserved proteins: DROSHA, DGCR8, EXP5, RAN, DICER TARBP2, AGO and PIWI. In mussels, we recognized several other proteins participating in the miRNA biogenesis or in the subsequent RNA silencing. According to digital expression analysis, these genes display low and not inducible expression levels in adult mussels and oysters whereas they are considerably expressed during development. As miRNAs play an important role also in the antiviral responses, knowledge on their production and regulative effects can shed light on essential molecular processes and provide new hints for disease prevention in bivalves. creator: Umberto Rosani creator: Alberto Pallavicini creator: Paola Venier uri: https://doi.org/10.7717/peerj.1763 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rosani et al. title: Aboveground carbon in Quebec forests: stock quantification at the provincial scale and assessment of temperature, precipitation and edaphic properties effects on the potential stand-level stocking link: https://peerj.com/articles/1767 last-modified: 2016-03-03 description: Biological carbon sequestration by forest ecosystems plays an important role in the net balance of greenhouse gases, acting as a carbon sink for anthropogenic CO2 emissions. Nevertheless, relatively little is known about the abiotic environmental factors (including climate) that control carbon storage in temperate and boreal forests and consequently, about their potential response to climate changes. From a set of more than 94,000 forest inventory plots and a large set of spatial data on forest attributes interpreted from aerial photographs, we constructed a fine-resolution map (∼375 m) of the current carbon stock in aboveground live biomass in the 435,000 km2 of managed forests in Quebec, Canada. Our analysis resulted in an area-weighted average aboveground carbon stock for productive forestland of 37.6 Mg ha−1, which is lower than commonly reported values for similar environment. Models capable of predicting the influence of mean annual temperature, annual precipitation, and soil physical environment on maximum stand-level aboveground carbon stock (MSAC) were developed. These models were then used to project the future MSAC in response to climate change. Our results indicate that the MSAC was significantly related to both mean annual temperature and precipitation, or to the interaction of these variables, and suggest that Quebec’s managed forests MSAC may increase by 20% by 2041–2070 in response to climate change. Along with changes in climate, the natural disturbance regime and forest management practices will nevertheless largely drive future carbon stock at the landscape scale. Overall, our results allow accurate accounting of carbon stock in aboveground live tree biomass of Quebec’s forests, and provide a better understanding of possible feedbacks between climate change and carbon storage in temperate and boreal forests. creator: Louis Duchesne creator: Daniel Houle creator: Rock Ouimet creator: Marie-Claude Lambert creator: Travis Logan uri: https://doi.org/10.7717/peerj.1767 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Duchesne et al. title: The effect of weight controllability beliefs on prejudice and self-efficacy link: https://peerj.com/articles/1764 last-modified: 2016-03-03 description: An experiment was conducted to test for the presence of prejudice towards obesity and whether weight controllability beliefs information reduces this prejudice and impacts on a person’s own healthy eating self-efficacy. The experiment randomly allocated 346 participants (49 males) into one of three conditions: controllable contributors toward obesity condition (e.g., information about personal control about diet and exercise); uncontrollable contributors toward obesity condition (e.g., information about genes, factors in society); and a control condition with no information given. Prejudice was present in 81% of the sample. High prejudice was predicted by low self-efficacy for exercise and weight. Weight controllability beliefs information had no significant effect on prejudice levels or exercise or healthy eating self-efficacy levels. Future research directions are discussed. creator: Einar B. Thorsteinsson creator: Natasha M. Loi creator: Dana Breadsell uri: https://doi.org/10.7717/peerj.1764 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Thorsteinsson et al. title: The beneficial effects of cumulus cells and oocyte-cumulus cell gap junctions depends on oocyte maturation and fertilization methods in mice link: https://peerj.com/articles/1761 last-modified: 2016-03-03 description: Cumulus cells are a group of closely associated granulosa cells that surround and nourish oocytes. Previous studies have shown that cumulus cells contribute to oocyte maturation and fertilization through gap junction communication. However, it is not known how