title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-10
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Two different approaches to the affective profiles model: median splits (variable-oriented) and cluster analysis (person-oriented)
link: https://peerj.com/articles/1380
last-modified: 2015-10-29
description: Background. The notion of the affective system as being composed of two dimensions led Archer and colleagues to the development of the affective profiles model. The model consists of four different profiles based on combinations of individuals’ experience of high/low positive and negative affect: self-fulfilling, low affective, high affective, and self-destructive. During the past 10 years, an increasing number of studies have used this person-centered model as the backdrop for the investigation of between and within individual differences in ill-being and well-being. The most common approach to this profiling is by dividing individuals’ scores of self-reported affect using the median of the population as reference for high/low splits. However, scores just-above and just-below the median might become high and low by arbitrariness, not by reality. Thus, it is plausible to criticize the validity of this variable-oriented approach. Our aim was to compare the median splits approach with a person-oriented approach, namely, cluster analysis.Method. The participants (N = 2, 225) were recruited through Amazons’ Mechanical Turk and asked to self-report affect using the Positive Affect Negative Affect Schedule. We compared the profiles’ homogeneity and Silhouette coefficients to discern differences in homogeneity and heterogeneity between approaches. We also conducted exact cell-wise analyses matching the profiles from both approaches and matching profiles and gender to investigate profiling agreement with respect to affectivity levels and affectivity and gender. All analyses were conducted using the ROPstat software.Results. The cluster approach (weighted average of cluster homogeneity coefficients = 0.62, Silhouette coefficients = 0.68) generated profiles with greater homogeneity and more distinctive from each other compared to the median splits approach (weighted average of cluster homogeneity coefficients = 0.75, Silhouette coefficients = 0.59). Most of the participants (n = 1,736, 78.0%) were allocated to the same profile (Rand Index = .83), however, 489 (21.98%) were allocated to different profiles depending on the approach. Both approaches allocated females and males similarly in three of the four profiles. Only the cluster analysis approach classified men significantly more often than chance to a self-fulfilling profile (type) and females less often than chance to this very same profile (antitype).Conclusions. Although the question whether one approach is more appropriate than the other is still without answer, the cluster method allocated individuals to profiles that are more in accordance with the conceptual basis of the model and also to expected gender differences. More importantly, regardless of the approach, our findings suggest that the model mirrors a complex and dynamic adaptive system.
creator: Danilo Garcia
creator: Shane MacDonald
creator: Trevor Archer
uri: https://doi.org/10.7717/peerj.1380
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Garcia et al.

title: Biotransformation of Momordica charantia fresh juice by Lactobacillus plantarum BET003 and its putative anti-diabetic potential
link: https://peerj.com/articles/1376
last-modified: 2015-10-29
description: Lactobacillus plantarum BET003 isolated from Momordica charantia fruit was used to ferment its juice. Momordica charantia fresh juice was able to support good growth of the lactic acid bacterium. High growth rate and cell viability were obtained without further nutrient supplementation. In stirred tank reactor batch fermentation, agitation rate showed significant effect on specific growth rate of the bacterium in the fruit juice. After the fermentation, initially abundant momordicoside 23-O-β-Allopyranosyle-cucurbita-5,24-dien-7α,3β,22(R),23(S)-tetraol-3-O-β-allopyranoside was transformed into its corresponding aglycone in addition to the emergence of new metabolites. The fermented M. charantia juice consistently reduced glucose production by 27.2%, 14.5%, 17.1% and 19.2% at 15-minute intervals respectively, when compared against the negative control. This putative anti-diabetic activity can be attributed to the increase in availability and concentration of aglycones as well as other phenolic compounds resulting from degradation of glycosidic momordicoside. Biotransformation of M. charantia fruit juice via lactic acid bacterium fermentation reduced its bitterness, reduced its sugar content, produced aglycones and other metabolites as well as improved its inhibition of α-glucosidase activity compared with the fresh, non-fermented juice.
creator: Farhaneen Afzal Mazlan
creator: M. Suffian M. Annuar
creator: Yusrizam Sharifuddin
uri: https://doi.org/10.7717/peerj.1376
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Mazlan et al.

title: The association between negative attention biases and symptoms of depression in a community sample of adolescents
link: https://peerj.com/articles/1372
last-modified: 2015-10-29
description: Adolescence is a vulnerable time for the onset of depression. Recent evidence from adult studies suggests not only that negative attention biases are correlated with symptoms of depression, but that reducing negative attention biases through training can in turn reduce symptomology. The role and plasticity of attention biases in adolescent depression, however, remains unclear. This study examines the association between symptoms of depression and attention biases, and whether such biases are modifiable, in a community sample of adolescents. We report data from 105 adolescents aged 13–17 who completed a dot-probe measure of attention bias before and after a single session of visual search-based cognitive bias modification training. This is the first study to find a significant association between negative attention biases and increased symptoms of depression in a community sample of adolescents. Contrary to expectations, we were unable to manipulate attention biases using a previously successful cognitive bias modification task. There were no significant effects of the training on positive affect and only modest effects of the training, identified in post-hoc analyses, were observed on negative affect. Our data replicate those from the adult literature, which suggest that adolescent depression is a disorder associated with negative attention biases, although we were unable to modify attention biases in our study. We identify numerous parameters of our methodology which may explain these null training effects, and which could be addressed in future cognitive bias modification studies of adolescent depression.
creator: Belinda Platt
creator: Susannah E. Murphy
creator: Jennifer Y.F. Lau
uri: https://doi.org/10.7717/peerj.1372
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Platt et al.

title: Genetic models reveal historical patterns of sea lamprey population fluctuations within Lake Champlain
link: https://peerj.com/articles/1369
last-modified: 2015-10-29
description: The origin of sea lamprey (Petromyzon marinus) in Lake Champlain has been heavily debated over the past decade. Given the lack of historical documentation, two competing hypotheses have emerged in the literature. First, it has been argued that the relatively recent population size increase and concomitant rise in wounding rates on prey populations are indicative of an invasive population that entered the lake through the Champlain Canal. Second, recent genetic evidence suggests a post-glacial colonization at the end of the Pleistocene, approximately 11,000 years ago. One limitation to resolving the origin of sea lamprey in Lake Champlain is a lack of historical and current measures of population size. In this study, the issue of population size was explicitly addressed using nuclear (nDNA) and mitochondrial DNA (mtDNA) markers to estimate historical demography with genetic models. Haplotype network analysis, mismatch analysis, and summary statistics based on mtDNA noncoding sequences for NCI (479 bp) and NCII (173 bp) all indicate a recent population expansion. Coalescent models based on mtDNA and nDNA identified two potential demographic events: a population decline followed by a very recent population expansion. The decline in effective population size may correlate with land-use and fishing pressure changes post-European settlement, while the recent expansion may be associated with the implementation of the salmonid stocking program in the 1970s. These results are most consistent with the hypothesis that sea lamprey are native to Lake Champlain; however, the credibility intervals around parameter estimates demonstrate that there is uncertainty regarding the magnitude and timing of past demographic events.
creator: Cassidy C. D’Aloia
creator: Christina B. Azodi
creator: Sallie P. Sheldon
creator: Stephen C. Trombulak
creator: William R. Ardren
uri: https://doi.org/10.7717/peerj.1369
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Getting the most out of RNA-seq data analysis
link: https://peerj.com/articles/1360
last-modified: 2015-10-29
description: Background. A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally, or use them for downstream systems biology analysis. Producing a coherent differential gene expression analysis from RNA-seq count data requires an understanding of how numerous sources of variation such as the replicate size, the hypothesized biological effect size, and the specific method for making differential expression calls interact. We believe an explicit demonstration of such interactions in real RNA-seq data sets is of practical interest to biologists.Results. Using two large public RNA-seq data sets—one representing strong, and another mild, biological effect size—we simulated different replicate size scenarios, and tested the performance of several commonly-used methods for calling differentially expressed genes in each of them. We found that, when biological effect size was mild, RNA-seq experiments should focus on experimental validation of differentially expressed gene candidates. Importantly, at least triplicates must be used, and the differentially expressed genes should be called using methods with high positive predictive value (PPV), such as NOISeq or GFOLD. In contrast, when biological effect size was strong, differentially expressed genes mined from unreplicated experiments using NOISeq, ASC and GFOLD had between 30 to 50% mean PPV, an increase of more than 30-fold compared to the cases of mild biological effect size. Among methods with good PPV performance, having triplicates or more substantially improved mean PPV to over 90% for GFOLD, 60% for DESeq2, 50% for NOISeq, and 30% for edgeR. At a replicate size of six, we found DESeq2 and edgeR to be reasonable methods for calling differentially expressed genes at systems level analysis, as their PPV and sensitivity trade-off were superior to the other methods’.Conclusion. When biological effect size is weak, systems level investigation is not possible using RNAseq data, and no meaningful result can be obtained in unreplicated experiments. Nonetheless, NOISeq or GFOLD may yield limited numbers of gene candidates with good validation potential, when triplicates or more are available. When biological effect size is strong, NOISeq and GFOLD are effective tools for detecting differentially expressed genes in unreplicated RNA-seq experiments for qPCR validation. When triplicates or more are available, GFOLD is a sharp tool for identifying high confidence differentially expressed genes for targeted qPCR validation; for downstream systems level analysis, combined results from DESeq2 and edgeR are useful.
creator: Tsung Fei Khang
creator: Ching Yee Lau
uri: https://doi.org/10.7717/peerj.1360
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Khang and Lau

title: Overexpression of IFITM3 predicts the high risk of lymphatic metastatic recurrence in pN0 esophageal squamous cell carcinoma after Ivor-Lewis esophagectomy
link: https://peerj.com/articles/1355
last-modified: 2015-10-29
description: Background. Recent studies have shown that the aberrant expression of IFITM3 is implicated in the lymph node metastasis of many malignancies. Our research aimed to investigate the expression of IFITM3 in pathological N0 (pN0) esophageal squamous cell carcinoma (ESCC) and its relationship with lymph node metastatic recurrence.Methods. Immunohistochemistry (IHC) was used to examine the expression profile of IFITM3 in 104 pairs of samples. Each pair consisted of ESCC tissue and its adjacent normal mucosa (ANM). This aberrant expression was verified by reverse transcription-polymerase chain reaction (RT-PCR) with 20 tumor specimens with strong immunostaining and their mucosal tissues. In addition, 20 samples of low expression tissues and their ANMs were evaluated. Moreover, the correlations between the IFITM3 expression level and the clinicopathological variables, recurrence risk and overall survival (OS) of patients were analyzed.Results. Both IHC and RT-PCR demonstrated that the IFITM3 expression level was significantly higher in tumor tissue than in ANM. Statistical analysis showed a significant correlation of IFITM3 expression with the T status of esophageal cancer (p = 0.015). In addition, IFITM3 overexpression was demonstrated to be not only an important risk factor of lymphatic metastatic recurrence but a significant prognostic factor in pN0 ESCC (p < 0.005).Conclusions. Even pN0 ESCC patients will still experience lymphatic metastatic recurrence. The IFITM3 gene could be a predictor of lymphatic metastatic recurrence in pN0 ESCC after Ivor-Lewis esophagectomy.
creator: Yang Jia
creator: Miao Zhang
creator: Wenpeng Jiang
creator: Zhiping Zhang
creator: Shiting Huang
creator: Zhou Wang
uri: https://doi.org/10.7717/peerj.1355
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Jia et al.

title: Effects of the acanthocephalan Polymorphus minutus and the microsporidian Dictyocoela duebenum on energy reserves and stress response of cadmium exposed Gammarus fossarum
link: https://peerj.com/articles/1353
last-modified: 2015-10-29
description: Amphipods are commonly parasitized by acanthocephalans and microsporidians and co-infections are found frequently. Both groups of parasites are known to have severe effects on their host. For example, microsporidians can modify host sex ratio and acanthocephalans can manipulate the behavior of the amphipod to promote transmission to the final host. These effects influence host metabolism in general and will also affect the ability of amphipods to cope with additional stressors such as environmental pollution, e.g., by toxic metals. Here we tested the effects of sub-lethal concentrations of cadmium on glycogen and lipid levels, as well as on the 70kDa heat shock protein (hsp70) response of field collected Gammarus fossarum, which were naturally infected with microsporidians and the acanthocephalan Polymorphus minutus. Infected and uninfected G. fossarum were exposed to a nominal Cd concentration of 4 µg/L, which resembled measured aqueous Cd concentration of 2.9 µg/L in reconstituted water for 7 d at 15 °C in parallel to an unexposed control. After exposure gammarids were snap frozen, weighed, sexed and tested for microsporidian infection by PCR. Only individuals containing the microsporidian Dictyocoela duebenum were used for the further biochemical and metal analyses. P. minutus infected amphipods were significantly smaller than their uninfected conspecifics. Mortality was insignificantly increased due to cadmium exposure, but not due to parasite infection. Microsporidian infection in combination with cadmium exposure led to increased glycogen levels in female gammarids. An increase of glycogen was also found due to interaction of acanthocephalan and microsporidian infection. Elevated lipid levels were observed in all groups infected with microsporidians, while acanthocephalans had the opposite effect. A positive correlation of lipid and glycogen levels was observed. The general stress response measured in form of hsp70 was significantly increased in microsporidian infected gammarids exposed to cadmium. P. minutus did not affect the stress response of its host. Lipid levels were correlated negatively with hsp70 response, and indicated a possible increased stress susceptibility of individuals with depleted energy reserves. The results of our study clearly demonstrate the importance of parasitic infections, especially of microsporidians, for ecotoxicological research.
creator: Hui-Yu Chen
creator: Daniel S. Grabner
creator: Milen Nachev
creator: Hsiu-Hui Shih
creator: Bernd Sures
uri: https://doi.org/10.7717/peerj.1353
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Chen et al.

title: An investigation of the genus Mesacanthus (Chordata: Acanthodii) from the Orcadian Basin and Midland Valley areas of Northern and Central Scotland using traditional morphometrics
link: https://peerj.com/articles/1331
last-modified: 2015-10-29
description: Mesacanthus is a common and speciose genus of acanthodian fish from Lower Old Red Sandstone and Middle Old Red Sandstone assemblages (representing the Lower Devonian and Middle Devonian respectively) and is well represented in many palaeoichthyology collections in the UK. Based upon descriptions given during the 19th century, specimens of the genus Mesacanthus from the Orcadian Basin and Midland Valley areas of Northern and Central Scotland have historically been referred to a number of different species; of these, the most frequently discussed in the literature are M. mitchelli, M. peachi and M. pusillus. In order to test the validity of these three species, traditional morphometric analyses were carried out on over 100 specimens of Mesacanthus, from both the Lower Devonian and the Middle Devonian, that cover the full range of known localities for these taxa in Northern and Central Scotland. Based upon morphological and morphometric comparisons, this investigation has found that at least two species of Mesacanthus are valid (M. mitchelli and M. pusillus) as specimens from the Lower Devonian and Middle Devonian have been shown to differ significantly in a number of important ways. However, no evidence has been found for the validity of the second and distinct Middle Devonian species, M. peachi.
creator: Matthew G. Baron
uri: https://doi.org/10.7717/peerj.1331
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Baron

title: Brain-derived neurotrophic factor serum levels in genetically isolated populations: gender-specific association with anxiety disorder subtypes but not with anxiety levels or Val66Met polymorphism
link: https://peerj.com/articles/1252
last-modified: 2015-10-29
description: Anxiety disorders (ADs) are disabling chronic disorders with exaggerated behavioral response to threats. This study was aimed at testing the hypothesis that ADs may be associated with reduced neurotrophic activity, particularly of Brain-derived neurotrophic factor (BDNF), and determining possible effects of genetics on serum BDNF concentrations. In 672 adult subjects from six isolated villages in North-Eastern Italy with high inbreeding, we determined serum BDNF levels and identified subjects with different ADs subtypes such as Social and Specific Phobias (PHSOC, PHSP), Generalized Anxiety Disorder (GAD), and Panic Disorder (PAD). Analysis of the population as a whole or individual village showed no significant correlation between serum BDNF levels and Val66Met polymorphism and no association with anxiety levels. Stratification of subjects highlighted a significant decrease in serum BDNF in females with GAD and males with PHSP. This study indicates low heritability and absence of any impact of the Val66Met polymorphism on circulating concentrations of BDNF. Our results show that BDNF is not a general biomarker of anxiety but serum BDNF levels correlate in a gender-specific manner with ADs subtypes.
creator: Davide Carlino
creator: Ruggiero Francavilla
creator: Gabriele Baj
creator: Karolina Kulak
creator: Pio d’Adamo
creator: Sheila Ulivi
creator: Stefania Cappellani
creator: Paolo Gasparini
creator: Enrico Tongiorgi
uri: https://doi.org/10.7717/peerj.1252
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Carlino et al.

