title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-08 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI link: https://peerj.com/articles/1225 last-modified: 2015-08-27 description: In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea. creator: Yan-Lue Lim creator: Robson Ee creator: Kah-Yan How creator: Siew-Kim Lee creator: Delicia Yong creator: Kok Keng Tee creator: Wai-Fong Yin creator: Kok-Gan Chan uri: https://doi.org/10.7717/peerj.1225 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lim et al. title: A global phylogeny of Pelomedusoides turtles with new material of Neochelys franzeni Schleich, 1993 (Testudines, Podocnemididae) from the middle Eocene, Messel Pit, of Germany link: https://peerj.com/articles/1221 last-modified: 2015-08-27 description: Background. Neochelys franzeni Schleich, 1993 is the only pleurodire or side-necked turtle from the middle Eocene, Messel Pit (the first UNESCO, World Natural Heritage Site in Germany, since 1995). The original description of the species is based on two specimens SMF ME 1091 (Holotype) and 715 (Paratype) housed at the Senckenberg Museum Frankfurt. The excellent preservation of complete and articulated skeletons of this species makes it a key taxon for understanding the evolution and phylogeny of the European Neochelys genus and its relationships with South American and African-Madagascar podocnemidids.Results. Five new specimens of Neochelys franzeni from Messel Pit are described here, together with the redescription of SMF ME 1091 and 715. Specimens correspond to individuals of different ontogenetic stages showing conservative morphology from hatching to adults. A revised diagnosis for the species is presented here, together with its inclusion in a global phylogenetic analysis of Pelomedusoides that shows that this species and the whole Neochelys spp. is sister to the Erymnochelys madagascariensis-Peltocephalus dumerilianus clade within Podocnemididae. creator: Edwin Cadena uri: https://doi.org/10.7717/peerj.1221 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Cadena title: Can 13C stable isotope analysis uncover essential amino acid provisioning by termite-associated gut microbes? link: https://peerj.com/articles/1218 last-modified: 2015-08-27 description: Gut-associated microbes of insects are postulated to provide a variety of nutritional functions including provisioning essential amino acids (EAAs). Demonstrations of EAA provisioning in insect-gut microbial systems, nonetheless, are scant. In this study, we investigated whether the eastern subterranean termite Reticulitermes flavipes sourced EAAs from its gut-associated microbiota. δ13CEAA data from termite carcass, termite gut filtrate and dietary (wood) samples were determined following 13C stable isotope analysis. Termite carcass samples (−27.0 ± 0.4‰, mean ± s.e.) were significantly different from termite gut filtrate samples (−27.53 ± 0.5‰), but not the wood diet (−26.0 ± 0.5‰) (F(2,64) = 6, P < 0.0052). δ13CEAA-offsets between termite samples and diet suggested possible non-dietary EAA input. Predictive modeling identified gut-associated bacteria and fungi, respectively as potential major and minor sources of EAAs in both termite carcass and gut filtrate samples, based on δ13CEAA data of four and three EAAs from representative bacteria, fungi and plant data. The wood diet, however, was classified as fungal rather than plant in origin by the model. This is attributed to fungal infestation of the wood diet in the termite colony. This lowers the confidence with which gut microbes (bacteria and fungi) can be attributed with being the source of EAA input to the termite host. Despite this limitation, this study provides tentative data in support of hypothesized EAA provisioning by gut microbes, and also a baseline/framework upon which further work can be carried out to definitively verify this function. creator: Paul A. Ayayee creator: Susan C. Jones creator: Zakee L. Sabree uri: https://doi.org/10.7717/peerj.1218 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ayayee et al. title: Watch-wearing as a marker of conscientiousness link: https://peerj.com/articles/1210 last-modified: 2015-08-27 description: Several aspects of an individual’s appearance have been shown to predict personality and related behaviour. While some of these cues are grounded in biology (e.g., the human face), other aspects of a person’s appearance can be actively controlled (e.g., clothing). In this paper, we consider a common fashion accessory, the wristwatch. In an exploratory sample (N > 100) and a confirmatory sample (N > 600), we compared big-five personality traits between individuals who do or do not regularly wear a standard wristwatch. Significantly higher levels of conscientiousness were observed in participants who wore a watch. In a third study (N = 85), watch wearers arrived significantly earlier to appointments in comparison to controls. These results are discussed in relation to enclothed cognition and the rise of wearable technology including smartwatches. creator: David A. Ellis creator: Rob Jenkins uri: https://doi.org/10.7717/peerj.1210 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ellis and Jenkins title: Association between serum interleukin-6 concentrations and chronic obstructive pulmonary disease: a systematic review and meta-analysis link: https://peerj.com/articles/1199 last-modified: 2015-08-27 description: Background. Interleukin-6 (IL-6) is an important pro-inflammatory cytokine and has been implicated to play a role in the systemic inflammation of patients with chronic obstructive pulmonary disease (COPD). We conducted this meta-analysis to assess the association between serum IL-6 concentrations and COPD.Methods. PubMed and Embase were searched for eligible studies. Data were extracted by two investigators (Wei J, Xiong XF) independently and analyzed using Review Manager 5.3 and STATA 12.0 software. Standard mean differences (SMDs) and 95% confidence intervals (CI) were calculated.Results. Thirty-three studies were included in this meta-analysis. The serum IL-6 concentrations were higher in patients with stable COPD than healthy controls (SMD = 0.65, 95% CI [0.51–0.79]). COPD patients without major comorbidities also showed higher IL-6 levels than healthy controls (SMD = 0.74, 95% CI [0.56–0.91]). COPD patients with an forced expiratory volume in one second (FEV1) of either <50% predicted or >50% predicted had increased IL-6 concentrations compared to healthy controls (SMD = 0.77, 95% CI [0.48–1.05], SMD = 1.01, 95% CI [0.43–1.59], respectively). The serum IL-6 concentrations between mild-moderate and severe-very severe COPD patient groups were not found to be significant (SMD = −0.1, 95% CI [−0.65–0.44]).Conclusions. This meta-analysis indicated that patients with stable COPD had higher serum IL-6 concentrations than healthy controls. No evidence showing positive or negative association between IL-6 concentrations and the severity of pulmonary function impairment was found. The correlation between IL-6 levels and pulmonary function was weak in different severities of stable COPD patients. creator: Jia Wei creator: Xiao-feng Xiong creator: Yi-hua Lin creator: Bi-xia Zheng creator: De-yun Cheng uri: https://doi.org/10.7717/peerj.1199 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wei et al. title: Orthostatic stability with intravenous levodopa link: https://peerj.com/articles/1198 last-modified: 2015-08-27 description: Intravenous levodopa has been used in a multitude of research studies due to its more predictable pharmacokinetics compared to the oral form, which is used frequently as a treatment for Parkinson’s disease (PD). Levodopa is the precursor for dopamine, and intravenous dopamine would strongly affect vascular tone, but peripheral decarboxylase inhibitors are intended to block such effects. Pulse and blood pressure, with orthostatic changes, were recorded before and after intravenous levodopa or placebo—after oral carbidopa—in 13 adults with a chronic tic disorder and 16 tic-free adult control subjects. Levodopa caused no statistically or clinically significant changes in blood pressure or pulse. These data add to previous data that support the safety of i.v. levodopa when given with adequate peripheral inhibition of DOPA decarboxylase. creator: Shan H. Siddiqi creator: Mary L. Creech creator: Kevin J. Black uri: https://doi.org/10.7717/peerj.1198 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Siddiqi et al. title: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities link: https://peerj.com/articles/1165 last-modified: 2015-08-27 description: Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. It automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat. creator: Dongwan D. Kang creator: Jeff Froula creator: Rob Egan creator: Zhong Wang uri: https://doi.org/10.7717/peerj.1165 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kang et al. title: The atherosclerosis of the sinus node artery is associated with an increased history of supra-ventricular arrhythmias: a retrospective study on 541 standard coronary angiograms link: https://peerj.com/articles/1156 last-modified: 2015-08-27 description: Background. The ischemic damage of the sinus node (SN) is a well known cause of cardiac arrhythmias and can be a consequence of any flow abnormality in the sinus node artery (SNA). Accordingly we aimed this retrospective study to: (1) evaluate the suitability of the standard coronary angiography to study the SNA and (2) determine if the percentage of subjects with a positive retrospective history of supra-ventricular arrhythmias (SVA) differs in patients with normal and diseased SNA ascertained at the time of coronary angiography.Methods and Results. Out of the 541 coronary angiograms reviewed the SNA was visible for its entire course in 486 cases (89.8%). It was found to arise from the right side of the coronary circulation in 266 cases (54.7%) slightly more often than from the left, 219 cases (45.1%). One patient had 2 distinct SNA arising from either side of the coronary circulation. For the second objective, we studied the 333 patients with: (a) coronary artery disease (CAD), (b) properly evaluable SNA and (c) complete clinical history available. In 51 (15.3%) a SNA disease was found, 41.2% of them had a positive SVA history, mainly atrial fibrillation (AF), whereas only 7.4% of patients with a positive history of SVA could be found in the non-SNA diseased. This difference was statistically significant (P < 0.001).Conclusions. (1) The evaluation of the SNA is feasible in clinical practice during a standard coronary angiography; (2) this may be relevant since angiographically detectable SNA disease was significantly associated with a positive history of SVA. creator: Michele M. Ciulla creator: Matteo Astuti creator: Stefano Carugo uri: https://doi.org/10.7717/peerj.1156 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ciulla et al. title: Interactions between Drosophila and its natural yeast symbionts—Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship? link: https://peerj.com/articles/1116 last-modified: 2015-08-25 description: Yeasts play an important role in the biology of the fruit fly, Drosophila melanogaster. In addition to being a valuable source of nutrition, yeasts affect D. melanogaster behavior and interact with the host immune system. Most experiments investigating the role of yeasts in D. melanogaster biology use the baker’s yeast, Saccharomyces cerevisiae. However, S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species. Moreover, the strain of S. cerevisiae used most often in D. melanogaster experiments is a commercially and industrially important strain that, to the best of our knowledge, was not isolated from flies. Since disrupting natural host–microbe interactions can have profound effects on host biology, the results from D. melanogaster–S. cerevisiae laboratory experiments may not be fully representative of host–microbe interactions in nature. In this study, we explore the D. melanogaster-yeast relationship using five different strains of yeast that were isolated from wild Drosophila populations. Ingested live yeasts have variable persistence in the D. melanogaster gastrointestinal tract. For example, Hanseniaspora occidentalis persists relative to S. cerevisiae, while Brettanomyces naardenensis is removed. Despite these differences in persistence relative to S. cerevisiae, we find that all yeasts decrease in total abundance over time. Reactive oxygen species (ROS) are an important component of the D. melanogaster anti-microbial response and can inhibit S. cerevisiae growth in the intestine. To determine if sensitivity to ROS explains the differences in yeast persistence, we measured yeast growth in the presence and absence of hydrogen peroxide. We find that B. naardenesis is completely inhibited by hydrogen peroxide, while H. occidentalis is not, which is consistent with yeast sensitivity to ROS affecting persistence within the D. melanogaster gastrointestinal tract. We also compared the feeding preference of D. melanogaster when given the choice between a naturally associated yeast and S. cerevisiae. We do not find a correlation between preferred yeasts and those that persist in the intestine. Notably, in no instances is S. cerevisiae preferred over the naturally associated strains. Overall, our results show that D. melanogaster-yeast interactions are more complex than might be revealed in experiments that use only S. cerevisiae. We propose that future research utilize other yeasts, and especially those that are naturally associated with Drosophila, to more fully understand the role of yeasts in Drosophila biology. Since the genetic basis of host–microbe interactions is shared across taxa and since many of these genes are initially discovered in D. melanogaster, a more realistic fly-yeast model system will benefit our understanding of host–microbe interactions throughout the animal kingdom. creator: Don Hoang creator: Artyom Kopp creator: James Angus Chandler uri: https://doi.org/10.7717/peerj.1116 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hoang et al. title: Strong geographical variation in wing aspect ratio of a damselfly, Calopteryx maculata (Odonata: Zygoptera) link: https://peerj.com/articles/1219 last-modified: 2015-08-25 description: Geographical patterns in body size have been described across a wide range of species, leading to the development of a series of fundamental biological rules. However, shape variables are less well-described despite having substantial consequences for organism performance. Wing aspect ratio (AR) has been proposed as a key shape parameter that determines function in flying animals, with high AR corresponding to longer, thinner wings that promote high manoeuvrability, low speed flight, and low AR corresponding to shorter, broader wings that promote high efficiency long distance flight. From this principle it might be predicted that populations living in cooler areas would exhibit low AR wings to compensate for reduced muscle efficiency at lower temperatures. I test this hypothesis using the riverine damselfly, Calopteryx maculata, sampled from 34 sites across its range margin in North America. Nine hundred and seven male specimens were captured from across the 34 sites (mean = 26.7 ± 2.9 SE per site), dissected and measured to quantify the area and length of all four wings. Geometric morphometrics were employed to investigate geographical variation in wing shape. The majority of variation in wing shape involved changes in wing aspect ratio, confirmed independently by geometric morphometrics and wing measurements. There was a strong negative relationship between wing aspect ratio and the maximum temperature of the warmest month which varies from west-east in North America, creating a positive relationship with longitude. This pattern suggests that higher aspect ratio may be associated with areas in which greater flight efficiency is required: regions of lower temperatures during the flight season. I discuss my findings in light of research of the functional ecology of wing shape across vertebrate and invertebrate taxa. creator: Christopher Hassall uri: https://doi.org/10.7717/peerj.1219 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hassall title: Inconsistent year-to-year fluctuations limit the conclusiveness of global higher education rankings for university management link: https://peerj.com/articles/1217 last-modified: 2015-08-25 description: Backround. University rankings are getting very high international media attention, this holds particularly true for the Times Higher Education Ranking (THE) and the Shanghai Jiao Tong University’s Academic Ranking of World Universities Ranking (ARWU). We therefore aimed to investigate how reliable the rankings are, especially for universities with lower ranking positions, that often show inconclusive year-to-year fluctuations in their rank, and if these rankings are thus a suitable basis for management purposes.Methods. We used the public available data from the web pages of the THE and the ARWU ranking to analyze the dynamics of change in score and ranking position from year to year, and we investigated possible causes for inconsistent fluctuations in the rankings by the means of regression analyses.Results. Regression analyses of results from the THE and ARWU from 2010–2014 show inconsistent fluctuations in the rank and score for universities with lower rank positions (below position 50) which lead to inconsistent “up and downs” in the total results, especially in the THE and to a lesser extent also in the ARWU. In both rankings, the mean year-to-year fluctuation of universities in groups of 50 universities aggregated by descending rank increases from less than 10% in the group of the 50 highest ranked universities to up to 60% in the group of the lowest ranked universities. Furthermore, year-to-year results do not correspond in THES- and ARWU-Rankings for universities below rank 50.Discussion. We conclude that the observed fluctuations in the THE do not correspond to actual university performance and ranking results are thus of limited conclusiveness for the university management of universities below a rank of 50. While the ARWU rankings seems more robust against inconsistent fluctuations, its year to year changes in the scores are very small, so essential changes from year to year could not be expected. Furthermore, year-to-year results do not correspond in THES- and ARWU-Rankings for universities below rank 50. Neither the THES nor the ARWU offer great value as a tool for university management in their current forms for universities ranked below 50, thus we suggest that both rankings alter their ranking procedure insofar as universities below position 50 should be ranked summarized only in groups of 25 or 50. Additionally, the THE should omit the peer reputation survey, which most likely contributes heavily to the inconsistent year-to-year fluctuations in ranks, and ARWU should be published less often to increase its validity. creator: Johannes Sorz creator: Bernard Wallner creator: Horst Seidler creator: Martin Fieder uri: https://doi.org/10.7717/peerj.1217 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sorz et al. title: Transdifferentiation is a driving force of regeneration in Halisarca dujardini (Demospongiae, Porifera) link: https://peerj.com/articles/1211 last-modified: 2015-08-25 description: The ability to regenerate is widespread in the animal kingdom, but the regenerative capacities and mechanisms vary widely. To understand the evolutionary history of the diverse regeneration mechanisms, the regeneration processes must be studied in early-evolved metazoans in addition to the traditional bilaterian and cnidarian models. For this purpose, we have combined several microscopy techniques to study mechanisms of regeneration in the demosponge Halisarca dujardini. The objectives of this work are to detect the cells and morphogenetic processes involved in Halisarca regeneration. We show that in Halisarca there are three main sources of the new exopinacoderm during regeneration: choanocytes, archaeocytes and (rarely) endopinacocytes. Here we show that epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET) occur during Halisarca regeneration. EMT is the principal mechanism during the first stages of regeneration, soon after the injury. Epithelial cells from damaged and adjacent intact choanocyte chambers and aquiferous canals assume mesenchymal phenotype and migrate into the mesohyl. Together with archaeocytes, these cells form an undifferentiated cell mass beneath of wound, which we refer to as a blastema. After the blastema is formed, MET becomes the principal mechanism of regeneration. Altogether, we demonstrate that regeneration in demosponges