this gap junction signaling affects in vivo versus in vitro maturation of oocytes, and their subsequent fertilization and embryonic development following insemination. Therefore, in our study, we performed mouse oocyte maturation and insemination using in vivo- or in vitro-matured oocyte-cumulus complexes (OCCs, which retain gap junctions between the cumulus cells and the oocytes), in vitro-matured, denuded oocytes co-cultured with cumulus cells (DCs, which lack gap junctions between the cumulus cells and the oocytes), and in vitro-matured, denuded oocytes without cumulus cells (DOs). Using these models, we were able to analyze the effects of gap junction signaling on oocyte maturation, fertilization, and early embryo development. We found that gap junctions were necessary for both in vivo and in vitro oocyte maturation. In addition, for oocytes matured in vivo, the presence of cumulus cells during insemination improved fertilization and blastocyst formation, and this improvement was strengthened by gap junctions. Moreover, for oocytes matured in vitro, the presence of cumulus cells during insemination improved fertilization, but not blastocyst formation, and this improvement was independent of gap junctions. Our results demonstrate, for the first time, that the beneficial effect of gap junction signaling from cumulus cells depends on oocyte maturation and fertilization methods. creator: Cheng-Jie Zhou creator: Sha-Na Wu creator: Jiang-Peng Shen creator: Dong-Hui Wang creator: Xiang-Wei Kong creator: Angeleem Lu creator: Yan-Jiao Li creator: Hong-Xia Zhou creator: Yue-Fang Zhao creator: Cheng-Guang Liang uri: https://doi.org/10.7717/peerj.1761 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhou et al. title: Genetic structure of the threatened West-Pannonian population of Great Bustard (Otis tarda) link: https://peerj.com/articles/1759 last-modified: 2016-03-03 description: The genetic diversity, population structure and gene flow of the Great Bustards (Otis tarda) living in Austria-Slovakia-West Hungary (West-Pannonian region), one of the few populations of this globally threatened species that survives across the Palaearctic, has been assessed for the first time in this study. Fourteen recently developed microsatellite loci identified one single population in the study area, with high values of genetic diversity and gene flow between two different genetic subunits. One of these subunits (Heideboden) was recognized as a priority for conservation, as it could be crucial to maintain connectivity with the central Hungarian population and thus contribute to keeping contemporary genetic diversity. Current conservation efforts have been successful in saving this threatened population from extinction two decades ago, and should continue to guarantee its future survival. creator: Jose L. Horreo creator: Rainer Raab creator: Péter Spakovszky creator: Juan Carlos Alonso uri: https://doi.org/10.7717/peerj.1759 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Horreo et al. title: Cell cycle progression in glioblastoma cells is unaffected by pathophysiological levels of hypoxia link: https://peerj.com/articles/1755 last-modified: 2016-03-03 description: Hypoxia is associated with the increased malignancy of a broad range of solid tumours. While very severe hypoxia has been widely shown to induce cell cycle arrest, the impact of pathophysiological hypoxia on tumour cell proliferation is poorly understood. The aim of this study was to investigate the effect of different oxygen levels on glioblastoma (GBM) cell proliferation and survival. GBM is an extremely aggressive brain tumour with a heterogeneous oxygenation pattern. The effects of a range of oxygen tensions on GBM cell lines and primary cells were assessed using flow cytometry. Results indicate that cell cycle distribution and viability are unaffected by long term exposure (24–96 h) to pathophysiological levels of oxygen (1–8% O2). Both transient cell cycle arrest and small amounts of cell death could only be detected when cells were exposed to severe hypoxia (0.1% O2). No significant changes in p21 protein expression levels were detected. These findings reinforce the importance of using physiologically relevant oxygen tensions when investigating tumour hypoxia, and help to explain how solid tumours can be both hypoxic and highly proliferative, as is the case with GBM. creator: Rosalie Richards creator: Michael D. Jenkinson creator: Brian J. Haylock creator: Violaine See uri: https://doi.org/10.7717/peerj.1755 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Richards et al. title: The pretreatment albumin to globulin ratio predicts survival in patients with natural killer/T-cell lymphoma link: https://peerj.com/articles/1742 last-modified: 2016-03-03 description: Background. The pretreatment albumin to globulin ratio (AGR) has been reported to be a