title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2016-02 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Broad-scale sampling of primary freshwater fish populations reveals the role of intrinsic traits, inter-basin connectivity, drainage area and latitude on shaping contemporary patterns of genetic diversity link: https://peerj.com/articles/1694 last-modified: 2016-02-29 description: Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern.Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins) in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences.Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary) seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins.Discussion. Targeting multiple co-distributed species of primary freshwater fish allowed us to assess the relative role of historical versus contemporary factors affecting genetic diversity. Since different patterns were detected for species with identical distribution areas we postulate that contemporary determinants of genetic diversity (species’ intrinsic traits and landscape features) must have played a more significant role than historical factors. Implications for conservation in a context of climate change and highly disturbed habitats are detailed, namely the need to focus management and conservation actions on intraspecific genetic data and to frequently conduct combined genetic and demographic surveys. creator: Carla Sousa-Santos creator: Joana I. Robalo creator: Ana M. Pereira creator: Paulo Branco creator: José Maria Santos creator: Maria Teresa Ferreira creator: Mónica Sousa creator: Ignacio Doadrio uri: https://doi.org/10.7717/peerj.1694 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sousa-Santos et al. title: A large abelisaurid (Dinosauria, Theropoda) from Morocco and comments on the Cenomanian theropods from North Africa link: https://peerj.com/articles/1754 last-modified: 2016-02-29 description: We describe the partially preserved femur of a large-bodied theropod dinosaur from the Cenomanian “Kem Kem Compound Assemblage” (KKCA) of Morocco. The fossil is housed in the Museo Geologico e Paleontologico “Gaetano Giorgio Gemmellaro” in Palermo (Italy). The specimen is compared with the theropod fossil record from the KKCA and coeval assemblages from North Africa. The combination of a distally reclined head, a not prominent trochanteric shelf, distally placed lesser trochanter of stout, alariform shape, a stocky shaft with the fourth trochanter placed proximally, and rugose muscular insertion areas in the specimen distinguishes it from Carcharodontosaurus, Deltadromeus and Spinosaurus and supports referral to an abelisaurid. The estimated body size for the individual from which this femur was derived is comparable to Carnotaurus and Ekrixinatosaurus (up to 9 meters in length and 2 tons in body mass). This find confirms that abelisaurids had reached their largest body size in the “middle Cretaceous,” and that large abelisaurids coexisted with other giant theropods in Africa. We review the taxonomic status of the theropods from the Cenomanian of North Africa, and provisionally restrict the Linnean binomina Carcharodontosaurus iguidensis and Spinosaurus aegyptiacus to the type specimens. Based on comparisons among the theropod records from the Aptian-Cenomanian of South America and Africa, a partial explanation for the so-called “Stromer’s riddle” (namely, the coexistence of many large predatory dinosaurs in the “middle Cretaceous” record from North Africa) is offered in term of taphonomic artifacts among lineage records that were ecologically and environmentally non-overlapping. Although morphofunctional and stratigraphic evidence supports an ecological segregation between spinosaurids and the other lineages, the co-occurrence of abelisaurids and carcharodontosaurids, two groups showing several craniodental convergences that suggest direct resource competition, remains to be explained. creator: Alfio Alessandro Chiarenza creator: Andrea Cau uri: https://doi.org/10.7717/peerj.1754 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chiarenza & Cau title: How do colonial Eurasian Griffon Vultures prevent extra-pair mating? link: https://peerj.com/articles/1749 last-modified: 2016-02-29 description: In colonial breeding species, preventive measures to reduce the risks of extra-pair copulations (EPCs) should reflect the actual risk perceived by males (e.g., proximity of neighbors, intrusions into the nest) mainly during the fertile period. In colonial vultures, specific studies examining the preventive measures that minimize the risks of EPCs occurring within the competitive context of colonial breeding have not been conducted. Here we tested at Eurasian Griffon Vulture (Gyps fulvus) nesting sites the intensity of paternity assurance behavior, shown as frequency and duration of within-pair copulations (WPCs), potential mate vigilance or nest attendance, and levels of aggressivity. This was measured according to the frequency of territorial intrusions and comparison of the fertile vs. the non-fertile period. Our findings suggest that the frequency of WPCs and their duration increased significantly during the presumed fertile period, regarded as the period when Griffon pairs spent significantly more time together at their nests. In addition, low levels of territorial intrusions were observed, an aggressive response of pairs towards intruders, and a relatively high presence of pairs at the nests during the fertile period. Thus, although nesting sites are subject to low exposure to EPC attempts, the increased frequency and duration of copulations during the fertile period suggests that, under pressure from the colonial breeding system, a higher rate of copulations is the most effective preventive mechanism against relative uncertainty of paternity. creator: Joan Bertran creator: Francesc Xavier Macià creator: Antoni Margalida uri: https://doi.org/10.7717/peerj.1749 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bertran et al. title: Potential contribution of fish restocking to the recovery of deteriorated coral reefs: an alternative restoration method? link: https://peerj.com/articles/1732 last-modified: 2016-02-29 description: Counteracting the worldwide trend of coral reef degeneration is a major challenge for the scientific community. A crucial management approach to minimizing stress effects on healthy reefs and helping the recovery of disturbed reefs is reef protection. However, the current rapid decline of the world’s reefs suggests that protection might be insufficient as a viable stand-alone management approach for some reefs. We thus suggest that the ecological restoration of coral reefs (CRR) should be considered as a valid component of coral reef management, in addition to protection, if the applied method is economically applicable and scalable. This theoretical study examines the potential applicability and outcomes of restocking grazers as a restoration tool for coral reef recovery—a tool that has not been applied so far in reef restoration projects. We studied the effect of restocking grazing fish as a restoration method using a mathematical model of degrading reefs, and analyzed the financial outcomes of the restocking intervention. The results suggest that applying this restoration method, in addition to protection, can facilitate reef recovery. Moreover, our analysis suggests that the restocking approach almost always becomes profitable within several years. Considering the relatively low cost of this restoration approach and the feasibility of mass production of herbivorous fish, we suggest that this approach should be considered and examined as an additional viable restoration tool for coral reefs. creator: Uri Obolski creator: Lilach Hadany creator: Avigdor Abelson uri: https://doi.org/10.7717/peerj.1732 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Obolski et al. title: A hierarchical model of daily stream temperature using air-water temperature synchronization, autocorrelation, and time lags link: https://peerj.com/articles/1727 last-modified: 2016-02-29 description: Water temperature is a primary driver of stream ecosystems and commonly forms the basis of stream classifications. Robust models of stream temperature are critical as the climate changes, but estimating daily stream temperature poses several important challenges. We developed a statistical model that accounts for many challenges that can make stream temperature estimation difficult. Our model identifies the yearly period when air and water temperature are synchronized, accommodates hysteresis, incorporates time lags, deals with missing data and autocorrelation and can include external drivers. In a small stream network, the model performed well (RMSE = 0.59°C), identified a clear warming trend (0.63 °C decade−1) and a widening of the synchronized period (29 d decade−1). We also carefully evaluated how missing data influenced predictions. Missing data within a year had a small effect on performance (∼0.05% average drop in RMSE with 10% fewer days with data). Missing all data for a year decreased performance (∼0.6 °C jump in RMSE), but this decrease was moderated when data were available from other streams in the network. creator: Benjamin H. Letcher creator: Daniel J. Hocking creator: Kyle O’Neil creator: Andrew R. Whiteley creator: Keith H. Nislow creator: Matthew J. O’Donnell uri: https://doi.org/10.7717/peerj.1727 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: The origin of the medial circumflex femoral artery: a meta-analysis and proposal of a new classification system link: https://peerj.com/articles/1726 last-modified: 2016-02-29 description: Background and Objectives. The medial circumflex femoral artery (MCFA) is a common branch of the deep femoral artery (DFA) responsible for supplying the femoral head and the greater trochanteric fossa. The prevalence rates of MCFA origin, its branching patterns and its distance to the mid-inguinal point (MIP) vary significantly throughout the literature. The aim of this study was to determine the true prevalence of these characteristics and to study their associated anatomical and clinical relevance.Methods. A search of the major electronic databases Pubmed, EMBASE, Scopus, ScienceDirect, Web of Science, SciELO, BIOSIS, and CNKI was performed to identify all articles reporting data on the origin of the MCFA, its branching patterns and its distance to the MIP. No data or language restriction was set. Additionally, an extensive search of the references of all relevant articles was performed. All data on origin, branching and distance to MIP was extracted and pooled into a meta-analysis using MetaXL v2.0.Results. A total of 38 (36 cadaveric and 2 imaging) studies (n = 4,351 lower limbs) were included into the meta-analysis. The pooled prevalence of the MCFA originating from the DFA was 64.6% (95% CI [58.0–71.5]), while the pooled prevalence of the MCFA originating from the CFA was 32.2% (95% CI [25.9–39.1]). The CFA-derived MCFA was found to originate as a single branch in 81.1% (95% CI [70.1–91.7]) of cases with a mean pooled distance of 50.14 mm (95% CI [42.50–57.78]) from the MIP.Conclusion. The MCFA’s variability must be taken into account by surgeons, especially during orthopedic interventions in the region of the hip to prevent iatrogenic injury to the circulation of the femoral head. Based on our analysis, we present a new proposed classification system for origin of the MCFA. creator: Krzysztof A. Tomaszewski creator: Brandon M. Henry creator: Jens Vikse creator: Joyeeta Roy creator: Przemysław A. Pękala creator: Maren Svensen creator: Daniel L. Guay creator: Karolina Saganiak creator: Jerzy A. Walocha uri: https://doi.org/10.7717/peerj.1726 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tomaszewski et al. title: Identifying key conservation threats to Alpine birds through expert knowledge link: https://peerj.com/articles/1723 last-modified: 2016-02-29 description: Alpine biodiversity is subject to a range of increasing threats, but the scarcity of data for many taxa means that it is difficult to assess the level and likely future impact of a given threat. Expert opinion can be a useful tool to address knowledge gaps in the absence of adequate data. Experts with experience in Alpine ecology were approached to rank threat levels for 69 Alpine bird species over the next 50 years for the whole European Alps in relation to ten categories: land abandonment, climate change, renewable energy, fire, forestry practices, grazing practices, hunting, leisure, mining and urbanization. There was a high degree of concordance in ranking of perceived threats among experts for most threat categories. The major overall perceived threats to Alpine birds identified through expert knowledge were land abandonment, urbanization, leisure and forestry, although other perceived threats were ranked highly for particular species groups (renewable energy and hunting for raptors, hunting for gamebirds). For groups of species defined according to their breeding habitat, open habitat species and treeline species were perceived as the most threatened. A spatial risk assessment tool based on summed scores for the whole community showed threat levels were highest for bird communities of the northern and western Alps. Development of the approaches given in this paper, including addressing biases in the selection of experts and adopting a more detailed ranking procedure, could prove useful in the future in identifying future threats, and in carrying out risk assessments based on levels of threat to the whole bird community. creator: Dan E. Chamberlain creator: Paolo Pedrini creator: Mattia Brambilla creator: Antonio Rolando creator: Marco Girardello uri: https://doi.org/10.7717/peerj.1723 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chamberlain et al. title: Head capsule stacking by caterpillars: morphology complements behaviour to provide a novel defence link: https://peerj.com/articles/1714 last-modified: 2016-02-29 description: Herbivores employ a variety of chemical, behavioural and morphological defences to reduce mortality from natural enemies. In some caterpillars the head capsules of successive instars are retained and stacked on top of each other and it has been suggested that this could serve as a defence against natural enemies. We tested this hypothesis by comparing the survival of groups of the gumleaf skeletoniser Uraba lugens Walker caterpillars, allocated to one of three treatments: “−HC,” where stacked head capsules were removed from all individuals, “+HC,” where the caterpillars retained their stacked head capsules, and “mixed,” where only half of the caterpillars in a group had their stacked head capsules removed. We found no difference in predation rate between the three treatments, but within the mixed treatment, caterpillars with head capsules were more than twice as likely to survive. During predator choice trials, conducted to observe how head capsule stacking acts as a defence, the predatory pentatomid bug attacked the −HC caterpillar in four out of six trials. The two attacks on +HC caterpillars took over 10 times longer because the bug would poke its rostrum through the head capsule stack, while the caterpillar used its head capsule stack to deflect the bug’s rostrum. Our results support the hypothesis that the retention of moulted head capsules by U. lugens provides some protection against their natural enemies and suggest that this is because stacked head capsules can function as a false target for natural enemies as well as a weapon to fend off attackers. This represents the first demonstration of a defensive function. creator: Petah A. Low creator: Clare McArthur creator: Dieter F. Hochuli uri: https://doi.org/10.7717/peerj.1714 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Low et al. title: Distinguishing between enamel fluorosis and other enamel defects in permanent teeth of children link: https://peerj.com/articles/1745 last-modified: 2016-02-25 description: Background. The inconsistent prevalence of fluorosis for a given level of fluoride in drinking water suggests developmental defects of enamel (DDEs) other than fluorosis were being misdiagnosed as fluorosis. The imprecise definition and subjective perception of fluorosis indices could result in misdiagnosis of dental fluorosis. This study was conducted to distinguish genuine fluorosis from fluorosis-resembling defects that could have adverse health-related events as a cause using Early Childhood Events Life-grid method (ECEL).Methods. A study was conducted on 400 9-year-old children from areas with high, optimal and low levels of fluoride in the drinking water of Fars province, Iran. Fluorosis cases were diagnosed on the standardized one view photographs of the anterior teeth using Dean’s and TF (Thylstrup and Fejerskov) Indices by calibrated dentists. Agreements between examiners were tested. Early childhood health-related data collected retrospectively by ECEL method were matched with the position of enamel defects.Results. Using both Dean and TF indices three out of four dentists diagnosed that 31.3% (115) children had fluorosis, 58.0%, 29.1%, and 10.0% in high (2.12–2.85 ppm), optimal (0.62–1.22 ppm), and low (0.24–0.29 ppm) fluoride areas respectively (p < 0.001). After matching health-related events in the 115 (31.3%) of children diagnosed with fluorosis, 31 (8.4%) of children had fluorosis which could be matched with their adverse health-related events. This suggests that what was diagnosed as fluorosis were non-fluoride related DDEs that resemble fluorosis.Discussion. The frequently used measures of fluorosis appear to overscore fluorosis. Use of ECEL method to consider health related events relevant to DDEs could help to differentiate between genuine fluorosis and fluorosis-resembling defects. creator: Aira Sabokseir creator: Ali Golkari creator: Aubrey Sheiham uri: https://doi.org/10.7717/peerj.1745 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sabokseir et al. title: Effects of personal relevance and simulated darkness on the affective appraisal of a virtual environment link: https://peerj.com/articles/1743 last-modified: 2016-02-25 description: This study investigated whether personal relevance influences the affective appraisal of a desktop virtual environment (VE) in simulated darkness. In the real world, darkness often evokes thoughts of vulnerability, threat, and danger, and may automatically precipitate emotional responses consonant with those thoughts (fear of darkness). This influences the affective appraisal of a given environment after dark and the way humans behave in that environment in conditions of low lighting. Desktop VEs are increasingly deployed to study the effects of environmental qualities and (architectural or lighting) interventions on human behaviour and feelings of safety. Their (ecological) validity for these purposes depends critically on their ability to correctly address the user’s cognitive and affective experience. Previous studies with desktop (i.e., non-immersive) VEs found that simulated darkness only slightly affects the user’s behavioral and emotional responses to the represented environment, in contrast to the responses observed for immersive VEs. We hypothesize that the desktop VE scenarios used in previous studies less effectively induced emotional and behavioral responses because they lacked personal relevance. In addition, factors like signs of social presence and relatively high levels of ambient lighting may also have limited these responses. In this study, young female volunteers explored either a daytime or a night-time (low ambient light level) version of a desktop VE representing a deserted (no social presence) prototypical Dutch polder landscape. To enhance the personal relevance of the simulation, a fraction of the participants were led to believe that the virtual exploration tour would prepare them for a follow-up tour through the real world counterpart of the VE. The affective appraisal of the VE and the emotional response of the participants were measured through self-report. The results show that the VE was appraised as slightly less pleasant and more arousing in simulated darkness (compared to a daylight) condition, as expected. However, the fictitious follow-up assignment had no emotional effects and did not influence the affective appraisal of the VE. Further research is required to establish the qualities that may enhance the validity of desktop VEs for both etiological (e.g., the effects of signs of darkness on navigation behaviour and fear of crime) and intervention (e.g., effects of street lighting on feelings of safety) research. creator: Alexander Toet creator: Joske M. Houtkamp creator: Paul E. Vreugdenhil uri: https://doi.org/10.7717/peerj.1743 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Toet et al. title: Metamorphosis of the invasive ascidian Ciona savignyi: environmental variables and chemical exposure link: https://peerj.com/articles/1739 last-modified: 2016-02-25 description: In this study, the effects of environmental variables on larval metamorphosis of the solitary ascidian Ciona savignyi were investigated in a laboratory setting. The progression of metamorphic changes were tracked under various temperature, photoperiod, substrate, larval density, and vessel size regimes. Metamorphosis was maximised at 18 °C, 12:12 h subdued light:dark, smooth polystyrene substrate, and 10 larvae mL−1 in a twelve-well tissue culture plate. Eliminating the air-water interface by filling culture vessels to capacity further increased the proportion of metamorphosed larvae; 87 ± 5% of larvae completed metamorphosis within 5 days compared to 45 ± 5% in control wells. The effects of the reference antifouling compounds polygodial, portimine, oroidin, chlorothalonil, and tolylfluanid on C. savignyi were subsequently determined, highlighting (1) the sensitivity of C. savignyi metamorphosis to chemical exposure and (2) the potential to use C. savignyi larvae to screen for bioactivity in an optimised laboratory setting. The compounds were bioactive in the low ng mL−1 to high µg mL−1 range. Polygodial was chosen for additional investigations, where it was shown that mean reductions in the proportions of larvae reaching stage E were highly repeatable both within (repeatability = 14 ± 9%) and between (intermediate precision = 17 ± 3%) independent experiments. An environmental extract had no effect on the larvae but exposing larvae to both the extract and polygodial reduced potency relative to polygodial alone. This change in potency stresses the need for caution when working with complex samples, as is routinely implemented when isolating natural compounds from their biological source. Overall, the outcomes of this study highlight the sensitivity of C. savignyi metamorphosis to environmental variations and chemical exposure. creator: Patrick L. Cahill creator: Javier Atalah creator: Andrew I. Selwood creator: Jeanne M. Kuhajek uri: https://doi.org/10.7717/peerj.1739 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cahill et al. title: Attitudes towards preventive tuberculosis treatment among hospital staff link: https://peerj.com/articles/1738 last-modified: 2016-02-25 description: Background. Healthcare workers have an increased risk of latent tuberculosis infection (LTBI), but previous studies suggested that they might be reluctant to accept preventive tuberculosis (TB) treatment. We aimed to examine doctors’ and nurses’ experience of TB screening and to explore their attitudes towards preventive TB treatment.Methods. We conducted a survey among randomly selected healthcare workers at a tertiary hospital in Sydney, Australia, using a paper-based questionnaire.Results. A total of 1,304 questionnaires were distributed and 311 (24%) responses were received. The majority of hospital staff supported preventive TB treatment in health care workers with evidence of latent TB infection (LTBI) in general (74%, 164/223) and for them personally (81%, 198/244) while 80 and 53 healthcare workers respectively had no opinion on the topic. Staff working in respiratory medicine were significantly less likely to support preventive TB treatment in health care workers in general or for them personally if they would have evidence of LTBI compared to other specialties (p = 0.001). Only 13% (14/106) of respondents with evidence of LTBI indicated that they had been offered preventive TB treatment. Twenty-one percent (64/306) of respondents indicated that they did not know the difference between active and latent TB. Among staff who had undergone testing for LTBI, only 33% (75/230) felt adequately informed about the meaning of their test results.Discussion. Hospital staff in general had positive attitudes towards preventive TB treatment, but actual treatment rates were low and perceived knowledge about LTBI was insufficient among a significant proportion of staff. The gap between high support for preventive TB treatment among staff and low treatment rates needs to be addressed. Better education on the concept of LTBI and the meaning of screening test results is required. creator: Vidya Pathak creator: Zinta Harrington creator: Claudia C. Dobler uri: https://doi.org/10.7717/peerj.1738 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pathak et al. title: Global miRNA expression is temporally correlated with acute kidney injury in mice link: https://peerj.com/articles/1729 last-modified: 2016-02-25 description: MicroRNAs (miRNAs) are negative regulators of gene expression and protein abundance. Current evidence shows an association of miRNAs with acute kidney injury (AKI) leading to substantially increased morbidity and mortality. Here, we investigated whether miRNAs are inductive regulators responsible for the pathological development of AKI. Microarray analysis was used to detect temporal changes in global miRNA expression within 48 h after AKI in mice. Results indicated that global miRNA expression gradually increased over 24 h from ischemia reperfusion injury after 24 h, and then decreased from 24 h to 48 h. A similar trend was observed for the index of tubulointerstitial injury and the level of serum creatinine, and there was a significant correlation between the level of total miRNA expression and the level of serum creatinine (p < 0.05). This expression-phenotype correlation was validated by quantitative reverse transcription PCR on individual miRNAs, including miR-18a, -134, -182, -210 and -214. Increased global miRNA expression may lead to widespread translational repression and reduced cellular activity. Furthermore, significant inflammatory cytokine release and peritubular capillary loss were observed, suggesting that the initiation of systematic destruction programs was due to AKI. Our findings provide new understanding of the dominant role of miRNAs in promoting the pathological development of AKI. creator: Rui Cui creator: Jia Xu creator: Xiao Chen creator: Wenliang Zhu uri: https://doi.org/10.7717/peerj.1729 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cui et al. title: Familiarity breeds content: assessing bird species popularity with culturomics link: https://peerj.com/articles/1728 last-modified: 2016-02-25 description: Understanding public perceptions of biodiversity is essential to ensure continued support for conservation efforts. Despite this, insights remain scarce at broader spatial scales, mostly due to a lack of adequate methods for their assessment. The emergence of new technologies with global reach and high levels of participation provide exciting new opportunities to study the public visibility of biodiversity and the factors that drive