involves a variety of processes utilized during regeneration in other animals (e.g., cell migration, dedifferentiation, blastema formation) and points to the particular importance of transdifferentiation in this process. Further studies will be needed to uncover the molecular mechanisms governing regeneration in sponges. creator: Ilya E. Borisenko creator: Maja Adamska creator: Daria B. Tokina creator: Alexander V. Ereskovsky uri: https://doi.org/10.7717/peerj.1211 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Borisenko et al. title: Frog eat frog: exploring variables influencing anurophagy link: https://peerj.com/articles/1204 last-modified: 2015-08-25 description: Background. Frogs are generalist predators of a wide range of typically small prey items. But descriptions of dietary items regularly include other anurans, such that frogs are considered to be among the most important of anuran predators. However, the only existing hypothesis for the inclusion of anurans in the diet of post-metamorphic frogs postulates that it happens more often in bigger frogs. Moreover, this hypothesis has yet to be tested.Methods. We reviewed the literature on frog diet in order to test the size hypothesis and determine whether there are other putative explanations for anurans in the diet of post-metamorphic frogs. In addition to size, we recorded the habitat, the number of other sympatric anuran species, and whether or not the population was invasive. We controlled for taxonomic bias by including the superfamily in our analysis.Results. Around one fifth of the 355 records included anurans as dietary items of populations studied, suggesting that frogs eating anurans is not unusual. Our data showed a clear taxonomic bias with ranids and pipids having a higher proportion of anuran prey than other superfamilies. Accounting for this taxonomic bias, we found that size in addition to being invasive, local anuran diversity, and habitat produced a model that best fitted our data. Large invasive frogs that live in forests with high anuran diversity are most likely to have a higher proportion of anurans in their diet.Conclusions. We confirm the validity of the size hypothesis for anurophagy, but show that there are additional significant variables. The circumstances under which frogs eat frogs are likely to be complex, but our data may help to alert conservationists to the possible dangers of invading frogs entering areas with threatened anuran species. creator: G. John Measey creator: Giovanni Vimercati creator: F. André de Villiers creator: Mohlamatsane M. Mokhatla creator: Sarah J. Davies creator: Shelley Edwards creator: Res Altwegg uri: https://doi.org/10.7717/peerj.1204 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Measey et al. title: Fear of becoming pregnant among female healthcare students in Spain link: https://peerj.com/articles/1200 last-modified: 2015-08-25 description: The inconsistent use of hormonal contraceptive methods can result, during the first year of use, in one in twelve women still having an undesired pregnancy. This may lead to women experiencing fear of becoming pregnant (FBP). We have only found one study examining the proportion of FBP among women who used hormonal contraceptives. To gather further scientific evidence we undertook an observational, cross-sectional study involving 472 women at a Spanish university in 2005–2009. The inclusion criteria were having had vaginal intercourse with a man in the previous three months and usual use for contraception of a male condom or hormonal contraceptives, or no method of contraception. The outcome was FBP. The secondary variables were contraceptive method used (oral contraceptives; condom; none), desire to increase the frequency of sexual relations, frequency of sexual intercourse with the partner, the sexual partner not always able to ejaculate, desire to increase the partner’s time before orgasm, age and being in a stable relationship. A multivariate logistic regression model was used to determine the associated factors. Of the 472 women, 171 experienced FBP (36.2%). Factors significantly associated (p < 0.05) with this FBP were method of contraception (condom and none), desire to increase the partner’s ability to delay orgasm and higher frequency of sexual intercourse with the partner. There was a high proportion of FBP, depending on the use of efficient contraceptive methods. A possible solution to this problem may reside in educational programmes. Qualitative studies would be useful to design these programmes. creator: Felipe Navarro-Cremades creator: Antonio Palazón-Bru creator: María del Ángel Arroyo-Sebastián creator: Luis Gómez-Pérez creator: Armina Sepehri creator: Salvador Martínez-Pérez creator: Dolores Marhuenda-Amorós creator: María Mercedes Rizo-Baeza creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.1200 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Navarro-Cremades et al. title: The relationship of female physical attractiveness to body fatness link: https://peerj.com/articles/1155 last-modified: 2015-08-25 description: Aspects of the female body may be attractive because they signal evolutionary fitness. Greater body fatness might reflect greater potential to survive famines, but individuals carrying larger fat stores may have poor health and lower fertility in non-famine conditions. A mathematical statistical model using epidemiological data linking fatness to fitness traits, predicted a peaked relationship between fatness and attractiveness (maximum at body mass index (BMI) = 22.8 to 24.8 depending on ethnicity and assumptions). Participants from three Caucasian populations (Austria, Lithuania and the UK), three Asian populations (China, Iran and Mauritius) and four African populations (Kenya, Morocco, Nigeria and Senegal) rated attractiveness of a series of female images varying in fatness (BMI) and waist to hip ratio (WHR). There was an inverse linear relationship between physical attractiveness and body fatness or BMI in all populations. Lower body fat was more attractive, down to at least BMI = 19. There was no peak in the relationship over the range we studied in any population. WHR was a significant independent but less important factor, which was more important (greater r2) in African populations. Predictions based on the fitness model were not supported. Raters appeared to use body fat percentage (BF%) and BMI as markers of age. The covariance of BF% and BMI with age indicates that the role of body fatness alone, as a marker of attractiveness, has been overestimated. creator: Guanlin Wang creator: Kurosh Djafarian creator: Chima A. Egedigwe creator: Asmaa El Hamdouchi creator: Robert Ojiambo creator: Harris Ramuth creator: Sandra Johanna Wallner-Liebmann creator: Sonja Lackner creator: Adama Diouf creator: Justina Sauciuvenaite creator: Catherine Hambly creator: Lobke M. Vaanholt creator: Mark D. Faries creator: John R. Speakman uri: https://doi.org/10.7717/peerj.1155 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wang et al. title: Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls link: https://peerj.com/articles/1140 last-modified: 2015-08-25 description: The role of the human microbiome in schizophrenia remains largely unexplored. The microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. This study reports findings from a shotgun metagenomic analysis of the oropharyngeal microbiome in 16 individuals with schizophrenia and 16 controls. High-level differences were evident at both the phylum and genus levels, with Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria dominating both schizophrenia patients and controls, and Ascomycota being more abundant in schizophrenia patients than controls. Controls were richer in species but less even in their distributions, i.e., dominated by fewer species, as opposed to schizophrenia patients. Lactic acid bacteria were relatively more abundant in schizophrenia, including species of Lactobacilli and Bifidobacterium, which have been shown to modulate chronic inflammation. We also found Eubacterium halii, a lactate-utilizing species. Functionally, the microbiome of schizophrenia patients was characterized by an increased number of metabolic pathways related to metabolite transport systems including siderophores, glutamate, and vitamin B12. In contrast, carbohydrate and lipid pathways and energy metabolism were abundant in controls. These findings suggest that the oropharyngeal microbiome in individuals with schizophrenia is significantly different compared to controls, and that particular microbial species and metabolic pathways differentiate both groups. Confirmation of these findings in larger and more diverse samples, e.g., gut microbiome, will contribute to elucidating potential links between schizophrenia and the human microbiota. creator: Eduardo Castro-Nallar creator: Matthew L. Bendall creator: Marcos Pérez-Losada creator: Sarven Sabuncyan creator: Emily G. Severance creator: Faith B. Dickerson creator: Jennifer R. Schroeder creator: Robert H. Yolken creator: Keith A. Crandall uri: https://doi.org/10.7717/peerj.1140 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Castro-Nallar et al. title: Oyster reef restoration supports increased nekton biomass and potential commercial fishery value link: https://peerj.com/articles/1111 last-modified: 2015-08-25 description: Across the globe, discussions centered on the value of nature drive many conservation and restoration decisions. As a result, justification for management activities increasingly asks for two lines of evidence: (1) biological proof of augmented ecosystem function or service, and (2) monetary valuation of these services. For oyster reefs, which have seen significant global declines and increasing restoration work, the need to provide both biological and monetary evidence of reef services on a local-level has become more critical in a time of declining resources. Here, we quantified species biomass and potential commercial value of nekton collected from restored oyster (Crassostrea virginica) reefs in coastal Louisiana over a 3-year period, providing multiple snapshots of biomass support over time. Overall, and with little change over time, fish and invertebrate biomass is 212% greater at restored oyster reefs than mud-bottom, or 0.12 kg m−2. The additional biomass of commercial species is equivalent to an increase of local fisheries value by 226%, or $0.09 m−2. Understanding the ecosystem value of restoration projects, and how they interact with regional management priorities, is critical to inform local decision-making and provide testable predictions. Quantitative estimates of potential commercial fisheries enhancement by oyster reef restoration such as this one can be used directly by local managers to determine the expected return on investment. creator: Austin T. Humphries creator: Megan K. La Peyre uri: https://doi.org/10.7717/peerj.1111 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Adaptation of the Critical Care Family Need Inventory to the Turkish population and its psychometric properties link: https://peerj.com/articles/1208 last-modified: 2015-08-20 description: In the complex environment of intensive care units, needs of patients’ relatives might be seen as the lowest priority. On the other hand, because of their patients’ critical and often uncertain conditions, stress levels of relatives are quite high. This study aims to adapt the Critical Care Family Need Inventory, which assesses the needs of patients’ relatives, for use with the Turkish-speaking population and to assess psychometric properties of the resulting inventory. The study was conducted in a state hospital with the participation of 191 critical care patient relatives. Content validity was assessed by expert opinions, and construct validity was examined by exploratory factor analysis (EFA). Cronbach’s alpha coefficient was used to determine internal consistency. The translated inventory has a content validity ratio higher than the minimum acceptable level. Its construct validity was established by the EFA. Cronbach’s alpha coefficient for the entire scale was 0.93 and higher than 0.80 for subscales, thus demonstrating the translated version’s reliability. The Turkish adaptation appropriately reflects all dimensions of needs in the original CCFNI, and its psychometric properties were acceptable. The revised tool could be useful for helping critical care healthcare workers provide services in a holistic approach and for policymakers to improve quality of service. creator: Sibel Büyükçoban creator: Meltem Çiçeklioğlu creator: Nilüfer Demiral Yılmaz creator: M. Murat Civaner uri: https://doi.org/10.7717/peerj.1208 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Büyükçoban et al. title: Polymorphism of amyloid-like fibrils can be defined by the concentration of seeds link: https://peerj.com/articles/1207 last-modified: 2015-08-20 description: Prions are infectious proteins where the same protein may express distinct strains. The strains are enciphered by different misfolded conformations. Strain-like phenomena have also been reported in a number of other amyloid-forming proteins. One of the features of amyloid strains is the ability to self-propagate, maintaining a constant set of physical properties despite being propagated under conditions different from those that allowed initial formation of the strain. Here we report a cross-seeding experiment using strains formed under different conditions. Using high concentrations of seeds results in rapid elongation and new fibrils preserve the properties of the seeding fibrils. At low seed concentrations, secondary nucleation plays the major role and new fibrils gain properties predicted by the environment rather than the structure of the seeds. Our findings could explain conformational switching between amyloid strains observed in a wide variety of in vivo and in vitro experiments. creator: Tomas Sneideris creator: Katažyna Milto creator: Vytautas Smirnovas uri: https://doi.org/10.7717/peerj.1207 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sneideris et al. title: Winter Aconite (Eranthis hyemalis) Lectin as a cytotoxic effector in the lifecycle of Caenorhabditis elegans link: https://peerj.com/articles/1206 last-modified: 2015-08-20 description: The lectin found in the tubers of the Winter Aconite (Eranthis hyemalis) plant is an N-acetyl-D-galactosamine specific Type II Ribosome Inactivating Protein (RIP); Type II RIPs have shown anti-cancer properties, and hence have potential as therapeutic agents. Here we present a modified protocol for the extraction and purification of the E. hyemalis lectin (EHL) using affinity chromatography. De novo amino acid sequencing of EHL confirms its classification as a Type II Ribosome Inactivating Protein. The biocidal properties of EHL have been investigated against the nematode Caenorhabditis elegans. Arrested first stage larvae treated with EHL have shown some direct mortality, with surviving larvae subsequently showing a range of phenotypes including food avoidance, reduced fecundity, developmental delay and constitutive dauer larvae formation. Both inappropriate dauer larvae development and failure to locate to bacterial food source are consistent with the disruption of chemosensory function and the ablation of amphid neurons. Further investigation indicates that mutations that disrupt normal amphid formation can block the EHL-induced dauer larvae formation. In combination, these phenotypes indicate that EHL is cytotoxic and suggest a cell specific activity against the amphid neurons of C. elegans. creator: Marie-Therese McConnell creator: David R. Lisgarten creator: Lee J. Byrne creator: Simon C. Harvey creator: Emilia Bertolo uri: https://doi.org/10.7717/peerj.1206 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McConnell et al. title: Low relative error in consumer-grade GPS units make them ideal for measuring small-scale animal movement patterns link: https://peerj.com/articles/1205 last-modified: 2015-08-20 description: Consumer-grade GPS units are a staple of modern field ecology, but the relatively large error radii reported by manufacturers (up to 10 m) ostensibly precludes their utility in measuring fine-scale movement of small animals such as insects. Here we demonstrate that for data collected at fine spatio-temporal scales, these devices can produce exceptionally accurate data on step-length and movement patterns of small animals. With an understanding of the properties of GPS error and how it arises, it is possible, using a simple field protocol, to use consumer grade GPS units to collect step-length data for the movement of small animals that introduces a median error as small as 11 cm. These small error rates were measured in controlled observations of real butterfly movement. Similar conclusions were reached using a ground-truth test track prepared with a field tape and compass and subsequently measured 20 times using the same methodology as the butterfly tracking. Median error in the ground-truth track was slightly higher than the field data, mostly between 20 and 30 cm, but even for the smallest ground-truth step (70 cm), this is still a signal-to-noise ratio of 3:1, and for steps of 3 m or more, the ratio is greater than 10:1. Such small errors relative to the movements being measured make these inexpensive units useful for measuring insect and other small animal movements on small to intermediate scales with budgets orders of magnitude lower than survey-grade units used in past studies. As an additional advantage, these units are simpler to operate, and insect or other small animal trackways can be collected more quickly than either survey-grade units or more traditional ruler/gird approaches. creator: Greg A. Breed creator: Paul M. Severns uri: https://doi.org/10.7717/peerj.1205 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Breed and Severns title: Neutering of cats and dogs in Ireland; pet owner self-reported perceptions of enabling and disabling factors in the decision to neuter link: https://peerj.com/articles/1196 last-modified: 2015-08-20 description: Background. Failure among pet owners to neuter their pets results in increased straying and overpopulation problems. Variations in neutering levels can be explained by cultural differences, differences in economic status in rural and urban locations, and owner perceptions about their pet. There are also differences between male and female pet owners. There is no research pertaining to Irish pet owner attitudes towards neutering their pets. This paper identified the perceptions of a sample of Irish cat and dog owners that influenced their decisions on pet neutering.Methods. This study was conducted using social science (qualitative) methods, including an interview-administered survey questionnaire and focus group discussions. Data was coded and managed using Nvivo 8 qualitative data analysis software.Results. Focus groups were conducted with 43 pet (cats and dogs) owners. Two major categories relating to the decision to neuter were identified: (1) enabling perceptions in the decision to neuter (subcategories were: controlling unwanted pet behaviour; positive perceptions regarding pet health and welfare outcomes; perceived owner responsibility; pet function; and the influence of veterinary advice), and (2) disabling perceptions in the decision to neuter (subcategories were: perceived financial cost of neutering; perceived adequacy of existing controls; and negative perceptions regarding pet health and welfare outcomes).Discussion. Pet owner sense of responsibility and control are two central issues to the decision to neuter their pets. Understanding how pet owners feel about topics such as pet neutering, can help improve initiatives aimed at emphasising the responsibility of population control of cats and dogs. creator: Martin J. Downes creator: Catherine Devitt creator: Marie T. Downes creator: Simon J. More uri: https://doi.org/10.7717/peerj.1196 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Downes et al. title: Personality and intelligence: persistence, not self-directedness, cooperativeness or self-transcendence, is related to twins’ cognitive abilities link: https://peerj.com/articles/1195 last-modified: 2015-08-20 description: Background. A person-centered approach focusing on the interaction of an individual’s temperament-character-life events is essential in the path of individuals’ well-being. In this context, three character traits, Self-directedness (e.g., self-acceptance, self-control, goal-directed behavior), Cooperativeness (e.g., social affiliation, social tolerance, empathy and helpfulness) and Self-transcendence (e.g., spiritual acceptance, transpersonal identification), measured using Cloninger’s model of personality are suggested to help the individual to