title: Taking account of uncertainties in digital land suitability assessment
link: https://peerj.com/articles/1366
last-modified: 2015-10-27
description: Simulations are used to generate plausible realisations of soil and climatic variables for input into an enterprise land suitability assessment (LSA). Subsequently we present a case study demonstrating a LSA (for hazelnuts) which takes into account the quantified uncertainties of the biophysical model input variables. This study is carried out in the Meander Valley Irrigation District, Tasmania, Australia. It is found that when comparing to a LSA that assumes inputs to be error free, there is a significant difference in the assessment of suitability. Using an approach that assumes inputs to be error free, 56% of the study area was predicted to be suitable for hazelnuts. Using the simulation approach it is revealed that there is considerable uncertainty about the ‘error free’ assessment, where a prediction of ‘unsuitable’ was made 66% of the time (on average) at each grid cell of the study area. The cause of this difference is that digital soil mapping of both soil pH and conductivity have a high quantified uncertainty in this study area. Despite differences between the comparative methods, taking account of the prediction uncertainties provide a realistic appraisal of enterprise suitability. It is advantageous also because suitability assessments are provided as continuous variables as opposed to discrete classifications. We would recommend for other studies that consider similar FAO (Food and Agriculture Organisation of the United Nations) land evaluation framework type suitability assessments, that parameter membership functions (as opposed to discrete threshold cutoffs) together with the simulation approach are used in concert.
creator: Brendan P. Malone
creator: Darren B. Kidd
creator: Budiman Minasny
creator: Alex B. McBratney
uri: https://doi.org/10.7717/peerj.1366
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Malone et al.

title: Differences in unilateral chest press muscle activation and kinematics on a stable versus unstable surface while holding one versus two dumbbells
link: https://peerj.com/articles/1365
last-modified: 2015-10-27
description: Training the bench press exercise on a traditional flat bench does not induce a level of instability as seen in sport movements and activities of daily living. Twenty participants were recruited to test two forms of instability: using one dumbbell rather than two and lifting on the COR bench compared to a flat bench. Electromyography (EMG) amplitudes of the pectoralis major, middle trapezius, external oblique, and internal oblique were recorded and compared. Differences in range of motion (ROM) were evaluated by measuring an angular representation of the shoulder complex. Four separate conditions of unilateral bench press were tested while lifting on a: flat bench with one dumbbell, flat bench with two dumbbells, COR Bench with one dumbbell, and COR Bench with two dumbbells. The results imply that there are no differences in EMG amplitude or ROM between the COR bench and traditional bench. However, greater ROM was found to be utilized in the single dumbbell condition, both in the COR bench and the flat bench.
creator: Jeffrey M. Patterson
creator: Andrew D. Vigotsky
creator: Nicole E. Oppenheimer
creator: Erin H. Feser
uri: https://doi.org/10.7717/peerj.1365
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Patterson et al.

title: Quotation accuracy in medical journal articles—a systematic review and meta-analysis
link: https://peerj.com/articles/1364
last-modified: 2015-10-27
description: Background. Quotations and references are an indispensable element of scientific communication. They should support what authors claim or provide important background information for readers. Studies indicate, however, that quotations not serving their purpose—quotation errors—may be prevalent.Methods. We carried out a systematic review, meta-analysis and meta-regression of quotation errors, taking account of differences between studies in error ascertainment.Results. Out of 559 studies screened we included 28 in the main analysis, and estimated major, minor and total quotation error rates of 11,9%, 95% CI [8.4, 16.6] 11.5% [8.3, 15.7], and 25.4% [19.5, 32.4]. While heterogeneity was substantial, even the lowest estimate of total quotation errors was considerable (6.7%). Indirect references accounted for less than one sixth of all quotation problems. The findings remained robust in a number of sensitivity and subgroup analyses (including risk of bias analysis) and in meta-regression. There was no indication of publication bias.Conclusions. Readers of medical journal articles should be aware of the fact that quotation errors are common. Measures against quotation errors include spot checks by editors and reviewers, correct placement of citations in the text, and declarations by authors that they have checked cited material. Future research should elucidate if and to what degree quotation errors are detrimental to scientific progress.
creator: Hannah Jergas
creator: Christopher Baethge
uri: https://doi.org/10.7717/peerj.1364
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Jergas and Baethge

title: Contributions to a neurophysiology of meaning: the interpretation of written messages could be an automatic stimulus-reaction mechanism before becoming conscious processing of information
link: https://peerj.com/articles/1361
last-modified: 2015-10-27
description: Background. Even though the interpretation of natural language messages is generally conceived as the result of a conscious processing of the message content, the influence of unconscious factors is also well known. What is still insufficiently known is the way such factors work. We have tackled interpretation assuming it is a process, whose basic features are the same for the whole humankind, and employing a naturalistic approach (careful observation of phenomena in conditions the closest to “natural” ones, and precise description before and independently of data statistical analysis).Methodology. Our field research involved a random sample of 102 adults. We presented them with a complete real world-like case of written communication using unabridged message texts. We collected data (participants’ written reports on their interpretations) in controlled conditions through a specially designed questionnaire (closed and opened answers); then, we treated it through qualitative and quantitative methods.Principal Findings. We gathered some evidence that, in written message interpretation, between reading and the attribution of conscious meaning, an intermediate step could exist (we named it “disassembling”) which looks like an automatic reaction to the text words/expressions. Thus, the process of interpretation would be a discontinuous sequence of three steps having different natures: the initial “decoding” step (i.e., reading, which requires technical abilities), disassembling (the automatic reaction, an unconscious passage) and the final conscious attribution of meaning. If this is true, words and expressions would firstly function like physical stimuli, before being taken into account as symbols. Such hypothesis, once confirmed, could help explaining some links between the cultural (human communication) and the biological (stimulus-reaction mechanisms as the basis for meanings) dimension of humankind.
creator: Roberto Maffei
creator: Livia S. Convertini
creator: Sabrina Quatraro
creator: Stefania Ressa
creator: Annalisa Velasco
uri: https://doi.org/10.7717/peerj.1361
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Maffei et al.

title: Combining environmental suitability and population abundances to evaluate the invasive potential of the tunicate Ciona intestinalis along the temperate South American coast
link: https://peerj.com/articles/1357
last-modified: 2015-10-27
description: The tunicate Ciona intestinalis is an opportunistic invader with high potential for causing economic losses in aquaculture centers. Recent phylogenetic and population genetic analysis support the existence of a genetic complex described as C. intestinalis with two main dominant species (sp A and B) occurring worldwide. In Chile, the species has been observed around 30°S of latitude, but no official reports exist for the presence of C. intestinalis in southern regions (above 40°S), where most of the mollusk aquaculture centers are located. Here, we used occurrences from multiple invaded regions and extensive field sampling to model and validate the environmental conditions that allow the species to persist and to find the geographic areas with the most suitable environmental conditions for the spread of C. intestinalis in the Chilean coast. By studying the potential expansion of C. intestinalis southward in the Chilean Coast, we aimed to provide valuable information that might help the development of control plans before the species becomes a significant problem, especially above 40°S. Our results highlight that, by using portions of the habitat that are apparently distinguishable, the species seem to be not only genetically distinct, but ecologically distinct as well. The two regional models fitted for sp A and for sp B showed disagreement on which sections of Chilean coastline are considered more suitable for these species. While the model for sp A identifies moderately to highly suitable areas between 30° and 40°S, the model for sp B classifies the areas around 45°S as the most appropriate. Data from field sampling show a positive linear relationship between density of C. intestinalis and the index of suitability for sp A in aquaculture centers. Understanding the relation of the distinct species with the surrounding environment provided valuable insights about probable routes of dispersion in Chile, especially into those areas considered suitable for aquaculture activities but where the species has not yet been recorded. We discuss the implications of our findings as a useful tool to anticipate the invasion of such harmful invasive species with regard to the most relevant environmental variables.
creator: Stella M. Januario
creator: Sergio A. Estay
creator: Fabio A. Labra
creator: Mauricio Lima
uri: https://doi.org/10.7717/peerj.1357
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Januario et al.

title: Modeling the effects of cyclodextrin on intracellular membrane vesicles from Cos-7 cells prepared by sonication and carbonate treatment
link: https://peerj.com/articles/1351
last-modified: 2015-10-27
description: Cholesterol has important functions in the organization of membrane structure and this may be mediated via the formation of cholesterol-rich, liquid-ordered membrane microdomains often referred to as lipid rafts. Methyl-beta-cyclodextrin (cyclodextrin) is commonly used in cell biology studies to extract cholesterol and therefore disrupt lipid rafts. However, in this study we reassessed this experimental strategy and investigated the effects of cyclodextrin on the physical properties of sonicated and carbonate-treated intracellular membrane vesicles isolated from Cos-7 fibroblasts. We treated these membranes, which mainly originate from the trans-Golgi network and endosomes, with cyclodextrin and measured the effects on their equilibrium buoyant density, protein content, represented by the palmitoylated protein phosphatidylinositol 4-kinase type IIα, and cholesterol. Despite the reduction in mass stemming from cholesterol removal, the vesicles became denser, indicating a possible large volumetric decrease, and this was confirmed by measurements of hydrodynamic vesicle size. Subsequent mathematical analyses demonstrated that only half of this change in membrane size was attributable to cholesterol loss. Hence, the non-selective desorption properties of cyclodextrin are also involved in membrane size and density changes. These findings may have implications for preceding studies that interpreted cyclodextrin-induced changes to membrane biochemistry in the context of lipid raft disruption without taking into account our finding that cyclodextrin treatment also reduces membrane size.
creator: Peter Kilbride
creator: Holly J. Woodward
creator: Kuan Boone Tan
creator: Nguyễn T.K. Thanh
creator: K.M. Emily Chu
creator: Shane Minogue
creator: Mark G. Waugh
uri: https://doi.org/10.7717/peerj.1351
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kilbride et al.

title: Person-centered osteopathic practice: patients’ personality (body, mind, and soul) and health (ill-being and well-being)
link: https://peerj.com/articles/1349
last-modified: 2015-10-27
description: Background. Osteopathic philosophy and practice are congruent with the biopsychosocial model, a patient-centered approach when treating disease, and the view of the person as a unity (i.e., body, mind, and soul). Nevertheless, a unity of being should involve a systematic person-centered understanding of the patient’s personality as a biopsychosociospiritual construct that influences health (i.e., well-being and ill-being). We suggest Cloninger’s personality model, comprising temperament (i.e., body) and character (i.e., mind and soul), as a genuine paradigm for implementation in osteopathic practice. As a first step, we investigated (1) the relationships between personality and health among osteopathic patients, (2) differences in personality between patients and a control group, and (3) differences in health within patients depending on the presenting problem and gender.Method. 524 osteopathic patients in Sweden (age mean = 46.17, SD = 12.54, 388 females and 136 males) responded to an online survey comprising the Temperament and Character Inventory and measures of health (well-being: life satisfaction, positive affect, harmony in life, energy, and resilience; ill-being: negative affect, anxiety, depression, stress, and dysfunction and suffering associated to the presenting problem). We conducted two structural equation models to investigate the association personality-health; graphically compared the patients’ personality T-scores to those of the control group and compared the mean raw scores using t-tests; and conducted two multivariate analyses of variance, using age as covariate, to compare patients’ health in relation to their presenting problem and gender.Results. The patients’ personality explained the variance of all of the well-being (R2 between .19 and .54) and four of the ill-being (R2 between .05 and .43) measures. Importantly, self-transcendence, the spiritual aspect of personality, was associated to high levels of positive emotions and resilience. Osteopathic patients, compared to controls, scored higher in six of the seven personality dimensions. These differences were, however, not considerably large (divergences in T-scores were <1 SD, Cohen’s d between 0.12 and 0.40). Presenting problem and gender did not have an effect on any of the health measures.Conclusion. The patient’s personality as a ternary construct (i.e., body, mind, and soul), which is in line with osteopathy, is associated to both well-being and ill-being. The lack of substantial differences in personality between patients and controls implies that the patients had not any personality disorders. Hence, osteopaths might, with proper education, be able to coach their patients to self-awareness. The lack of differences in health variables between osteopathic patients with different presenting problems suggests that practitioners should focus on the person’s health regardless of the type of presenting problem.
creator: Elin Fahlgren
creator: Ali A. Nima
creator: Trevor Archer
creator: Danilo Garcia
uri: https://doi.org/10.7717/peerj.1349
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Fahlgren et al.

title: Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry
link: https://peerj.com/articles/1318
last-modified: 2015-10-27
description: Cattle commonly raised in Thailand have characteristics of Bos indicus (zebu). We do not know when or how cattle domestication in Thailand occurred, and so questions remain regarding their origins and relationships to other breeds. We obtained genome-wide SNP genotypic data of 28 bovine individuals sampled from four regions: North (Kho-Khaolampoon), Northeast (Kho-Isaan), Central (Kho-Lan) and South (Kho-Chon) Thailand. These regional varieties have distinctive traits suggestive of breed-like genetic variations. From these data, we confirmed that all four Thai varieties are Bos indicus and that they are distinct from other indicine breeds. Among these Thai cattle, a distinctive ancestry pattern is apparent, which is the purest within Kho-Chon individuals. This ancestral component is only present outside of Thailand among other indicine breeds in Southeast Asia. From this pattern, we conclude that a unique Bos indicus ancestor originated in Southeast Asia, and native Kho-Chon Thai cattle retain the signal of this ancestry with limited admixture of other bovine ancestors.
creator: Pongsakorn Wangkumhang
creator: Alisa Wilantho
creator: Philip J. Shaw
creator: Laurence Flori
creator: Katayoun Moazami-Goudarzi
creator: Mathieu Gautier
creator: Monchai Duangjinda
creator: Anunchai Assawamakin
creator: Sissades Tongsima
uri: https://doi.org/10.7717/peerj.1318
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wangkumhang et al.

title: Is there a hybridization barrier between Gentiana lutea color morphs?
link: https://peerj.com/articles/1308
last-modified: 2015-10-27
description: In Gentiana lutea two varieties are described: G. lutea var. aurantiaca with orange corolla colors and G. lutea var. lutea with yellow corolla colors. Both color varieties co-occur in NW Spain, and pollinators select flower color in this species. It is not known whether a hybridization barrier exists between these G. lutea color varieties. We aim to test the compatibility between flower color varieties in G. lutea and its dependence on pollen vectors. Within a sympatric population containing both flower color morphs, we analyzed differences in reproductive success (number, weight, viability and germinability of seeds) depending on fertilization treatments (autogamy and xenogamy within variety and among varieties). We found a 93% reduction in number of seeds and a 37% reduction in seed weight respectively of autogamy treatments compared to xenogamy crossings. Additionally, reproductive success is higher within color varieties than among varieties, due to a 45% seed viability reduction on hybrids from different varieties. Our results show that G. lutea reproductive success is strongly dependent on pollinators and that a partial hybridization barrier exists between G. lutea varieties.
creator: María Losada
creator: Tania Veiga
creator: Javier Guitián
creator: José Guitián
creator: Pablo Guitián
creator: Mar Sobral
uri: https://doi.org/10.7717/peerj.1308
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Losada et al.

title: Effects of in situ climate warming on monarch caterpillar (Danaus plexippus) development
link: https://peerj.com/articles/1293
last-modified: 2015-10-27
description: Climate warming will fundamentally alter basic life history strategies of many ectothermic insects. In the lab, rising temperatures increase growth rates of lepidopteran larvae but also reduce final pupal mass and increase mortality. Using in situ field warming experiments on their natural host plants, we assessed the impact of climate warming on development of monarch (Danaus plexippus) larvae. Monarchs were reared on Asclepias tuberosa grown under ‘Ambient’ and ‘Warmed’ conditions. We quantified time to pupation, final pupal mass, and survivorship. Warming significantly decreased time to pupation, such that an increase of 1 °C corresponded to a 0.5 day decrease in pupation time. In contrast, survivorship and pupal mass were not affected by warming. Our results indicate that climate warming will speed the developmental rate of monarchs, influencing their ecological and evolutionary dynamics. However, the effects of climate warming on larval development in other monarch populations and at different times of year should be investigated.
creator: Nathan P. Lemoine
creator: Jillian N. Capdevielle
creator: John D. Parker
uri: https://doi.org/10.7717/peerj.1293
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: The nonlinear variation of drought and its relation to atmospheric circulation in Shandong Province, East China
link: https://peerj.com/articles/1289
last-modified: 2015-10-27
description: Considerable attention has recently been devoted to the linear trend of drought at the decadal to inter-decadal time scale; however, the nonlinear variation of drought at multi-decadal scales and its relation to atmospheric circulation need to be further studied. The linear and nonlinear variations of the Palmer drought severity index (PDSI) in Shandong from 1900 to 2012 and its relations to the Pacific decadal oscillation (PDO), El Niño-Southern Oscillation (ENSO), Siberian high (SH) and Southern Oscillation (SO) phase changes from multi-scale are detected using linear regression, the Mann–Kendall test, ensemble empirical mode decomposition (EEMD) and the Pearson correlation analysis method. The results indicate that the PDSI shows no statistically significant linear change trend from 1900 to 2012; however, before (after) the late 1950s, PDSI shows a significant upward (downward) trend (P < 0.01) with a linear rate of 0.28/decade (−0.48/decade). From 1900 to 2012, the PDSI also exhibits a nonlinear variation trend at the inter-annual scale (quasi-3 and quasi-7-year), inter-decadal scale (quasi-14-year) and multi-decadal scale (quasi-46 and quasi-65-year). The variance contribution rate of components from the inter-annual scale is the largest, reaching 38.7%, and that from the inter-decadal scale and multi-decadal scale are 18.9% and 19.0%, respectively, indicating that the inter-annual change exerts a huge influence on the overall PDSI change. The results also imply that the effect of the four atmospheric circulations (PDO, ENSO, SH, SO) on PDSI at the multi-decadal variability scale are more important than that at the other scales. Consequently, we state that PDSI variation at the inter-annual scale has more instability, while that at the inter-decadal and multi-decadal scale is more strongly influenced by natural factors.
creator: Baofu Li
creator: Zhongsheng Chen
creator: Xingzhong Yuan
uri: https://doi.org/10.7717/peerj.1289
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Li et al.