predictor of survival in several types of cancer. The aim of this study was to evaluate the prognostic impact of AGR in patients with natural killer/T-cell lymphoma (NKTCL).Methods. We retrospectively reviewed the available serum biochemistry results for 331 NKTCL patients before treatment. AGR was calculated as albumin/(total protein—albumin), and a cut-off value of 1.3 was used to define AGR as low or high. Survival analysis was used to assess the prognostic value of AGR.Results. A low AGR (<1.3) was associated with significantly more adverse clinical features, including old age, poor performance status, advanced stage, elevated lactate dehydrogenase, B symptoms, and high International Prognostic Index (IPI) and natural killer/T-cell lymphoma prognostic index (NKPI) scores. Patients with a low AGR had a significantly lower 5-year overall survival (44.5 vs. 65.2%, P < 0.001) and progression-free survival (33.1 vs. 57.4%, P < 0.001). In the multivariate analysis, a low AGR remained an independent predictor of poorer survival. Additionally, AGR distinguished patients with different outcomes in the IPI low-risk group and in the NKPI high-risk group.Discussion. Pretreatment AGR may serve as a simple and effective predictor of prognosis in patients with NKTCL. creator: Xi-wen Bi creator: Liang Wang creator: Wen-wen Zhang creator: Shu-mei Yan creator: Peng Sun creator: Yi Xia creator: Zhi-ming Li creator: Wen-qi Jiang uri: https://doi.org/10.7717/peerj.1742 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bi et al. title: Iflavirus increases its infectivity and physical stability in association with baculovirus link: https://peerj.com/articles/1687 last-modified: 2016-03-03 description: Virus transmission and the prevalence of infection depend on multiple factors, including the interaction with other viral pathogens infecting the same host. In this study, active replication of an iflavirus, Spodoptera exigua iflavirus 1 (order Picornavirales) was observed in the offspring of insects that survived following inoculation with a pathogenic baculovirus, Spodoptera exigua multiple nucleopolyhedrovirus. Tracking the origin of the iflavirus suggested the association of this virus with the occlusion bodies of the baculovirus. Here we investigated the effect of this association on the stability and infectivity of both viruses. A reduction in baculovirus pathogenicity, without affecting its infectivity and productivity, was observed when associated with the iflavirus. In contrast, viral association increased the infectivity of the iflavirus and its resistance to ultraviolet radiation and high temperature, two of the main factors affecting virus stability in the field. In addition, electron microscopy analysis revealed the presence of particles resembling iflavirus virions inside the occlusion bodies of the baculovirus, suggesting the possible co-occlusion of both viruses. Results reported here are indicative of facultative phoresis of a virus and suggest that virus–virus interactions may be more common than currently recognized, and may be influential in the ecology of baculovirus and host populations and in consequence in the use of baculoviruses as biological insecticides. creator: Agata K. Jakubowska creator: Rosa Murillo creator: Arkaitz Carballo creator: Trevor Williams creator: Jan W.M. van Lent creator: Primitivo Caballero creator: Salvador Herrero uri: https://doi.org/10.7717/peerj.1687 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jakubowska et al. title: Increasing land use drives changes in plant phylogenetic diversity and prevalence of specialists link: https://peerj.com/articles/1740 last-modified: 2016-03-01 description: Increased human land use has resulted in the increased homogenization of biodiversity between sites, yet we lack sufficient indicators to predict which species decline and the consequence of their potential loss on ecosystem services. We used comparative phylogenetic analysis to (1) characterize how increasing conversion of forest and grasslands to grazing pasturelands changes plant diversity and composition; (2) examine how changes in land use relate to declines in functional trait diversity; and (3) specifically investigate how these changes in plant composition affect the prevalence of zygomorphy and the possible consequences that these changes may have on pollinator functional groups. As predicted, we found that the conversion to grazing pasturelands negatively impacted species richness and phylogenetic composition. Clades with significantly more represented taxa in grasslands (GL) were genera with a high representation of agricultural weeds, while the composition was biased towards clades of subalpine herbaceous wildflowers in Mixed Forest (MF). Changes in community composition and structure had strong effects on the prevalence of zygomorphic species likely driven by