it. Here, we use a measure of internet saliency to assess the national and international visibility of species within four taxa of Brazilian birds (toucans, hummingbirds, parrots and woodpeckers), and evaluate how much of this visibility can be explained by factors associated with familiarity, aesthetic appeal and conservation interest. Our results strongly indicate that familiarity (human population within the range of a species) is the most important factor driving internet saliency within Brazil, while aesthetic appeal (body size) best explains variation in international saliency. Endemism and conservation status of a species had small, but often negative, effects on either metric of internet saliency. While further studies are needed to evaluate the relationship between internet content and the cultural visibility of different species, our results strongly indicate that internet saliency can be considered as a broad proxy of cultural interest. creator: Ricardo A. Correia creator: Paul R. Jepson creator: Ana C. M. Malhado creator: Richard J. Ladle uri: https://doi.org/10.7717/peerj.1728 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Correia et al. title: Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases link: https://peerj.com/articles/1725 last-modified: 2016-02-25 description: The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work indicates that San1 is not a unique case, and that several other yeast and human E3 ligases have sequence properties that may allow them to recognize substrates by a similar mechanism as San1. creator: Wouter Boomsma creator: Sofie V. Nielsen creator: Kresten Lindorff-Larsen creator: Rasmus Hartmann-Petersen creator: Lars Ellgaard uri: https://doi.org/10.7717/peerj.1725 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Boomsma et al. title: A comparison of clustering methods for biogeography with fossil datasets link: https://peerj.com/articles/1720 last-modified: 2016-02-25 description: Cluster analysis is one of the most commonly used methods in palaeoecological studies, particularly in studies investigating biogeographic patterns. Although a number of different clustering methods are widely used, the approach and underlying assumptions of many of these methods are quite different. For example, methods may be hierarchical or non-hierarchical in their approaches, and may use Euclidean distance or non-Euclidean indices to cluster the data. In order to assess the effectiveness of the different clustering methods as compared to one another, a simulation was designed that could assess each method over a range of both cluster distinctiveness and sampling intensity. Additionally, a non-hierarchical, non-Euclidean, iterative clustering method implemented in the R Statistical Language is described. This method, Non-Euclidean Relational Clustering (NERC), creates distinct clusters by dividing the data set in order to maximize the average similarity within each cluster, identifying clusters in which each data point is on average more similar to those within its own group than to those in any other group. While all the methods performed well with clearly differentiated and well-sampled datasets, when data are less than ideal the linkage methods perform poorly compared to non-Euclidean based k-means and the NERC method. Based on this analysis, Unweighted Pair Group Method with Arithmetic Mean and neighbor joining methods are less reliable with incomplete datasets like those found in palaeobiological analyses, and the k-means and NERC methods should be used in their place. creator: Matthew J. Vavrek uri: https://doi.org/10.7717/peerj.1720 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Vavrek title: A systematic review of pediatric clinical trials of high dose vitamin D link: https://peerj.com/articles/1701 last-modified: 2016-02-25 description: Background. Due to inadequate UV exposure, intake of small quantities of vitamin D is recommended to prevent musculoskeletal disease. Both basic science and observational literature strongly suggest that higher doses may benefit specific populations and have non-musculoskeletal roles. Evaluating the evidence surrounding high dose supplementation can be challenging given a relatively large and growing body of clinical trial evidence spanning time, geography, populations and dosing regimens. Study objectives were to identify and summarize the clinical trial literature, recognize areas with high quality evidence, and develop a resource database that makes the literature more immediately accessible to end users.Methods. Medline (1946 to January 2015), Embase (1974 to January 2015), and Cochrane databases (January 2015), were searched for trials. All pediatric (0–18 years) trials administering doses higher than 400 IU (<1 year) or 600 IU (≥1 year) were included. Data was extracted independently by two of the authors. An online searchable database of trials was developed containing relevant extracted information (http://www.cheori.org/en/pedvitaminddatabaseOverview). Sensitivity and utility were assessed by comparing the trials in the database with those from systematic reviews of vitamin D supplementation including children.Results. A total of 2,579 candidate papers were identified, yielding 169 trials having one or more arms meeting eligibility criteria. The publication rate has increased significantly from 1 per year (1970–1979) to 14 per year (2010–2015). Although 84% of the total trials focused on healthy children or known high risk populations (e.g., renal, prematurity), this proportion has declined in recent years due to the rise in trials evaluating populations and outcomes not directly related to the musculoskeletal actions of vitamin D (27% in 2010s). Beyond healthy children, the only pediatric populations with more than 50 participants from low risk of bias trials evaluating a clinically relevant outcome were prematurity and respiratory illness. Finally, we created and validated the online searchable database using 13 recent systematic reviews. Of the 38 high dose trials identified by the systematic review, 36 (94.7%) could be found within the database. When compared with the search strategy reported in each systematic review, use of the database reduced the number of full papers to assess for eligibility by 85.2% (±13.4%).Conclusion. The pediatric vitamin D field is highly active, with a significant increase in trials evaluating non-classical diseases and outcomes. Despite the large overall number there are few high quality trials of sufficient size to provide answers on clinical efficacy of high-dose vitamin D. An open access online searchable data should assist end users in the rapid and comprehensive identification and evaluation of trials relevant to their population or question of interest. creator: Nassr Nama creator: Kusum Menon creator: Klevis Iliriani creator: Supichaya Pojsupap creator: Margaret Sampson creator: Katie O’Hearn creator: Linghong (Linda) Zhou creator: Lauralyn McIntyre creator: Dean Fergusson creator: James D. McNally uri: https://doi.org/10.7717/peerj.1701 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nama et al. title: Sexual behaviour and risk of sexually transmitted infections in young female healthcare students in Spain link: https://peerj.com/articles/1699 last-modified: 2016-02-25 description: Background. Several authors have examined the risk for sexually transmitted infections (STI), but no study has yet analyzed it solely in relation with sexual behaviour in women. We analyzed the association of sexual behaviour with STI risk in female university students of healthcare sciences.Methods. We designed a cross-sectional study assessing over three months vaginal intercourse with a man. The study involved 175 female university students, without a stable partner, studying healthcare sciences in Spain. Main outcome variable: STI risk (not always using male condoms). Secondary variables: sexual behaviour, method of orgasm, desire to increase the frequency of sexual relations, desire to have more variety in sexual relations, frequency of sexual intercourse with the partner, and age. The information was collected with an original questionnaire. A logistic regression model was used to estimate the adjusted odds ratios (ORs) in order to analyze the association between the STI risk and the study variables.Results. Of the 175 women, 52 were positive for STI risk (29.7%, 95% CI [22.9–36.5%]). Factors significantly associated with STI risk (p < 0.05) included: orgasm (not having orgasms →OR = 7.01, 95% CI [1.49–33.00]; several methods →OR = 0.77, 95% CI [0.31–1.90]; one single method →OR = 1; p = 0.008) and desiring an increased frequency of sexual activities (OR = 0.27, 95% CI [0.13–0.59], p < 0.001).Conclusions. Women’s desire for sexual activities and their sexual function were significant predictors of their risk for STI. Information about sexual function is an intrinsic aspect of sexual behaviour and should be taken into consideration when seeking approaches to reduce risks for STI. creator: Felipe Navarro-Cremades creator: Antonio Palazón-Bru creator: Dolores Marhuenda-Amorós creator: María Isabel Tomás-Rodríguez creator: Fina Antón-Ruiz creator: Josefina Belda-Ibañez creator: Ángel Luis Montejo creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.1699 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Navarro-Cremades et al. title: Comparison of three clustering approaches for detecting novel environmental microbial diversity link: https://peerj.com/articles/1692 last-modified: 2016-02-25 description: Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR2) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR2. Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity. creator: Dominik Forster creator: Micah Dunthorn creator: Thorsten Stoeck creator: Frédéric Mahé uri: https://doi.org/10.7717/peerj.1692 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Forster et al. title: Low-frequency, low-magnitude vibrations (LFLM) enhances chondrogenic differentiation potential of human adipose derived mesenchymal stromal stem cells (hASCs) link: https://peerj.com/articles/1637 last-modified: 2016-02-25 description: The aim of this study was to evaluate if low-frequency, low-magnitude vibrations (LFLM) could enhance chondrogenic differentiation potential of human adipose derived mesenchymal stem cells (hASCs) with simultaneous inhibition of their adipogenic properties for biomedical purposes. We developed a prototype device that induces low-magnitude (0.3 g) low-frequency vibrations with the following frequencies: 25, 35 and 45 Hz. Afterwards, we used human adipose derived mesenchymal stem cell (hASCS), to investigate their cellular response to the mechanical signals. We have also evaluated hASCs morphological and proliferative activity changes in response to each frequency. Induction of chondrogenesis in hASCs, under the influence of a 35 Hz signal leads to most effective and stable cartilaginous tissue formation through highest secretion of Bone Morphogenetic Protein 2 (BMP-2), and Collagen type II, with low concentration of Collagen type I. These results correlated well with appropriate gene expression level. Simultaneously, we observed significant up-regulation of α3, α4, β1 and β3 integrins in chondroblast progenitor cells treated with 35 Hz vibrations, as well as Sox-9. Interestingly, we noticed that application of 35 Hz frequencies significantly inhibited adipogenesis of hASCs. The obtained results suggest that application of LFLM vibrations together with stem cell therapy might be a promising tool in cartilage regeneration. creator: Krzysztof Marycz creator: Daniel Lewandowski creator: Krzysztof A. Tomaszewski creator: Brandon M. Henry creator: Edward B. Golec creator: Monika Marędziak uri: https://doi.org/10.7717/peerj.1637 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Marycz et al. title: Samples and data accessibility in research biobanks: an explorative survey link: https://peerj.com/articles/1613 last-modified: 2016-02-25 description: Biobanks, which contain human biological samples and/or data, provide a crucial contribution to the progress of biomedical research. However, the effective and efficient use of biobank resources depends on their accessibility. In fact, making bio-resources promptly accessible to everybody may increase the benefits for society. Furthermore, optimizing their use and ensuring their quality will promote scientific creativity and, in general, contribute to the progress of bio-medical research. Although this has become a rather common belief, several laboratories are still secretive and continue to withhold samples and data. In this study, we conducted a questionnaire-based survey in order to investigate sample and data accessibility in research biobanks operating all over the world. The survey involved a total of 46 biobanks. Most of them gave permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seemed not to be common practice. The analysis of the guidelines regarding the accessibility to resources of the biobanks that responded to the survey highlights three issues: (i) the request for applicants to explain what they would like to do with the resources requested; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) the request of co-authorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sample and data sharing stored in biobanks. As a second step of this study, we investigated the reasons behind the high diversity of requirements to access biobank resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where the biobanks operate. creator: Marco Capocasa creator: Paolo Anagnostou creator: Flavio D’Abramo creator: Giulia Matteucci creator: Valentina Dominici creator: Giovanni Destro Bisol creator: Fabrizio Rufo uri: https://doi.org/10.7717/peerj.1613 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Capocasa et al. title: Genome-wide discovered psychosis-risk gene ZNF804A impacts on white matter microstructure in health, schizophrenia and bipolar disorder link: https://peerj.com/articles/1570 last-modified: 2016-02-25 description: Background. Schizophrenia (SZ) and bipolar disorder (BD) have both been associated with reduced microstructural white matter integrity using, as a proxy, fractional anisotropy (FA) detected using diffusion tensor imaging (DTI). Genetic susceptibility for both illnesses has also been positively correlated in recent genome-wide association studies with allele A (adenine) of single nucleotide polymorphism (SNP) rs1344706 of the ZNF804A gene. However, little is known about how the genomic linkage disequilibrium region tagged by this SNP impacts on the brain to increase risk for psychosis. This study aimed to assess the impact of this risk variant on FA in patients with SZ, in those with BD and in healthy controls.Methods. 230 individuals were genotyped for the rs1344706 SNP and underwent DTI. We used tract-based spatial statistics (TBSS) followed by an analysis of variance, with threshold-free cluster enhancement (TFCE), to assess underlying effects of genotype, diagnosis and their interaction, on FA.Results. As predicted, statistically significant reductions in FA across a widely distributed brain network (p < 0.05, TFCE-corrected) were positively associated both with a diagnosis of SZ or BD and with the double (homozygous) presence of the ZNF804A rs1344706 risk variant (A). The main effect of genotype was medium (d = 0.48 in a 44,054-voxel cluster) and the effect in the SZ group alone was large (d = 1.01 in a 51,260-voxel cluster), with no significant effects in BD or controls, in isolation. No areas under a significant diagnosis by genotype interaction were found.Discussion. We provide the first evidence in a predominantly Caucasian clinical sample, of an association between ZNF804A rs1344706 A-homozygosity and reduced FA, both irrespective of diagnosis and particularly in SZ (in overlapping brain areas). This suggests that the previously observed involvement of this genomic region in psychosis susceptibility, and in impaired functional connectivity, may be conferred through it inducing abnormalities in white matter microstructure. creator: Emma-Jane Mallas creator: Francesco Carletti creator: Christopher A. Chaddock creator: James Woolley creator: Marco M. Picchioni creator: Sukhwinder S. Shergill creator: Fergus Kane creator: Matthew P.G. Allin creator: Gareth J. Barker creator: Diana P. Prata uri: https://doi.org/10.7717/peerj.1570 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Mallas et al. title: Spider phylogenomics: untangling the Spider Tree of Life link: https://peerj.com/articles/1719 last-modified: 2016-02-23 description: Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs. creator: Nicole L. Garrison creator: Juanita Rodriguez creator: Ingi Agnarsson creator: Jonathan A. Coddington creator: Charles E. Griswold creator: Christopher A. Hamilton creator: Marshal Hedin creator: Kevin M. Kocot creator: Joel M. Ledford creator: Jason E. Bond uri: https://doi.org/10.7717/peerj.1719 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Garrison et al. title: A novel computed method to reconstruct the bilateral digital interarticular channel of atlas and its use on the anterior upper cervical screw fixation link: https://peerj.com/articles/1737 last-modified: 2016-02-23 description: Purpose. To investigate a novel computed method to reconstruct the bilateral digital interarticular channel of atlas and its potential use on the anterior upper cervical screw fixation.Methods. We have used the reverse engineering software (image-processing software and computer-aided design software) to create the approximate and optimal digital interarticular channel of atlas for 60 participants. Angles of channels, diameters of inscribed circles, long and short axes of ellipses were measured and recorded, and gender-specific analysis was also performed.Results. The channels provided sufficient space for one or two screws, and the parameters of channels are described. While the channels of females were smaller than that of males, no significant difference of angles between males and females were observed.Conclusion. Our study demonstrates the radiological features of approximate digital interarticular channels, optimal digital interarticular channels of atlas, and provides the reference trajectory of anterior transarticular screws and anterior occiput-to-axis screws. Additionally, we provide a protocol that can help make a pre-operative plan for accurate placement of anterior transarticular screws and anterior occiput-to-axis screws. creator: Ai-Min Wu creator: Wenhai Wang creator: Hui Xu creator: Zhong-Ke Lin creator: Xin-Dong Yang creator: Xiang-Yang Wang creator: Hua-Zi Xu creator: Yong-Long Chi uri: https://doi.org/10.7717/peerj.1737 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wu et al. title: Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis link: https://peerj.com/articles/1734 last-modified: 2016-02-23 description: Citrus canker is a major disease affecting citrus production in Brazil. It’s mainly caused by Xanthomonas citri subsp. citri strain 306 pathotype A (Xac). We analysed the differential expression of proteins secreted by wild type Xac and an asymptomatic mutant for hrpB4 (ΔhrpB4) grown in Nutrient Broth (NB) and a medium mimicking growth conditions in the plant (XAM1). This allowed the identification of 55 secreted proteins, of which 37 were secreted by both strains when cultured in XAM1. In this secreted protein repertoire, the following stand out: Virk, Polyphosphate-selective porin, Cellulase, Endoglucanase, Histone-like protein, Ribosomal proteins, five hypothetical proteins expressed only in the wild type strain, Lytic murein transglycosylase, Lipoprotein, Leucyl-tRNA synthetase, Co-chaperonin, Toluene tolerance, C-type cytochrome biogenesis membrane protein, Aminopeptidase and two hypothetical proteins expressed only in the ΔhrpB4 mutant. Furthermore, Peptidoglycan-associated outer membrane protein, Regulator of pathogenicity factor, Outer membrane proteins, Endopolygalacturonase, Chorismate mutase, Peptidyl-prolyl cis-trans isomerase and seven hypothetical proteins were detected in both strains, suggesting that there was no relationship with the secretion mediated by the type III secretory system, which is not functional in the mutant strain. Also worth mentioning is the Elongation factor Tu (EF-Tu), expressed only the wild type strain, and Type IV pilus assembly protein, Flagellin (FliC) and Flagellar hook-associated protein, identified in the wild-type strain secretome when grown only in NB. Noteworthy, that FliC, EF-Tu are classically characterized as PAMPs (Pathogen-associated molecular patterns), responsible for a PAMP-triggered immunity response. Therefore, our results highlight proteins potentially involved with the virulence. Overall, we conclude that the use of secretome data is a valuable approach that may bring more knowledge of the biology of this important plant pathogen, which ultimately can lead to the establishment of new strategies to combat citrus canker. creator: Rafael M. Ferreira creator: Leandro M. Moreira creator: Jesus A. Ferro creator: Marcia R.R. Soares creator: Marcelo L. Laia creator: Alessandro M. Varani creator: Julio C.F. de Oliveira creator: Maria Ines T. Ferro uri: https://doi.org/10.7717/peerj.1734 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ferreira et al. title: The past, present and future distribution of a deep-sea shrimp in the Southern Ocean link: https://peerj.com/articles/1713 last-modified: 2016-02-23 description: Shrimps have a widespread distribution across the shelf, slope and seamount regions of the Southern Ocean. Studies of Antarctic organisms have shown that individual species and higher taxa display different degrees of sensitivity and adaptability in response to environmental change. We use species distribution models to predict changes in the geographic range of the deep-sea Antarctic shrimp Nematocarcinus lanceopes under changing climatic conditions from the Last Glacial Maximum to the present and to the year 2100. The present distribution range indicates a pole-ward shift of the shrimp population since the last glaciation. This occurred by colonization of slopes from nearby refugia located around the northern part of Scotia Arc, southern tip of South America, South Georgia, Bouvet Island, southern tip of the Campbell plateau and Kerguelen plateau. By 2100, the shrimp are likely to expand their distribution in east Antarctica but have a continued pole-ward contraction in west Antarctica. The range extension and contraction process followed by the deep-sea shrimp provide a geographic context of how other deep-sea Antarctic species may have survived during the last glaciation and may endure with projected changing climatic conditions in the future. creator: Zeenatul Basher creator: Mark J. Costello uri: https://doi.org/10.7717/peerj.1713 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Basher and Costello title: Western scrub-jays do not appear to attend to functionality in Aesop’s Fable experiments link: https://peerj.com/articles/1707 last-modified: 2016-02-23 description: Western scrub-jays are known for their highly discriminatory and flexible behaviors in a caching (food storing) context. However, it is unknown whether their cognitive abilities are restricted to a caching context. To explore this question, we tested scrub-jays in a non-caching context using the Aesop’s Fable paradigm, where a partially filled tube of water contains a floating food reward and objects must be inserted to displace the water and bring the food within reach. We tested four birds, but only two learned to drop stones proficiently. Of these, one bird participated in 4/5 experiments and one in 2/5 experiments. Both birds passed one experiment, but without attending to the functional differences of the objects, and failed the other experiments. Scrub-jays were not motivated to participate in these experiments, suggesting that either this paradigm was ecologically irrelevant or perhaps their flexibility is restricted to a caching context. creator: Corina J. Logan creator: Brigit D. Harvey creator: Barney A. Schlinger creator: Michelle Rensel uri: https://doi.org/10.7717/peerj.1707 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Logan et al. title: Cardiovascular manifestations of renovascular hypertension in diabetic mice link: https://peerj.com/articles/1736 last-modified: 2016-02-22 description: Purpose. Type 2 diabetes is the leading cause of end stage renal disease in the United States. Atherosclerotic renal artery stenosis is commonly observed in diabetic patients and impacts the rate of renal and cardiovascular disease progression. We sought to test the hypothesis that renovascular hypertension, induced by unilateral renal artery stenosis, exacerbates cardiac remodeling in leptin-deficient (db/db) mice, which serves as a model of human type II diabetes.Methods. We employed a murine model of renovascular hypertension through placement of a polytetrafluoroethylene cuff on the right renal artery in db/db mice. We studied 109 wild-type (non-diabetic, WT) and 95 db/db mice subjected to renal artery stenosis (RAS) or sham surgery studied at 1, 2, 4, and 6+ weeks following surgery. Cardiac remodeling was assessed by quantitative analysis of the percent of myocardial surface area occupied by interstitial fibrosis tissue, as delineated by trichrome stained slides. Aortic pathology was assessed by histologic sampling of grossly apparent structural abnormalities or by section of ascending aorta of vessels without apparent abnormalities.Results. We noted an increased mortality in db/db mice subjected to RAS. The mortality rate of db/db RAS mice was about 23.5%, whereas the mortality rate of WT RAS mice was only 1.5%. Over 60% of mortality in the db/db mice occurred in the first two weeks following RAS surgery. Necropsy showed massive intrathoracic hemorrhage associated with aortic dissection, predominantly in the ascending aorta and proximal descending aorta. Aortas from db/db RAS mice showed more smooth muscle dropout, loss of alpha smooth muscle actin expression, medial disruption, and hemorrhage than aortas from WT mice with RAS. Cardiac tissue from db/db RAS mice had more fibrosis than did cardiac tissue from WT RAS mice.Conclusions. db/db mice subjected to RAS are prone to develop fatal aortic dissection, which is not observed in WT mice with RAS. The db/db RAS model provides the basis for future studies directed towards defining basic mechanisms underlying the interaction of hypertension and diabetes on the development of aortic lesions. creator: Sonu Kashyap creator: Sean Engel creator: Mazen Osman creator: Yousif Al-Saiegh creator: Asarn Wongjarupong creator: Joseph P. Grande uri: https://doi.org/10.7717/peerj.1736 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kashyap et al. title: Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.) link: https://peerj.com/articles/1735 last-modified: 2016-02-22 description: Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop. creator: Peng-cheng Fu creator: Yan-Zhao Zhang creator: Hui-yuan Ya creator: Qing-bo Gao uri: https://doi.org/10.7717/peerj.1735 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Fu et al. title: Ultrasound estimates of muscle quality in older adults: reliability and comparison of Photoshop and ImageJ for the grayscale analysis of muscle echogenicity link: https://peerj.com/articles/1721 last-modified: 2016-02-22 description: Background. Quantitative diagnostic ultrasound imaging has been proposed as a method of estimating muscle quality using measures of echogenicity. The Rectangular Marquee