title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2018-01 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: On the morphological variability of Ichniotherium tracks and evolution of locomotion in the sistergroup of amniotes link: https://peerj.com/articles/4346 last-modified: 2018-01-31 description: Ichniotherium tracks with a relatively short pedal digit V (digit length ratio V/IV < 0.6) form the majority of yet described Late Carboniferous to Early Permian diadectomorph tracks and can be related to a certain diadectid clade with corresponding phalangeal reduction that includes Diadectes and its close relatives. Here we document the variation of digit proportions and trackway parameters in 25 trackways (69 step cycles) from nine localities and seven further specimens with incomplete step cycles from the type locality of Ichniotherium cottae (Gottlob quarry) in order to find out whether this type of Ichniotherium tracks represents a homogeneous group or an assemblage of distinct morphotypes and includes variability indicative for evolutionary change in trackmaker locomotion. According to our results, the largest sample of tracks from three Lower Permian sites of the Thuringian Forest, commonly referred to I. cottae, is not homogeneous but shows a clear distinction in pace length, pace angulation, apparent trunk length and toe proportions between tracks from Bromacker quarry and those from the stratigraphically older sites Birkheide and Gottlob quarry. Three Late Carboniferous trackways of Ichniotherium with relatively short pedal digit V from Haine’s Farm, Ohio, and Alveley near Birmingham, United Kingdom, that have been referred to the ichnotaxa “Baropus hainesi,” “Megabaropus hainesi” and “Ichniotherium willsi,” respectively, share a marked outward rotation of foot imprints with respect to walking direction. Apart from this feature they are in many aspects similar to the Birkheide and Gottlob records of I. cottae. With the possible exception of the Maroon Formation (Early Permian, Colorado) sample, Early Permian Ichniotherium trackways with a relatively short pedal digit V fall into the morphological spectrum of the three well defined “Hainesi–Willsi,” “Birkheide–Gottlob” and “Bromacker” morphotypes. With their more obtuse pace angulations and higher body-size-normalized pace and stride lengths the Bromacker type tracks imply higher walking speeds of their trackmakers compared to all other Ichniotherium tracks. More generally, a trend towards higher locomotion capability from the last common ancestor of all Ichniotherium producers to the last common ancestor of all “Ichniotherium with relatively short pedal digit V” and from the latter to the trackmakers of the mid-Early Permian Bromacker type can be deduced—with the reservation that overall sample size is relatively small, making this scenario a preliminary assessment. Whether the presumed advancements represent a more general pattern within diadectomorphs remains open until the non-European Ichniotherium trackway record improves. Ichnotaxonomic implications are discussed. creator: Michael Buchwitz creator: Sebastian Voigt uri: https://doi.org/10.7717/peerj.4346 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Buchwitz and Voigt title: A review of bottom-up vs. top-down control of sponges on Caribbean fore-reefs: what’s old, what’s new, and future directions link: https://peerj.com/articles/4343 last-modified: 2018-01-31 description: Interest in the ecology of sponges on coral reefs has grown in recent years with mounting evidence that sponges are becoming dominant members of reef communities, particularly in the Caribbean. New estimates of water column processing by sponge pumping activities combined with discoveries related to carbon and nutrient cycling have led to novel hypotheses about the role of sponges in reef ecosystem function. Among these developments, a debate has emerged about the relative effects of bottom-up (food availability) and top-down (predation) control on the community of sponges on Caribbean fore-reefs. In this review, we evaluate the impact of the latest findings on the debate, as well as provide new insights based on older citations. Recent studies that employed different research methods have demonstrated that dissolved organic carbon (DOC) and detritus are the principal sources of food for a growing list of sponge species, challenging the idea that the relative availability of living picoplankton is the sole proxy for sponge growth or abundance. New reports have confirmed earlier findings that reef macroalgae release labile DOC available for sponge nutrition. Evidence for top-down control of sponge community structure by fish predation is further supported by gut content studies and historical population estimates of hawksbill turtles, which likely had a much greater impact on relative sponge abundances on Caribbean reefs of the past. Implicit to investigations designed to address the bottom-up vs. top-down debate are appropriate studies of Caribbean fore-reef environments, where benthic communities are relatively homogeneous and terrestrial influences and abiotic effects are minimized. One recent study designed to test both aspects of the debate did so using experiments conducted entirely in shallow lagoonal habitats dominated by mangroves and seagrass beds. The top-down results from this study are reinterpreted as supporting past research demonstrating predator preferences for sponge species that are abundant in these lagoonal habitats, but grazed away in fore-reef habitats. We conclude that sponge communities on Caribbean fore-reefs of the past and present are largely structured by predation, and offer new directions for research, such as determining the environmental conditions under which sponges may be food-limited (e.g., deep sea, lagoonal habitats) and monitoring changes in sponge community structure as populations of hawksbill turtles rebound. creator: Joseph R. Pawlik creator: Tse-Lynn Loh creator: Steven E. McMurray uri: https://doi.org/10.7717/peerj.4343 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Pawlik et al. title: The association between chronic bullying victimization with weight status and body self-image: a cross-national study in 39 countries link: https://peerj.com/articles/4330 last-modified: 2018-01-31 description: BackgroundChildhood obesity and school bullying are pervasive public health issues and known to co-occur in adolescents. However, the association between underweight or thinness and chronic bullying victimization is unclear. The current study examined whether chronic bullying victimization is associated with weight status and body self-image.MethodsA school-based, cross-sectional study in 39 North American and European countries and regions was conducted. A total of 213,595 adolescents aged 11, 13, and 15 years were surveyed in 2009/10. Chronic bullying victimization was identified using the Revised Olweus Bully/Victim Questionnaire. Weight status was determined using self-reported height and weight and the body mass index (BMI), and body self-image was based on perceived weight. We tested associations between underweight and bullying victimization using three-level logistic regression models.ResultsOf the 213,595 adolescents investigated, 11.28% adolescents reported chronic bullying victimization, 14.80% were classified as overweight/obese according to age- and sex-specific BMI criteria, 12.97% were underweight, and 28.36% considered themselves a little bit fat or too fat, 14.57% were too thin. Bullying victimization was less common in older adolescent boys and girls. Weight status was associated with chronic bullying victimization (adjusted ORunderweight = 1.10, 95% CI = 1.05–1.16, p = 0.002; adjusted ORoverweight = 1.40, 95% CI = 1.32–1.49, p < 0.0001; adjusted ORobese = 1.91, 95% CI = 1.71–2.14, p < 0.0001). Body self-image also related to chronic bullying victimization (adjusted ORtoo thin = 1.42, 95% CI = 1.36–1.49, p < 0.0001; adjusted ORa little bit fat = 1.54, 95% CI = 1.48–1.61, p < 0.0001; adjusted ORtoo fat = 3.30, 95% CI = 2.96–3.68, p < 0.0001).ConclusionBoth perceived weight and self-rated overweight are associated with chronic bullying victimization. Both overweight and underweight children are at risk of being chronically bullied. creator: Qiguo Lian creator: Qiru Su creator: Ruili Li creator: Frank J. Elgar creator: Zhihao Liu creator: Dongpeng Zheng uri: https://doi.org/10.7717/peerj.4330 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lian et al. title: The role of awareness of repetition during the development of automaticity in a dot-counting task link: https://peerj.com/articles/4329 last-modified: 2018-01-31 description: This study examined whether being aware of the repetition of stimuli in a simple numerosity task could aid the development of automaticity. The numerosity task used in this study was a simple counting task. Thirty-four participants were divided into two groups. One group was instructed that the stimuli would repeat many times throughout the experiment. The results showed no significant differences in the way automatic processing developed between the groups. Similarly, there was no correlation between the point at which automatic processing developed and the point at which participants felt they benefitted from the repetition of stimuli. These results suggest that extra-trial features of a task may have no effect on the development of automaticity, a finding consistent with the instance theory of automatisation. creator: Craig P. Speelman creator: Emma Shadbolt uri: https://doi.org/10.7717/peerj.4329 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Speelman and Shadbolt title: Evidence for widespread dysregulation of circadian clock progression in human cancer link: https://peerj.com/articles/4327 last-modified: 2018-01-31 description: The ubiquitous daily rhythms in mammalian physiology are guided by progression of the circadian clock. In mice, systemic disruption of the clock can promote tumor growth. In vitro, multiple oncogenes can disrupt the clock. However, due to the difficulties of studying circadian rhythms in solid tissues in humans, whether the clock is disrupted within human tumors has remained unknown. We sought to determine the state of the circadian clock in human cancer using publicly available transcriptome data. We developed a method, called the clock correlation distance (CCD), to infer circadian clock progression in a group of samples based on the co-expression of 12 clock genes. Our method can be applied to modestly sized datasets in which samples are not labeled with time of day and coverage of the circadian cycle is incomplete. We used the method to define a signature of clock gene co-expression in healthy mouse organs, then validated the signature in healthy human tissues. By then comparing human tumor and non-tumor samples from twenty datasets of a range of cancer types, we discovered that clock gene co-expression in tumors is consistently perturbed. Subsequent analysis of data from clock gene knockouts in mice suggested that perturbed clock gene co-expression in human cancer is not caused solely by the inactivation of clock genes. Furthermore, focusing on lung cancer, we found that human lung tumors showed systematic changes in expression in a large set of genes previously inferred to be rhythmic in healthy lung. Our findings suggest that clock progression is dysregulated in many solid human cancers and that this dysregulation could have broad effects on circadian physiology within tumors. In addition, our approach opens the door to using publicly available data to infer circadian clock progression in a multitude of human phenotypes. creator: Jarrod Shilts creator: Guanhua Chen creator: Jacob J. Hughey uri: https://doi.org/10.7717/peerj.4327 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shilts et al. title: Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics link: https://peerj.com/articles/4322 last-modified: 2018-01-31 description: Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines the convergence of functional overrepresentation of genes previously implicated in plant carnivory. Gene Ontology (GO) coding was used to quantitatively score functional representation in these taxa, in terms of proportion of carnivory-associated functions relative to all functional sequence. Statistical analysis revealed that, in carnivorous plants as a group, only two of the 24 functions tested showed a signal of substantial overrepresentation. However, when the four carnivorous taxa were analyzed individually, 11 functions were found to be significant in at least one taxon. Though carnivorous plants collectively may show overrepresentation in functions from the predicted set, the specific functions that are overrepresented vary substantially from taxon to taxon. While it is possible that some functions serve a similar practical purpose such that one taxon does not need to utilize both to achieve the same result, it appears that there are multiple approaches for the evolution of carnivorous function in plant genomes. Our approach could be applied to tests of functional convergence in other systems provided on the availability of genomes and annotation data for a group. creator: Gregory L. Wheeler creator: Bryan C. Carstens uri: https://doi.org/10.7717/peerj.4322 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wheeler and Carstens title: Detours in long-distance migration across the Qinghai-Tibetan Plateau: individual consistency and habitat associations link: https://peerj.com/articles/4304 last-modified: 2018-01-31 description: Migratory birds often follow detours when confronted with ecological barriers, and understanding the extent and the underlying drivers of such detours can provide important insights into the associated cost to the annual energy budget and the migration strategies. The Qinghai-Tibetan Plateau is the most daunting geographical barrier for migratory birds because the partial pressure of oxygen is dramatically reduced and flight costs greatly increase. We analyzed the repeated migration detours and habitat associations of four Pallas’s Gulls Larus ichthyaetus across the Qinghai-Tibetan Plateau over 22 migration seasons. Gulls exhibited notable detours, with the maximum distance being more than double that of the expected shortest route, that extended rather than reduced the passage across the plateau. The extent of longitudinal detours significantly increased with latitude, and detours were longer in autumn than in spring. Compared with the expected shortest routes, proximity to water bodies increased along autumn migration routes, but detour-habitat associations were weak along spring migration routes. Thus, habitat availability was likely one, but not the only, factor shaping the extent of detours, and migration routes were determined by different mechanisms between seasons. Significant between-individual variation but high individual consistency in migration timing and routes were revealed in both seasons, indicating a stronger influence of endogenous schedules than local environmental conditions. Gulls may benefit from repeated use of familiar routes and stopover sites, which may be particularly significant in the challenging environment of the Qinghai-Tibetan Plateau. creator: Dongping Liu creator: Guogang Zhang creator: Hongxing Jiang creator: Jun Lu uri: https://doi.org/10.7717/peerj.4304 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al. title: The first report of the prevalence of Nosema ceranae in Bulgaria link: https://peerj.com/articles/4252 last-modified: 2018-01-31 description: Nosema apis and Nosema ceranae are the two main microsporidian parasites causing nosematosis in the honey bee Apis mellifera. The aim of the present study is to investigate the presence of Nosema apis and Nosema ceranae in the area of Bulgaria. The 16S (SSU) rDNA gene region was chosen for analysis. A duplex PCR assay was performed on 108 honey bee samples from three different parts of the country (South, North and West Bulgaria). The results showed that the samples from the northern part of the country were with the highest prevalence (77.2%) for Nosema ceranae while those from the mountainous parts (the Rodopa Mountains, South Bulgaria) were with the lowest rate (13.9%). Infection with Nosema apis alone and co-infection N. apis/N. ceranae were not detected in any samples. These findings suggest that Nosema ceranae is the dominant species in the Bulgarian honey bee. It is not known when the introduction of Nosema ceranae in Bulgaria has occurred, but as in the rest of the world, this species has become the dominant one in Bulgarian Apis mellifera. In conclusion, this is the first report for molecular detection of Nosema infection of honey bee in Bulgaria. The results showed that N. ceranae is the main Nosema species in Bulgaria. creator: Rositsa Shumkova creator: Ani Georgieva creator: Georgi Radoslavov creator: Daniela Sirakova creator: Gyulnas Dzhebir creator: Boyko Neov creator: Maria Bouga creator: Peter Hristov uri: https://doi.org/10.7717/peerj.4252 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shumkova et al. title: Signals of forest degradation in the demography of common Asian amphibians link: https://peerj.com/articles/4220 last-modified: 2018-01-31 description: BackgroundLowland areas in tropical East and Southeast Asia have a long history of conversion from forestland to agricultural land, with many remaining forests being chronically degraded by wood cutting, livestock grazing, and burning. Wetland-breeding amphibians that have evolved in lowland forests in the region have adjusted to changes in habitat composition caused by humans’ activities, and populations continue to persist. However, we have little understanding of the impacts of forest disturbance on these species beyond assessments of abundance and distribution, and species considered to be common and widespread have been largely neglected.MethodsWe examined body condition and sex ratios of toads (Duttaphrynus melanostictus), predation risk in treefrogs (2 Polypedates spp.), and growth and survival of leaf litter frogs (2 Microhyla spp.) in agricultural land, degraded forest, and intact forest in two study areas, Thailand and Hong Kong.ResultsToad populations exhibited higher body condition and female-biased sex ratios in intact forest. Predation of treefrog embryos by flies was lower in intact and degraded forests than in agricultural land. Embryonic survival and larval growth and survival in leaf litter frogs were lower in intact forests than in agricultural land. Results for each study were similar between study areas.DiscussionFor three of five of these common amphibian species, we documented signals of forest loss and disturbance in their populations. Although these species occur in disturbed habitats, loss of forest cover continues to degrade aspects of their population demography. We urge conservation biologists to consider that populations of species appearing to be common, widespread, and tolerant of human disturbance may be eroding over time. creator: Nancy E. Karraker creator: Samantha Fischer creator: Anchalee Aowphol creator: Jennifer Sheridan creator: Sinlan Poo uri: https://doi.org/10.7717/peerj.4220 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Karraker et al. title: Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing link: https://peerj.com/articles/4198 last-modified: 2018-01-31 description: BackgroundThe Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks.MethodsTo genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed.ResultsOne hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (Hd = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected.DiscussionOur samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while. creator: Nikolett Csizmár creator: Sándor Mihók creator: András Jávor creator: Szilvia Kusza uri: https://doi.org/10.7717/peerj.4198 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Csizmár et al. title: Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A link: https://peerj.com/articles/4276 last-modified: 2018-01-30 description: Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade. creator: Shelby S. Calkins creator: Nicole C. Elledge creator: Katherine E. Mueller creator: Stephen M. Marek creator: MB Couger creator: Mostafa S. Elshahed creator: Noha H. Youssef uri: https://doi.org/10.7717/peerj.4276 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Calkins et al. title: Novel NAC-loaded poly(lactide-co-glycolide acid) nanoparticles for cataract treatment: preparation, characterization, evaluation of structure, cytotoxicity, and molecular docking studies link: https://peerj.com/articles/4270 last-modified: 2018-01-30 description: BackgroundN-acetylcarnosine (NAC), a dipeptide with powerful antioxidant properties that is extensively used as a pharmaceutical prodrug for the treatment of cataract and acute gastric disease, was investigated by molecular dynamics with the GROMACS program in order to understand the solvent effect on peptide conformation of the peptide molecule used as a component of a drug and which presents substantial information on where drug molecules bind and how they exert their effects. Besides, molecular docking simulation was performed by using the AutoDock Vina program which identify the kind of interaction between the drug and proteins. A delivery system based on poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) loaded with NAC (NAC-PLGA-NPs) for the treatment of cataract was prepared for the first time in this study in order to enhance drug bioavailability and biocompatibility. The objective of this work was to prepare and evaluate the structural formulation, characterization, and cytotoxicity studies of NAC-loaded NPs based on PLGA for cataract treatment.MethodsPLGA and NAC-loaded PLGA NPs were prepared using the double emulsion (w/o/w) method, and characterizations of the NPs were carried out with UV–Vis spectrometer to determine drug concentration, the Zeta-sizer system to analyze size and zeta potential, FTIR spectrometer to determine the incorporation of drug and PLGA, and TEM analysis for morphological evaluation.ResultsNAC-loaded PLGA NPs were successfully obtained according to UV–Vis and FTIR spectroscopy, Zeta-sizer system. And it was clearly observed from the TEM analysis that the peptide-loaded NPs had spherical and non-aggregated morphology. Also, the NPs had low toxicity at lower concentrations, and toxicity was augmented by increasing the concentration of the drug.DiscussionThe NAC molecule, which has been investigated as a drug molecule due to its antioxidant and oxidative stress-reducing properties, especially in cataract treatment, was encapsulated with a PLGA polymer in order to increase drug bioavailability. This study may contribute to the design of drugs for cataract treatment with better reactivity and stability. creator: Yasemin Budama-Kilinc creator: Rabia Cakir-Koc creator: Serda Kecel-Gunduz creator: Yagmur Kokcu creator: Bilge Bicak creator: Hande Mutlu creator: Aysen E. Ozel uri: https://doi.org/10.7717/peerj.4270 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Budama-Kilinc et al. title: Ant mosaics in Bornean primary rain forest high canopy depend on spatial scale, time of day, and sampling method link: https://peerj.com/articles/4231 last-modified: 2018-01-30 description: BackgroundCompetitive interactions in biological communities can be thought of as giving rise to “assembly rules” that dictate the species that are able to co-exist. Ant communities in tropical canopies often display a particular pattern, an “ant mosaic”, in which competition between dominant ant species results in a patchwork of mutually exclusive territories. Although ant mosaics have been well-documented in plantation landscapes, their presence in pristine tropical forests remained contentious until recently. Here we assess presence of ant mosaics in a hitherto under-investigated forest stratum, the emergent trees of the high canopy in primary tropical rain forest, and explore how the strength of any ant mosaics is affected by spatial scale, time of day, and sampling method.MethodsTo test whether these factors might impact the detection of ant mosaics in pristine habitats, we sampled ant communities from emergent trees, which rise above the highest canopy layers in lowland dipterocarp rain forests in North Borneo (38.8–60.2 m), using both baiting and insecticide fogging. Critically, we restricted sampling to only the canopy of each focal tree. For baiting, we carried out sampling during both the day and the night. We used null models of species co-occurrence to assess patterns of segregation at within-tree and between-tree scales.ResultsThe numerically dominant ant species on the emergent trees sampled formed a diverse community, with differences in the identity of dominant species between times of day and sampling methods. Between trees, we found patterns of ant species segregation consistent with the existence of ant mosaics using both methods. Within trees, fogged ants were segregated, while baited ants were segregated only at night.DiscussionWe conclude that ant mosaics are present within the emergent trees of the high canopy of tropical rain forest in Malaysian Borneo, and that sampling technique, spatial scale, and time of day interact to determine observed patterns of segregation. Restricting sampling to only emergent trees reveals segregatory patterns not observed in ground-based studies, confirming previous observations of stronger segregation with increasing height in the canopy. creator: Kalsum M. Yusah creator: William A. Foster creator: Glen Reynolds creator: Tom M. Fayle uri: https://doi.org/10.7717/peerj.4231 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yusah et al. title: Positive end expiratory pressure in acute hypoxemic respiratory failure due to community acquired pneumonia: do we need a personalized approach? link: https://peerj.com/articles/4211 last-modified: 2018-01-30 description: BackgroundAcute respiratory failure (ARF) is a life-threatening complication in patients with community acquired pneumonia (CAP). The use of non-invasive ventilation is controversial. With this prospective, observational study we aimed to describe a protocol to assess whether a patient with moderate-to-severe hypoxemic ARF secondary to CAP benefits, in clinical and laboratoristic terms, from the application of a positive end expiratory pressure (PEEP) + oxygen vs oxygen alone.MethodsPatients who benefit from PEEP application (PEEP-responders) were defined as those with partial pressure of arterial oxygen to the fraction of inspired oxygen (PaO2/FiO2) increase >20% and/or reduction of respiratory distress during PEEP + oxygen therapy compared to oxygen therapy alone. Clinical characteristics and outcomes were compared between PEEP-responders and PEEP-non responders.ResultsOut of 41 patients, 27 (66%) benefit from PEEP application (PEEP-responders), the best response was obtained with a PEEP of 10 cmH2O in 13 patients, 7.5 cmH2O in eight and 5 cmH2O in six. PEEP-responders were less likely to present comorbidities compared to PEEP-non responders. No differences between groups were found in regards to endotracheal intubation criteria fullfillment, intensive care unit admission and in-hospital mortality, while PEEP-responders had a shorter length of hospital stay.DiscussionThe application of a protocol to evaluate PEEP responsiveness might be useful in patients with moderate-to-severe hypoxemic ARF due to CAP in order to personalize and maximize the effectiveness of therapy, and prevent the inappropriate PEEP use. PEEP responsiveness does not seem to be associated with better outcomes, with the exception of a shorter length of hospital stay. creator: Valentina Paolini creator: Paola Faverio creator: Stefano Aliberti creator: Grazia Messinesi creator: Giuseppe Foti creator: Oriol Sibila creator: Anna Monzani creator: Federica De Giacomi creator: Anna Stainer creator: Alberto Pesci uri: https://doi.org/10.7717/peerj.4211 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Paolini et al. title: Comparative proteomics reveals that YK51, a 4-Hydroxypandurantin-A analogue, downregulates the expression of proteins associated with dengue virus infection link: https://peerj.com/articles/3939 last-modified: 2018-01-30 description: Dengue is endemic throughout tropical and subtropical regions of the world. Currently, there is no clinically approved therapeutic drug available for this acute viral infection. Although the first dengue vaccine Dengvaxia has been approved for use in certain countries, it is limited to those without a previous dengue infection while the safety and efficacy of the vaccine in those elderly and younger children still need to be identified. Therefore, it is becoming increasingly important to develop therapeutics/drugs to combat dengue virus (DENV) infection. YK51 is a synthetic analogue of 4-Hydroxypandurantin A (a compound found in the crude extract of the rhizomes of Boesenbergia rotunda) that has been extensively studied by our research group. It has been shown to possess outstanding antiviral activity due to its inhibitory activity against NS2B/NS3 DENV2 protease. However, it is not known how YK51 affects the proteome of DENV infected cells. Therefore, we performed a comparative proteomics analysis to identify changes in protein expression in DENV infected HepG2 cells treated with YK51. Classical two-dimensional gel electrophoresis followed by protein identification using tandem mass spectrometry was employed in this study. Thirty proteins were found to be down-regulated with YK51 treatment. In silico analysis predicted that the down-regulation of eight of these proteins may inhibit viral infection. Our results suggested that apart from inhibiting the NS2B/NS3 DENV2 protease, YK51 may also be causing the down-regulation of a number of proteins that may be responsible in, and/or essential to virus infection. However, functional characterization of these proteins will be necessary before we can conclusively determine their roles in DENV infection. creator: Wei-Lian Tan creator: Yean Kee Lee creator: Yen Fong Ho creator: Rohana Yusof creator: Noorsaadah Abdul Rahman creator: Saiful Anuar Karsani uri: https://doi.org/10.7717/peerj.3939 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tan et al. title: Incidence of and social-demographic and obstetric factors associated with postpartum depression: differences among ethnic Han and Kazak women of Northwestern China link: https://peerj.com/articles/4335 last-modified: 2018-01-29 description: BackgroundStudies on postpartum depression (PPD) in China have focused primarily on women of Han ethnicity, whereas work on other ethnic groups has proven limited. This study explored the ethnic differences of associated social-demographic and obstetric factors for PPD between Han-majority and Kazak-minority women in northwestern China.MethodsHan and Kazak women who received routine examinations at four hospitals in a multi-ethnic area of China six weeks after childbirth between March 2016 and December 2016 were included in the study. Data on the women’s socio-demographic characteristics, obstetric factors, and possible depression at six weeks after childbirth were collected. We examined the associated factors of PPD using multivariable logistic regression analyses by ethnic group.ResultsThe overall incidence of PPD was 14.6% (184/1,263) at six weeks after childbirth. PPD was detected more frequently among Kazak (16.1%) than Han women (13.1%). Kazak women exhibited a higher risk of PPD (adjusted OR = 1.561, 95% CI [1.108–2.198], P = 0.011). Urinary incontinence (UI) represented a significant risk factor of PPD for Kazak compared with Han women (OR = 1.720, 95% CI [1.056–2.804], P = 0.003). In contrast, the presence of the mother-in-law as a caregiver after childbirth demonstrated a positive association with PPD among Han (OR = 2.600, 95% CI [1.499–4.512], P = 0.001), but not with Kazak women.ConclusionsKazak women were more likely to develop PPD than Han women, even after controlling for confounders. Moreover, distinct risk factors for PPD existed for Han and Kazak women. Future research that explores the relationships between Han women and their mothers-in-law as well as Kazak women’s attitudes toward UI could help us further understand PPD in these populations. creator: Ling Chen creator: Li Ding creator: Ming Qi creator: Chao Jiang creator: Xin-Min Mao creator: Wen-Zhi Cai uri: https://doi.org/10.7717/peerj.4335 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chen et al. title: Evaluating outcomes of young forest management on a target species of conservation concern link: https://peerj.com/articles/4319 last-modified: 2018-01-29 description: BackgroundAssessing outcomes of habitat management is critical for informing and adapting conservation plans. From 2013–2019, a multi-stage management initiative aims to create >26,000 ha of shrubland and early-successional vegetation to benefit Golden-winged Warblers (Vermivora chrysoptera) in managed forested landscapes of the western Great Lakes region. We studied a dense breeding population of Golden-winged Warblers at Rice Lake National Wildlife Refuge (NWR) in Minnesota, USA, where shrubs and young trees were sheared during the winter of 2014–2015 in a single treatment supported in part by the American Bird Conservancy (ABC) and in part by other funding source(s) to benefit Golden-winged Warblers and other species associated with young forest [e.g., American Woodcock (Scalopax minor)] and as part of maintenance of early successional forest cover on the refuge.MethodsWe monitored abundance of Golden-winged Warblers before (2013–2014) and after (2015–2016) management at the treatment site and a control site, and we estimated full-season productivity (i.e., young recruited into the fall population) on the treatment site from predictive, spatially explicit models, informed by nest and fledgling survival data collected at sites in the western Great Lakes region, including Rice Lake NWR, during 2011 and 2012. Then, using biologically informed models of Golden-winged Warbler response to observed and predicted vegetation succession, we estimated the cumulative change in population recruitment over various scenarios of vegetation succession and demographic response.ResultsWe observed a 32% decline in abundance of Golden-winged Warbler breeding pairs on the treatment site and estimated a 27% decline in per-pair full-season productivity following management, compared to no change in a nearby control site. In models that ranged from highly optimistic to progressively more realistic scenarios, we estimated a net loss of 72–460 juvenile Golden-winged Warblers produced from the treatment site in the 10–20 years following management. Even if our well-informed and locally validated productivity models produced erroneous estimates and the management resulted in only a temporary reduction in abundance (i.e., no change in productivity), our forecast models still predicted a net loss of 61–260 juvenile Golden-winged Warblers from the treatment site over the same time frame.ConclusionsOur study sites represent only a small portion of a large young-forest management initiative directed at Golden-winged Warblers in the western Great Lakes region; however, the brush management, or shearing of shrubs and small trees, that was applied at our study site is a common treatment applied by contractors funded by ABC and its partners on public lands across Minnesota with the expressed intent of benefiting Golden-winged Warblers and related species. Furthermore, the resulting vegetation structure at our treatment site is consistent with that of other areas managed under the initiative, and ABC documents include our study site as successful Golden-winged Warbler management based on observations of ≥1 Golden-winged Warbler at the treatment site since the management. Our assessment demonstrates that, at least for the only site for which pre- and post-management data on Golden-winged Warblers exist, the shearing of shrubs and small trees has had a substantial and likely enduring negative impact on Golden-winged Warblers. We suggest that incorporating region-specific, empirical information about Golden-winged Warbler—habitat relations into habitat management efforts would increase the likelihood of a positive response by Golden-winged Warblers and also suggest that management directed generically at young forest may not benefit Golden-winged Warblers. creator: Henry M. Streby creator: Gunnar R. Kramer creator: Sean M. Peterson creator: David E. Andersen uri: https://doi.org/10.7717/peerj.4319 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Equine glucagon-like peptide-1 receptor physiology link: https://peerj.com/articles/4316 last-modified: 2018-01-29 description: BackgroundEquine metabolic syndrome (EMS) is associated with insulin dysregulation, which often manifests as post-prandial hyperinsulinemia. Circulating concentrations of the incretin hormone, glucagon-like peptide-1 (GLP-1) correlate with an increased insulin response to carbohydrate intake in animals with EMS. However, little is known about the equine GLP-1 receptor (eGLP-1R), or whether GLP-1 concentrations can be manipulated. The objectives were to determine (1) the tissue localisation of the eGLP-1R, (2) the GLP-1 secretory capacity of equine intestine in response to glucose and (3) whether GLP-1 stimulated insulin secretion from isolated pancreatic islets can be attenuated.MethodsArchived and abattoir-sourced tissues from healthy horses were used. Reverse transcriptase PCR was used to determine the tissue distribution of the eGLP-1R gene, with immunohistochemical confirmation of its pancreatic location. The GLP-1 secretion from intestinal explants in response to 4 and 12 mM glucose was quantified in vitro. Pancreatic islets were freshly isolated to assess the insulin secretory response to GLP-1 agonism and antagonism in vitro, using concentration-response experiments.ResultsThe eGLP-1R gene is widely distributed in horses (pancreas, heart, liver, kidney, duodenum, digital lamellae, tongue and gluteal skeletal muscle). Within the pancreas the eGLP-1R was immunolocalised to the pancreatic islets. Insulin secretion from pancreatic islets was concentration-dependent with human GLP-1, but not the synthetic analogue exendin-4. The GLP-1R antagonist exendin 9-39 (1 nM) reduced (P = 0.08) insulin secretion by 27%.DiscussionThe distribution of the eGLP-1R across a range of tissues indicates that it may have functions beyond insulin release. The ability to reduce insulin secretion, and therefore hyperinsulinemia, through eGLP-1R antagonism is a promising and novel approach to managing equine insulin dysregulation. creator: Murad H. Kheder creator: Simon R. Bailey creator: Kevin J. Dudley creator: Martin N. Sillence creator: Melody A. de Laat uri: https://doi.org/10.7717/peerj.4316 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kheder et al. title: Gene-based association study for lipid traits in diverse cohorts implicates BACE1 and SIDT2 regulation in triglyceride levels link: https://peerj.com/articles/4314 last-modified: 2018-01-29 description: Plasma lipid levels are risk factors for cardiovascular disease, a leading cause of death worldwide. While many studies have been conducted on lipid genetics, they mainly focus on Europeans and thus their transferability to diverse populations is unclear. We performed SNP- and gene-level genome-wide association studies (GWAS) of four lipid traits in cohorts from Nigeria and the Philippines and compared them to the results of larger, predominantly European meta-analyses. Two previously implicated loci met genome-wide significance in our SNP-level GWAS in the Nigerian cohort, rs34065661 in CETP associated with HDL cholesterol (P = 9.0 × 10−10) and rs1065853 upstream of APOE associated with LDL cholesterol (P = 6.6 × 10−9). The top SNP in the Filipino cohort associated with triglyceride levels (rs662799; P = 2.7 × 10−16) and has been previously implicated in other East Asian studies. While this SNP is located directly upstream of well known APOA5, we show it may also be involved in the regulation of BACE1 and SIDT2. Our gene-based association analysis, PrediXcan, revealed decreased expression of BACE1 and decreased expression of SIDT2 in several tissues, all driven by rs662799, significantly associate with increased triglyceride levels in Filipinos (FDR <0.1). In addition, our PrediXcan analysis implicated gene regulation as the mechanism underlying the associations of many other previously discovered lipid loci. Our novel BACE1 and SIDT2 findings were confirmed using summary statistics from the Global Lipids Genetic Consortium (GLGC) meta-GWAS. creator: Angela Andaleon creator: Lauren S. Mogil creator: Heather E. Wheeler uri: https://doi.org/10.7717/peerj.4314 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Andaleon et al. title: Cost-benefit analysis for invasive species control: the case of greater Canada goose Branta canadensis in Flanders (northern Belgium) link: https://peerj.com/articles/4283 last-modified: 2018-01-29 description: BackgroundSound decisions on control actions for established invasive alien species (IAS) require information on ecological as well as socio-economic impact of the species and of its management. Cost-benefit analysis provides part of this information, yet has received relatively little attention in the scientific literature on IAS.MethodsWe apply a bio-economic model in a cost-benefit analysis framework to greater Canada goose Branta canadensis, an IAS with documented social, economic and ecological impacts in Flanders (northern Belgium). We compared a business as usual (BAU) scenario which involved non-coordinated hunting and egg destruction with an enhanced scenario based on a continuation of these activities but supplemented with coordinated capture of moulting birds. To assess population growth under the BAU scenario we fitted a logistic growth model to the observed pre-moult capture population. Projected damage costs included water eutrophication and damage to cultivated grasslands and were calculated for all scenarios. Management costs of the moult captures were based on a representative average of the actual cost of planning and executing moult captures.ResultsComparing the scenarios with different capture rates, different costs for eutrophication and various discount rates, showed avoided damage costs were in the range of 21.15 M€ to 45.82 M€ under the moult capture scenario. The lowest value for the avoided costs applied to the scenario where we lowered the capture rate by 10%. The highest value occurred in the scenario where we lowered the real discount rate from 4% to 2.5%.DiscussionThe reduction in damage costs always outweighed the additional management costs of moult captures. Therefore, additional coordinated moult captures could be applied to limit the negative economic impact of greater Canada goose at a regional scale. We further discuss the strengths and weaknesses of our approach and its potential application to other IAS. creator: Nikolaas Reyns creator: Jim Casaer creator: Lieven De Smet creator: Koen Devos creator: Frank Huysentruyt creator: Peter A. Robertson creator: Tom Verbeke creator: Tim Adriaens uri: https://doi.org/10.7717/peerj.4283 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Reyns et al. title: Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea link: https://peerj.com/articles/4272 last-modified: 2018-01-29 description: The eutrophic Bohai Sea receives large amount of suspended material, nutrients and contaminant from terrestrial runoff, and exchanges waters with the northern Yellow Sea through a narrow strait. This coastal region provides an ideal model system to study microbial biogeography. We performed high-throughput sequencing to investigate the distribution of bacterial taxa along spatial and environmental gradients. The results showed bacterial communities presented remarkable horizontal and vertical distribution under coastal gradients of spatial and environmental factors. Fourteen abundant taxa clustered the samples into three distinctive groups, reflecting typical habitats in shallow coastal water (seafloor depth ≤ 20 m), sunlit surface layer (at water surface with seafloor depth >20 m) and bottom water (at 2–3 m above sediment with seafloor depth >20 m). The most significant taxa of each cluster were determined by the least discriminant analysis effect size, and strongly correlated with spatial and environmental variables. Environmental factors (especially turbidity and nitrite) exhibited significant influences on bacterial beta-diversity in surface water (at 0 m sampling depth), while community similarity in bottom water (at 2–3 m above sediment) was mainly determined by depth. In both surface and bottom water, we found bacterial community similarity and the number of OTUs shared between every two sites decreased with increasing geographic distance. Bacterial dispersal was also affected by phosphate, which was possible due to the high ratios of IN/IP in this coastal sea area. creator: Shu-Xian Yu creator: Yun-Long Pang creator: Yin-Chu Wang creator: Jia-Lin Li creator: Song Qin uri: https://doi.org/10.7717/peerj.4272 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yu et al. title: Intra-colonial diversity in the scleractinian coral, Acropora millepora: identifying the nutritional gradients underlying physiological integration and compartmentalised functioning link: https://peerj.com/articles/4239 last-modified: 2018-01-29 description: Scleractinian corals are colonial organisms comprising multiple physiologically integrated polyps and branches. Colonialism in corals is highly beneficial, and allows a single colony to undergo several life processes at once through physiological integration and compartmentalised functioning. Elucidating differences in the biochemical composition of intra-colonial branch positions will provide valuable insight into the nutritional reserves underlying different regions in individual coral colonies. This will also ascertain prudent harvesting strategies of wild donor-colonies to generate coral stock with high survival and vigour prospects for reef-rehabilitation efforts and captive husbandry. This study examined the effects of colony branch position on the nutritional profile of two different colony sizes of the common scleractinian, Acropora millepora. For smaller colonies, branches were sampled at three locations: the colony centre (S-centre), 50% of the longitudinal radius length (LRL) (S-50), and the colony edge (S-edge). For larger colonies, four locations were sampled: the colony centre (L-centre), 33.3% of the LRL (L-33), 66.6% of the LRL (L-66), and the edge (L-edge). Results demonstrate significant branch position effects, with the edge regions containing higher protein, likely due to increased tissue synthesis and calcification. Meanwhile, storage lipid and total fatty acid concentrations were lower at the edges, possibly reflecting catabolism of high-energy nutrients to support proliferating cells. Results also showed a significant effect of colony size in the two classes examined. While the major protein and structural lipid sink was exhibited at the edge for both sizes, the major sink for high-energy lipids and fatty acids appeared to be the L-66 position of the larger colonies and the S-centre and S-50 positions for the smaller colonies. These results confirm that the scleractinian coral colony is not nutritionally homogeneous, and while different regions of the coral colony are functionally specialised, so too are their nutritional profiles geared toward meeting specific energetic demands. creator: Jessica A. Conlan creator: Craig A. Humphrey creator: Andrea Severati creator: David S. Francis uri: https://doi.org/10.7717/peerj.4239 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Conlan et al. title: Establishment of an immortalized mouse dermal papilla cell strain with optimized culture strategy link: https://peerj.com/articles/4306 last-modified: 2018-01-26 description: Dermal papilla (DP) plays important roles in hair follicle regeneration. Long-term culture of mouse DP cells can provide enough cells for research and application of DP cells. We optimized the culture strategy for DP cells from three dimensions: stepwise dissection, collagen I coating, and optimized culture medium. Based on the optimized culture strategy, we immortalized primary DP cells with SV40 large T antigen, and established several immortalized DP cell strains. By comparing molecular expression and morphologic characteristics with primary DP cells, we found one cell strain named iDP6 was similar with primary DP cells. Further identifications illustrate that iDP6 expresses FGF7 and α-SMA, and has activity of alkaline phosphatase. During the process of characterization of immortalized DP cell strains, we also found that cells in DP were heterogeneous. We successfully optimized culture strategy for DP cells, and established an immortalized DP cell strain suitable for research and application of DP cells. creator: Haiying Guo creator: Yizhan Xing creator: Yiming Zhang creator: Long He creator: Fang Deng creator: Xiaogen Ma creator: Yuhong Li uri: https://doi.org/10.7717/peerj.4306 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Guo et al. title: Remote collection of microorganisms at two depths in a freshwater lake using an unmanned surface vehicle (USV) link: https://peerj.com/articles/4290 last-modified: 2018-01-26 description: Microorganisms are ubiquitous in freshwater aquatic environments, but little is known about their abundance, diversity, and transport. We designed and deployed a remote-operated water-sampling system onboard an unmanned surface vehicle (USV, a remote-controlled boat) to collect and characterize microbes in a freshwater lake in Virginia, USA. The USV collected water samples simultaneously at 5 and 50 cm below the surface of the water at three separate locations over three days in October, 2016. These samples were plated on a non-selective medium (TSA) and on a medium selective for the genus Pseudomonas (KBC) to estimate concentrations of culturable bacteria in the lake. Mean concentrations ranged from 134 to 407 CFU/mL for microbes cultured on TSA, and from 2 to 8 CFU/mL for microbes cultured on KBC. There was a significant difference in the concentration of microbes cultured on KBC across three sampling locations in the lake (P = 0.027), suggesting an uneven distribution of Pseudomonas across the locations sampled. There was also a significant difference in concentrations of microbes cultured on TSA across the three sampling days (P = 0.038), demonstrating daily fluctuations in concentrations of culturable bacteria. There was no significant difference in concentrations of microbes cultured on TSA (P = 0.707) and KBC (P = 0.641) across the two depths sampled, suggesting microorganisms were well-mixed between 5 and 50 cm below the surface of the water. About 1 percent (7/720) of the colonies recovered across all four sampling missions were ice nucleation active (ice+) at temperatures warmer than −10 °C. Our work extends traditional manned observations of aquatic environments to unmanned systems, and highlights the potential for USVs to understand the distribution and diversity of microbes within and above freshwater aquatic environments. creator: Craig Powers creator: Regina Hanlon creator: David G. Schmale III uri: https://doi.org/10.7717/peerj.4290 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Powers et al. title: Identification by shape-based virtual screening and evaluation of new tyrosinase inhibitors link: https://peerj.com/articles/4206 last-modified: 2018-01-26 description: Targeting tyrosinase is considered to be an effective way to control the production of melanin. Tyrosinase inhibitor is anticipated to provide new therapy to prevent skin pigmentation, melanoma and neurodegenerative diseases. Herein, we report our results in identifying new tyrosinase inhibitors. The shape-based virtual screening was performed to discover new tyrosinase inhibitors. Thirteen potential hits derived from virtual screening were tested by biological determinations. Compound 5186-0429 exhibited the most potent inhibitory activity. It dose-dependently inhibited the activity of tyrosinase, with the IC50 values 6.2 ± 2.0 µM and 10.3 ± 5.4 µM on tyrosine and L-Dopa formation, respectively. The kinetic study of 5186-0429 demonstrated that this compound acted as a competitive inhibitor. We believe the discoveries here could serve as a good starting point for further design of potent tyrosinase inhibitor. creator: Qi Li creator: Hongyu Yang creator: Jun Mo creator: Yao Chen creator: Yue Wu creator: Chen Kang creator: Yuan Sun creator: Haopeng Sun uri: https://doi.org/10.7717/peerj.4206 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: The oldest Archaeopteryx (Theropoda: Avialiae): a new specimen from the Kimmeridgian/Tithonian boundary of Schamhaupten, Bavaria link: https://peerj.com/articles/4191 last-modified: 2018-01-26 description: The iconic primeval bird Archaeopteryx was so far mainly known from the Altmühltal Formation (early Tithonian) of Bavaria, southern Germany, with one specimen having been found in the overlying Mörnsheim Formation. A new specimen (the 12th skeletal specimen) from the earliest Tithonian Painten Formation of Schamhaupten (Bavaria) represents the so far oldest representative of the genus. The new specimen shows several interesting anatomical details, including the presence of a postorbital in contact with the jugal, the presence of a separate prefrontal and coronoid, and opisthocoelous mid-cervical vertebrae. Based on observations on the new specimen, we discuss several problematic issues concerning Archaeopteryx, including the monophyly and diagnosis of the genus, the absence/presence of the sternum, the position of the gastralia, and variation in morphometrics and dental morphology in that genus. Based on a new diagnosis for the genus Archaeopteryx, the Berlin, Eichstätt, Solnhofen, Munich, Daiting, Thermopolis, 11th, and 12th specimens can be referred to this genus with high certainty. The Maxberg specimen is very probably also an Archaeopteryx, based on overall similarity, although none of the diagnostic characters can be evaluated with certainty. The ninth specimen (‘chicken wing’) might be Archaeopteryx, but cannot be referred to the genus with any certainty. In comparison with other paravians, the presence of distally thickened anterior pectoral ribs indicates that a rather large cartilagenous sternum was present in this taxon. In contrast to non-opisthopubic theropods, opisthopubic taxa, such as Archaeopteryx and many other paravians, have the posterior end of the gastral basket preserved at about half-length of the pubis, which might reflect the post-mortem collapse of enlarged abdominal air sacs in these taxa. Specimens that can be referred to Archaeopteryx show a high amount of variation, both in the morphometrics of the limb bones as well as in the dentition. In respect to the latter aspect, variation is found in tooth number, spacing, orientation, and morphology, with no two specimens showing the exact same pattern. The significance of this variation is unclear, and possible explanations reach from high intraspecific (and possibly ontogenetic and/or sexual dimorphic) variation to the possibility that the known specimens represent a ‘species flock’ of Archaeopteryx, possibly due to island speciation after the initial dispersal of the genus into the Solnhofen Archipelago. creator: Oliver W.M. Rauhut creator: Christian Foth creator: Helmut Tischlinger uri: https://doi.org/10.7717/peerj.4191 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rauhut et al. title: Linking pangenomes and metagenomes: the Prochlorococcus metapangenome link: https://peerj.com/articles/4320 last-modified: 2018-01-25 description: Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available. creator: Tom O. Delmont creator: A. Murat Eren uri: https://doi.org/10.7717/peerj.4320 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Delmont and Eren title: Tissue material properties and computational modelling of the human tibiofemoral joint: a critical review link: https://peerj.com/articles/4298 last-modified: 2018-01-25 description: Understanding how structural and functional alterations of individual tissues impact on whole-joint function is challenging, particularly in humans where direct invasive experimentation is difficult. Finite element (FE) computational models produce quantitative predictions of the mechanical and physiological behaviour of multiple tissues simultaneously, thereby providing a means to study changes that occur through healthy ageing and disease such as osteoarthritis (OA). As a result, significant research investment has been placed in developing such models of the human knee. Previous work has highlighted that model predictions are highly sensitive to the various inputs used to build them, particularly the mathematical definition of material properties of biological tissues. The goal of this systematic review is two-fold. First, we provide a comprehensive summation and evaluation of existing linear elastic material property data for human tibiofemoral joint tissues, tabulating numerical values as a reference resource for future studies. Second, we review efforts to model tibiofemoral joint mechanical behaviour through FE modelling with particular focus on how studies have sourced tissue material properties. The last decade has seen a renaissance in material testing fuelled by development of a variety of new engineering techniques that allow the mechanical behaviour of both soft and hard tissues to be characterised at a spectrum of scales from nano- to bulk tissue level. As a result, there now exists an extremely broad range of published values for human tibiofemoral joint tissues. However, our systematic review highlights gaps and ambiguities that mean quantitative understanding of how tissue material properties alter with age and OA is limited. It is therefore currently challenging to construct FE models of the knee that are truly representative of a specific age or disease-state. Consequently, recent tibiofemoral joint FE models have been highly generic in terms of material properties even relying on non-human data from multiple species. We highlight this by critically evaluating current ability to quantitatively compare and model (1) young and old and (2) healthy and OA human tibiofemoral joints. We suggest that future research into both healthy and diseased knee function will benefit greatly from a subject- or cohort-specific approach in which FE models are constructed using material properties, medical imagery and loading data from cohorts with consistent demographics and/or disease states. creator: Abby E. Peters creator: Riaz Akhtar creator: Eithne J. Comerford creator: Karl T. Bates uri: https://doi.org/10.7717/peerj.4298 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Peters et al. title: Molecular and serological dynamics of Chlamydia pecorum infection in a longitudinal study of prime lamb production link: https://peerj.com/articles/4296 last-modified: 2018-01-25 description: BackgroundChlamydia pecorum is a globally significant livestock pathogen causing pathology and production losses. The on-farm infection and serological dynamics and the relevance of existing diagnostic tools for diagnosing C. pecorum in livestock remains poorly characterized. In this study, we characterized the antigen and antibody dynamics of this pathogen in a longitudinal study of prime lamb production, utilizing the infection focused C. pecorum-specific 16S rRNA qPCR assay and serology based chlamydial Complement fixation Test (CFT).MethodsThe study consisted of 76 Border Leicester mixed sex lambs (39 females and 37 males) that were sampled bimonthly from 2–10 months of age in a commercial farm operating in Central NSW, Australia. Blood/plasma was analysed for CFT antibodies, and swabs from conjunctival, rectal and vaginal sites were analysed for C. pecorum shedding using qPCR. We assessed the temporal and overall dynamics of C. pecorum in lambs, including detailed description and comparison of qPCR and CFT, the timing of first detection by either diagnostic method, the lag between infection and antibody response; and the distribution of qPCR load and CFT antibody titre over time.ResultsOver the study period, C. pecorum was highly prevalent (71.0% by qPCR, 92.1% by CFT, 96.0% by both), with 21.1% (16/76) lambs shedding ≥1, 000 qPCR copies/µl (denoted as high shedders). C. pecorum shedding (as evidence of infection) were first observed at two months of age (14.4%) with a significant peak of infection occurring at six months of age (34.2%), whereas seroconversions peaked at eight months of age (81.5%). 