title: Evaluation of nutritional and economic feed values of spent coffee grounds and Artemisia princeps residues as a ruminant feed using in vitro ruminal fermentation
link: https://peerj.com/articles/1343
last-modified: 2015-10-22
description: Much research on animal feed has focused on finding alternative feed ingredients that can replace conventional ones (e.g., grains and beans) to reduce feed costs. The objective of this study was to evaluate the economic, as well as nutritional value of spent coffee grounds (SCG) and Japanese mugwort (Artemisia princeps) residues (APR) as alternative feed ingredients for ruminants. We also investigated whether pre-fermentation using Lactobacillus spp. was a feasible way to increase the feed value of these by-products. Chemical analyses and an in vitro study were conducted for SCG, APR, and their pre-fermented forms. All the experimental diets for in vitro ruminal fermentation were formulated to contain a similar composition of crude protein, neutral detergent fiber and total digestible nutrients at 1x maintenance feed intake based on the dairy National Research Council (NRC). The control diet was composed of ryegrass, corn, soybean meal, whereas the treatments consisted of SCG, SCG fermented with Lactobacillus spp. (FSCG), APR, and its fermented form (FAPR). The treatment diets replaced 100 g/kg dry matter (DM) of the feed ingredients in the control. Costs were lower for the all treatments, except FAPR, than that of the control. After 24-h incubation, the NDF digestibility of the diets containing SCG and its fermented form were significantly lower than those of the other diets (P < 0.01); pre-fermentation tended to increase NDF digestibility (P = 0.07), especially for APR. Supplementation of SCG significantly decreased total gas production (ml/g DM) after 24-h fermentation in comparison with the control (P < 0.05); however, there were no significant differences between the control and the SCG or the APR diets in total gas production, as expressed per Korean Won (KRW). Diets supplemented with SCG or FSCG tended to have a higher total volatile fatty acid (VFA) concentration, expressed as per KRW, compared with the control (P = 0.06). Conversely, the fermentation process of SCG and APR significantly decreased total gas production and VFA production as expressed per KRW (P < 0.05). Because of their nutrient composition and relatively lower cost, we concluded that SCG and APR could be used as alternative feed sources, replacing conventional feed ingredients. However, pre-fermentation of agricultural by-products, such as SCG and APR, may be inappropriate for improving their nutritive considering the increase in production costs.
creator: Jakyeom Seo
creator: Jae Keun Jung
creator: Seongwon Seo
uri: https://doi.org/10.7717/peerj.1343
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Seo et al.

title: Mammalian bone palaeohistology: a survey and new data with emphasis on island forms
link: https://peerj.com/articles/1358
last-modified: 2015-10-22
description: The interest in mammalian palaeohistology has increased dramatically in the last two decades. Starting in 1849 via descriptive approaches, it has been demonstrated that bone tissue and vascularisation types correlate with several biological variables such as ontogenetic stage, growth rate, and ecology. Mammalian bone displays a large variety of bone tissues and vascularisation patterns reaching from lamellar or parallel-fibred to fibrolamellar or woven-fibred bone, depending on taxon and individual age. Here we systematically review the knowledge and methods on cynodont and mammalian bone microstructure as well as palaeohistology and discuss potential future research fields and techniques. We present new data on the bone microstructure of two extant marsupial species and of several extinct continental and island placental mammals. Extant marsupials display mainly parallel-fibred primary bone with radial and oblique but mainly longitudinal vascular canals. Three juvenile specimens of the dwarf island hippopotamid Hippopotamus minor from the Late Pleistocene of Cyprus show reticular to plexiform fibrolamellar bone. The island murid Mikrotia magna from the Late Miocene of Gargano, Italy displays parallel-fibred primary bone with reticular vascularisation and strong remodelling in the middle part of the cortex. Leithia sp., the dormouse from the Pleistocene of Sicily, is characterised by a primary bone cortex consisting of lamellar bone and a high amount of compact coarse cancellous bone. The bone cortex of the fossil continental lagomorph Prolagus oeningensis and three fossil species of insular Prolagus displays mainly parallel-fibred primary bone and reticular, radial as well as longitudinal vascularisation. Typical for large mammals, secondary bone in the giant rhinocerotoid Paraceratherium sp. from the Late Oligocene of Turkey is represented by dense Haversian bone. The skeletochronological features of Sinomegaceros yabei, a large-sized deer from the Pleistocene of Japan closely related to Megaloceros, indicate a high growth rate. These examples and the synthesis of existing data show the potential of bone microstructure to reveal essential information on life history evolution. The bone tissue and the skeletochronological data of the sampled island species suggest the presence of various modes of bone histological modification and mammalian life history evolution on islands to depend on factors of island evolution such as island size, distance from mainland, climate, phylogeny, and time of evolution.
creator: Christian Kolb
creator: Torsten M. Scheyer
creator: Kristof Veitschegger
creator: Analia M. Forasiepi
creator: Eli Amson
creator: Alexandra A.E. Van der Geer
creator: Lars W. Van den Hoek Ostende
creator: Shoji Hayashi
creator: Marcelo R. Sánchez-Villagra
uri: https://doi.org/10.7717/peerj.1358
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kolb et al.

title: Urban habitat complexity affects species richness but not environmental filtering of morphologically-diverse ants
link: https://peerj.com/articles/1356
last-modified: 2015-10-22
description: Habitat complexity is a major determinant of structure and diversity of ant assemblages. Following the size-grain hypothesis, smaller ant species are likely to be advantaged in more complex habitats compared to larger species. Habitat complexity can act as an environmental filter based on species size and morphological traits, therefore affecting the overall structure and diversity of ant assemblages. In natural and semi-natural ecosystems, habitat complexity is principally regulated by ecological successions or disturbance such as fire and grazing. Urban ecosystems provide an opportunity to test relationships between habitat, ant assemblage structure and ant traits using novel combinations of habitat complexity generated and sustained by human management. We sampled ant assemblages in low-complexity and high-complexity parks, and high-complexity woodland remnants, hypothesizing that (i) ant abundance and species richness would be higher in high-complexity urban habitats, (ii) ant assemblages would differ between low- and high-complexity habitats and (iii) ants living in high-complexity habitats would be smaller than those living in low-complexity habitats. Contrary to our hypothesis, ant species richness was higher in low-complexity habitats compared to high-complexity habitats. Overall, ant assemblages were significantly different among the habitat complexity types investigated, although ant size and morphology remained the same. Habitat complexity appears to affect the structure of ant assemblages in urban ecosystems as previously observed in natural and semi-natural ecosystems. However, the habitat complexity filter does not seem to be linked to ant morphological traits related to body size.
creator: Alessandro Ossola
creator: Michael A. Nash
creator: Fiona J. Christie
creator: Amy K. Hahs
creator: Stephen J. Livesley
uri: https://doi.org/10.7717/peerj.1356
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ossola et al.

title: Frailty severity is significantly associated with electrocardiographic QRS duration in chronic dialysis patients
link: https://peerj.com/articles/1354
last-modified: 2015-10-22
description: End-stage renal disease (ESRD) patients are at increased risk of sudden cardiac death, the risk of which is presumably related to arrhythmia. Electrocardiographic (ECG) parameters have been found to correlate with arrhythmia and predict cardiovascular outcomes in ESRD patients. Frailty is also a common feature in this population. We investigate whether the severity of dialysis frailty is associated with ECG findings, including PR interval, QRS duration, and QTc interval. Presence and severity of frailty was ascertained using six different self-report questionnaires with proven construct validity. Correlation analysis between frailty severity and ECG was made, and those with significant association entered into multiple regression analysis for confirmation. Among a cohort of chronic hemodialysis patients, we found that frailty severity, assessed by the Edmonton frailty scale, is significantly associated with QRS duration (r = − 0.3, p < 0.05). Dialysis patients with QRS longer than 120 ms had significantly lower severity of frailty than those with QRS less than 120 ms (p = 0.01 for the Edmonton frailty scale and 0.05 for simple FRAIL scale). Regression analysis showed that frailty severity, assessed by the Edmonton frailty scale and simple FRAIL scale, was significantly associated with QRS duration independent of serum electrolyte levels. In conclusion, a significant relationship exists between the severity of frailty and QRS duration in ESRD patients. This might be an under-recognized link between frailty and its adverse cardiovascular impact in these patients.
creator: Chia-Ter Chao
creator: Jenq-Wen Huang
uri: https://doi.org/10.7717/peerj.1354
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Chao and Huang

title: Migration in the social stage of Dictyostelium discoideum amoebae impacts competition
link: https://peerj.com/articles/1352
last-modified: 2015-10-22
description: Interaction conditions can change the balance of cooperation and conflict in multicellular groups. After aggregating together, cells of the social amoeba Dictyostelium discoideum may migrate as a group (known as a slug) to a new location. We consider this migration stage as an arena for social competition and conflict because the cells in the slug may not be from a genetically homogeneous population. In this study, we examined the interplay of two seemingly diametric actions, the solitary action of kin recognition and the collective action of slug migration in D. discoideum, to more fully understand the effects of social competition on fitness over the entire lifecycle. We compare slugs composed of either genetically homogenous or heterogeneous cells that have migrated or remained stationary in the social stage of the social amoeba Dictyostelium discoideum. After migration of chimeric slugs, we found that facultative cheating is reduced, where facultative cheating is defined as greater contribution to spore relative to stalk than found for that clone in the clonal state. In addition our results support previous findings that competitive interactions in chimeras diminish slug migration distance. Furthermore, fruiting bodies have shorter stalks after migration, even accounting for cell numbers at that time. Taken together, these results show that migration can alleviate the conflict of interests in heterogeneous slugs. It aligns their interest in finding a more advantageous place for dispersal, where shorter stalks suffice, which leads to a decrease in cheating behavior.
creator: Chandra N. Jack
creator: Neil Buttery
creator: Boahemaa Adu-Oppong
creator: Michael Powers
creator: Christopher R.L. Thompson
creator: David C. Queller
creator: Joan E. Strassmann
uri: https://doi.org/10.7717/peerj.1352
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Jack et al.

title: Astrocyte activation in the anterior cingulate cortex and altered glutamatergic gene expression during paclitaxel-induced neuropathic pain in mice
link: https://peerj.com/articles/1350
last-modified: 2015-10-22
description: Spinal astrocyte activation contributes to the pathogenesis of paclitaxel-induced neuropathic pain (PINP) in animal models. We examined glial fibrillary acidic protein (GFAP; an astrocyte marker) immunoreactivity and gene expression of GFAP, glutamate transporters and receptor subunits by real time PCR in the anterior cingulate cortex (ACC) at 7 days post first administration of paclitaxel, a time point when mice had developed thermal hyperalgesia. The ACC, an area in the brain involved in pain perception and modulation, was chosen because changes in this area might contribute to the pathophysiology of PINP. GFAP transcripts levels were elevated by more than fivefold and GFAP immunoreactivity increased in the ACC of paclitaxel-treated mice. The 6 glutamate transporters (GLAST, GLT-1 EAAC1, EAAT4, VGLUT-1 and VGLUT-2) quantified were not significantly altered by paclitaxel treatment. Of the 12 ionotropic glutamate receptor subunits transcripts analysed 6 (GLuA1, GLuA3, GLuK2, GLuK3, GLuK5 and GLuN1) were significantly up-regulated, whereas GLuA2, GLuK1, GLuK4, GLuN2A and GLuN2B were not significantly altered and GLuA4 was lowly expressed. Amongst the 8 metabotropic receptor subunits analysed only mGLuR8 was significantly elevated. In conclusion, during PINP there is astrocyte activation, with no change in glutamate transporter expression and differential up-regulation of glutamate receptor subunits in the ACC. Thus, targeting astrocyte activation and the glutamatergic system might be another therapeutic avenue for management of PINP.
creator: Willias Masocha
uri: https://doi.org/10.7717/peerj.1350
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Masocha

title: Cheetahs (Acinonyx jubatus) running the gauntlet: an evaluation of translocations into free-range environments in Namibia
link: https://peerj.com/articles/1346
last-modified: 2015-10-22
description: Following dramatic range and population declines, the cheetah is Africa’s most endangered large felid. In Namibia, private land managers still trap cheetahs but increasingly consider moving animals instead of killing them. Across Africa, managers have translocated perceived conflict carnivores for decades, but rarely evaluated their actions. We analyse the outcomes of 15 cheetah translocations (for 23 adults and 10 dependent offspring) into free-range environments in Namibia. We released cheetahs at an average distance of 419.6 km ± 216.1 km SD (range: 71–816 km) after captive periods ranging from 1–1,184 days (350.6 days ± 439.0 days SD). An individual’s ability to survive the first year predominantly determined the overall translocation success of 40%. Post-release conflict and homing had less impact on success. Cheetah survival was lowest in the first three months after release. Human persecution (50% of deaths) and spotted hyaenas (29% of deaths) had the highest effect on survival. The degree of habituation to humans acquired during captivity significantly influenced chances of survival. Cheetahs surviving the initial post-release period (∼90 days) often settled into ranges and females reproduced successfully. However, all individuals exhibited extensive movements, frequently roaming >4,000 km2 in the first six months after release (with a maximum of 19,743 km2 in 112 days), resulting in low release site fidelity. Soft release and larger recipient area size did not improve site fidelity. Based on these outcomes, we evaluated which unfenced conservation areas in Namibia could potentially receive cheetahs. We found that there are currently few public and/or private reserves large enough to contain the movement profiles we observed in this study. This suggests that most translocations will result in cheetahs re-entering farmlands where they face a high risk of persecution. In conclusion, translocations into unconfined areas can successfully conserve individual cheetahs. Due to high mortality and unpredictable outcomes, however, conservation efforts need to focus on improving tolerance of cheetahs in commercial livestock and game farming areas in order to reduce the number of indiscriminately trapped animals.
creator: Florian J. Weise
creator: Joseph R. Lemeris
creator: Stuart J. Munro
creator: Andrew Bowden
creator: Cicelia Venter
creator: Marlice van Vuuren
creator: Rudie J. van Vuuren
uri: https://doi.org/10.7717/peerj.1346
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Weise et al.

title: Gluten-free food database: the nutritional quality and cost of packaged gluten-free foods
link: https://peerj.com/articles/1337
last-modified: 2015-10-22
description: Notwithstanding a growth in popularity and consumption of gluten-free (GF) food products, there is a lack of substantiated analysis of the nutritional quality compared with their gluten-containing counterparts. To put GF foods into proper perspective both for those who need it (patients with celiac disease) and for those who do not, we provide contemporary data about cost and nutritional quality of GF food products. The objective of this study is to develop a food composition database for seven discretionary food categories of packaged GF products. Nutrient composition, nutritional information and cost of foods from 63 GF and 126 gluten-containing counterparts were systematically obtained from 12 different Austrian supermarkets. The nutrition composition (macro and micronutrients) was analyzed by using two nutrient composition databases in a stepwise approximation process. A total of 63 packaged GF foods were included in the analysis representing a broad spectrum of different GF categories (flour/bake mix, bread and bakery products, pasta and cereal-based food, cereals, cookies and cakes, snacks and convenience food). Our results show that the protein content of GF products is >2 fold lower across 57% of all food categories. In 65% of all GF foods, low sodium content was observed (defined as <120 mg/100 g). Across all GF products, 19% can be classified as source high in fiber (defined as >6g/100 g). On average, GF foods were substantially higher in cost, ranging from +205% (cereals) to +267% (bread and bakery products) compared to similar gluten-containing products. In conclusion, our results indicate that for GF foods no predominant health benefits are indicated; in fact, some critical nutrients must be considered when being on a GF diet. For individuals with celiac disease, the GF database provides a helpful tool to identify the food composition of their medical diet. For healthy consumers, replacing gluten-containing products with GF foods is aligned with substantial cost differences but GF foods do not provide additional health benefits from a nutritional perspective.
creator: Benjamin Missbach
creator: Lukas Schwingshackl
creator: Alina Billmann
creator: Aleksandra Mystek
creator: Melanie Hickelsberger
creator: Gregor Bauer
creator: Jürgen König
uri: https://doi.org/10.7717/peerj.1337
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Missbach et al.