Tool (RMT) and the Free Hand Tool (FHT) are two types of editing features used in Photoshop and ImageJ for determining a region of interest (ROI) within an ultrasound image. The primary objective of this study is to determine the intrarater and interrater reliability of Photoshop and ImageJ for the estimate of muscle tissue echogenicity in older adults via grayscale histogram analysis. The secondary objective is to compare the mean grayscale values obtained using both the RMT and FHT methods across both image analysis platforms.Methods. This cross-sectional observational study features 18 community-dwelling men (age = 61.5 ± 2.32 years). Longitudinal views of the rectus femoris were captured using B-mode ultrasound. The ROI for each scan was selected by 2 examiners using the RMT and FHT methods from each software program. Their reliability is assessed using intraclass correlation coefficients (ICCs) and the standard error of the measurement (SEM). Measurement agreement for these values is depicted using Bland-Altman plots. A paired t-test is used to determine mean differences in echogenicity expressed as grayscale values using the RMT and FHT methods to select the post-image acquisition ROI. The degree of association among ROI selection methods and image analysis platforms is analyzed using the coefficient of determination (R2).Results. The raters demonstrated excellent intrarater and interrater reliability using the RMT and FHT methods across both platforms (lower bound 95% CI ICC = .97–.99, p < .001). Mean differences between the echogenicity estimates obtained with the RMT and FHT methods was .87 grayscale levels (95% CI [.54–1.21], p < .0001) using data obtained with both programs. The SEM for Photoshop was .97 and 1.05 grayscale levels when using the RMT and FHT ROI selection methods, respectively. Comparatively, the SEM values were .72 and .81 grayscale levels, respectively, when using the RMT and FHT ROI selection methods in ImageJ. Uniform coefficients of determination (R2 = .96–.99, p < .001) indicate strong positive associations among the grayscale histogram analysis measurement conditions independent of the ROI selection methods and imaging platform.Conclusion. Our method for evaluating muscle echogenicity demonstrated a high degree of intrarater and interrater reliability using both the RMT and FHT methods across 2 common image analysis platforms. The minimal measurement error exhibited by the examiners demonstrates that the ROI selection methods used with Photoshop and ImageJ are suitable for the post-acquisition image analysis of tissue echogenicity in older adults. creator: Michael O. Harris-Love creator: Bryant A. Seamon creator: Carla Teixeira creator: Catheeja Ismail uri: https://doi.org/10.7717/peerj.1721 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Structural modeling of the flagellum MS ring protein FliF reveals similarities to the type III secretion system and sporulation complex link: https://peerj.com/articles/1718 last-modified: 2016-02-22 description: The flagellum is a large proteinaceous organelle found at the surface of many bacteria, whose primary role is to allow motility through the rotation of a long extracellular filament. It is an essential virulence factor in many pathogenic species, and is also a priming component in the formation of antibiotic-resistant biofilms. The flagellum consists of the export apparatus on the cytosolic side; the basal body and rotor, spanning the bacterial membrane(s) and periplasm; and the hook-filament, that protrudes away from the bacterial surface. Formation of the basal body MS ring region, constituted of multiple copies of the protein FliF, is one of the initial steps of flagellum assembly. However, the precise architecture of FliF is poorly understood. Here, I report a bioinformatics analysis of the FliF sequence from various bacterial species, suggesting that its periplasmic region is composed of three globular domains. The first two are homologous to that of the type III secretion system injectisome proteins SctJ, and the third possesses a similar fold to that of the sporulation complex component SpoIIIAG. I also describe that Chlamydia possesses an unusual FliF protein, lacking part of the SctJ homology domain and the SpoIIIAG-like domain, and fused to the rotor component FliG at its C-terminus. Finally, I have combined the sequence analysis of FliF with the EM map of the MS ring, to propose the first atomic model for the FliF oligomer, suggesting that FliF is structurally akin to a fusion of the two injectisome components SctJ and SctD. These results further define the relationship between the flagellum, injectisome and sporulation complex, and will facilitate future structural characterization of the flagellum basal body. creator: Julien R. Bergeron uri: https://doi.org/10.7717/peerj.1718 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bergeron title: Comparison of the synergistic effect of lipid nanobubbles and SonoVue microbubbles for high intensity focused ultrasound thermal ablation of tumors link: https://peerj.com/articles/1716 last-modified: 2016-02-22 description: Microbubbles (MBs) are considered as an important enhancer for high intensity focused ultrasound (HIFU) treatment of benign or malignant tumors. Recently, different sizes of gas-filled bubbles have been investigated to improve the therapeutic efficiency of HIFU thermal ablation and reduce side effects associated with ultrasound power and irradiation time. However, nanobubbles (NBs) as an ultrasound contrast agent for synergistic therapy of HIFU thermal ablation remain controversial due to their small nano-size in diameter. In this study, phospholipid-shell and gas-core NBs with a narrow size range of 500–600 nm were developed. The synergistic effect of NBs for HIFU thermal ablation was carefully studied both in excised bovine livers and in breast tumor models of rabbits, and made a critical comparison with that of commercial SonoVue microbubbles (SonoVue MBs). In addition, the pathological changes of the targeted area in tumor tissue after HIFU ablation were further investigated. Phosphate buffer saline (PBS) was used as the control. Under the same HIFU parameters, the quantitative echo intensity of B-mode ultrasound image and the volume of coagulative necrosis in lipid NBs groups were significantly higher and larger than that in PBS groups, but could not be demonstrated a difference to that in SonoVue MBs groups both ex vivo and in vivo. These results showed that the synergistic effect of lipid NBs for HIFU thermal ablation were similar with that of SonoVue MBs, and further indicate that lipid NBs could potentially become an enhancer for HIFU thermal ablation of tumors. creator: Yuanzhi Yao creator: Ke Yang creator: Yang Cao creator: Xuan Zhou creator: Jinshun Xu creator: Jianxin Liu creator: Qi Wang creator: Zhigang Wang creator: Dong Wang uri: https://doi.org/10.7717/peerj.1716 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yao et al. title: Do Tonkean macaques (Macaca tonkeana) perceive what conspecifics do and do not see? link: https://peerj.com/articles/1693 last-modified: 2016-02-22 description: The understanding of the visual perception of others, also named visual perspective taking, is a component of Theory of Mind. Although strong evidence of visual perspective taking has been reported in great apes, the issue is more open to discussion in monkeys. We investigated whether Tonkean macaques (Macaca tonkeana) know what conspecifics do and do not see, using a food competition paradigm originally developed in great apes. We tested individuals in pairs, after establishing the dominance relationship within each pair. Twenty-one pairs were tested in four different conditions. In one condition, the subordinate had the choice between two pieces of food, one that was visible only to it and another that was also visible to the dominant. It was predicted that if the subordinate understands that the dominant cannot see both pieces of food because one is hidden from its view, the subordinate should preferentially go for the food visible only to itself. In the three other conditions, we varied the temporal and visual access to food for both individuals, to control for alternative explanations based on dominance. We recorded the first movement direction chosen by subjects, i.e. towards a) visible food b) hidden food or c) elsewhere; and the outcome of the test, i.e. the quantity of food obtained. Results showed that subordinates moved preferentially for the hidden food when released simultaneously with the dominant and also with a head start on the dominant. By contrast, dominants’ choices of the two pieces of food were random. We also describe and discuss some of the strategies used by subordinates in these tests. According to the whole of our results, Tonkean macaques seem capable of visual perspective taking despite the fact that a low-level explanation as behavior reading has not been totally excluded. creator: Charlotte Canteloup creator: Emilie Piraux creator: Nicolas Poulin creator: Hélène Meunier uri: https://doi.org/10.7717/peerj.1693 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Canteloup et al. title: Internal seed dispersal by parrots: an overview of a neglected mutualism link: https://peerj.com/articles/1688 last-modified: 2016-02-22 description: Despite the fact that parrots (Psitacifformes) are generalist apex frugivores, they have largely been considered plant antagonists and thus neglected as seed dispersers of their food plants. Internal dispersal was investigated by searching for seeds in faeces opportunistically collected at communal roosts, foraging sites and nests of eleven parrot species in different habitats and biomes in the Neotropics. Multiple intact seeds of seven plant species of five families were found in a variable proportion of faeces from four parrot species. The mean number of seeds of each plant species per dropping ranged between one and about sixty, with a maximum of almost five hundred seeds from the cacti Pilosocereus pachycladus in a single dropping of Lear’s Macaw (Anodorhynchus leari). All seeds retrieved were small (<3 mm) and corresponded to herbs and relatively large, multiple-seeded fleshy berries and infrutescences from shrubs, trees and columnar cacti, often also dispersed by stomatochory. An overview of the potential constraints driving seed dispersal suggest that, despite the obvious size difference between seeds dispersed by endozoochory and stomatochory, there is no clear difference in fruit size depending on the dispersal mode. Regardless of the enhanced or limited germination capability after gut transit, a relatively large proportion of cacti seeds frequently found in the faeces of two parrot species were viable according to the tetrazolium test and germination experiments. The conservative results of our exploratory sampling and a literature review clearly indicate that the importance of parrots as endozoochorous dispersers has been largely under-appreciated due to the lack of research systematically searching for seeds in their faeces. We encourage the evaluation of seed dispersal and other mutualistic interactions mediated by parrots before their generalized population declines contribute to the collapse of key ecosystem processes. creator: Guillermo Blanco creator: Carolina Bravo creator: Erica C. Pacifico creator: Daniel Chamorro creator: Karina L. Speziale creator: Sergio A. Lambertucci creator: Fernando Hiraldo creator: José L. Tella uri: https://doi.org/10.7717/peerj.1688 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Blanco et al. title: Insight into the maintenance of odontogenic potential in mouse dental mesenchymal cells based on transcriptomic analysis link: https://peerj.com/articles/1684 last-modified: 2016-02-22 description: Background. Mouse dental mesenchymal cells (mDMCs) from tooth germs of cap or later stages are frequently used in the context of developmental biology or whole-tooth regeneration due to their odontogenic potential. In vitro-expanded mDMCs serve as an alternative cell source considering the difficulty in obtaining primary mDMCs; however, cultured mDMCs fail to support tooth development as a result of functional failures of specific genes or pathways. The goal of this study was to identify the genes that maintain the odontogenic potential of mDMCs in culture.Methods. We examined the odontogenic potential of freshly isolated versus cultured mDMCs from the lower first molars of embryonic day 14.5 mice. The transcriptome of mDMCs was detected using RNA sequencing and the data were validated by qRT-PCR. Differential expression analysis and pathway analysis were conducted to identify the genes that contribute to the loss of odontogenic potential.Results. Cultured mDMCs failed to develop into well-structured tooth when they were recombined with dental epithelium. Compared with freshly isolated mDMCs, we found that 1,004 genes were upregulated and 948 were downregulated in cultured mDMCs. The differentially expressed genes were clustered in the biological processes and signaling pathways associated with tooth development. Following in vitro culture, genes encoding a wide array of components of MAPK, TGF-β/BMP, and Wnt pathways were significantly downregulated. Moreover, the activities of Bdnf, Vegfα, Bmp2, and Bmp7 were significantly inhibited in cultured mDMCs. Supplementation of VEGFα, BMP2, and BMP7 restored the expression of a subset of downregulated genes and induced mDMCs to form dentin-like structures in vivo.Conclusions.Vegfα, Bmp2, and Bmp7 play a role in the maintenance of odontogenic potential in mDMCs. creator: Yunfei Zheng creator: Lingfei Jia creator: Pengfei Liu creator: Dandan Yang creator: Waner Hu creator: Shubin Chen creator: Yuming Zhao creator: Jinglei Cai creator: Duanqing Pei creator: Lihong Ge creator: Shicheng Wei uri: https://doi.org/10.7717/peerj.1684 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zheng et al. title: Could biorational insecticides be used in the management of aflatoxigenic Aspergillus parasiticus and its insect vectors in stored wheat? link: https://peerj.com/articles/1665 last-modified: 2016-02-22 description: Insect pests in stored wheat cause significant losses and play an important role in the dispersal of viable fungal spores of various species including aflatoxin producing Aspergillus parasiticus. The problem of insecticide resistance in stored insects and environmental hazards associated with fumigants and conventional grain protectants underscore the need to explore reduced risk insecticides to control stored insects with the ultimate effect on aflatoxin production. The purpose of this study was to investigate the insecticidal potential of four biorational insecticides: spinosad, thiamethoxam, imidacloprid and indoxacarb, on wheat grains artificially infested with Rhyzopertha dominica/Sitophilus oryzae and/or A. parasiticus spores, and the subsequent effect on aflatoxin production. Spinosad and thiamethoxam were the most effective insecticides against R. dominica compared to S. oryzae followed by imidacloprid. Spinosad applied at 0.25–1 ppm and thiamethoxam at 2 and 4 ppm concentrations resulted in complete mortality of R. dominica. However, indoxacarb was more toxic against S. oryzae compared to R. dominica. Wheat grains inoculated with R. dominica/S. oryzae +spores elicited higher aflatoxin levels than wheat grains inoculated with or without insecticide+spores. In all the treatment combinations containing insects, aflatoxin production was dependent on insects’ survival rate. In addition, thiamethoxam and imidacloprid had also a significant direct effect on reducing aflatoxin production. Aflatoxin levels were lower in the treatment combinations with any concentration of thiamethoxam/imidacloprid+spores as compared to wheat grains inoculated with spores only. Correlation analyses revealed highly significant and positive association between moisture contents/insect survival rate and production of aflatoxin levels, and insect survival rate and moisture contents of the wheat grains. In conclusion, the results of the present study provide baseline data on the use of biorational insecticides against R. dominica and S. oryzae and subsequent effect on aflatoxin production. creator: Tiyyabah Khan creator: Ahmad Ali Shahid creator: Hafiz Azhar Ali Khan uri: https://doi.org/10.7717/peerj.1665 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Khan et al. title: Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA) link: https://peerj.com/articles/1664 last-modified: 2016-02-22 description: Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy.Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features.Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study.Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The model codes can be accessed at http://mybiodiversityontologies.um.edu.my/Otolith/ and https://peerj.com/preprints/1517/. The current model has flexibility to be used for more species and families in future studies. creator: Nima Salimi creator: Kar Hoe Loh creator: Sarinder Kaur Dhillon creator: Ving Ching Chong uri: https://doi.org/10.7717/peerj.1664 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Salimi et al. title: Plating versus intramedullary fixation for mid-shaft clavicle fractures: a systemic review and meta-analysis link: https://peerj.com/articles/1540 last-modified: 2016-02-22 description: Background. Plate fixation and intramedullary fixation are the most commonly used surgical treatment options for mid-shaft clavicle fractures; the latter method has demonstrated better performance in some studies.Objectives. Our aim was to critically review and summarize the literature comparing the outcomes of mid-shaft clavicle fracture treatment with plate fixation or intramedullary fixation to identify the better approach.Search Methods. Potential academic articles were identified from the Cochrane Library, MEDLINE (1966-2015.5), PubMed (1966-2015.5), EMBASE (1980-2015.5) and ScienceDirect (1966-2015.5). Gray studies were identified from the references of the included literature.Selection Criteria. Randomized controlled trials (RCTs) and non-RCTs comparing plate fixation and intramedullary fixation for mid-shaft clavicle fracture were included.Data Collection and Analysis. Two reviewers performed independent data abstraction. The I2 statistic was used to assess heterogeneity. A fixed- or random-effects model was used for the meta-analysis.Results. Six RCTs and nine non-RCTs were retrieved, including 513 patients in the intramedullary fixation group and 521 patients in the plating group. No significant differences in terms of the union rate and shoulder function were found between the groups. Patients in the intramedullary fixation group had a shorter operative time, less blood loss, smaller wound size, and shorter union time than those in the plating group. With respect to complications, significant differences were identified for all complications and major complications (wound infection, nonunion, implant failures, transient brachial plexopathy, and pain after 6 months). Similar secondary complications (symptomatic hardware, hardware irritation, prominence, numbness, hypertrophic callus) were observed in both groups.Conclusions. Intramedullary fixation may be superior to plate fixation in the treatment of mid-shaft clavicle fractures, with similar performance in terms of the union rate and shoulder function, better operative parameters and fewer complications. creator: Yan Gao creator: Wei Chen creator: Yue-Jv Liu creator: Xu Li creator: Hai-Li Wang creator: Zhao-yu Chen uri: https://doi.org/10.7717/peerj.1540 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gao et al. title: Responses of microbial community from tropical pristine coastal soil to crude oil contamination link: https://peerj.com/articles/1733 last-modified: 2016-02-18 description: Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg−1), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required. creator: Daniel Morais creator: Victor Pylro creator: Ian M. Clark creator: Penny R. Hirsch creator: Marcos R. Tótola uri: https://doi.org/10.7717/peerj.1733 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Morais et al. title: Phenotypical expression of reduced mobility during limb ontogeny in frogs: the knee-joint case link: https://peerj.com/articles/1730 last-modified: 2016-02-18 description: Movement is one of the most important epigenetic factors for normal development of the musculoskeletal system, particularly during genesis and joint development. Studies regarding alterations to embryonic mobility, performed on anurans, chickens and mammals, report important phenotypical similarities as a result of the reduction or absence of this stimulus. The precise stage of development at which the stimulus modification generates phenotypic modifications however, is yet to be determined. In this work we explore whether the developmental effects of abnormal mobility can appear at any time during development or whether they begin to express themselves in particular phases of tadpole ontogeny. We conducted five experiments that showed that morphological abnormalities are not visible until Stages 40–42. Morphology in earlier stages remains normal, probably due to the fact that the bones/muscles/tendons have not yet developed and therefore are not affected by immobilization. These results suggest the existence of a specific period of phenotypical expression in which normal limb movement is necessary for the correct development of the joint tissue framework. creator: Maria Laura Ponssa creator: Virginia Abdala uri: https://doi.org/10.7717/peerj.1730 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ponssa and Abdala title: Problems in using p-curve analysis and text-mining to detect rate of p-hacking and evidential value link: https://peerj.com/articles/1715 last-modified: 2016-02-18 description: Background. The p-curve is a plot of the distribution of p-values reported in a set of scientific studies. Comparisons between ranges of p-values have been used to evaluate fields of research in terms of the extent to which studies have genuine evidential value, and the extent to which they suffer from bias in the selection of variables and analyses for publication, p-hacking.Methods.p-hacking can take various forms. Here we used R code to simulate the use of ghost variables, where an experimenter gathers data on several dependent variables but reports only those with statistically significant effects. We also examined a text-mined dataset used by Head et al. (2015) and assessed its suitability for investigating p-hacking.Results. We show that when there is ghost p-hacking, the shape of the p-curve depends on whether dependent variables are intercorrelated. For uncorrelated variables, simulated p-hacked data do not give the “p-hacking bump” just below .05 that is regarded as evidence of p-hacking, though there is a negative skew when simulated variables are inter-correlated. The way p-curves vary according to features of underlying data poses problems when automated text mining is used to detect p-values in heterogeneous sets of published papers.Conclusions. The absence of a bump in the p-curve is not indicative of lack of p-hacking. Furthermore, while studies with evidential value will usually generate a right-skewed p-curve, we cannot treat a right-skewed p-curve as an indicator of the extent of evidential value, unless we have a model specific to the type of p-values entered into the analysis. We conclude that it is not feasible to use the p-curve to estimate the extent of p-hacking and evidential value unless there is considerable control over the type of data entered into the analysis. In particular, p-hacking with ghost variables is likely to be missed. creator: Dorothy V.M. Bishop creator: Paul A. Thompson uri: https://doi.org/10.7717/peerj.1715 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bishop and Thompson title: First record of hybridization between green Chelonia mydas and hawksbill Eretmochelys imbricata sea turtles in the Southeast Pacific link: https://peerj.com/articles/1712 last-modified: 2016-02-18 description: Hybridization among sea turtle species has been widely reported in the Atlantic Ocean, but their detection in the Pacific Ocean is limited to just two individual hybrid turtles, in the northern hemisphere. Herein, we report, for the first time in the southeast Pacific, the presence of a sea turtle hybrid between the green turtle Chelonia mydas and the hawksbill turtle Eretmochelys imbricata. This juvenile sea turtle was captured in northern Peru (4°13′S; 81°10′W) on the 5th of January, 2014. The individual exhibited morphological characteristics of C. mydas such as dark green coloration, single pair of pre-frontal scales, four post-orbital scales, and mandibular median ridge, while the presence of two claws in each frontal flipper, and elongated snout resembled the features of E. imbricata. In addition to morphological evidence, we confirmed the hybrid status of this animal using genetic analysis of the mitochondrial gene cytochrome oxidase I, which revealed that the hybrid individual resulted from the cross between a female E. imbricata and a male C. mydas. Our report extends the geographical range of occurrence of hybrid sea turtles in the Pacific Ocean, and is a significant observation of interspecific breeding between one of the world’s most critically endangered populations of sea turtles, the east Pacific E. imbricata, and a relatively healthy population, the east Pacific C. mydas. creator: Shaleyla Kelez creator: Ximena Velez-Zuazo creator: Aldo S. Pacheco uri: https://doi.org/10.7717/peerj.1712 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kelez et al. title: Contrasting response of biomass and grain yield to severe drought in Cappelle Desprez and Plainsman V wheat cultivars link: https://peerj.com/articles/1708 last-modified: 2016-02-18 description: We report a case study of natural variations and correlations of some photosynthetic parameters, green biomass and grain yield in Cappelle Desprez and Plainsman V winter wheat (Triticum aestivum L.) cultivars, which are classified as being drought sensitive and tolerant, respectively. We monitored biomass accumulation from secondary leaves in the vegetative phase and grain yield from flag leaves in the grain filling period. Interestingly, we observed higher biomass production, but lower grain yield stability in the sensitive Cappelle cultivar, as compared to the tolerant Plainsman cv. Higher biomass production in the sensitive variety was correlated with enhanced water-use efficiency. Increased cyclic electron flow around PSI was also observed in the Cappelle cv. under drought stress as shown by light intensity dependence of the ratio of maximal quantum yields of Photosystem I and Photosystem II, as well by the plot of the Photosystem I electron transport rate as a function of Photosystem II electron transport rate. Higher CO2 uptake rate in flag leaves of the drought-stressed Plainsman cv. during grain filling period correlates well with its higher grain yield and prolonged transpiration rate through spikes. The increase in drought factor (DFI) and performance (PI) indices calculated from variable chlorophyll fluorescence parameters of secondary leaves also showed correlation with higher biomass in the Cappelle cultivar during the biomass accumulation period. However, during the grain filling period, DFI and PI parameters of the flag leaves were higher in the tolerant Plainsman V cultivar and showed correlation with grain yield stability. Our results suggest that overall