52.6% of C. pecorum qPCR and CFT positive lambs became qPCR negative by 10 months of age, indicating clearance of chlamydial infection. Although CFT is utilised for on-farm detection of active infection, we confirm that it lagged behind qPCR detection (average lag 1.7 ± 2.1 months) and that the proportion of qPCR positives simultaneously identified by CFT was low with 2/11 (18.1%), 0/13, 17/25 (68.0%), 5/7 (71.4%) and 1/10 (10.0%) concurrent seroconversions occurring at two, four, six, eight and 10 months of age, respectively.DiscussionThis work reveals rapid rates of C. pecorum infection and widespread exposure during lamb production. The comparison of molecular and serological diagnostic agreement longitudinally, supports the use of qPCR as an important ancillary tool for the detection of active infections in conjunction with chlamydial CFT for routine veterinary diagnostics. Development of rapid Point-of-Care (POC) tools for diagnosing active infection would be valuable for producers and veterinarians. creator: Sankhya Bommana creator: Evelyn Walker creator: Marion Desclozeaux creator: Martina Jelocnik creator: Peter Timms creator: Adam Polkinghorne creator: Scott Carver uri: https://doi.org/10.7717/peerj.4296 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bommana et al. title: Characterization of sympatric Platanthera bifolia and Platanthera chlorantha (Orchidaceae) populations with intermediate plants link: https://peerj.com/articles/4256 last-modified: 2018-01-25 description: Platanthera bifolia and P. chlorantha are terrestrial and rewarding orchids with a wide Eurasian distribution. Although genetically closely related, they exhibit significant morphological, phenological and ecological differences that maintain reproductive isolation between the species. However, where both species co-occur, individuals with intermediate phenotypic traits, often considered as hybrids, are frequently observed. Here, we combined neutral genetic markers (AFLPs), morphometrics and floral scent analysis (GC-MS) to investigate two mixed Platanthera populations where morphologically intermediate plants were found. Self-pollination experiments revealed a low level of autogamy and artificial crossings combined with assessments of fruit set and seed viability, showed compatibility between the two species. The results of the genetic analyses showed that morphologically intermediate plants had similar genetic patterns as the P. bifolia group. These results are corroborated also by floral scent analyses, which confirmed a strong similarity in floral scent composition between intermediate morphotypes and P. bifolia. Therefore, this study provided a much more detailed picture of the genetic structure of a sympatric zone between two closely allied species and supports the hypothesis that intermediate morphotypes in sympatry could reflect an adaptive evolution in response to local pollinator-mediated selection. creator: Fabiana Esposito creator: Nicolas J. Vereecken creator: Maddalena Gammella creator: Rosita Rinaldi creator: Pascal Laurent creator: Daniel Tyteca uri: https://doi.org/10.7717/peerj.4256 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Esposito et al. title: Breeding and multiple waves of primary molt in common ground doves of coastal Sinaloa link: https://peerj.com/articles/4243 last-modified: 2018-01-25 description: For adult Common Ground Doves from Sinaloa we demonstrate that the primaries are a single molt series, which sometimes feature two (in one case three) waves of feather replacement. Such stepwise primary replacement is found in many large birds but, at 40 g, this dove is much the smallest species reported to have multiple waves of replacement proceeding through its primaries simultaneously. Pre-breeding juvenile Common Ground Doves never feature two waves of primary replacement. Juveniles usually have more than two adjacent feathers growing simultaneously and replace their primaries in about 100 days. In contrast adults, which extensively overlap molt and breeding, usually grow just a single primary at a time, and require at least 145 days to replace their primaries. Molt arrests are thought to drive the generation of new waves of primary replacement in a diversity of large birds. For adult Common Ground Doves, we found molt arrests to be strongly associated with active crop glands, suggesting that the demands of parental care cause arrests in primary replacement in this dove. For those adults with two primary molt waves, initiation of an inner wave was most frequently observed once the outer wave had reached P10. Thus, unlike reports for large birds, Common Ground Doves usually suppress the initiation of a new wave of molt starting at P1 when the preceding wave arrests before reaching the distal primaries. This assures that relatively fresh inner primaries are not replaced redundantly, overcoming a serious flaw in stepwise molting in large birds (Rohwer, 1999). creator: Sievert Rohwer creator: Vanya G. Rohwer uri: https://doi.org/10.7717/peerj.4243 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rohwer and Rohwer title: Species identification by conservation practitioners using online images: accuracy and agreement between experts link: https://peerj.com/articles/4157 last-modified: 2018-01-25 description: Emerging technologies have led to an increase in species observations being recorded via digital images. Such visual records are easily shared, and are often uploaded to online communities when help is required to identify or validate species. Although this is common practice, little is known about the accuracy of species identification from such images. Using online images of newts that are native and non-native to the UK, this study asked holders of great crested newt (Triturus cristatus) licences (issued by UK authorities to permit surveying for this species) to sort these images into groups, and to assign species names to those groups. All of these experts identified the native species, but agreement among these participants was low, with some being cautious in committing to definitive identifications. Individuals’ accuracy was also independent of both their experience and self-assessed ability. Furthermore, mean accuracy was not uniform across species (69–96%). These findings demonstrate the difficulty of accurate identification of newts from a single image, and that expert judgements are variable, even within the same knowledgeable community. We suggest that identification decisions should be made on multiple images and verified by more than one expert, which could improve the reliability of species data. creator: Gail E. Austen creator: Markus Bindemann creator: Richard A. Griffiths creator: David L. Roberts uri: https://doi.org/10.7717/peerj.4157 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Austen et al. title: Do patients with chronic unilateral orofacial pain due to a temporomandibular disorder show increased attending to somatosensory input at the painful side of the jaw? link: https://peerj.com/articles/4310 last-modified: 2018-01-24 description: BackgroundPatients with chronic orofacial pain due to temporomandibular disorders (TMD) display alterations in somatosensory processing at the jaw, such as amplified perception of tactile stimuli, but the underlying mechanisms remain unclear. This study investigated one possible explanation, namely hypervigilance, and tested if TMD patients with unilateral pain showed increased attending to somatosensory input at the painful side of the jaw.MethodsTMD patients with chronic unilateral orofacial pain (n = 20) and matched healthy volunteers (n = 20) performed a temporal order judgment (TOJ) task indicated which one of two tactile stimuli, presented on each side of the jaw, they had perceived first. TOJ methodology allows examining spatial bias in somatosensory processing speed. Furthermore, after each block of trials, the participants rated the perceived intensity of tactile stimuli separately for both sides of the jaw. Finally, questionnaires assessing pain catastrophizing, fear-avoidance beliefs, and pain vigilance, were completed.ResultsTMD patients tended to perceive tactile stimuli at the painful jaw side as occurring earlier in time than stimuli at the non-painful side but this effect did not reach conventional levels of significance (p = .07). In the control group, tactile stimuli were perceived as occurring simultaneously. Secondary analyses indicated that the magnitude of spatial bias in the TMD group is positively associated with the extent of fear-avoidance beliefs. Overall, intensity ratings of tactile stimuli were significantly higher in the TMD group than in the control group, but there was no significant difference between the painful and non-painful jaw side in the TMD patients.DiscussionThe hypothesis that TMD patients with chronic unilateral orofacial pain preferentially attend to somatosensory information at the painful side of the jaw was not statistically supported, although lack of power could not be ruled out as a reason for this. The findings are discussed within recent theories of pain-related attention. creator: Stefaan Van Damme creator: Charlotte Vanden Bulcke creator: Linda Van Den Berghe creator: Louise Poppe creator: Geert Crombez uri: https://doi.org/10.7717/peerj.4310 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Van Damme et al. title: Historical baselines of coral cover on tropical reefs as estimated by expert opinion link: https://peerj.com/articles/4308 last-modified: 2018-01-24 description: Coral reefs are important habitats that represent global marine biodiversity hotspots and provide important benefits to people in many tropical regions. However, coral reefs are becoming increasingly threatened by climate change, overfishing, habitat destruction, and pollution. Historical baselines of coral cover are important to understand how much coral cover has been lost, e.g., to avoid the ‘shifting baseline syndrome’. There are few quantitative observations of coral reef cover prior to the industrial revolution, and therefore baselines of coral reef cover are difficult to estimate. Here, we use expert and ocean-user opinion surveys to estimate baselines of global coral reef cover. The overall mean estimated baseline coral cover was 59% (±19% standard deviation), compared to an average of 58% (±18% standard deviation) estimated by professional scientists. We did not find evidence of the shifting baseline syndrome, whereby respondents who first observed coral reefs more recently report lower estimates of baseline coral cover. These estimates of historical coral reef baseline cover are important for scientists, policy makers, and managers to understand the extent to which coral reefs have become depleted and to set appropriate recovery targets. creator: Tyler D. Eddy creator: William W.L. Cheung creator: John F. Bruno uri: https://doi.org/10.7717/peerj.4308 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Eddy et al. title: Isolation and culture of primary adult skin fibroblasts from the Asian elephant (Elephas maximus) link: https://peerj.com/articles/4302 last-modified: 2018-01-24 description: BackgroundPrimary cultures from Asian elephants (Elephas maximus) allow scientists to obtain representative cells that have conserved most of their original characteristics, function, physiology and biochemistry. This technique has thus gained significant importance as a foundation for further cellular, cell biology and molecular research. Therefore, the aim of this study was to describe conditions for the successful establishment of primary adult fibroblasts from Asian elephant carcasses.MethodsEar tissue sample collection from Asian elephant carcasses and our recommendations are given. We describe here a simple modified protocol for successful isolation and maintenance of primary adult fibroblasts from elephant ear skin. Ear samples from each individual (five 3 × 3 cm2 pieces) were brought to the laboratory within 3 h after collection, kept in transportation medium at 0–4 °C. The ear tissues were prepared by a combination of 10% collagenase type II digestion procedure together with a simple explant procedure. Primary fibroblasts were cultured at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM) with 20% fetal calf serum (FCS) in a humidified atmosphere containing 5% CO2. After the third passage, fibroblasts were routinely trypsinized with 0.25% trypsin/EDTA and cultured in DMEM with 10% FCS at 37 °C and 5% CO2. Traditional cell counting method was used to measure cell viability and growth curve. Long-term storage of cells used freezing medium consisting of 40% FCS (v/v).ResultsWe explored the most suitable conditions during sample collection (post-mortem storage time and sample storage temperature), which is the most important step in determining primary outgrowth. Our study successfully established and cultured primary adult skin fibroblasts obtained from post-mortem E. maximus ear skin tissues from six carcasses, with a success rate of around 83.3%. Outgrowth could be seen 4–12 days after explantation, and epithelial-like cells were found after 4–7 days of culture, while fibroblasts appeared at around day 7–10. The fibroblasts had viability and post-freezing recovery rates of around 97.3 ± 4.3% and 95.5 ± 7.3%, respectively, and doubling time was about 25 h (passage 6).DiscussionTo our knowledge, this report is the first to describe primary cell cultures derived from adult Asian elephant skin. Future studies should benefit from the information and useful suggestions herein, which may be used as a standard method for establishing primary skin fibroblast cultures in future experiments. creator: Puntita Siengdee creator: Sarisa Klinhom creator: Chatchote Thitaram creator: Korakot Nganvongpanit uri: https://doi.org/10.7717/peerj.4302 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Siengdee et al. title: Are pumas subordinate carnivores, and does it matter? link: https://peerj.com/articles/4293 last-modified: 2018-01-24 description: BackgroundInterspecific competition affects species fitness, community assemblages and structure, and the geographic distributions of species. Established dominance hierarchies among species mitigate the need for fighting and contribute to the realized niche for subordinate species. This is especially important for apex predators, many of which simultaneous contend with the costs of competition with more dominant species and the costs associated with human hunting and lethal management.MethodsPumas are a widespread solitary felid heavily regulated through hunting to reduce conflicts with livestock and people. Across their range, pumas overlap with six apex predators (gray wolf, grizzly bear, American black bear, jaguar, coyote, maned wolf), two of which (gray wolf, grizzly bear) are currently expanding in North America following recovery efforts. We conducted a literature search to assess whether pumas were subordinate or dominant with sympatric apex predators, as well as with three felid mesocarnivores with similar ecology (ocelot, bobcat, Canada lynx). We also conducted an analysis of the spatial distributions of pumas and their dominant sympatric competitors to estimate in what part of their range, pumas are dominant versus subordinate.ResultsWe used 64 sources to assess dominance among pumas and other apex predators, and 13 sources to assess their relationships with felid mesocarnivores. Evidence suggested that wolves, grizzly bears, black bears, and jaguars are dominant over pumas, but that pumas are dominant over coyotes and maned wolves. Evidence suggested that pumas are also dominant over all three felid mesocarnivores with which they share range. More broadly, pumas are subordinate to at least one other apex carnivore in 10,799,252 (47.5%) of their 22,735,268 km2 range across North and South America.DiscussionSubordinate pumas change their habitat use, suffer displacement at food sources, likely experience increased energetic demands from harassment, exhibit increased starvation, and are sometimes directly killed in competitive interactions with dominant competitors. Nevertheless, we lack research clearly linking the costs of competition to puma fitness. Further, we lack research that assesses the influence of human effects simultaneous with the negative effects of competition with other sympatric carnivores. Until the time that we understand whether competitive effects are additive with human management, or even potentially synergistic, we encourage caution among managers responsible for determining harvest limits for pumas and other subordinate, apex carnivores in areas where they are sympatric with dominant species. This may be especially important information for managers working in regions where wolves and brown bears are recolonizing and recovering, and historic competition scenarios among multiple apex predators are being realized. creator: L. Mark Elbroch creator: Anna Kusler uri: https://doi.org/10.7717/peerj.4293 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Elbroch and Kusler title: Genomic signal processing for DNA sequence clustering link: https://peerj.com/articles/4264 last-modified: 2018-01-24 description: Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring data is cluster analysis which refers to the unsupervised classification of patterns in data. In this paper, we propose a novel approach for performing cluster analysis of DNA sequences that is based on the use of GSP methods and the K-means algorithm. We also propose a visualization method that facilitates the easy inspection and analysis of the results and possible hidden behaviors. Our results support the feasibility of employing the proposed method to find and easily visualize interesting features of sets of DNA data. creator: Gerardo Mendizabal-Ruiz creator: Israel Román-Godínez creator: Sulema Torres-Ramos creator: Ricardo A. Salido-Ruiz creator: Hugo Vélez-Pérez creator: J. Alejandro Morales uri: https://doi.org/10.7717/peerj.4264 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mendizabal-Ruiz et al. title: EU protected area network did not prevent a country wide population decline in a threatened grassland bird link: https://peerj.com/articles/4284 last-modified: 2018-01-23 description: BackgroundFew studies have assessed the effectiveness of the Protected Area networks on the conservation status of target species. Here, we assess the effectiveness of the Portuguese Natura 2000 (the European Union network of protected areas) in maintaining a species included in the Annex I of the Bird Directive, namely the population of a priority farmland bird, the little bustard Tetrax tetrax.MethodsWe measured the effectiveness of the Natura 2000 by comparing population trends across time (2003–2006 and 2016) in 51 areas, 21 of which within 12 Special Protection Areas (SPA) that were mostly designated for farmland bird conservation and another 30 areas without EU protection.ResultsOverall, the national population is estimated to have declined 49% over the last 10–14 years. This loss was found to be proportionally larger outside SPA (64% decline) compared to losses within SPA (25% decline). However, the absolute male density decline was significantly larger within SPA .DiscussionIn spite of holding higher population densities and having prevented habitat loss, we conclude that Natura 2000 was not effective in buffering against the overall bustard population decline. Results show that the mere designation of SPA in farmland is not enough to secure species populations and has to be combined with agricultural policies and investment to maintain not only habitat availability but also habitat quality. creator: João P. Silva creator: Ricardo Correia creator: Hany Alonso creator: Ricardo C. Martins creator: Marcello D’Amico creator: Ana Delgado creator: Hugo Sampaio creator: Carlos Godinho creator: Francisco Moreira uri: https://doi.org/10.7717/peerj.4284 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Silva et al. title: Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa link: https://peerj.com/articles/4260 last-modified: 2018-01-23 description: Portunoidea is a diverse lineage of ecologically and economically important marine crabs comprising 8 families and 14 subfamilies. Closely related portunid subfamilies Caphyrinae and Thalamitinae constitute some of this group’s greatest morphological and taxonomic diversity, and are the only known lineages to include symbiotic taxa. Emergence of symbiosis in decapods remains poorly studied and portunoid crabs provide an interesting, but often overlooked example. Yet the paucity of molecular phylogenetic data available for Portunoidea makes it challenging to investigate the evolution and systematics of the group. Phylogenetic analyses, though limited, suggest that many putative portunoid taxa are para- or polyphyletic. Here I augment existing molecular data—significantly increasing taxon sampling of Caphyrinae, Thalamitinae, and several disparate portunoid lineages—to investigate the phylogenetic origin of symbiosis within Portunoidea and reevaluate higher- and lower-level portunoid classifications. Phylogenetic analyses were carried out on sequences of H3, 28S rRNA, 16S rRNA, and CO1 for up to 168 portunoid taxa; this included, for the first time, molecular data from the genera Atoportunus, Brusinia, Caphyra, Coelocarcinus, Gonioinfradens, Raymanninus, and Thalamonyx. Results support the placement of all symbiotic taxa (Caphyra, Lissocarcinus, and two Thalamita) in a single clade derived within the thalamitine genus Thalamita. Caphyrina Paulson, 1875, nom. trans. is recognized here as a subtribe within the subfamily Thalamitinae. Results also support the following taxonomic actions: Cronius is reclassified as a thalamitine genus; Thalamonyx is reestablished as a valid genus; Goniosupradens is raised to the generic rank; and three new genera (Zygita gen. nov., Thranita gen. nov., and Trierarchus gen. nov.) are described to accommodate some Thalamita s.l. taxa rendered paraphyletic by Caphyrina. A new diagnosis of Thalamitinae is provided. Results also support a more conservative classification of Portunoidea comprising three instead of eight extant families: Geryonidae (Geryonidae + Ovalipidae; new diagnosis provided), Carcinidae (Carcinidae + Pirimelidae + Polybiidae + Thiidae + Coelocarcinus; new diagnosis provided) and Portunidae. Finally, 16s rRNA data suggests family Brusiniidae might not be a portunoid lineage. creator: Nathaniel Evans uri: https://doi.org/10.7717/peerj.4260 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Evans title: Identification of the fungal endophyte of Ammophila breviligulata (American beachgrass) as Epichloë amarillans link: https://peerj.com/articles/4300 last-modified: 2018-01-22 description: The grass Ammophila breviligulata (American beachgrass) is known to host an endophyte of the genus Epichloë. Based on morphological characteristics it was originally identified as Acremonium typhinum var. ammophilae and is currently designated as Epichloë typhina var. ammophilae. However, the Epichloë species has not previously been identified based on DNA sequence data. Based on phylogenetic placement of beta-tubulin and translation elongation factor 1-alpha DNA sequences the endophyte is identified as a member of E. amarillans rather than E. typhina. creator: Ian Drake creator: James F. White Jr creator: Faith C. Belanger uri: https://doi.org/10.7717/peerj.4300 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Drake et al. title: Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome link: https://peerj.com/articles/4282 last-modified: 2018-01-22 description: Patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) often suffer from gastrointestinal symptoms and many are diagnosed with irritable bowel syndrome (IBS). Previous studies, including from our laboratory, have demonstrated that the ME/CFS gut bacterial composition is altered and less diverse when compared to healthy individuals. Patients have increased biomarkers of inflammation and leaky gut syndrome. To further investigate dysbiosis in the ME/CFS gut microbiome, we sought to characterize the eukaryotes present in the gut of 49 individuals with ME/CFS and 39 healthy controls. Using 18S rRNA sequencing, we have identified eukaryotes in stool samples of 17 healthy individuals and 17 ME/CFS patients. Our analysis demonstrates a small, nonsignificant decrease in eukaryotic diversity in ME/CFS patients compared to healthy individuals. In addition, ME/CFS patients show a nonsignificant increase in the ratio of fungal phyla Basidiomycota to Ascomycota, which is consistent with ongoing inflammation in ME/CFS. We did not identify specific eukaryotic taxa that are associated with ME/CFS disease status. creator: Alexandra H. Mandarano creator: Ludovic Giloteaux creator: Betsy A. Keller creator: Susan M. Levine creator: Maureen R. Hanson uri: https://doi.org/10.7717/peerj.4282 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mandarano et al. title: Antifibrotic effect of xanthohumol in combination with praziquantel is associated with altered redox status and reduced iron accumulation during liver fluke-associated cholangiocarcinogenesis link: https://peerj.com/articles/4281 last-modified: 2018-01-22 description: Cholangiocarcinoma (CCA) caused by infection of the liver fluke Opisthorchis viverrini, (Ov) is the major public health problem in northeast Thailand. Following Ov infection the subsequent molecular changes can be associated by reactive oxygen species (ROS) induced chronic inflammation, advanced periductal fibrosis, and cholangiocarcinogenesis. Notably, resistance to an activation of cell death in prolonged oxidative stress conditions can occur but some damaged/mutated cells could survive and enable clonal expansion. Our study used a natural product, xanthohumol (XN), which is an anti-oxidant and anti-inflammatory compound, to examine whether it could prevent Ov-associated CCA carcinogenesis. We measured the effect of XN with or without praziquantel (PZ), an anti-helminthic treatment, on DNA damage, redox status change including iron accumulation and periductal fibrosis during CCA genesis induced by administration of Ov and N-dinitrosomethylamine (NDMA) in hamsters. Animals were randomly divided into four groups: group I, Ov infection and NDMA administration (ON); group II, Ov infection and NDMA administration and PZ treatment (ONP); the latter 2 groups were similar to group I and II, but group III received additional XN (XON) and group IV received XN plus PZ (XONP). The results showed that high 8-oxodG (a marker of DNA damage) was observed throughout cholangiocarcinogenesis. Moreover, increased expression of CD44v8-10 (a cell surface in regulation of the ROS defense system), whereas decreased expression of phospho-p38MAPK (a major ROS target), was found during the progression of the bile duct cell transformation. In addition, high accumulation of iron and expression of transferrin receptor-1 (TfR-1) in both malignant bile ducts and inflammatory cells were detected. Furthermore, fibrosis also increased with the highest level being on day 180. On the other hand, the groups of XN with or without PZ supplementations showed an effective reduction in all the markers examined, including fibrosis when compared with the ON group. In particular, the XONP group, in which a significant reduction DNA damage occurred, was also found to have iron accumulation and fibrosis compared to the other groups. Our results show that XN administered in combination with PZ could efficiently prevent CCA development and hence provide potential chemopreventive benefits in Ov-induced cholangiocarcinogenesis. creator: Wassana Jamnongkan creator: Malinee Thanee creator: Puangrat Yongvanit creator: Watcharin Loilome creator: Raynoo Thanan creator: Phongsaran Kimawaha creator: Tidarat Boonmars creator: Runglawan Silakit creator: Nisana Namwat creator: Anchalee Techasen uri: https://doi.org/10.7717/peerj.4281 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jamnongkan et al. title: Morphology and structure of Homo erectus humeri from Zhoukoudian, Locality 1 link: https://peerj.com/articles/4279 last-modified: 2018-01-19 description: BackgroundRegional diversity in the morphology of the H. erectus postcranium is not broadly documented, in part, because of the paucity of Asian sites preserving postcranial fossils. Yet, such an understanding of the initial hominin taxon to spread throughout multiple regions of the world is fundamental to documenting the adaptive responses to selective forces operating during this period of human evolution.MethodsThe current study reports the first humeral rigidity and strength properties of East Asian H. erectus and places its diaphyseal robusticity into broader regional and temporal contexts. We estimate true cross-sectional properties of Zhoukoudian Humerus II and quantify new diaphyseal properties of Humerus III using high resolution computed tomography. Comparative data for African H. erectus and Eurasian Late Pleistocene H. sapiens were assembled, and new data were generated from two modern Chinese populations.ResultsDifferences between East Asian and African H. erectus were inconsistently expressed in humeral cortical thickness. In contrast, East Asian H. erectus appears to exhibit greater humeral robusticity compared to African H. erectus when standardizing diaphyseal properties by the product of estimated body mass and humeral length. East Asian H. erectus humeri typically differed less in standardized properties from those of side-matched Late Pleistocene hominins (e.g., Neanderthals and more recent Upper Paleolithic modern humans) than did African H. erectus, and often fell in the lower range of Late Pleistocene humeral rigidity or strength properties.DiscussionQuantitative comparisons indicate that regional variability in humeral midshaft robusticity may characterize H. erectus to a greater extent than presently recognized. This may suggest a temporal difference within H. erectus, or possibly different ecogeographical trends and/or upper limb loading patterns across the taxon. Both discovery and analysis of more adult H. erectus humeri are critical to further evaluating and potentially distinguishing between these possibilities. creator: Song Xing creator: Kristian J. Carlson creator: Pianpian Wei creator: Jianing He creator: Wu Liu uri: https://doi.org/10.7717/peerj.4279 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Xing et al. title: CoMiniGut—a small volume in vitro colon model for the screening of gut microbial fermentation processes link: https://peerj.com/articles/4268 last-modified: 2018-01-19 description: Driven by the growing recognition of the influence of the gut microbiota (GM) on human health and disease, there is a rapidly increasing interest in understanding how dietary components, pharmaceuticals and pre- and probiotics influence GM. In vitro colon models represent an attractive tool for this purpose. With the dual objective of facilitating the investigation of rare and expensive compounds, as well as an increased throughput, we have developed a prototype in vitro parallel gut microbial fermentation screening tool with a working volume of only 5 ml consisting of five parallel reactor units that can be expanded with multiples of five to increase throughput. This allows e.g., the investigation of interpersonal variations in gut microbial dynamics and the acquisition of larger data sets with enhanced statistical inference. The functionality of the in vitro colon model, Copenhagen MiniGut (CoMiniGut) was first demonstrated in experiments with two common prebiotics using the oligosaccharide inulin and the disaccharide lactulose at 1% (w/v). We then investigated fermentation of the scarce and expensive human milk oligosaccharides (HMOs) 3-Fucosyllactose, 3-Sialyllactose, 6-Sialyllactose and the more common Fructooligosaccharide in fermentations with infant gut microbial communities. Investigations of microbial community composition dynamics in the CoMiniGut reactors by MiSeq-based 16S rRNA gene amplicon high throughput sequencing showed excellent experimental reproducibility and allowed us to extract significant differences in gut microbial composition after 24 h of fermentation for all investigated substrates and fecal donors. Furthermore, short chain fatty acids (SCFAs) were quantified for all treatments and donors. Fermentations with inulin and lactulose showed that inulin leads to a microbiota dominated by obligate anaerobes, with high relative abundance of Bacteroidetes, while the more easily fermented lactulose leads to higher relative abundance of Proteobacteria. The subsequent study on the influence of HMOs on two infant GM communities, revealed the strongest bifidogenic effect for 3′SL for both infants. Inter-individual differences of infant GM, especially with regards to the occurrence of Bacteroidetes and differences in bifidobacterial species composition, correlated with varying degrees of HMO utilization foremost of 6′SL and 3′FL, indicating species and strain related differences in HMO utilization which was also reflected in SCFAs concentrations, with 3′SL and 6′SL resulting in significantly higher butyrate production compared to 3′FL. In conclusion, the increased throughput of CoMiniGut strengthens experimental conclusions through elimination of statistical interferences originating from low number of repetitions. Its small working volume moreover allows the investigation of rare and expensive bioactives. creator: Maria Wiese creator: Bekzod Khakimov creator: Sebastian Nielsen creator: Helena Sørensen creator: Frans van den Berg creator: Dennis Sandris Nielsen