title: Local-scale topoclimate effects on treeline elevations: a country-wide investigation of New Zealand’s southern beech treelines
link: https://peerj.com/articles/1334
last-modified: 2015-10-22
description: Although treeline elevations are limited globally by growing season temperature, at regional scales treelines frequently deviate below their climatic limit. The cause of these deviations relate to a host of climatic, disturbance, and geomorphic factors that operate at multiple scales. The ability to disentangle the relative effects of these factors is currently hampered by the lack of reliable topoclimatic data, which describe how regional climatic characteristics are modified by topographic effects in mountain areas. In this study we present an analysis of the combined effects of local- and regional-scale factors on southern beech treeline elevation variability at 28 study areas across New Zealand. We apply a mesoscale atmospheric model to generate local-scale (200 m) meteorological data at these treelines and, from these data, we derive a set of topoclimatic indices that reflect possible detrimental and ameliorative influences on tree physiological functioning. Principal components analysis of meteorological data revealed geographic structure in how study areas were situated in multivariate space along gradients of topoclimate. Random forest and conditional inference tree modelling enabled us to tease apart the relative effects of 17 explanatory factors on local-scale treeline elevation variability. Overall, modelling explained about 50% of the variation in treeline elevation variability across the 28 study areas, with local landform and topoclimatic effects generally outweighing those from regional-scale factors across the 28 study areas. Further, the nature of the relationships between treeline elevation variability and the explanatory variables were complex, frequently non-linear, and consistent with the treeline literature. To our knowledge, this is the first study where model-generated meteorological data, and derived topoclimatic indices, have been developed and applied to explain treeline variation. Our results demonstrate the potential of such an approach for ecological research in mountainous environments.
creator: Bradley S. Case
creator: Hannah L. Buckley
uri: https://doi.org/10.7717/peerj.1334
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Case and Buckley

title: Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages
link: https://peerj.com/articles/1320
last-modified: 2015-10-22
description: Horizontal gene transfer and recombination occur across many groups of viruses and play key roles in important viral processes such as host-range expansion and immune-system avoidance. To have any predictive power regarding the ability of viruses to readily recombine, we must determine the extent to which epistasis restricts the success of recombinants, particularly as it relates to the genetic divergence between parental strains. In any hybridization event, the evolutionary success or failure of hybrids is largely determined by the pervasiveness of epistasis in the parental genomes. Recombination has previously been shown to incur steep fitness costs in highly divergent viruses as a result of disrupted epistatic interactions. We used a pair of bacteriophages of the family Microviridae to demonstrate that epistasis may evidence itself in the form of fitness costs even in the case of the exchange of alleles at a locus with amino acid divergence as low as 1%. We explored a possible biophysical source of epistasis in the interaction of viral coat and scaffolding proteins and examined a recovery mutation that likely repairs interactions disrupted by recombination.
creator: Andrew M. Sackman
creator: Danielle Reed
creator: Darin R. Rokyta
uri: https://doi.org/10.7717/peerj.1320
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sackman et al.

title: ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins
link: https://peerj.com/articles/1344
last-modified: 2015-10-20
description: We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.
creator: Anders S. Larsen
creator: Lars A. Bratholm
creator: Anders S. Christensen
creator: Maher Channir
creator: Jan H. Jensen
uri: https://doi.org/10.7717/peerj.1344
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Larsen et al.

title: What do giant titanosaur dinosaurs and modern Australasian megapodes have in common?
link: https://peerj.com/articles/1341
last-modified: 2015-10-20
description: Titanosauria is a globally distributed clade of sometimes extremely large Mesozoic herbivorous sauropod dinosaurs. On the basis of current evidence these giant dinosaurs seem to have reproduced in specific and localized nesting sites. However, no investigations have been performed to understand the possible ecological and geological biases that acted for the selection of these nesting sites worldwide. In this study, observations were performed on the best-known Cretaceous nesting sites around the world. Our observations strongly suggest their eggs were incubated with environmental sources of heat, in burial conditions. Taking into account the clutch composition and geometry, the nature and properties of the sediments, the eggshells’ structures and conductance, it would appear that titanosaurs adopted nesting behaviors comparable to the modern Australasian megapodes, using burrow-nesting in diverse media and mound-building strategies.
creator: E. Martín Hechenleitner
creator: Gerald Grellet-Tinner
creator: Lucas E. Fiorelli
uri: https://doi.org/10.7717/peerj.1341
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hechenleitner et al.

title: Epidemiological evidence on extra-medical use of prescription pain relievers: transitions from newly incident use to dependence among 12–21 year olds in the United States using meta-analysis, 2002–13
link: https://peerj.com/articles/1340
last-modified: 2015-10-20
description: Background. When 12-to-21-year-olds start using prescription pain relievers extra-medically, some of them transition into opioid dependence within 12 months after such use. Our main aim for this epidemiological research on 12-to-21-year-olds in the United States (US) is to estimate the risk of becoming a newly incident case of opioid dependence within 12 months after onset of using prescription pain relievers extra-medically (EMPPR).Methods. Meta-analyses from multiple independent replication samples now are possible, based upon nationally representative survey samples of US adolescents age 12–21 years. All 12-to-21-year-olds were sampled and recruited for the US National Surveys on Drug Use and Health, with standardized assessments of EMPPR use and opioid dependence (NSDUH, 2002–2013).Results. Peak risk for a transition from start of EMPPR use to opioid dependence within 12 months is seen at mid-adolescence among 14-to-15-year-olds (6.3%, 8.7% per year), somewhat earlier than peak risk for starting EMPPR use (seen for 16-to-19-year-olds at 4.1%, 5.9% per year). Applied to 12-to-21-year-olds in the US between 2002–2013, an estimated 8 million started using PPR extra-medically. Each year, roughly 42,000 to 58,000 transitioned into opioid dependence within 12 months after onset of such use.Discussion. These epidemiological estimates for the US in recent years teach us to expect one transition into adolescent-onset opioid dependence within 12 months for every 11–16 newly incident EMPPR users, yielding perhaps 120 newly incident opioid dependent cases in need of practitioner attention or treatment services, each day of each year. This evidence can be used to motivate more effective public health prevention, outreach, and early intervention programs as might prevent or delay occurrence of EMPPR use and opioid dependence.
creator: Maria A. Parker
creator: James C. Anthony
uri: https://doi.org/10.7717/peerj.1340
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Parker and Anthony

title: Two continents and two names for a Neotropical colletid bee species (Hymenoptera: Colletidae: Neopasiphaeinae): Hoplocolletes ventralis (Friese, 1924)
link: https://peerj.com/articles/1338
last-modified: 2015-10-20
description: Neopasiphaeine bees (Apoidea: Colletidae) are known for their Amphinotic distribution in the Australian and Neotropical regions. Affinities between colletid taxa in Australia and South America have been speculated for decades, and have been confirmed by recent phylogenetic hypotheses that indicate a biogeographic scenario compatible with a trans-Antarctic biotic connection during the Paleogene. No neopasiphaeine species occurs on both sides of the Pacific Ocean, but the Neotropical species Hoplocolletes ventralis (Friese, 1924) was described as an Australian taxon due to an error in the specimen labels. This mistake was recognized by CD Michener 50 years ago. We herein report that the same labeling problem also happened with Dasycolletes chalceusFriese, 1924, which remained as a tentatively placed species in the Australian genus Leioproctus until now. Moreover, Dasycolletes chalceus is interpreted as a synonym of Hoplocolletes ventralis. We also provide a revised diagnosis for Hoplocolletes, describe the male of H. ventralis in detail for the first time, including a comparative study of its genitalia and associated sterna.
creator: Eduardo A.B. Almeida
creator: Fábio B. Quinteiro
uri: https://doi.org/10.7717/peerj.1338
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Almeida and Quinteiro

title: miRMOD: a tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data
link: https://peerj.com/articles/1332
last-modified: 2015-10-20
description: In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
creator: Abhinav Kaushik
creator: Shradha Saraf
creator: Sunil K. Mukherjee
creator: Dinesh Gupta
uri: https://doi.org/10.7717/peerj.1332
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kaushik et al.

title: Replacement of native by non-native animal communities assisted by human introduction and management on Isla Victoria, Nahuel Huapi National Park
link: https://peerj.com/articles/1328
last-modified: 2015-10-20
description: One of the possible consequences of biological invasions is the decrease of native species abundances or their replacement by non-native species. In Andean Patagonia, southern Argentina and Chile, many non-native animals have been introduced and are currently spreading. On Isla Victoria, Nahuel Huapi National Park, many non-native vertebrates were introduced ca. 1937. Records indicate that several native vertebrates were present before these species were introduced. We hypothesize that seven decades after the introduction of non-native species and without appropriate management to maintain native diversity, non-native vertebrates have displaced native species (given the known invasiveness and impacts of some of the introduced species). We conducted direct censuses in linear transects 500 m long (n = 10) in parallel with camera-trapping (1,253 camera-days) surveys in two regions of the island with different levels of disturbance: high (n = 4) and low (n = 6) to study the community of terrestrial mammals and birds and the relative abundances of native and non-native species. Results show that currently non-native species are dominant across all environments; 60.4% of census records and 99.7% of camera trapping records are of non-native animals. We detected no native large mammals; the assemblage of large vertebrates consisted of five non-native mammals and one non-native bird. Native species detected were one small mammal and one small bird. Species with the highest trapping rate were red and fallow deer, wild boar, silver pheasant (all four species are non-native) and chucao (a native bird). These results suggest that native species are being displaced by non-natives and are currently in very low numbers.
creator: Valeria L. Martin-Albarracin
creator: Martin A. Nuñez
creator: Guillermo C. Amico
uri: https://doi.org/10.7717/peerj.1328
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Martin-Albarracin et al.

title: A reappraisal of the morphology and systematic position of the theropod dinosaur Sigilmassasaurus from the “middle” Cretaceous of Morocco
link: https://peerj.com/articles/1323
last-modified: 2015-10-20
description: Sigilmassasaurus brevicollis is an enigmatic theropod dinosaur from the early Late Cretaceous (Cenomanian) of Morocco, originally based on a few isolated cervical vertebrae. Ever since its original description, both its taxonomic validity and systematic affinities were contentious. Originally considered to represent its own family, Sigilmassasauridae, the genus has variously been suggested to represent a carcharodontosaurid, an ornithischian, and, more recently, a spinosaurid. Here we describe new remains referrable to this taxon and re-evaluate its taxonomic status and systematic affinities. Based on the new remains, a re-evaluation of the original materials, and comparisons with other spinosaurids, the holotype of Sigilmassasaurus brevicollis is identified as an anterior dorsal, rather than a cervical vertebra, and differences between elements referred to this taxon can be explained by different positions of the elements in question within the vertebral column. Many characters used previously to diagnose the genus and species are found to be more widespread among basal tetanurans, and specifically spinosaurids. However, the taxon shows several autapomorphies that support its validity, including the presence of a strongly rugose, ventrally offset triangular platform that is confluent with a ventral keel anteriorly in the mid-cervical vertebral centra and a strongly reduced lateral neural arch lamination, with no or an incomplete distinction between anterior and posterior centrodiapophyseal laminae in the posterior cervical and anterior dorsal vertebrae. We argue furthermore that Spinosaurus maroccanus, also described on the basis of isolated cervical vertebrae from the same stratigraphic unit and in the same paper as Sigilmassasaurus brevicollis, is a subjective synonym of the latter. Both a detailed comparison of this taxon with other theropods and a formal phylogenetic analysis support spinosaurid affintities for Sigilmassasaurus. However, we reject the recently proposed synonymy of both Spinosaurus maroccanus and Sigilmassasurus brevicollis with Spinosaurus aegyptiacus from the Cenomanian of Egypt, as there are clear differences between the vertebrae of these taxa, and they do not share any derived character that is not found in other spinosaurids. Together with a comparison with other spinosaurid vertebral material from the Kem Kem, this suggests that more than one taxon of spinosaurid was present in the Kem Kem assemblage of Morocco, so the referral of non-overlapping material from this unit to a single taxon should be regarded with caution.
creator: Serjoscha W. Evers
creator: Oliver W.M. Rauhut
creator: Angela C. Milner
creator: Bradley McFeeters
creator: Ronan Allain
uri: https://doi.org/10.7717/peerj.1323
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Evers et al.

title: Allocation trade-off under climate warming in experimental amphibian populations
link: https://peerj.com/articles/1326
last-modified: 2015-10-20
description: Climate change could either directly or indirectly cause population declines via altered temperature, rainfall regimes, food availability or phenological responses. However few studies have focused on allocation trade-offs between growth and reproduction under marginal resources, such as food scarce that may be caused by climate warming. Such critical changes may have an unpredicted impact on amphibian life-history parameters and even population dynamics. Here, we report an allocation strategy of adult anuran individuals involving a reproductive stage under experimental warming. Using outdoor mesocosm experiments we simulated a warming scenario likely to occur at the end of this century. We examined the effects of temperature (ambient vs. pre-/post-hibernation warming) and food availability (normal vs. low) on reproduction and growth parameters of pond frogs (Pelophylax nigromaculatus). We found that temperature was the major factor influencing reproductive time of female pond frogs, which showed a significant advancing under post-hibernation warming treatment. While feeding rate was the major factor influencing reproductive status of females, clutch size, and variation of body size for females, showed significant positive correlations between feeding rate and reproductive status, clutch size, or variation of body size. Our results suggested that reproduction and body size of amphibians might be modulated by climate warming or food availability variation. We believe this study provides some new evidence on allocation strategies suggesting that amphibians could adjust their reproductive output to cope with climate warming.
creator: Xu Gao
creator: Changnan Jin
creator: Arley Camargo
creator: Yiming Li
uri: https://doi.org/10.7717/peerj.1326
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gao et al.

title: Growing coral larger and faster: micro-colony-fusion as a strategy for accelerating coral cover
link: https://peerj.com/articles/1313
last-modified: 2015-10-20
description: Fusion is an important life history strategy for clonal organisms to increase access to shared resources, to compete for space, and to recover from disturbance. For reef building corals, fragmentation and colony fusion are key components of resilience to disturbance. Observations of small fragments spreading tissue and fusing over artificial substrates prompted experiments aimed at further characterizing Atlantic and Pacific corals under various conditions. Small (∼1–3 cm2) fragments from the same colony spaced regularly over ceramic tiles resulted in spreading at rapid rates (e.g., tens of square centimeters per month) followed by isogenic fusion. Using this strategy, we demonstrate growth, in terms of area encrusted and covered by living tissue, of Orbicella faveolata, Pseudodiploria clivosa, and Porites lobata as high as 63, 48, and 23 cm2 per month respectively. We found a relationship between starting and ending size of fragments, with larger fragments growing at a faster rate. Porites lobata showed significant tank effects on rates of tissue spreading indicating sensitivity to biotic and abiotic factors. The tendency of small coral fragments to encrust and fuse over a variety of surfaces can be exploited for a variety of applications such as coral cultivation, assays for coral growth, and reef restoration.
creator: Zac H. Forsman
creator: Christopher A. Page
creator: Robert J. Toonen
creator: David Vaughan
uri: https://doi.org/10.7717/peerj.1313
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Forsman et al.

title: The development of Negative Self-Beliefs Inventory (NSBI): cultural adaptation and psychometric validation
link: https://peerj.com/articles/1312
last-modified: 2015-10-20
description: Social anxiety is an emotional disorder common to various populations around the world. The newly developed Self-Beliefs Related to Social Anxiety Scale (SBSA) aims to assess three kinds of self-beliefs through 15 items that include self-related cognitive factors that evidently result in social anxiety. This study explored the psychometric characteristics of SBSA among 978 Chinese. An eight-item Negative Self-beliefs Inventory (NSBI) was developed through qualitative and quantitative analyses. Exploratory factor analysis, confirmatory factor analysis, and multi-group confirmatory factor analysis suggested that NSBI contained clear, meaningful, stable, and invariant three-factor structure consistent with the original SBSA. Further analyses showed that the three subscales and the entire scale exhibited high internal consistency (0.779–0.837), good criterion validity, and good convergent and divergent validity (i.e., negative associations with flourishing and positive associations with anxiety, depression, and stress). These findings indicated that NSBI is reliable and valid for measuring negative self-beliefs in the Chinese population. A higher total score of NSBI indicates the more serious negative self-beliefs. Limitations of the present study and implications for research and practice were also discussed. Further studies are needed to evaluate the predictive ability, incremental validity, and potential role of NSBI in clinical and large-scale populations.
creator: Xiaoqing Tang
creator: Wenjie Duan
creator: Ying Wang
creator: Pengfei Guo
uri: https://doi.org/10.7717/peerj.1312
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Tang et al.