biomass and grain yield may respond differentially to drought stress in different wheat cultivars and therefore phenotyping for green biomass cannot be used as a general approach to predict grain yield. We also conclude that photosynthetic efficiency of flag and secondary leaves is correlated with grain yield and green biomass, respectively. In addition, secondary trait associated mechanisms like delayed senescence and higher water-use efficiency also contribute to biomass stability. Our studies further prove that photosynthetic parameters could be used to characterize environmental stress responses. creator: Kenny Paul creator: János Pauk creator: Zsuzsanna Deák creator: László Sass creator: Imre Vass uri: https://doi.org/10.7717/peerj.1708 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Paul et al. title: The structure and diversity of freshwater diatom assemblages from Franz Josef Land Archipelago: a northern outpost for freshwater diatoms link: https://peerj.com/articles/1705 last-modified: 2016-02-18 description: We examined diatom assemblages from 18 stream and pond samples in the Franz Josef Land Archipelago (FJL), the most northern land of Eurasia. More than 216 taxa were observed, revealing a rich circumpolar diatom flora, including many undescribed taxa. Widely distributed taxa were the most abundant by cell densities, while circumpolar taxa were the most species rich. Stream and pond habitats hosted different assemblages, and varied along a pH gradient. Diatoma tenuis was the most abundant and ubiquitous taxon. However, several circumpolar taxa such as Chamaepinnularia gandrupii, Cymbella botellus, Psammothidium sp. and Humidophila laevissima were also found in relatively high abundances. Aerophilic taxa were an important component of FJL diatom assemblages (Humidophila spp., Caloneis spp. and Pinnularia spp.), reflecting the large and extreme seasonal changes in Arctic conditions. We predict a decrease in the abundance of circumpolar taxa, an increase in local (α-) freshwater diatom diversity, but a decrease in regional diversity (circumpolar homogenization) as a result of current warming trends and to a lesser extent the increasing human footprint in the region. creator: Sergi Pla-Rabés creator: Paul B. Hamilton creator: Enric Ballesteros creator: Maria Gavrilo creator: Alan M. Friedlander creator: Enric Sala uri: https://doi.org/10.7717/peerj.1705 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pla-Rabés et al. title: May arsenic pollution contribute to limiting Artemia franciscana invasion in southern Spain? link: https://peerj.com/articles/1703 last-modified: 2016-02-18 description: Limited information exists regarding the complex interactions between biological invasions, pollution, and climate change. Most studies indicate that pollution tends to favor invasive species. Here, we provide evidence that arsenic (As) pollution may have a role in limiting the invasion of the exotic brine shrimp Artemia franciscana. We tested As toxicity in natural populations of Artemia parthenogenetica (a native taxon) and A. franciscana from localities in southern Spain with differing degrees of As contamination. Tests were conducted both under current mean temperature conditions (25 °C), and as per a future climate scenario (i.e., an increase in mean temperature of 4 °C). Acute toxicity was estimated on the basis of the median lethal concentration (at 24 h), and chronic toxicity was evaluated by measuring Artemia survival and growth under sublethal exposures (after 26 days). At 25 °C, native A. parthenogenetica from the highly polluted Odiel and Tinto estuary was much more resistant to acute As stress (LC50-24 h, 24.67 mg L−1) than A. franciscana (15.78 mg L−1) and A. parthenogenetica from unpolluted sites (12.04 mg L−1)–suggesting that local adaptation to polluted conditions may occur. At 29 °C, resistance of A. parthenogenetica from Odiel decreased significantly, and there were no statistical differences in sensitivity between the three species/populations, suggesting that climate change may enhance the probability of invasion. Resistance increased with developmental stage from nauplii to adults, and was extremely high in cysts which still hatched at As concentrations of up to 6400 mg L−1. Under sublethal chronic exposure A. franciscana performed better (survival and growth) than A. parthenogenetica, and both species experienced a faster growth when exposed to As, compared with unexposed (control) individuals, probably due to the hormesis. We discuss the ecological implications of our results. creator: Marta I. Sánchez creator: Cathleen Petit creator: Mónica Martínez-Haro creator: Mark A. Taggart creator: Andy J. Green uri: https://doi.org/10.7717/peerj.1703 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sánchez et al. title: Stratigraphy, palaeoenvironments and palaeoecology of the Loch Humphrey Burn lagerstätte and other Mississippian palaeobotanical localities of the Kilpatrick Hills, southwest Scotland link: https://peerj.com/articles/1700 last-modified: 2016-02-18 description: Background and Aims. The largely Mississippian strata of the Kilpatrick Hills, located at the western end of the Scottish Midland Valley, enclose several macrofossil floras that together contain ca 21 organ-species of permineralised plants and ca 44 organ-species of compressed plants, here estimated to represent 25 whole-plant species (Glenarbuck = nine, Loch Humphrey Burn Lower = 11, Upper = seven). The most significant locality is the internationally important volcanigenic sequence that is reputedly intercalated within the Clyde Plateau Lava Formation at Loch Humphrey Burn, where ca 30 m of reworked tuffs and other clastic sediments enclose one of the world’s most important terrestrial lagerstätten of this period. We here explore the palaeoecology and palaeoenvironments of the locality, and elucidate its controversial age.Methods. Repeated re-excavation of key exposures allowed recognition of five main depositional units, differing in thickness from 4 m to 12 m. It also permitted detailed sampling for plant macrofossils and microfossils throughout the succession. Several approaches are integrated to re-assess the taphonomy and preservation of these exceptional plant fossils.Key Results. The deposits are rich in taxonomically diverse miospores and in toto contain at least six well-developed compression floras, together with two beds yielding nodules that enclose well-researched anatomically preserved plants permineralised in calcite. Bulk geochemistry shows that the upper nodules formed by migration of Ca with subordinate Mn and Na. Some phylogenetically important plant fossils recovered in the early 20th century have been traced to their source horizons. Trends in relative proportions of macrofossil and microfossil taxa through the sequence are only moderately congruent, perhaps reflecting the likelihood that microfossils sample the regional rather than the local flora.Conclusions. The Loch Humphrey Burn sequence encompasses a wide range of depositional environments that intercalates high-energy fluvial channels (possibly developed during flash floods in a seasonally arid environment) with lower energy flood plains and a brief lacustrine interval; all yield macrofloras typically dominated by allochthonous pteridosperms. The uppermost unit represents clastic swamps dominated by (hypo)autochthonous lycopsids and ferns s.l., and is tentatively correlated with the entire—reputedly mid-Visean—exposure at nearby Glenarbuck. Other nearby localities with rooted tree-lycopsids appear to have immediately pre-dated the onset of regional volcanism. These interpretations allow revised provenancing and dating of historical collections of key plant fossils. The late Tournaisian date previously attributed on palynological evidence to the lowest unit at Loch Humphrey Burn appears increasingly improbable when our re-appraisal of the macrofloras and microfloras is placed in the context of (a) statistical comparison with other permineralised Mississippian assemblages and (b) recent stratigraphic and geochronologic studies in the region; rather, we ascribe the entire Kilpatrick Hills sequence to the mid-Visean. Stratigraphic and palaeoenvironmental interpretations of the Mississippian rocks of the Kilpatrick Hills have especially profound implications for our understanding of the physical evolution of Scotland during the Variscan orogeny and formation of Pangea. creator: Richard M. Bateman creator: Liadan G. Stevens creator: Jason Hilton uri: https://doi.org/10.7717/peerj.1700 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bateman et al. title: Comparison of miRNA expression profiles in pituitary–adrenal axis between Beagle and Chinese Field dogs after chronic stress exposure link: https://peerj.com/articles/1682 last-modified: 2016-02-18 description: MicoRNAs (miRNAs), usually as gene regulators, participate in various biological processes, including stress responses. The hypothalamus–pituitary–adrenal axis (HPA axis) is an important pathway in regulating stress response. Although the mechanism that HPA axis regulates stress response has been basically revealed, the knowledge that miRNAs regulate stress response within HPA axis, still remains poor. The object of this study was to investigate the miRNAs in the pituitary and adrenal cortex that regulate chronic stress response with high-throughput sequencing. The pituitary and adrenal cortex of beagles and Chinese Field dogs (CFD) from a stress exposure group (including beagle pituitary 1 (BP1), CFD pituitary 1 (CFDP1), beagle adrenal cortex 1 (BAC1), CFD adrenal cortex 1 (CFDAC1)) and a control group (including beagle pituitary 2 (BP2), CFD pituitary 2 (CFDP2), beagle adrenal cortex 2 (BAC2), CFD adrenal cortex 2 (CFDAC2)), were selected for miRNA-seq comparisons. Comparisons, that were made in pituitary (including BP1 vs. BP2, CFDP1 vs. CFDP2, BP1 vs. CFDP1 and BP2 vs. CFDP2) and adrenal cortex (including BAC1 vs. BAC2, CFDAC1 vs. CFDAC2, BAC1 vs. CFDAC1 and BAC2 vs. CFDAC2), showed that a total of 39 and 18 common differentially expressed miRNAs (DE-miRNAs) (Total read counts > 1,000, Fold change > 2 & p-value < 0.001), that shared in at least two pituitary comparisons and at least two adrenal cortex comparisons, were detected separately. These identified DE-miRNAs were predicted for target genes, thus resulting in 3,959 and 4,010 target genes in pituitary and adrenal cortex, respectively. Further, 105 and 10 differentially expressed genes (DEGs) (Fold change > 2 & p-value < 0.05) from those target genes in pituitary and adrenal cortex were obtained separately, in combination with our previous corresponding transcriptome study. Meanwhile, in line with that miRNAs usually negatively regulated their target genes and the dual luciferase reporter assay, we finally identified cfa-miR-205 might play an important role by upregulating MMD in pituitary and hippocampus, thus enhancing the immune response, under chronic stress exposure. Our results shed light on the miRNA expression profiles in the pituitary and adrenal cortex with and without chronic stress exposure, and provide a new insight into miR-205 with its feasible role in regulating chronic stress in the pituitary and hippocampus through targeting MMD. creator: Wei Luo creator: Meixia Fang creator: Haiping Xu creator: Huijie Xing creator: Jiangnan Fu creator: Qinghua Nie uri: https://doi.org/10.7717/peerj.1682 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Luo et al. title: Seasonal availability of edible underground and aboveground carbohydrate resources to human foragers on the Cape south coast, South Africa link: https://peerj.com/articles/1679 last-modified: 2016-02-18 description: The coastal environments of South Africa’s Cape Floristic Region (CFR) provide some of the earliest and most abundant evidence for the emergence of cognitively modern humans. In particular, the south coast of the CFR provided a uniquely diverse resource base for hunter-gatherers, which included marine shellfish, game, and carbohydrate-bearing plants, especially those with Underground Storage Organs (USOs). It has been hypothesized that these resources underpinned the continuity of human occupation in the region since the Middle Pleistocene. Very little research has been conducted on the foraging potential of carbohydrate resources in the CFR. This study focuses on the seasonal availability of plants with edible carbohydrates at six-weekly intervals over a two-year period in four vegetation types on South Africa’s Cape south coast. Different plant species were considered available to foragers if the edible carbohydrate was directly (i.e. above-ground edible portions) or indirectly (above-ground indications to below-ground edible portions) visible to an expert botanist familiar with this landscape. A total of 52 edible plant species were recorded across all vegetation types. Of these, 33 species were geophytes with edible USOs and 21 species had aboveground edible carbohydrates. Limestone Fynbos had the richest flora, followed by Strandveld, Renosterveld and lastly, Sand Fynbos. The availability of plant species differed across vegetation types and between survey years. The number of available USO species was highest for a six-month period from winter to early summer (Jul–Dec) across all vegetation types. Months of lowest species’ availability were in mid-summer to early autumn (Jan–Apr); the early winter (May–Jun) values were variable, being highest in Limestone Fynbos. However, even during the late summer carbohydrate “crunch,” 25 carbohydrate bearing species were visible across the four vegetation types. To establish a robust resource landscape will require additional spatial mapping of plant species abundances. Nonetheless, our results demonstrate that plant-based carbohydrate resources available to Stone Age foragers of the Cape south coast, especially USOs belonging to the Iridaceae family, are likely to have comprised a reliable and nutritious source of calories over most of the year. creator: Jan C. De Vynck creator: Richard M. Cowling creator: Alastair J. Potts creator: Curtis W. Marean uri: https://doi.org/10.7717/peerj.1679 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 De Vynck et al. title: Genotypic richness predicts phenotypic variation in an endangered clonal plant link: https://peerj.com/articles/1633 last-modified: 2016-02-18 description: Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species. However, the strong link between genotypic and phenotypic variation suggests that a range of genotypes is still the best case scenario for adaptation to and recovery from predicted environmental change. creator: Suzanna M. Evans creator: Elizabeth A. Sinclair creator: Alistair G.B. Poore creator: Keryn F. Bain creator: Adriana Vergés uri: https://doi.org/10.7717/peerj.1633 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Evans et al. title: Comparisons of eccentric knee flexor strength and asymmetries across elite, sub-elite and school level cricket players link: https://peerj.com/articles/1594 last-modified: 2016-02-18 description: Background. There has been a continual increase in injury rates in cricket, with hamstring strain injuries (HSIs) being the most prominent. Eccentric knee flexor weakness and bilateral asymmetries are major modifiable risk factors for future HSIs. However, there is a lack of data relating to eccentric hamstring strength in cricket at any skill level. The objective of this study was to compare eccentric knee flexor strength and bilateral asymmetries in elite, sub-elite and school level cricket players; and to determine if playing position and limb role influenced these eccentric knee flexor strength indices.Methods. Seventy four male cricket players of three distinct skill levels performed three repetitions of the Nordic hamstring exercise on the experimental device. Strength was assessed as the absolute and relative mean peak force output for both limbs, with bilateral asymmetries. Differences in mean peak force outputs between skill level and playing positions were measured.Results. There were no significant differences between elite, sub-elite and school level athletes for mean peak force and bilateral asymmetries of the knee flexors. There were no significant differences observed between bowler’s and batter’s mean peak force and bilateral asymmetries. There were no significant differences between front and back limb mean peak force outputs.Discussion. Skill level, playing position and limb role appeared to have no significant effect on eccentric knee flexor strength and bilateral asymmetries. Future research should seek to determine whether eccentric knee flexor strength thresholds are predictive of HSIs in cricket and if specific eccentric knee flexor strengthening can reduce these injuries. creator: Wade J. Chalker creator: Anthony J. Shield creator: David A. Opar creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.1594 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chalker et al. title: Ketamine modulates subgenual cingulate connectivity with the memory-related neural circuit—a mechanism of relevance to resistant depression? link: https://peerj.com/articles/1710 last-modified: 2016-02-16 description: Background. Ketamine has been reported to have efficacy as an antidepressant in several studies of treatment-resistant depression. In this study, we investigate whether an acute administration of ketamine leads to reductions in the functional connectivity of subgenual anterior cingulate cortex (sgACC) with other brain regions.Methods. Thirteen right-handed healthy male subjects underwent a 15 min resting state fMRI with an infusion of intravenous ketamine (target blood level = 150 ng/ml) starting at 5 min. We used a seed region centred on the sgACC and assessed functional connectivity before and during ketamine administration.Results. Before ketamine administration, positive coupling with the sgACC seed region was observed in a large cluster encompassing the anterior cingulate and negative coupling was observed with the anterior cerebellum. Following ketamine administration, sgACC activity became negatively correlated with the brainstem, hippocampus, parahippocampal gyrus, retrosplenial cortex, and thalamus.Discussion. Ketamine reduced functional connectivity of the sgACC with brain regions implicated in emotion, memory and mind wandering. It is possible the therapeutic effects of ketamine may be mediated via this mechanism, although further work is required to test this hypothesis. creator: Jing J. Wong creator: Owen O’Daly creator: Mitul A. Mehta creator: Allan H. Young creator: James M. Stone uri: https://doi.org/10.7717/peerj.1710 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wong et al. title: Ischemic postconditioning influences electron transport chain protein turnover in Langendorff-perfused rat hearts link: https://peerj.com/articles/1706 last-modified: 2016-02-16 description: Ischemia postconditioning (IPo) is a promising strategy in reducing myocardial ischemia reperfusion (I/R) injury (MIRI), but its specific molecular mechanism is incompletely understood. Langendorff-perfused isolated rat hearts were subjected to global I/R and received IPo in the absence or presence of the mitochondrial ATP-sensitive potassium channel (mitoKATP) blocker 5-hydroxydecanoate (5-HD). Myocardial mitochondria were extracted and mitochondrial comparative proteomics was analyzed. IPo significantly reduces post-ischemic myocardial infarction and improved cardiac function in I/R rat hearts, while 5-HD basically cancelled IPo’s myocardial protective effect. Joint application of two-dimensional polyacrylamide gel electrophoresis (2DE) and MALDI-TOF MS identified eight differentially expressed proteins between groups. Expression of cardiac succinate dehydrogenase (ubiquinone) flavoprotein subunit (SDHA) increased more than two-fold after I/R, while IPo led to overexpression of dihydrolipoyl dehydrogenase (DLD), NADH dehydrogenase (ubiquinone) flavoprotein 1 and isoform CRA_b (NDUFV1). When the mitoKATP was blocked, MICOS complex subunit Mic60 (IMMT) and Stress-70 protein (Grp75) were over expressed, while DLDH, ATPase subunit A (ATPA) and rCG44606 were decreased. Seven of the differential proteins belong to electron transport chain (ETC) or metabolism regulating proteins, and five of them were induced by closing mitoKATP in I/R hearts. We thus conclude that IPo’s myocardial protective effect relies on energy homeostasis regulation. DLD, SDHA, NDUFV1, Grp75, ATPA and rCG44606 may contribute to IPo’s cardial protective effect. creator: Song Cao creator: Yun Liu creator: Haiying Wang creator: Xiaowen Mao creator: Jincong Chen creator: Jiming Liu creator: Zhengyuan Xia creator: Lin Zhang creator: Xingkui Liu creator: Tian Yu uri: https://doi.org/10.7717/peerj.1706 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cao et al. title: Can macroalgae provide promising anti-tumoral compounds? A closer look at Cystoseira tamariscifolia as a source for antioxidant and anti-hepatocarcinoma compounds link: https://peerj.com/articles/1704 last-modified: 2016-02-16 description: Marine organisms are a prolific source of drug leads in a variety of therapeutic areas. In the last few years, biomedical, pharmaceutical and nutraceutical industries have shown growing interest in novel compounds from marine organisms, including macroalgae. Cystoseira is a genus of Phaeophyceae (Fucales) macroalgae known to contain bioactive compounds. Organic extracts (hexane, diethyl ether, ethyl acetate and methanol extracts) from three Cystoseira species (C. humilis, C. tamariscifolia and C. usneoides) were evaluated for their total phenolic content, radical scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radicals, and antiproliferative activity against a human hepatocarcinoma cell line (HepG2 cells). C. tamariscifolia had the highest TPC and RSA. The hexane extract of C. tamariscifolia (CTH) had the highest cytotoxic activity (IC50 = 2.31 µg/mL), and was further tested in four human tumor (cervical adenocarcinoma HeLa; gastric adenocarcinoma AGS; colorectal adenocarcinoma HCT-15; neuroblastoma SH-SY5Y), and two non-tumor (murine bone marrow stroma S17 and human umbilical vein endothelial HUVEC) cell lines in order to determine its selectivity. CTH strongly reduced viability of all tumor cell lines, especially of HepG2 cells. Cytotoxicity was particularly selective for the latter cells with a selectivity index = 12.6 as compared to non-tumor cells. Incubation with CTH led to a 2-fold decrease of HepG2 cell proliferation as shown by the bromodeoxyuridine (BrdU) incorporation assay. CTH-treated HepG2 cells presented also pro-apoptotic features, such as increased Annexin V/propidium iodide (PI) binding and dose-dependent morphological alterations in DAPI-stained cells. Moreover, it had a noticeable disaggregating effect on 3D multicellular tumor spheroids. Demethoxy cystoketal chromane, a derivative of the meroditerpenoid cystoketal, was identified as the active compound in CTH and was shown to display selective in vitro cytotoxicity towards HepG2 cells. creator: Catarina Vizetto-Duarte creator: Luísa Custódio creator: Gerardo Acosta creator: João H.G. Lago creator: Thiago R. Morais creator: Carolina Bruno de Sousa creator: Katkam N. Gangadhar creator: Maria João Rodrigues creator: Hugo Pereira creator: Raquel T. Lima creator: M. Helena Vasconcelos creator: Luísa Barreira creator: Amélia P. Rauter creator: Fernando Albericio creator: João Varela uri: https://doi.org/10.7717/peerj.1704 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Vizetto-Duarte et al. title: A comparison of postnatal arterial patterns in a growth series of giraffe (Artiodactyla: Giraffa camelopardalis) link: https://peerj.com/articles/1696 last-modified: 2016-02-16 description: Nearly all living artiodactyls (even-toed ungulates) possess a derived cranial arterial pattern that is highly distinctive from most other mammals. Foremost among a suite of atypical arterial configurations is the functional and anatomical replacement of the internal carotid artery with an extensive, subdural arterial meshwork called the carotid rete. This interdigitating network branches from the maxillary artery and is housed within the cavernous venous sinus. As the cavernous sinus receives cooled blood draining from the nasal mucosa, heat rapidly dissipates across the high surface area of the rete to be carried away from the brain by the venous system. This combination yields one of the most effective mechanisms of selective brain cooling. Although arterial development begins from the same embryonic scaffolding typical of mammals, possession of a rete is typically accompanied by obliteration of the internal carotid artery. Among taxa with available ontogenetic data, the point at which the internal carotid obliterates is variable throughout development. In small-bodied artiodactyls, the internal carotid typically obliterates prior to parturition, but in larger species, the vessel may remain patent for several years. In this study, we use digital anatomical data collection methods to describe the cranial arterial patterns for a growth series of giraffe (Giraffa camelopardalis), from parturition to senescence. Giraffes, in particular, have unique cardiovascular demands and adaptations owing to their exceptional body form and may not adhere to previously documented stages of cranial arterial development. We find the carotid arterial system to be conserved between developmental stages and that obliteration of the giraffe internal carotid artery occurs prior to parturition. creator: Haley D. O’Brien creator: Paul M. Gignac creator: Tobin L. Hieronymus creator: Lawrence M. Witmer uri: https://doi.org/10.7717/peerj.1696 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 O’Brien et al. title: Initiating a watch list for Ebola virus antibody escape mutations link: https://peerj.com/articles/1674 last-modified: 2016-02-16 description: The 2014 Ebola virus (EBOV) outbreak in West Africa is the largest in recorded history and resulted in over 11,000 deaths. It is essential that strategies for treatment and containment be developed to avoid future epidemics of this magnitude. With the development of vaccines and antibody-based therapies using the envelope glycoprotein (GP) of the 1976 Mayinga strain, one important strategy is to anticipate how the evolution of EBOV might compromise these efforts. In this study we have initiated a watch list of potential antibody escape mutations of EBOV by modeling interactions between GP and the antibody KZ52. The watch list was generated using molecular modeling to estimate stability changes due to mutation. Every possible mutation of GP was considered and the list was generated from those that are predicted to disrupt GP-KZ52 binding but not to disrupt the ability of GP to fold and to form trimers. The resulting watch list contains 34 mutations (one of which has already been seen in humans) at six sites in the GP2 subunit. Should mutations from the watch list appear and spread during an epidemic, it warrants attention as these mutations may reflect an evolutionary response from the virus that could reduce the effectiveness of interventions such as vaccination. However, this watch list is incomplete and emphasizes the need for more experimental structures of EBOV interacting with antibodies in order to expand the watch list to other epitopes. We hope that this work provokes experimental research on evolutionary escape in both Ebola and other viral pathogens. creator: Craig R. Miller creator: Erin L. Johnson creator: Aran Z. Burke creator: Kyle P. Martin creator: Tanya A. Miura