regulate and resolve the conflicts derived from her/his temperament combinations as a reaction to life events. However, if character is related to the individual’s cognitive ability, then this association might limit any intervention that focuses on character development. We used data from the Child and Adolescent Twin Study in Sweden (CATSS) to investigate the relationship between personality and cognitive ability.Method. The sample consisted of 370 15-year-old twins (159 girls/211 boys), 192 of whom screen-positive with various types of mental health problems. We used the Temperament and Character Inventory to measure personality and the Wechsler Intelligence Scales for Children (WISC-IV) to measure intelligence. The relationship was investigated using correlation analyses using random-selected twins from each dyad and separately for monozygotic and dizygotic twins. Additional analyses investigated the genetic and environmental effects on personality and cognitive ability in this specific sample.Results. There were no significant correlations between the WISC-IV indices and any of the character traits (i.e., Self-directedness, Cooperativeness, and Self-transcendence). Persistence was significantly related, if weak, to four WISC-IV indices: Verbal Comprehension, Perceptual Reasoning, Working Memory, and the Full WISC-IV Scale. Post-hoc cross-twin/cross-trait analyses showed that the Persistence-cognitive ability correlation might depend on common genetic effects. The WISC-IV indices showed a relatively large genetic influence, while earlier findings about the etiology of temperament and character traits using the whole CATSS sample were replicated in this sub-sample of twins.Conclusions. The results indicate that what individuals make of themselves intentionally (i.e., their character) was not associated to intelligence. Persistence, a temperament dimension that measures heritable individual differences in eagerness of effort, ambition, perfectionism, and resistance to discouragement despite frustration and fatigue, was weakly linked to intelligence. Suggesting that, at least during adolescence, interventions targeting character development are not limited by the individual’s intelligence. creator: Fariba Mousavi creator: Sandor Rozsa creator: Thomas Nilsson creator: Trevor Archer creator: Henrik Anckarsäter creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.1195 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Mousavi et al. title: A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae) link: https://peerj.com/articles/1193 last-modified: 2015-08-20 description: Silene ciliata Pourr. (Caryophyllaceae) is a species with a highly disjunct distribution which inhabits the alpine mountains of the Mediterranean Basin. We investigated the phylogeny and phylogeography of the species to (a) clarify the long-suggested division of S. ciliata into two subspecies, (b) evaluate its phylogenetic origin and (c) assess whether the species’ diversification patterns were affected by the Mediterranean relief. For this purpose, we collected DNA from 25 populations of the species that inhabit the mountains of Portugal, Spain, France, Italy, former Yugoslav Republic of Macedonia, Bulgaria and Greece and studied the plastid regions rbcL, rps16 and trnL. Major intraspecific variation was supported by all analyses, while the possibility of the existence of more varieties or subspecies was not favoured. Plastid DNA (cpDNA) evidence was in accordance with the division of S. ciliata into the two subspecies, one spreading west (Iberian Peninsula and Central Massif) and the other east of the Alps region (Italian and Balkan Peninsula). This study proposes that the species’ geographically disconnected distribution has probably derived from vicariance processes and from the Alps acting as a barrier to the species’ dispersal. The monophyletic origin of the species is highly supported. cpDNA patterns were shown independent of the chromosome evolution in the populations and could have resulted from a combination of geographic factors providing links and barriers, climatic adversities and evolutionary processes that took place during Quaternary glaciations. creator: Ifigeneia Kyrkou creator: José María Iriondo creator: Alfredo García-Fernández uri: https://doi.org/10.7717/peerj.1193 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kyrkou et al. title: A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite link: https://peerj.com/articles/1191 last-modified: 2015-08-20 description: Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium. creator: David Hone creator: Donald M. Henderson creator: François Therrien creator: Michael B. Habib uri: https://doi.org/10.7717/peerj.1191 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hone et al. title: Irrigation and avifaunal change in coastal Northwest Mexico: has irrigated habit attracted threatened migratory species? link: https://peerj.com/articles/1187 last-modified: 2015-08-20 description: Irrigation in desert ecosystems can either reduce or increase species diversity. Groundwater pumping often lowers water tables and reduces natural wetlands, whereas canal irrigation often creates mesic habitat, resulting in great increases in avian diversity from irrigation. Here we compare a dataset of potential natural vegetation to recent datasets from areal and satellite imagery to show that 60% of the land in the coastal plain of southern Sonora and northern Sinaloa lying below 200 m elevation has been converted by irrigation to more mesic habitats. We then use the record of bird specimens in the world’s museums from this same region of Mexico to examine the avian community before and after the development of extensive irrigation. In general these museum records show an increase in the abundance and diversity of breeding birds associated with mesic habitats. Although thorn forest birds have likely decreased in total numbers, most are common enough in the remaining thorn forest that collection records did not indicate their probable decline. Four migrants having most of their breeding ranges in the US or Canada, Yellow-billed Cuckoo, Cliff Swallow, Bell’s Vireo, and Orchard Oriole, apparently have increased dramatically as breeders in irrigated habitats of NW Mexico. Because these species have decreased or even largely disappeared as breeding birds in parts of the US or Canada, further research should assess whether their increases in new mesic habitats of NW Mexico are linked to their declines as breeding birds in Canada and the US For Bell’s Vireo recent specimens from Sinaloa suggest its new breeding population in NW Mexico may be composed partly of the endangered Least Bell’s Vireo. creator: Sievert Rohwer creator: Emily Grason creator: Adolfo G. Navarro-Sigüenza uri: https://doi.org/10.7717/peerj.1187 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Rohwer et al. title: Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA) link: https://peerj.com/articles/1182 last-modified: 2015-08-20 description: Within highly diverse ecosystems, the majority of bacterial taxa are present in low abundance as members of the rare biosphere. The rationale for the occurrence and maintenance of the rare biosphere, and the putative ecological role(s) and dynamics of its members within a specific ecosystem is currently debated. We hypothesized that in highly diverse ecosystems, a fraction of the rare biosphere acts as a backup system that readily responds to environmental disturbances. We tested this hypothesis by subjecting sediments from Zodletone spring, a sulfide- and sulfur-rich spring in Southwestern OK, to incremental levels of salinity (1, 2, 3, 4, and 10% NaCl), or temperature (28°, 30°, 32°, and 70 °C), and traced the trajectories of rare members of the community in response to these manipulations using 16S rRNA gene analysis. Our results indicate that multiple rare bacterial taxa are promoted from rare to abundant members of the community following such manipulations and that, in general, the magnitude of such recruitment is directly proportional to the severity of the applied manipulation. Rare members that are phylogenetically distinct from abundant taxa in the original sample (unique rare biosphere) played a more important role in the microbial community response to environmental disturbances, compared to rare members that are phylogenetically similar to abundant taxa in the original sample (non-unique rare biosphere). The results emphasize the dynamic nature of the rare biosphere, and highlight its complexity and non-monolithic nature. creator: Suzanne Coveley creator: Mostafa S. Elshahed creator: Noha H. Youssef uri: https://doi.org/10.7717/peerj.1182 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Coveley et al. title: The effects of leaf litter nutrient pulses on Alliaria petiolata performance link: https://peerj.com/articles/1166 last-modified: 2015-08-20 description: Nutrient pulses can facilitate species establishment and spread in new habitats, particularly when one species more effectively uses that nutrient pulse. Biological differences in nutrient acquisition between native and exotic species may facilitate invasions into a variety of habitats including deciduous forest understories. Alliaria petiolata (Bieb.) Cavara & Grande is an important invader of deciduous forest understories throughout much of North America. These understory communities contain many species which perform the majority of their growth and reproduction before canopy closure in spring. Because A. petiolata is a wintergreen biennial that can be active during autumn and winter, it may utilize nutrients released from decaying leaf litter before its competitors. To investigate this we manipulated the timing of leaf litter addition (fall or spring) and experimentally simulated the nutrient pulse from decaying leaves using artificial fertilizer. To determine whether A. petiolata affected the abundance of understory competitors, we also removed A. petiolata from one treatment. A. petiolata that received early nutrients exhibited greater growth. Treatments receiving fall leaf litter or artificial nutrients had greater A. petiolata adult biomass than plots receiving spring nutrient additions (leaf litter or artificial nutrients). However, fall leaf litter addition had no effect on the richness of competitor species. Thus, wintergreen phenology may contribute to the spread of A. petiolata through deciduous forest understories, but may not explain community-level impacts of A. petiolata in deciduous forests. creator: Robert W. Heckman creator: David E. Carr uri: https://doi.org/10.7717/peerj.1166 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Heckman and Carr title: Mental disorder recovery correlated with centralities and interactions on an online social network link: https://peerj.com/articles/1163 last-modified: 2015-08-20 description: Recent research has established both a theoretical basis and strong empirical evidence that effective social behavior plays a beneficial role in the maintenance of physical and psychological well-being of people. To test whether social behavior and well-being are also associated in online communities, we studied the correlations between the recovery of patients with mental disorders and their behaviors in online social media. As the source of the data related to the social behavior and progress of mental recovery, we used PatientsLikeMe (PLM), the world’s first open-participation research platform for the development of patient-centered health outcome measures. We first constructed an online social network structure based on patient-to-patient ties among 200 patients obtained from PLM. We then characterized patients’ online social activities by measuring the numbers of “posts and views” and “helpful marks” each patient obtained. The patients’ recovery data were obtained from their self-reported status information that was also available on PLM. We found that some node properties (in-degree, eigenvector centrality and PageRank) and the two online social activity measures were significantly correlated with patients’ recovery. Furthermore, we re-collected the patients’ recovery data two months after the first data collection. We found significant correlations between the patients’ social behaviors and the second recovery data, which were collected two months apart. Our results indicated that social interactions in online communities such as PLM were significantly associated with the current and future recoveries of patients with mental disorders. creator: Xinpei Ma creator: Hiroki Sayama uri: https://doi.org/10.7717/peerj.1163 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ma and Sayama title: Environmental influences on the Indo–Pacific octocoral Isis hippuris Linnaeus 1758 (Alcyonacea: Isididae): genetic fixation or phenotypic plasticity? link: https://peerj.com/articles/1128 last-modified: 2015-08-20 description: As conspicuous modular components of benthic marine habitats, gorgonian (sea fan) octocorals have perplexed taxonomists for centuries through their shear diversity, particularly throughout the Indo–Pacific. Phenotypic incongruence within and between seemingly unitary lineages across contrasting environments can provide the raw material to investigate processes of disruptive selection. Two distinct phenotypes of the Isidid Isis hippurisLinnaeus, 1758 partition between differing reef environments: long-branched bushy colonies on degraded reefs, and short-branched multi/planar colonies on healthy reefs within the Wakatobi Marine National Park (WMNP), Indonesia. Multivariate analyses reveal phenotypic traits between morphotypes were likely integrated primarily at the colony level with increased polyp density and consistently smaller sclerite dimensions at the degraded site. Sediment load and turbidity, hence light availability, primarily influenced phenotypic differences between the two sites. This distinct morphological dissimilarity between the two sites is a reliable indicator of reef health; selection primarily acting on colony morphology, porosity through branching structure, as well as sclerite diversity and size. ITS2 sequence and predicted RNA secondary structure further revealed intraspecific variation between I. hippuris morphotypes relative to such environments (ΦST = 0.7683, P < 0.001). This evidence suggests—but does not confirm—that I. hippuris morphotypes within the WMNP are two separate species; however, to what extent and taxonomic assignment requires further investigation across its full geographic distribution. Incongruence between colonies present in the WMNP with tenuously described Isis alternatives (Isis reticulataNutting, 1910, Isis minorbrachyblastaZou, Huang & Wang, 1991), questions the validity of such assignments. Furthermore, phylogenetic analyses confirm early taxonomic suggestion that the characteristic jointed axis of the Isididae is in fact a convergent trait. Thus the polyphyletic nature of the Isididae lies in its type species I. hippuris, being unrelated to the rest of its family members. creator: Sonia J. Rowley creator: Xavier Pochon creator: Les Watling uri: https://doi.org/10.7717/peerj.1128 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Rowley et al. title: In vitro biomechanical evaluation of internal fixation techniques on the canine lumbosacral junction link: https://peerj.com/articles/1094 last-modified: 2015-08-20 description: Few biomechanical studies have evaluated the effect of internal stabilization techniques after decompressive surgery on the stability of the canine lumbosacral junction. The purpose of this canine cadaver study is to evaluate the stability of the canine lumbosacral (LS) spine in flexion and extension following laminectomy and discectomy and then stabilization with each of the three techniques: pins and polymethylmethacrylate (P/PMMA), two dorsal locking plates (SOP) or bilateral transarticular facet screws (FACET).Using a cantilever biomechanical system, bending moments were applied to the LS and range of motion (ROM) was recorded via a rotational potentiometer. With 3 Nm, the ROM (n = 4 in each group) for P/PMMA, SOP and FACET were 1.92 ± 0.96°, 2.56 ± 0.55°and 3.18 ± 1.14°, respectively. With moments up to 35 Nm, the P/PMMA specimens appeared stable. Sacroiliac motion in the SOP and FACET groups invalidated further comparisons. Each of the stabilization techniques (P/PMMA, SOP, and FACET) significantly decreased the range of motion in flexion and extension for low bending moments. creator: Peter Early creator: Peter Mente creator: Stacy Dillard creator: Simon Roe uri: https://doi.org/10.7717/peerj.1094 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Early et al. title: Coalescent: an open-science framework for importance sampling in coalescent theory link: https://peerj.com/articles/1203 last-modified: 2015-08-18 description: Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner.Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable.Conclusions. In coalescent theory, many studies of computational efficiency consider only effective sample size. Here, we evaluate proposals in the coalescent literature, to discover that the order of efficiency among the three importance sampling schemes changes when one considers running time as well as effective sample size. We also describe a computational technique called “just-in-time delegation” available to improve the trade-off between running time and precision by constructing improved importance sampling schemes from existing ones. Thus, our systems approach is a potential solution to the “28 programs problem” highlighted by Felsenstein, because it provides the flexibility to include or exclude various features of similar coalescent models or importance sampling schemes. creator: Susanta Tewari creator: John L. Spouge uri: https://doi.org/10.7717/peerj.1203 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Biological and ecological traits of marine species link: https://peerj.com/articles/1201 last-modified: 2015-08-18 description: This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the ‘status’ of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them. creator: Mark John Costello creator: Simon Claus creator: Stefanie Dekeyzer creator: Leen Vandepitte creator: Éamonn Ó Tuama creator: Dan Lear creator: Harvey Tyler-Walters uri: https://doi.org/10.7717/peerj.1201 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Costello et al. title: The application of fractional Mel cepstral coefficient in deceptive speech detection link: https://peerj.com/articles/1194 last-modified: 2015-08-18 description: The inconvenience operation of EEG P300 or functional magnetic resonance imaging (FMRI) will be overcome, when the deceptive information can be effectively detected from speech signal analysis. In this paper, the fractional Mel cepstral coefficient (FrCC) is proposed as the speech character for deception detection. The different fractional order can reveal various personalities of the speakers. The linear discriminant analysis (LDA) model (which has the ability of global optimal vector mapping) is introduced, and the performance of FrCC and MFCC in deceptive detection is compared when all the data are mapped to low dimensional. Then, the hidden Markov model (HMM) is introduced as a long-term signal analysis tool. Twenty-five male and 25 female participants are involved in the experiment. The results show that the clustering effect of optimal fractional order FrCC is better than that of MFCC. The average accuracy for male and female speaker is 59.9% and 56.2%, respectively, by using the FrCC under the LDA model. When MFCC is used, the accuracy is reduced by 3.2% and 5.9%, respectively, for male and female. The accuracy can be increased to 71.0% and 70.2% for male and female speakers when HMM is used. Moreover, some individual accuracy is increased over 20%, or even more than 85%, when FrCC is introduced. The results show that the deceptive information is indeed hidden in the speech signals. Therefore, speech-based psychophysiology calculating may be a valuable research field. creator: Xinyu Pan creator: Heming Zhao creator: Yan Zhou uri: https://doi.org/10.7717/peerj.1194 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pan et al. title: Perivascular mast cells regulate vein graft neointimal formation and remodeling link: https://peerj.com/articles/1192 last-modified: 2015-08-18 description: Objective. Emerging evidence suggests an important role for mast cells in vein graft failure. This study addressed the hypothesis that perivascular mast cells regulate in situ vascular inflammatory and proliferative responses and subsequent vein graft neointimal lesion formation, using an optimized local mast cell reconstitution method.Methods and Results. Neointimal hyperplasia was induced by