title: Interaction of Wnt pathway related variants with type 2 diabetes in a Chinese Han population
link: https://peerj.com/articles/1304
last-modified: 2015-10-20
description: Aims. Epistasis from gene set based on the function-related genes may confer to the susceptibility of type 2 diabetes (T2D). The Wnt pathway has been reported to play an important role in the pathogenesis of T2D. Here we applied tag SNPs to explore the association between epistasis among genes from Wnt and T2D in the Han Chinese population.Methods. Variants of fourteen genes selected from Wnt pathways were performed to analyze epistasis. Gene–gene interactions in case-control samples were identified by generalized multifactor dimensionality reduction (GMDR) method. We performed a case-controlled association analysis on a total of 1,026 individual with T2D and 1,157 controls via tag SNPs in Wnt pathway.Results. In single-locus analysis, SNPs in four genes were significantly associated with T2D adjusted for multiple testing (rs7903146C in TCF7L2, p = 3.21∗10−3, OR = 1.39, 95% CI [1.31–1.47], rs12904944G in SMAD3, p = 2.51∗10−3, OR = 1.39, 95% CI [1.31–1.47], rs2273368C in WNT2B, p = 4.46∗10−3, OR = 1.23, 95% CI [1.11–1.32], rs6902123C in PPARD, p = 1.14∗10−2, OR = 1.40, 95% CI [1.32–1.48]). The haplotype TGC constructed by TCF7L2 (rs7903146), DKK1 (rs2241529) and BTRC (rs4436485) showed a significant association with T2D (OR = 0.750, 95% CI [0.579–0.972], P = 0.03). For epistasis analysis, the optimized combination was the two locus model of WNT2B rs2273368 and TCF7L2rs7903146, which had the maximum cross-validation consistency. This was 9 out of 10 for the sign test at 0.0107 level. The best combination increased the risk of T2D by 1.47 times (95% CI [1.13–1.91], p = 0.0039).Conclusions. Epistasis between TCF7L2 and WNT2B is associated with the susceptibility of T2D in a Han Chinese population. Our results were compatible with the idea of the complex nature of T2D that would have been missed using conventional tools.
creator: Jian-Bo Zhou
creator: Jin-Kui Yang
creator: Bao-Hong Zhang
creator: Jing Lu
uri: https://doi.org/10.7717/peerj.1304
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhou et al.

title: Multifaceted interventions to decrease mortality in patients with severe sepsis/septic shock—a quality improvement project
link: https://peerj.com/articles/1290
last-modified: 2015-10-20
description: Despite knowledge that EGDT improves outcomes in septic patients, staff education on EGDT and compliance with the CPOE order set has been variable. Based on results of a resident survey to identify barriers to decrease severe sepsis/septic shock mortality in the medical intensive care unit (MICU), multifaceted interventions such as educational interventions to improve awareness to the importance of early goal-directed therapy (EGDT), and the use of the Computerized Physician Order Entry (CPOE) order set, were implemented in July 2013. CPOE order set was established to improve compliance with the EGDT resuscitation bundle elements. Orders were reviewed and compared for patients admitted to the MICU with severe sepsis/septic shock in July and August 2013 (controls) and 2014 (following the intervention). Similarly, educational slide sets were used as interventions for residents before the start of their ICU rotations in July and August 2013. While CPOE order set compliance did not significantly improve (78% vs. 76%, p = 0.74), overall EGDT adherence improved from 43% to 68% (p = 0.0295). Although there was a trend toward improved mortality, this did not reach statistical significance. This study shows that education interventions can be used to increase awareness of severe sepsis/septic shock and improve overall EGDT adherence.
creator: Brittany Siontis
creator: Jennifer Elmer
creator: Richard Dannielson
creator: Catherine Brown
creator: John Park
creator: Salim Surani
creator: Kannan Ramar
uri: https://doi.org/10.7717/peerj.1290
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Siontis et al.

title: Grunt variation in the oyster toadfish Opsanus tau: effect of size and sex
link: https://peerj.com/articles/1330
last-modified: 2015-10-15
description: As in insects, frogs and birds, vocal activity in fishes tends to be more developed in males than in females, and sonic swimbladder muscles may be sexually dimorphic, i.e., either larger in males or present only in males. Male oyster toadfish Opsanus tau L produce a long duration, tonal boatwhistle advertisement call, and both sexes grunt, a short duration more pulsatile agonistic call. Sonic muscles are present in both sexes but larger in males. We tested the hypothesis that males would call more than females by inducing grunts in toadfish of various sizes held in a net and determined incidence of calling and developmental changes in grunt parameters. A small number of fish were recorded twice to examine call repeatability. Both sexes were equally likely to grunt, and grunt parameters (sound pressure level (SPL), individual range in SPL, number of grunts, and fundamental frequency) were similar in both sexes. SPL increased with fish size before leveling off in fish >200 g, and fundamental frequency and other parameters did not change with fish size. Number of grunts in a train, grunt duration and inter-grunt interval were highly variable in fish recorded twice suggesting that grunt parameters reflect internal motivation rather than different messages. Grunt production may explain the presence of well-developed sonic muscles in females and suggests that females have an active but unexplored vocal life.
creator: Michael L. Fine
creator: Tyler D. Waybright
uri: https://doi.org/10.7717/peerj.1330
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Fine and Waybright

title: Stable isotope analyses of web-spinning spider assemblages along a headwater stream in Puerto Rico
link: https://peerj.com/articles/1324
last-modified: 2015-10-15
description: Web-spinning spiders that inhabit stream channels are considered specialists of aquatic ecosystems and are major consumers of emerging aquatic insects, while other spider taxa are more commonly found in riparian forests and as a result may consume more terrestrial insects. To determine if there was a difference in spider taxa abundance between riverine web-spinning spider assemblages within the stream channel and the assemblages 10 m into the riparian forest, we compared abundances for all web-spinning spiders along a headwater stream in El Yunque National Forest in northeast Puerto Rico. By using a nonmetric dimensional scaling (NMDS) abundance analysis we were able to see a clear separation of the two spider assemblages. The second objective of the study was to determine if aquatic insects contributed more to the diet of the spider assemblages closest to the stream channel and therefore stable isotope analyses of δ15N and δ13C for web-spinning spiders along with their possible prey were utilized. The results of the Bayesian mixing model (SIAR) however showed little difference in the diets of riverine (0 m), riparian (10 m) and upland (25 m) spiders. We found that aquatic insects made up ∼50% of the diet for web-spinning spiders collected at 0 m, 10 m, and 25 m from the stream. This study highlights the importance of aquatic insects as a food source for web-spinning spiders despite the taxonomic differences in assemblages at different distances from the stream.
creator: Sean P. Kelly
creator: Elvira Cuevas
creator: Alonso Ramírez
uri: https://doi.org/10.7717/peerj.1324
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kelly et al.

title: Persistent and extreme outliers in causes of death by state, 1999–2013
link: https://peerj.com/articles/1336
last-modified: 2015-10-13
description: In the United States, state-specific mortality rates that are high relative to national rates can result from legitimate reasons or from variability in coding practices. This paper identifies instances of state-specific mortality rates that were at least twice the national rate in each of three consecutive five-year periods (termed persistent outliers), along with rates that were at least five times the national rate in at least one five-year period (termed extreme outliers). The resulting set of 71 outliers, 12 of which appear on both lists, illuminates mortality variations within the country, including some that are amenable to improvement either because they represent preventable causes of death or highlight weaknesses in coding techniques. Because the approach used here is based on relative rather than absolute mortality, it is not dominated by the most common causes of death such as heart disease and cancer.
creator: Francis P. Boscoe
uri: https://doi.org/10.7717/peerj.1336
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Boscoe

title: The vibrating reed frequency meter: digital investigation of an early cochlear model
link: https://peerj.com/articles/1333
last-modified: 2015-10-13
description: The vibrating reed frequency meter, originally employed by Békésy and later by Wilson as a cochlear model, uses a set of tuned reeds to represent the cochlea’s graded bank of resonant elements and an elastic band threaded between them to provide nearest-neighbour coupling. Here the system, constructed of 21 reeds progressively tuned from 45 to 55 Hz, is simulated numerically as an elastically coupled bank of passive harmonic oscillators driven simultaneously by an external sinusoidal force. To uncover more detail, simulations were extended to 201 oscillators covering the range 1–2 kHz. Calculations mirror the results reported by Wilson and show expected characteristics such as traveling waves, phase plateaus, and a response with a broad peak at a forcing frequency just above the natural frequency. The system also displays additional fine-grain features that resemble those which have only recently been recognised in the cochlea. Thus, detailed analysis brings to light a secondary peak beyond the main peak, a set of closely spaced low-amplitude ripples, rapid rotation of phase as the driving frequency is swept, frequency plateaus, clustering, and waxing and waning of impulse responses. Further investigation shows that each reed’s vibrations are strongly localised, with small energy flow along the chain. The distinctive set of equally spaced ripples is an inherent feature which is found to be largely independent of boundary conditions. Although the vibrating reed model is functionally different to the standard transmission line, its cochlea-like properties make it an intriguing local oscillator model whose relevance to cochlear mechanics needs further investigation.
creator: Andrew Bell
creator: Hero P. Wit
uri: https://doi.org/10.7717/peerj.1333
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bell and Wit

title: No apparent correlation between honey bee forager gut microbiota and honey production
link: https://peerj.com/articles/1329
last-modified: 2015-10-13
description: One of the best indicators of colony health for the European honey bee (Apis mellifera) is its performance in the production of honey. Recent research into the microbial communities naturally populating the bee gut raise the question as to whether there is a correlation between microbial community structure and colony productivity. In this work, we used 16S rRNA amplicon sequencing to explore the microbial composition associated with forager bees from honey bee colonies producing large amounts of surplus honey (productive) and compared them to colonies producing less (unproductive). As supported by previous work, the honey bee microbiome was found to be dominated by three major phyla: the Proteobacteria, Bacilli and Actinobacteria, within which we found a total of 23 different bacterial genera, including known “core” honey bee microbiome members. Using discriminant function analysis and correlation-based network analysis, we identified highly abundant members (such as Frischella and Gilliamella) as important in shaping the bacterial community; libraries from colonies with high quantities of these Orbaceae members were also likely to contain fewer Bifidobacteria and Lactobacillus species (such as Firm-4). However, co-culture assays, using isolates from these major clades, were unable to confirm any antagonistic interaction between Gilliamella and honey bee gut bacteria. Our results suggest that honey bee colony productivity is associated with increased bacterial diversity, although this mechanism behind this correlation has yet to be determined. Our results also suggest researchers should not base inferences of bacterial interactions solely on correlations found using sequencing. Instead, we suggest that depth of sequencing and library size can dramatically influence statistically significant results from sequence analysis of amplicons and should be cautiously interpreted.
creator: Melissa A. Horton
creator: Randy Oliver
creator: Irene L. Newton
uri: https://doi.org/10.7717/peerj.1329
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Horton et al.

title: Successful childhood obesity management in primary care in Canada: what are the odds?
link: https://peerj.com/articles/1327
last-modified: 2015-10-13
description: Background. The management of a child presenting with obesity in a primary care setting can be viewed as a multi-step behavioral process with many perceived and actual barriers for families and primary care providers. In order to achieve the goal of behavior change and, ultimately, clinically meaningful weight management outcomes in a child who is considered obese, all steps in this process should ideally be completed. We sought to review the evidence for completing each step, and to estimate the population effect of secondary prevention of childhood obesity in Canada.Methods. Data from the 2009/2010 Canadian Community Health Survey and from a review of the literature were used to estimate the probabilities for completion of each step. A flow chart based on these probabilities was used to determine the proportion of children with obesity that would undergo and achieve clinically meaningful weight management outcomes each year in Canada.Results. We estimated that the probability of a child in Canada who presents with obesity achieving clinically meaningful weight management outcomes through secondary prevention in primary care is around 0.6% per year, with a range from 0.01% to 7.2% per year. The lack of accessible and effective weight management programs appeared to be the most important bottleneck in the process.Conclusions. In order to make progress towards supporting effective pediatric obesity management, efforts should focus on population-based primary prevention and a systems approach to change our obesogenic society, alongside the allocation of resources toward weight management approaches that are comprehensively offered, equitably distributed and robustly evaluated.
creator: Stefan Kuhle
creator: Rachel Doucette
creator: Helena Piccinini-Vallis
creator: Sara F.L. Kirk
uri: https://doi.org/10.7717/peerj.1327
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kuhle et al.

title: Clustering symptoms of non-severe malaria in semi-immune Amazonian patients
link: https://peerj.com/articles/1325
last-modified: 2015-10-13
description: Malaria is a disease that generates a broad spectrum of clinical features. The purpose of this study was to evaluate the clinical spectrum of malaria in semi-immune populations. Patients were recruited in Mâncio Lima, a city situated in the Brazilian Amazon region. The study included 171 malaria cases, which were diagnosed via the use of a thick blood smear and confirmed by molecular methods. A questionnaire addressing 19 common symptoms was administered to all patients. Multiple correspondence analysis and hierarchical cluster analysis were performed to identify clusters of symptoms, and logistic regression was used to identify factors associated with the occurrence of symptoms. The cluster analysis revealed five groups of symptoms: the first cluster, which included algic- and fever-related symptoms, occurred in up to 95.3% of the cases. The second cluster, which comprised gastric symptoms (nausea, abdominal pain, inappetence, and bitter mouth), occurred in frequencies that ranged between 35.1% and 42.7%, and at least one of these symptoms was observed in 71.9% of the subjects. All respiratory symptoms were clustered and occurred in 42.7% of the malaria cases, and diarrhea occurred in 9.9% of the cases. Symptoms constituting the fifth cluster were vomiting and pallor, with a 14.6% and 11.7% of prevalence, respectively. A higher parasitemia count (more than 300 parasites/mm3) was associated with the presence of fever, vomiting, dizziness, and weakness (P < 0.05). Arthralgia and myalgia were associated with patients over the age of 14 years (P < 0.001). Having experienced at least eight malaria episodes prior to the study was associated with a decreased risk of chills and fever and an increased risk of sore throat (P < 0.05). None of the symptoms showed an association with gender or with species of Plasmodium. The clinical spectrum of malaria in semi-immune individuals can have a broad range of symptoms, the frequency and intensity of which are associated with age, past exposure to malaria, and parasitemia. Understanding the full spectrum of nonsevere malaria is important in endemic areas to guide both passive and active case detection, for the diagnosis of malaria in travelers returning to non-endemic areas, and for the development of vaccines aimed to decrease symptom severity.
creator: Antonio C. Martins
creator: Felipe M. Araújo
creator: Cássio B. Braga
creator: Maria G.S. Guimarães
creator: Rudi Nogueira
creator: Rayanne A. Arruda
creator: Lícia N. Fernandes
creator: Livia R. Correa
creator: Rosely dos S. Malafronte
creator: Oswaldo G. Cruz
creator: Cláudia T. Codeço
creator: Mônica da Silva-Nunes
uri: https://doi.org/10.7717/peerj.1325
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Martins et al.

title: Six simple questions to detect malnutrition or malnutrition risk in elderly women
link: https://peerj.com/articles/1316
last-modified: 2015-10-13
description: Of the numerous instruments available to detect nutritional risk, the most widely used is the Mini Nutritional Assessment (MNA), but it takes 15–20 min to complete and its systematic administration in primary care units is not feasible in practice. We developed a tool to evaluate malnutrition risk that can be completed more rapidly using just clinical variables. Between 2008 and 2013, we conducted a cross-sectional study of 418 women aged ≥60 years from Mexico. Our outcome was positive MNA and our secondary variables included were: physical activity, diabetes mellitus, hypertension, educational level, dentition, psychological problems, living arrangements, history of falls, age and the number of tablets taken daily. The sample was divided randomly into two groups: construction and validation. Construction: a risk table was constructed to estimate the likelihood of the outcome, and risk groups were formed. Validation: the area under the ROC curve (AUC) was calculated and we compared the expected and the observed outcomes. The following risk factors were identified: physical activity, hypertension, diabetes, dentition, psychological problems and living with the family. The AUC was 0.77 (95% CI [0.68–0.86], p < 0.001). No differences were found between the expected and the observed outcomes (p = 0.902). This study presents a new malnutrition screening test for use in elderly women. The test is based on six very simple, quick and easy-to-evaluate questions, enabling the MNA to be reserved for confirmation. However, it should be used with caution until validation studies have been performed in other geographical areas.
creator: Tranquilina Gutiérrez-Gómez
creator: Ernesto Cortés
creator: Antonio Palazón-Bru
creator: Isabel Peñarrieta-de Córdova
creator: Vicente Francisco Gil-Guillén
creator: Rosa María Ferrer-Diego
uri: https://doi.org/10.7717/peerj.1316
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gutiérrez-Gómez et al.

title: Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
link: https://peerj.com/articles/1310
last-modified: 2015-10-13
description: Transient Receptor Potential cation channel, subfamily Melastatin, member 8 (TRPM8) is involved in detection of cold temperature, different noxious compounds and in execution of thermo- as well as chemo-sensitive responses at cellular levels. Here we explored the molecular evolution of TRPM8 by analyzing sequences from various species. We elucidate that several regions of TRPM8 had different levels of selection pressure but the 4th–5th transmembrane regions remain highly conserved. Analysis of synteny suggests that since vertebrate origin, TRPM8 gene is linked with SPP2, a bone morphogen. TRPM8, especially the N-terminal region of it, seems to be highly variable in human population. We found 16,656 TRPM8 variants in 1092 human genomes with top variations being SNPs, insertions and deletions. A total of 692 missense mutations are also mapped to human TRPM8 protein of which 509 seem to be delateroiours in nature as supported by Polyphen V2, SIFT and Grantham deviation score. Using a highly specific antibody, we demonstrate that TRPM8 is expressed endogenously in the testis of rat and sperm cells of different vertebrates ranging from fish to higher mammals. We hypothesize that TRPM8 had emerged during vertebrate evolution (ca 450 MYA). We propose that expression of TRPM8 in sperm cell and its role in regulating sperm function are important factors that have guided its molecular evolution, and that these understandings may have medical importance.
creator: Rakesh Kumar Majhi
creator: Somdatta Saha
creator: Ashutosh Kumar
creator: Arijit Ghosh
creator: Nirlipta Swain
creator: Luna Goswami
creator: Pratyush Mohapatra
creator: Apratim Maity
creator: Vivek Kumar Sahoo
creator: Abhishek Kumar
creator: Chandan Goswami
uri: https://doi.org/10.7717/peerj.1310
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Majhi et al.