creator: Holly A. Wichman creator: Celeste J. Brown creator: F. Marty Ytreberg uri: https://doi.org/10.7717/peerj.1674 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Miller et al. title: A pan-cancer analysis of prognostic genes link: https://peerj.com/articles/1499 last-modified: 2016-02-16 description: Numerous studies have identified prognostic genes in individual cancers, but a thorough pan-cancer analysis has not been performed. In addition, previous studies have mostly used microarray data instead of RNA-SEQ, and have not published comprehensive lists of associations with survival. Using recently available RNA-SEQ and clinical data from The Cancer Genome Atlas for 6,495 patients, we have investigated every annotated and expressed gene’s association with survival across 16 cancer types. The most statistically significant harmful and protective genes were not shared across cancers, but were enriched in distinct gene sets which were shared across certain groups of cancers. These groups of cancers were independently recapitulated by both unsupervised clustering of Cox coefficients (a measure of association with survival) for individual genes, and for gene programs. This analysis has revealed unappreciated commonalities among cancers which may provide insights into cancer pathogenesis and rationales for co-opting treatments between cancers. creator: Jordan Anaya creator: Brian Reon creator: Wei-Min Chen creator: Stefan Bekiranov creator: Anindya Dutta uri: https://doi.org/10.7717/peerj.1499 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Anaya title: Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice link: https://peerj.com/articles/1702 last-modified: 2016-02-15 description: The digestive tract of mammals and other animals is colonized by trillions of metabolically-active microorganisms. Changes in the gut microbiota have been associated with obesity in both humans and laboratory animals. Dietary modifications can often modulate the obese gut microbial ecosystem towards a more healthy state. This phenomenon should preferably be studied using dietary ingredients that are relevant to human nutrition. This study was designed to evaluate the influence of whole-wheat, a food ingredient with several beneficial properties, on gut microorganisms of obese diabetic mice. Diabetic (db/db) mice were fed standard (obese-control) or whole-wheat isocaloric diets (WW group) for eight weeks; non-obese mice were used as control (lean-control). High-throughput sequencing using the MiSeq platform coupled with freely-available computational tools and quantitative real-time PCR were used to analyze fecal bacterial 16S rRNA gene sequences. Short-chain fatty acids were measured in caecal contents using quantitative high-performance liquid chromatography photo-diode array analysis. Results showed no statistical difference in final body weights between the obese-control and the WW group. The bacterial richness (number of Operational Taxonomic Units) did not differ among the treatment groups. The abundance of Ruminococcaceae, a family containing several butyrate-producing bacteria, was found to be higher in obese (median: 6.9%) and WW-supplemented mice (5.6%) compared to lean (2.7%, p = 0.02, Kruskal-Wallis test). Caecal concentrations of butyrate were higher in obese (average: 2.91 mmol/mg of feces) but especially in WW-supplemented mice (4.27 mmol/mg) compared to lean controls (0.97 mmol/mg), while caecal succinic acid was lower in the WW group compared to obese but especially to the lean group. WW consumption was associated with ∼3 times higher abundances of Lactobacillus spp. compared to both obese and lean control mice. Analysis of weighted UniFrac distances revealed a distinctive clustering of lean microbial communities separately from both obese and WW-supplemented mice (p = 0.001, ANOSIM test). Predictive metagenome analysis revealed significant differences in several metabolic features of the microbiota among the treatment groups, including carbohydrate, amino acids and vitamin metabolism (p < 0.01, Kruskal-Wallis test). However, obese and WW groups tended to share more similar abundances of gene families compared to lean mice. Using an in vivo model of obesity and diabetes, this study suggests that daily WW supplementation for eight weeks may not be enough to influence body weight or to output a lean-like microbiome, both taxonomically and metabolically. However, WW-supplementation was associated with several statistically significant differences in the gut microbiome compared to obese controls that deserve further investigation. creator: Jose F. Garcia-Mazcorro creator: Ivan Ivanov creator: David A. Mills creator: Giuliana Noratto uri: https://doi.org/10.7717/peerj.1702 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Garcia-Mazcorro et al. title: Apparent source levels and active communication space of whistles of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in the Pearl River Estuary and Beibu Gulf, China link: https://peerj.com/articles/1695 last-modified: 2016-02-15 description: Background. Knowledge of species-specific vocalization characteristics and their associated active communication space, the effective range over which a communication signal can be detected by a conspecific, is critical for understanding the impacts of underwater acoustic pollution, as well as other threats.Methods. We used a two-dimensional cross-shaped hydrophone array system to record the whistles of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in shallow-water environments of the Pearl River Estuary (PRE) and Beibu Gulf (BG), China. Using hyperbolic position fixing, which exploits time differences of arrival of a signal between pairs of hydrophone receivers, we obtained source location estimates for whistles with good signal-to-noise ratio (SNR ≥10 dB) and not polluted by other sounds and back-calculated their apparent source levels (ASL). Combining with the masking levels (including simultaneous noise levels, masking tonal threshold, and the Sousa auditory threshold) and the custom made site-specific sound propagation models, we further estimated their active communication space (ACS).Results. Humpback dolphins produced whistles with average root-mean-square ASL of 138.5 ± 6.8 (mean ± standard deviation) and 137.2 ± 7.0 dB re 1 µPa in PRE (N = 33) and BG (N = 209), respectively. We found statistically significant differences in ASLs among different whistle contour types. The mean and maximum ACS of whistles were estimated to be 14.7 ± 2.6 (median ± quartile deviation) and 17.1± 3.5 m in PRE, and 34.2 ± 9.5 and 43.5 ± 12.2 m in BG. Using just the auditory threshold as the masking level produced the mean and maximum ACSat of 24.3 ± 4.8 and 35.7 ± 4.6 m for PRE, and 60.7 ± 18.1 and 74.3 ± 25.3 m for BG. The small ACSs were due to the high ambient noise level. Significant differences in ACSs were also observed among different whistle contour types.Discussion. Besides shedding some light for evaluating appropriate noise exposure levels and information for the regulation of underwater acoustic pollution, these baseline data can also be used for aiding the passive acoustic monitoring of dolphin populations, defining the boundaries of separate groups in a more biologically meaningful way during field surveys, and guiding the appropriate approach distance for local dolphin-watching boats and research boat during focal group following. creator: Zhi-Tao Wang creator: Whitlow W.L. Au creator: Luke Rendell creator: Ke-Xiong Wang creator: Hai-Ping Wu creator: Yu-Ping Wu creator: Jian-Chang Liu creator: Guo-Qin Duan creator: Han-Jiang Cao creator: Ding Wang uri: https://doi.org/10.7717/peerj.1695 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Spatial structure arising from neighbour-dependent bias in collective cell movement link: https://peerj.com/articles/1689 last-modified: 2016-02-15 description: Mathematical models of collective cell movement often neglect the effects of spatial structure, such as clustering, on the population dynamics. Typically, they assume that individuals interact with one another in proportion to their average density (the mean-field assumption) which means that cell–cell interactions occurring over short spatial ranges are not accounted for. However, in vitro cell culture studies have shown that spatial correlations can play an important role in determining collective behaviour. Here, we take a combined experimental and modelling approach to explore how individual-level interactions give rise to spatial structure in a moving cell population. Using imaging data from in vitro experiments, we quantify the extent of spatial structure in a population of 3T3 fibroblast cells. To understand how this spatial structure arises, we develop a lattice-free individual-based model (IBM) and simulate cell movement in two spatial dimensions. Our model allows an individual’s direction of movement to be affected by interactions with other cells in its neighbourhood, providing insights into how directional bias generates spatial structure. We consider how this behaviour scales up to the population level by using the IBM to derive a continuum description in terms of the dynamics of spatial moments. In particular, we account for spatial correlations between cells by considering dynamics of the second spatial moment (the average density of pairs of cells). Our numerical results suggest that the moment dynamics description can provide a good approximation to averaged simulation results from the underlying IBM. Using our in vitro data, we estimate parameters for the model and show that it can generate similar spatial structure to that observed in a 3T3 fibroblast cell population. creator: Rachelle N. Binny creator: Parvathi Haridas creator: Alex James creator: Richard Law creator: Matthew J. Simpson creator: Michael J. Plank uri: https://doi.org/10.7717/peerj.1689 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Binny et al. title: Bagworm bags as portable armour against invertebrate predators link: https://peerj.com/articles/1686 last-modified: 2016-02-15 description: Some animals have evolved the use of environmental materials as “portable armour” against natural enemies. Portable bags that bagworm larvae (Lepidoptera: Psychidae) construct using their own silk and plant parts are generally believed to play an important role as a physical barrier against natural enemies. However, no experimental studies have tested the importance of bags as portable armour against predators. To clarify the defensive function, I studied the bagworm Eumeta minuscula and a potential predator Calosoma maximoviczi (Coleoptera: Carabidae). Under laboratory conditions, all bagworm larvae were attacked by carabid adults, but successfully defended themselves against the predators’ mandibles using their own bags. The portable bags, which are composed mainly of host plant twigs, may function as a physical barrier against predator mandibles. To test this hypothesis, I removed the twig bags and replaced some with herb leaf bags; all bag-removed larvae were easily caught and predated by carabids, while all bag-replaced larvae could successfully defend themselves against carabid attacks. Therefore, various types of portable bags can protect bagworm larvae from carabid attacks. This is the first study to test the defensive function of bagworm portable bags against invertebrate predators. creator: Shinji Sugiura uri: https://doi.org/10.7717/peerj.1686 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sugiura title: Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets link: https://peerj.com/articles/1678 last-modified: 2016-02-15 description: In the Allonemobius socius complex of crickets, reproductive isolation is primarily accomplished via postmating prezygotic barriers. We tested seven protein-coding genes expressed in the male ejaculate for patterns of evolution consistent with a putative role as postmating prezygotic isolation genes. Our recently diverged species generally lacked sequence variation. As a result, ω-based tests were only mildly successful. Some of our genes showed evidence of elevated ω values on the internal branches of gene trees. In a couple of genes, these internal branches coincided with both species branching events of the species tree, between A. fasciatus and the other two species, and between A. socius and A. sp. nov. Tex. In comparison, more successful approaches were those that took advantage of the varying degrees of lineage sorting and allele sharing among our young species. These approaches were particularly powerful within the contact zone. Among the genes we tested we found genes with genealogies that indicated relatively advanced degrees of lineage sorting across both allopatric and contact zone alleles. Within a contact zone between two members of the species complex, only a subset of genes maintained allelic segregation despite evidence of ongoing gene flow in other genes. The overlap in these analyses was arginine kinase (AK) and apolipoprotein A-1 binding protein (APBP). These genes represent two of the first examples of sperm maturation, capacitation, and motility proteins with fixed non-synonymous substitutions between species-specific alleles that may lead to postmating prezygotic isolation. Both genes express ejaculate proteins transferred to females during copulation and were previously identified through comparative proteomics. We discuss the potential function of these genes in the context of the specific postmating prezygotic isolation phenotype among our species, namely conspecific sperm precedence and the superior ability of conspecific males to induce oviposition in females. creator: Suegene Noh creator: Jeremy L. Marshall uri: https://doi.org/10.7717/peerj.1678 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Noh and Marshall title: Bodily action penetrates affective perception link: https://peerj.com/articles/1677 last-modified: 2016-02-15 description: Fantoni & Gerbino (2014) showed that subtle postural shifts associated with reaching can have a strong hedonic impact and affect how actors experience facial expressions of emotion. Using a novel Motor Action Mood Induction Procedure (MAMIP), they found consistent congruency effects in participants who performed a facial emotion identification task after a sequence of visually-guided reaches: a face perceived as neutral in a baseline condition appeared slightly happy after comfortable actions and slightly angry after uncomfortable actions. However, skeptics about the penetrability of perception (Zeimbekis & Raftopoulos, 2015) would consider such evidence insufficient to demonstrate that observer’s internal states induced by action comfort/discomfort affect perception in a top-down fashion. The action-modulated mood might have produced a back-end memory effect capable of affecting post-perceptual and decision processing, but not front-end perception.Here, we present evidence that performing a facial emotion detection (not identification) task after MAMIP exhibits systematic mood-congruent sensitivity changes, rather than response bias changes attributable to cognitive set shifts; i.e., we show that observer’s internal states induced by bodily action can modulate affective perception. The detection threshold for happiness was lower after fifty comfortable than uncomfortable reaches; while the detection threshold for anger was lower after fifty uncomfortable than comfortable reaches. Action valence induced an overall sensitivity improvement in detecting subtle variations of congruent facial expressions (happiness after positive comfortable actions, anger after negative uncomfortable actions), in the absence of significant response bias shifts. Notably, both comfortable and uncomfortable reaches impact sensitivity in an approximately symmetric way relative to a baseline inaction condition. All of these constitute compelling evidence of a genuine top-down effect on perception: specifically, facial expressions of emotion are penetrable by action-induced mood. Affective priming by action valence is a candidate mechanism for the influence of observer’s internal states on properties experienced as phenomenally objective and yet loaded with meaning. creator: Carlo Fantoni creator: Sara Rigutti creator: Walter Gerbino uri: https://doi.org/10.7717/peerj.1677 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Fantoni et al. title: A method to construct a points system to predict cardiovascular disease considering repeated measures of risk factors link: https://peerj.com/articles/1673 last-modified: 2016-02-15 description: Current predictive models for cardiovascular disease based on points systems use the baseline situation of the risk factors as independent variables. These models do not take into account the variability of the risk factors over time. Predictive models for other types of disease also exist that do consider the temporal variability of a single biological marker in addition to the baseline variables. However, due to their complexity these other models are not used in daily clinical practice. Bearing in mind the clinical relevance of these issues and that cardiovascular diseases are the leading cause of death worldwide we show the properties and viability of a new methodological alternative for constructing cardiovascular risk scores to make predictions of cardiovascular disease with repeated measures of the risk factors and retaining the simplicity of the points systems so often used in clinical practice (construction, statistical validation by simulation and explanation of potential utilization). We have also applied the system clinically upon a set of simulated data solely to help readers understand the procedure constructed. creator: Antonio Palazón-Bru creator: Julio Antonio Carbayo-Herencia creator: Maria Isabel Vigo creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.1673 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Palazón-Bru et al. title: Effectiveness of adaptive silverware on range of motion of the hand link: https://peerj.com/articles/1667 last-modified: 2016-02-15 description: Background. Hand function is essential to a person’s self-efficacy and greatly affects quality of life. Adapted utensils with handles of increased diameters have historically been used to assist individuals with arthritis or other hand disabilities for feeding, and other related activities of daily living. To date, minimal research has examined the biomechanical effects of modified handles, or quantified the differences in ranges of motion (ROM) when using a standard versus a modified handle. The aim of this study was to quantify the ranges of motion (ROM) required for a healthy hand to use different adaptive spoons with electrogoniometry for the purpose of understanding the physiologic advantages that adapted spoons may provide patients with limited ROM.Methods. Hand measurements included the distal interphalangeal joint (DIP), proximal interphalangeal joint (PIP), and metacarpophalangeal joint (MCP) for each finger and the interphalangeal (IP) and MCP joint for the thumb. Participants were 34 females age 18–30 (mean age 20.38 ± 1.67) with no previous hand injuries or abnormalities. Participants grasped spoons with standard handles, and spoons with handle diameters of 3.18 cm (1.25 inch), and 4.45 cm (1.75 inch). ROM measurements were obtained with an electrogoniometer to record the angle at each joint for each of the spoon handle sizes.Results. A 3 × 3 × 4 repeated measures ANOVA (Spoon handle size by Joint by Finger) found main effects on ROM of Joint (F(2, 33) = 318.68, Partial η2 = .95, p < .001), Spoon handle size (F(2, 33) = 598.73, Partial η2 = .97, p < .001), and Finger (F(3, 32) = 163.83, Partial η2 = .94, p < .001). As the spoon handle diameter size increased, the range of motion utilized to grasp the spoon handle decreased in all joints and all fingers (p < 0.01).Discussion. This study confirms the hypothesis that less range of motion is required to grip utensils with larger diameter handles, which in turn may reduce challenges for patients with limited ROM of the hand. creator: Susan S. McDonald creator: David Levine creator: Jim Richards creator: Lauren Aguilar uri: https://doi.org/10.7717/peerj.1667 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 McDonald et al. title: Effects of early and late cheiloplasty on anterior part of maxillary dental arch development in infants with unilateral complete cleft lip and palate link: https://peerj.com/articles/1620 last-modified: 2016-02-15 description: Objectives. The objective of this study is to compare the impact of early and late reconstruction of complete unilateral cleft lip and palate on the growth and development of the front of the dentoalveolar arch. Methods. This study was carried out in the years 2012–2015 at the Clinic of Plastic, Reconstructive and Aesthetic Surgery in Banska Bystrica. Infants with unilateral complete cleft lip and palate were divided into 2 groups according to the timing of lip reconstruction. Group A consisted of infants with early lip reconstruction–realised in the first 14 days of life. Group B consisted of infants with later lip reconstruction–realised in the third month of age. Maxillary dental casts were obtained for each child in four periods–in the first 14 days of life, in the third month, in the sixth month and in the age of one year. These were followed by the identification, measurement and evaluation of anthropometric parameters. Results. Significant differences were occurred after the reconstruction of the lips in linear and angle measurements between infants in the A and B groups. Conclusion. The early surgical reconstruction of the lips in the first 14 days of life has a positive effect on the growth and development of the anterior segment of the dentoalveolar arch. Early lip reconstruction forms a continuous pressure on the frontal segment, resulting in the earlier remedy of anatomical properties and creates appropriate conditions for the best development of this area. creator: Silvia Valentová-Strenáčiková creator: Radovan Malina uri: https://doi.org/10.7717/peerj.1620 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Valentová-Strenáčiková & Malina title: RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity link: https://peerj.com/articles/1616 last-modified: 2016-02-15 description: Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling. O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system. creator: David A. Anderson creator: Marcus E. Walz creator: Ernesto Weil creator: Peter Tonellato creator: Matthew C. Smith uri: https://doi.org/10.7717/peerj.1616 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Anderson et al. title: Validation of reference genes for quantitative RT-PCR normalization in Suaeda aralocaspica, an annual halophyte with heteromorphism and C4 pathway without Kranz anatomy link: https://peerj.com/articles/1697 last-modified: 2016-02-11 description: Reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful analytical technique for the measurement of gene expression, which depends on the stability of the reference gene used for data normalization. Suaeda aralocaspica, an annual halophyte with heteromorphic seeds and possessing C4 photosynthesis pathway without Kranz anatomy, is an ideal plant species to identify stress tolerance-related genes and compare relative expression at transcriptional level. So far, no molecular information is available for this species. In the present study, six traditionally used reference genes were selected and their expression stability in two types of seeds of S. aralocaspica under different experimental conditions was evaluated. Three analytical programs, geNorm, NormFinder and BestKeeper, were used to assess and rank the stability of reference gene expression. Results revealed that although some reference genes may display different transcriptional profiles between the two types of seeds, β-TUB and GAPDH appeared to be the most suitable references under different developmental stages and tissues. GAPDH was the appropriate reference gene under different germination time points and salt stress conditions, and ACTIN was suitable for various abiotic stress treatments for the two types of seeds. For all the sample pools, β-TUB served as the most stable reference gene, whereas 18S rRNA and 28S rRNA performed poorly and presented as the least stable genes in our study. UBQ seemed to be unsuitable as internal control under different salt treatments. In addition, the expression of a photosynthesis-related gene (PPDK) of C4 pathway and a salt tolerance-related gene (SAT) of S. aralocaspica were used to validate the best performance reference genes. This is the first systematic comparison of reference gene selection for qRT-PCR work in S. aralocaspica and these data will facilitate further studies on gene expression in this species and other euhalophytes. creator: Jing Cao creator: Lu Wang creator: Haiyan Lan uri: https://doi.org/10.7717/peerj.1697 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cao et al. title: Heat shock protein 90 is involved in the regulation of HMGA2-driven growth and epithelial-to-mesenchymal transition of colorectal cancer cells link: https://peerj.com/articles/1683 last-modified: 2016-02-11 description: High Mobility Group AT-hook 2 (HMGA2) is a nonhistone chromatin-binding protein which acts as a transcriptional regulating factor involved in gene transcription. In particular, overexpression of HMGA2 has been demonstrated to associate with neoplastic transformation and tumor progression in Colorectal Cancer (CRC). Thus, HMGA2 is a potential therapeutic target in cancer therapy. Heat Shock Protein 90 (Hsp90) is a chaperone protein required for the stability and function for a number of proteins that promote the growth, mobility, and survival of cancer cells. Moreover, it has shown strong positive connections were observed between Hsp90 inhibitors and CRC, which indicated their potential for use in CRC treatment by using combination of data mining and experimental designs. However, little is known about the effect of Hsp90 inhibition on HMGA2 protein expression in CRC. In this study, we tested the hypothesis that Hsp90 may regulate HMGA2 expression and investigated the relationship between Hsp90 and HMGA2 signaling. The use of the second-generation Hsp90 inhibitor, NVP-AUY922, considerably knocked down HMGA2 expression, and the effects of Hsp90 and HMGA2 knockdown were similar. In addition, Hsp90 knockdown abrogates colocalization of Hsp90 and HMGA2 in CRC cells. Moreover, the suppression of HMGA2 protein expression in response to NVP-AUY922 treatment resulted in ubiquitination and subsequent proteasome-dependant degradation of HMGA2. Furthermore, RNAi-mediated silencing of HMGA2 reduced the survival of CRC cells and increased the sensitivity of these cells to chemotherapy. Finally, we found that the NVP-AUY922-dependent mitigation of HMGA2 signaling occurred also through indirect reactivation of the tumor suppressor microRNA (miRNA), let-7a, or the inhibition of ERK-regulated HMGA2 involved in regulating the growth of CRC cells. Collectively, our studies identify the crucial role for the Hsp90-HMGA2 interaction in maintaining CRC cell survival and migration. These findings have significant implications for inhibition HMGA2-dependent tumorigenesis by clinically available Hsp90 inhibitors. creator: Chun-Yu Kao creator: Pei-Ming Yang creator: Ming-Heng Wu creator: Chi-Chen Huang creator: Yi-Chao Lee creator: Kuen-Haur Lee uri: https://doi.org/10.7717/peerj.1683 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kao et al. title: Testing the effects of perimeter