uri: https://doi.org/10.7717/peerj.4268 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wiese et al. title: The importance of local settings: within-year variability in seawater temperature at South Bay, Western Antarctic Peninsula link: https://peerj.com/articles/4289 last-modified: 2018-01-18 description: The Western Antarctic Peninsula (WAP) has undergone significant changes in air and seawater temperatures during the last 50 years. Although highly stenotherm Antarctic organisms are expected to be severely affected by the increase of seawater temperature, high-resolution datasets of seawater temperature within coastal areas of the WAP (where diverse marine communities have been reported) are not commonly available. Here we report on within-year (2016–2017) variation in seawater temperature at three sites on Doumer Island, Palmer Archipelago, WAP. Within a year, Antarctic organisms in South Bay were exposed to water temperatures in excess of 2 °C for more than 25 days and 2.5 °C for more than 10 days. We recorded a temperature range between −1.7° to 3.0 °C. Warming of seawater temperature was 3.75 times faster after October 2016 than it was before October. Results from this study indicate that organisms at South Bay are already exposed to temperatures that are being used in experimental studies to evaluate physiological responses to thermal stress in WAP organisms. Continuous measurements of short to long-term variability in seawater temperature provides important information for parametrizing meaningful experimental treatments that aim to assess the local effects of environmental variation on Antarctic organisms under future climate scenarios. creator: César A. Cárdenas creator: Marcelo González-Aravena creator: Pamela A. Santibañez uri: https://doi.org/10.7717/peerj.4289 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cárdenas et al. title: The French press: a repeatable and high-throughput approach to exercising zebrafish (Danio rerio) link: https://peerj.com/articles/4292 last-modified: 2018-01-17 description: Zebrafish are increasingly used as a vertebrate model organism for various traits including swimming performance, obesity and metabolism, necessitating high-throughput protocols to generate standardized phenotypic information. Here, we propose a novel and cost-effective method for exercising zebrafish, using a coffee plunger and magnetic stirrer. To demonstrate the use of this method, we conducted a pilot experiment to show that this simple system provides repeatable estimates of maximal swim performance (intra-class correlation [ICC] = 0.34–0.41) and observe that exercise training of zebrafish on this system significantly increases their maximum swimming speed. We propose this high-throughput and reproducible system as an alternative to traditional linear chamber systems for exercising zebrafish and similarly sized fishes. creator: Takuji Usui creator: Daniel W.A. Noble creator: Rose E. O’Dea creator: Melissa L. Fangmeier creator: Malgorzata Lagisz creator: Daniel Hesselson creator: Shinichi Nakagawa uri: https://doi.org/10.7717/peerj.4292 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Usui et al. title: Alpha-actinin of the chlorarchiniophyte Bigelowiella natans link: https://peerj.com/articles/4288 last-modified: 2018-01-17 description: The genome of the chlorarchiniophyte Bigelowiella natans codes for a protein annotated as an α-actinin-like protein. Analysis of the primary sequence indicate that this protein has the same domain structure as other α-actinins, a N-terminal actin-binding domain and a C-terminal calmodulin-like domain. These two domains are connected by a short rod domain, albeit long enough to form a single spectrin repeat. To analyse the functional properties of this protein, the full-length protein as well as the separate domains were cloned and isolated. Characerisation showed that the protein is capable of cross-linking actin filaments into dense bundles, probably due to dimer formation. Similar to human α-actinin, calcium-binding occurs to the most N-terminal EF-hand motif in the calmodulin-like C-terminal domain. The results indicate that this Bigelowiella protein is a proper α-actinin, with all common characteristics of a typical α-actinin. creator: Lars Backman uri: https://doi.org/10.7717/peerj.4288 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Backman title: Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques (Macaca mulatta) link: https://peerj.com/articles/4271 last-modified: 2018-01-17 description: In group-living animals, heterogeneity in individuals’ social connections may mediate the sharing of microbial infectious agents. In this regard, the genetic relatedness of individuals’ commensal gut bacterium Escherichia coli may be ideal to assess the potential for pathogen transmission through animal social networks. Here we use microbial phylogenetics and population genetics approaches, as well as host social network reconstruction, to assess evidence for the contact-mediated sharing of E. coli among three groups of captively housed rhesus macaques (Macaca mulatta), at multiple organizational scales. For each group, behavioral data on grooming, huddling, and aggressive interactions collected for a six-week period were used to reconstruct social network communities via the Data Cloud Geometry (DCG) clustering algorithm. Further, an E. coli isolate was biochemically confirmed and genotypically fingerprinted from fecal swabs collected from each macaque. Population genetics approaches revealed that Group Membership, in comparison to intrinsic attributes like age, sex, and/or matriline membership of individuals, accounted for the highest proportion of variance in E. coli genotypic similarity. Social network approaches revealed that such sharing was evident at the community-level rather than the dyadic level. Specifically, although we found no links between dyadic E. coli similarity and social contact frequencies, similarity was significantly greater among macaques within the same social network communities compared to those across different communities. Moreover, tests for one of our study-groups confirmed that E. coli isolated from macaque rectal swabs were more genotypically similar to each other than they were to isolates from environmentally deposited feces. In summary, our results suggest that among frequently interacting, spatially constrained macaques with complex social relationships, microbial sharing via fecal-oral, social contact-mediated routes may depend on both individuals’ direct connections and on secondary network pathways that define community structure. They lend support to the hypothesis that social network communities may act as bottlenecks to contain the spread of infectious agents, thereby encouraging disease control strategies to focus on multiple organizational scales. Future directions includeincreasing microbial sampling effort per individual to better-detect dyadic transmission events, and assessments of the co-evolutionary links between sociality, infectious agent risk, and host immune function. creator: Krishna Balasubramaniam creator: Brianne Beisner creator: Jiahui Guan creator: Jessica Vandeleest creator: Hsieh Fushing creator: Edward Atwill creator: Brenda McCowan uri: https://doi.org/10.7717/peerj.4271 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Balasubramaniam et al. title: Effects of chronic exposure to thiamethoxam on larvae of the hoverfly Eristalis tenax (Diptera, Syrphidae) link: https://peerj.com/articles/4258 last-modified: 2018-01-17 description: There is widespread concern over the use of neonicotinoid pesticides in the agro-ecosystem, due in part to their high water solubility which can lead to widespread contamination of non-target areas including standing surface water. Most studies investigating the negative fitness consequences of neonicotinoids have focused on bees, with little research on the impact on other non-target insects. Here we examined the effect of exposure on the aquatic larval stages of the hoverfly Eristalis tenax L. (Diptera: Syrphidae) to a range of concentrations (control, 5, 15, 50, 100 and 500 ppb) of the neonicotinoid thiamethoxam; no published studies have thus far examined the effects of neonicotinoids on hoverflies. Survival was significantly lower when exposed to 500 ppb thiamethoxam, but this concentration exceeds that likely to be found in the field. We observed no effect on survival, development or any latent effects on adult activity budgets resulting from exposure to lower concentrations (up to 100 ppb). Our results suggest that E. tenax exposed as larvae to thiamethoxam are unlikely to be negatively impacted by this neonicotinoid under field conditions. creator: Kate Basley creator: Balin Davenport creator: Kate Vogiatzis creator: Dave Goulson uri: https://doi.org/10.7717/peerj.4258 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Basley et al. title: Expression status and clinical significance of lncRNA APPAT in the progression of atherosclerosis link: https://peerj.com/articles/4246 last-modified: 2018-01-17 description: BackgroundLong non-coding RNAs (lncRNAs) have been reported to modulate cardiovascular diseases, and expression dynamics of lncRNAs in the bloodstream were proposed to be potential biomarkers for clinical diagnosis. However, few cardiovascular diseases-related circulating lncRNAs were identified and their prediction power has not been investigated in depth. Here we report a new circulating lncRNA, atherosclerotic plaque pathogenesis associated transcript (APPAT), and evaluated its role and predicting ability in atherosclerotic development.MethodsAPPAT was analyzed and screened by high-throughput sequencing, and then detected in vitro and in vivo. Immunofluorescence-fluorescence in situ hybridization (IF-FISH) was utilized to explore distribution and subcellular location of APPAT. The expressing alteration of APPAT in samples of healthy and pathological coronary artery was explored further. We also assessed the level of circulating APPAT in blood samples from healthy individuals, and patients with angina pectoris (AP) or myocardial infarction (MI). Additionally, we predicted and validated microRNA targets of APPAT, then showed the expression level of a candidate target which was primarily measured in human VSMCs cell line, coronary artery, and blood samples. Lastly, we examined the potential indicating ability of APPAT for the risk of AP or MI.ResultsAPPAT showed significant reduction in ox-LDL treated human VSMCs in vitro. It enriched in contractile VSMCs of artery tunica media and mainly existed in cytoplasm. Significant down-regulation of APPAT was found in coronary artery samples with severe stenosis. More importantly, we observed decreased expression of APPAT in blood samples accompanying disease progression. ROC and correlation analyses further verified the relatively high predicting ability of APPAT. We also observed the predicted miRNA exhibited opposite expression direction to that of APPAT.ConclusionsThis study revealed that circulating lncRNA-APPAT may perform an important function and have some indicating ability on the development of atherosclerosis. creator: Fanming Meng creator: Jie Yan creator: Qiongshan Ma creator: Yunjuan Jiao creator: Luyang Han creator: Jing Xu creator: Fan Yang creator: Junwen Liu uri: https://doi.org/10.7717/peerj.4246 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Meng et al. title: FUSTr: a tool to find gene families under selection in transcriptomes link: https://peerj.com/articles/4234 last-modified: 2018-01-17 description: BackgroundThe recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved in the process of adaptation. This is a tool that finds genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis.ResultsWhen applied to previously studied spider transcriptomic data as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection in relatively little time.ConclusionsFUSTr provides a useful tool for novice bioinformaticians to characterize the molecular evolution of organisms throughout the tree of life using large transcriptomic biodiversity datasets and can utilize multi-processor high-performance computational facilities. creator: T. Jeffrey Cole creator: Michael S. Brewer uri: https://doi.org/10.7717/peerj.4234 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cole and Brewer title: Distributional dynamics of a vulnerable species in response to past and future climate change: a window for conservation prospects link: https://peerj.com/articles/4287 last-modified: 2018-01-16 description: BackgroundThe ongoing change in climate is predicted to exert unprecedented effects on Earth’s biodiversity at all levels of organization. Biological conservation is important to prevent biodiversity loss, especially for species facing a high risk of extinction. Understanding the past responses of species to climate change is helpful for revealing response mechanisms, which will contribute to the development of effective conservation strategies in the future.MethodsIn this study, we modelled the distributional dynamics of a ‘Vulnerable’ species, Pseudolarix amabilis, in response to late Quaternary glacial-interglacial cycles and future 2080 climate change using an ecological niche model (MaxEnt). We also performed migration vector analysis to reveal the potential migration of the population over time.ResultsHistorical modelling indicates that the range dynamics of P. amabilis is highly sensitive to climate change and that its long-distance dispersal ability and potential for evolutionary adaption are limited. Compared to the current climatically suitable areas for this species, future modelling showed significant migration northward towards future potential climatically suitable areas.DiscussionIn combination with the predicted future distribution, the mechanism revealed by the historical response suggests that this species will not be able to fully occupy the future expanded areas of suitable climate or adapt to the unsuitable climate across the future contraction regions. As a result, we suggest assisted migration as an effective supplementary means of conserving this vulnerable species in the face of the unprecedentedly rapid climate change of the 21st century. As a study case, this work highlights the significance of introducing historical perspectives while researching species conservation, especially for currently vulnerable or endangered taxa that once had a wider distribution in geological time. creator: Yunjun Bai creator: Xueping Wei creator: Xiaoqiang Li uri: https://doi.org/10.7717/peerj.4287 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bai et al. title: Local genic base composition impacts protein production and cellular fitness link: https://peerj.com/articles/4286 last-modified: 2018-01-16 description: The maintenance of a G + C content that is higher than the mutational input to a genome provides support for the view that selection serves to increase G + C contents in bacteria. Recent experimental evidence from Escherichia coli demonstrated that selection for increasing G + C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G + C content acts across all sites within a gene or is confined to particular genic regions or nucleotide positions. We systematically altered the G + C contents of the GFP gene and assayed its effects on the fitness of strains harboring each variant. Fitness differences were attributable to the base compositional variation in the terminal portion of the gene, suggesting a connection to the folding of a specific protein feature. Variants containing sequence features that are thought to result in rapid translation, such as low G + C content and high levels of codon adaptation, displayed highly reduced growth rates. Taken together, our results show that purifying selection acting against A and T mutations most likely results from their tendency to increase the rate of translation, which can perturb the dynamics of protein folding. creator: Erik M. Quandt creator: Charles C. Traverse creator: Howard Ochman uri: https://doi.org/10.7717/peerj.4286 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Quandt et al. title: Attentional biases toward body images in males at high risk of muscle dysmorphia link: https://peerj.com/articles/4273 last-modified: 2018-01-16 description: ObjectiveAlthough research on muscle dysmorphia (MD), a body dysmorphic disorder subtype, has recently increased, the causes and mechanisms underlying this disorder remain unclear. Results from studies examining disorders associated with body image suggest the involvement of self-schema in biasing attention toward specific body information. The present study examined whether individuals at higher risk of MD also display attentional biases toward specific types of body images.MethodsThe validated Chinese version of the Muscle Appearance Satisfaction Scale was used to distinguish men at higher and lower risk of MD. Sixty-five adult Chinese men at higher (HRMD, n = 33) and lower risk of MD (LRMD, n = 32) performed a visual probe task. Initially, an image of a bodybuilder with either larger or smaller musculature was presented on one side of a central point, with a neutral image of a car exterior presented on the other side along the horizontal plane for 2,000 ms. The paired images were removed, and a visual target (a dot) was displayed in the location of one of the previously shown images. Participants were asked to indicate the location of the target, and their eye movements were recorded during the entire visual presentation. Participant reaction time and three eye movement measurements (gaze direction, first saccade latency, and first fixation duration) were recorded for use in determining attentional bias.ResultsThe HRMD group revealed biases in orienting and maintaining their attention on images of bodybuilders with larger musculatures. Participants in this group consequently had a shorter reaction time in identifying the target that appeared at the location in which an image of a bodybuilder with a larger musculature had been previously displayed. They also directed their initial gaze more frequently, had shorter saccade latency, and had longer first fixation duration on images of bodybuilders with larger musculatures (all p < .0001). In comparison, the LRMD group had longer reaction times, slower attention orientation toward body images, and shorter fixation duration for images of bodybuilders with larger musculatures (all p < .0001), indicating weaker or mixed responses.DiscussionAdult Chinese men at higher risk of MD displayed biases in orienting and maintaining their visual attention toward images of bodybuilders with larger musculatures, and these biases facilitated their information processing. These results suggest that development of MD may be due in part to attentional biases associated with established negative self-schema of specific body information. These findings provide insight into understanding and identifying the cognitive characteristics of MD in an Asian population. creator: Xinhong Jin creator: Yahong Jin creator: Shi Zhou creator: Shun-nan Yang creator: Shuzhi Chang creator: Hui Li uri: https://doi.org/10.7717/peerj.4273 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jin et al. title: Long-horned Ceratopsidae from the Foremost Formation (Campanian) of southern Alberta link: https://peerj.com/articles/4265 last-modified: 2018-01-16 description: The horned Ceratopsidae represent one of the last radiations of dinosaurs, and despite a decade of intense work greatly adding to our understanding of this diversification, their early evolution is still poorly known. Here, two postorbital horncores from the upper Foremost Formation (Campanian) of Alberta are described, and at ∼78.5 Ma represent some of the geologically oldest ceratopsid material. The larger of these specimens is incorporated into a fused supraorbital complex, and preserves a massive, straight, postorbital horncore that is vertical in lateral view, but canted dorsolaterally in rostral view. Medially, the supracranial sinus is composed of a small, restricted caudal chamber, and a large rostral chamber that forms the cornual diverticulum. This morphology is distinct from that of the long-horned Chasmosaurinae, and similar to, but still different from, those of younger Centrosaurinae taxa. The smaller specimen represents an ontogenetically younger individual, and although showing consistent morphology to the larger specimen, is less taxonomically useful. Although not certain, these postorbital horns may be referable to a long-horned basal (i.e., early-branching, non-pachyrhinosaurini, non-centrosaurini) centrosaurine, potentially the contemporaneous Xenoceratops, largely known from the parietosquamosal frill. These specimens indicate the morphology of the supracranial sinus in early, long-horned members of the Ceratopsidae, and add to our understanding of the evolution of the cranial display structures in this iconic dinosaur clade. creator: Caleb M. Brown uri: https://doi.org/10.7717/peerj.4265 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brown title: Phylogenetic relationships and genetic diversity of the Polypedates leucomystax complex in Thailand link: https://peerj.com/articles/4263 last-modified: 2018-01-16 description: Taxonomic uncertainty of the Asian tree frog Polypedates leucomystax complex presents the challenging task of inferring its biogeographical history. Here, we describe its dispersion and the genetic relationships among different populations in Thailand, where we connect the population of the P. leucomystax complex of the Sunda Islands to the Indochina (mainland) population based on analyses of 266 sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A: Polypedates sp.), Nan (clade B: P. cf. impresus), Southern (clade C: P. cf. leucomystax) and Northern D (clade D: P. cf. megacephalus), with Bayesian posterior probability >0.9. Phylogeny and haplotype networks indicate that clades A, B and D are sympatric. In contrast, clade C (P. cf. leucomystax) and clade D (P. cf. megacephalus) are genetically divergent due to the geographical barrier of the Isthmus of Kra, resulting in an allopatric distribution. Climatic conditions, in particular differences in rainfall on each side of the Isthmus of Kra, may play an important role in limiting the immigration of both clades. For the within-populations of either clades C or D, there was no significant correlation between geographic and genetic distance by the isolation-by-distance test, indicating intraspecific-dispersal of each clade. Population expansion occurred in clade C, whereas clade D showed a constant population. Taken together, the P. leucomystax complex in South East Asia may have diversified under climatic pressure, leading to allopatric and/or sympatric speciation. creator: Kittisak Buddhachat creator: Chatmongkon Suwannapoom uri: https://doi.org/10.7717/peerj.4263 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Buddhachat and Suwannapoom title: Sicegar: R package for sigmoidal and double-sigmoidal curve fitting link: https://peerj.com/articles/4251 last-modified: 2018-01-16 description: Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmoidal data. The package categorizes data into one of three categories, “no signal,” “sigmoidal,” or “double-sigmoidal,” by rigorously fitting a series of mathematical models to the data. The data is labeled as “ambiguous” if neither the sigmoidal nor double-sigmoidal model fit the data well. In addition to performing the classification, the package also reports a wealth of metrics as well as biologically meaningful parameters describing the sigmoidal or double-sigmoidal curves. In extensive simulations, we find that the package performs well, can recover the original dynamics even under fairly high noise levels, and will typically classify curves as “ambiguous” rather than misclassifying them. The package is available on CRAN and comes with extensive documentation and usage examples. creator: M. Umut Caglar creator: Ashley I. Teufel creator: Claus O. Wilke uri: https://doi.org/10.7717/peerj.4251 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Caglar et al. title: Giant ants and their shape: revealing relationships in the genus Titanomyrma with geometric morphometrics link: https://peerj.com/articles/4242 last-modified: 2018-01-16 description: Shape is a natural phenomenon inherent to many different lifeforms. A modern technique to analyse shape is geometric morphometrics (GM), which offers a whole range of methods concerning the pure shape of an object. The results from these methods have provided new insights into biological problems and have become especially useful in the fields of entomology and palaeontology. Despite the conspicuous successes in other hymenopteran groups, GM analysis of wings and fossil wings of Formicidae has been neglected. Here we tested if landmarks defining the wing shape of fossil ants that belong to the genus Titanomyrma are reliable and if this technique is able to expose relationships among different groups of the largest Hymenoptera that ever lived. This study comprises 402 wings from 362 ants that were analysed and assigned with the GM methods linear discriminant function analysis, principal component analysis, canonical variate analysis, and regression. The giant ant genus Titanomyrma and the parataxon Formicium have different representatives that are all very similar but these modern methods were able to distinguish giant ant types even to the level of the sex. Thirty-five giant ant specimens from the Eckfeld Maar were significantly differentiable from a collection of Messel specimens that consisted of 187 Titanomyrma gigantea females and 42 T. gigantea males, and from 74 Titanomyrma simillima females and 21 T. simillima males. Out of the 324 Messel ants, 127 are newly assigned to a species and 223 giant ants are newly assigned to sex with GM analysis. All specimens from Messel fit to the two species. Moreover, shape affinities of these groups and the species Formicium brodiei, Formicium mirabile, and Formicium berryi, which are known only from wings, were investigated. T. gigantea stands out with a possible female relative in one of the Eckfeld specimens whereas the other groups show similar shape patterns that are possibly plesiomorphic. Formicidae are one of the most dominant taxa in the animal kingdom and new methods can aid in investigating their diversity in the present and in deep time. GM of the ant wing delivers significant results and this core of methods is able to enhance the toolset we have now to analyse the complex biology of the ants. It can prove as especially useful in the future when incorporated into better understanding aspects of evolutionary patterns and ant palaeontology. creator: Julian Katzke creator: Phillip Barden creator: Manuel Dehon creator: Denis Michez creator: Torsten Wappler uri: https://doi.org/10.7717/peerj.4242 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Katzke et al. title: Population genetic structure of Patagonian toothfish (Dissostichus eleginoides) in the Southeast Pacific and Southwest Atlantic Ocean link: https://peerj.com/articles/4173 last-modified: 2018-01-16 description: Previous studies of population genetic structure in Dissostichus eleginoides have shown that oceanographic and geographic discontinuities drive in this species population differentiation. Studies have focused on the genetics of D. eleginoides in the Southern Ocean; however, there is little knowledge of their genetic variation along the South American continental shelf. In this study, we used a panel of six microsatellites to test whether D. eleginoides shows population genetic structuring in this region. We hypothesized that this species would show zero or very limited genetic structuring due to the habitat continuity along the South American shelf from Peru in the Pacific Ocean to the Falkland Islands in the Atlantic Ocean. We used Bayesian and traditional analyses to evaluate population genetic structure, and we estimated the number of putative migrants and effective population size. Consistent with our predictions, our results showed no significant genetic structuring among populations of the South American continental shelf but supported two significant and well-defined genetic clusters of D. eleginoides between regions (South American continental shelf and South Georgia clusters). Genetic connectivity between these two clusters was 11.3% of putative migrants from the South American cluster to the South Georgia Island and 0.7% in the opposite direction. Effective population size was higher in locations from the South American continental shelf as compared with the South Georgia Island. Overall, our results support that the continuity of the deep-sea habitat along the continental shelf and the biological features of the study species are plausible drivers of intraspecific population genetic structuring across the distribution of D. eleginoides on the South American continental shelf. creator: Cristian B. Canales-Aguirre creator: Sandra Ferrada-Fuentes creator: Ricardo Galleguillos creator: Fernanda X. Oyarzun creator: Cristián E. Hernández uri: https://doi.org/10.7717/peerj.4173 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Canales-Aguirre et al. title: Differential response to stress in Ostrea lurida as measured by gene expression link: https://peerj.com/articles/4261 last-modified: 2018-01-15 description: Olympia oysters are the only oyster native to the west coast of North America. The population within Puget Sound, WA has been decreasing significantly since the early 1900’s. Current restoration efforts are focused on supplementing local populations with hatchery bred oysters. A recent study by Heare et al. (2017) has shown differences in stress response in oysters from different locations in Puget Sound however, nothing is known about the underlying mechanisms associated with these observed differences. In this study, expression of genes associated with growth, immune function, and gene regulatory activity in oysters from Oyster Bay, Dabob Bay, and Fidalgo Bay were characterized following temperature and mechanical stress. We found that heat stress and mechanical stress significantly changed expression in molecular regulatory activity and immune response, respectively. We also found that oysters from Oyster Bay had the most dramatic response to stress at the gene expression level. These data provide important baseline information on the physiological response of Ostrea lurida to stress and provide clues to underlying performance differences in the three populations examined. creator: J. Emerson Heare creator: Samuel J. White creator: Brent Vadopalas creator: Steven B. Roberts uri: https://doi.org/10.7717/peerj.4261 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Heare et al. title: ­Comparative spigot ontogeny across the spider tree of life link: https://peerj.com/articles/4233 last-modified: 2018-01-15 description: Spiders are well known for their silk and its varying use across taxa. Very few studies have examined the silk spigot ontogeny of the entire spinning field of a spider. Historically the spider phylogeny was based on morphological data and behavioral data associated with silk. Recent phylogenomics studies have shifted major paradigms in our understanding of silk use evolution, reordering phylogenetic relationships that were once thought to be monophyletic. Considering this, we explored spigot ontogeny in 22 species, including Dolomedes tenebrosus and Hogna