title: Antityrosinase activity of Euphorbia characias extracts
link: https://peerj.com/articles/1305
last-modified: 2015-10-13
description: Tyrosinase is a well-known key enzyme in melanin biosynthesis and its inhibitors have become increasingly important because of their potential use as hypopigmenting agents. In the present study, the anti-melanogenic effect of aqueous and ethanolic extracts from Euphorbia characias leaves, stems, and flowers in cell-free and cellular systems was examined. All the extracts showed inhibitory effects against mushroom tyrosinase with leaf extracts exhibiting the lowest IC50 values of 24 and 97 µg/mL for aqueous and ethanolic extracts respectively. Enzyme kinetic analysis indicated that leaf aqueous extract acts as a mixed type inhibitor, while ethanolic extract shows a competitive inhibition effect on mushroom tyrosinase using L-DOPA as substrate. In addition, the inhibitory effect of leaf extracts on tyrosinase activity and melanin production was examined in murine melanoma B16F10 cells. Cellular tyrosinase activity as well as levels of melanin synthesis are reduced in a dose-dependent manner by extracts in cells treated with α-melanocyte stimulating hormone (α-MSH). The effects are comparable, and sometimes even better, than that of kojic acid, a well known tyrosinase inhibitor used for reference. All these results suggest that E. characias could be a great source of the natural inhibitors from tyrosinase and has the potential to be used as a whitening agent in therapeutic fields.
creator: Francesca Pintus
creator: Delia Spanò
creator: Angela Corona
creator: Rosaria Medda
uri: https://doi.org/10.7717/peerj.1305
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Pintus et al.

title: Validation experiments on finite element models of an ostrich (Struthio camelus) cranium
link: https://peerj.com/articles/1294
last-modified: 2015-10-13
description: The first finite element (FE) validation of a complete avian cranium was performed on an extant palaeognath, the ostrich (Struthio camelus). Ex-vivo strains were collected from the cranial bone and rhamphotheca. These experimental strains were then compared to convergence tested, specimen-specific finite element (FE) models. The FE models contained segmented cortical and trabecular bone, sutures and the keratinous rhamphotheca as identified from micro-CT scan data. Each of these individual materials was assigned isotropic material properties either from the literature or from nanoindentation, and the FE models compared to the ex-vivo results. The FE models generally replicate the location of peak strains and reflect the correct mode of deformation in the rostral region. The models are too stiff in regions of experimentally recorded high strain and too elastic in regions of low experimentally recorded low strain. The mode of deformation in the low strain neurocranial region is not replicated by the FE models, and although the models replicate strain orientations to within 10° in some regions, in most regions the correlation is not strong. Cranial sutures, as has previously been found in other taxa, are important for modifying both strain magnitude and strain patterns across the entire skull, but especially between opposing the sutural junctions. Experimentally, we find that the strains on the surface of the rhamphotheca are much lower than those found on nearby bone. The FE models produce much higher principal strains despite similar strain ratios across the entirety of the rhamphotheca. This study emphasises the importance of attempting to validate FE models, modelling sutures and rhamphothecae in birds, and shows that whilst location of peak strain and patterns of deformation can be modelled, replicating experimental data in digital models of avian crania remains problematic.
creator: Andrew R. Cuff
creator: Jen A. Bright
creator: Emily J. Rayfield
uri: https://doi.org/10.7717/peerj.1294
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Cuff et al.

title: Under which conditions can introverts achieve happiness? Mediation and moderation effects of the quality of social relationships and emotion regulation ability on happiness
link: https://peerj.com/articles/1300
last-modified: 2015-10-08
description: Personality traits have been directly associated with happiness. One consistent finding is a strong link between extraversion and happiness: extraverts are happier than introverts. Although happy introverts exist, it is currently unclear under what conditions they can achieve happiness. The present study analyzes, generally, how the quality of social relationships and emotion regulation ability influence happiness and, specifically, how these factors can lead introverts to be happy. In the present study, 1,006 participants aged 18–80 (42% males) completed measures of extraversion, neuroticism, quality of social relationships, emotion regulation ability, and happiness. We found that extraverts had significantly higher happiness, quality of social relationships and emotion regulation ability scores than introverts. In addition, people with high quality social relationships or high emotion regulation ability were happier. Serial mediation analyses indicated that greater levels of extraversion were associated with greater happiness, with small effect size, via two indirect mechanisms: (a) higher quality of social relationships, and (b) higher quality of social relationships followed serially by higher emotion regulation ability. We also found a moderating effect due to the three-way interaction of extraversion, quality of social relationships, and emotion regulation ability: introverts were happier when they had high scores for these two variables, though the effect size was small. These results suggest that the quality of social relationships and emotion regulation ability are relevant to our understanding of complex associations between extraversion and happiness.
creator: Rosario Cabello
creator: Pablo Fernandez-Berrocal
uri: https://doi.org/10.7717/peerj.1300
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Cabello and Fernandez-Berrocal

title: Promoting an active form of learning out-of-class via answering online “study questions” leads to higher than expected exam scores in General Biology
link: https://peerj.com/articles/1322
last-modified: 2015-10-08
description: A rising need for workers in science, technology, engineering and mathematics (STEM) fields has fueled interest in improving teaching within STEM disciplines. Numerous studies have demonstrated the benefits of active learning approaches on student learning outcomes. However, many of these studies have been conducted in experimental, rather than real-life class, settings. In addition, most of these studies have focused on in-class active learning exercises. This study tested the effects of answering questions outside of class on exam performance for General Biology students at the University of Minnesota. An online database of 1,020 multiple-choice questions covering material from the first half of the course was generated. Students in seven course sections (with an average of ∼265 students per section) were given unlimited access to the online study questions. These students made extensive use of the online questions, with students answering an average of 1,323 questions covering material from the half of the semester for which the questions were available. After students answered a set of questions, they were shown the correct answers for those questions. More specific feedback describing how to arrive at the correct answer was provided for the 73% of the questions for which the correct answers were not deemed to be self-explanatory. The extent to which access to the online study questions improved student learning outcomes was assessed by comparing the performance on exam questions of students in the seven course sections with access to the online study questions with the performance of students in course sections without access to the online study questions. Student performance was analyzed for a total of 89 different exams questions that were not included in the study questions, but that covered the same material covered by the study questions. Each of these 89 questions was used on one to five exams given to students in course sections that had access to the online study questions and on three to 77 exams given to students in sections that lacked such access. Data from over 1,800 students in sections with access to the online study questions show that those students scored a statistically significant average of 6.6% points higher on the exam questions analyzed than students in sections without access to the study questions. This difference was greater than the average amount necessary to raise students’ exam grades by one grade (e.g., from a “B-” to a “B”). In addition, there was a higher correlation between number of questions answered and success on exam questions on material related to the study questions than between number of questions answered and success on exam questions on material unrelated to the study questions. The online study question system required substantial effort to set up, but required minimal effort to maintain and was effective in significantly raising average exam scores for even very large course sections.
creator: Susan I. Gibson
uri: https://doi.org/10.7717/peerj.1322
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Gibson

title: Interdisciplinary, interinstitutional and international collaboration of family medicine researchers in Taiwan
link: https://peerj.com/articles/1321
last-modified: 2015-10-08
description: The family medicine researches flourished worldwide in the past decade. However, the collaborative patterns of family medicine publications had not been reported. Our study analyzed the collaborative activity of family medicine researchers in Taiwan. We focused on the types of collaboration among disciplines, institutions and countries. We searched “family medicine” AND “Taiwan” in address field from Web of Science and documented the disciplines, institutions and countries of all authors. We analyzed the collaborative patterns of family medicine researchers in Taiwan from 2010 to 2014. The journal’s impact factor of each article in the same publication year was also retrieved. Among 1,217 articles from 2010 to 2014, interdisciplinary collaboration existed in 1,185 (97.3%) articles, interinstitutional in 1,012 (83.2%) and international in 142 (11.7%). Public health was the most common collaborative discipline. All international researches were also interdisciplinary and interinstitutional. The United States (75 articles), the United Kingdom (21) and the People’s Republic of China (20) were the top three countries with which family medicine researchers in Taiwan had collaborated. We found a high degree of interdisciplinary and interinstitutional collaboration of family medicine researches in Taiwan. However, the collaboration of family medicine researchers in Taiwan with family medicine colleagues of other domestic or foreign institutions was insufficient. The future direction of family medicine studies could focus on the promotion of communication among family medicine researchers.
creator: Yi-Hsuan Lin
creator: Yen-Han Tseng
creator: Hsiao-Ting Chang
creator: Ming-Hwai Lin
creator: Yen-Chiang Tseng
creator: Tzeng-Ji Chen
creator: Shinn-Jang Hwang
uri: https://doi.org/10.7717/peerj.1321
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Lin et al.

title: Anvi’o: an advanced analysis and visualization platform for ‘omics data
link: https://peerj.com/articles/1319
last-modified: 2015-10-08
description: Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
creator: A. Murat Eren
creator: Özcan C. Esen
creator: Christopher Quince
creator: Joseph H. Vineis
creator: Hilary G. Morrison
creator: Mitchell L. Sogin
creator: Tom O. Delmont
uri: https://doi.org/10.7717/peerj.1319
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Eren et al.

title: Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria
link: https://peerj.com/articles/1291
last-modified: 2015-10-08
description: Fertilizer application is a common anthropogenic alteration to terrestrial systems. Increased nutrient input can impact soil microbial diversity or function directly through altered soil environments, or indirectly through plant-microbe feedbacks, with potentially important effects on ecologically-important plant-associated mutualists. We investigated the impacts of plant fertilizer, containing all common macro and micronutrients on symbiotic nitrogen-fixing bacteria (rhizobia), a group of bacteria that are important for plant productivity and ecosystem function. We collected rhizobia nodule isolates from natural field soil that was treated with slow-release plant fertilizer over a single growing season and compared phenotypic traits related to free-living growth and host partner quality in these isolates to those of rhizobia from unfertilized soils. Through a series of single inoculation assays in controlled glasshouse conditions, we found that isolates from fertilized field soil provided legume hosts with higher mutualistic benefits. Through growth assays on media containing variable plant fertilizer concentrations, we found that plant fertilizer was generally beneficial for rhizobia growth. Rhizobia isolated from fertilized field soil had higher growth rates in the presence of plant fertilizer compared to isolates from unfertilized field soil, indicating that plant fertilizer application favoured rhizobia isolates with higher abilities to utilize fertilizer for free-living growth. We found a positive correlation between growth responses to fertilizer and mutualism benefits among isolates from fertilized field soil, demonstrating that variable plant fertilizer induces context-dependent genetic correlations, potentially changing the evolutionary trajectory of either trait through increased trait dependencies. Our study shows that short-term application is sufficient to alter the composition of rhizobia isolates in the population or community, either directly though changes in the soil chemistry or indirectly through altered host legume feedbacks, and is potentially a strong selective agent acting on natural rhizobia populations.
creator: Anna K. Simonsen
creator: Shery Han
creator: Phil Rekret
creator: Christine S. Rentschler
creator: Katy D. Heath
creator: John R. Stinchcombe
uri: https://doi.org/10.7717/peerj.1291
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Simonsen et al.

title: Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs
link: https://peerj.com/articles/1272
last-modified: 2015-10-08
description: In a number of recent studies we used computer modeling to investigate the evolution of muscle leverage (moment arms) and function in extant and extinct archosaur lineages (crocodilians, dinosaurs including birds and pterosaurs). These studies sought to quantify the level of disparity and convergence in muscle moment arms during the evolution of bipedal and quadrupedal posture in various independent archosaur lineages, and in doing so further our understanding of changes in anatomy, locomotion and ecology during the group’s >250 million year evolutionary history. Subsequent work by others has led us to re-evaluate our models, which revealed a methodological error that impacted on the results obtained from the abduction–adduction and long-axis rotation moment arms in our published studies. In this paper we present corrected abduction–adduction and long axis rotation moment arms for all our models, and evaluate the impact of this new data on the conclusions of our previous studies. We find that, in general, our newly corrected data differed only slightly from that previously published, with very few qualitative changes in muscle moments (e.g., muscles originally identified as abductors remained abductors). As a result the majority of our previous conclusions regarding the functional evolution of key muscles in these archosaur groups are upheld.
creator: Karl Bates
creator: Susannah C.R. Maidment
creator: Emma R. Schachner
creator: Paul M. Barrett
uri: https://doi.org/10.7717/peerj.1272
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bates et al.

title: Competition from native hydrophytes reduces establishment and growth of invasive dense-flowered cordgrass (Spartina densiflora)
link: https://peerj.com/articles/1260
last-modified: 2015-10-08
description: Experimental studies to determine the nature of ecological interactions between invasive and native species are necessary for conserving and restoring native species in impacted habitats. Theory predicts that species boundaries along environmental gradients are determined by physical factors in stressful environments and by competitive ability in benign environments, but little is known about the mechanisms by which hydrophytes exclude halophytes and the life history stage at which these mechanisms are able to operate. The ongoing invasion of the South American Spartina densiflora in European marshes is causing concern about potential impacts to native plants along the marsh salinity gradient, offering an opportunity to evaluate the mechanisms by which native hydrophytes may limit, or even prevent, the expansion of invasive halophytes. Our study compared S. densiflora seedling establishment with and without competition with Phragmites australis and Typha domingensis, two hydrophytes differing in clonal architecture. We hypothesized that seedlings of the stress tolerant S. densiflora would be out-competed by stands of P. australis and T. domingensis. Growth, survivorship, biomass patterns and foliar nutrient content were recorded in a common garden experiment to determine the effect of mature P. australis and T. domingensis on the growth and colonization of S. densiflora under fresh water conditions where invasion events are likely to occur. Mature P. australis stands prevented establishment of S. densiflora seedlings and T. domingensis reduced S. densiflora establishment by 38%. Seedlings grown with P. australis produced fewer than five short shoots and all plants died after ca. 2 yrs. Our results showed that direct competition, most likely for subterranean resources, was responsible for decreased growth rate and survivorship of S. densiflora. The presence of healthy stands of P. australis, and to some extent T. domingensis, along river channels and in brackish marshes may prevent the invasion of S. densiflora by stopping the establishment of its seedlings.
creator: Ahmed M. Abbas
creator: Adam M. Lambert
creator: Alfredo E. Rubio-Casal
creator: Alfonso De Cires
creator: Enrique M. Figueroa
creator: Jesús M. Castillo
uri: https://doi.org/10.7717/peerj.1260
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Abbas et al.

title: Assessing shoreline exposure and oyster habitat suitability maximizes potential success for sustainable shoreline protection using restored oyster reefs
link: https://peerj.com/articles/1317
last-modified: 2015-10-06
description: Oyster reefs provide valuable ecosystem services that contribute to coastal resilience. Unfortunately, many reefs have been degraded or removed completely, and there are increased efforts to restore oysters in many coastal areas. In particular, much attention has recently been given to the restoration of shellfish reefs along eroding shorelines to reduce erosion. Such fringing reef approaches, however, often lack empirical data to identify locations where reefs are most effective in reducing marsh erosion, or fully take into account habitat suitability. Using monitoring data from 5 separate fringing reef projects across coastal Louisiana, we quantify shoreline exposure (fetch + wind direction + wind speed) and reef impacts on shoreline retreat. Our results indicate that fringing oyster reefs have a higher impact on shoreline retreat at higher exposure shorelines. At higher exposures, fringing reefs reduced marsh edge erosion an average of 1.0 m y−1. Using these data, we identify ranges of shoreline exposure values where oyster reefs are most effective at reducing marsh edge erosion and apply this knowledge to a case study within one Louisiana estuary. In Breton Sound estuary, we calculate shoreline exposure at 500 random points and then overlay a habitat suitability index for oysters. This method and the resulting visualization show areas most likely to support sustainable oyster populations as well as significantly reduce shoreline erosion. Our results demonstrate how site selection criteria, which include shoreline exposure and habitat suitability, are critical to ensuring greater positive impacts and longevity of oyster reef restoration projects.
creator: Megan K. La Peyre
creator: Kayla Serra
creator: T. Andrew Joyner
creator: Austin Humphries
uri: https://doi.org/10.7717/peerj.1317
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 La Peyre et al.