insertion of a vein graft into the right carotid artery in wild type and mast cell deficient KitW−sh/W−sh mice. In some experiments, mast cells were reconstituted systemically (tail vein injection of bone marrow-derived mast cells) or locally (directly into the right neck area) prior to vein grafting. Vein graft neointimal lesion formation was significantly (P < 0.05) reduced in KitW−sh/W−sh mice. Mast cell deficiency reduced the number of proliferating cells, and inhibited L-selectin, CCL2, M-CSF and MIP-3α expression in the vein grafts. Local but not systemic mast cell reconstitution restored a perivascular mast cell population that subsequently promoted neointimal formation in mast cell deficient mice.Conclusion. Our data demonstrate that perivascular mast cells play a key role in promoting neointima formation by inducing local acute inflammatory and proliferative responses. These results suggest that ex vivo intraoperative targeting of mast cells may have therapeutic potential for the prevention of pathological vein graft remodeling. creator: Junxi Wu creator: Gianluca Grassia creator: Helen Cambrook creator: Armando Ialenti creator: Neil MacRitchie creator: Jaclyn Carberry creator: Roger M. Wadsworth creator: Catherine Lawrence creator: Simon Kennedy creator: Pasquale Maffia uri: https://doi.org/10.7717/peerj.1192 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wu et al. title: Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota link: https://peerj.com/articles/1190 last-modified: 2015-08-18 description: Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of the methods tested here, and base their choice according to practical considerations such as prior use, cost, and availability in the field, although we still advise that all samples within a study be handled in an identical manner when possible. We also suggest that, in large-scale molecular studies of hundreds of insect specimens, surface sterilization may not be worth the time and effort involved. This information should help researchers design sampling strategies and will facilitate cross-comparisons and meta-analyses of microbial community data obtained from insect specimens preserved in different ways. creator: Tobin J. Hammer creator: Jacob C. Dickerson creator: Noah Fierer uri: https://doi.org/10.7717/peerj.1190 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hammer et al. title: Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions link: https://peerj.com/articles/1186 last-modified: 2015-08-18 description: The ichthyoplankton assemblage structure in the Yangtze Estuary was analyzed based on four springs in 1999, 2001, 2004 and 2007 in order to provide detailed characterizations of the ichthyoplankton assemblage in springs, examine the long-term dynamics of spring ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. Forty-two ichthyoplankton species belonging to 23 families were collected. Engraulidae was the most abundant family, including six species and comprising 67.91% of the total catch. Only four species (Coilia mystus, Engraulis japonicus, Trachidermis fasciatus and Allanetta bleekeri) could be considered dominant, accounting for 88.70% of total abundance. The structure of the ichthyoplankton spring assemblage persisted on an annual basis, with the dominant species reappearing consistently even though their abundance fluctuated from year to year. This inter-annual variation probably reflects variable environmental conditions influenced by jellyfish blooms, declining river flow, and overfishing. Canonical correspondence analysis indicated aspatial structure of the ichthyoplankton assemblage in three areas: (1) an inner assemblage dominated by C. mystus; (2) a central assemblage dominated by A. bleekeri and T. fasciatus; and (3) a shelf assemblage featuring E. japonicus. The observed ichthyoplankton assemblage structure appears to be strongly influenced by depth, salinity and suspended particulate matter gradients. creator: Hui Zhang creator: Weiwei Xian creator: Shude Liu uri: https://doi.org/10.7717/peerj.1186 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Zhang et al. title: Face matching in a long task: enforced rest and desk-switching cannot maintain identification accuracy link: https://peerj.com/articles/1184 last-modified: 2015-08-18 description: In face matching, observers have to decide whether two photographs depict the same person or different people. This task is not only remarkably difficult but accuracy declines further during prolonged testing. The current study investigated whether this decline in long tasks can be eliminated with regular rest-breaks (Experiment 1) or room-switching (Experiment 2). Both experiments replicated the accuracy decline for long face-matching tasks and showed that this could not be eliminated with rest or room-switching. These findings suggest that person identification in applied settings, such as passport control, might be particularly error-prone due to the long and repetitive nature of the task. The experiments also show that it is difficult to counteract these problems. creator: Hamood M. Alenezi creator: Markus Bindemann creator: Matthew C. Fysh creator: Robert A. Johnston uri: https://doi.org/10.7717/peerj.1184 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Alenezi et al. title: External morphology of eyes and Nebenaugen of caridean decapods–ecological and systematic considerations link: https://peerj.com/articles/1176 last-modified: 2015-08-18 description: Most caridean decapods have compound eyes of the reflecting superposition kind, and additionally some possess an accessory eye-like organ of unknown function, also referred to as the nebenauge. We examined 308 caridean genera to assess the general morphology of the eye, rostrum length, eye diameter and the presence or absence and, when present, the diameter of the nebenauge. We have attempted to relate these data to ecological and taxonomic considerations. We consider there to be 6 distinct eye types based on the margin between the eyestalk and cornea. The presence of nebenaugen appears to be generally linked to an active lifestyle, as evidenced by the fact that species that have nebenaugen tend to have larger eyes and are more likely to have a distinct rostrum. We suggest that the inconsistencies in its presence/absence under both systematic and ecological lenses may indicate that when present it has various roles relating to behavioural and physiological rhythms. creator: Magnus L. Johnson creator: Nicola Dobson creator: Sammy De Grave uri: https://doi.org/10.7717/peerj.1176 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Johnson et al. title: Parametric estimation of P(X > Y) for normal distributions in the context of probabilistic environmental risk assessment link: https://peerj.com/articles/1164 last-modified: 2015-08-18 description: Estimating the risk, P(X > Y), in probabilistic environmental risk assessment of nanoparticles is a problem when confronted by potentially small risks and small sample sizes of the exposure concentration X and/or the effect concentration Y. This is illustrated in the motivating case study of aquatic risk assessment of nano-Ag. A non-parametric estimator based on data alone is not sufficient as it is limited by sample size. In this paper, we investigate the maximum gain possible when making strong parametric assumptions as opposed to making no parametric assumptions at all. We compare maximum likelihood and Bayesian estimators with the non-parametric estimator and study the influence of sample size and risk on the (interval) estimators via simulation. We found that the parametric estimators enable us to estimate and bound the risk for smaller sample sizes and small risks. Also, the Bayesian estimator outperforms the maximum likelihood estimators in terms of coverage and interval lengths and is, therefore, preferred in our motivating case study. creator: Rianne Jacobs creator: Andriëtte A. Bekker creator: Hilko van der Voet creator: Cajo J.F. ter Braak uri: https://doi.org/10.7717/peerj.1164 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Jacobs et al. title: Too much of a good thing? An observational study of prolific authors link: https://peerj.com/articles/1154 last-modified: 2015-08-18 description: Introduction. Researchers’ productivity is usually measured in terms of their publication output. A minimum number of publications is required for some medical qualifications and professional appointments. However, authoring an unfeasibly large number of publications might indicate disregard of authorship criteria or even fraud. We therefore examined publication patterns of highly prolific authors in 4 medical specialties.Methods. We analysed Medline publications from 2008–12 using bespoke software to disambiguate individual authors focusing on 4 discrete topics (to further reduce the risk of combining publications from authors with the same name and affiliation). This enabled us to assess the number and type of publications per author per year.Results. While 99% of authors were listed on fewer than 20 publications in the 5-year period, 24 authors in the chosen areas were listed on at least 25 publications in a single year (i.e., >1 publication per 10 working days). Types of publication by the prolific authors varied but included substantial numbers of original research papers (not simply editorials or letters).Conclusions. Institutions and funders should be alert to unfeasibly prolific authors when measuring and creating incentives for researcher productivity. creator: Elizabeth Wager creator: Sanjay Singhvi creator: Sabine Kleinert uri: https://doi.org/10.7717/peerj.1154 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Wager et al. title: Understanding text-based persuasion and support tactics of concerned significant others link: https://peerj.com/articles/1151 last-modified: 2015-08-18 description: The behavior of concerned significant others (CSOs) can have a measurable impact on the health and wellness of individuals attempting to meet behavioral and health goals, and research is needed to better understand the attributes of text-based CSO language when encouraging target significant others (TSOs) to achieve those goals. In an effort to inform the development of interventions for CSOs, this study examined the language content of brief text-based messages generated by CSOs to motivate TSOs to achieve a behavioral goal. CSOs generated brief text-based messages for TSOs for three scenarios: (1) to help TSOs achieve the goal, (2) in the event that the TSO is struggling to meet the goal, and (3) in the event that the TSO has given up on meeting the goal. Results indicate that there was a significant relationship between the tone and compassion of messages generated by CSOs, the CSOs’ perceptions of TSO motivation, and their expectation of a grateful or annoyed reaction by the TSO to their feedback or support. Results underscore the importance of attending to patterns in language when CSOs communicate with TSOs about goal achievement or failure, and how certain variables in the CSOs’ perceptions of their TSOs affect these characteristics. creator: Katherine van Stolk-Cooke creator: Marie Hayes creator: Amit Baumel creator: Frederick Muench uri: https://doi.org/10.7717/peerj.1151 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Van Stolk-Cooke et al. title: Response of Microtermes mycophagus (Isoptera: Termitidae) to twenty one wood species link: https://peerj.com/articles/1132 last-modified: 2015-08-18 description: The responses of termite species to bait depend upon the quality of the food used in the stations. Woods are the most common food sources for termites but different termite species behave differently to different wood species and types. The knowledge of the preference status of different wood species to a termite species helps in effective monitoring and baiting program. The current study was carried out to evaluate the preference of 21 wood species to the termite, Microtermes mycophagus in the field by no-choice and choice feeding tests. The results indicated silk cotton tree and sacred fig woods as the most preferred wood species with mean mass losses of 71.21 ± 5.09% and 68.38 ± 7.27% in no-choice test and 95.02 ± 1.65% and 91.69 ± 2.07% in choice tests, respectively. White cedar was the least preferred wood species with mean mass losses of 7.49 ± 1.64% and 13.92 ± 1.89% in no choice and choice feeding tests, respectively. Based on present studies, sapwood of silk cotton tree and sacred fig may be used in effective monitoring and baiting program against M. mycophagus. creator: Naeem Iqbal creator: Hafiz Azhar Ali Khan creator: Shafqat Saeed uri: https://doi.org/10.7717/peerj.1132 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Iqbal et al. title: Interactions between donor Agreeableness and recipient characteristics in predicting charitable donation and positive social evaluation link: https://peerj.com/articles/1089 last-modified: 2015-08-18 description: Agreeable people are more likely to display prosocial attitudes and helpful behavior in a broad range of situations. Here we show that this tendency interacts with the personal characteristics of interaction partners. In an online study (n = 284), participants were given the opportunity to report attitudes toward and make monetary donations to needy individuals who were described in dynamically generated biographies. Using a machine learning and multilevel modeling framework, we tested three potential explanations for the facilitatory influence of Agreeableness on charitable behavior. We find that Agreeableness preferentially increased donations and prosocial attitudes toward targets normatively rated as being more deserving. Our results advance understanding of person-by-situation interactions in the context of charitable behavior and prosocial attitudes. creator: Tal Yarkoni creator: Yoni K. Ashar creator: Tor D. Wager uri: https://doi.org/10.7717/peerj.1089 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Yarkoni et al. title: Cranial and mandibular shape variation in the genus Carollia (Mammalia: Chiroptera) from Colombia: biogeographic patterns and morphological modularity link: https://peerj.com/articles/1197 last-modified: 2015-08-13 description: Neotropical bats of the genus Carollia are widely studied due to their abundance, distribution and relevance for ecosystems. However, the ecomorphological boundaries of these species are poorly differentiated, and consequently correspondence between their geographic distribution, ecological plasticity and morphological variation remains unclear. In this study, patterns of cranial and mandibular morphological variation were assessed for Carollia brevicauda, C. castanea and C. perspicillata from Colombia. Using geometric morphometrics, morphological variation was examined with respect to: differences in intraspecific variation, morphological modularity and integration, and biogeographic patterns. Patterns of intraspecific variation were different for each species in both cranial and mandibular morphology, with functional differences apparent according to diet. Cranial modularity varied between species whereas mandibular modularity did not. High cranial and mandibular correlation reflects Cranium-Mandible integration as a functional unit. Similarity between the biogeographic patterns in C. brevicauda and C. perspicillata indicates that the Andes do not act as a barrier but rather as an independent region, isolating the morphology of Andean populations of larger-bodied species. The biogeographic pattern for C. castanea was not associated with the physiography of the Andes, suggesting that large body size does not benefit C. brevicauda and C. perspicillata in maintaining homogeneous morphologies among populations. creator: Camilo López-Aguirre creator: Jairo Pérez-Torres creator: Laura A. B. Wilson uri: https://doi.org/10.7717/peerj.1197 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 López-Aguirre et al. title: Cell death of spinal cord ED1+ cells in a rat model of multiple sclerosis link: https://peerj.com/articles/1189 last-modified: 2015-08-13 description: Infiltration of macrophages into the central nervous system and activation of microglia are hallmarks of multiple sclerosis and its animal model—experimental autoimmune encephalomyelitis (EAE). Cell death in EAE has been demonstrated as an essential mechanism in the local regulation of the inflammatory reaction, but also as one of the major factors contributing to the destruction of the nervous tissue. The focus of this study was on detection of cell death among ED1+ cells (macrophages/activated microglia) in the spinal cord of Dark Agouti rats at the peak of EAE. Cell death was assessed using the TUNEL assay and immunostaining for cleaved caspase 3, as markers for cell death in general and “classical” apoptosis, respectively. Major infiltrates of immune cells were detected both in white matter and gray matter of spinal cords in rats at the disease peak. ED1, TUNEL, and caspase 3 positive cells were detected within, but also outside the infiltrates. There were more dying ED1+ cells in white matter than in gray matter, both in the general population and in infiltrated regions. The observed discrepancy in the proportion of dying ED1+ cells in spinal cord gray and white matter indicated that in EAE rat macrophages/microglia within gray matter are less prone to cell death induction. This is of special interest in the context of the increasingly appreciated contribution of spinal cord gray matter inflammation to multiple sclerosis pathogenesis. Our findings suggest that activated macrophages/microglia of gray matter are less susceptible to cell death induction. Alternatively, it can be assumed that intrinsic cell death-inductive mechanisms of nervous tissue differ in white and gray matter. Thus, further research on the gray matter macrophages/microglia cell death during EAE is warranted. They should be aimed at identification of the reasons for the observed differences and finding suitable ways to stimulate gray matter activated macrophages/microglia death. creator: Dragana Trifunović creator: Neda Djedović creator: Irena Lavrnja creator: Katrin Sophie Wendrich creator: François Paquet-Durand creator: Djordje Miljković uri: https://doi.org/10.7717/peerj.1189 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Trifunović et al. title: Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success link: https://peerj.com/articles/1188 last-modified: 2015-08-13 description: Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing. creator: Tom Kashiwagi creator: Elisabeth A. Maxwell creator: Andrea D. Marshall creator: Ana B. Christensen uri: https://doi.org/10.7717/peerj.1188 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kashiwagi et al. title: Effects of disputes and easement violations on the cost-effectiveness of land conservation link: https://peerj.com/articles/1185 last-modified: 2015-08-13 description: Conservation initiatives to protect and restore valued species communities in human-dominated landscapes face challenges linked to their potential costs. Conservation easements on private land may represent a cost-effective alternative to land purchase, but long-term costs to monitor and enforce easements, or defend legal challenges, remain uncertain. We explored the cost-effectiveness of conservation easements, defined here as the fraction of the high-biodiversity landscape potentially protected via investment in easements versus land purchase. We show that easement violation and dispute rates substantially affect the estimated long-term cost-effectiveness of an easement versus land purchase strategy. Our results suggest that conservation easements can outperform land purchase as a strategy to protect biodiversity as long as the rate of disputes and legal challenges is low, pointing to a critical need for monitoring data to reduce costs and maximize the value of conservation investments. creator: Richard Schuster creator: Peter Arcese uri: https://doi.org/10.7717/peerj.1185 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Schuster and Arcese title: A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes link: https://peerj.com/articles/1183 last-modified: 2015-08-13 description: Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances. creator: Baldiri Salvado creator: Ester Vilaprinyo creator: Albert Sorribas creator: Rui Alves uri: https://doi.org/10.7717/peerj.1183 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Salvado et al. title: Low serum albumin and total lymphocyte count as predictors of 30 day hospital readmission in patients 65 years of age or older link: https://peerj.com/articles/1181 last-modified: 2015-08-13 description: Introduction. Hospital readmission within 30 days of discharge is a target for health care cost savings through the medicare Value Based Purchasing initiative. Because of this focus, hospitals and health systems are investing considerable resources into the identification of patients at risk of hospital readmission and designing interventions to reduce the rate of hospital readmission. Malnutrition is a known risk factor for hospital readmission.Materials and Methods. All medical patients 65 years of age or older discharged from Memorial Medical Center from January 1, 2012 to March 31, 2012 who had a determination of serum albumin level and total lymphocyte count on hospital admission were studied retrospectively. Admission serum albumin levels and total lymphocyte counts were used to classify the nutritional status of all patients in the study. Patients with a serum albumin less than 3.5 grams/dL and/or a TLC less than 1,500 cells per mm3 were classified as having protein energy malnutrition. The primary outcome investigated in this study was hospital readmission for any reason within 30 days of discharge.Results. The study population included 1,683 hospital discharges with an average age of 79 years. The majority of the patients were female (55.9%) and had a DRG weight of 1.22 (0.68). 