fencing and elephant exclosures on lion predation patterns in a Kenyan wildlife conservancy link: https://peerj.com/articles/1681 last-modified: 2016-02-11 description: The use of fences to segregate wildlife can change predator and prey behaviour. Predators can learn to incorporate fencing into their hunting strategies and prey can learn to avoid foraging near fences. A twelve-strand electric predator-proof fence surrounds our study site. There are also porous one-strand electric fences used to create exclosures where elephant (and giraffe) cannot enter in order to protect blocs of browse vegetation for two critically endangered species, the black rhinoceros (Diceros bicornis) and the Grevy’s zebra (Equus grevyi). The denser vegetation in these exclosures attracts both browsing prey and ambush predators. In this study we examined if lion predation patterns differed near the perimeter fencing and inside the elephant exclosures by mapping the location of kills. We used a spatial analysis to compare the predation patterns near the perimeter fencing and inside the exclosures to predation in the rest of the conservancy. Predation was not over-represented near the perimeter fence but the pattern of predation near the fence suggests that fences may be a contributing factor to predation success. Overall, we found that predation was over-represented inside and within 50 m of the exclosures. However, by examining individual exclosures in greater detail using a hot spot analysis, we found that only a few exclosures contained lion predation hot spots. Although some exclosures provide good hunting grounds for lions, we concluded that exclosures did not necessarily create prey-traps per se and that managers could continue to use this type of exclusionary fencing to protect stands of dense vegetation. creator: Marc Dupuis-Desormeaux creator: Zeke Davidson creator: Laura Pratt creator: Mary Mwololo creator: Suzanne E. MacDonald uri: https://doi.org/10.7717/peerj.1681 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dupuis-Desormeaux et al. title: The effect of agmatine on trichothecene type B and zearalenone production in Fusarium graminearum, F. culmorum and F. poae link: https://peerj.com/articles/1672 last-modified: 2016-02-11 description: Agmatine and other putrescines are known for being strong inducers of deoxynivalenol (DON) production in Fusarium graminearum. Other important species produce DON and/or other trichothecene type B toxins (3 acetylated DON, 15 acetylated DON, Fusarenon-X, Nivalenol), such as F. culmorum and F. poae. In order to verify whether the mechanism of the regulation of trichothecene type B induction by agmatine is shared by different species of Fusarium, we tested the hypothesis on 19 strains belonging to 3 Fusarium species (F. graminearum, F. culmorum, F. poae) with diverse genetic chemotypes (3ADON, 15ADON, NIV) by measuring trichothecene B toxins such as DON, NIV, Fusarenon-X, 3ADON and 15ADON. Moreover, we tested whether other toxins like zearalenone were also boosted by agmatine. The trichothecene type B boosting effect was observed in the majority of strains (13 out of 19) in all the three species. Representative strains from all three genetic chemotypes were able to boost toxin production after agmatine treatment. We identified the non-responding strains to the agmatine stimulus, which may contribute to deciphering the regulatory mechanisms that link toxin production to agmatine (and, more generally, polyamines). creator: Matias Pasquali creator: Emmanuelle Cocco creator: Cédric Guignard creator: Lucien Hoffmann uri: https://doi.org/10.7717/peerj.1672 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pasquali et al. title: Comparison of upper body strength gains between men and women after 10 weeks of resistance training link: https://peerj.com/articles/1627 last-modified: 2016-02-11 description: Resistance training (RT) offers benefits to both men and women. However, the studies about the differences between men and women in response to an RT program are not conclusive and few data are available about upper body strength response. The aim of this study was to compare elbow flexor strength gains in men and women after 10 weeks of RT. Forty-four college-aged men (22.63 ± 2.34 years) and forty-seven college-aged women (21.62 ± 2.96 years) participated in the study. The RT program was performed two days a week for 10 weeks. Before and after the training period, peak torque (PT) of the elbow flexors was measured with an isokinetic dynamometer. PT values were higher in men in comparison to women in pre- and post-tests (p < 0.01). Both males and females significantly increased elbow flexor strength (p < 0.05); however, strength changes did not differ between genders after 10 weeks of RT program (11.61 and 11.76% for men and women, respectively; p > 0.05). Effect sizes were 0.57 and 0.56 for men and women, respectively. In conclusion, the present study suggests that men and women have a similar upper body strength response to RT. creator: Paulo Gentil creator: James Steele creator: Maria C. Pereira creator: Rafael P.M. Castanheira creator: Antonio Paoli creator: Martim Bottaro uri: https://doi.org/10.7717/peerj.1627 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gentil et al. title: On the impact of masking and blocking hypotheses for measuring the efficacy of new tuberculosis vaccines link: https://peerj.com/articles/1513 last-modified: 2016-02-11 description: Over the past 60 years, the Mycobacterium bovis bacille Calmette–Guérin (BCG) has been used worldwide to prevent tuberculosis (TB). However, BCG has shown a very variable efficacy in different trials, offering a wide range of protection in adults against pulmonary TB. One of the most accepted hypotheses to explain these inconsistencies points to the existence of a pre-existing immune response to antigens that are common to environmental sources of mycobacterial antigens and Mycobacterium tuberculosis. Specifically, two different mechanisms have been hypothesized to explain this phenomenon: the masking and the blocking effects. According to masking hypothesis, previous sensitization confers some level of protection against TB that masks vaccine’s effects. In turn, the blocking hypothesis postulates that previous immune response prevents vaccine taking of a new TB vaccine. In this work we introduce a series of models to discriminate between masking and blocking mechanisms and address their relative likelihood. We apply our methodology to the data reported by BCG-REVAC clinical trials, which were specifically designed for studying BCG efficacy variability. Our results yield estimates that are consistent with high levels of blocking (41% in Manaus -95% CI [14–68]- and 96% in Salvador -95% CI [52–100]-). Moreover, we also show that masking does not play any relevant role in modifying vaccine’s efficacy either alone or in addition to blocking. The quantification of these effects around a plausible model constitutes a relevant step towards impact evaluation of novel anti-tuberculosis vaccines, which are susceptible of being affected by similar effects, especially if applied on individuals previously exposed to mycobacterial antigens. creator: Sergio Arregui creator: Joaquín Sanz creator: Dessislava Marinova creator: Carlos Martín creator: Yamir Moreno uri: https://doi.org/10.7717/peerj.1513 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Arregui et al. title: The furculae of the dromaeosaurid dinosaur Dakotaraptor steini are trionychid turtle entoplastra link: https://peerj.com/articles/1691 last-modified: 2016-02-09 description: Dakotaraptor steini is a recently described dromaeosaurid dinosaur from the Upper Cretaceous (Maastrichtian) Hell Creek Formation of South Dakota. Included within the D. steini hypodigm are three elements originally identified as furculae, one of which was made part of the holotype specimen. We show that the elements described as D. steini ‘furculae’ are not theropod dinosaur furculae, but are rather trionychid turtle entoplastra referable to cf. Axestemys splendida. The hypodigm of D. steini should be adjusted accordingly. creator: Victoria M. Arbour creator: Lindsay E. Zanno creator: Derek W. Larson creator: David C. Evans creator: Hans-Dieter Sues uri: https://doi.org/10.7717/peerj.1691 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Arbour et al. title: Is type-D personality trait(s) or state? An examination of type-D temporal stability in older Israeli adults in the community link: https://peerj.com/articles/1690 last-modified: 2016-02-09 description: Background. Type D personality was suggested as a marker of poorer prognosis for patients of cardiovascular disease. It is defined by having a score of 10 or more on both sub-scales of the DS14 questionnaire, Social Inhibition (SI) and Negative Affectivity (NA). As Type D was designed to predict risk, its temporal stability is of prime importance.Methods. Participants in the current study were 285 community volunteers, who completed the DS14, and other personality scales, at a mean interval of six years.Results. The prevalence of Type D did not change. The component traits of Type D showed rank order stability. Type D caseness temporal stability was improved by using the sub-scales product as a criterion. Logistic hierarchical regression predicting Type D classification from Time1 demonstrated that the best predictors were Time1 scores on NA and SI, with the character trait of Cooperation, and the alexithymia score adding some predictive power.Conclusions. The temporal stability of the component traits, and of the prevalence of Type D were excellent. Temporal stability of Type D caseness may be improved by using a product threshold, rather than the current rule. Research is required in order to formulate the optimal timing for Type D measurement for predictive purposes. creator: Ada H. Zohar uri: https://doi.org/10.7717/peerj.1690 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zohar title: Four-dimensional noise reduction using the time series of medical computed tomography datasets with short interval times: a static-phantom study link: https://peerj.com/articles/1680 last-modified: 2016-02-09 description: Backgrounds. This study examines the hypothesis that four-dimensional noise reduction (4DNR) with short interval times reduces noise in cardiac computed tomography (CCT) using “padding” phases. Furthermore, the capability of reducing the reduction dose in CCT using this post-processing technique was assessed.Methods. Using base and quarter radiation doses for CCT (456 and 114 mAs/rot with 120 kVp), a static phantom was scanned ten times with retrospective electrocardiogram gating, and 4DNR with short interval times (50 ms) was performed using a post-processing technique. Differences in the computed tomography (CT) attenuation, contrast-to-noise ratio (CNR) and spatial resolution with modulation transfer function in each dose image obtained with and without 4DNR were assessed by conducting a Tukey–Kramer’s test and non-inferiority test.Results. For the base dose, by using 4DNR, the CNR was improved from 1.18 ± 0.15 to 2.08 ± 0.20 (P = 0.001), while the CT attenuation and spatial resolution of the image of 4DNR did not were significantly inferior to those of reference image (P < 0.001). CNRs of the quarter-dose image in 4DNR also improved to 1.28 ± 0.11, and were not inferior to those of the non-4DNR images of the base dose (P < 0.001).Conclusions. 4DNR with short interval times significantly reduced noise. Furthermore, applying this method to CCT would have the potential of reducing the radiation dose by 75%, while maintaining a similar image noise level. creator: Tatsuya Nishii creator: Atsushi K. Kono creator: Wakiko Tani creator: Erina Suehiro creator: Noriyuki Negi creator: Satoru Takahashi creator: Kazuro Sugimura uri: https://doi.org/10.7717/peerj.1680 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nishii et al. title: Improving the peer-review process and editorial quality: key errors escaping the review and editorial process in top scientific journals link: https://peerj.com/articles/1670 last-modified: 2016-02-09 description: We apply a novel mistake index to assess trends in the proportion of corrections published between 1993 and 2014 in Nature, Science and PNAS. The index revealed a progressive increase in the proportion of corrections published in these three high-quality journals. The index appears to be independent of the journal impact factor or the number of items published, as suggested by a comparative analyses among 16 top scientific journals of different impact factors and disciplines. A more detailed analysis suggests that the trend in the time-to-correction increased significantly over time and also differed among journals (Nature 233 days; Science 136 days; PNAS 232 days). A detailed review of 1,428 errors showed that 60% of corrections were related to figures, authors, references or results. According to the three categories established, 34.7% of the corrections were considered mild, 47.7% moderate and 17.6% severe, also differing among journals. Errors occurring during the printing process were responsible for 5% of corrections in Nature, 3% in Science and 18% in PNAS. The measurement of the temporal trends in the quality of scientific manuscripts can assist editors and reviewers in identifying the most common mistakes, increasing the rigor of peer-review and improving the quality of published scientific manuscripts. creator: Antoni Margalida creator: Mª Àngels Colomer uri: https://doi.org/10.7717/peerj.1670 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Margalida and Colomer title: Taxonomic and systematic revisions to the North American Nimravidae (Mammalia, Carnivora) link: https://peerj.com/articles/1658 last-modified: 2016-02-09 description: The Nimravidae is a family of extinct carnivores commonly referred to as “false saber-tooth cats.” Since their initial discovery, they have prompted difficulty in taxonomic assignments and number of valid species. Past revisions have only examined a handful of genera, while recent advances in cladistic and morphometric analyses have granted us additional avenues to answering questions regarding our understanding of valid nimravid taxa and their phylogenetic relationships. To resolve issues of specific validity, the phylogenetic species concept (PSC) was utilized to maintain consistency in diagnosing valid species, while simultaneously employing character and linear morphometric analyses for confirming the validity of taxa. Determined valid species and taxonomically informative characters were then employed in two differential cladistic analyses to create competing hypotheses of interspecific relationships. The results suggest the validity of twelve species and six monophyletic genera. The first in depth reviews of Pogonodon and Dinictis returned two valid species (P. platycopis, P. davisi) for the former, while only one for the latter (D. felina). The taxonomic validity of Nanosmilus is upheld. Two main clades with substantial support were returned for all cladistic analyses, the Hoplophoneini and Nimravini, with ambiguous positions relative to these main clades for the European taxa: Eofelis, Dinailurictis bonali, and Quercylurus major; and the North American taxa Dinictis and Pogonodon. Eusmilus is determined to represent a non-valid genus for North American taxa, suggesting non-validity for Old World nimravid species as well. Finally, Hoplophoneus mentalis is found to be a junior synonym of Hoplophoneus primaevus, while the validity of Hoplophoneus oharrai is reinstated. creator: Paul Z. Barrett uri: https://doi.org/10.7717/peerj.1658 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Barrett title: PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes link: https://peerj.com/articles/1603 last-modified: 2016-02-08 description: Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have.Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods.Availability.PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki. creator: Ivan Gregor creator: Johannes Dröge creator: Melanie Schirmer creator: Christopher Quince creator: Alice C. McHardy uri: https://doi.org/10.7717/peerj.1603 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gregor et al. title: Examining perceptions of the usefulness and usability of a mobile-based system for pharmacogenomics clinical decision support: a mixed methods study link: https://peerj.com/articles/1671 last-modified: 2016-02-08 description: Background. Pharmacogenomic testing has the potential to improve the safety and efficacy of pharmacotherapy, but clinical application of pharmacogenetic knowledge has remained uncommon. Clinical Decision Support (CDS) systems could help overcome some of the barriers to clinical implementation. The aim of this study was to evaluate the perception and usability of a web- and mobile-enabled CDS system for pharmacogenetics-guided drug therapy–the Medication Safety Code (MSC) system–among potential users (i.e., physicians and pharmacists). Furthermore, this study sought to collect data on the practicability and comprehensibility of potential layouts of a proposed personalized pocket card that is intended to not only contain the machine-readable data for use with the MSC system but also human-readable data on the patient’s pharmacogenomic profile. Methods. We deployed an emergent mixed methods design encompassing (1) qualitative interviews with pharmacists and pharmacy students, (2) a survey among pharmacogenomics experts that included both qualitative and quantitative elements and (3) a quantitative survey among physicians and pharmacists. The interviews followed a semi-structured guide including a hypothetical patient scenario that had to be solved by using the MSC system. The survey among pharmacogenomics experts focused on what information should be printed on the card and how this information should be arranged. Furthermore, the MSC system was evaluated based on two hypothetical patient scenarios and four follow-up questions on the perceived usability. The second survey assessed physicians’ and pharmacists’ attitude towards the MSC system. Results. In total, 101 physicians, pharmacists and PGx experts coming from various relevant fields evaluated the MSC system. Overall, the reaction to the MSC system was positive across all investigated parameters and among all user groups. The majority of participants were able to solve the patient scenarios based on the recommendations displayed on the MSC interface. A frequent request among participants was to provide specific listings of alternative drugs and concrete dosage instructions. Negligence of other patient-specific factors for choosing the right treatment such as renal function and co-medication was a common concern related to the MSC system, while data privacy and cost-benefit considerations emerged as the participants’ major concerns regarding pharmacogenetic testing in general. The results of the card layout evaluation indicate that a gene-centered and tabulated presentation of the patient’s pharmacogenomic profile is helpful and well-accepted. Conclusions. We found that the MSC system was well-received among the physicians and pharmacists included in this study. A personalized pocket card that lists a patient’s metabolizer status along with critically affected drugs can alert physicians and pharmacists to the availability of essential therapy modifications. creator: Kathrin Blagec creator: Katrina M. Romagnoli creator: Richard D. Boyce creator: Matthias Samwald uri: https://doi.org/10.7717/peerj.1671 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Blagec et al. title: The dark cube: dark and light character profiles link: https://peerj.com/articles/1675 last-modified: 2016-02-08 description: Background. Research addressing distinctions and similarities between people’s malevolent character traits (i.e., the Dark Triad: Machiavellianism, narcissism, and psychopathy) has detected inconsistent linear associations to temperament traits. Additionally, these dark traits seem to have a common core expressed as uncooperativeness. Hence, some researchers suggest that the dark traits are best represented as one global construct (i.e., the unification argument) rather than as ternary construct (i.e., the uniqueness argument). We put forward the dark cube (cf. Cloninger’s character cube) comprising eight dark profiles that can be used to compare individuals who differ in one dark character trait while holding the other two constant. Our aim was to investigate in which circumstances individuals who are high in each one of the dark character traits differ in Cloninger’s “light” character traits: self-directedness, cooperativeness, and self-transcendence. We also investigated if people’s dark character profiles were associated to their light character profiles.Method. A total of 997 participants recruited from Amazon’s Mechanical Turk (MTurk) responded to the Short Dark Triad and the Short Character Inventory. Participants were allocated to eight different dark profiles and eight light profiles based on their scores in each of the traits and any possible combination of high and low scores. We used three-way interaction regression analyses and t-tests to investigate differences in light character traits between individuals with different dark profiles. As a second step, we compared the individuals’ dark profile with her/his character profile using an exact cell-wise analysis conducted in the ROPstat software (http://www.ropstat.com).Results. Individuals who expressed high levels of Machiavellianism and those who expressed high levels of psychopathy also expressed low self-directedness and low cooperativeness. Individuals with high levels of narcissism, in contrast, scored high in self-directedness. Moreover, individuals with a profile low in the dark traits were more likely to end up with a profile high in cooperativeness. The opposite was true for those individuals with a profile high in the dark traits. The rest of the cross-comparisons revealed some of the characteristics of human personality as a non-linear complex dynamic system.Conclusions. Our study suggests that individuals who are high in Machiavellianism and psychopathy share a unified non-agentic and uncooperative character (i.e., irresponsible, low in self-control, unempathetic, unhelpful, untolerant), while individuals high in narcissism have a more unique character configuration expressed as high agency and, when the other dark traits are high, highly spiritual but uncooperative. In other words, based on differences in their associations to the light side of character, the Dark Triad seems to be a dyad rather than a triad. creator: Danilo Garcia creator: Patricia Rosenberg uri: https://doi.org/10.7717/peerj.1675 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Garcia and Rosenberg title: The personality trait of behavioral inhibition modulates perceptions of moral character and performance during the trust game: behavioral results and computational modeling link: https://peerj.com/articles/1631 last-modified: 2016-02-08 description: Decisions based on trust are critical for human social interaction. We judge the trustworthiness of partners in social interactions based on a number of partner characteristics as well as experiences with those partners. These decisions are also influenced by personality. The current study examined how the personality trait of behavioral inhibition, which involves the tendency to avoid or withdraw from novelty in both social and non-social situations, is related to explicit ratings of trustworthiness as well as decisions made in the trust game. In the game, healthy young adults interacted with three fictional partners who were portrayed as trustworthy, untrustworthy or neutral through biographical information. Participants could choose to keep $1 or send $3 of virtual money to a partner. The partner could then choose to send $1.5 back to the participant or to keep the entire amount. On any trial in which the participant chose to send, the partner always reciprocated with 50% probability, irrespective of how that partner was portrayed in the biography. Behavioral inhibition was assessed through a self-report questionnaire. Finally, a reinforcement learning computational model was fit to the behavior of each participant. Self-reported ratings of trust confirmed that all participants, irrespective of behavioral inhibition, perceived differences in the moral character of the three partners (trustworthiness of good > neutral > bad partner). Decisions made in the game showed that inhibited participants tended to trust the neutral partner less than uninhibited participants. In contrast, this was not reflected in the ratings of the neutral partner (either pre- or post-game), indicating a dissociation between ratings of trustworthiness and decisions made by inhibited participants. Computational modeling showed that this was due to lower initial trust of the neutral partner rather than a higher learning rate associated with loss, suggesting an implicit bias against the neutral partner. Overall, the results suggest inhibited individuals may be predisposed to interpret neutral or ambiguous information more negatively which could, at least in part, account for the tendency to avoid unfamiliar people characteristic of behaviorally inhibited temperament, as well as its relationship to anxiety disorders. creator: Milen L. Radell creator: Rosanna Sanchez creator: Noah Weinflash creator: Catherine E. Myers uri: https://doi.org/10.7717/peerj.1631 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Identification of fibrillogenic regions in human triosephosphate isomerase link: https://peerj.com/articles/1676 last-modified: 2016-02-04 description: Background. Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate into toxic or functional amyloids. Structural characteristics differ greatly among amyloid proteins reported, so it has been difficult to link the fibrillogenic propensity with structural topology. However, there are ubiquitous topologies not represented in the amyloidome that could be considered as amyloid-resistant attributable to structural features, such is the case of TIM barrel topology.Methods. This work was aimed to study the fibrillogenic propensity of human triosephosphate isomerase (HsTPI) as a model of TIM barrels. In order to do so, aggregation of HsTPI was evaluated under native-like and destabilizing conditions. Fibrillogenic regions were identified by bioinformatics approaches, protein fragmentation and peptide aggregation.Results. We identified four fibrillogenic regions in the HsTPI corresponding to the β3, β6, β7 y α8 of the TIM barrel. From these, the β3-strand region (residues 59–66) was highly fibrillogenic. In aggregation assays, HsTPI under native-like conditions led to amorphous assemblies while under partially denaturing conditions (urea 3.2 M) formed more structured aggregates. This slightly structured aggregates exhibited residual cross-β structure, as demonstrated by the recognition of the WO1 antibody and ATR-FTIR analysis.Discussion. Despite the fibrillogenic regions present in HsTPI, the enzyme maintained under native-favoring conditions displayed low fibrillogenic propensity. This amyloid-resistance can be attributed to the three-dimensional arrangement of the protein, where β-strands, susceptible to aggregation, are protected in the core of the molecule. Destabilization of the protein structure may expose inner regions promoting β-aggregation, as well as the formation of hydrophobic disordered aggregates. Being this last pathway kinetically favored over the thermodynamically more stable fibril aggregation pathway. creator: Edson N. Carcamo-Noriega creator: Gloria Saab-Rincon uri: https://doi.org/10.7717/peerj.1676 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Carcamo-Noriega and Saab-Rincon title: Role of heparan sulfate in mediating CXCL8-induced endothelial cell migration link: https://peerj.com/articles/1669 last-modified: 2016-02-04 description: CXCL8 (Interleukin-8, IL-8) plays an important role in angiogenesis and wound healing by prompting endothelial cell migration. It has been suggested that heparan sulfate (HS) could provide binding sites on endothelial cells to retain and activate highly diffusible cytokines and inflammatory chemokines. In the present study, we aimed to test the hypothesis that HS is essential for enhancement of endothelial cell migration by CXCL8, and to explore the underlying mechanism by detecting the changes in expression and activity of Rho GTPases and in the organization of actin cytoskeleton after enzymatic removal of HS on human umbilical vein endothelial cells (HUVECs) by using heparinase III. Our results revealed that the wound healing induced by CXCL8 was greatly attenuated by removal of HS. The CXCL8-upregulated Rho GTPases including Cdc42, Rac1, and RhoA, and CXCL8-increased Rac1/Rho activity were suppressed by removal of HS. The polymerization and polarization of actin cytoskeleton, and the increasing of stress fibers induced by CXCL8 were also abolished by heparinase III. Taken together, our results demonstrated an essential role of HS in mediating CXCL8-induced endothelial cell migration, and highlighted the biological importance of the interaction between CXCL8 and heparan sulfate in wound healing. creator: Zhiping Yan creator: Jingxia Liu creator: Linshen Xie creator: Xiaoheng Liu creator: Ye Zeng uri: https://doi.org/10.7717/peerj.1669 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yan et al. title: Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution link: https://peerj.com/articles/1668 last-modified: 2016-02-04 description: Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions.Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams’s Kmult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data.Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root point, and the length between the inner root point and the dent point. The species on M. buchanani evolved larger, more robust anchors; those on L. subviridis evolved smaller, more delicate anchors. Anchor shape and size were significantly correlated, suggesting constraints in anchor evolution. Tight integration between the root and the point compartments within anchors confirms the anchor as a single, fully integrated module. The correlation between male copulatory organ morphology and size with anchor shape was consistent with predictions from the Rohde-Hobbs hypothesis.Conclusions. Monogenean anchors are tightly integrated structures, and their shape variation correlates strongly with phylogeny, thus underscoring their value for systematic and evolutionary biology studies. Our MonogeneaGM R package provides tools for researchers to mine biological insights from geometric morphometric data of speciose monogenean genera. creator: Tsung Fei Khang creator: Oi Yoon Michelle Soo creator: Wooi Boon Tan creator: Lee Hong Susan Lim uri: https://doi.org/10.7717/peerj.1668 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Khang et al. title: The use and evaluation of self-regulation techniques can predict health goal attainment in adults: an explorative study link: https://peerj.com/articles/1666 last-modified: 2016-02-04 description: Background. Self-regulation tools are not always used optimally, and implementation intention plans often lack quality. Therefore, this study explored participants’ use and evaluation of self-regulation techniques and their impact on goal attainment.Methods. Data were obtained from 452 adults in a proof of concept (POC) intervention of ‘MyPlan’, an eHealth intervention using self-regulation techniques to promote three healthy behaviours (physical activity (PA), fruit intake, or vegetable intake). Participants applied self-regulation techniques to a self-selected health behaviour, and evaluated the self-regulation techniques. The quality of implementation intentions was rated by the authors as a function of instrumentality (instrumental and non-instrumental) and specificity (non-specific and medium to highly specific). Logistic regression analyses were conducted to predict goal attainment.Results. Goal attainment was significantly predicted by the motivational value of the personal advice (OR:1.86), by the specificity of the implementation intentions (OR:3.5), by the motivational value of the action plan (OR:1.86), and by making a new action plan at follow-up (OR:4.10). Interaction-effects with behaviour showed that the specificity score of the implementation intention plans (OR:4.59), the motivational value of the personal advice (OR:2.38), selecting hindering factors and solutions(OR:2.00) and making a new action plan at follow-up (OR:7.54) were predictive of goal attainment only for fruit or vegetable intake. Also, when participants in the fruit and vegetable group made more than three plans, they were more likely to attain their goal (OR:1.73), whereas the reverse was the case in the PA group (OR:0.34).Discussion. The chance that adults reach fruit and vegetable goals can be increased by including motivating personal advice, self-formulated action plans, and instructions/strategies to make specific implementation intentions into eHealth interventions. To increase the chance that adults reach short-term PA goals, it is suggested to keep eHealth PA interventions simple and focus only on developing a few implementation intentions. However, more research is needed to identify behaviour change techniques that can increase health goal attainment at long-term. creator: Jolien Plaete creator: Ilse De Bourdeaudhuij creator: Maite Verloigne creator: Geert Crombez uri: https://doi.org/10.7717/peerj.1666 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Plaete et al. title: LPS- or Pseudomonas aeruginosa-mediated activation of the macrophage TLR4 signaling cascade depends on membrane lipid composition link: https://peerj.com/articles/1663 last-modified: 2016-02-04 description: It is well known that PUFA impede the LPS-mediated activation of the transcription factor NFkappaB. However, the underlying mode of action has not been clarified yet. To address this issue in a comprehensive approach, we used the monocyte/macrophage cell line RAW264.7 to investigate the consequences of a PUFA supplementation on the TLR4 pathway with a focus on (i) the gene expression of TLR4 itself as well as of its downstream mediators, (ii) the membrane microdomain localization of TLR4 and CD14, (iii) the stimulation-induced interaction of TLR4 and CD14. Our data indicate that the impairment of the TLR4-mediated cell activation by PUFA supplementation is not due to changes in gene expression of mediator proteins of the signaling cascade. Rather, our data provide evidence that the PUFA enrichment of macrophages affects the TLR4 pathway at the membrane level. PUFA incorporation into membrane lipids induces a reordering of membrane microdomains thereby affecting cellular signal transduction. It is important to note that this remodeling of macrophage rafts has no adverse effect on cell viability. Hence, microdomain disruption via macrophage PUFA supplementation has a potential as non-toxic strategy to attenuate inflammatory signaling. creator: Axel Schoeniger creator: Herbert Fuhrmann creator: Julia Schumann uri: https://doi.org/10.7717/peerj.1663 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Schoeniger et al. title: A model for HIV disclosure of a parent’s and/or a child’s illness link: https://peerj.com/articles/1662 last-modified: 2016-02-04 description: HIV prevalence in Kenya remains steady at 5.6% for adults 15 years and older, and 0.9% among children aged below 14 years. Parents and children are known to practice unprotected sex, which has implications for continued HIV spread within the country. Additionally, due to increased accessibility of antiretroviral therapy, more HIV-positive persons are living longer. Therefore, the need for HIV disclosure of a parent’s and/or a child’s HIV status within the country will continue for years to come. We conducted a qualitative phenomenological study to understand the entire process of disclosure from the time of initial HIV diagnosis of an index person within an HIV-affected family, to the time of full disclosure of a parent’s and/or a child’s HIV status to one or more HIV-positive, negative, or untested children within these households. Participants were purposively selected and included 16 HIV-positive parents, seven HIV-positive children, six healthcare professionals (physician, clinical officer, psychologist, registered nurse, social worker, and a peer educator), and five HIV-negative children. All participants underwent an in-depth individualized semistructured interview that was digitally recorded. Interviews were transcribed and analyzed in NVivo 8 using the modified Van Kaam method. Six themes emerged from the data indicating that factors such as HIV testing, living with HIV, evolution of disclosure, questions, emotions, benefits, and consequences of disclosure interact with each other and either impede or facilitate the HIV disclosure process. Kenya currently does not have guidelines for HIV disclosure of a parent’s and/or a child’s HIV status. HIV disclosure is a process that may result in poor outcomes in both parents and children. Therefore, understanding how these factors affect the disclosure process is key to achieving optimal disclosure outcomes in both parents and children. To this end, we propose an HIV disclosure model incorporating these six themes that is geared at helping healthcare professionals provide routine, clinic-based, targeted, disclosure-related counseling/advice and services to HIV-positive parents and their HIV-positive, HIV-negative, and untested children during the HIV disclosure process. The model should help improve HIV disclosure levels within HIV-affected households. Future researchers should test the utility and viability of our HIV disclosure model in different settings and cultures. creator: Grace Gachanja creator: Gary J. Burkholder uri: https://doi.org/10.7717/peerj.1662 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gachanja and Burkholder title: Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution link: https://peerj.com/articles/1661 last-modified: 2016-02-04 description: Background. Highly stable, evolutionarily conserved, small, non-integrative plasmids are commonly found in members of the Chlamydiaceae and, in some species, these plasmids have been strongly linked to virulence. To date, evidence for such a plasmid in Chlamydia pecorum has been ambiguous. In a recent comparative genomic study of porcine, ovine, bovine, and koala C. pecorum isolates, we identified plasmids (pCpec) in a pig and three koala strains, respectively. Screening of further porcine, ovine, bovine, and koala C. pecorum isolates for pCpec showed that pCpec is common, but not ubiquitous in C. pecorum from all of the infected hosts.Methods. We used a combination of (i) bioinformatic mining of previously sequenced C. pecorum genome data sets and (ii) pCpec PCR-amplicon sequencing to characterise a further 17 novel pCpecs in C. pecorum isolates obtained from livestock, including pigs, sheep, and cattle, as well as those from koala.Results and Discussion. This analysis revealed that pCpec is conserved with all eight coding domain sequences (CDSs) present in isolates from each of the hosts studied. Sequence alignments revealed that the 21 pCpecs show 99% nucleotide sequence identity, with 83 single nucleotide polymorphisms (SNPs) shown to differentiate all of the plasmids analysed in this study. SNPs were found to be mostly synonymous and were distributed evenly across all eight pCpec CDSs as well as in the intergenic regions. Although conserved, analyses of the 21 pCpec sequences resolved plasmids into 12 distinct genotypes, with five shared between pCpecs from different isolates, and the remaining seven genotypes being unique to a single pCpec. Phylogenetic analysis revealed congruency and co-evolution of pCpecs with their cognate chromosome, further supporting polyphyletic origin of the koala C. pecorum. This study provides further understanding of the complex epidemiology of this pathogen in livestock and koala hosts and paves the way for studies to evaluate the function of this putative C. pecorum virulence factor. creator: Martina Jelocnik creator: Nathan L. Bachmann creator: Helena Seth-Smith creator: Nicholas R. Thomson creator: Peter Timms creator: Adam M. Polkinghorne uri: https://doi.org/10.7717/peerj.1661 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jelocnik et al. title: Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate link: https://peerj.com/articles/1654 last-modified: 2016-02-04 description: Plant-parasitic nematodes (PPN) need to be adapted to survive in the absence of a suitable host or in hostile environmental conditions. Various forms of developmental arrest including hatching inhibition and dauer stages are used by PPN in order to survive these conditions and spread to other areas. Potato cyst nematodes (PCN) (Globodera pallida and G. rostochiensis) are frequently in an anhydrobiotic state, with unhatched nematode persisting for extended periods of time inside the cyst in the absence of the host. This paper shows fundamental changes in the response of quiescent and diapaused eggs of G. pallida to hydration and following exposure to tomato root diffusate (RD) using microarray gene expression analysis encompassing a broad set of genes. For the quiescent eggs, 547 genes showed differential expression following hydration vs. hydratation and RD (H-RD) treatment whereas 708 genes showed differential regulation for the diapaused eggs following these treatments. The comparison between hydrated quiescent and diapaused eggs showed marked differences, with 2,380 genes that were differentially regulated compared with 987 genes following H-RD. Hydrated quiescent and diapaused eggs were markedly different indicating differences in adaptation for long-term survival. Transport activity is highly up-regulated following H-RD and few genes were coincident between both kinds of eggs. With the quiescent eggs, the majority of genes were related to ion transport (mainly sodium), while the diapaused eggs showed a major diversity of transporters (amino acid transport, ion transport, acetylcholine or other molecules). creator: Juan Emilio Palomares-Rius creator: Pete Hedley creator: Peter J.A. Cock creator: Jenny A. Morris creator: John T. Jones creator: Vivian C. Blok uri: https://doi.org/10.7717/peerj.1654 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Palomares-Rius et al. title: Inside-out flowers of Lacandonia brasiliana (Triuridaceae) provide new insights into fundamental aspects of floral patterning link: https://peerj.com/articles/1653 last-modified: 2016-02-04 description: Background and Aims. A recently described Brazilian species, Lacandonia brasiliana, shares with its longer established putative sister species from Mexico, L. schismatica, inverted floral patterning (carpels surrounding stamens) that is almost unique among angiosperms. We present a detailed ontogenetic study of L. brasiliana for comparison with other members of the tribe Triurideae (Triuridaceae) to explore the possible evolutionary origins of “inside-out” flowers.Methods. Wild-source populations of L. brasiliana were compared morphologically and ontogenetically with related species of Triurideae, using light and scanning electron microscopy.Key Results. Relatively few morphological differences separate flowers of L. brasiliana and L. schismatica. Both species have tepals with late-developing subapical appendages. In both species, the three central (almost sessile) anthers develop precociously with respect to the carpels; the anthers remain closed, and fertilization is achieved via pollen-tube growth from germinating pollen grains of the same cleistogamous flower. Carpels are initiated on fascicles.Conclusions. The close similarity between the two Lacandonia species makes it unlikely that they arose independently from two separate homeotic transformation events; they could either represent sister species or two populations of a single disjunct species. Our study underlines the problematic generic and species boundaries within Triurideae. We present an evolutionary scenario of character evolution in Triuridaceae. The inside-out Lacandonia flower could have resulted from a stabilized homeotic transformation; this hypothesis is not in conflict with constrasting theories of the origin of the Triuridaceae flower, which coincided with a shift to unisexuality. The unisexual yet highly plastic flowers that are typical of Triuridaceae could have pre-adapted the origin of the extraordinary Lacandonia morphology. creator: Paula J. Rudall creator: Marccus Alves creator: Maria das Graças Sajo uri: https://doi.org/10.7717/peerj.1653 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rudall et al. title: The semantic basis of taste-shape associations link: https://peerj.com/articles/1644 last-modified: 2016-02-04 description: Previous research shows that people systematically match tastes with shapes. Here, we assess the extent to which matched taste and shape stimuli share a common semantic space and whether semantically congruent versus incongruent taste/shape associations can influence the speed with which people respond to both shapes and taste words. In Experiment 1, semantic differentiation was used to assess the semantic space of both taste words and shapes. The results suggest a common semantic space containing two principal components (seemingly, intensity and hedonics) and two principal clusters, one including round shapes and the taste word “sweet,” and the other including angular shapes and the taste words “salty,” “sour,” and “bitter.” The former cluster appears more positively-valenced whilst less potent than the latter. In Experiment 2, two speeded classification tasks assessed whether congruent versus incongruent mappings of stimuli and responses (e.g., sweet with round versus sweet with angular) would influence the speed of participants’ responding, to both shapes and taste words. The results revealed an overall effect of congruence with congruent trials yielding faster responses than their incongruent counterparts. These results are consistent with previous evidence suggesting a close relation (or crossmodal correspondence) between tastes and shape curvature that may derive from common semantic coding, perhaps along the intensity and hedonic dimensions. creator: Carlos Velasco creator: Andy T. Woods creator: Lawrence E. Marks creator: Adrian David Cheok creator: Charles Spence uri: https://doi.org/10.7717/peerj.1644 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Velasco et al. title: An inferential study of the phenotype for the chromosome 15q24 microdeletion syndrome: a bootstrap analysis link: https://peerj.com/articles/1641 last-modified: 2016-02-04 description: In January 2012, a review of the cases of chromosome 15q24 microdeletion syndrome was published. However, this study did not include inferential statistics. The aims of the present study were to update the literature search and calculate confidence intervals for the prevalence of each phenotype using bootstrap methodology. Published case reports of patients with the syndrome that included detailed information about breakpoints and phenotype were sought and 36 were included. Deletions in megabase (Mb) pairs were determined to calculate the size of the interstitial deletion of the phenotypes studied in 2012. To determine confidence intervals for the prevalence of the phenotype and the interstitial loss, we used bootstrap methodology. Using the bootstrap percentiles method, we found wide variability in the prevalence of the different phenotypes (3–100%). The mean interstitial deletion size was 2.72 Mb (95% CI [2.35–3.10 Mb]). In comparison with our work, which expanded the literature search by 45 months, there were differences in the prevalence of 17% of the phenotypes, indicating that more studies are needed to analyze this rare disease. creator: Antonio Palazón-Bru creator: Dolores Ramírez-Prado creator: Ernesto Cortés creator: María Soledad Aguilar-Segura creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.1641 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Palazón-Bru et al. title: miR-27b attenuates apoptosis induced by transmissible gastroenteritis virus (TGEV) infection via targeting runt-related transcription factor 1 (RUNX1) link: https://peerj.com/articles/1635 last-modified: 2016-02-04 description: Transmissible gastroenteritis virus (TGEV), belonging to the coronaviridae family, is the key cause of the fatal diarrhea of piglets and results in many pathological processes. microRNAs (miRNAs) play a key role in the regulation of virus-induced apoptosis. During the process of apoptosis induced by TGEV infection in PK-15 cells, the miR-27b is notably down-regulated. Thus, we speculate that miR-27b is involved in regulating the process of apoptosis in PK-15 cells. In this study we demonstrated that the over-expression of miR-27b led to the inhibition of TGEV-induced apoptosis, reduction of Bax protein level, and decrease of caspase-3 and −9 activities. Conversely, silencing of miR-27b by miR-27b inhibitors enhanced apoptosis via up-regulating Bax expression and promoting the activities of caspase-3 and −9 in TGEV-infected cells. Subsequently, the runt-related transcription factor 1 (RUNX1) is a candidate target of miR-27b predicted by bioinformatics search. We further identified that the miR-27b directly bound to the 3′ UTR of RUNX1 mRNA and suppressed RUNX1 expression, which indicates RUNX1 is the direct target gene of miR-27b. The over-expression of RUNX1 increased apoptosis and knockdown RUNX1blocked apoptosis of viral-infected cells via regulating Bax expression and the activities of caspase-3 and −9. Our data reveal that miR-27b may repress the mitochondrial pathway of apoptosis by targeting RUNX1, indicating that TGEV may induce apoptosis via down-regulating miR-27b and that miR-27b may act as a target for therapeutic intervention. creator: Xiaomin Zhao creator: Xiangjun Song creator: Xiaoyuan Bai creator: Naijiao Fei creator: Yong Huang creator: Zhimin Zhao creator: Qian Du creator: Hongling Zhang creator: Liang Zhang creator: Dewen Tong uri: https://doi.org/10.7717/peerj.1635 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhao et al. title: A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms link: https://peerj.com/articles/1599 last-modified: 2016-02-04 description: Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M2 = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed. creator: Nagaraju Indugu creator: Kyle Bittinger creator: Sanjay Kumar creator: Bonnie Vecchiarelli creator: Dipti Pitta uri: https://doi.org/10.7717/peerj.1599 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Indugu et al. title: Can we set a global threshold age to define mature forests? link: https://peerj.com/articles/1595 last-modified: 2016-02-04 description: Globally, mature forests appear to be increasing in biomass density (BD). There is disagreement whether these increases are the result of increases in atmospheric CO2 concentrations or a legacy effect of previous land-use. Recently, it was suggested that a threshold of 450 years should be used to define mature forests and that many forests increasing in BD may be younger than this. However, the study making these suggestions failed to account for the interactions between forest age and climate. Here we revisit the issue to identify: (1) how climate and forest age control global forest BD and (2) whether we can set a threshold age for mature forests. Using data from previously published studies we modelled the impacts of forest age and climate on BD using linear mixed effects models. We examined the potential biases in the dataset by comparing how representative it was of global mature forests in terms of its distribution, the climate space it occupied, and the ages of the forests used. BD increased with forest age, mean annual temperature and annual precipitation. Importantly, the effect of forest age increased with increasing temperature, but the effect of precipitation decreased with increasing temperatures. The dataset was biased towards northern hemisphere forests in relatively dry, cold climates. The dataset was also clearly biased towards forests <250 years of age. Our analysis suggests that there is not a single threshold age for forest maturity. Since climate interacts with forest age to determine BD, a threshold age at which they reach equilibrium can only be determined locally. We caution against using BD as the only determinant of forest maturity since this ignores forest biodiversity and tree size structure which may take longer to recover. Future research should address the utility and cost-effectiveness of different methods for determining whether forests should be classified as mature. creator: Philip Martin creator: Martin Jung creator: Francis Q. Brearley creator: Relena R. Ribbons creator: Emily R. Lines creator: Aerin L. Jacob uri: https://doi.org/10.7717/peerj.1595 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Martin et al. title: Examining the role of red background in magnocellular contribution to face perception link: https://peerj.com/articles/1617 last-modified: 2016-02-04 description: This study examines the role of the magnocellular system in the early stages of face perception, in particular sex categorization. Utilizing the specific property of magnocellular suppression in red light, we investigated visually guided reaching to low and high spatial frequency hybrid faces against red and grey backgrounds. The arm movement curvature measure shows that reduced response of the magnocellular pathway interferes with the low spatial frequency component of face perception. This finding provides behavioral evidence for magnocellular contribution to non-emotional aspect of face perception. creator: Bhuvanesh Awasthi creator: Mark A. Williams creator: Jason Friedman uri: https://doi.org/10.7717/peerj.1617 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Awasthi et al. title: Ship noise extends to frequencies used for echolocation by endangered killer whales link: https://peerj.com/articles/1657 last-modified: 2016-02-02 description: Combining calibrated hydrophone measurements with vessel location data from the Automatic Identification System, we estimate underwater sound pressure levels for 1,582 unique ships that transited the core critical habitat of the endangered Southern Resident killer whales during 28 months between March, 2011, and October, 2013. Median received spectrum levels of noise from 2,809 isolated transits are elevated relative to median background levels not only at low frequencies (20–30 dB re 1 µPa2/Hz from 100 to 1,000 Hz), but also at high frequencies (5–13 dB from 10,000 to 96,000 Hz). Thus, noise received from ships at ranges less than 3 km extends to frequencies used by odontocetes. Broadband received levels (11.5–40,000 Hz) near the shoreline in Haro Strait (WA, USA) for the entire ship population were 110 ± 7 dB re 1 µPa on average. Assuming near-spherical spreading based on a transmission loss experiment we