nitrogen-fixing abilities of certain clades with zygomorphic flowers (e.g., Fabaceae). Land conversion can thus have unexpected impacts on trait distributions relevant for the functioning of the community in other capacities (e.g., cascading effects to other trophic levels (i.e., pollinators). Finally, the combination of traits represented by the current composition of species in GL and MF might enhance the diagnostic value of productivity and ecosystem processes in the most eroded ecosystems. creator: Soraya Villalobos creator: Jana C. Vamosi uri: https://doi.org/10.7717/peerj.1740 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Villalobos and Vamosi title: The (mis)measurement of the Dark Triad Dirty Dozen: exploitation at the core of the scale link: https://peerj.com/articles/1748 last-modified: 2016-03-01 description: Background. The dark side of human character has been conceptualized in the Dark Triad Model: Machiavellianism, psychopathy, and narcissism. These three dark traits are often measured using single long instruments for each one of the traits. Nevertheless, there is a necessity of short and valid personality measures in psychological research. As an independent research group, we replicated the factor structure, convergent validity and item response for one of the most recent and widely used short measures to operationalize these malevolent traits, namely, Jonason’s Dark Triad Dirty Dozen. We aimed to expand the understanding of what the Dirty Dozen really captures because the mixed results on construct validity in previous research.Method. We used the largest sample to date to respond to the Dirty Dozen (N = 3,698). We firstly investigated the factor structure using Confirmatory Factor Analysis and an exploratory distribution analysis of the items in the Dirty Dozen. Secondly, using a sub-sample (n = 500) and correlation analyses, we investigated the Dirty Dozen dark traits convergent validity to Machiavellianism measured by the Mach-IV, psychopathy measured by Eysenck’s Personality Questionnaire Revised, narcissism using the Narcissism Personality Inventory, and both neuroticism and extraversion from the Eysenck’s questionnaire. Finally, besides these Classic Test Theory analyses, we analyzed the responses for each Dirty Dozen item using Item Response Theory (IRT).Results. The results confirmed previous findings of a bi-factor model fit: one latent core dark trait and three dark traits. All three Dirty Dozen traits had a striking bi-modal distribution, which might indicate unconcealed social undesirability with the items. The three Dirty Dozen traits did converge too, although not strongly, with the contiguous single Dark Triad scales (r between .41 and .49). The probabilities of filling out steps on the Dirty Dozen narcissism-items were much higher than on the Dirty Dozen items for Machiavellianism and psychopathy. Overall, the Dirty Dozen instrument delivered the most predictive value with persons with average and high Dark Triad traits (theta > −0.5). Moreover, the Dirty Dozen scale was better conceptualized as a combined Machiavellianism-psychopathy factor, not narcissism, and is well captured with item 4: ‘I tend to exploit others towards my own end.’Conclusion. The Dirty Dozen showed a consistent factor structure, a relatively convergent validity similar to that found in earlier studies. Narcissism measured using the Dirty Dozen, however, did not contribute with information to the core of the Dirty Dozen construct. More importantly, the results imply that the core of the Dirty Dozen scale, a manipulative and anti-social trait, can be measured by a Single Item Dirty Dark Dyad (SIDDD). creator: Petri J. Kajonius creator: Björn N. Persson creator: Patricia Rosenberg creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.1748 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kajonius et al. title: Looking upstream: enhancers of child nutritional status in post-flood rural settings link: https://peerj.com/articles/1741 last-modified: 2016-03-01 description: Background. Child undernutrition and flooding are highly prevalent public health issues in many developing countries, yet we have little understanding of preventive strategies for effective coping in these circumstances. Education has been recently highlighted as key to reduce the societal impacts of extreme weather events under climate change, but there is a lack of studies assessing to what extent parental education may prevent post-flood child undernutrition.Methods and Materials. One year after large floods in 2008, we conducted a two-stage cluster population-based survey of 6–59 months children inhabiting flooded and non-flooded communities of Jagatsinghpur district, Odisha (India), and collected anthropometric measurements on children along with child, parental and household level variables through face-to-face