219 patients (13%) were readmitted within 30 days of hospital discharge. Protein energy malnutrition was common in this population. Low albumin was found in 973 (58%) patients and a low TLC was found in 1,152 (68%) patients. Low albumin and low TLC was found in 709 (42%) of patients. Kaplan–Meier analysis shows any laboratory evidence of PEM is a significant (p < 0.001) predictor of hospital readmission. Low serum albumin (p < 0.001) and TLC (p = 0.018) show similar trends. Cox proportional-hazards regression analysis showed low serum albumin (Hazard Ratio 3.27, 95% CI [2.30–4.63]) and higher DRG weight (Hazard Ratio 1.19, 95% CI [1.03–1.38]) to be significant independent predictors of hospital readmission within 30 days.Discussion. This study investigated the relationship of PEM to the rate of hospital readmission within 30 days of discharge in patients 65 years of age or older. These results indicate that laboratory markers of PEM can identify patients at risk of hospital readmission within 30 days of discharge. This risk determination is simple and identifies a potentially modifiable risk factor for readmission: protein energy malnutrition. creator: Robert Robinson uri: https://doi.org/10.7717/peerj.1181 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Robinson title: Mammalian cycles: internally defined periods and interaction-driven amplitudes link: https://peerj.com/articles/1180 last-modified: 2015-08-13 description: The cause of mammalian cycles—the rise and fall of populations over a predictable period of time—has remained controversial since these patterns were first observed over a century ago. In spite of extensive work on observable mammalian cycles, the field has remained divided upon what the true cause is, with a majority of opinions attributing it to either predation or to intra-species mechanisms. Here we unite the eigenperiod hypothesis, which describes an internal, maternal effect-based mechanism to explain the cycles’ periods with a recent generalization explaining the amplitude of snowshoe hare cycles in northwestern North America based on initial predator abundance. By explaining the period and the amplitude of the cycle with separate mechanisms, a unified and consistent view of the causation of cycles is reached. Based on our suggested theory, we forecast the next snowshoe hare cycle (predicted peak in 2016) to be of extraordinarily low amplitude. creator: LR Ginzburg creator: CJ Krebs uri: https://doi.org/10.7717/peerj.1180 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ginzburg and Krebs title: A new species of Brachycephalus (Anura: Brachycephalidae) from the Quiriri mountain range of southern Brazil link: https://peerj.com/articles/1179 last-modified: 2015-08-13 description: A new miniaturized toadled of the genus Brachycephalus (Anura: Brachycephalidae) is described from Serra do Quiriri in the municipality of Campo Alegre, Santa Catarina, southern Brazil. Specimens were collected from the leaf litter between from 1,263 and 1,318 m above sea level. The new species is distinguished from all its congeners by the combination of the following characters: snout–vent length 9.9–13.1 mm; skin on head and dorsum without dermal co-ossification; snout mucronate in dorsal view; dorsum rugose; general color brown, with a narrow orange vertebral stripe. The region where the new species is located is also shared with other endemic anuran species and has experienced strong anthropogenic impacts,suggesting that immediate actions should be taken to ensure their long-term preservation. creator: Marcio R. Pie creator: Luiz F. Ribeiro uri: https://doi.org/10.7717/peerj.1179 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pie and Ribeiro title: Artificial light pollution increases nocturnal vigilance in peahens link: https://peerj.com/articles/1174 last-modified: 2015-08-13 description: Artificial light pollution is drastically changing the sensory environments of animals. Even though many animals are now living in these changed environments, the effect light pollution has on animal behavior is poorly understood. We investigated the effect of light pollution on nocturnal vigilance in peahens (Pavo cristatus). Captive peahens were exposed to either artificial lighting or natural lighting at night. We employed a novel method to record their vigilance behavior by attaching accelerometers to their heads and continuously monitoring their large head movements. We found that light pollution significantly increases nocturnal vigilance in peahens. Furthermore, the birds faced a trade-off between vigilance and sleep at night: peahens that were more vigilant spent less time sleeping. Given the choice, peahens preferred to roost away from high levels of artificial lighting but showed no preference for roosting without artificial lighting or with low levels of artificial lighting. Our study demonstrates that light pollution can have a substantial impact on animal behavior that can potentially result in fitness consequences. creator: Jessica L. Yorzinski creator: Sarah Chisholm creator: Sydney D Byerley creator: Jeanee R. Coy creator: Aisyah Aziz creator: Jamie A. Wolf creator: Amanda C. Gnerlich uri: https://doi.org/10.7717/peerj.1174 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Yorzinski et al. title: A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications link: https://peerj.com/articles/1171 last-modified: 2015-08-13 description: Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features.Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively.Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an “anterodorsal tympanic sinus” not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group ‘Allodaposuchia’ at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae.Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high-specialized auditory system. Further, the large cranial cavities could help to reduce the weight of the cranium. Concerning the postcranial skeleton, Allodaposuchus hulki shows massive and robust vertebrae and forelimb bones, suggesting it could have a bulky body. The myological study performed on the anterior limb elements supports this interpretation. In addition, several bone and muscular features seem to point at a semi-erected position of the forelimbs during terrestrial locomotion. Taking all the above results into consideration, it seems plausible to suggest that A. hulki could conduct large incursions out of the water and have a semi-terrestrial lifestyle. creator: Alejandro Blanco creator: Josep Fortuny creator: Alba Vicente creator: Àngel H. Luján creator: Jordi Alexis García-Marçà creator: Albert G. Sellés uri: https://doi.org/10.7717/peerj.1171 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Blanco et al. title: Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway link: https://peerj.com/articles/1161 last-modified: 2015-08-13 description: Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those from Scandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012–0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018–0.022). The NJ tree does not show evidence of any single clades grouping together all individuals from the same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations. creator: Irene Pellegrino creator: Marco Cucco creator: Arne Follestad creator: Mathieu Boos uri: https://doi.org/10.7717/peerj.1161 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pellegrino et al. title: Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda) link: https://peerj.com/articles/1167 last-modified: 2015-08-13 description: In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae. creator: Sammy De Grave creator: Charles H.J.M. Fransen creator: Timothy J. Page uri: https://doi.org/10.7717/peerj.1167 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 De Grave et al. title: An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago link: https://peerj.com/articles/1160 last-modified: 2015-08-13 description: Background. The Cretaceous of southern Europe was characterized by an archipelago setting with faunas of mixed composition of endemic, Laurasian and Gondwanan elements. However, little is known about the relative timing of these faunal influences. The Lower Cretaceous of East-Central Europe holds a great promise for understanding the biogeographic history of Cretaceous European biotas because of the former proximity of the area to Gondwana (as part of the Apulian microcontinent). However, East-Central European vertebrates are typically poorly known from this time period. Here, we report on a ziphodont crocodyliform tooth discovered in the Lower Cretaceous (Albian) Alsópere Bauxite Formation of Olaszfalu, western Hungary.Methods. The morphology of the tooth is described and compared with that of other similar Cretaceous crocodyliforms.Results. Based on the triangular, slightly distally curved, constricted and labiolingually flattened crown, the small, subequal-sized true serrations on the carinae mesially and distally, the longitudinal fluting labially, and the extended shelves along the carinae lingually the tooth is most similar to some peirosaurid, non-baurusuchian sebecosuchian, and uruguaysuchid notosuchians. In addition, the paralligatorid Wannchampsus also possesses similar anterior teeth, thus the Hungarian tooth is referred here to Mesoeucrocodylia indet.Discussion. Supposing a notosuchian affinity, this tooth is the earliest occurrence of the group in Europe and one of the earliest in Laurasia. In case of a paralligatorid relationship the Hungarian tooth would represent their first European record, further expanding their cosmopolitan distribution. In any case, the ziphodont tooth from the Albian bauxite deposit of western Hungary belongs to a group still unknown from the Early Cretaceous European archipelago and therefore implies a hidden diversity of crocodyliforms in the area. creator: Attila Ősi creator: Márton Rabi creator: László Makádi uri: https://doi.org/10.7717/peerj.1160 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ősi et al. title: Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua) link: https://peerj.com/articles/1153 last-modified: 2015-08-13 description: The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen. creator: Lisa A. Beirn creator: Ruying Wang creator: Bruce B. Clarke creator: Jo Anne Crouch uri: https://doi.org/10.7717/peerj.1153 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: To beat or not to beat a tick: comparison of DNA extraction methods for ticks (Ixodes scapularis) link: https://peerj.com/articles/1147 last-modified: 2015-08-13 description: Background. Blacklegged ticks (Ixodes scapularis) are important disease vectors in the United States, known to transmit a variety of pathogens to humans, including bacteria, protozoa, and viruses. Their importance as a disease vector necessitates reliable and comparable methods for extracting microbial DNA from ticks. Furthermore, to explore the population genetics or genomics of this tick, appropriate DNA extraction techniques are needed for both the vector and its microbes. Although a few studies have investigated different methods of DNA isolation from ticks, they are limited in the number and types of DNA extraction and lack species-specific quantification of DNA yield.Methods. Here we determined the most efficient and consistent method of DNA extraction from two different developmental stages of I. scapularis—nymph and adult—that are the most important for disease transmission. We used various methods of physical disruption of the hard, chitinous exoskeleton, as well as commercial and non-commercial DNA isolation kits. To gauge the effectiveness of these methods, we quantified the DNA yield and confirmed the DNA quality via PCR of both tick and microbial genetic material.Results. DNA extraction using the Thermo GeneJET Genomic DNA Purification Kit resulted in the highest DNA yields and the most consistent PCR amplification when combined with either cutting or bead beating with select matrices across life stages. DNA isolation methods using ammonium hydroxide as well as the MoBio PowerSoil kit also produced strong and successful PCR amplification, but only for females.Discussion. We contrasted a variety of readily available methods of DNA extraction from single individual blacklegged ticks and presented the results through a quantitative and qualitative assessment. creator: Alyssa D. Ammazzalorso creator: Christine P. Zolnik creator: Thomas J. Daniels creator: Sergios-Orestis Kolokotronis uri: https://doi.org/10.7717/peerj.1147 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ammazzalorso et al. title: Rapid eye movement-sleep is reduced in patients with acute uncomplicated diverticulitis—an observational study link: https://peerj.com/articles/1146 last-modified: 2015-08-13 description: Introduction. Sleep disturbances are commonly found in patients in the postoperative period. Sleep disturbances may give rise to several complications including cardiopulmonary instability, transient cognitive dysfunction and prolonged convalescence. Many factors including host inflammatory responses are believed to cause postoperative sleep disturbances, as inflammatory responses can alter sleep architecture through cytokine-brain interactions. Our aim was to investigate alteration of sleep architecture during acute infection and its relationships to inflammation and clinical symptoms.Materials & Methods. In this observational study, we included patients with acute uncomplicated diverticulitis as a model to investigate the isolated effects of inflammatory responses on sleep. Eleven patients completed the study. Patients were admitted and treated with antibiotics for two nights, during which study endpoints were measured by polysomnography recordings, self-reported discomfort scores and blood samples of cytokines. One month later, the patients, who now were in complete remission, were readmitted and the endpoints were re-measured (the baseline values).Results. Total sleep time was reduced 4% and 7% the first (p = 0.006) and second (p = 0.014) nights of diverticulitis, compared to baseline, respectively. The rapid eye movement sleep was reduced 33% the first night (p = 0.016), compared to baseline. Moreover, plasma IL-6 levels were correlated to non-rapid eye movement sleep, rapid eye movement sleep and fatigue.Conclusion. Total sleep time and rapid eye movement sleep were reduced during nights with active diverticulitis and correlated with markers of inflammation. creator: Chenxi Huang creator: Mahdi Alamili creator: Claus Henrik Nielsen creator: Jacob Rosenberg creator: Ismail Gögenur uri: https://doi.org/10.7717/peerj.1146 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Huang et al. title: Seasonal variation in microhabitat of salamanders: environmental variation or shift of habitat selection? link: https://peerj.com/articles/1122 last-modified: 2015-08-13 description: Relationships between species and their habitats are not always constant. Different processes may determine changes in species-habitat association: individuals may prefer different habitat typologies in different periods, or they may be forced to occupy a different habitat in order to follow the changing environment. The aim of our study was to assess whether cave salamanders change their habitat association pattern through the year, and to test whether such changes are determined by environmental changes or by changes in preferences. We monitored multiple caves in Central Italy through one year, and monthly measured biotic and abiotic features of microhabitat and recorded Italian cave salamanders distribution. We used mixed models and niche similarity tests to assess whether species-habitat relationships remain constant through the year. Microhabitat showed strong seasonal variation, with the highest variability in the superficial sectors. Salamanders were associated to relatively cold and humid sectors in summer, but not during winter. Such apparent shift in habitat preferences mostly occurred because the environmental gradient changed through the year, while individuals generally selected similar conditions. Nevertheless, juveniles were more tolerant to dry sectors during late winter, when food demand was highest. This suggests that tolerance for suboptimal abiotic conditions may change through time, depending on the required resources. Differences in habitat use are jointly determined by environmental variation through time, and by changes in the preferred habitat. The trade-offs between tolerance and resources requirement are major determinant of such variation. creator: Enrico Lunghi creator: Raoul Manenti creator: Gentile Francesco Ficetola uri: https://doi.org/10.7717/peerj.1122 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lunghi et al. title: Wireless laptop-based phonocardiograph and diagnosis link: https://peerj.com/articles/1178 last-modified: 2015-08-11 description: Auscultation is used to evaluate heart health, and can indicate when it’s needed to refer a patient to a cardiologist. Advanced phonocardiograph (PCG) signal processing algorithms are developed to assist the physician in the initial diagnosis but they are primarily designed and demonstrated with research quality equipment. Therefore, there is a need to demonstrate the applicability of those techniques with consumer grade instrument. Furthermore, routine monitoring would benefit from a wireless PCG sensor that allows continuous monitoring of cardiac signals of patients in physical activity, e.g., treadmill or weight exercise. In this work, a low-cost portable and wireless healthcare monitoring system based on PCG signal is implemented to validate and evaluate the most advanced algorithms. Off-the-shelf electronics and a notebook PC are used with MATLAB codes to record and analyze PCG signals which are collected with a notebook computer in tethered and wireless mode. Physiological parameters based on the S1 and S2 signals and MATLAB codes are demonstrated. While the prototype is based on MATLAB, the later is not an absolute requirement. creator: Amy T. Dao uri: https://doi.org/10.7717/peerj.1178 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Dao title: Enigmatic declines in bird numbers in lowland forest of eastern Ecuador may be a consequence of climate change link: https://peerj.com/articles/1177 last-modified: 2015-08-11 description: Bird populations have declined in many parts of the world but most of those declines can be attributed to effects of human activities (e.g., habitat fragmentation); declines in areas unaffected by human activities are not common. We have been sampling bird populations at an undisturbed site in lowland forest of eastern Ecuador annually since 2001 using a combination of mist nets and direct observations on two 100-ha plots. Bird numbers fluctuated on both plots during the first 8 years but did not show a consistent pattern of change. Since about 2008, numbers of birds on both plots have declined; capture rates in 2014 were ∼40% less than at the start of the study and observation rates were ∼50% less. Both understory and canopy species declined in abundance. Overall, insectivores showed the most pronounced declines but declines varied among trophic groups. The period from 2008 onward also was a period of stronger La Niña events which, at this study site, are associated with increased rainfall. The mechanism for the declines is not known but likely reflects a combination of reduced reproductive success coupled with reduced survival associated with changing climate. creator: John G. Blake creator: Bette A. Loiselle