title: Autophagic flux inhibition and lysosomogenesis ensuing cellular capture and retention of the cationic drug quinacrine in murine models
link: https://peerj.com/articles/1314
last-modified: 2015-10-06
description: The proton pump vacuolar (V)-ATPase is the driving force that mediates the concentration of cationic drugs (weak bases) in the late endosome-lysosome continuum; secondary cell reactions include the protracted transformation of enlarged vacuoles into autophagosomes. We used the inherently fluorescent tertiary amine quinacrine in murine models to further assess the accumulation and signaling associated with cation trapping. Primary fibroblasts concentrate quinacrine ∼5,000-fold from their culture medium (KM 9.8 µM; transport studies). The drug is present in perinuclear granules that are mostly positive for Rab7 and LAMP1 (microscopy). Both drug uptake and retention are extensively inhibited by treatments with the V-ATPase inhibitor bafilomycin A1. The H+ ionophore monensin also prevented quinacrine concentration by fibroblasts. However, inhibition of plasma membrane transporters or of the autophagic process with spautin-1 did not alter quinacrine transport parameters. Ancillary experiments did not support that low micromolar concentrations of quinacrine are substrates for organic cation transporters-1 to -3 or P-glycoprotein. The secondary autophagy induced by quinacrine in cells may derive from the accumulation of incompetent autophagolysosomes, as judged from the accumulation of p62/SQSTM1 and LC3 II (immunoblots). Accordingly, protracted lysosomogenesis is evidenced by increased expression of LAMP1 and LAMP2 in quinacrine-treated fibroblasts (48 h, immunoblots), a response that follows the nuclear translocation of the lysosomal genesis transcription factor TFEB and upregulation of LAMP1 and −2 mRNAs (24 h). Quinacrine administration to live mice evidenced variable distribution to various organs and heterogeneous accumulation within the lung (stereo-microscopy, extraction). Dose-dependent in vivo autophagic and lysosomal accumulation was observed in the lung (immunoblots). No evidence has been found for transport or extrusion mechanisms modulating the cellular uptake of micromolar quinacrine at the plasma membrane level. As shown in vitro and in vivo, V-ATPase-mediated cation sequestration is associated, above a certain threshold, to autophagic flux inhibition and feed-back lysosomogenesis.
creator: Alexandre Parks
creator: Xavier Charest-Morin
creator: Michael Boivin-Welch
creator: Johanne Bouthillier
creator: Francois Marceau
uri: https://doi.org/10.7717/peerj.1314
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Parks et al.

title: Metacarpal torsion in apes, humans, and early Australopithecus: implications for manipulatory abilities
link: https://peerj.com/articles/1311
last-modified: 2015-10-06
description: Human hands, when compared to that of apes, have a series of adaptations to facilitate manipulation. Numerous studies have shown that Australopithecus afarensis and Au. africanus display some of these adaptations, such as a longer thumb relative to the other fingers, asymmetric heads on the second and fifth metacarpals, and orientation of the second metacarpal joints with the trapezium and capitate away from the sagittal plane, while lacking others such as a very mobile fifth metacarpal, a styloid process on the third, and a flatter metacarpo-trapezium articulation, suggesting some adaptation to manipulation but more limited than in humans. This paper explores variation in metacarpal torsion, a trait said to enhance manipulation, in humans, apes, early australopithecines and specimens from Swartkrans. This study shows that humans are different from large apes in torsion of the third and fourth metacarpals. Humans are also characterized by wedge-shaped bases of the third and fourth metacarpals, making the metacarpal-base row very arched mediolaterally and placing the ulnar-most metacarpals in a position that facilitate opposition to the thumb in power or cradle grips. The third and fourth metacarpals of Au. afarensis are very human-like, suggesting that the medial palm was already well adapted for these kinds of grips in that taxon. Au. africanus present a less clear human-like morphology, suggesting, perhaps, that the medial palm was less suited to human-like manipulation in that taxa than in Au. afarensis. Overall, this study supports previous studies on Au. afarensis and Au. africanus that these taxa had derived hand morphology with some adaptation to human-like power and precision grips and support the hypothesis that dexterous hands largely predated Homo.
creator: Michelle S.M. Drapeau
uri: https://doi.org/10.7717/peerj.1311
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Drapeau

title: Variations in leopard cat (Prionailurus bengalensis) skull morphology and body size: sexual and geographic influences
link: https://peerj.com/articles/1309
last-modified: 2015-10-06
description: The leopard cat, Prionailurus bengalensis (Kerr, 1792), is one of the most widespread Asian cats, occurring in continental eastern and southeastern Asia. Since 1929, several studies have focused on the morphology, ecology, and taxonomy of leopard cats. Nevertheless, hitherto there has been no agreement on basic aspects of leopard cat biology, such as the presence or absence of sexual dimorphism, morphological skull and body differences between the eleven recognized subspecies, and the biogeography of the different morphotypes. Twenty measurements on 25 adult leopard cat skulls from different Asian localities were analyzed through univariate and multivariate statistical approaches. Skull and external body measurements from studies over the last 77 years were assembled and organized in two categories: full data and summary data. Most of this database comprises small samples, which have never been statistically tested and compared with each other. Full data sets were tested with univariate and multivariate statistical analyses; summary data sets (i.e., means, SDs, and ranges) were analyzed through suitable univariate approaches. The independent analyses of the data from these works confirmed our original results and improved the overview of sexual dimorphism and geographical morphological variation among subspecies. Continental leopard cats have larger skulls and body dimensions. Skulls of Indochinese morphotypes have broader and higher features than those of continental morphotypes, while individuals from the Sunda Islands have skulls with comparatively narrow and low profiles. Cranial sexual dimorphism is present in different degrees among subspecies. Most display subtle sex-related variations in a few skull features. However, in some cases, sexual dimorphism in skull morphology is absent, such as in P. b. sumatranus and P. b. borneoensis. External body measurement comparisons also indicate the low degree of sexual dimorphism. Apart from the gonads, the longer hind foot of male leopard cats is the main feature of sexual dimorphism among P. b. bengalensis (and probably among P. b. horsfieldii too). External body measurements also indicated the absence of sexual dimorphism among individuals of P. b. borneoensis. Inter-subspecific skull comparisons provided a morphometric basis for differentiating some subspecies. Prionailurus b. horsfieldii and P. b. bengalensis were distinguished only by a subtle difference in PM4 size, indicating that overall skull morphology does not appear to support their separate taxonomical status, in spite of the marked differences reported in their coat patterns. Geological events affecting the Sunda Shelf connection between the Sunda Islands and the mainland during the Last Glacial Maximum seem to have influenced directly the morphological pattern shown by leopard cat subspecies nowadays.
creator: Fernando L. Sicuro
creator: Luiz Flamarion B. Oliveira
uri: https://doi.org/10.7717/peerj.1309
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sicuro and Oliveira

title: A taste for exotic food: Neotropical land planarians feeding on an invasive flatworm
link: https://peerj.com/articles/1307
last-modified: 2015-10-06
description: Invasive species establish successfully in new habitats especially due to their ability to include new species in their diet and due to the freedom from natural enemies. However, native species may also adapt to the use of new elements in their ecosystem. The planarian Endeavouria septemlineata, first recorded in Hawaii, was later found in Brazil. Recently, we found it in human-disturbed areas in southern Brazil and here we investigate its interactions with other invertebrates both in the field and in the laboratory. We observed the species in the field during collecting activities and hence maintained some specimens alive in small terraria in the laboratory, where we offered different invertebrate species as potential prey and also put them in contact with native land planarians in order to examine their interaction. Both in the field and in the laboratory, E. septemlineata showed a gregarious behavior and was found feeding on woodlice, millipedes, earwigs and gastropods. In the laboratory, specimens often did not attack live prey, but immediately approached dead specimens, indicating a scavenging behavior. In an experiment using the slug Deroceras laeve and the woodlouse Atlantoscia floridana, there was a higher consumption of dead specimens of woodlice and slugs compared to live specimens, as well as a higher consumption of dead woodlice over dead slugs. Four native land planarians of the genus Obama and one of the genus Paraba attacked and consumed E. septemlineata, which, after the beginning of the attack, tried to escape by tumbling or using autotomy. As a scavenger, E. septemlineata would have no impact on the populations of species used as food, but could possibly exclude native scavengers by competition. On the other hand, its consumption by native land planarians may control its spread and thus reduce its impact on the ecosystem.
creator: Piter K. Boll
creator: Ilana Rossi
creator: Silvana V. Amaral
creator: Ana Leal-Zanchet
uri: https://doi.org/10.7717/peerj.1307
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Boll et al.

title: Intraspecific variation of phragmocone chamber volumes throughout ontogeny in the modern nautilid Nautilus and the Jurassic ammonite Normannites
link: https://peerj.com/articles/1306
last-modified: 2015-10-06
description: Nautilus remains of great interest to palaeontologists after a long history of actualistic comparisons and speculations on aspects of the palaeoecology of fossil cephalopods, which are otherwise impossible to assess. Although a large amount of work has been dedicated to Nautilus ecology, conch geometry and volumes of shell parts and chambers have been studied less frequently. In addition, although the focus on volumetric analyses for ammonites has been increasing recently with the development of computed tomographic technology, the intraspecific variation of volumetric parameters has never been examined. To investigate the intraspecific variation of the phragmocone chamber volumes throughout ontogeny, 30 specimens of Recent Nautilus pompilius and two Middle Jurassic ammonites (Normannites mitis) were reconstructed using computed tomography and grinding tomography, respectively. Both of the ontogenetic growth trajectories from the two Normannites demonstrate logistic increase. However, a considerable difference in Normannites has been observed between their entire phragmocone volumes (cumulative chamber volumes), in spite of their similar morphology and size. Ontogenetic growth trajectories from Nautilus also show a high variation. Sexual dimorphism appears to contribute significantly to this variation. Finally, covariation between chamber widths and volumes was examined. The results illustrate the strategic difference in chamber construction between Nautilus and Normannites. The former genus persists to construct a certain conch shape, whereas the conch of the latter genus can change its shape flexibly under some constraints.
creator: Amane Tajika
creator: Naoki Morimoto
creator: Ryoji Wani
creator: Carole Naglik
creator: Christian Klug
uri: https://doi.org/10.7717/peerj.1306
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Tajika et al.

title: Effects of mediated social touch on affective experiences and trust
link: https://peerj.com/articles/1297
last-modified: 2015-10-06
description: This study investigated whether communication via mediated hand pressure during a remotely shared experience (watching an amusing video) can (1) enhance recovery from sadness, (2) enhance the affective quality of the experience, and (3) increase trust towards the communication partner. Thereto participants first watched a sad movie clip to elicit sadness, followed by a funny one to stimulate recovery from sadness. While watching the funny clip they signaled a hypothetical fellow participant every time they felt amused. In the experimental condition the participants responded by pressing a hand-held two-way mediated touch device (a Frebble), which also provided haptic feedback via simulated hand squeezes. In the control condition they responded by pressing a button and they received abstract visual feedback. Objective (heart rate, galvanic skin conductance, number and duration of joystick or Frebble presses) and subjective (questionnaires) data were collected to assess the emotional reactions of the participants. The subjective measurements confirmed that the sad movie successfully induced sadness while the funny movie indeed evoked more positive feelings. Although their ranking agreed with the subjective measurements, the physiological measurements confirmed this conclusion only for the funny movie. The results show that recovery from movie induced sadness, the affective experience of the amusing movie, and trust towards the communication partner did not differ between both experimental conditions. Hence, feedback via mediated hand touching did not enhance either of these factors compared to visual feedback. Further analysis of the data showed that participants scoring low on Extraversion (i.e., persons that are more introvert) or low on Touch Receptivity (i.e., persons who do not like to be touched by others) felt better understood by their communication partner when receiving mediated touch feedback instead of visual feedback, while the opposite was found for participants scoring high on these factors. The implications of these results for further research are discussed, and some suggestions for follow-up experiments are presented.
creator: Stefanie M. Erk
creator: Alexander Toet
creator: Jan B.F. Van Erp
uri: https://doi.org/10.7717/peerj.1297
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Erk et al.

title: Pore size is a critical parameter for obtaining sustained protein release from electrochemically synthesized mesoporous silicon microparticles
link: https://peerj.com/articles/1277
last-modified: 2015-10-06
description: Mesoporous silicon has become a material of high interest for drug delivery due to its outstanding internal surface area and inherent biodegradability. We have previously reported the preparation of mesoporous silicon microparticles (MS-MPs) synthesized by an advantageous electrochemical method, and showed that due to their inner structure they can adsorb proteins in amounts exceeding the mass of the carrier itself. Protein release from these MS-MPs showed low burst effect and fast delivery kinetics with complete release in a few hours. In this work, we explored if tailoring the size of the inner pores of the particles would retard the protein release process. To address this hypothesis, three new MS-MPs prototypes were prepared by electrochemical synthesis, and the resulting carriers were characterized for morphology, particle size, and pore structure. All MS-MP prototypes had 90 µm mean particle size, but depending on the current density applied for synthesis, pore size changed between 5 and 13 nm. The model protein α-chymotrypsinogen was loaded into MS-MPs by adsorption and solvent evaporation. In the subsequent release experiments, no burst release of the protein was detected for any prototype. However, prototypes with larger pores (>10 nm) reached 100% release in 24–48 h, whereas prototypes with small mesopores (<6 nm) still retained most of their cargo after 96 h. MS-MPs with ∼6 nm pores were loaded with the osteogenic factor BMP7, and sustained release of this protein for up to two weeks was achieved. In conclusion, our results confirm that tailoring pore size can modify protein release from MS-MPs, and that prototypes with potential therapeutic utility for regional delivery of osteogenic factors can be prepared by convenient techniques.
creator: Ester L. Pastor
creator: Elaine Reguera-Nuñez
creator: Eugenia Matveeva
creator: Marcos Garcia-Fuentes
uri: https://doi.org/10.7717/peerj.1277
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Pastor et al.

title: Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus)
link: https://peerj.com/articles/1253
last-modified: 2015-10-06
description: The white-spotted sandbass (Paralabrax albomaculatus) is a commercially important species in the Galapagos Marine Reserve, but is classified as endangered in the IUCN Red List. For this study, 10 microsatellite loci were isolated and characterized using Illumina paired-end sequencing. These loci can be used for genetic studies of population structure and connectivity to aid in the management of the white-spotted sandbass and other closely-related species. The 10 characterized loci were polymorphic, with 11–49 alleles per locus, and observed heterozygosity ranged from 0.575 to 0.964. This set of markers is the first to be developed for this species.
creator: Alicia C. Bertolotti
creator: Sarah M. Griffiths
creator: Nathan K. Truelove
creator: Stephen J. Box
creator: Richard F. Preziosi
creator: Pelayo Salinas de Leon
uri: https://doi.org/10.7717/peerj.1253
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bertolotti et al.

title: Spider crabs of the Western Atlantic with special reference to fossil and some modern Mithracidae
link: https://peerj.com/articles/1301
last-modified: 2015-10-01
description: Spider crabs (Majoidea) are well-known from modern oceans and are also common in the western part of the Atlantic Ocean. When spider crabs appeared in the Western Atlantic in deep time, and when they became diverse, hinges on their fossil record. By reviewing their fossil record, we show that (1) spider crabs first appeared in the Western Atlantic in the Late Cretaceous, (2) they became common since the Miocene, and (3) most species and genera are found in the Caribbean region from the Miocene onwards. Furthermore, taxonomic work on some modern and fossil Mithracidae, a family that might have originated in the Western Atlantic, was conducted. Specifically, Maguimithrax gen. nov. is erected to accommodate the extant species Damithrax spinosissimus, while Damithrax cf. pleuracanthus is recognized for the first time from the fossil record (late Pliocene–early Pleistocene, Florida, USA). Furthermore, two new species are described from the lower Miocene coral-associated limestones of Jamaica (Mithrax arawakum sp. nov. and Nemausa windsorae sp. nov.). Spurred by a recent revision of the subfamily, two known species from the same deposits are refigured and transferred to new genera: Mithrax donovani to Nemausa, and Mithrax unguis to Damithrax. The diverse assemblage of decapods from these coral-associated limestones underlines the importance of reefs for the abundance and diversity of decapods in deep time. Finally, we quantitatively show that these crabs possess allometric growth in that length/width ratios drop as specimens grow, a factor that is not always taken into account while describing and comparing among taxa.
creator: Adiël A. Klompmaker
creator: Roger W. Portell
creator: Aaron T. Klier
creator: Vanessa Prueter
creator: Alyssa L. Tucker
uri: https://doi.org/10.7717/peerj.1301
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Klompmaker et al.