carolinensis, reported here for the first time. This is the first study of its kind and the first to incorporate the Araneae Tree of Life. After rigorous testing for phylogenetic signal and model fit, we performed 60 phylogenetic generalized least squares analyses on adult female and second instar spigot morphology. Six analyses had significant correlation coefficients, suggesting that instar, strategy, and spigot variety are good predictors of spigot number in spiders, after correcting for bias of shared evolutionary history. We performed ancestral character estimation of singular, fiber producing spigots on the posterior lateral spinneret whose potential homology has long been debated. We found that the ancestral root of our phylogram of 22 species, with the addition of five additional cribellate and ecribellate lineages, was more likely to have either none or a modified spigot rather than a pseudoflagelliform gland spigot or a flagelliform spigot. This spigot ontogeny approach is novel and we can build on our efforts from this study by growing the dataset to include deeper taxon sampling and working towards the capability to incorporate full ontogeny in the analysis. creator: Rachael E. Alfaro creator: Charles E. Griswold creator: Kelly B. Miller uri: https://doi.org/10.7717/peerj.4233 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Alfaro et al. title: Prediction of life stress on athletes’ burnout: the dual role of perceived stress link: https://peerj.com/articles/4213 last-modified: 2018-01-15 description: Although many studies adopted Smith’s (1986) cognitive–affective model of athletic burnout in examining stress–burnout relationship, very few studies examined the mediating/moderating role of perceived stress on the stress–burnout relationship. We sampled 195 college student-athletes and assessed their life stress, perceived stress, and burnout. Correlation analyses found all study variables correlated. Two separate hierarchical regression analyses found that the “distress” component of perceived stress mediated athletes’ two types of life stress–burnout relationship but “counter-stress” component of perceived stress-moderated athletes’ general-life stress–burnout relationship. We concluded that interweaving relationships among athletes’ life stress, perceived stress, and burnout are not straightforward. Future research should consider the nature of athletes life stress, and dual role of perceived stress in examining its’ association with related psychological responses in athletic settings. creator: Theresa Chyi creator: Frank Jing-Horng Lu creator: Erica T.W. Wang creator: Ya-Wen Hsu creator: Ko-Hsin Chang uri: https://doi.org/10.7717/peerj.4213 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chyi et al. title: Ergonomic risk and preventive measures of musculoskeletal disorders in the dentistry environment: an umbrella review link: https://peerj.com/articles/4154 last-modified: 2018-01-15 description: IntroductionDental practitioners are exposed to different occupational hazards during the course of their professional activity, such as physical, chemical, biological, ergonomic factors. The ergonomic hazards, caused by strained posture and prolonged repetitive movements, can induce musculoskeletal disorders. It occurs in 54–93% of dental professionals and involve the spine, shoulder and hand-wrist tract. Through a systematic review of international literature, we analyzed specific ergonomic risk factors and preventive measures of musculoskeletal disorders in professional dental activity.MethodsThis systematic review is coherent with the PRISMA statement. The scientific research on the major online databases was based on the following keywords: dentist, prevention, ergonomic, dentistry, musculoskeletal, neck pain, posture, ergonomics, work and occupational. The studies included in this review focus on disorders related to ergonomics and on the most effective preventive measures to be adopted. No restrictions were applied for language or publication type. We excluded reports not related to ergonomic prevention in dentistry, reports of minor academic significance, editorial articles, individual contributions, and studies published in scientific conferences.ResultsOnline research indicated 4188 references: PubMed (2919), Scopus (1257) e Cochrane Library (12). We excluded 3012 of these, because they were unrelated to ergonomics theme and 187 due to duplication. From the remaining 989 studies, 960 papers did not meet inclusion criteria and they were excluded. Therefore, we analyzed 29 articles, including 16 narrative reviews and 13 original article. The main risk factor for the development of musculoskeletal disorders found in our analysis is static posture adopted during work, highlighted in 87.5% of reviews and 84% of original articles. With regard to preventive measures, 75% of the reviews highlighted the importance of stretching after each working session and at the end of the working day, while 61.5% of the original articles emphasized the use of modern and ergonomic instruments.DiscussionThis review showed that static postures are strongly responsible in the etiology of musculoskeletal disorders. The awkward postures more frequently identified among dental professionals are: extreme forward-head and neck flexion; trunk inclination and rotation towards one side; lifting one or both shoulders; increased curvature of the thoracic vertebral column; incorrect positioning of the lower limbs with thigh-leg angle of less than 90°. It is really important to use of a modern workstation with appropriate ergonomic supports. Among the preventive ergonomic measures, literature has widely recognized the role of physical activity and of a neutral and balanced posture. The present review has some limits: a large part of the selected studies did not have a high methodological quality score and an inadequate statistical analysis. creator: Simone De Sio creator: Veronica Traversini creator: Francesca Rinaldo creator: Valerio Colasanti creator: Giuseppe Buomprisco creator: Roberto Perri creator: Federica Mormone creator: Giuseppe La Torre creator: Fabrizio Guerra uri: https://doi.org/10.7717/peerj.4154 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 De Sio et al. title: Habitat use in south-west European skinks (genus Chalcides) link: https://peerj.com/articles/4274 last-modified: 2018-01-12 description: BackgroundCongeneric species of reptiles frequently exhibit partitioning in terms of their use of habitats or trophic resources in order to reduce competition. In this study, we investigated habitat use by two species of European skinks: Chalcides bedriagai and Chalcides striatus, based on 49 records from southern France, Spain, and Portugal.MethodsWe measured three levels of niche descriptors: macroscale (climate, topography, and substrate), mesoscale (plant associations), and microscale (vegetation cover and shelters). We assessed the associations between these environmental descriptors and the occurrence of the skinks.ResultsOur results showed that the two species occupied opposite extremes of the ecological gradient i.e., C. bedriagai in semi-arid environments and C. striatus in temperate-oceanic environments, but there was broad ecological overlap in transitional climates at all of the habitat scales examined. This overlap was demonstrated by the presence of syntopy in geographically distant sites with different environmental characteristics.DiscussionThe morphological differences between the two species, and possibly their different use of microhabitats, might favor this mesoscale overlap between congeneric species, which is relatively unusual in Mediterranean lizards. creator: Daniel Escoriza creator: Guillem Pascual creator: Alberto Sánchez-Vialas uri: https://doi.org/10.7717/peerj.4274 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Escoriza et al. title: Response of methane production via propionate oxidation to carboxylated multiwalled carbon nanotubes in paddy soil enrichments link: https://peerj.com/articles/4267 last-modified: 2018-01-12 description: Carboxylated multiwalled carbon nanotubes (MWCNTs-COOH) have become a growing concern in terms of their fate and toxicity in aqueous environments. Methane (CH4) is a major product of organic matter degradation in waterlogged environments. In this study, we determined the effect of MWCNTs-COOH on the production of CH4 from propionate oxidation in paddy soil enrichments. The results showed that the methanogenesis from propionate degradation was accelerated in the presence of MWCNTs-COOH. In addition, the rates of CH4 production and propionate degradation increased with increasing concentrations of MWCNTs-COOH. Scanning electron microscopy (SEM) observations showed that the cells were intact and maintained their structure in the presence of MWCNTs-COOH. In addition, SEM and fluorescence in situ hybridization (FISH) images revealed that the cells were in direct contact with the MWCNTs and formed cell-MWCNTs aggregates that contained both bacteria and archaea. On the other hand, nontoxic magnetite nanoparticles (Fe3O4) had similar effects on the CH4 production and cell integrity as the MWCNTs-COOH. Compared with no nanomaterial addition, the relative abundances of Geobacter and Methanosarcina species increased in the presence of MWCNTs-COOH. This study suggests that MWCNTs-COOH exerted positive rather than cytotoxic effects on the syntrophic oxidation of propionate in paddy soil enrichments and affected the bacterial and archaeal community structure at the test concentrations. These findings provide novel insight into the consequences of nanomaterial release into anoxic natural environments. creator: Jianchao Zhang creator: Xingxuan Xia creator: Siliang Li creator: Wei Ran uri: https://doi.org/10.7717/peerj.4267 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration link: https://peerj.com/articles/4262 last-modified: 2018-01-12 description: BackgroundWith the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA’s role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS) analysis.MethodsThe package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs.ResultsBy incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow.ConclusionsWith RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS). More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865). creator: Jing Zhang creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4262 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang and Storey title: The relationships between exercise and affective states: a naturalistic, longitudinal study of recreational runners link: https://peerj.com/articles/4257 last-modified: 2018-01-12 description: BackgroundAlthough people generally feel more positive and more energetic in the aftermath of exercise than before, longitudinal research on how exercise relates to within-person fluctuations in affect over the course of everyday life is still relatively limited. One constraint on doing such research is the need to provide participants with accelerometers to objectively record their exercise, and pagers to capture affective reports.AimsWe aimed to develop a methodology for studying affect and exercise using only technology that participants already possess, namely GPS running watches and smartphones. Using this methodology, we aimed to characterize within-individual fluctuations in affective valence and arousal in relation to bouts of exercise, and explore possible moderators of these fluctuations.MethodsWe recruited a sample of 38 recreational runners. Participants provided daily affective reports for six weeks using their smartphones. Information on their runs was harvested from their own GPS devices via an online platform for athletes.ResultsAverage valence and arousal were higher on days when the person had run than on the next day, and higher the day after a run than on the days after that. Over the course of the day of a run, valence and arousal declined significantly as the time since the run increased. Physically fitter participants had more positive valence overall, and this was particularly true when they had not run recently. There was some evidence of higher-dose (i.e., longer and faster) runs being associated with lower arousal on the next and subsequent days. Gender did not moderate associations between running and valence or arousal.DiscussionOur study demonstrated the potential for studying the associations between affect and exercise in a way that is precise, undemanding for participants, and convenient for researchers, using technologies that participants already own and use. creator: Tim Bonham creator: Gillian V. Pepper creator: Daniel Nettle uri: https://doi.org/10.7717/peerj.4257 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bonham et al. title: Integrated genomic analyses of lung squamous cell carcinoma for identification of a possible competitive endogenous RNA network by means of TCGA datasets link: https://peerj.com/articles/4254 last-modified: 2018-01-12 description: The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play important roles in the initiation, progression, and metastasis of human cancers. Nonetheless, a mechanistic understanding of noncoding RNA functions in lung squamous cell carcinoma (LUSC) is lacking. To fill this critical gap in knowledge, we obtained mRNA, miRNA, and lncRNA expression data on patients with LUSC from the updated Cancer Genome Atlas (TCGA) database (2016). We successfully identified 3,366 mRNAs, 79 miRNAs, and 151 lncRNAs as key contributing factors of a high risk of LUSC. Furthermore, we hypothesized that the lncRNA–miRNA–mRNA regulatory axis positively correlates with LUSC and constructed a competitive endogenous RNA (ceRNA) network of LUSC by targeting interrelations with significantly aberrant expression data between miRNA and mRNA or lncRNA. Six ceRNAs (PLAU, miR-31-5p, miR-455-3p, FAM83A-AS1, MIR31HG, and MIR99AHG) significantly correlated with survival (P < 0.05). Finally, real-time quantitative PCR analysis showed that PLAU is significantly upregulated in SK-MES-1 cells compared with 16-BBE-T cells. Taken together, our findings represent new knowledge for a better understanding the ceRNA network in LUSC biology and pave the way to improved diagnosis and prognosis of LUSC. creator: Pengbo Ning creator: Zhongxing Wu creator: Aoxue Hu creator: Xuepeng Li creator: Jun He creator: Xiaocheng Gong creator: Yuqiong Xia creator: Yukui Shang creator: Huijie Bian uri: https://doi.org/10.7717/peerj.4254 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ning et al. title: Depth- and range-dependent variation in the performance of aquatic telemetry systems: understanding and predicting the susceptibility of acoustic tag–receiver pairs to close proximity detection interference link: https://peerj.com/articles/4249 last-modified: 2018-01-12 description: BackgroundPassive acoustic telemetry using coded transmitter tags and stationary receivers is a popular method for tracking movements of aquatic animals. Understanding the performance of these systems is important in array design and in analysis. Close proximity detection interference (CPDI) is a condition where receivers fail to reliably detect tag transmissions. CPDI generally occurs when the tag and receiver are near one another in acoustically reverberant settings. Here we confirm transmission multipaths reflected off the environment arriving at a receiver with sufficient delay relative to the direct signal cause CPDI. We propose a ray-propagation based model to estimate the arrival of energy via multipaths to predict CPDI occurrence, and we show how deeper deployments are particularly susceptible.MethodsA series of experiments were designed to develop and validate our model. Deep (300 m) and shallow (25 m) ranging experiments were conducted using Vemco V13 acoustic tags and VR2-W receivers. Probabilistic modeling of hourly detections was used to estimate the average distance a tag could be detected. A mechanistic model for predicting the arrival time of multipaths was developed using parameters from these experiments to calculate the direct and multipath path lengths. This model was retroactively applied to the previous ranging experiments to validate CPDI observations. Two additional experiments were designed to validate predictions of CPDI with respect to combinations of deployment depth and distance. Playback of recorded tags in a tank environment was used to confirm multipaths arriving after the receiver’s blanking interval cause CPDI effects.ResultsAnalysis of empirical data estimated the average maximum detection radius (AMDR), the farthest distance at which 95% of tag transmissions went undetected by receivers, was between 840 and 846 m for the deep ranging experiment across all factor permutations. From these results, CPDI was estimated within a 276.5 m radius of the receiver. These empirical estimations were consistent with mechanistic model predictions. CPDI affected detection at distances closer than 259–326 m from receivers. AMDR determined from the shallow ranging experiment was between 278 and 290 m with CPDI neither predicted nor observed. Results of validation experiments were consistent with mechanistic model predictions. Finally, we were able to predict detection/nondetection with 95.7% accuracy using the mechanistic model’s criterion when simulating transmissions with and without multipaths.DiscussionClose proximity detection interference results from combinations of depth and distance that produce reflected signals arriving after a receiver’s blanking interval has ended. Deployment scenarios resulting in CPDI can be predicted with the proposed mechanistic model. For deeper deployments, sea-surface reflections can produce CPDI conditions, resulting in transmission rejection, regardless of the reflective properties of the seafloor. creator: Stephen R. Scherrer creator: Brendan P. Rideout creator: Giacomo Giorli creator: Eva-Marie Nosal creator: Kevin C. Weng uri: https://doi.org/10.7717/peerj.4249 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Scherrer et al. title: Weekend effect in upper gastrointestinal bleeding: a systematic review and meta-analysis link: https://peerj.com/articles/4248 last-modified: 2018-01-12 description: AimTo perform a systematic review and meta-analysis of the weekend effect on the mortality of patients with upper gastrointestinal bleeding(UGIB).MethodsThe review protocol has been registered in the PROSPERO International Prospective Register of Systematic Reviews (registration number: CRD42017073313) and was written according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. We conducted a search of the PUBMED, COCHRANE, EMBASE and CINAHL databases from inception to August 2017. All observational studies comparing mortality between UGIB patients with weekend versus weekday admissions were included. Articles that were published only in abstract form or not published in a peer-reviewed journal were excluded. The quality of articles was assessed using the Newcastle-Ottawa Scale. We pooled results from the articles using random-effect models. Heterogeneity was evaluated by the chi-square-based Q-test and I2test. To address heterogeneity, we performed sensitivity and subgroup analyses. Potential publication bias was assessed via funnel plot.ResultsEighteen observational cohort studies involving 1,232,083 study patients were included. Weekend admission was associated with significantly higher 30-day or in-hospital mortality in all studies (OR = 1.12, 95% CI [1.07–1.17], P < 0.00001). Increased in-hospital mortality was also associated with weekend admission (OR = 1.12, 95% CI [1.08–1.17], P < 0.00001). No significant difference in in-hospital mortality was observed between patients admitted with variceal bleeding during the weekend or on weekdays (OR = 0.99, 95% CI [0.91–1.08], P = 0.82); however, weekend admission was associated with a 15% increase in in-hospital mortality for patients with non-variceal bleeding (OR = 1.15, 95% CI [1.09–1.21], P < 0.00001). The time to endoscopy for weekday admission was significantly less than that obtained for weekend admission (MD = −2.50, 95% CI [−4.08–−0.92], P = 0.002).ConclusionsThe weekend effect is associated with increased mortality of UGIB patients, particularly in non-variceal bleeding. The timing of endoscopic intervention might be a factor that influences mortality of UGIB patients. creator: Pei-Ching Shih creator: Shu-Jung Liu creator: Sung-Tse Li creator: Ai-Chen Chiu creator: Po-Chuan Wang creator: Lawrence Yu-Min Liu uri: https://doi.org/10.7717/peerj.4248 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shih et al. title: Isolation, identification, and pathological effects of beach sand bacterial extract on human skin keratinocytes in vitro link: https://peerj.com/articles/4245 last-modified: 2018-01-12 description: BackgroundBeaches are recreational spots for people. However, beach sand contains harmful microbes that affect human health, and there are no established methods for either sampling and identifying beach-borne pathogens or managing the quality of beach sand.MethodThis study was conducted with the aim of improving human safety at beaches and augmenting the quality of the beach experience. Beach sand was used as a resource to isolate bacteria due to its distinctive features and the biodiversity of the beach sand biota. A selected bacterial isolate termed FSRS was identified as Pseudomonas stutzeri using 16S rRNA sequencing and phylogenetic analysis, and the sequence was deposited in the NCBI GenBank database under the accession number MF599548. The isolated P. stutzeri bacterium was cultured in Luria–Bertani growth medium, and a crude extract was prepared using ethyl acetate to examine the potential pathogenic effect of P. stutzeri on human skin. A human skin keratinocyte cell line (HaCaT) was used to assess cell adhesion, cell viability, and cell proliferation using a morphological analysis and a WST-1 assay.ResultThe crude P. stutzeri extract inhibited cell adhesion and decreased cell viability in HaCaT cells. We concluded that the crude extract of P. stutzeri FSRS had a strong pathological effect on human skin cells.DiscussionBeach visitors frequently get skin infections, but the exact cause of the infections is yet to be determined. The beach sand bacterium P. stutzeri may, therefore, be responsible for some of the dermatological problems experienced by people visiting the beach. creator: Fazli Subhan creator: Raheem Shahzad creator: Isfahan Tauseef creator: Kashif Syed Haleem creator: Atta-Ur Rehman creator: Sajid Mahmood creator: In-Jung Lee uri: https://doi.org/10.7717/peerj.4245 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Subhan et al. title: Effects of the visual-feedback-based force platform training with functional electric stimulation on the balance and prevention of falls in older adults: a randomized controlled trial link: https://peerj.com/articles/4244 last-modified: 2018-01-12 description: BackgroundForce platform training with functional electric stimulation aimed at improving balance may be effective in fall prevention for older adults. Aim of the study is to evaluate the effects of the visual-feedback-based force platform balance training with functional electric stimulation on balance and fall prevention in older adults.MethodsA single-centre, unblinded, randomized controlled trial was conducted. One hundred and twenty older adults were randomly allocated to two groups: the control group (n = 60, one-leg standing balance exercise, 12 min/d) or the intervention group (n = 60, force platform training with functional electric stimulation, 12 min/d). The training was provided 15 days a month for 3 months by physical therapists. Medial–lateral and anterior–posterior maximal range of sway with eyes open and closed, the Berg Balance Scale, the Barthel Index, the Falls Efficacy scale-International were assessed at baseline and after the 3-month intervention. A fall diary was kept by each participant during the 6-month follow-up.ResultsOn comparing the two groups, the intervention group showed significantly decreased (p < 0.01) medial–lateral and anterior–posterior maximal range of sway with eyes open and closed. There was significantly higher improvement in the Berg Balance Scale (p < 0.05), the Barthel Index (p < 0.05) and the Falls Efficacy Scale-International (p < 0.05), along with significantly lesser number of injurious fallers (p < 0.05), number of fallers (p < 0.05), and fall rates (p < 0.05) during the 6-month follow-up in the intervention group.ConclusionThis study showed that the visual feedback-based force platform training with functional electric stimulation improved balance and prevented falls in older adults. creator: Zhen Li creator: Xiu-Xia Wang creator: Yan-Yi Liang creator: Shu-Yan Chen creator: Jing Sheng creator: Shao-Jun Ma uri: https://doi.org/10.7717/peerj.4244 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Urban heat island effect on cicada densities in metropolitan Seoul link: https://peerj.com/articles/4238 last-modified: 2018-01-12 description: BackgroundUrban heat island (UHI) effect, the ubiquitous consequence of urbanization, is considered to play a major role in population expansion of numerous insects. Cryptotympana atrata and Hyalessa fuscata are the most abundant cicada species in the Korean Peninsula, where their population densities are higher in urban than in rural areas. We predicted a positive relationship between the UHI intensities and population densities of these two cicada species in metropolitan Seoul.MethodsTo test this prediction, enumeration surveys of cicada exuviae densities were conducted in 36 localities located within and in the vicinity of metropolitan Seoul. Samples were collected in two consecutive periods from July to August 2015. The abundance of each species was estimated by two resource-weighted densities, one based on the total geographic area, and the other on the total number of trees. Multiple linear regression analyses were performed to identify factors critical for the prevalence of cicada species in the urban habitat.ResultsC. atrata and H. fuscata were major constituents of cicada species composition collected across all localities. Minimum temperature and sampling period were significant factors contributing to the variation in densities of both species, whereas other environmental factors related to urbanization were not significant. More cicada exuviae were collected in the second rather than in the first samplings, which matched the phenological pattern of cicadas in metropolitan Seoul. Cicada population densities increased measurably with the increase in temperature. Age of residential complex also exhibited a significantly positive correlation to H. fuscata densities, but not to C. atrata densities.DiscussionEffects of temperature on cicada densities have been discerned from other environmental factors, as cicada densities increased measurably in tandem with elevated temperature. Several mechanisms may contribute to the abundance of cicadas in urban environments, such as higher fecundity of females, lower mortality rate of instars, decline in host plant quality, and local adaptation of organisms, but none of them were tested in the current study.ConclusionsIn sum, results of the enumeration surveys of cicada exuviae support the hypothesis that the UHI effect underlies the population expansion of cicadas in metropolitan Seoul. Nevertheless, the underlying mechanisms for this remain untested. creator: Hoa Q. Nguyen creator: Desiree K. Andersen creator: Yuseob Kim creator: Yikweon Jang uri: https://doi.org/10.7717/peerj.4238 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Nguyen et al. title: A diagnostic model for minimal change disease based on biological parameters link: https://peerj.com/articles/4237 last-modified: 2018-01-12 description: BackgroundMinimal change disease (MCD) is a kind of nephrotic syndrome (NS). In this study, we aimed to establish a mathematical diagnostic model based on biological parameters to classify MCD.MethodsA total of 798 NS patients were divided into MCD group and control group. The comparison of biological indicators between two groups were performed with t-tests. Logistic regression was used to establish the diagnostic model, and the diagnostic value of the model was estimated using receiver operating characteristic (ROC) analysis.ResultsThirteen indicators including Anti-phospholipase A2 receptor (anti-PLA2R) (P = 0.000), Total protein (TP) (P = 0.000), Albumin (ALB) (P = 0.000), Direct bilirubin (DB) (P = 0.002), Creatinine (Cr) (P = 0.000), Total cholesterol (CH) (P = 0.000), Lactate dehydrogenase (LDH) (P = 0.007), High density lipoprotein cholesterol (HDL) (P = 0.000), Low density lipoprotein cholesterol (LDL) (P = 0.000), Thrombin time (TT) (P = 0.000), Plasma fibrinogen (FIB) (P = 0.000), Immunoglobulin A (IgA) (P = 0.008) and Complement 3 (C3) (P = 0.019) were significantly correlated with MCD. Furthermore, the area under ROC curves of CH, HDL, LDL, TT and FIB were more than 0.70. Logistic analysis demonstrated that CH and TT were risk factors for MCD. According to the ROC of “CH+TT”, the AUC was 0.827, with the sensitivity of 83.0% and the specificity of 69.8% (P = 0.000).ConclusionThe established diagnostic model with CH and TT could be used for classified diagnosis of MCD. creator: Hanyu Zhu creator: Qiuxia Han creator: Dong Zhang creator: Yong Wang creator: Jing Gao creator: Wenjia Geng creator: Xiaoli Yang creator: Xiangmei Chen uri: https://doi.org/10.7717/peerj.4237 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhu et al. title: Risk factors for osteoporosis in male patients with chronic obstructive pulmonary disease in Taiwan link: https://peerj.com/articles/4232 last-modified: 2018-01-12 description: ObjectiveTo investigate the risk factors for osteoporosis in male Taiwanese patients with chronic obstructive pulmonary disease (COPD).MethodsThis cross-sectional study evaluated male COPD outpatients and age-matched male subjects at a regional teaching hospital. The following data were obtained and analyzed: bone mineral density of the lumbar spine and hip on dual-energy X-ray absorptiometry, demographic characteristics, questionnaire interview results, pulmonary function test results, chest posterior–anterior radiographic findings, and biochemical and high-sensitivity C-reactive protein (hs-CRP) levels.ResultsFifty-nine male COPD patients and 36 age-matched male subjects were enrolled. COPD patients had lower body mass index (BMI) (23.6 ± 4.1 vs. 25.2 ± 3.0 kg/m2) and higher total prevalence for osteoporosis and osteopenia than controls. Among COPD patients, patients with osteoporosis had lower BMI, body weight, waist circumference, and triglyceride level but higher hs-CRP level, and tended to have lower creatinine level. Binary logistic regression analysis for factors including age, BMI, creatinine, hs-CRP, smoking, steroid use, and forced expiratory volume in one second (FEV1) revealed that an hs-CRP level ≥5 and decreased creatinine level were independent risk factors for osteoporosis in COPD patients. Lower BMI tended to be associated with osteoporosis development, although it did not reach statistical significance, and hs-CRP was associated with COPD severity and steroid use history.ConclusionThe total prevalence of osteoporosis and osteopenia in male Taiwanese COPD patients is higher than that in age-matched male subjects and systemic inflammation is an independent risk factors for osteoporosis. Low creatinine