uri: https://doi.org/10.7717/peerj.1177 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Blake and Loiselle title: A novel biomechanical analysis of gait changes in the MPTP mouse model of Parkinson’s disease link: https://peerj.com/articles/1175 last-modified: 2015-08-11 description: Parkinson’s disease (PD) is an age-associated neurodegenerative disorder hallmarked by a loss of mesencephalic dopaminergic neurons. Accurate recapitulation of the PD movement phenotype in animal models of the disease is critical for understanding disease etiology and developing novel therapeutic treatments. However, most existing behavioral assays currently applied to such animal models fail to adequately detect and subsequently quantify the subtle changes associated with the progressive stages of PD. In this study, we used a video-based analysis system to develop and validate a novel protocol for tracking locomotor performance in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. We anticipated that (1) treated mice should use slower, shorter, and less frequent strides and (2) that gait deficits should monotonically increase following MPTP administration, as the effects of neurodegeneration become manifest. Video-based biomechanical analyses, utilizing behavioral measures motivated by the comparative biomechanics literature, were used to quantify gait dynamics over a seven-day period following MPTP treatment. Analyses revealed shuffling behaviors consistent with the gait symptoms of advanced PD in humans. Here we also document dramatic gender-based differences in locomotor performance during the progression of the MPTP-induced lesion, despite male and female mice showing similar losses of striatal dopaminergic cells following MPTP administration. Whereas female mice appeared to be protected against gait deficits, males showed multiple changes in gait kinematics, consistent with the loss of locomotor agility and stability. Overall, these data show that the novel video analysis protocol presented here is a robust method capable of detecting subtle changes in gait biomechanics in a mouse model of PD. Our findings indicate that this method is a useful means by which to easily and economically screen preclinical therapeutic compounds for protecting against or reversing neuropathology associated with PD neurodegeneration. creator: Werner J. Geldenhuys creator: Tamara L. Guseman creator: Ilse S. Pienaar creator: Dean E. Dluzen creator: Jesse W. Young uri: https://doi.org/10.7717/peerj.1175 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Geldenhuys et al. title: Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution link: https://peerj.com/articles/1172 last-modified: 2015-08-11 description: Almost all extant testudinids are highly associated with terrestrial habitats and the few tortoises with high affinity to aquatic environments are found within the genus Manouria. Manouria belongs to a clade which forms a sister taxon to all remaining tortoises and is suitable as a model for studying evolutionary transitions within modern turtles. We analysed the feeding behaviour of Manouria emys and due to its phylogenetic position, we hypothesise that the species might have retained some ancestral features associated with an aquatic lifestyle. We tested whether M. emys is able to feed both in aquatic and terrestrial environments. In fact, M. emys repetitively tried to reach submerged food items in water, but always failed to grasp them—no suction feeding mechanism was applied. When feeding on land, M. emys showed another peculiar behaviour; it grasped food items by its jaws—a behaviour typical for aquatic or semiaquatic turtles—and not by the tongue as generally accepted as the typical feeding mode in all tortoises studied so far. In M. emys, the hyolingual complex remained retracted during all food uptake sequences, but the food transport was entirely lingual based. The kinematical profiles significantly differed from those described for other tortoises and from those proposed from the general models on the function of the feeding systems in lower tetrapods. We conclude that the feeding behaviour of M. emys might reflect a remnant of the primordial condition expected in the aquatic ancestor of the tortoises. creator: Nikolay Natchev creator: Nikolay Tzankov creator: Ingmar Werneburg creator: Egon Heiss uri: https://doi.org/10.7717/peerj.1172 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Natchev et al. title: Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla link: https://peerj.com/articles/1159 last-modified: 2015-08-11 description: Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer. creator: Nicole M. Kollars creator: Stacy A. Krueger-Hadfield creator: James E. Byers creator: Thomas W. Greig creator: Allan E. Strand creator: Florian Weinberger creator: Erik E. Sotka uri: https://doi.org/10.7717/peerj.1159 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kollars et al. title: Selection in the dopamine receptor 2 gene: a candidate SNP study link: https://peerj.com/articles/1149 last-modified: 2015-08-11 description: Dopamine is a major neurotransmitter in the human brain and is associated with various diseases. Schizophrenia, for example, is treated by blocking the dopamine receptors type 2. Shaner, Miller & Mintz (2004) stated that schizophrenia was the low fitness variant of a highly variable mental trait. We therefore explore whether the dopamine receptor 2 gene (DRD2) underwent any selection processes. We acquired genotype data of the 1,000 Genomes project (phase I), which contains 1,093 individuals from 14 populations. We included single nucleotide polymorphisms (SNPs) with two minor allele frequencies (MAFs) in the analysis: MAF over 0.05 and over 0.01. This is equivalent to 151 SNPs (MAF > 0.05) and 246 SNPs (MAF > 0.01) for DRD2. We used two different approaches (an outlier approach and a Bayesian approach) to detect loci under selection. The combined results of both approaches yielded nine (MAF > 0.05) and two candidate SNPs (MAF > 0.01), under balancing selection. We also found weak signs for directional selection on DRD2, but in our opinion these were too weak to draw any final conclusions on directional selection in DRD2. All candidates for balancing selection are in the intronic region of the gene and only one (rs12574471) has been mentioned in the literature. Two of our candidate SNPs are located in specific regions of the gene: rs80215768 lies within a promoter flanking region and rs74751335 lies within a transcription factor binding site. We strongly encourage research on our candidate SNPs and their possible effects. creator: Tobias Göllner creator: Martin Fieder uri: https://doi.org/10.7717/peerj.1149 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Göllner and Fieder title: Field-measured drag area is a key correlate of level cycling time trial performance link: https://peerj.com/articles/1144 last-modified: 2015-08-11 description: Drag area (Ad) is a primary factor determining aerodynamic resistance during level cycling and is therefore a key determinant of level time trial performance. However, Ad has traditionally been difficult to measure. Our purpose was to determine the value of adding field-measured Ad as a correlate of level cycling time trial performance. In the field, 19 male cyclists performed a level (22.1 km) time trial. Separately, field-determined Ad and rolling resistance were calculated for subjects along with projected frontal area assessed directly (AP) and indirectly (Est AP). Also, a graded exercise test was performed to determine $\dot {V}{O}_{2}$V̇O2 peak, lactate threshold (LT), and economy. $\dot {V}{O}_{2}$V̇O2 peak ($\mathrm{l}~\min ^{-1}$lmin−1) and power at LT were significantly correlated to power measured during the time trial (r = 0.83 and 0.69, respectively) but were not significantly correlated to performance time (r = − 0.42 and −0.45). The correlation with performance time improved significantly (p < 0.05) when these variables were normalized to Ad. Of note, Ad alone was better correlated to performance time (r = 0.85, p < 0.001) than any combination of non-normalized physiological measure. The best correlate with performance time was field-measured power output during the time trial normalized to Ad (r = − 0.92). AP only accounted for 54% of the variability in Ad. Accordingly, the correlation to performance time was significantly lower using power normalized to AP (r = − 0.75) or Est AP (r = − 0.71). In conclusion, unless normalized to Ad, level time trial performance in the field was not highly correlated to common laboratory measures. Furthermore, our field-measured Ad is easy to determine and was the single best predictor of level time trial performance. creator: James E. Peterman creator: Allen C. Lim creator: Ryan I. Ignatz creator: Andrew G. Edwards creator: William C. Byrnes uri: https://doi.org/10.7717/peerj.1144 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Peterman et al. title: Prey type and foraging ecology of Sanderlings Calidris alba in different climate zones: are tropical areas more favourable than temperate sites? link: https://peerj.com/articles/1125 last-modified: 2015-08-11 description: Sanderlings (Calidris alba) are long-distance migratory shorebirds with a non-breeding range that spans temperate and tropical coastal habitats. Breeding in the High Arctic combined with non-breeding seasons in the tropics necessitate long migrations, which are energetically demanding. On an annual basis, the higher energy expenditures during migration might pay off if food availability in the tropics is higher than at temperate latitudes. We compared foraging behaviour of birds at a north temperate and a tropical non-breeding site in the Netherlands and Ghana, respectively. In both cases the birds used similar habitats (open beaches), and experienced similar periods of daylight, which enabled us to compare food abundance and availability, and behavioural time budgets and food intake. During the non-breeding season, Sanderlings in the Netherlands spent 79% of their day foraging; in Ghana birds spent only 38% of the daytime period foraging and the largest proportion of their time resting (58%). The main prey item in the Netherlands was the soft-bodied polychaete Scolelepis squamata, while Sanderlings in Ghana fed almost exclusively on the bivalve Donax pulchellus, which they swallowed whole and crushed internally. Average availability of polychaete worms in the Netherlands was 7.4 g ash free dry mass (AFDM) m−2, which was one tenth of the 77.1 g AFDM m−2 estimated for the beach in Ghana. In the tropical environment of Ghana the Sanderlings combined relatively low energy requirements with high prey intake rates (1.64 mg opposed to 0.13 mg AFDM s−1 for Ghana and the Netherlands respectively). Although this may suggest that the Ghana beaches are the most favourable environment, processing the hard-shelled bivalve (D. pulchellus) which is the staple food could be costly. The large amount of daytime spent resting in Ghana may be indicative of the time needed to process the shell fragments, rather than indicate rest. creator: Kirsten Grond creator: Yaa Ntiamoa-Baidu creator: Theunis Piersma creator: Jeroen Reneerkens uri: https://doi.org/10.7717/peerj.1125 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Grond et al. title: Choosing mates based on the diet of your ancestors: replication of non-genetic assortative mating in Drosophila melanogaster link: https://peerj.com/articles/1173 last-modified: 2015-08-06 description: Assortative mating has been a focus of considerable research because of its potential to influence biodiversity at many scales. Sharon et al. (2010) discovered that an inbred strain of Drosophila melanogaster mated assortatively based on the diet of previous generations, leading to initial reproductive isolation without genetic evolution. This behavior was reproduced by manipulating the microbiome independently of the diet, pointing to extracellular bacterial symbionts as the assortative mating cue. To further investigate the biological significance of this result, we attempted to reproduce this phenomenon in an independent laboratory using different genotypes and additional mating assays. Supporting the previous result, we found that a different inbred strain also mated assortatively based on the diets of previous generations. However, we were unable to generate assortative mating in an outbred strain from North Carolina. Our results support the potential for non-genetic mechanisms to influence reproductive isolation, but additional work is needed to investigate the importance of this mechanism in natural populations of Drosophila. creator: Michael A. Najarro creator: Matt Sumethasorn creator: Alexandra Lamoureux creator: Thomas L. Turner uri: https://doi.org/10.7717/peerj.1173 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Najarro et al. title: Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific link: https://peerj.com/articles/1170 last-modified: 2015-08-06 description: Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella) caerulea from the Caribbean to Palmyra Atoll via Hawaiʻi using morphological characteristics and genetic analyses based on one nuclear (18s rDNA) and three mitochondrial (COI, the barcoding COI extension (COI ext.) and rnl rDNA) markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68%) between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawaiʻi and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawaiʻi remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms. creator: Ingrid S. Knapp creator: Zac H. Forsman creator: Gareth J. Williams creator: Robert J. Toonen creator: James J. Bell uri: https://doi.org/10.7717/peerj.1170 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Knapp et al. title: Sight or smell? Behavioural and heart rate responses in subordinate rainbow trout exposed to cues from dominant fish link: https://peerj.com/articles/1169 last-modified: 2015-08-06 description: Many animals, including fish, can utilize both vision and the chemical senses in intra-specific communication. However, the relative influence of these sensory modalities on behavioral and physiological responses in social interactions is not well understood. The aim of this study was therefore to investigate the relative effects of visual and chemical stimuli from dominant individuals on the behavioral and physiological responses of subordinate rainbow trout (Oncorhynchus mykiss). External electrodes were used to detect ECG signals from free-swimming fish. This method allowed the simultaneous recording of behavioral and physiological responses, and possible sex differences in these responses were also investigated. The results suggest that, in this context, visual cues are more important than chemical cues in settling the social hierarchy in rainbow trout because a combination of chemical and visual exposure generally yielded a response in focal fish that was similar to the response elicited by visual exposure alone. Both activity and physiological responses were most pronounced during the first ten seconds after exposure, with subordinate fish moving closer to the dominant, accompanied by a strong bradycardic response. Furthermore, females acted more boldly and moved closer to the dominant fish than males, but here the effect of the modes was additive, with a stronger effect of the combined visual and chemical exposure. Overall, the extra information furnished to the fish in the form of chemical cues did not change either the behavioral or the physiological response. This result suggests that visual cues are more important than chemically mediated ones for social communication and individual recognition in rainbow trout. creator: Johan Höjesjö creator: Michael Axelsson creator: Ronja Dahy creator: Lena Gustavsson creator: Jörgen I. Johnsson uri: https://doi.org/10.7717/peerj.1169 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Höjesjö et al. title: Non-repeatable science: assessing the frequency of voucher specimen deposition reveals that most arthropod research cannot be verified link: https://peerj.com/articles/1168 last-modified: 2015-08-06 description: Scientific findings need to be verifiable and grounded in repeatability. With specimen-level research this is in part achieved with the deposition of voucher specimens. These are labeled, curated, data-based specimens that have been deposited in a collection or museum, available for verification of the work and to ensure researchers are calling the same taxa by the same names. Voucher specimens themselves are the subject of research, from the discovery of new species by taxonomists to ecologists documenting historical records of invasive species. Our objective was to quantify the frequency of voucher specimen deposition in biodiversity and community ecology research through a survey of the peer-reviewed literature about arthropods, from 1989 until 2014. Overall rates of voucher deposition were alarmingly low, at under 25%. This rate increased significantly over time, with 35% of papers reporting on vouchers in 2014. Relative to the global mean, entomological research had a significantly higher rate of voucher deposition (46%), whereas researchers studying crustaceans deposited vouchers less than 6% of the time, significantly less than the mean. Researchers working in museums had a significantly higher frequency of voucher deposition. Our results suggest a significant culture shift about the process of vouchering specimens is required. There must be more education and mentoring about voucher specimens within laboratories and across different fields of study. Principal investigators and granting agencies need a proactive approach to ensuring specimen-level data are properly, long-term curated. Editorial boards and journals can also adopt policies to ensure papers are published only if explicit statements about the deposition of voucher specimens is provided. Although the gap is significant, achieving a higher rate of voucher specimen deposition is a worthy goal to ensure all research efforts are preserved for future generations. creator: Shaun Turney creator: Elyssa R. Cameron creator: Christopher A. Cloutier creator: Christopher M. Buddle uri: https://doi.org/10.7717/peerj.1168 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Turney et al. title: Modeling absolute differences in life expectancy with a censored skew-normal regression approach link: https://peerj.com/articles/1162 last-modified: 2015-08-06 description: Parameter estimates from commonly used multivariable parametric survival regression models do not directly quantify differences in years of life expectancy. Gaussian linear regression models give results in terms of absolute mean differences, but are not appropriate in modeling life expectancy, because in many situations time to death has a negative skewed distribution. A regression approach using a skew-normal distribution would be an alternative to parametric survival models in the modeling of life expectancy, because parameter estimates can be interpreted in terms of survival time differences while allowing for skewness of the distribution. In this paper we show how to use the skew-normal regression so that censored and left-truncated observations are accounted for. With this we model differences in life expectancy using data from the Swiss National Cohort Study and from official life expectancy estimates and compare the results with those derived from commonly used survival regression models. We conclude that a censored skew-normal survival regression approach for left-truncated observations can be used to model differences in life expectancy across covariates of interest. creator: André Moser creator: Kerri Clough-Gorr creator: Marcel Zwahlen uri: https://doi.org/10.7717/peerj.1162 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Moser et al. title: Predictors of exercise participation in ambulatory and non-ambulatory older people with multiple sclerosis link: https://peerj.com/articles/1158 last-modified: 2015-08-06 description: Background. Exercise at moderate intensity may confer neuroprotective benefits in multiple sclerosis (MS), however it has been reported that people with MS (PwMS) exercise less than national guideline recommendations. We aimed to determine predictors of moderate to vigorous exercise among a sample of older Canadians with MS who were divided into ambulatory (less disabled) and non-ambulatory (more disabled) groups.Methods. We analysed data collected as part of a national survey of health, lifestyle and aging with MS. Participants (n = 743) were Canadians over 55 years of age with MS for 20 or more years. We identified ‘a priori’ variables (demographic, personal, socioeconomic, physical health, exercise history and health care support) that may