title: Home range and use of diurnal shelters by the Etendeka round-eared sengi, a newly discovered Namibian endemic desert mammal
link: https://peerj.com/articles/1302
last-modified: 2015-10-01
description: To understand habitat use by the newly described Etendeka round-eared sengi (Macroscelides micus) in northwestern Namibia, we radio-tracked five individuals for nearly a month. Home ranges (100% convex polygons) in the rocky desert habitat were remarkably large (mean 14.9 ha) when compared to sengi species in more mesic habitats (<1.5 ha). The activity pattern of M. micus was strictly nocturnal, which contrasts to the normal diurnal or crepuscular activity of other sengis. The day shelters of M. micus were under single rocks and they likely were occupied by single sengis. One tagged sengi used 22 different day shelters during the study. On average, only 7% of the day shelters were used more than once by the five tagged sengis. The shelters were also unusual for a small mammal in that they were unmodified in terms of excavation or nesting material. Shelter entrances were significantly oriented to face south by south west (average 193°), away from the angle of the prevailing midday sun. This suggests that solar radiation is probably an important aspect of M. micus thermal ecology, similar to other sengis. Compared to published data on other sengis, M. micus generally conforms to the unique sengi adaptive syndrome, but with modifications related to its hyper-arid habitat.
creator: Galen B. Rathbun
creator: John P. Dumbacher
uri: https://doi.org/10.7717/peerj.1302
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Rathbun and Dumbacher

title: Unraveling mysteries of personal performance style; biomechanics of left-hand position changes (shifting) in violin performance
link: https://peerj.com/articles/1299
last-modified: 2015-10-01
description: Instrumental music performance ranks among the most complex of learned human behaviors, requiring development of highly nuanced powers of sensory and neural discrimination, intricate motor skills, and adaptive abilities in a temporal activity. Teaching, learning and performing on the violin generally occur within musico-cultural parameters most often transmitted through aural traditions that include both verbal instruction and performance modeling. In most parts of the world, violin is taught in a manner virtually indistinguishable from that used 200 years ago. The current study uses methods from movement science to examine the “how” and “what” of left-hand position changes (shifting), a movement skill essential during violin performance. In doing so, it begins a discussion of artistic individualization in terms of anthropometry, the performer-instrument interface, and the strategic use of motor behaviors. Results based on 540 shifting samples, a case series of 6 professional-level violinists, showed that some elements of the skill were individualized in surprising ways while others were explainable by anthropometry, ergonomics and entrainment. Remarkably, results demonstrated each violinist to have developed an individualized pacing for shifts, a feature that should influence timing effects and prove foundational to aesthetic outcomes during performance. Such results underpin the potential for scientific methodologies to unravel mysteries of performance that are associated with a performer’s personal artistic style.
creator: Peter Visentin
creator: Shiming Li
creator: Guillaume Tardif
creator: Gongbing Shan
uri: https://doi.org/10.7717/peerj.1299
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Visentin et al.

title: Identification of limiting climatic and geographical variables for the distribution of the tortoise Chelonoidis chilensis (Testudinidae): a baseline for conservation actions
link: https://peerj.com/articles/1298
last-modified: 2015-10-01
description: Background. Just as for most other tortoise species, the once common Chaco tortoise, Chelonoidis chilensis (Testudinidae), is under constant threat across it distribution in Argentina, Bolivia and Paraguay. Despite initial qualitative description of the species distribution and further individual reports of new locations for the species, there is no description of the species distribution in probabilistic terms. With this work we aim to produce an updated predictive distribution map for C. chilensis to serve as a baseline management tool for directed strategic conservation planning.Methods. We fitted a spatially expanded logistic regression model within the Bayesian framework that accounts for uncertainty on presence-only and generated pseudo-absence data into the parameter estimates. We contrast the results with reported data for the national networks of protected areas to assess the inclusion of the species in area-based conservation strategies.Results. We obtained maps with predictions of the occurrence of the species and reported the model’s uncertainty spatially. The model suggests that potential suitable habitats for the species are continuous across Argentina, West Paraguay and South Bolivia, considering the variables, the scale and the resolution used. The main limiting variables were temperature-related variables, and precipitation in the reproductive period.Discussion. Given the alarming low density and coverage of protected areas over the distribution area of C. chilensis, the map produced provides a baseline to identify areas where directed strategic conservation management actions would be more efficient for this and other associated species.
creator: Alejandro Ruete
creator: Gerardo C. Leynaud
uri: https://doi.org/10.7717/peerj.1298
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ruete and Leynaud

title: Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair
link: https://peerj.com/articles/1296
last-modified: 2015-10-01
description: The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.
creator: Yuchen Zhang
creator: Richard J. Alsop
creator: Asfia Soomro
creator: Fei-Chi Yang
creator: Maikel C. Rheinstädter
uri: https://doi.org/10.7717/peerj.1296
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhang et al.

title: Dispersal and metapopulation stability
link: https://peerj.com/articles/1295
last-modified: 2015-10-01
description: Metapopulation dynamics are jointly regulated by local and spatial factors. These factors may affect the dynamics of local populations and of the entire metapopulation differently. Previous studies have shown that dispersal can stabilize local populations; however, as dispersal also tends to increase spatial synchrony, its net effect on metapopulation stability has been controversial. Here we present a simple metapopulation model to study how dispersal, in interaction with other spatial and local processes, affects the temporal variability of metapopulations in a stochastic environment. Our results show that in homogeneous metapopulations, the local stabilizing and spatial synchronizing effects of dispersal cancel each other out, such that dispersal has no effect on metapopulation variability. This result is robust to moderate heterogeneities in local and spatial parameters. When local and spatial dynamics exhibit high heterogeneities, however, dispersal can either stabilize or destabilize metapopulation dynamics through various mechanisms. Our findings have important theoretical and practical implications. We show that dispersal functions as a form of spatial intraspecific mutualism in metapopulation dynamics and that its effect on metapopulation stability is opposite to that of interspecific competition on local community stability. Our results also suggest that conservation corridors should be designed with appreciation of spatial heterogeneities in population dynamics in order to maximize metapopulation stability.
creator: Shaopeng Wang
creator: Bart Haegeman
creator: Michel Loreau
uri: https://doi.org/10.7717/peerj.1295
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wang et al.

title: Investigation into the effects of antioxidant-rich extract of Tamarindus indica leaf on antioxidant enzyme activities, oxidative stress and gene expression profiles in HepG2 cells
link: https://peerj.com/articles/1292
last-modified: 2015-10-01
description: The leaf extract of Tamarindus indica L. (T. indica) had been reported to possess high phenolic content and showed high antioxidant activities. In this study, the effects of the antioxidant-rich leaf extract of the T. indica on lipid peroxidation, antioxidant enzyme activities, H2O2-induced ROS production and gene expression patterns were investigated in liver HepG2 cells. Lipid peroxidation and ROS production were inhibited and the activity of antioxidant enzymes superoxide dismutase, catalase and glutathione peroxidase was enhanced when the cells were treated with the antioxidant-rich leaf extract. cDNA microarray analysis revealed that 207 genes were significantly regulated by at least 1.5-fold (p < 0.05) in cells treated with the antioxidant-rich leaf extract. The expression of KNG1, SERPINC1, SERPIND1, SERPINE1, FGG, FGA, MVK, DHCR24, CYP24A1, ALDH6A1, EPHX1 and LEAP2 were amongst the highly regulated. When the significantly regulated genes were analyzed using Ingenuity Pathway Analysis software, “Lipid Metabolism, Small Molecule Biochemistry, Hematological Disease” was the top biological network affected by the leaf extract, with a score of 36. The top predicted canonical pathway affected by the leaf extract was the coagulation system (P < 2.80 × 10−6) followed by the superpathway of cholesterol biosynthesis (P < 2.17 × 10−4), intrinsic prothrombin pathway (P < 2.92 × 10−4), Immune Protection/Antimicrobial Response (P < 2.28 × 10−3) and xenobiotic metabolism signaling (P < 2.41 × 10−3). The antioxidant-rich leaf extract of T. indica also altered the expression of proteins that are involved in the Coagulation System and the Intrinsic Prothrombin Activation Pathway (KNG1, SERPINE1, FGG), Superpathway of Cholesterol Biosynthesis (MVK), Immune protection/antimicrobial response (IFNGR1, LEAP2, ANXA3 and MX1) and Xenobiotic Metabolism Signaling (ALDH6A1, ADH6). In conclusion, the antioxidant-rich leaf extract of T. indica inhibited lipid peroxidation and ROS production, enhanced antioxidant enzyme activities and significantly regulated the expression of genes and proteins involved with consequential impact on the coagulation system, cholesterol biosynthesis, xenobiotic metabolism signaling and antimicrobial response.
creator: Nurhanani Razali
creator: Azlina Abdul Aziz
creator: Chor Yin Lim
creator: Sarni Mat Junit
uri: https://doi.org/10.7717/peerj.1292
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Razali et al.

title: Association among smoking, depression, and anxiety: findings from a representative sample of Korean adolescents
link: https://peerj.com/articles/1288
last-modified: 2015-10-01
description: This study investigated the relationship between smoking and depression and anxiety using data from a nationwide survey representing Korean adolescents. Subjects were 6,489 adolescents in middle and high school (age 13–18) who had participated in the 2011 Korean Study of Promotion Policies on Children and Adolescents—Mental Health (KSPCAM). Daily smoking number of times for current smokers was classified as 1–2 times, 2–4 times and over 5 times. The odds ratio for the statistical test was presented using hierarchical logistic regression. When adjusted for covariates (gender, age, household economy, type of residing city, type of school, school record, satisfaction with school life, subjective health status, satisfaction with relationship with parents, and drinking experience), smokers more significantly likely to have depression (OR = 1.27, 95% CI [1.02–1.57]), and anxiety (OR = 1.49, 95% CI [1.14–1.96]) than non-smokers (p < 0.05). In addition, adolescents who smoke more than 5 cigarettes a day were 1.5 times more likely to have depression (OR = 1.48, 95% CI [1.13–1.92]) and anxiety (OR = 1.49, 95% CI [1.07–2.08]) than those who do not smoke. Smoking in adolescence was found to be significantly related with depression and anxiety. To promote the mental health of adolescents, effective smoking cessation programs are required.
creator: Haewon Byeon
uri: https://doi.org/10.7717/peerj.1288
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Byeon

title: Nodes with high centrality in protein interaction networks are responsible for driving signaling pathways in diabetic nephropathy
link: https://peerj.com/articles/1284
last-modified: 2015-10-01
description: In spite of huge efforts, chronic diseases remain an unresolved problem in medicine. Systems biology could assist to develop more efficient therapies through providing quantitative holistic sights to these complex disorders. In this study, we have re-analyzed a microarray dataset to identify critical signaling pathways related to diabetic nephropathy. GSE1009 dataset was downloaded from Gene Expression Omnibus database and the gene expression profile of glomeruli from diabetic nephropathy patients and those from healthy individuals were compared. The protein-protein interaction network for differentially expressed genes was constructed and enriched. In addition, topology of the network was analyzed to identify the genes with high centrality parameters and then pathway enrichment analysis was performed. We found 49 genes to be variably expressed between the two groups. The network of these genes had few interactions so it was enriched and a network with 137 nodes was constructed. Based on different parameters, 34 nodes were considered to have high centrality in this network. Pathway enrichment analysis with these central genes identified 62 inter-connected signaling pathways related to diabetic nephropathy. Interestingly, the central nodes were more informative for pathway enrichment analysis compared to all network nodes and also 49 differentially expressed genes. In conclusion, we here show that central nodes in protein interaction networks tend to be present in pathways that co-occur in a biological state. Also, this study suggests a computational method for inferring underlying mechanisms of complex disorders from raw high-throughput data.
creator: Maryam Abedi
creator: Yousof Gheisari
uri: https://doi.org/10.7717/peerj.1284
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Abedi and Gheisari

title: Risk factors and prognosis of hypoalbuminemia in surgical septic patients
link: https://peerj.com/articles/1267
last-modified: 2015-10-01
description: The aim of this study was to investigate the risk factors of hypoalbuminemia and effects of different albumin levels on the prognosis of surgical septic patients. We preformed a retrospective clinical study including 135 adult patients from September 2011 to June 2014. The albumin levels and severity markers were recorded during the first 48 h after enrollment, and logistic regression analyses were used to determine the risk factors. The outcomes of patients with different albumin levels were also compared. The acute physiology and chronic health evaluation II (APACHE II) score (OR 1.786, 95% CI [1.379–2.314], P < 0.001), C-reactive protein (CRP) (OR 1.016, 95% CI [1.005–1.027], P = 0.005), and blood lactate (OR 1.764, 95% CI [1.141–2.726], P = 0.011) were established as the independent risk factors of hypoalbuminemia in patients with surgical sepsis. The severity markers and outcomes of patients with albumin levels ≤20 g/L were significantly worse than that of 21–25 g/L and ≥26 g/L, whereas the latter two groups had similar prognosis. Every 1 g/L decrease of albumin level below the optimal cut-off (23 g/L) was associated with a 19.4% increase in hospital mortality and a 28.7% increase in the incidence of multiple organ dysfunction syndrome. In conclusion, APACHE II score (≥14.5), CRP (≥34.25 mg/L), and blood lactate (≥.35 mmol/L) were established as the independent risk factors of hypoalbuminemia in the early stage of surgical sepsis. Patients with baseline albumin level ≤20 g/L had worse prognosis than that of albumin level ≥21 g/L. Albumin levels were negatively correlated the prognosis of surgical sepsis when below about 23 g/L.
creator: Jia-Kui Sun
creator: Fang Sun
creator: Xiang Wang
creator: Shou-Tao Yuan
creator: Shu-Yun Zheng
creator: Xin-Wei Mu
uri: https://doi.org/10.7717/peerj.1267
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sun et al.

title: Measuring the well-being of health care professionals in the Punjab: a psychometric evaluation of the Warwick–Edinburgh Mental Well-being Scale in a Pakistani population
link: https://peerj.com/articles/1264
last-modified: 2015-10-01
description: Background. There is growing awareness of the public health importance of mental well-being both in the general population and in specific groups. The well-being of health professionals is likely to influence the quality of the care they deliver. This study was carried out to examine the well-being of Pakistani healthcare professionals, and to evaluate the psychometric performance of the Warwick–Edinburgh Mental Well-being Scale (WEMWBS) in this population.Methods. A cross-sectional survey was carried out from June, 2013 to December, 2014 among 1,271 Pakistani health care providers (HCPs) working in seven different cities in Punjab province, Pakistan, to examine the acceptability, internal consistency, test-retest reliability and content and construct validity of the English version of the WEMWBS in a Pakistani population sample. All data were analyzed in SPSS v. 21.Results. Our analysis demonstrated unidimensional construct validity, high internal consistency (0.89) and test-retest reliability, good validity and easy readability of WEMWBS in our sample of Pakistani HCPs. The mean WEMWBS score was 48.1 (SD 9.4), which is lower than in the general population in other countries. Male HCPs scored significantly higher on the WEMWBS than their female counterparts (P < 0.05), and older respondents had higher scores.Conclusion. The WEMWBS appears acceptable for use in Pakistani HCPs, and findings from this study verify its validity and internal consistency for this population sample. Our respondents had lower well-being scores than those reported in general population surveys in the UK.
creator: Ahmed Waqas
creator: Waqas Ahmad
creator: Mark Haddad
creator: Frances M. Taggart
creator: Zerwah Muhammad
creator: Muhammad Hamza Bukhari
creator: Shahzad Ahmed Sami
creator: Sayyeda Mehak Batool
creator: Fiza Najeeb
creator: Ayesha Hanif
creator: Zehra Ali Rizvi
creator: Sumbul Ejaz
uri: https://doi.org/10.7717/peerj.1264
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Waqas et al.

title: The prevalence and anatomical characteristics of the accessory head of the flexor pollicis longus muscle: a meta-analysis
link: https://peerj.com/articles/1255
last-modified: 2015-10-01
description: Background and Objectives. The accessory head of the flexor pollicis longus muscle (AHFPL), also known as the Gantzer’s muscle, was first described in 1813. The prevalence rates of an AHFPL significantly vary between studies, and no consensus has been reached on the numerous variations reported in its origin, innervation, and relationships to the Anterior Interosseous Nerve (AIN) and the Median Nerve (MN). The aim of our study was to determine the true prevalence of AHFPL and to study its associated anatomical characteristics.Methods. A search of the major electronic databases PubMed, EMBASE, Scopus, ScienceDirect, and Web of Science was performed to identify all articles reporting data on the prevalence of AHPFL in the population. No date or language restriction was set. Additionally, an extensive search of the references of all relevant articles was performed. Data on the prevalence of the AHFPL in upper limbs and its anatomical characteristics and relationships including origin, insertion, innervation, and position was extracted and pooled into a meta-analysis using MetaXL version 2.0.Results. A total of 24 cadaveric studies (n = 2,358 upper limb) were included in the meta-analysis. The pooled prevalence of an AHFPL was 44.2% (95% CI [0.347–0.540]). An AHFPL was found more commonly in men than in women (41.1% vs. 24.1%), and was slightly more prevalent on the right side than on the left side (52.8% vs. 45.2%). The most common origin of the AHFPL was from the medial epicondyle of the humerus with a pooled prevalence of 43.6% (95% CI [0.166–0.521]). In most cases, the AHFPL inserted into the flexor pollicis longus muscle (94.6%, 95% CI [0.731–1.0]) and was innervated by the AIN (97.3%, 95% CI [0.924–0.993]).Conclusion. The AHFPL should be considered as more a part of normal anatomy than an anatomical variant. The variability in its anatomical characteristics, and its potential to cause compression of the AIN and MN, must be taken into account by physicians to avoid iatrogenic injury during decompression procedures and to aid in the diagnosis and treatment of Anterior Interosseous Nerve Syndrome.
creator: Joyeeta Roy
creator: Brandon M. Henry
creator: Przemysław A. Pękala
creator: Jens Vikse
creator: Piravin Kumar Ramakrishnan
creator: Jerzy A. Walocha
creator: Krzysztof A. Tomaszewski
uri: https://doi.org/10.7717/peerj.1255
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Roy et al.