level in COPD patients should raise the suspicion of sarcopenia and associated increased risk of osteoporosis. creator: Chu-Hsu Lin creator: Kai-Hua Chen creator: Chien-Min Chen creator: Chia-Hao Chang creator: Tung-Jung Huang creator: Chia-Hung Lin uri: https://doi.org/10.7717/peerj.4232 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lin et al. title: FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data link: https://peerj.com/articles/4227 last-modified: 2018-01-12 description: With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets. creator: Saima Sultana Tithi creator: Frank O. Aylward creator: Roderick V. Jensen creator: Liqing Zhang uri: https://doi.org/10.7717/peerj.4227 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tithi et al. title: A revised cranial description of Massospondylus carinatus Owen (Dinosauria: Sauropodomorpha) based on computed tomographic scans and a review of cranial characters for basal Sauropodomorpha link: https://peerj.com/articles/4224 last-modified: 2018-01-12 description: Massospondylus carinatus is a basal sauropodomorph dinosaur from the early Jurassic Elliot Formation of South Africa. It is one of the best-represented fossil dinosaur taxa, known from hundreds of specimens including at least 13 complete or nearly complete skulls. Surprisingly, the internal cranial anatomy of M. carinatus has never been described using computed tomography (CT) methods. Using CT scans and 3D digital representations, we digitally reconstruct the bones of the facial skeleton, braincase, and palate of a complete, undistorted cranium of M. carinatus (BP/1/5241). We describe the anatomical features of the cranial bones, and compare them to other closely related sauropodomorph taxa such as Plateosaurus erlenbergiensis, Lufengosaurus huenei, Sarahsaurus aurifontanalis and Efraasia minor. We identify a suite of character states of the skull and braincase for M. carinatus that sets it apart from other taxa, but these remain tentative due to the lack of comparative sauropodomorph braincase descriptions in the literature. Furthermore, we hypothesize 27 new cranial characters useful for determining relationships in non-sauropodan Sauropodomorpha, delete five pre-existing characters and revise the scores of several existing cranial characters to make more explicit homology statements. All the characters that we hypothesized or revised are illustrated. Using parsimony as an optimality criterion, we then test the relationships of M. carinatus (using BP/1/5241 as a specimen-level exemplar) in our revised phylogenetic data matrix. creator: Kimberley E.J. Chapelle creator: Jonah N. Choiniere uri: https://doi.org/10.7717/peerj.4224 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chapelle and Choiniere title: DNA barcode-based survey of Trichoptera in the Crooked River reveals three new species records for British Columbia link: https://peerj.com/articles/4221 last-modified: 2018-01-12 description: Anthropogenic pressures on aquatic systems have placed a renewed focus on biodiversity of aquatic macroinvertebrates. By combining classical taxonomy and DNA barcoding we identified 39 species of caddisflies from the Crooked River, a unique and sensitive system in the southernmost arctic watershed in British Columbia. Our records include three species never before recorded in British Columbia: Lepidostoma togatum (Lepidostomatidae), Ceraclea annulicornis (Leptoceridae), and possibly Cheumatopsyche harwoodi (Hydropsychidae). Three other specimens may represent new occurrence records and a number of other records seem to be substantial observed geographic range expansions within British Columbia. creator: Daniel J. Erasmus creator: Emily A. Yurkowski creator: Dezene P.W. Huber uri: https://doi.org/10.7717/peerj.4221 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Erasmus et al. title: Achilles heel of a powerful invader: restrictions on distribution and disappearance of feral pigs from a protected area in Northern Pantanal, Western Brazil link: https://peerj.com/articles/4200 last-modified: 2018-01-12 description: This paper focuses on a rare case of natural disappearance of feral pigs (Sus scrofa) in an extensive area without using traditional methods of eradication programs. The study was conducted both in the Private Reserve of Natural Heritage (PRNH) Sesc Pantanal and in an adjacent traditional private cattle ranch. In 1998, feral pigs were abundant and widely distributed in the PRNH. However, the feral pigs gradually disappeared from the area and currently, the absence of pigs in the PRNH contrasts with the adjacent cattle ranch where the species is abundant. To understand the current distribution of the species in the region we partitioned the effects of variation of feral pigs’ presence considering the habitat structure (local), landscape composition and the occurrence of potential predators. Additionally, we modeled the distributions of the species in Northern Pantanal, projecting into the past using the classes of vegetation cover before the PRNH implementation (year 1988). Our results show areas with more suitability for feral pigs in regions where the landscape is dominated by pastures and permeated by patches of Seasonal Dry Forest. The species tends to avoid predominantly forested areas. Additionally, we recorded that the environmental suitability decreases exponentially as the distance from water bodies increases. The disappearance of feral pigs in the PRNH area seems to be associated with changes in the landscape and vegetation structure after the removal of the cattle. In the Brazilian Pantanal, the feral pigs’ occurrence seems strongly conditioned to environmental changes associated to livestock activity. creator: Jose L.P. Cordeiro creator: Gabriel S. Hofmann creator: Carlos Fonseca creator: Luiz Flamarion B. Oliveira uri: https://doi.org/10.7717/peerj.4200 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cordeiro et al. title: Crustacean amphipods from marsh ponds: a nutritious feed resource with potential for application in Integrated Multi-Trophic Aquaculture link: https://peerj.com/articles/4194 last-modified: 2018-01-12 description: Coastal protection, nutrient cycling, erosion control, water purification, and carbon sequestration are ecosystem services provided by salt marshes. Additionally, salt ponds offer coastal breeding and a nursery habitat for fishes and they provide abundant invertebrates, such as amphipods, which are potentially useful as a resource in aquaculture. Fishmeal and fish oil are necessary food resources to support aquaculture of carnivorous species due to their omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). Currently, aquaculture depends on limited fisheries and feed with elevated n-3 LC-PUFA levels, but the development of more sustainable food sources is necessary. Amphipods appear to be a potential high quality alternative feed resource for aquaculture. Hence, a nutritional study was carried out for several main amphipod species—Microdeutopus gryllotalpa, Monocorophium acherusicum, Gammarus insensibilis, Melita palmata and Cymadusa filosa—in terrestrial ponds in the South of Spain. These species showed high protein content (up to 40%), high n-3 PUFA and phospholipid levels, and high levels of phophatidylcholine (PC), phosphatidylethanolamine (PE) and triacylglycerols (TAG), the latter being significantly high for M. acherusicum. M. gryllotalpa and M. acherusicum showed the highest proportion of lipids (19.15% and 18.35%, respectively). Isoleucine, glycine and alanine were the dominant amino acids in all species. In addition, amphipods collected from ponds showed low levels of heavy metals. Furthermore, the biochemical profiles of the five species of amphipods have been compared with other studied alternative prey. Therefore, pond amphipods are good candidates to be used as feed, and are proposed as a new sustainable economic resource to be used in aquaculture. G. insensibilis may be the best for intensive culture as an alternative feed resource because it shows: (1) adequate n-3 PUFA and PL composition; (2) high levels of glycine, alanine, tyrosine, isoleucine and lysine; (3) high natural densities; (4) large body size (≥1 cm), and (5) high concentration of calcium. Moreover, a combined culture of amphipods and fishes in these marsh ponds seems a promising and environmentally sustainable way to develop Integrate Multi-Trophic Aquaculture (IMTA) in these ecosystems. creator: Pablo Jiménez-Prada creator: Ismael Hachero-Cruzado creator: Inmaculada Giráldez creator: Catalina Fernández-Diaz creator: César Vilas creator: José Pedro Cañavate creator: José Manuel Guerra-García uri: https://doi.org/10.7717/peerj.4194 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jiménez-Prada et al. title: A new small-bodied ornithopod (Dinosauria, Ornithischia) from a deep, high-energy Early Cretaceous river of the Australian–Antarctic rift system link: https://peerj.com/articles/4113 last-modified: 2018-01-11 description: A new small-bodied ornithopod dinosaur, Diluvicursor pickeringi, gen. et sp. nov., is named from the lower Albian of the Eumeralla Formation in southeastern Australia and helps shed new light on the anatomy and diversity of Gondwanan ornithopods. Comprising an almost complete tail and partial lower right hindlimb, the holotype (NMV P221080) was deposited as a carcass or body-part in a log-filled scour near the base of a deep, high-energy river that incised a faunally rich, substantially forested riverine floodplain within the Australian–Antarctic rift graben. The deposit is termed the ‘Eric the Red West Sandstone.’ The holotype, interpreted as an older juvenile ∼1.2 m in total length, appears to have endured antemortem trauma to the pes. A referred, isolated posterior caudal vertebra (NMV P229456) from the holotype locality, suggests D. pickeringi grew to at least 2.3 m in length. D. pickeringi is characterised by 10 potential autapomorphies, among which dorsoventrally low neural arches and transversely broad caudal ribs on the anterior-most caudal vertebrae are a visually defining combination of features. These features suggest D. pickeringi had robust anterior caudal musculature and strong locomotor abilities. Another isolated anterior caudal vertebra (NMV P228342) from the same deposit, suggests that the fossil assemblage hosts at least two ornithopod taxa. D. pickeringi and two stratigraphically younger, indeterminate Eumeralla Formation ornithopods from Dinosaur Cove, NMV P185992/P185993 and NMV P186047, are closely related. However, the tail of D. pickeringi is far shorter than that of NMV P185992/P185993 and its pes more robust than that of NMV P186047. Preliminary cladistic analysis, utilising three existing datasets, failed to resolve D. pickeringi beyond a large polytomy of Ornithopoda. However, qualitative assessment of shared anatomical features suggest that the Eumeralla Formation ornithopods, South American Anabisetia saldiviai and Gasparinisaura cincosaltensis, Afro-Laurasian dryosaurids and possibly Antarctic Morrosaurus antarcticus share a close phylogenetic progenitor. Future phylogenetic analysis with improved data on Australian ornithopods will help to test these suggested affinities. creator: Matthew C. Herne creator: Alan M. Tait creator: Vera Weisbecker creator: Michael Hall creator: Jay P. Nair creator: Michael Cleeland creator: Steven W. Salisbury uri: https://doi.org/10.7717/peerj.4113 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Herne et al. title: Positive selection on human gamete-recognition genes link: https://peerj.com/articles/4259 last-modified: 2018-01-11 description: Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2. We also identified one candidate site under positive selection in C4BPA, which encodes a repetitive protein similar to the mouse protein ZP3R that is expressed in the sperm head and binds to the ZP at fertilization. Results from several additional analyses that applied population genetic models to the same data were consistent with the hypothesis of selection on those candidate sites leading to coevolution of sperm- and egg-expressed genes. By contrast, we found no candidate sites under selection in a fourth gene (ZP1) that encodes an egg coat structural protein not directly involved in sperm binding. Finally, we found that two of the candidate sites (in C4BPA and ZP2) were correlated with variation in family size and birth rate among Hutterite couples, and those two candidate sites were also in linkage disequilibrium in the same Hutterite study population. All of these lines of evidence are consistent with predictions from a previously proposed hypothesis of balancing selection on epistatic interactions between C4BPA and ZP3 at fertilization that lead to the evolution of co-adapted allele pairs. Such patterns also suggest specific molecular traits that may be associated with both natural reproductive variation and clinical infertility. creator: Michael W. Hart creator: Daryn A. Stover creator: Vanessa Guerra creator: Sahar V. Mozaffari creator: Carole Ober creator: Carina F. Mugal creator: Ingemar Kaj uri: https://doi.org/10.7717/peerj.4259 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hart et al. title: A streptomycin resistance marker in H. parasuis based on site-directed mutations in rpsL gene to perform unmarked in-frame mutations and to verify natural transformation link: https://peerj.com/articles/4253 last-modified: 2018-01-11 description: Haemophilus parasuis is a member of the family Pasteurellaceae and a major causative agent of Glässer’s disease. This bacterium is normally a benign swine commensal but may become a deadly pathogen upon penetration into multiple tissues, contributing to severe lesions in swine. We have established a successive natural transformation-based markerless mutation system in this species. However, the two-step mutation system requires screening of natural competent cells, and cannot delete genes which regulate natural competence per se. In this study, we successfully obtained streptomycin-resistant derivatives from H. parasuis wild type strain SC1401 by using ethyl methane sulfonate (EMS, CH3SO2OC2H5). Upon sequencing and site-directed mutations, we uncovered that the EMS-induced point mutation in rpsL at codon 43rd (AAA → AGA; K43R) or at 88th (AAA → AGA; K88R) confers a much higher streptomycin resistance than clinical isolates. We have applied the streptomycin resistance marker as a positive selection marker to perform homologous recombination through conjugation and successfully generated a double unmarked in-frame targeted mutant 1401D88△tfox△arcA. Combined with a natural transformation-based knockout system and this genetic technique, multiple deletion mutants or attenuated strains of H. parasuis can be easily constructed. Moreover, the mutant genetic marker rpsL and streptomycin resistant phenotypes can serve as an effective tool to select naturally competent strains, and to verify natural transformation quantitatively. creator: Ke Dai creator: Xintian Wen creator: Yung-Fu Chang creator: Sanjie Cao creator: Qin Zhao creator: Xiaobo Huang creator: Rui Wu creator: Yong Huang creator: Qigui Yan creator: Xinfeng Han creator: Xiaoping Ma creator: Yiping Wen uri: https://doi.org/10.7717/peerj.4253 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dai et al. title: Stat-tracks and mediotypes: powerful tools for modern ichnology based on 3D models link: https://peerj.com/articles/4247 last-modified: 2018-01-11 description: Vertebrate tracks are subject to a wide distribution of morphological types. A single trackmaker may be associated with a range of tracks reflecting individual pedal anatomy and behavioural kinematics mediated through substrate properties which may vary both in space and time. Accordingly, the same trackmaker can leave substantially different morphotypes something which must be considered in creating ichnotaxa. In modern practice this is often captured by the collection of a series of 3D track models. We introduce two concepts to help integrate these 3D models into ichnological analysis procedures. The mediotype is based on the idea of using statistically-generated three-dimensional track models (median or mean) of the type specimens to create a composite track to support formal recognition of a ichno type. A representative track (mean and/or median) is created from a set of individual reference tracks or from multiple examples from one or more trackways. In contrast, stat-tracks refer to other digitally generated tracks which may explore variance. For example, they are useful in: understanding the preservation variability of a given track sample; identifying characteristics or unusual track features; or simply as a quantitative comparison tool. Both concepts assist in making ichnotaxonomical interpretations and we argue that they should become part of the standard procedure when instituting new ichnotaxa. As three-dimensional models start to become a standard in publications on vertebrate ichnology, the mediotype and stat-track concepts have the potential to help guiding a revolution in the study of vertebrate ichnology and ichnotaxonomy. creator: Matteo Belvedere creator: Matthew R. Bennett creator: Daniel Marty creator: Marcin Budka creator: Sally C. Reynolds creator: Rashid Bakirov uri: https://doi.org/10.7717/peerj.4247 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Belvedere et al. title: An exploratory study of adolescent response to fluoxetine using psychological and biological predictors link: https://peerj.com/articles/4240 last-modified: 2018-01-10 description: BackgroundNot enough is known about predicting therapeutic response to serotonin-specific reuptake inhibitors, and specifically to fluoxetine. This exploratory study used psychological and biological markers for (retrospective) prediction of treatment-response to fluoxetine in depressed and/or anxious adolescents.MethodsForty-one consecutive adolescent outpatients with a primary diagnosis of severe affective and/or anxiety disorders were assessed and treated with an open-label 8-week trial of fluoxetine. Type D personality was assessed with the 14-item questionnaire, the DS14. In addition, TNFα, IL-6, and IL-1b were measured pre- and post-treatment.ResultsThere was an elevation of Type D personality in patients, compared to the adolescent population rate. Post-treatment, 44% of patients were classified as non-responders; the relative risk of non-response for Type D personality patients was 2.8. Binary logistic regression predicting response vs. non-response showed a contribution of initial TNFα levels as well as Type D personality to non-response.ConclusionsIn this exploratory study, the most significant contributor to non-response was Type D personality. However, the measurement of Type D was not prospective, and thus may be confounded with psychiatric morbidity. The measurement of personality in psychiatric settings may contribute to the understanding of treatment response and have clinical utility. creator: Ada H. Zohar creator: Tamar Eilat creator: Maya Amitai creator: Michal Taler creator: Romi Bari creator: Alon Chen creator: Alan Apter creator: Avraham Weizman creator: Silvana Fennig uri: https://doi.org/10.7717/peerj.4240 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zohar et al. title: Refining amino acid hydrophobicity for dynamics simulation of membrane proteins link: https://peerj.com/articles/4230 last-modified: 2018-01-10 description: Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems. creator: Ronald D. Hills, Jr uri: https://doi.org/10.7717/peerj.4230 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hills, Jr title: Using underwater video to evaluate the performance of the Fukui trap as a mitigation tool for the invasive European green crab (Carcinus maenas) in Newfoundland, Canada link: https://peerj.com/articles/4223 last-modified: 2018-01-10 description: The European green crab (Carcinus maenas) is a destructive marine invader that was first discovered in Newfoundland waters in 2007 and has since become established in nearshore ecosystems on the south and west coast of the island. Targeted fishing programs aimed at removing green crabs from invaded Newfoundland ecosystems use Fukui traps, but the capture efficiency of these traps has not been previously assessed. We assessed Fukui traps using in situ observation with underwater video cameras as they actively fished for green crabs. From these videos, we recorded the number of green crabs that approached the trap, the outcome of each entry attempt (success or failure), and the number of exits from the trap. Across eight videos, we observed 1,226 green crab entry attempts, with only a 16% rate of success from these attempts. Based on these observations we believe there is scope to improve the performance of the Fukui trap through modifications in order to achieve a higher catch per unit effort (CPUE), maximizing trap usage for mitigation. Ultimately, a more efficient Fukui trap will help to control green crab populations in order to preserve the function and integrity of ecosystems invaded by the green crab. creator: Jonathan A. Bergshoeff creator: Cynthia H. McKenzie creator: Kiley Best creator: Nicola Zargarpour creator: Brett Favaro uri: https://doi.org/10.7717/peerj.4223 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bergshoeff et al. title: Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory link: https://peerj.com/articles/4218 last-modified: 2018-01-10 description: BackgroundMicrobial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics—including clinicians, laboratorians, epidemiologists, and researchers—is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results.MethodsWe used Design Study Methodology—a human centered approach drawn from the information visualization domain—to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report.ResultsWe recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design comparisons, participants preferred the alternative prototype designs over the existing version, and that both clinicians and non-clinicians expressed similar design preferences. Participants showed clearer design preferences when asked to compare individual design elements versus entire reports. Both the quantitative and qualitative data informed the design of a revised report, available online as a LaTeX template.ConclusionsWe show how a human-centered design approach integrating quantitative and qualitative feedback can be used to design an alternative report for representing complex microbial genomic data. We suggest experimental and design guidelines to inform future design studies in the bioinformatics and microbial genomics domains, and suggest that this type of mixed-methods study is important to facilitate the successful translation of pathogen genomics in the clinic, not only for clinical reports but also more complex bioinformatics data visualization software. creator: Anamaria Crisan creator: Geoffrey McKee creator: Tamara Munzner creator: Jennifer L. Gardy uri: https://doi.org/10.7717/peerj.4218 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Crisan et al. title: Annual and spatial variation in composition and activity of terrestrial mammals on two replicate plots in lowland forest of eastern Ecuador link: https://peerj.com/articles/4241 last-modified: 2018-01-09 description: Terrestrial mammals are important components of lowland forests in Amazonia (as seed dispersal agents, herbivores, predators) but there are relatively few detailed studies from areas that have not been affected by human activities (e.g., hunting, logging). Yet, such information is needed to evaluate effects of humans elsewhere. We used camera traps to sample medium to large-sized terrestrial mammals at a site in lowland forests of eastern Ecuador, one of the most biologically rich areas in the world. We deployed cameras on two study plots in terra firme forest at Tiputini Biodiversity Station. Sixteen cameras were arranged 200 m apart in a 4 × 4 grid on each plot. Cameras were operated for  60 days in January–March, 2014–2017, for a total of 3,707 and 3,482 trap-days on the two plots (Harpia, Puma). A total of 28 species were recorded; 26 on Harpia and 25 on Puma. Number of species recorded each year was slightly greater on Harpia whereas overall capture rates (images/100 trap-days) were higher on Puma. Although most species were recorded on each plot, differences in capture rates meant that yearly samples on a given plot were more similar to each other than to samples on the other plot. Images of most species showed a clumped distribution pattern on each plot; Panthera onca was the only species that did not show a clumped distribution on either plot. Images at a given camera location showed no evidence of autocorrelation with numbers of images at nearby camera locations, suggesting that species were responding to small-scale differences in habitat conditions. A redundancy analysis showed that environmental features within 50 or 100 m of camera locations (e.g., elevation, variation in elevation, slope, distance to streams) accounted for significant amounts of variation in distribution patterns of species. Composition and relative importance based on capture rates were very similar to results from cameras located along trails at the same site; similarities decreased at increasing spatial scales based on comparisons with results from other sites in Ecuador and Peru. creator: John G. Blake creator: Bette A. Loiselle uri: https://doi.org/10.7717/peerj.4241 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Blake and Loiselle title: The old and the new plankton: ecological replacement of associations of mollusc plankton and giant filter feeders after the Cretaceous? link: https://peerj.com/articles/4219 last-modified: 2018-01-09 description: Owing to their great diversity and abundance, ammonites and belemnites represented key elements in Mesozoic food webs. Because of their extreme ontogenetic size increase by up to three orders of magnitude, their position in the food webs likely changed during ontogeny. Here, we reconstruct the number of eggs laid by large adult females of these cephalopods and discuss developmental shifts in their ecologic roles. Based on similarities in conch morphology, size, habitat and abundance, we suggest that similar niches occupied in the Cretaceous by juvenile ammonites and belemnites were vacated during the extinction and later partially filled by holoplanktonic gastropods. As primary consumers, these extinct cephalopod groups were important constituents of the plankton and a principal food source for planktivorous organisms. As victims or, respectively, profiteers of this case of ecological replacement, filter feeding chondrichthyans and cetaceans likely filled the niches formerly occupied by large pachycormid fishes during the Jurassic and Cretaceous. creator: Amane Tajika creator: Alexander Nützel creator: Christian Klug uri: https://doi.org/10.7717/peerj.4219 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tajika et al. title: Preventive effects of Salvia officinalis leaf extract on insulin resistance and inflammation in a model of high fat diet-induced obesity in mice that responds to rosiglitazone link: https://peerj.com/articles/4166 last-modified: 2018-01-09 description: BackgroundSalvia officinalis (sage) is a native plant to the Mediterranean region and has been used for a long time in traditional medicine for various diseases. We investigated possible anti-diabetic, anti-inflammatory and anti-obesity effects of sage methanol (MetOH) extract in a nutritional mouse model of obesity, inflammation and insulin resistance, as well as its effects on lipolysis and lipogenesis in 3T3-L1 cells.MethodsDiet-induced obese (DIO) mice were treated for five weeks with sage methanol extract (100 and 400 mg kg−1/day bid), or rosiglitazone (3 mg kg−1/day bid), as a positive control. Energy expenditure, food intake, body weight, fat mass, liver glycogen and lipid content were evaluated. Blood glucose, and plasma levels of insulin, lipids leptin and pro- and anti-inflammatory cytokines were measured throughout the experiment. The effects of sage MetOH extract on lipolysis and lipogenesis were tested in vitro in 3T3-L1 cells.ResultsAfter two weeks of treatment, the lower dose of sage MetOH extract decreased blood glucose and plasma insulin levels during an oral glucose tolerance test (OGTT). An insulin tolerance test (ITT), performed at day 29 confirmed that sage improved insulin sensitivity. Groups treated with low dose sage and rosiglitazone showed very similar effects on OGTT and ITT. Sage also improved HOMA-IR, triglycerides and NEFA. Treatment with the low dose increased the plasma levels of the anti-inflammatory cytokines IL-2, IL-4 and IL-10 and reduced the plasma level of the pro-inflammatory cytokines IL-12, TNF-α, and KC/GRO. The GC analysis revealed the presence of two PPARs agonist in sage MetOH extract. In vitro, the extract reduced in a dose-related manner the accumulation of lipid droplets; however no effect on lipolysis was observed.ConclusionsSage MetOH extract at low dose exhibits similar effects to rosiglitazone. It improves insulin sensitivity, inhibits lipogenesis in adipocytes and reduces inflammation as judged by plasma cytokines. Sage presents an alternative to pharmaceuticals for the treatment of diabetes and associated inflammation. creator: Mohamed R. Ben Khedher creator: Mohamed Hammami creator: Jonathan R.S. Arch creator: David C. Hislop creator: Dominic Eze creator: Edward T. Wargent creator: Małgorzata A. Kępczyńska creator: Mohamed S. Zaibi uri: https://doi.org/10.7717/peerj.4166 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ben Khedher et al. title: A new species of Cretalamna sensu stricto (Lamniformes, Otodontidae) from the Late Cretaceous (Santonian-Campanian) of Alabama, USA link: https://peerj.com/articles/4229 last-modified: 2018-01-08 description: Decades of collecting from exposures of the Upper Cretaceous Tombigbee Sand Member of the Eutaw Formation and Mooreville Chalk in Alabama, USA has produced large numbers of isolated Cretalamna (sensu stricto) teeth. Many of these teeth had formerly been assigned to the extinct Late Cretaceous shark Cretalamna appendiculata (Agassiz, 1843), a taxon that is now considered largely restricted to the Turonian of Europe. Recent studies have shed light on the diversity of Late Cretaceous Cretalamna (s.s.) taxa, and here we recognize a new species from Alabama, Cretalamna bryanti. The teeth of C. bryanti sp. nov. appear aligned with the members of the Cretalamna borealis species group, but can be distinguished from these other species by a combination of the following: anterior teeth with a more pronounced and triangular lingual root protuberance, broader triangular cusp, and a taller root relative to the height of the crown; anteriorly situated lateroposterior teeth have a distally inclined or hooked main cusp and more than one pair of lateral cusplets; and lateroposterior teeth have a strong distally hooked main cusp and a root that is largely symmetrical in basal view. At present, C. bryanti sp. nov. is stratigraphically confined to the Santonian/Campanian Dicarinella asymetricaSigal, 1952 and Globotruncanita elevataBrotzen, 1934 Planktonic Foraminiferal Zones within the Tombigbee Sand Member of the Eutaw Formation and Mooreville Chalk, and teeth have been collected from only four counties in central and western Alabama. The recognition of C. bryanti sp. nov. in Alabama adds to our knowledge on