predict exercise at moderate to vigorous intensity (>6.75 metabolic equivalent hours/week). Predictive variables were entered into stepwise logistic regression until best fit was achieved.Results. There was no difference in explanatory models between ambulatory and non-ambulatory groups. The model predicting exercise included the ability to walk independently (OR 1.90, 95% CI [1.24–2.91]); low disability (OR 1.50, 95% CI [1.34–1.68] for each 10 point difference in Barthel Index score), perseverance (OR 1.17, 95% CI [1.08–1.26] for each additional point on the scale of 0–14), less fatigue (OR 2.01, 95% CI [1.32–3.07] for those in the lowest quartile), fewer years since MS diagnosis (OR 1.58, 95% CI [1.11–2.23] below the median of 23 years) and fewer cardiovascular comorbidities (OR 1.55 95% CI [1.02–2.35] one or no comorbidities). It was also notable that the factors, age, gender, social support, health care support and financial status were not predictive of exercise.Conclusions. This is the first examination of exercise and exercise predictors among older, more disabled PwMS. Disability is a major predictor of exercise participation (at moderate to vigorous levels) in both ambulatory and non-ambulatory groups suggesting that more exercise options must be developed for people with greater disability. Perseverance, fatigue, and cardiovascular comorbidities are predictors that are modifiable and potential targets for exercise adherence interventions. creator: Michelle Ploughman creator: Chelsea Harris creator: Elizabeth M. Wallack creator: Olivia Drodge creator: Serge Beaulieu creator: Nancy Mayo uri: https://doi.org/10.7717/peerj.1158 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ploughman et al. title: Characteristics of ambulatory care visits to family medicine specialists in Taiwan: a nationwide analysis link: https://peerj.com/articles/1145 last-modified: 2015-08-06 description: Although family medicine (FM) is the most commonly practiced specialty among all the medical specialties, its practice patterns have seldom been analyzed. Looking at data from Taiwan’s National Health Insurance Research Database, the current study analyzed ambulatory visits to FM specialists nationwide. From a sample dataset that randomly sampled one out of every 500 cases among a total of 309,880,000 visits in 2012, it was found that 18.8% (n = 116, 551) of the 619,760 visits in the dataset were made to FM specialists. Most of the FM services were performed by male FM physicians. Elderly patients above 80 years of age accounted for only 7.1% of FM visits. The most frequent diagnoses (22.8%) were associated acute upper respiratory infections (including ICD 460, 465 and 466). Anti-histamine agents were prescribed in 25.6% of FM visits. Hypertension, diabetes and dyslipidemia were the causes of 20.7% of the ambulatory visits made to FM specialists of all types, while those conditions accounted for only 10.6% of visits to FM clinics. The study demonstrated the relatively low proportion of chronic diseases that was managed in FM clinics in Taiwan, and our detailed results could contribute to evidence-based discussions on healthcare policymaking and residency training. creator: An-Min Lynn creator: Tzu-Chien Shih creator: Cheng-Hao Hung creator: Ming-Hwai Lin creator: Shinn-Jang Hwang creator: Tzeng-Ji Chen uri: https://doi.org/10.7717/peerj.1145 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lynn et al. title: Variation in phenology of hibernation and reproduction in the endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus) link: https://peerj.com/articles/1138 last-modified: 2015-08-06 description: Hibernation is a key life history feature that can impact many other crucial aspects of a species’ biology, such as its survival and reproduction. I examined the timing of hibernation and reproduction in the federally endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus), which occurs across a broad range of latitudes and elevations in the American Southwest. Data from museum specimens and field studies supported predictions for later emergence and shorter active intervals in montane populations relative to lower elevation valley populations. A low-elevation population located at Bosque del Apache National Wildlife Refuge (BANWR) in the Rio Grande valley was most similar to other subspecies of Z. hudsonius: the first emergence date was in mid-May and there was an active interval of 162 days. In montane populations of Z. h. luteus, the date of first emergence was delayed until mid-June and the active interval was reduced to ca 124–135 days, similar to some populations of the western jumping mouse (Z. princeps). Last date of immergence into hibernation occurred at about the same time in all populations (mid to late October). In montane populations pregnant females are known from July to late August and evidence suggests that they have a single litter per year. At BANWR two peaks in reproduction were expected based on similarity of active season to Z. h. preblei. However, only one peak was clearly evident, possibly due to later first reproduction and possible torpor during late summer. At BANWR pregnant females are known from June and July. Due to the short activity season and geographic variation in phenology of key life history events of Z. h. luteus, recommendations are made for the appropriate timing for surveys for this endangered species. creator: Jennifer K. Frey uri: https://doi.org/10.7717/peerj.1138 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Frey title: Space-use, movement and dispersal of sub-adult cougars in a geographically isolated population link: https://peerj.com/articles/1118 last-modified: 2015-08-06 description: Cougar (Puma concolor) observations have increased in Midwest North America, with breeding populations re-establishing in several regions east of their contemporary range. The Cypress Hills Uplands, located in southwest Saskatchewan and southeast Alberta, was recently re-colonized by cougars and now supports the easternmost confirmed breeding population of cougars in Canada. A number of factors contribute to this cougar range expansion, but it is dispersal that provides the mechanism for re-colonization of historic range. We used GPS-collar data to examine space-use and movement behavior of sub-adult cougars, the age class associated with dispersal, in the Cypress Hills. Conditional logistic regression and a two-stage modeling approach were used to estimate resource selection functions (RSF) of sub-adult cougars during two distinct ranging behaviors: transient movements (i.e., dispersal and exploratory forays) and localizing movements (i.e., temporary home ranges). Linear regression was used to model movement rates, measured as the distance between consecutive 3-h GPS-relocations, of sub-adult cougars relative to different habitats, times of day and between transient and localizing behavior. All individual sub-adult cougars displayed bouts of transient and localizing behavior. All male cougars dispersed from their natal ranges and travelled considerably farther distances than female cougars. One male dispersed over 750 km eastward through the agricultural belt of northern Montana and southern Saskatchewan. Males occupied temporary home ranges in more open habitats on the fringes of the insular Cypress Hills, while females appeared to be recruited into the adult population, occupying treed habitat that provided more suitable cover. During both ranging behaviors, sub-adult cougars selected for rugged terrain and proximity to hydrological features (likely supporting riparian habitats) and avoided open cover types. Differences in habitat selection between ranging behaviors were observed in response to open water, roads and elevation. Although certain habitat characteristics were preferred, transient and localizing cougars used fast-paced nocturnal movements and shortened daytime movements when traversing open habitats to effectively limit their residency and exposure in less-suitable landscapes. Additionally, cougars moved greater distances at night during transient behavior compared to localizing behavior indicating cougars used cover of darkness to traverse novel terrain. In doing so, sub-adult cougars can successfully disperse several hundred kilometres across a matrix of open habitat in search of resources and mates. creator: Carl D. Morrison creator: Mark S. Boyce creator: Scott E. Nielsen uri: https://doi.org/10.7717/peerj.1118 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Morrison et al. title: Whole genome sequencing enables the characterization of BurI, a LuxI homologue of Burkholderia cepacia strain GG4 link: https://peerj.com/articles/1117 last-modified: 2015-08-06 description: Quorum sensing is a mechanism for regulating proteobacterial gene expression in response to changes in cell population. In proteobacteria, N-acyl homoserine lactone (AHL) appears to be the most widely used signalling molecules in mediating, among others, the production of extracellular virulence factors for survival. In this work, the genome of B. cepacia strain GG4, a plasmid-free strain capable of AHL synthesis was explored. In silico analysis of the 6.6 Mb complete genome revealed the presence of a LuxI homologue which correspond to Type I quorum sensing. Here, we report the molecular cloning and characterization of this LuxI homologue, designated as BurI. This 609 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was approximately 25 kDa and is highly similar to several autoinducer proteins of the LuxI family among Burkholderia species. To verify the AHL synthesis activity of this protein, high resolution liquid chromatography-mass spectrometry analysis revealed the production of 3-oxo-hexanoylhomoserine lactone, N-octanoylhomoserine lactone and 3-hydroxy-octanoylhomoserine lactone from induced E. coli BL21 harboring the recombinant BurI. Our data show, for the first time, the cloning and characterization of the LuxI homologue from B. cepacia strain GG4 and confirmation of its AHL synthesis activity. creator: Kah Yan How creator: Kar Wai Hong creator: Kok-Gan Chan uri: https://doi.org/10.7717/peerj.1117 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 How et al. title: Allantoin ameliorates chemically-induced pancreatic β-cell damage through activation of the imidazoline I3 receptors link: https://peerj.com/articles/1105 last-modified: 2015-08-06 description: Objective. Allantoin is the primary active compound in yams (Dioscorea spp.). Recently, allantoin has been demonstrated to activate imidazoline 3 (I3) receptors located in pancreatic tissues. Thus, the present study aimed to investigate the role of allantoin in the effect to improve damage induced in pancreatic β-cells by streptozotocin (STZ) via the I3 receptors.Research Design and Methods. The effect of allantoin on STZ-induced apoptosis in pancreatic β-cells was examined using the ApoTox-Glo triplex assay, live/dead cell double staining assay, flow cytometric analysis, and Western blottings. The potential mechanism was investigated using KU14R: an I3 receptor antagonist, and U73122: a phospholipase C (PLC) inhibitor. The effects of allantoin on serum glucose and insulin secretion were measured in STZ-treated rats.Results. Allantoin attenuated apoptosis and cytotoxicity and increased the viability of STZ-induced β-cells in a dose-dependent manner; this effect was suppressed by KU14R and U73112. Allantoin decreased the level of caspase-3 and increased the level of phosphorylated B-cell lymphoma 2 (Bcl-2) expression detected by Western blotting. The improvement in β-cells viability was confirmed using flow cytometry analysis. Daily injection of allantoin for 8 days in STZ-treated rats significantly lowered plasma glucose and increased plasma insulin levels. This action was inhibited by treatment with KU14R.Conclusion. Allantoin ameliorates the damage of β-cells induced by STZ. The blockade by pharmacological inhibitors indicated that allantoin can activate the I3 receptors through a PLC-related pathway to decrease this damage. Therefore, allantoin and related analogs may be effective in the therapy for β-cell damage. creator: Marie Amitani creator: Kai-Chun Cheng creator: Akihiro Asakawa creator: Haruka Amitani creator: Timothy Sean Kairupan creator: Nanami Sameshima creator: Toshiaki Shimizu creator: Teruto Hashiguchi creator: Akio Inui uri: https://doi.org/10.7717/peerj.1105 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Amitani et al. title: Correlates of condom use among female sex workers in The Gambia: results of a cross-sectional survey link: https://peerj.com/articles/1076 last-modified: 2015-08-06 description: Objectives. This study examined correlates of condom use among 248 female sex workers (FSW) in The Gambia.Methods. Between July and August 2011, FSW in The Gambia who were older than 16 years of age, the age of consent in The Gambia, were recruited for the study using venue-based sampling and snowball sampling, beginning with seeds who were established clients with the Network of AIDS Services Organizations. To be eligible, FSW must have reported selling sex for money, favors, or goods in the past 12 months. Bivariate and multivariate logistic regressions were used to determine associations and the relative odds of the independent variables with condom use. Four different condom use dependent variables were used: consistent condom use in the past six months during vaginal or anal sex with all clients and partners; consistent condom use in the past month during vaginal sex with new clients; consistent condom use in the past month during vaginal sex with nonpaying partners (including boyfriends, husbands, or casual sexual partners); and condom use at last vaginal or anal sex with a nonpaying partner.Results. Many FSW (67.34%, n = 167) reported it was not at all difficult to negotiate condom use with clients in all applicable situations, and these FSW were more likely to report consistent condom use with all clients and partners in the past 6 months (aOR 3.47, 95% CI [1.70–7.07]) compared to those perceiving any difficulty in condom negotiation. In addition, FSW were more likely to report using condoms in the past month with new clients (aOR 8.04, 95% CI [2.11–30.65]) and in the past month with nonpaying partners (aOR 2.93, 95% CI [1.09–7.89]) if they had been tested for HIV in the past year. Women who bought all their condoms were less likely than those who received all of their condoms for free (aOR 0.38, 95% CI [0.15–0.97]) to have used a condom at last vaginal or anal sex with a nonpaying partner.Conclusions. HIV and sexually transmitted infection (STI) prevention interventions for FSW should aim to improve condom negotiation self-efficacy since women who report less difficulty negotiating condom use are more likely to use condoms with clients. Interventions should also be aimed at structural issues such as increasing access to free condoms and HIV testing since these were positively associated with condom use among FSW. creator: Ashley L. Grosso creator: Esther L. Lei creator: Sosthenes C. Ketende creator: Sarah Peitzmeier creator: Krystal Mason creator: Nuha Ceesay creator: Daouda Diouf creator: Fatou Maria Drame creator: Jaegan Loum creator: Erin Papworth creator: Stefan Baral uri: https://doi.org/10.7717/peerj.1076 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Grosso et al. title: Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree link: https://peerj.com/articles/1066 last-modified: 2015-08-06 description: Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways. creator: Nagesh A. Kuravadi creator: Vijay Yenagi creator: Kannan Rangiah creator: HB Mahesh creator: Anantharamanan Rajamani creator: Meghana D. Shirke creator: Heikham Russiachand creator: Ramya Malarini Loganathan creator: Chandana Shankara Lingu creator: Shilpa Siddappa creator: Aishwarya Ramamurthy creator: BN Sathyanarayana creator: Malali Gowda uri: https://doi.org/10.7717/peerj.1066 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kuravadi et al. title: Functional flexibility in wild bonobo vocal behaviour link: https://peerj.com/articles/1124 last-modified: 2015-08-04 description: A shared principle in the evolution of language and the development of speech is the emergence of functional flexibility, the capacity of vocal signals to express a range of emotional states independently of context and biological function. Functional flexibility has recently been demonstrated in the vocalisations of pre-linguistic human infants, which has been contrasted to the functionally fixed vocal behaviour of non-human primates. Here, we revisited the presumed chasm in functional flexibility between human and non-human primate vocal behaviour, with a study on our closest living primate relatives, the bonobo (Pan paniscus). We found that wild bonobos use a specific call type (the “peep”) across a range of contexts that cover the full valence range (positive-neutral-negative) in much of their daily activities, including feeding, travel, rest, aggression, alarm, nesting and grooming. Peeps were produced in functionally flexible ways in some contexts, but not others. Crucially, calls did not vary acoustically between neutral and positive contexts, suggesting that recipients take pragmatic information into account to make inferences about call meaning. In comparison, peeps during negative contexts were acoustically distinct. Our data suggest that the capacity for functional flexibility has evolutionary roots that predate the evolution of human speech. We interpret this evidence as an example of an evolutionary early transition away from fixed vocal signalling towards functional flexibility. creator: Zanna Clay creator: Jahmaira Archbold creator: Klaus Zuberbühler uri: https://doi.org/10.7717/peerj.1124 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Clay et al. title: Awake fMRI reveals a specialized region in dog temporal cortex for face processing link: https://peerj.com/articles/1115 last-modified: 2015-08-04 description: Recent behavioral evidence suggests that dogs, like humans and monkeys, are capable of visual face recognition. But do dogs also exhibit specialized cortical face regions similar to humans and monkeys? Using functional magnetic resonance imaging (fMRI) in six dogs trained to remain motionless during scanning without restraint or sedation, we found a region in the canine temporal lobe that responded significantly more to movies of human faces than to movies of everyday objects. Next, using a new stimulus set to investigate face selectivity in this predefined candidate dog face area, we found that this region responded similarly to images of human faces and dog faces, yet significantly more to both human and dog faces than to images of objects. Such face selectivity was not found in dog primary visual cortex. Taken together, these findings: (1) provide the first evidence for a face-selective region in the temporal cortex of dogs, which cannot be explained by simple low-level visual feature extraction; (2) reveal that neural machinery dedicated to face processing is not unique to primates; and (3) may help explain dogs’ exquisite sensitivity to human social cues. creator: Daniel D. Dilks creator: Peter Cook creator: Samuel K. Weiller creator: Helen P. Berns creator: Mark Spivak creator: Gregory S. Berns uri: https://doi.org/10.7717/peerj.1115 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Dilks et al. title: Differential use of salmon by vertebrate consumers: implications for conservation link: https://peerj.com/articles/1157 last-modified: 2015-08-04 description: Salmon and other anadromous fish are consumed by vertebrates with distinct life history strategies to capitalize on this ephemeral pulse of resource availability. Depending on the timing of salmon arrival, this resource may be in surplus to the needs of vertebrate consumers if, for instance, their populations are limited by food availability during other times of year. However, the life history of some consumers enables more efficient exploitation of these ephemeral resources. Bears can deposit fat and then hibernate to avoid winter food scarcity, and highly mobile consumers such as eagles, gulls, and other birds can migrate to access asynchronous pulses of salmon availability. We used camera traps on pink, chum, and sockeye salmon spawning grounds with various run times and stream morphologies, and on individual salmon carcasses, to discern potentially different use patterns among consumers. Wildlife use of salmon was highly heterogeneous. Ravens were the only avian consumer that fed heavily on pink salmon in small streams. Eagles and gulls did not feed on early pink salmon runs in streams, and only moderately at early sockeye runs, but were the dominant consumers at late chum salmon runs, particularly on