compute mean broadband source levels for the ship population of 173 ± 7 dB re 1 µPa 1 m without accounting for frequency-dependent absorption. Mean ship speed was 7.3 ± 2.0 m/s (14.1 ± 3.9 knots). Most ship classes show a linear relationship between source level and speed with a slope near +2 dB per m/s (+1 dB/knot). Spectrum, 1/12-octave, and 1/3-octave source levels for the whole population have median values that are comparable to previous measurements and models at most frequencies, but for select studies may be relatively low below 200 Hz and high above 20,000 Hz. Median source spectrum levels peak near 50 Hz for all 12 ship classes, have a maximum of 159 dB re 1 µPa2/Hz @ 1 m for container ships, and vary between classes. Below 200 Hz, the class-specific median spectrum levels bifurcate with large commercial ships grouping as higher power noise sources. Within all ship classes spectrum levels vary more at low frequencies than at high frequencies, and the degree of variability is almost halved for classes that have smaller speed standard deviations. This is the first study to present source spectra for populations of different ship classes operating in coastal habitats, including at higher frequencies used by killer whales for both communication and echolocation. creator: Scott Veirs creator: Val Veirs creator: Jason D. Wood uri: https://doi.org/10.7717/peerj.1657 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Veirs et al. title: Late Pleistocene fishes of the Tennessee River Basin: an analysis of a late Pleistocene freshwater fish fauna from Bell Cave (site ACb-2) in Colbert County, Alabama, USA link: https://peerj.com/articles/1648 last-modified: 2016-02-02 description: The Tennessee River Basin is considered one of the most important regions for freshwater biodiversity anywhere on the globe. The Tennessee River Basin currently includes populations of at least half of the described contemporary diversity of extant North American freshwater fishes, crayfish, mussel, and gastropod species. However, comparatively little is known about the biodiversity of this basin from the Pleistocene Epoch, particularly the late Pleistocene (∼10,000 to 30,000 years B.P.) leading to modern Holocene fish diversity patterns. The objective of this study was to describe the fish assemblages of the Tennessee River Basin from the late Pleistocene using a series of faunas from locales throughout the basin documented from published literature, unpublished reports, and an undocumented fauna from Bell Cave (site ACb-2, Colbert County, AL). Herein we discuss 41 unequivocal taxa from 10 late Pleistocene localities within the basin and include a systematic discussion of 11 families, 19 genera, and 24 identifiable species (28 unequivocal taxa) specific to the Bell Cave locality. Among the described fauna are several extirpated (e.g., Northern Pike Esox lucius, Northern Madtom Noturus stigmosus) and a single extinct (Harelip Sucker Moxostoma lacerum) taxa that suggest a combination of late Pleistocene displacement events coupled with more recent changes in habitat that have resulted in modern basin diversity patterns. The Bell Cave locality represents one of the most intact Pleistocene freshwater fish deposits anywhere in North America. Significant preservational, taphonomic, sampling, and identification biases preclude the identification of additional taxa. Overall, this study provides a detailed look into paleo-river ecology, as well as freshwater fish diversity and distribution leading up to the contemporary biodiversity patterns of the Tennessee River Basin and Mississippi River Basin as a whole. creator: Stephen J. Jacquemin creator: Jun A. Ebersole creator: William C. Dickinson creator: Charles N. Ciampaglio uri: https://doi.org/10.7717/peerj.1648 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jacquemin et al. title: Poultry consumption and prostate cancer risk: a meta-analysis link: https://peerj.com/articles/1646 last-modified: 2016-02-02 description: Background. Several kinds of foods are hypothesized to be potential factors contributing to the variation of prostate cancer (PCa) incidence. But the effect of poultry on PCa is still inconsistent and no quantitative assessment has been published up to date. So we conducted this meta-analysis to clarify the association between them.Materials and Methods. We conducted a literature search of PubMed and Embase for studies examining the association between poultry consumption and PCa up to June, 2015. Pooled risk ratio (RR) and corresponding 95% confidence interval (CI) of the highest versus lowest poultry consumption categories were calculated by fixed-effect model or random-effect model.Results. A total of 27 (12 cohort and 15 case-control) studies comprising 23,703 cases and 469,986 noncases were eligible for inclusion. The summary RR of total PCa incidence was 1.03 (95% CI [0.95–1.11]) for the highest versus lowest categories of poultry intake. The heterogeneity between studies was not statistically significant (P = 0.768, I2 = 28.5%). Synthesized analysis of 11 studies on high stage PCa and 8 studies on chicken exposure also demonstrated null association. We also did not obtain significant association in the subgroup of cohort study (RR = 1.04, 95% CI [0.98–1.10]), as well as in the subgroups of population-based case-control study and hospital-based case-control study. Then the studies were divided into three geographic groups: Western countries, Asia and South America. The pooled RRs in these areas did not reveal statistically significant association between poultry and PCa.Conclusions. This meta-analysis suggests no association between poultry consumption and PCa risk. Further well-designed studies are warranted to confirm the result. creator: Qian He creator: Zheng-ce Wan creator: Xiao-bing Xu creator: Jing Wu creator: Guang-lian Xiong uri: https://doi.org/10.7717/peerj.1646 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 He et al. title: Physiological response of the cold-water coral Desmophyllum dianthus to thermal stress and ocean acidification link: https://peerj.com/articles/1606 last-modified: 2016-02-02 description: Rising temperatures and ocean acidification driven by anthropogenic carbon emissions threaten both tropical and temperate corals. However, the synergistic effect of these stressors on coral physiology is still poorly understood, in particular for cold-water corals. This study assessed changes in key physiological parameters (calcification, respiration and ammonium excretion) of the widespread cold-water coral Desmophyllum dianthus maintained for ∼8 months at two temperatures (ambient 12 °C and elevated 15 °C) and two pCO2 conditions (ambient 390 ppm and elevated 750 ppm). At ambient temperatures no change in instantaneous calcification, respiration or ammonium excretion rates was observed at either pCO2 levels. Conversely, elevated temperature (15 °C) significantly reduced calcification rates, and combined elevated temperature and pCO2 significantly reduced respiration rates. Changes in the ratio of respired oxygen to excreted nitrogen (O:N), which provides information on the main sources of energy being metabolized, indicated a shift from mixed use of protein and carbohydrate/lipid as metabolic substrates under control conditions, to less efficient protein-dominated catabolism under both stressors. Overall, this study shows that the physiology of D. dianthus is more sensitive to thermal than pCO2 stress, and that the predicted combination of rising temperatures and ocean acidification in the coming decades may severely impact this cold-water coral species. creator: Andrea Gori creator: Christine Ferrier-Pagès creator: Sebastian J. Hennige creator: Fiona Murray creator: Cécile Rottier creator: Laura C. Wicks creator: J. Murray Roberts uri: https://doi.org/10.7717/peerj.1606 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gori et al. title: The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome link: https://peerj.com/articles/1605 last-modified: 2016-02-02 description: An ever expanding body of research investigates the human microbiome in general and the skin microbiome in particular. Microbiomes vary greatly from individual to individual. Understanding the factors that account for this variation, however, has proven challenging, with many studies able to account statistically for just a small proportion of the inter-individual variation in the abundance, species richness or composition of bacteria. The human armpit has long been noted to host a high biomass bacterial community, and recent studies have highlighted substantial inter-individual variation in armpit bacteria, even relative to variation among individuals for other body habitats. One obvious potential explanation for this variation has to do with the use of personal hygiene products, particularly deodorants and antiperspirants. Here we experimentally manipulate product use to examine the abundance, species richness, and composition of bacterial communities that recolonize the armpits of people with different product use habits. In doing so, we find that when deodorant and antiperspirant use were stopped, culturable bacterial density increased and approached that found on individuals who regularly do not use any product. In addition, when antiperspirants were subsequently applied, bacterial density dramatically declined. These culture-based results are in line with sequence-based comparisons of the effects of long-term product use on bacterial species richness and composition. Sequence-based analyses suggested that individuals who habitually use antiperspirant tended to have a greater richness of bacterial OTUs in their armpits than those who use deodorant. In addition, individuals who used antiperspirants or deodorants long-term, but who stopped using product for two or more days as part of this study, had armpit communities dominated by Staphylococcaceae, whereas those of individuals in our study who habitually used no products were dominated by Corynebacterium. Collectively these results suggest a strong effect of product use on the bacterial composition of armpits. Although stopping the use of deodorant and antiperspirant similarly favors presence of Staphylococcaceae over Corynebacterium, their differential modes of action exert strikingly different effects on the richness of other bacteria living in armpit communities. creator: Julie Urban creator: Daniel J. Fergus creator: Amy M. Savage creator: Megan Ehlers creator: Holly L. Menninger creator: Robert R. Dunn creator: Julie E. Horvath uri: https://doi.org/10.7717/peerj.1605 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Urban et al. title: Auditory ERP response to successive stimuli in infancy link: https://peerj.com/articles/1580 last-modified: 2016-02-02 description: Background. Auditory Event-Related Potentials (ERPs) are useful for understanding early auditory development among infants, as it allows the collection of a relatively large amount of data in a short time. So far, studies that have investigated development in auditory ERPs in infancy have mainly used single sounds as stimuli. Yet in real life, infants must decode successive rather than single acoustic events. In the present study, we tested 4-, 8-, and 12-month-old infants’ auditory ERPs to musical melodies comprising three piano notes, and examined ERPs to each individual note in the melody. Methods. Infants were presented with 360 repetitions of a three-note melody while EEG was recorded from 128 channels on the scalp through a Geodesic Sensor Net. For each infant, both latency and amplitude of auditory components P1 and N2 were measured from averaged ERPs for each individual note. Results. Analysis was restricted to response collected at frontal central site. For all three notes, there was an overall reduction in latency for both P1 and N2 over age. For P1, latency reduction was significant from 4 to 8 months, but not from 8 to 12 months. N2 latency, on the other hand, decreased significantly from 4 to 8 to 12 months. With regard to amplitude, no significant change was found for either P1 or N2. Nevertheless, the waveforms of the three age groups were qualitatively different: for the 4-month-olds, the P1–N2 deflection was attenuated for the second and the third notes; for the 8-month-olds, such attenuation was observed only for the middle note; for the 12-month-olds, the P1 and N2 peaks show relatively equivalent amplitude and peak width across all three notes. Conclusion. Our findings indicate that the infant brain is able to register successive acoustic events in a stream, and ERPs become better time-locked to each composite event over age. Younger infants may have difficulties in responding to late occurring events in a stream, and the onset response to the late events may overlap with the incomplete response to preceding events. creator: Ao Chen creator: Varghese Peter creator: Denis Burnham uri: https://doi.org/10.7717/peerj.1580 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chen et al. title: Performance of women with fibromyalgia in walking up stairs while carrying a load link: https://peerj.com/articles/1656 last-modified: 2016-02-01 description: Background. Fibromyalgia is a chronic disease characterized by widespread pain and other associated symptoms. It has a relevant impact on physical fitness and the ability to perform daily living tasks. The objective of the study was to analyze the step-by-step-performance and the trunk tilt of women with fibromyalgia in the 10-step stair climbing test compared with healthy controls.Methods. A cross-sectional study was carried out. Twelve women suffering from fibromyalgia and eight healthy controls were recruited from a local association. Participants were asked to climb 10 stairs without carrying a load and 10 stairs carrying a load of 5 kg in each hand. Mediolateral trunk tilt was assessed using the “Functional Assessment of Biomechanics (FAB)” wireless motion capture device, and the time between steps was assessed via weight-bearing insoles.Results. Trunk tilt in the stair-climbing task carrying a load was significantly higher in women with fibromyalgia when compared to the healthy controls (2.31 (0.63) vs. 1.69 (0.51) respectively). The effect of carrying a load was significantly higher for women with fibromyalgia compared with healthy controls at the intermediate and final part of the task.Discussion. Trunk tilt during stair climbing while carrying a load was higher in women with FM, which could increase the risk of falling. Additionally, women with FM experienced a higher pace slowdown as a consequence of the load, which supports the need of including specific strength and resistance training to physical therapies for this population. creator: Daniel Collado-Mateo creator: José C. Adsuar creator: Pedro R. Olivares creator: Francisco J. Dominguez-Muñoz creator: Cristina Maestre-Cascales creator: Narcis Gusi uri: https://doi.org/10.7717/peerj.1656 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Collado-Mateo et al. title: Patterns of bird-window collisions inform mitigation on a university campus link: https://peerj.com/articles/1652 last-modified: 2016-02-01 description: Bird-window collisions cause an estimated one billion bird deaths annually in the United States. Building characteristics and surrounding habitat affect collision frequency. Given the importance of collisions as an anthropogenic threat to birds, mitigation is essential. Patterned glass and UV-reflective films have been proven to prevent collisions. At Duke University’s West campus in Durham, North Carolina, we set out to identify the buildings and building characteristics associated with the highest frequencies of collisions in order to propose a mitigation strategy. We surveyed six buildings, stratified by size, and measured architectural characteristics and surrounding area variables. During 21 consecutive days in spring and fall 2014, and spring 2015, we conducted carcass surveys to document collisions. In addition, we also collected ad hoc collision data year-round and recorded the data using the app iNaturalist. Consistent with previous studies, we found a positive relationship between glass area and collisions. Fitzpatrick, the building with the most window area, caused the most collisions. Schwartz and the Perk, the two small buildings with small window areas, had the lowest collision frequencies. Penn, the only building with bird deterrent pattern, caused just two collisions, despite being almost completely made out of glass. Unlike many research projects, our data collection led to mitigation action. A resolution supported by the student government, including news stories in the local media, resulted in the application of a bird deterrent film to the building with the most collisions: Fitzpatrick. We present our collision data and mitigation result to inspire other researchers and organizations to prevent bird-window collisions. creator: Natalia Ocampo-Peñuela creator: R. Scott Winton creator: Charlene J. Wu creator: Erika Zambello creator: Thomas W. Wittig creator: Nicolette L. Cagle uri: https://doi.org/10.7717/peerj.1652 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ocampo-Peñuela et al. title: New material and revision of Melanorosaurus thabanensis, a basal sauropodomorph from the Upper Triassic of Lesotho link: https://peerj.com/articles/1639 last-modified: 2016-02-01 description: Melanorosaurus is a genus of basal sauropodomorph that currently includes two species from Southern Africa. In this paper, we redescribe the holotype femur of Melanorosaurus thabanensis from the Elliot Formation of Lesotho, as well as associated remains. The stratigraphic position of this taxon is reviewed, and it is clear that it comes from the Lower Elliot Formation being, therefore, Late Triassic in age, and not Early Jurassic as originally described. The knowledge of the anatomy of the basal sauropodomorph of Thabana Morena is enhanced by the description of six new skeletal elements from the type locality. The femur and the ilium from Thabana Morena are diagnostic and characterized by unusual proportions. The first phylogenetic analysis including both this specimen and Melanorosaurus is conducted. This analysis leads to the conclusion that the femur described in the original publication of Melanorosaurus thabanensis can no longer be referred to Melanorosaurus. For these reasons, we hereby create Meroktenos gen. nov. to encompass Meroktenos thabanensis comb. nov. creator: Claire Peyre de Fabrègues creator: Ronan Allain uri: https://doi.org/10.7717/peerj.1639 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Peyre de Fabrègues and Allain title: Exploration of the “larval pool”: development and ground-truthing of a larval transport model off leeward Hawai‘i link: https://peerj.com/articles/1636 last-modified: 2016-02-01 description: Most adult reef fish show site fidelity thus dispersal is limited to the mobile larval stage of the fish, and effective management of such species requires an understanding of the patterns of larval dispersal. In this study, we assess larval reef fish distributions in the waters west of the Big Island of Hawai‘i using both in situ and model data. Catches from Cobb midwater trawls off west Hawai‘i show that reef fish larvae are most numerous in offshore waters deeper than 3,000 m and consist largely of pre-settlement Pomacanthids, Acanthurids and Chaetodontids. Utilizing a Lagrangian larval dispersal model, we were able to replicate the observed shore fish distributions from the trawl data and we identified the 100 m depth strata as the most likely depth of occupancy. Additionally, our model showed that for larval shore fish with a pelagic larval duration longer than 40 days there was no significant change in settlement success in our model. By creating a general additive model (GAM) incorporating lunar phase and angle we were able to explain 67.5% of the variance between modeled and in situ Acanthurid abundances. We took steps towards creating a predictive larval distribution model that will greatly aid in understanding the spatiotemporal nature of the larval pool in west Hawai‘i, and the dispersal of larvae throughout the Hawaiian archipelago. creator: Johanna L.K. Wren creator: Donald R. Kobayashi uri: https://doi.org/10.7717/peerj.1636 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wren and Kobayashi title: Estimating and comparing microbial diversity in the presence of sequencing errors link: https://peerj.com/articles/1634 last-modified: 2016-02-01 description: Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes. creator: Chun-Huo Chiu creator: Anne Chao uri: https://doi.org/10.7717/peerj.1634 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chiu & Chao title: Climate envelope predictions indicate an enlarged suitable wintering distribution for Great Bustards (Otis tarda dybowskii) in China for the 21st century link: https://peerj.com/articles/1630 last-modified: 2016-02-01 description: The rapidly changing climate makes humans realize that there is a critical need to incorporate climate change adaptation into conservation planning. Whether the wintering habitats of Great Bustards (Otis tarda dybowskii), a globally endangered migratory subspecies whose population is approximately 1,500–2,200 individuals in China, would be still suitable in a changing climate environment, and where this could be found, is an important protection issue. In this study, we selected the most suitable species distribution model for bustards using climate envelopes from four machine learning models, combining two modelling approaches (TreeNet and Random Forest) with two sets of variables (correlated variables removed or not). We used common evaluation methods area under the receiver operating characteristic curves (AUC) and the True Skill Statistic (TSS) as well as independent test data to identify the most suitable model. As often found elsewhere, we found Random Forest with all environmental variables outperformed in all assessment methods. When we projected the best model to the latest IPCC-CMIP5 climate scenarios (Representative Concentration Pathways (RCPs) 2.6, 4.5 and 8.5 in three Global Circulation Models (GCMs)), and averaged the project results of the three models, we found that suitable wintering habitats in the current bustard distribution would increase during the 21st century. The Northeast Plain and the south of North China were projected to become two major wintering areas for bustards. However, the models suggest that some currently suitable habitats will experience a reduction, such as Dongting Lake and Poyang Lake in the Middle and Lower Yangtze River Basin. Although our results suggested that suitable habitats in China would widen with climate change, greater efforts should be undertaken to assess and mitigate unstudied human disturbance, such as pollution, hunting, agricultural development, infrastructure construction, habitat fragmentation, and oil and mine exploitation. All of these are negatively and intensely linked with global change. creator: Chunrong Mi creator: Huettmann Falk creator: Yumin Guo uri: https://doi.org/10.7717/peerj.1630 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mi et al. title: New insights on Prestosuchus chiniquensis Huene, 1942 (Pseudosuchia, Loricata) based on new specimens from the “Tree Sanga” Outcrop, Chiniquá Region, Rio Grande do Sul, Brazil link: https://peerj.com/articles/1622 last-modified: 2016-02-01 description: The ‘rauisuchians’ are a group of Triassic pseudosuchian archosaurs that displayed a near global distribution. Their problematic taxonomic resolution comes from the fact that most taxa are represented only by a few and/or mostly incomplete specimens. In the last few decades, renewed interest in early archosaur evolution has helped to clarify some of these problems, but further studies on the taxonomic and paleobiological aspects are still needed. In the present work, we describe new material attributed to the ‘rauisuchian’ taxon Prestosuchus chiniquensis, of the Dinodontosaurus Assemblage Zone, Middle Triassic (Ladinian) of the Santa Maria Supersequence of southern Brazil, based on a comparative osteologic analysis. Additionally, we present well supported evidence that these represent juvenile forms, due to differences in osteological features (i.e., a subnarial fenestra) that when compared to previously described specimens can be attributed to ontogeny and indicate variation within a single taxon of a problematic but important osteological structure in the study of ‘rauisuchians.’ creator: Marcel B. Lacerda creator: Bianca M. Mastrantonio creator: Daniel C. Fortier creator: Cesar L. Schultz uri: https://doi.org/10.7717/peerj.1622 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Lacerda et al. title: Phylogenetic and morphologic evidence confirm the presence of a new montane cloud forest associated bird species in Mexico, the Mountain Elaenia (Elaenia frantzii; Aves: Passeriformes: Tyrannidae) link: https://peerj.com/articles/1598 last-modified: 2016-02-01 description: Here we provide evidence to support an extension of the recognized distributional range of the Mountain Elaenia (Elaenia frantzii) to include southern Mexico. We collected two specimens in breeding condition in northwestern Sierra Norte de Chiapas, Mexico. Morphologic and genetic evidence support their identity as Elaenia frantzii. We compared environmental parameters of records across the entire geographic range of the species to those at the northern Chiapas survey site and found no climatic differences among localities. creator: Zachary R. Hanna creator: Marco F. Ortiz-Ramírez creator: César A. Ríos-Muñoz creator: Héctor Cayetano-Rosas creator: Rauri C. K. Bowie creator: Adolfo G. Navarro-Sigüenza uri: https://doi.org/10.7717/peerj.1598 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hanna et al. title: Unequal contribution of native South African phylogeographic lineages to the invasion of the African clawed frog, Xenopus laevis, in Europe link: https://peerj.com/articles/1659 last-modified: 2016-02-01 description: Due to both deliberate and accidental introductions, invasive African Clawed Frog (Xenopus laevis) populations have become established worldwide. In this study, we investigate the geographic origins of invasive X. laevis populations in France and Portugal using the phylogeographic structure of X. laevis in its native South African range. In total, 80 individuals from the whole area known to be invaded in France and Portugal were analysed for two mitochondrial and three nuclear genes, allowing a comparison with 185 specimens from the native range. Our results show that native phylogeographic lineages have contributed differently to invasive European X. laevis populations. In Portugal, genetic and historical data suggest a single colonization event involving a small number of individuals from the south-western Cape region in South Africa. In contrast, French invasive X. laevis encompass two distinct native phylogeographic lineages, i.e., one from the south-western Cape region and one from the northern regions of South Africa. The French X. laevis population is the first example of a X. laevis invasion involving multiple lineages. Moreover, the lack of population structure based on nuclear DNA suggests a potential role for admixture within the invasive French population. creator: Charlotte De Busschere creator: Julien Courant creator: Anthony Herrel creator: Rui Rebelo creator: Dennis Rödder creator: G. John Measey creator: Thierry Backeljau uri: https://doi.org/10.7717/peerj.1659 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 De Busschere et al.