the diversity and distribution of Late Cretaceous otodontids in the region. creator: Jun A. Ebersole creator: Dana J. Ehret uri: https://doi.org/10.7717/peerj.4229 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ebersole and Ehret title: Beyond harm’s reach? Submersion of river turtle nesting areas and implications for restoration actions after Amazon hydropower development link: https://peerj.com/articles/4228 last-modified: 2018-01-08 description: The global expansion of energy demands combined with abundant rainfall, large water volumes and high flow in tropical rivers have led to an unprecedented expansion of dam constructions in the Amazon. This expansion generates an urgent need for refined approaches to river management; specifically a move away from decision-making governed by overly generalized guidelines. For the first time we quantify direct impacts of hydropower reservoir establishment on an Amazon fresh water turtle. We conducted surveys along 150 km of rivers upstream of a new dam construction during the low water months that correspond to the nesting season of Podocnemis unifilis in the study area. Comparison of nest-areas before (2011, 2015) and after (2016) reservoir filling show that reservoir impacts extend 13% beyond legally defined limits. The submerged nesting areas accounted for a total of 3.8 ha of nesting habitat that was inundated as a direct result of the reservoir filling in 2016. Our findings highlight limitations in the development and implementation of existing Brazilian environmental impact assessment process. We also propose potential ways to mitigate the negative impacts of dams on freshwater turtles and the Amazonian freshwater ecosystems they inhabit. creator: Darren Norris creator: Fernanda Michalski creator: James P. Gibbs uri: https://doi.org/10.7717/peerj.4228 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Norris et al. title: Boundaries in ground beetle (Coleoptera: Carabidae) and environmental variables at the edges of forest patches with residential developments link: https://peerj.com/articles/4226 last-modified: 2018-01-08 description: BackgroundFew studies of edge effects on wildlife objectively identify habitat edges or explore non-linear responses. In this paper, we build on ground beetle (Coleoptera: Carabidae) research that has begun to address these domains by using triangulation wombling to identify boundaries in beetle community structure and composition at the edges of forest patches with residential developments. We hypothesized that edges are characterized by boundaries in environmental variables that correspond to marked discontinuities in vegetation structure between maintained yards and forest. We expected environmental boundaries to be associated with beetle boundaries.MethodsWe collected beetles and measured environmental variables in 200 m by 200 m sampling grids centered at the edges of three forest patches, each with a rural, suburban, or urban context, in Charlotte, North Carolina, USA. We identified boundaries within each grid at two spatial scales and tested their significance and overlap using boundary statistics and overlap statistics, respectively. We complemented boundary delineation with k-means clustering.ResultsBoundaries in environmental variables, such as temperature, grass cover, and leaf litter depth, occurred at or near the edges of all three sites, in many cases at both scales. The beetle variables that exhibited the most pronounced boundary structure in relation to edges were total species evenness, generalist abundance, generalist richness, generalist evenness, and Agonum punctiforme abundance. Environmental and beetle boundaries also occurred within forest patches and residential developments, indicating substantial localized spatial variation on either side of edges. Boundaries in beetle and environmental variables that displayed boundary structure at edges significantly overlapped, as did boundaries on either side of edges. The comparison of boundaries and clusters revealed that boundaries formed parts of the borders of patches of similar beetle or environmental condition.DiscussionWe show that edge effects on ground beetle community structure and composition and environmental variation at the intersection of forest patches and residential developments can be described by boundaries and that these boundaries overlap in space. However, our results also highlight the complexity of edge effects in our system: environmental boundaries were located at or near edges whereas beetle boundaries related to edges could be spatially disjunct from them; boundaries incompletely delineated edges such that only parts of edges were well-described by sharp transitions in beetle and/or environmental variables; and the occurrence of boundaries related to edges was apparently influenced by individual property management practices, site-specific characteristics such as development geometry, and spatial scale. creator: Doreen E. Davis creator: Sara A. Gagné uri: https://doi.org/10.7717/peerj.4226 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Davis and Gagné title: Ontogeny reversal and phylogenetic analysis of Turritopsis sp.5 (Cnidaria, Hydrozoa, Oceaniidae), a possible new species endemic to Xiamen, China link: https://peerj.com/articles/4225 last-modified: 2018-01-08 description: Ontogeny reversal, as seen in some cnidarians, is an unprecedented phenomenon in the animal kingdom involving reversal of the ordinary life cycle. Three species of Turritopsis have been shown to be capable of inverted metamorphosis, a process in which the pelagic medusa transforms back into a juvenile benthic polyp stage when faced with adverse conditions. Turritopsis sp.5 is a species of Turritopsis collected from Xiamen, China which presents a similar ability, being able to reverse its life cycle if injured by mechanical stress. Phylogenetic analysis based on both 16S rDNA and cytochrome c oxidase subunit I (COI) genetic barcodes shows that Turritopsis sp.5 is phylogenetically clustered in a clade separate from other species of Turritopsis. The genetic distance between T. sp.5 and the Japanese species T. sp.2 is the shortest, when measured by the Kimura 2-Parameter metric, and the distance to the New Zealand species T. rubra is the largest. An experimental assay on the induction of reverse development in this species was initiated by cutting medusae into upper and lower parts. We show, for the first time, that the two dissected parts have significantly different potentials to transform into polyps. Also, a series of morphological changes of the reversed life cycle can be recognised, including medusa stage, contraction stage I, contraction stage II, cyst, cyst with stolons, and polyp. The discovery of species capable of reverse ontogeny caused by unfavorable conditions adds to the available systems with which to study the cell types that contribute to the developmental reversal and the molecular mechanisms of the directional determination of ontogeny. creator: Jun-yuan Li creator: Dong-hui Guo creator: Peng-cheng Wu creator: Li-sheng He uri: https://doi.org/10.7717/peerj.4225 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Resounding failure to replicate links between developmental language disorder and cerebral lateralisation link: https://peerj.com/articles/4217 last-modified: 2018-01-08 description: BackgroundIt has been suggested that failure to establish cerebral lateralisation may be related to developmental language disorder (DLD). There has been weak support for any link with handedness, but more consistent reports of associations with functional brain lateralisation for language. The consistency of lateralisation across different functions may also be important. We aimed to replicate previous findings of an association between DLD and reduced laterality on a quantitative measure of hand preference (reaching across the midline) and on language laterality assessed using functional transcranial Doppler ultrasound (fTCD).MethodsFrom a sample of twin children aged from 6;0 to 11;11 years, we identified 107 cases of DLD and 156 typically-developing comparison cases for whom we had useable data from fTCD yielding a laterality index (LI) for language function during an animation description task. Handedness data were also available for these children.ResultsIndices of handedness and language laterality for this twin sample were similar to those previously reported for single-born children. There were no differences between the DLD and TD groups on measures of handedness or language lateralisation, or on a categorical measure of consistency of left hemisphere dominance. Contrary to prediction, there was a greater incidence of right lateralisation for language in the TD group (19.90%) than the DLD group (9.30%), confirming that atypical laterality is not inconsistent with typical language development. We also failed to replicate associations between language laterality and language test scores.Discussion and ConclusionsGiven the large sample studied here and the range of measures, we suggest that previous reports of atypical manual or language lateralisation in DLD may have been false positives. creator: Alexander C. Wilson creator: Dorothy V.M. Bishop uri: https://doi.org/10.7717/peerj.4217 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wilson and Bishop title: Is there a link between aging and microbiome diversity in exceptional mammalian longevity? link: https://peerj.com/articles/4174 last-modified: 2018-01-08 description: A changing microbiome has been linked to biological aging in mice and humans, suggesting a possible role of gut flora in pathogenic aging phenotypes. Many bat species have exceptional longevity given their body size and some can live up to ten times longer than expected with little signs of aging. This study explores the anal microbiome of the exceptionally long-lived Myotis myotis bat, investigating bacterial composition in both adult and juvenile bats to determine if the microbiome changes with age in a wild, long-lived non-model organism, using non-lethal sampling. The anal microbiome was sequenced using metabarcoding in more than 50 individuals, finding no significant difference between the composition of juvenile and adult bats, suggesting that age-related microbial shifts previously observed in other mammals may not be present in Myotis myotis. Functional gene categories, inferred from metabarcoding data, expressed in the M. myotis microbiome were categorized identifying pathways involved in metabolism, DNA repair and oxidative phosphorylation. We highlight an abundance of ‘Proteobacteria’ relative to other mammals, with similar patterns compared to other bat microbiomes. Our results suggest that M. myotis may have a relatively stable, unchanging microbiome playing a role in their extended ‘health spans’ with the advancement of age, and suggest a potential link between microbiome and sustained, powered flight. creator: Graham M. Hughes creator: John Leech creator: Sébastien J. Puechmaille creator: Jose V. Lopez creator: Emma C. Teeling uri: https://doi.org/10.7717/peerj.4174 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hughes et al. title: Activities concentration of radiocesium in wild mushroom collected in Ukraine 30 years after the Chernobyl power plant accident link: https://peerj.com/articles/4222 last-modified: 2018-01-05 description: Mushrooms are recognized as one of the main contributors to internal radiation exposure from the activity concentration of radiocesium released by the accident at the Chernobyl nuclear power plant (CNNP). We evaluated the activity concentrations of the artificial radionuclides (radiocesium) in wild mushrooms collected in 2015 from Korosten and Lugine, Zhitomir region, Ukraine, located 120 km away from the CNPP. Cesium-137 was detected in 110 of 127 mushroom samples (86.6%). Based on the average mushroom consumption (5 kg per year), we calculated committed effective doses ranging from 0.001–0.12 mSv. Cesium-137 remains in the wild mushrooms even 30 years after the accident, but the committed effective doses are limited by the amount of contaminated mushrooms consumed. However, evaluation of internal radiation exposure and assessment of environmental radioactivity in the surrounding area affected by the nuclear accident are still necessary in order to relieve anxiety about internal radiation exposure, as long as the possibility of consumption of contaminated mushrooms remains. creator: Makiko Orita creator: Yuko Kimura creator: Yasuyuki Taira creator: Toshiki Fukuda creator: Jumpei Takahashi creator: Oleksandr Gutevych creator: Serghii Chornyi creator: Takashi Kudo creator: Shunichi Yamashita creator: Noboru Takamura uri: https://doi.org/10.7717/peerj.4222 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Orita et al. title: Lipid raft localization of TLR2 and its co-receptors is independent of membrane lipid composition link: https://peerj.com/articles/4212 last-modified: 2018-01-05 description: BackgroundToll like receptors (TLRs) are an important and evolutionary conserved class of pattern recognition receptors associated with innate immunity. The recognition of Gram-positive cell wall constituents strongly depends on TLR2. In order to be functional, TLR2 predominantly forms a heterodimer with TLR1 or TLR6 within specialized membrane microdomains, the lipid rafts. The membrane lipid composition and the physicochemical properties of lipid rafts are subject to modification by exogenous fatty acids. Previous investigations of our group provide evidence that macrophage enrichment with polyunsaturated fatty acids (PUFA) induces a reordering of lipid rafts and non-rafts based on the incorporation of supplemented PUFA as well as their elongation and desaturation products.MethodsIn the present study we investigated potential constraining effects of membrane microdomain reorganization on the clustering of TLR2 with its co-receptors TLR1 and TLR6 within lipid rafts. To this end, RAW264.7 macrophages were supplemented with either docosahexaenoic acid (DHA) or arachidonic acid (AA) and analyzed for receptor expression and microdomain localization in context of TLR stimulation.Results and ConclusionsOur analyses showed that receptor levels and microdomain localization were unchanged by PUFA supplementation. The TLR2 pathway, in contrast to the TLR4 signaling cascade, is not affected by exogenous PUFA at the membrane level. creator: Christine Hellwing creator: Axel Schoeniger creator: Claudia Roessler creator: Anja Leimert creator: Julia Schumann uri: https://doi.org/10.7717/peerj.4212 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hellwing et al. title: On revealing the gene targets of Ebola virus microRNAs involved in the human skin microbiome link: https://peerj.com/articles/4138 last-modified: 2018-01-05 description: Ebola virus, a negative-sense single-stranded RNA virus, causes severe viral hemorrhagic fever and has a high mortality rate. Histopathological and immunopathological analyses of Ebola virus have revealed that histopathological changes in skin tissue are associated with various degrees of endothelial cell swelling and necrosis. The interactions of microbes within or on a host are a crucial for the skin immune shield. The discovery of microRNAs (miRNAs) in Ebola virus implies that immune escape, endothelial cell rupture, and tissue dissolution during Ebola virus infection are a result of the effects of Ebola virus miRNAs. Keratinocytes obtained from normal skin can attach and spread through expression of the thrombospondin family of proteins, playing a role in initiation of cell-mediated immune responses in the skin. Several miRNAs have been shown to bind the 3′ untranslated region of thrombospondin mRNA, thereby controlling its stability and translational activity. In this study, we discovered short RNA sequences that may act as miRNAs from Propionibacterium acnes using a practical workflow of bioinformatics methods. Subsequently, we deciphered the common target gene. These RNA sequences tended to bind to the same thrombospondin protein, THSD4, emphasizing the potential importance of the synergistic binding of miRNAs from Ebola virus, Propionibacterium acnes, and humans to the target. These results provide important insights into the molecular mechanisms of thrombospondin proteins and miRNAs in Ebola virus infection. creator: Pei-Chun Hsu creator: Bin-Hao Chiou creator: Chun-Ming Huang uri: https://doi.org/10.7717/peerj.4138 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hsu et al. title: Pupillometry reveals the physiological underpinnings of the aversion to holes link: https://peerj.com/articles/4185 last-modified: 2018-01-04 description: An unusual, but common, aversion to images with clusters of holes is known as trypophobia. Recent research suggests that trypophobic reactions are caused by visual spectral properties also present in aversive images of evolutionary threatening animals (e.g., snakes and spiders). However, despite similar spectral properties, it remains unknown whether there is a shared emotional response to holes and threatening animals. Whereas snakes and spiders are known to elicit a fear reaction, associated with the sympathetic nervous system, anecdotal reports from self-described trypophobes suggest reactions more consistent with disgust, which is associated with activation of the parasympathetic nervous system. Here we used pupillometry in a novel attempt to uncover the distinct emotional response associated with a trypophobic response to holes. Across two experiments, images of holes elicited greater constriction compared to images of threatening animals and neutral images. Moreover, this effect held when controlling for level of arousal and accounting for the pupil grating response. This pattern of pupillary response is consistent with involvement of the parasympathetic nervous system and suggests a disgust, not a fear, response to images of holes. Although general aversion may be rooted in shared visual-spectral properties, we propose that the specific emotion is determined by cognitive appraisal of the distinct image content. creator: Vladislav Ayzenberg creator: Meghan R. Hickey creator: Stella F. Lourenco uri: https://doi.org/10.7717/peerj.4185 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ayzenberg et al. title: Joint damage is amplified in rheumatoid arthritis patients with positive thyroid autoantibodies link: https://peerj.com/articles/4216 last-modified: 2018-01-04 description: BackgroundAutoimmune thyroid disease (AITD), which is characterized by an increased presence of thyroid autoantibodies (TAbs), such as antibodies against thyroid peroxidase (TPOAbs) and antibodies against thyroglobulin (TgAbs), has been reported to be associated with rheumatoid arthritis (RA) because AITD and RA both involve autoimmunity. However, few data are available on the incidence of TAbs in Chinese RA patients, and studies on the association between TAbs and joint damage as well as synovitis in RA patients remain sparse. Here, we aimed to evaluate the incidence of TAbs in a consecutive Chinese RA cohort and to investigate whether the elevated presence of TAbs is associated with joint damage and synovitis in RA patients.MethodsA total of 125 hospitalized RA patients were consecutively recruited. Clinical data and available synovial tissues were collected at baseline, and TAbs and thyroid function were detected by chemiluminescent immunoassay. Patients who tested positive for TPOAbs or TgAbs were classified as the TAbs-positive group, and patients who tested positive for neither TPOAbs nor TgAbs were recruited as the TAbs-negative group. Disease activity was assessed using DAS28-ESR (the disease activity score in 28 joints and including the erythrocyte sedimentation rate). X-ray assessment of the hand/wrist was performed according to the Sharp/van der Heijde-modified Sharp score (mTSS), and patients with an mTSS score >10 were defined as having radiographic joint damage (RJD). Serial tissue sections were stained immunohistochemically for CD3, CD15, CD20, CD34, CD38, and CD68, and synovitis were assessed according to Krenn’s synovitis score.ResultsA total of 44 (35%) patients were positive for either TPOAbs or TgAbs. Importantly, there was a significantly greater percentage of patients with RJD in the TAbs-positive group versus the TAbs-negative group (68% vs. 42%, p = 0.005). Compared with the TAbs-negative group, significantly more CD38-positive plasma cells infiltrated the TAbs-positive synovium, and a higher percentage of patients with high-grade synovitis were observed in the TAbs-positive group (5/8, 63% vs. 5/14, 36%). Moreover, RF positivity and disease activity indicators, including TJC28, DAS28-ESR, and CDAI, were significantly higher in the TAbs-positive group (all p < 0.05). Adjusted logistic regression analysis revealed that positive TAbs (OR 2.999, 95% CI [1.301–6.913]; p = 0.010) and disease duration (OR 1.013, 95% CI [1.006–1.019]; p < 0.001) were independently associated with RJD, and an odds ratio of 2.845 (95% CI [1.062–7.622]) was found for RJD in women with positive TAbs (n = 37) compared with those without TAbs (n = 59) (p = 0.038).ConclusionOur data showed that joint destruction was amplified in RA patients with an elevated presence of TAbs, which supports the importance and necessity of TAbs and thyroid function screening and monitoring in RA patient management in clinical practice. creator: Yu-Lan Chen creator: Jian-Zi Lin creator: Ying-Qian Mo creator: Jin-Jian Liang creator: Qian-Hua Li creator: Cheng-Jing Zhou creator: Xiu-Ning Wei creator: Jian-Da Ma creator: Ze-Hong Yang creator: Dong-Hui Zheng creator: Lie Dai uri: https://doi.org/10.7717/peerj.4216 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chen et al. title: Geo-referencing bird-window collisions for targeted mitigation link: https://peerj.com/articles/4215 last-modified: 2018-01-04 description: Bird collisions with windows are an important conservation concern. Efficient mitigation efforts should prioritize retrofitting sections of glass exhibiting the highest mortality of birds. Most collision studies, however, record location meta-data at a spatial scale too coarse (i.e., compass direction of facing façade) to be useful for large buildings with complex geometries. Through spatial analysis of three seasons of survey data at a large building at a university campus, we found that GPS data were able to identify collision hotspots while compass directions could not. To demonstrate the broad applicability and utility of this georeferencing approach, we identified collision hotspots at two additional urban areas in North America. The data for this latter exercise were collected via the citizen science database, iNaturalist, which we review for its potential to generate the georeferenced data necessary for directing building retrofits and mitigating a major source of anthropogenic bird mortality. creator: R. Scott Winton creator: Natalia Ocampo-Peñuela creator: Nicolette Cagle uri: https://doi.org/10.7717/peerj.4215 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Winton et al. title: On the exponent in the Von Bertalanffy growth model link: https://peerj.com/articles/4205 last-modified: 2018-01-04 description: Von Bertalanffy proposed the differential equation m′(t) = p × m(t)a − q × m(t) for the description of the mass growth of animals as a function m(t) of time t. He suggested that the solution using the metabolic scaling exponent a = 2/3 (Von Bertalanffy growth function VBGF) would be universal for vertebrates. Several authors questioned universality, as for certain species other models would provide a better fit. This paper reconsiders this question. Based on 60 data sets from literature (37 about fish and 23 about non-fish species) it optimizes the model parameters, in particular the exponent 0 ≤ a < 1, so that the model curve achieves the best fit to the data. The main observation of the paper is the large variability in the exponent, which can vary over a very large range without affecting the fit to the data significantly, when the other parameters are also optimized. The paper explains this by differences in the data quality: variability is low for data from highly controlled experiments and high for natural data. Other deficiencies were biologically meaningless optimal parameter values or optimal parameter values attained on the boundary of the parameter region (indicating the possible need for a different model). Only 11 of the 60 data sets were free of such deficiencies and for them no universal exponent could be discerned. creator: Katharina Renner-Martin creator: Norbert Brunner creator: Manfred Kühleitner creator: Werner Georg Nowak creator: Klaus Scheicher uri: https://doi.org/10.7717/peerj.4205 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Renner-Martin et al. title: Amphibian and reptile biodiversity in the semi-arid region of the municipality of Nopala de Villagrán, Hidalgo, Mexico link: https://peerj.com/articles/4202 last-modified: 2018-01-04 description: Current global changes are putting both biodiversity and the processes that depend on it at risk. This is especially true for semi-arid regions and the flagship groups that inhabit them, such as amphibians and reptiles. Semi-arid regions are often thought to have lower biodiversity and thus have been overlooked, resulting in the underestimation of their biological richness. Therefore, the aim of this study was to conduct an inventory of amphibians and reptiles in the semi-arid municipality of Nopala de Villagrán, Mexico, and analyze its biodiversity in relation to the seasons, vegetation and microhabitat. During a year of fieldwork, we found 24 species in the area, most of them of low abundance, and one of which was recorded for the first time for the state of Hidalgo. We documented five amphibian species and 19 reptile species. We also found that observed species richness was higher in the rainy season and in xeric scrub vegetation, although only the season differences were significant according to rarefaction curves. Our findings highlight the importance of seasonality and vegetation type for the species that inhabit this semi-arid region. This study broadens our understanding of the importance of semi-arid regions and, by extension, that of other areas with similar characteristics. creator: Andrea J. Roth-Monzón creator: Andrés Alberto Mendoza-Hernández creator: Oscar Flores-Villela uri: https://doi.org/10.7717/peerj.4202 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Roth-Monzón et al. title: Small-scale screening of anticancer drugs acting specifically on neural stem/progenitor cells derived from human-induced pluripotent stem cells using a time-course cytotoxicity test link: https://peerj.com/articles/4187 last-modified: 2018-01-04 description: Since the development of human-induced pluripotent stem cells (hiPSCs), various types of hiPSC-derived cells have been established for regenerative medicine and drug development. Neural stem/progenitor cells (NSPCs) derived from hiPSCs (hiPSC-NSPCs) have shown benefits for regenerative therapy of the central nervous system. However, owing to their intrinsic proliferative potential, therapies using transplanted hiPSC-NSPCs carry an inherent risk of undesired growth in vivo. Therefore, it is important to find cytotoxic drugs that can specifically target overproliferative transplanted hiPSC-NSPCs without damaging the intrinsic in vivo stem-cell system. Here, we examined the chemosensitivity of hiPSC-NSPCs and human neural tissue—derived NSPCs (hN-NSPCs) to the general anticancer drugs cisplatin, etoposide, mercaptopurine, and methotrexate. A time-course analysis of neurospheres in a microsphere array identified cisplatin and etoposide as fast-acting drugs, and mercaptopurine and methotrexate as slow-acting drugs. Notably, the slow-acting drugs were eventually cytotoxic to hiPSC-NSPCs but not to hN-NSPCs, a phenomenon not evident in the conventional endpoint assay on day 2 of treatment. Our results indicate that slow-acting drugs can distinguish hiPSC-NSPCs from hN-NSPCs and may provide an effective backup safety measure in stem-cell transplant therapies. creator: Hayato Fukusumi creator: Yukako Handa creator: Tomoko Shofuda creator: Yonehiro Kanemura uri: https://doi.org/10.7717/peerj.4187 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fukusumi et al. title: Murine pluripotent stem cells that escape differentiation inside teratomas maintain pluripotency link: https://peerj.com/articles/4177 last-modified: 2018-01-04 description: BackgroundPluripotent stem cells (PSCs) offer immense potential as a source for regenerative therapies. The teratoma assay is widely used in the field of stem cells and regenerative medicine, but the cell composition of teratoma is still elusive.MethodsWe utilized PSCs expressing enhanced green fluorescent protein (EGFP) under the control of the Pou5f1 promoter to study the persistence of potential pluripotent cells during teratoma formation in vivo. OCT4-MES (mouse embryonic stem cells) were isolated from the blastocysts of 3.5-day OCT4-EGFP mice (transgenic mice express EGFP cDNA under the control of the Pou5f1 promoter) embryos, and TG iPS 1-7 (induced pluripotent stem cells) were generated from mouse embryonic fibroblasts (MEFs) from 13.5-day OCT4-EGFP mice embryos by infecting them with a virus carrying OCT4, SOX2, KLF4 and c-MYC. These pluripotent cells were characterized according to their morphology and expression of pluripotency markers. Their differentiation ability was studied with in vivo teratoma formation assays. Further differences between pluripotent cells were examined by real-time quantitative PCR (qPCR).ResultsThe results showed that several OCT4-expressing PSCs escaped differentiation inside of teratomas, and these escaped cells (MES-FT, GFP-positive cells separated from OCT4-MES-derived teratomas; and iPS-FT, GFP-positive cells obtained from teratomas formed by TG iPS 1-7) retained their pluripotency. Interestingly, a small number of GFP-positive cells in teratomas formed by MES-FT and iPS-FT (MES-ST, GFP-positive cells isolated from MES-FT-derived teratomas; iPS-ST, GFP-positive cells obtained from teratomas formed by iPS-FT) were still pluripotent, as shown by alkaline phosphatase (AP) staining, immunofluorescent staining and PCR. MES-FT, iPS-FT, MES-ST and iPS-ST cells also expressed several markers associated with germ cell formation, such as Dazl, Stella and Stra8.ConclusionsIn summary, a small number of PSCs escaped differentiation inside of teratomas, and these cells maintained pluripotency and partially developed towards germ cells. Both escaped PSCs and germ cells present a risk of tumor formation. Therefore, medical workers must be careful in preventing tumor formation when stem cells are used to treat specific diseases. creator: Yangli Pei creator: Liang Yue creator: Wei Zhang creator: Jinzhu Xiang creator: Zhu Ma creator: Jianyong Han uri: https://doi.org/10.7717/peerj.4177 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Pei et al. title: First record of Phormia regina (Meigen, 1826) (Diptera: Calliphoridae) from mummies at the Sant’Antonio Abate Cathedral of Castelsardo, Sardinia, Italy link: https://peerj.com/articles/4176 last-modified: 2018-01-04 description: The studies of insects from archaeological contexts can provide an important supplement of information to reconstruct past events, climate and environments. Furthermore, the list of the species present in an area in the past allows the reconstruction of