interviews. Using multivariate logistic regression models, we examined separately the effect of maternal and paternal education and other risk factors (mainly income, socio-demographic, and child and mother variables) on stunting and wasting in children from households inhabiting recurrently flooded communities (2006 and 2008; n = 299). As a comparison, separate analyses on children in non-flooded communities were carried out (n = 385). All analyses were adjusted by income as additional robustness check.Results. Overall, fathers with at least completed middle education (up to 14 years of age and compulsory in India) had an advantage in protecting their children from child wasting and stunting. For child stunting, the clearest result was a 100–200% lower prevalence associated with at least paternal secondary schooling (compared to no schooling) in flooded-areas. Again, only in flooded communities, an increase in per capita annual household income of 1,000 rupees was associated to a 4.7–4.9% lower prevalence of child stunting. For child wasting in flooded areas, delayed motherhood was associated to better nutritional outcomes (3.4% lower prevalence per year). In flooded communities, households dedicated to activities other than agriculture, a 50–51% lower prevalence of child wasting was estimated, suggesting farmers and fishermen as the most vulnerable livelihoods under flooding. In flooded areas, lower rank castes were at higher odds of both child wasting and stunting.Conclusions. In the short-term, protracted nutritional response in the aftermath of floods should be urgently implemented and target agricultural livelihoods and low-rank castes. Education promotion and schooling up to 14 years should have positive impacts on improving children nutritional health in the long run, especially under flooding. Policies effectively helping sustainable livelihood economic development and delayed motherhood are also recommended. creator: Jose Manuel Rodriguez-Llanes creator: Shishir Ranjan-Dash creator: Alok Mukhopadhyay creator: Debarati Guha-Sapir uri: https://doi.org/10.7717/peerj.1741 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rodriguez-Llanes et al. title: An examination of clinical differences between carriers and non-carriers of chromosome 8q24 risk alleles in a New Zealand Caucasian population with prostate cancer link: https://peerj.com/articles/1731 last-modified: 2016-03-01 description: Background. Prostate cancer makes up approximately 15% of all cancers diagnosed in men in developed nations and approximately 4% of cases in developing nations. Although it is clear that prostate cancer has a genetic component and single nucleotide polymorphisms (SNPs) can contribute to prostate cancer risk, detecting associations is difficult in multi-factorial diseases, as environmental and lifestyle factors also play a role. In this study, specific clinical characteristics, environmental factors and genetic risk factors were assessed for interaction with prostate cancer.Methods. A total of 489 prostate cancer cases and 427 healthy controls were genotyped for SNPs found on chromosome 8q24 and a genetic risk score was calculated. In addition the SNPs were tested for an association with a number of clinical and environmental factors.Results. Age and tobacco use were positively associated, whilst alcohol consumption was negatively associated with prostate cancer risk. The following SNPs found on chromosome 8q24 were statistically significantly associated with prostate cancer: rs10086908, rs16901979; rs1447295and rs4242382. No association between Gleason score and smoking status, or between Gleason score and genotype were detected.Conclusion. A genetic risk score was calculated based on the 15 SNPs tested and found to be significantly associated with prostate cancer risk. Smoking significantly contributed to the risk of developing prostate cancer, and this risk was further increased by the presence of four SNPs in the 8q24 chromosomal region. creator: Karen S. Bishop creator: Dug Yeo Han creator: Nishi Karunasinghe creator: Megan Goudie creator: Jonathan G. Masters creator: Lynnette R. Ferguson uri: https://doi.org/10.7717/peerj.1731 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bishop et al. title: New phiomorph rodents from the latest Eocene of Egypt, and the impact of Bayesian “clock”-based phylogenetic methods on estimates of basal hystricognath relationships and biochronology link: https://peerj.com/articles/1717 last-modified: 2016-03-01 description: The Fayum Depression of Egypt has yielded fossils of hystricognathous rodents from multiple Eocene and Oligocene horizons that range in age from ∼37 to ∼30 Ma and document several phases in the early evolution of crown Hystricognathi and one of its major subclades, Phiomorpha. Here we describe two new genera and species of basal phiomorphs, Birkamys korai