expansive river flats. Brown bears used all salmon resources far more than other terrestrial vertebrates. Notably, black bears were not observed on salmon spawning grounds despite being the most frequently observed vertebrate on roads and trails. From a conservation and management perspective, all salmon species and stream morphologies are used extensively by bears, but salmon spawning late in the year are disproportionately important to eagles and other highly mobile species that are seasonally limited by winter food availability. creator: Taal Levi creator: Rachel E. Wheat creator: Jennifer M. Allen creator: Christopher C. Wilmers uri: https://doi.org/10.7717/peerj.1157 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Levi et al. title: Sixty years of change in avian communities of the Pacific Northwest link: https://peerj.com/articles/1152 last-modified: 2015-08-04 description: Bird communities are influenced by local and regional processes. The degree to which communities are dynamic has implications for projecting responses in community composition as birds track geographic shifts of their habitats. Historic datasets offer a legacy of information that can be used to quantify changes over time in avian community composition. A rare, highly-detailed avian survey of multiple habitat types in the Willamette Valley, Oregon, was conducted in 1952. We resurveyed the same sites in 2013 and evaluated whether observed results agreed with theoretical patterns of community change. We compared alpha, beta, and gamma diversity between survey periods and evaluated shifts in categorical abundances of species. Most patterns of change were consistent with community turnover. Nearly 50% of species were replaced over six decades, with increased species richness and decreased evenness at local and regional spatial extents. Patterns of regional species turnover reflected local turnover. Evidence that local shifts in habitat type drove bird community change were not strongly supported, although historic data on habitats within study plots were limited to macro-level aerial photographs. Thus, regional factors and structural changes likely played important roles determining species composition and abundance. creator: Jenna R. Curtis creator: W. Douglas Robinson uri: https://doi.org/10.7717/peerj.1152 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Curtis and Robinson title: Intrasaccadic perception triggers pupillary constriction link: https://peerj.com/articles/1150 last-modified: 2015-08-04 description: It is commonly believed that vision is impaired during saccadic eye movements. However, here we report that some visual stimuli are clearly visible during saccades, and trigger a constriction of the eye’s pupil. Participants viewed sinusoid gratings that changed polarity 150 times per second (every 6.67 ms). At this rate of flicker, the gratings were perceived as homogeneous surfaces while participants fixated. However, the flickering gratings contained ambiguous motion: rightward and leftward motion for vertical gratings; upward and downward motion for horizontal gratings. When participants made a saccade perpendicular to the gratings’ orientation (e.g., a leftward saccade for a vertical grating), the eye’s peak velocity matched the gratings’ motion. As a result, the retinal image was approximately stable for a brief moment during the saccade, and this gave rise to an intrasaccadic percept: A normally invisible stimulus became visible when eye velocity was maximal. Our results confirm and extend previous studies by demonstrating intrasaccadic perception using a reflexive measure (pupillometry) that does not rely on subjective report. Our results further show that intrasaccadic perception affects all stages of visual processing, from the pupillary response to visual awareness. creator: Sebastiaan Mathôt creator: Jean-Baptiste Melmi creator: Eric Castet uri: https://doi.org/10.7717/peerj.1150 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Mathôt et al. title: No evidence that presence of sexually transmitted infection selects for reduced mating rate in the two spot ladybird, Adalia bipunctata link: https://peerj.com/articles/1148 last-modified: 2015-08-04 description: Sexually transmitted infections (STIs) are common in animals and plants, and frequently impair individual fertility. Theory predicts that natural selection will favour behaviours that reduce the chance of acquiring a STI. We investigated whether an STI, Coccipolipus hippodamiae has selected for increased rejection of mating by female Adalia bipunctata as a mechanism to avoid exposure. We first demonstrated that rejection of mating by females did indeed reduce the chance of acquiring the mite. We then examined whether rejection rate and mating rate differed between ladybirds from mite-present and mite-absent populations when tested in a common environment. No differences in rejection intensity or remating propensity were observed between the two populations. We therefore conclude there is no evidence that STIs have driven the evolution of female mating behaviour in this species. creator: Sophie L. Jones creator: Daria Pastok creator: Gregory D.D. Hurst uri: https://doi.org/10.7717/peerj.1148 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Jones et al. title: 210Po microsphere radiological design for tumor vascular disruption link: https://peerj.com/articles/1143 last-modified: 2015-08-04 description: The feasibility of disrupting a tumor’s vascular structure using 210Po microspheres is investigated using standard ion and photon absorbed dose methodologies. Calculated absorbed dose profiles for 210Po alpha particles are sufficient to disrupt a tumor’s arteriole structure while minimizing the dose outside the blood vessel wall. 210Po photons contribute minimal dose to healthy tissue. The requisite activity of 210Po to facilitate vascular disruption is calculated. creator: JJ Bevelacqua uri: https://doi.org/10.7717/peerj.1143 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Bevelacqua title: Remote sensing captures varying temporal patterns of vegetation between human-altered and natural landscapes link: https://peerj.com/articles/1141 last-modified: 2015-08-04 description: Global change has led to shifts in phenology, potentially disrupting species interactions such as plant–pollinator relationships. Advances in remote sensing techniques allow one to detect vegetation phenological diversity between different land use types, but it is not clear how this translates to other communities in the ecosystem. Here, we investigated the phenological diversity of the vegetation across a human-altered landscape including urban, agricultural, and natural land use types. We found that the patterns of change in the vegetation indices (EVI and NDVI) of human-altered landscapes are out of synchronization with the phenology in neighboring natural California grassland habitat. Comparing these findings to a spatio-temporal pollinator distribution dataset, EVI and NDVI were significant predictors of total bee abundance, a relationship that improved with time lags. This evidence supports the importance of differences in temporal dynamics between land use types. These findings also highlight the potential to utilize remote sensing data to make predictions for components of biodiversity that have tight vegetation associations, such as pollinators. creator: Misha Leong creator: George K. Roderick uri: https://doi.org/10.7717/peerj.1141 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Leong and Roderick title: Assessing the reproducibility of discriminant function analyses link: https://peerj.com/articles/1137 last-modified: 2015-08-04 description: Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the carefully curated research that the scientific community and public expects. creator: Rose L. Andrew creator: Arianne Y.K. Albert creator: Sebastien Renaut creator: Diana J. Rennison creator: Dan G. Bock creator: Tim Vines uri: https://doi.org/10.7717/peerj.1137 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2015 Andrew et al. title: The 2014 coral bleaching and freshwater flood events in Kāneʻohe Bay, Hawaiʻi link: https://peerj.com/articles/1136 last-modified: 2015-08-04 description: Until recently, subtropical Hawaiʻi escaped the major bleaching events that have devastated many tropical regions, but the continued increases in global long-term mean temperatures and the apparent ending of the Pacific Decadal Oscillation (PDO) cool phase have increased the risk of bleaching events. Climate models and observations predict that bleaching in Hawaiʻi will occur with increasing frequency and increasing severity over future decades. A freshwater “kill” event occurred during July 2014 in the northern part of Kāneʻohe Bay that reduced coral cover by 22.5% in the area directly impacted by flooding. A subsequent major bleaching event during September 2014 caused extensive coral bleaching and mortality throughout the bay and further reduced coral cover in the freshwater kill area by 60.0%. The high temperature bleaching event only caused a 1.0% reduction in live coral throughout the portion of the bay not directly impacted by the freshwater event. Thus, the combined impact of the low salinity event and the thermal bleaching event appears to be more than simply additive. The temperature regime during the September 2014 bleaching event was analogous in duration and intensity to that of the large bleaching event that occurred previously during August 1996, but resulted in a much larger area of bleaching and coral mortality. Apparently seasonal timing as well as duration and magnitude of heating is important. Coral spawning in the dominant coral species occurs early in the summer, so reservoirs of stored lipid in the corals had been depleted by spawning prior to the September 2014 event. Warm months above 27 °C result in lower coral growth and presumably could further decrease lipid reserves, leading to a bleaching event that was more severe than would have happened if the high temperatures occurred earlier in the summer. Hawaiian reef corals decrease skeletal growth at temperatures above 27 °C, so perhaps the “stress period” actually started long before the bleaching threshold of 29 °C was reached. Hawaiʻi is directly influenced by the PDO which may become a factor influencing bleaching events in subtropical Hawaiʻi in much the same manner as variations in the El Niño Southern Oscillation (ENSO) influences bleaching events at low latitudes in the tropical Pacific. Records show that offshore temperatures measured by satellite will not always predict inshore bleaching because other factors (high cloud cover, high wind and wave action, tidal exchange rate) can limit inshore heating and prevent temperatures in the bay from reaching the bleaching threshold. Low light levels due to cloud cover or high turbidity can also serve to prevent bleaching. creator: Keisha D. Bahr creator: Paul L. Jokiel creator: Kuʻulei S. Rodgers uri: https://doi.org/10.7717/peerj.1136 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Bahr et al. title: On reconstructing Giraffa sivalensis, an extinct giraffid from the Siwalik Hills, India link: https://peerj.com/articles/1135 last-modified: 2015-08-04 description: Giraffa sivalensis occurred during the Plio-Pleistocene period and probably represents the terminal species of the genus in Southern Asia. The holotype is an almost perfectly preserved cervical vertebra of disputed anatomical location. Although there is also uncertainty regarding this animal’s size, other specimens that have been assigned to this species include fragments of two humeri, a radius, metacarpi and teeth. Here we estimate neck length, leg length and body mass using interspecific and, unusually, ontogenetic allometry of extant giraffe skeletal parameters. The appropriateness of each equation to estimate body mass was evaluated by calculating the prediction error incurred in both extant giraffes (G. camelopardalis) and okapis (Okapia johnstoni). It followed that the equations with the lowest prediction error in both species were considered robust enough to use in G. sivalensis. The size of G. sivalensis, based on the holotype, is proposed as 400 kg (range 228 kg–575 kg), with a neck length of approximately 147 cm and a height of 390 cm. The molar lengths of tooth specimens considered agree with this size estimate. The humerus was the most appropriate long bone to establish body mass, which estimates a heavier animal of ca 790 kg. The discrepancy with the vertebral body weight estimate might indicate sexual dimorphism. Radial and metacarpal specimens estimate G. sivalensis to be as heavy as extant giraffes. This may indicate that the radius and metacarpus are unsuitable for body mass predictions in Giraffa spp. Alternatively, certain long bones may have belonged to another long legged giraffid that occurred during the same period and locality as G. sivalensis. We have concluded that if sexual dimorphism was present then males would have been about twice the size of females. If sexual dimorphism was not present and all bones were correctly attributed to this species, then G. sivalensis had a slender neck with a relatively stocky body. creator: Sybrand J. van Sittert creator: Graham Mitchell uri: https://doi.org/10.7717/peerj.1135 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 van Sittert and Mitchell title: Impact of copper toxicity on stone-head cabbage (Brassica oleracea var. capitata) in hydroponics link: https://peerj.com/articles/1119 last-modified: 2015-08-04 description: Arable soils are frequently subjected to contamination with copper as the consequence of imbalanced fertilization with manure and organic fertilizers and/or extensive use of copper-containing fungicides. In the present study, the exposure of stone-head cabbage (Brassica oleracea var. capitata) to elevated Cu2+ levels resulted in leaf chlorosis and lesser biomass yield at ≥2 µ M. Root nitrate content was not statistically affected by Cu2+ levels, although it was substantially decreased at ≥5 µ M Cu2+ in the shoot. The decrease in nitrate contents can be related to lower nitrate uptake rates because of growth inhibition by Cu-toxicity. Shoot sulfate content increased strongly at ≥2 µ M Cu2+ indicating an increase in demand for sulfur under Cu stress. Furthermore, at ≥2 µM concentration, concentration of water-soluble non-protein thiol increased markedly in the roots and to a smaller level in the shoot. When exposed to elevated concentrations of Cu2+ the improved sulfate and water-soluble non-protein thiols need further studies for the evaluation of their direct relation with the synthesis of metal-chelating compounds (i.e., phytochelatins). creator: Sajid Ali creator: Muhammad Shahbaz creator: Ahmad Naeem Shahzad creator: Hafiz Azhar Ali Khan creator: Moazzam Anees creator: Muhammad Saleem Haider creator: Ammara Fatima uri: https://doi.org/10.7717/peerj.1119 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ali et al. title: Vision in two cyprinid fish: implications for collective behavior link: https://peerj.com/articles/1113 last-modified: 2015-08-04 description: Many species of fish rely on their visual systems to interact with conspecifics and these interactions can lead to collective behavior. Individual-based models have been used to predict collective interactions; however, these models generally make simplistic assumptions about the sensory systems that are applied without proper empirical testing to different species. This could limit our ability to predict (and test empirically) collective behavior in species with very different sensory requirements. In this study, we characterized components of the visual system in two species of cyprinid fish known to engage in visually dependent collective interactions (zebrafish Danio rerio and golden shiner Notemigonus crysoleucas) and derived quantitative predictions about the positioning of individuals within schools. We found that both species had relatively narrow binocular and blind fields and wide visual coverage. However, golden shiners had more visual coverage in the vertical plane (binocular field extending behind the head) and higher visual acuity than zebrafish. The centers of acute vision (areae) of both species projected in the fronto-dorsal region of the visual field, but those of the zebrafish projected more dorsally than those of the golden shiner. Based on this visual sensory information, we predicted that: (a) predator detection time could be increased by >1,000% in zebrafish and >100% in golden shiners with an increase in nearest neighbor distance, (b) zebrafish schools would have a higher roughness value (surface area/volume ratio) than those of golden shiners, (c) and that nearest neighbor distance would vary from 8 to 20 cm to visually resolve conspecific striping patterns in both species. Overall, considering between-species differences in the sensory system of species exhibiting collective behavior could change the predictions about the positioning of individuals in the group as well as the shape of the school, which can have implications for group cohesion. We suggest that more effort should be invested in assessing the role of the sensory system in shaping local interactions driving collective behavior. creator: Diana Pita creator: Bret A. Moore creator: Luke P. Tyrrell creator: Esteban Fernández-Juricic uri: https://doi.org/10.7717/peerj.1113 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pita et al. title: Establishment of a lectotype for the species Plesiochelys langii Rütimeyer, 1873 link: https://peerj.com/articles/1108 last-modified: 2015-08-04 description: Background. In a recent paper, we proposed a lectotype for the species Plesiochelys langiiRütimeyer, 1873. However, we failed to register this publication in ZooBank as required by the International Commission on Zoological Nomenclature (ICZN) for electronic publication. Although our conclusions remain unchanged, this particular nomenclatural act cannot be considered as published under ICZN regulations.Results. The present work fulfills the requirements of the ICZN for a lectotype designation and has been registered in ZooBank. creator: Jérémy Anquetin uri: https://doi.org/10.7717/peerj.1108 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Anquetin title: Recursion to food plants by free-ranging Bornean elephant link: https://peerj.com/articles/1030 last-modified: 2015-08-04 description: Plant recovery rates after herbivory are thought to be a key factor driving recursion by herbivores to sites and plants to optimise resource-use but have not been investigated as an explanation for recursion in large herbivores. We investigated the relationship between plant recovery and recursion by elephants (Elephas maximus borneensis) in the Lower Kinabatangan Wildlife Sanctuary, Sabah. We identified 182 recently eaten food plants, from 30 species, along 14 × 50 m transects and measured their recovery growth each month over nine months or until they were re-browsed by elephants. The monthly growth in leaf and branch or shoot length for each plant was used to calculate the time required (months) for each species to recover to its pre-eaten length. Elephant returned to all but two transects with 10 eaten plants, a further 26 plants died leaving 146 plants that could be re-eaten. Recursion occurred to 58% of all plants and 12 of the 30 species. Seventy-seven percent of the re-eaten plants were grasses. Recovery times to all plants varied from two to twenty months depending on the species. Recursion to all grasses coincided with plant recovery whereas recursion to most browsed plants occurred four to twelve months before they had recovered to their previous length. The small sample size of many browsed plants that received recursion and uneven plant species distribution across transects limits our ability to generalise for most browsed species but a prominent pattern in plant-scale recursion did emerge. Plant recovery time was a good predictor of time to recursion but varied as a function of growth form (grass, ginger, palm, liana and woody) and differences between sites. Time to plant recursion coincided with plant recovery time for the elephant’s preferred food, grasses, and perhaps also gingers, but not the other browsed species. Elephants are bulk feeders so it is likely that they time their returns to bulk feed on these grass species when quantities have recovered sufficiently to meet their intake requirements. The implications for habitat and elephant management are discussed. creator: Megan English creator: Graeme Gillespie creator: Benoit Goossens creator: Sulaiman Ismail creator: Marc Ancrenaz creator: Wayne Linklater uri: https://doi.org/10.7717/peerj.1030 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 English et al.