the entomofauna on that area at that time, that can be different from the nowadays condition, providing information about biodiversity changes. In this work, the results of a funerary archaeoentomological study on samples collected from mummified corpses discovered during the restoration of the crypt of the Sant’Antonio Abate Cathedral of Castelsardo (Sardinia, Italy) are reported. The majority of the sampled specimens were Diptera puparia, whereas only few Lepidoptera cocoons and some Coleoptera fragments were isolated. Among Diptera, Calliphoridae puparia were identified as Phormia regina (Meigen, 1826) and Calliphora vicina, (Robineau-Desvoidy, 1830) both species typical of the first colonization waves of exposed bodies. Three puparia fragments were also identified as belonging to a Sarcophaga Meigen, 1826, species (Sarcophagidae). Several Muscidae puparia of the species Hydrotaea capensis (Weidmermann, 1818), a late colonizer of bodies, and typical of buried bodies were also collected. The few moth (Lepidoptera) cocoons were identified as belonging to the family Tineidae. This family comprises species feeding on dry tissues and hair typical of the later phases of the human decomposition. Among Coleoptera a single specimen in the family Histeridae, Saprinus semistriatus (Scriba, 1790) and a single elytra, potentially of a species in the family Tenebrionidae, were also collected. Overall, the samples collected indicated an initial colonization of the bodies in an exposed context, mainly in a warm season. This research allows the finding of elements indicating the presence, at least in the past, of P. regina in Sardinia. This species at the moment seems extinct from Sardinia while it is quite common in the continent. creator: Giorgia Giordani creator: Fabiola Tuccia creator: Ignazio Floris creator: Stefano Vanin uri: https://doi.org/10.7717/peerj.4176 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Giordani et al. title: Domestic carnivore interactions with wildlife in the Cape Horn Biosphere Reserve, Chile: husbandry and perceptions of impact from a community perspective link: https://peerj.com/articles/4124 last-modified: 2018-01-04 description: BackgroundHundreds of millions of domestic carnivores worldwide have diverse positive affiliations with humans, but can provoke serious socio-ecological impacts when free-roaming. Unconfined dogs (Canis familiaris) and cats (Felis catus) interact with wildlife as predators, competitors, and disease-transmitters; their access to wildlife depends on husbandry, perceptions, attitudes, and behaviors of pet owners and non-owners.MethodsTo better understand husbandry and perceptions of impacts by unconfined, domestic carnivores, we administered questionnaires (n = 244) to pet owners and non-owners living in one of the last wilderness areas of the world, the Cape Horn Biosphere Reserve, located in southern Chile. We used descriptive statistics to provide demographic pet and husbandry information, quantify free-roaming dogs and cats, map their sightings in nature, and report experiences and perceptions of the impact of free-roaming dogs and cats on wildlife. We corroborated our results with an analysis of prey remains in dog feces (n = 53). With generalized linear models, we examined which factors (i.e., food provisioning, reproductive state, rural/village households, sex, and size) predicted that owned dogs and cats bring wildlife prey home.ResultsThirty-one percent of village dogs (n = 121) and 60% of dogs in rural areas (n = 47) roamed freely day and/or night. Free-roaming dog packs were frequently observed (64% of participants) in the wild, including a feral dog population on Navarino Island. Dogs (31 of 168) brought home invasive muskrats (Ondatra zibethicus) and avian prey, and over half of all cats (27 of 51) brought home mainly avian prey. Birds were also the most harassed wildlife category, affected by one third of all dogs and cats. Nevertheless, dog-wildlife conflicts were hardly recognized (<9% of observed conflicts and suspected problems), and only 34% of the participants thought that cats might impact birds. Diet analysis revealed that dogs consumed livestock (64% of 59 prey occurrences), beavers (Castor canadensis, 14%), and birds (10%). The probability that dogs brought prey to owners’ homes was higher in rural locations and with larger dogs. There was also evidence that cats from rural households and with an inadequate food supply brought more prey home than village cats.DiscussionAlthough muskrat, beavers, and birds were brought home, harassed, or found in dog feces, free-roaming dogs and, to a lesser extent, cats are perceived predominantly in an anthropogenic context (i.e., as pets) and not as carnivores interacting with wildlife. Therefore, technical and legal measures should be applied to encourage neutering, increase confinement, particularly in rural areas, and stimulate social change via environmental education that draws attention to the possibility and consequences of unconfined pet interaction with wildlife in the southernmost protected forest ecoregion of the globe. creator: Elke Schüttler creator: Lorena Saavedra-Aracena creator: Jaime E. Jiménez uri: https://doi.org/10.7717/peerj.4124 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Schüttler et al. title: Characterization and toxicity of citral incorporated with nanostructured lipid carrier link: https://peerj.com/articles/3916 last-modified: 2018-01-04 description: The nanoparticle as a cancer drug delivery vehicle is rapidly under investigation due to its promising applicability as a novel drug delivery system for anticancer agents. This study describes the development, characterization and toxicity studies of a nanostructured lipid carrier (NLC) system for citral. Citral was loaded into the NLC using high pressure homogenization methods. The characterizations of NLC-citral were then determined through various methods. Based on Transmission Electron Microscope (TEM) analysis, NLC-Citral showed a spherical shape with an average diameter size of 54.12 ± 0.30 nm and a polydipersity index of 0.224 ± 0.005. The zeta potential of NLC-Citral was −12.73 ± 0.34 mV with an entrapment efficiency of 98.9 ± 0.124%, and drug loading of 9.84 ± 0.041%. Safety profile of the formulation was examined via in vitro and in vivo routes to study its effects toward normal cells. NLC-Citral exhibited no toxic effects towards the proliferation of mice splenocytes. Moreover, no mortality and toxic signs were observed in the treated groups after 28 days of treatment. There were also no significant alterations in serum biochemical analysis for all treatments. Increase in immunomodulatory effects of treated NLC-Citral and Citral groups was verified from the increase in CD4/CD3 and CD8/CD3 T cell population in both NLC-citral and citral treated splenocytes. This study suggests that NLC is a promising drug delivery system for citral as it has the potential in sustaining drug release without inducing any toxicity. creator: Noraini Nordin creator: Swee Keong Yeap creator: Nur Rizi Zamberi creator: Nadiah Abu creator: Nurul Elyani Mohamad creator: Heshu Sulaiman Rahman creator: Chee Wun How creator: Mas Jaffri Masarudin creator: Rasedee Abdullah creator: Noorjahan Banu Alitheen uri: https://doi.org/10.7717/peerj.3916 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Nordin et al. title: Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak link: https://peerj.com/articles/4210 last-modified: 2018-01-03 description: BackgroundUntil recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks.MethodsAll KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids.ResultsInitial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation.ConclusionA real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase-producing Enterobacteriaceae surveillance and management. creator: Jason C. Kwong creator: Courtney R. Lane creator: Finn Romanes creator: Anders Gonçalves da Silva creator: Marion Easton creator: Katie Cronin creator: Mary Jo Waters creator: Takehiro Tomita creator: Kerrie Stevens creator: Mark B. Schultz creator: Sarah L. Baines creator: Norelle L. Sherry creator: Glen P. Carter creator: Andre Mu creator: Michelle Sait creator: Susan A. Ballard creator: Torsten Seemann creator: Timothy P. Stinear creator: Benjamin P. Howden uri: https://doi.org/10.7717/peerj.4210 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kwong et al. title: Developmental effects of environmental light on male nuptial coloration in Lake Victoria cichlid fish link: https://peerj.com/articles/4209 last-modified: 2018-01-03 description: BackgroundEfficient communication requires that signals are well transmitted and perceived in a given environment. Natural selection therefore drives the evolution of different signals in different environments. In addition, environmental heterogeneity at small spatial or temporal scales may favour phenotypic plasticity in signaling traits, as plasticity may allow rapid adjustment of signal expression to optimize transmission. In this study, we explore signal plasticity in the nuptial coloration of Lake Victoria cichlids, Pundamilia pundamilia and Pundamilia nyererei. These two species differ in male coloration, which mediates species-assortative mating. They occur in adjacent depth ranges with different light environments. Given the close proximity of their habitats, overlapping at some locations, plasticity in male coloration could contribute to male reproductive success but interfere with reproductive isolation.MethodsWe reared P. pundamilia, P. nyererei, and their hybrids under light conditions mimicking the two depth ranges in Lake Victoria. From photographs, we quantified the nuptial coloration of males, spanning the entire visible spectrum. In experiment 1, we examined developmental colour plasticity by comparing sibling males reared in each light condition. In experiment 2, we assessed colour plasticity in adulthood, by switching adult males between conditions and tracking coloration for 100 days.ResultsWe found that nuptial colour in Pundamilia did respond plastically to our light manipulations, but only in a limited hue range. Fish that were reared in light conditions mimicking the deeper habitat were significantly greener than those in conditions mimicking shallow waters. The species-specific nuptial colours (blue and red) did not change. When moved to the opposing light condition as adults, males did not change colour.DiscussionOur results show that species-specific nuptial colours, which are subject to strong divergent selection by female choice, are not plastic. We do find plasticity in green coloration, a response that may contribute to visual conspicuousness in darker, red-shifted light environments. These results suggest that light-environment-induced plasticity in male nuptial coloration in P. pundamilia and P. nyererei is limited and does not interfere with reproductive isolation. creator: Daniel Shane Wright creator: Emma Rietveld creator: Martine E. Maan uri: https://doi.org/10.7717/peerj.4209 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wright et al. title: Formononetin inhibits lipopolysaccharide-induced release of high mobility group box 1 by upregulating SIRT1 in a PPARδ-dependent manner link: https://peerj.com/articles/4208 last-modified: 2018-01-03 description: BackgroundThe release of high mobility group box 1 (HMGB1) induced by inflammatory signals acts as a cellular alarmin to trigger a chain of inflammatory responses. Although the inflammatory actions of HMGB1 are well studied, less is known about the therapeutic agents that can impede its release. This study investigated whether the isoflavonoid formononetin can modulate HMGB1 release in cellular inflammatory responses.MethodsRAW264.7 murine macrophages were exposed to lipopolysaccharide (LPS) in the presence or absence of formononetin. The levels of HMGB1 release, sirtuin 1 (SIRT1) expression, and HMGB1 acetylation were analyzed by immunoblotting and real-time polymerase chain reaction. The effects of resveratrol and sirtinol, an activator and inhibitor of SIRT1, respectively, on LPS-induced HMGB1 release were also evaluated.ResultsFormononetin modulated cellular inflammatory responses by suppressing the release of HMGB1 by macrophages exposed to LPS. In RAW264.7 cells, formononetin significantly attenuated LPS-induced release of HMGB1 into the extracellular environment, which was accompanied by a reduction in its translocation from the nucleus to the cytoplasm. In addition, formononetin significantly induced mRNA and protein expression of SIRT1 in a peroxisome proliferator-activated receptor δ (PPARδ)-dependent manner. These effects of formononetin were dramatically attenuated in cells treated with small interfering RNA (siRNA) against PPARδ or with GSK0660, a specific inhibitor of PPARδ, indicating that PPARδ is involved in formononetin-mediated SIRT1 expression. In line with these effects, formononetin-mediated inhibition of HMGB1 release in LPS-treated cells was reversed by treatment with SIRT1-targeting siRNA or sirtinol, a SIRT1 inhibitor. By contrast, resveratrol, a SIRT1 activator, further potentiated the inhibitory effect of formononetin on LPS-induced HMGB1 release, revealing a possible mechanism by which formononetin regulates HMGB1 release through SIRT1. Furthermore, modulation of SIRT1 expression by transfection of SIRT1- or PPARδ-targeting siRNA significantly counteracted the inhibitory effects of formononetin on LPS-induced HMGB1 acetylation, which was responsible for HMGB1 release.DiscussionThis study shows for the first time that formononetin inhibits HMGB1 release by decreasing HMGB1 acetylation via upregulating SIRT1 in a PPARδ-dependent manner. Formononetin consequently exhibits anti-inflammatory activity. Identification of agents, such as formononetin, which can block HMGB1 release, may help to treat inflammation-related disorders. creator: Jung Seok Hwang creator: Eun Sil Kang creator: Sung Gu Han creator: Dae-Seog Lim creator: Kyung Shin Paek creator: Chi-Ho Lee creator: Han Geuk Seo uri: https://doi.org/10.7717/peerj.4208 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hwang et al. title: A historical legacy of antibiotic utilization on bacterial seed banks in sediments link: https://peerj.com/articles/4197 last-modified: 2018-01-03 description: The introduction of antibiotics for both medical and non-medical purposes has had a positive effect on human welfare and agricultural output in the past century. However, there is also an important ecological legacy regarding the use of antibiotics and the consequences of increased levels of these compounds in the environment as a consequence of their use and disposal. This legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond broadly to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence. creator: Laura Madueño creator: Christophe Paul creator: Thomas Junier creator: Zhanna Bayrychenko creator: Sevasti Filippidou creator: Karin Beck creator: Gilbert Greub creator: Helmut Bürgmann creator: Pilar Junier uri: https://doi.org/10.7717/peerj.4197 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Madueño et al. title: Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice link: https://peerj.com/articles/4195 last-modified: 2018-01-03 description: Cherries are fruits containing fiber and bioactive compounds (e.g., polyphenolics) with the potential of helping patients with diabetes and weight disorders, a phenomenon likely related to changes in the complex host-microbiota milieu. The objective of this study was to investigate the effect of cherry supplementation on the gut bacterial composition, concentrations of caecal short-chain fatty acids (SCFAs) and biomarkers of gut health using an in vivo model of obesity. Obese diabetic (db/db) mice received a supplemented diet with 10% cherry powder (supplemented mice, n = 12) for 12 weeks; obese (n = 10) and lean (n = 10) mice served as controls and received a standard diet without cherry. High-throughput sequencing of the 16S rRNA gene and quantitative real-time PCR (qPCR) were used to analyze the gut microbiota; SCFAs and biomarkers of gut health were also measured using standard techniques. According to 16S sequencing, supplemented mice harbored a distinct colonic microbiota characterized by a higher abundance of mucin-degraders (i.e., Akkermansia) and fiber-degraders (the S24-7 family) as well as lower abundances of Lactobacillus and Enterobacteriaceae. Overall this particular cherry-associated colonic microbiota did not resemble the microbiota in obese or lean controls based on the analysis of weighted and unweighted UniFrac distance metrics. qPCR confirmed some of the results observed in sequencing, thus supporting the notion that cherry supplementation can change the colonic microbiota. Moreover, the SCFAs detected in supplemented mice (caproate, methyl butyrate, propionate, acetate and valerate) exceeded those concentrations detected in obese and lean controls except for butyrate. Despite the changes in microbial composition and SCFAs, most of the assessed biomarkers of inflammation, oxidative stress, and intestinal health in colon tissues and mucosal cells were similar in all obese mice with and without supplementation. This paper shows that dietary supplementation with cherry powder for 12 weeks affects the microbiota and the concentrations of SCFAs in the lower intestinal tract of obese db/db diabetic mice. These effects occurred in absence of differences in most biomarkers of inflammation and other parameters of gut health. Our study prompts more research into the potential clinical implications of cherry consumption as a dietary supplement in diabetic and obese human patients. creator: Jose F. Garcia-Mazcorro creator: Nara N. Lage creator: Susanne Mertens-Talcott creator: Stephen Talcott creator: Boon Chew creator: Scot E. Dowd creator: Jorge R. Kawas creator: Giuliana D. Noratto uri: https://doi.org/10.7717/peerj.4195 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Garcia-Mazcorro et al. title: Sex differences in the use of social information emerge under conditions of risk link: https://peerj.com/articles/4190 last-modified: 2018-01-03 description: Social learning provides an effective route to gaining up-to-date information, particularly when information is costly to obtain asocially. Theoretical work predicts that the willingness to switch between using asocial and social sources of information will vary between individuals according to their risk tolerance. We tested the prediction that, where there are sex differences in risk tolerance, altering the variance of the payoffs of using asocial and social information differentially influences the probability of social information use by sex. In a computer-based task that involved building a virtual spaceship, men and women (N = 88) were given the option of using either asocial or social sources of information to improve their performance. When the asocial option was risky (i.e., the participant’s score could markedly increase or decrease) and the social option was safe (i.e., their score could slightly increase or remain the same), women, but not men, were more likely to use the social option than the asocial option. In all other conditions, both women and men preferentially used the asocial option to a similar degree. We therefore found both a sex difference in risk aversion and a sex difference in the preference for social information when relying on asocial information was risky, consistent with the hypothesis that levels of risk-aversion influence the use of social information. creator: Charlotte O. Brand creator: Gillian R. Brown creator: Catharine P. Cross uri: https://doi.org/10.7717/peerj.4190 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brand et al. title: Resistance strategies of Phragmites australis (common reed) to Pb pollution in flood and drought conditions link: https://peerj.com/articles/4188 last-modified: 2018-01-03 description: Resistance strategies of clonal organs, and parent and offspring shoots of Phragmites australis (common reed) to heavy metal pollution in soils are not well known. To clarify the tolerance or resistance strategies in reeds, we conducted a pot experiment with five levels of Pb concentration (0∼4,500 mg kg−1) in flood and drought conditions. Lead toxicity had no inhibitory effect on the number of offspring shoots in flood environment; however, biomass accumulation, and photosynthetic and clonal growth parameters were inhibited in both water environment. At each treatment of Pb concentration, offspring shoots had greater biomass and higher photosynthesis indicators than parent shoots. The lowest Pb allocation was found in rhizomes. More of the Pb transported to above-ground parts tended to accumulate in parent shoots rather than in offspring shoots. Biomass and photosynthesis of offspring shoots, rhizome length, and the number of buds, rhizomes and offspring shoots in the flooded treatment were significantly greater than those in the drought treatment. Our results indicated that the tolerance strategies used by reeds, including higher biomass accumulation and photosynthesis in offspring shoots, low allocation of Pb in rhizomes and offspring shoots, and stable clonal growth, maintained the stability of population propagation and productivity, improving the resistance of reeds to Pb pollution in flood environment. However, the resistance or tolerance was significantly reduced by the synergistic effect of Pb and drought, which significantly inhibited biomass accumulation, photosynthesis, and clonal growth of reeds. creator: Na Zhang creator: Jinwei Zhang creator: Zhiqiang Li creator: Jing Chen creator: Zhenhua Zhang creator: Chunsheng Mu uri: https://doi.org/10.7717/peerj.4188 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study link: https://peerj.com/articles/4207 last-modified: 2018-01-02 description: BackgroundClear aligners are well known for facilitating oral hygiene maintenance and decreasing susceptibility to periodontal diseases as compared to conventional fixed appliances. However, few research studies focus on the subgingival microbial community during clear aligner treatment (CAT). Hence, this study investigates changes of the subgingival microbial community and its association with clinical characteristics during the first three months of CAT.MethodsTen female patients with clear aligners were enrolled in this study. Subgingival plaque samples were obtained at three time points: before orthodontic treatment (T0), one month after orthodontic treatment (T1) and three months after orthodontic treatment (T2). DNA was then extracted from plaque samples and analyzed by 16S rRNA gene sequencing. Periodontal examinations, including plaque index (PI) and gingival bleeding index (GBI) measurements were also recorded.ResultsThe plaque indices (PIs) and gingival bleeding indices (GBIs) were slightly increased at T1 and T2, but no statistically significant difference was found. The alpha diversity indices, including the ACE, Chao1, Shannon indices, all showed a declining trend without significance, and a rising trend in the Simpson diversity index was observed. The weighted UniFrac distance was significantly higher at T1 and T2 compared with T0. Principal Coordinates Analysis (PCoA) demonstrated that the communities at T0 tended to cluster apart from the communities at T1 and T2. The relative abundance of the phylum Firmicutes and genus Mycoplasma was significantly increased at T0 compared with T2. There was no significant difference in the relative abundance of periodontal pathogens at the genus and species levels or core microorganisms at the genus level.ConclusionA slightly decreasing microbial diversity with a significant change of microbial structure was found during the first three-month clear aligner treatment (CAT). However, subjects receiving clear aligner treatment were free from periodontal diseases with relatively stable levels of periodontal microorganisms and core microorganisms. Thus, our preliminary findings indicated that clear aligners induced nonpathogenic changes of the subgingival microbiome in the first three-month treatment. creator: Runzhi Guo creator: Yunfei Zheng creator: Hao Liu creator: Xiaobei Li creator: Lingfei Jia creator: Weiran Li uri: https://doi.org/10.7717/peerj.4207 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Guo et al. title: A gene expression-based risk model reveals prognosis of gastric cancer link: https://peerj.com/articles/4204 last-modified: 2018-01-02 description: BackgroundThe prognosis of gastric cancer is difficult to determine, although clinical indicators provide valuable evidence.MethodsIn this study, using screened biomarkers of gastric cancer in combination with random forest variable hunting and multivariable Cox regression, a risk score model was developed to predict the survival of gastric cancer. Survival difference between high/low-risk groups were compared. The relationship between risk score and other clinicopathological indicators was evaluated. Gene set enrichment analysis (GSEA) was used to identify pathways associated with risk scores.ResultsThe patients with high risk scores (median overall survival: 20.2 months, 95% CI [16.9–26.0] months) tend to exhibit early events compared with those with low risk scores (median survival: 70.0 months, 95% CI [46.9–101] months, p = 1.80e–5). Further validation was implemented in another three independent datasets (GSE15459, GSE26253, GSE62254). Correlation analyses between clinical observations and risk scores were performed, and the results indicated that the risk score was not significantly associated with gender, age and primary tumor size but was significantly associated with grade and tumor stage. In addition, the risk score was also not influenced by radiation therapy. Cox multivariate regression and three-year survival nomogram suggest that the risk score is an important indicator of gastric cancer prognosis. GSEA was used to identified KEGG pathways significantly associated with risk score, and signaling pathways involved in focal adhesion and the TGF-beta signaling pathway were identified.ConclusionThe risk score model successfully predicted the survival of 1,294 gastric cancer samples from four independent datasets and is among the most important indicators in clinical clinicopathological information for the prognosis of gastric cancer. To our knowledge, it is the first report to predict the survival of gastric cancer using optimized expression panel. creator: Xiaorong Deng creator: Qun Xiao creator: Feng Liu creator: Cihua Zheng uri: https://doi.org/10.7717/peerj.4204 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Deng et al. title: Heteroassociative storage of hippocampal pattern sequences in the CA3 subregion link: https://peerj.com/articles/4203 last-modified: 2018-01-02 description: BackgroundRecent research suggests that the CA3 subregion of the hippocampus has properties of both autoassociative network, due to its ability to complete partial cues, tolerate noise, and store associations between memories, and heteroassociative one, due to its ability to store and retrieve sequences of patterns. Although there are several computational models of the CA3 as an autoassociative network, more detailed evaluations of its heteroassociative properties are missing.MethodsWe developed a model of the CA3 subregion containing 10,000 integrate-and-fire neurons with both recurrent excitatory and inhibitory connections, and which exhibits coupled oscillations in the gamma and theta ranges. We stored thousands of pattern sequences using a heteroassociative learning rule with competitive synaptic scaling.ResultsWe showed that a purely heteroassociative network model can (i) retrieve pattern sequences from partial cues with external noise and incomplete connectivity, (ii) achieve homeostasis regarding the number of connections per neuron when many patterns are stored when using synaptic scaling, (iii) continuously update the set of retrievable patterns, guaranteeing that the last stored patterns can be retrieved and older ones can be forgotten.DiscussionHeteroassociative networks with synaptic scaling rules seem sufficient to achieve many desirable features regarding connectivity homeostasis, pattern sequence retrieval, noise tolerance and updating of the set of retrievable patterns. creator: Raphael Y. de Camargo creator: Renan S. Recio creator: Marcelo B. Reyes uri: https://doi.org/10.7717/peerj.4203 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 de Camargo et al. title: Biotea: semantics for Pubmed Central link: https://peerj.com/articles/4201 last-modified: 2018-01-02 description: A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io. creator: Alexander Garcia creator: Federico Lopez creator: Leyla Garcia creator: Olga Giraldo creator: Victor Bucheli creator: Michel Dumontier uri: https://doi.org/10.7717/peerj.4201 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Garcia et al. title: Satellite tagging highlights the importance of productive Mozambican coastal waters to the ecology and conservation of whale sharks link: https://peerj.com/articles/4161 last-modified: 2018-01-02 description: The whale shark Rhincodon typus is an endangered, highly migratory species with a wide, albeit patchy, distribution through tropical oceans. Ten aerial survey flights along the southern Mozambican coast, conducted between 2004–2008, documented a relatively high density of whale sharks along a 200 km stretch of the Inhambane Province, with a pronounced hotspot adjacent to Praia do Tofo. To examine the residency and movement of whale sharks in coastal areas around Praia do Tofo, where they may be more susceptible to gill net entanglement, we tagged 15 juveniles with SPOT5 satellite tags and tracked them for 2–88 days (mean = 27 days) as they dispersed from this area. Sharks travelled between 10 and 2,737 km (mean = 738 km) at a mean horizontal speed of 28 ± 17.1 SD km day−1. While several individuals left shelf waters and travelled across international boundaries, most sharks stayed in Mozambican coastal waters over the tracking period. We tested for whale shark habitat preferences, using sea surface temperature, chlorophyll-a concentration and water depth as variables, by computing 100 random model tracks for each real shark based on their empirical movement characteristics. Whale sharks spent significantly more time in cooler, shallower water with higher chlorophyll-a concentrations than model sharks, suggesting that feeding in productive coastal waters is an important driver of their movements. To investigate what this coastal habitat choice means for their conservation in Mozambique, we mapped gill nets during two dedicated aerial surveys along the Inhambane coast and counted gill nets in 1,323 boat-based surveys near Praia do Tofo. Our results show that, while whale sharks are capable of long-distance oceanic movements, they can spend a disproportionate amount of time in specific areas, such as along the southern Mozambique coast. The increasing use of drifting gill nets in this coastal hotspot for whale sharks is likely to be a threat to regional populations of this iconic species. creator: Christoph A. Rohner creator: Anthony J. Richardson creator: Fabrice R. A. Jaine creator: Michael B. Bennett creator: Scarla J. Weeks creator: Geremy Cliff creator: David P. Robinson creator: Katie E. Reeve-Arnold creator: Simon J. Pierce uri: https://doi.org/10.7717/peerj.4161 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rohner et al.