and Mubhammys vadumensis, based on rostra and maxillary and mandibular remains from the terminal Eocene (∼34 Ma) Fayum Locality 41 (L-41). Birkamys is the smallest known Paleogene hystricognath, has very simple molars, and, like derived Oligocene-to-Recent phiomorphs (but unlike contemporaneous and older taxa) apparently retained dP4∕4 late into life, with no evidence for P4∕4 eruption or formation. Mubhammys is very similar in dental morphology to Birkamys, and also shows no evidence for P4∕4 formation or eruption, but is considerably larger. Though parsimony analysis with all characters equally weighted places Birkamys and Mubhammys as sister taxa of extant Thryonomys to the exclusion of much younger relatives of that genus, all other methods (standard Bayesian inference, Bayesian “tip-dating,” and parsimony analysis with scaled transitions between “fixed” and polymorphic states) place these species in more basal positions within Hystricognathi, as sister taxa of Oligocene-to-Recent phiomorphs. We also employ tip-dating as a means for estimating the ages of early hystricognath-bearing localities, many of which are not well-constrained by geological, geochronological, or biostratigraphic evidence. By simultaneously taking into account phylogeny, evolutionary rates, and uniform priors that appropriately encompass the range of possible ages for fossil localities, dating of tips in this Bayesian framework allows paleontologists to move beyond vague and assumption-laden “stage of evolution” arguments in biochronology to provide relatively rigorous age assessments of poorly-constrained faunas. This approach should become increasingly robust as estimates are combined from multiple independent analyses of distantly related clades, and is broadly applicable across the tree of life; as such it is deserving of paleontologists’ close attention. Notably, in the example provided here, hystricognathous rodents from Libya and Namibia that are controversially considered to be of middle Eocene age are instead estimated to be of late Eocene and late Oligocene age, respectively. Finally, we reconstruct the evolution of first lower molar size among Paleogene African hystricognaths using a Bayesian approach; the results of this analysis reconstruct a rapid latest Eocene dwarfing event along the lineage leading to Birkamys. creator: Hesham M. Sallam creator: Erik R. Seiffert uri: https://doi.org/10.7717/peerj.1717 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sallam and Seiffert title: Ultra-structural changes and expression of chondrogenic and hypertrophic genes during chondrogenic differentiation of mesenchymal stromal cells in alginate beads link: https://peerj.com/articles/1650 last-modified: 2016-03-01 description: Chondrogenic differentiation of mesenchymal stromal cells (MSCs) in the form of pellet culture and encapsulation in alginate beads has been widely used as conventional model for in vitro chondrogenesis. However, comparative characterization between differentiation, hypertrophic markers, cell adhesion molecule and ultrastructural changes during alginate and pellet culture has not been described. Hence, the present study was conducted comparing MSCs cultured in pellet and alginate beads with monolayer culture. qPCR was performed to assess the expression of chondrogenic, hypertrophic, and cell adhesion molecule genes, whereas transmission electron microscopy (TEM) was used to assess the ultrastructural changes. In addition, immunocytochemistry for Collagen type II and aggrecan and glycosaminoglycan (GAG) analysis were performed. Our results indicate that pellet and alginate bead cultures were necessary for chondrogenic differentiation of MSC. It also indicates that cultures using alginate bead demonstrated significantly higher (p < 0.05) chondrogenic but lower hypertrophic (p < 0.05) gene expressions as compared with pellet cultures. N-cadherin and N-CAM1 expression were up-regulated in second and third weeks of culture and were comparable between the alginate bead and pellet culture groups, respectively. TEM images demonstrated ultrastructural changes resembling cell death in pellet cultures. Our results indicate that using alginate beads, MSCs express higher chondrogenic but lower hypertrophic gene expression. Enhanced production of extracellular matrix and cell adhesion molecules was also observed in this group. These findings suggest that alginate bead culture may serve as a superior chondrogenic model, whereas pellet culture is more appropriate as a hypertrophic model of chondrogenesis. creator: Havva Dashtdar creator: Malliga Raman Murali creator: Lakshmi Selvaratnam creator: Hanumantharao Balaji Raghavendran creator: Abdulrazzaq Mahmod Suhaeb creator: Tunku Sara Ahmad creator: Tunku Kamarul uri: https://doi.org/10.7717/peerj.1650 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dashtdar et al.