title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2018-09 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Influence of sports expertise level on attention in multiple object tracking link: https://peerj.com/articles/5732 last-modified: 2018-09-28 description: BackgroundThis study aimed to investigate whether performance in a multiple object tracking (MOT) task could be improved incrementally with sports expertise, and whether differences between experienced and less experienced athletes, or non-athletes, were modulated by load.MethodsWe asked 22 elite and 20 intermediate basketball players, and 23 non-athletes, to perform an MOT task under three attentional load conditions (two, three, and four targets). Accuracies were analyzed to examine whether different levels of sports expertise influence MOT task performance.ResultsThe elite athletes displayed better tracking performance compared with the intermediate or non-athletes when tracking three or four targets. However, no significant difference was found between the intermediate athletes and the non-athletes. Further, no differences were observed among the three groups when tracking two targets.DiscussionThe results suggest that the effects of expertise in team ball sports could transfer to a non-sports-specific attention task. These transfer effects to general cognitive functions occur only in elite athletes with extensive training under higher attentional load. creator: Fanghui Qiu creator: Yanling Pi creator: Ke Liu creator: Xuepei Li creator: Jian Zhang creator: Yin Wu uri: https://doi.org/10.7717/peerj.5732 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Qiu et al. title: Sunset Yellow and Allura Red modulate Bcl2 and COX2 expression levels and confer oxidative stress-mediated renal and hepatic toxicity in male rats link: https://peerj.com/articles/5689 last-modified: 2018-09-28 description: Studies on the adverse health effects caused by azo dyes are insufficient and quite contradictory. This work aims to investigate the possible toxic effect of two types of widely used food additives, Sunset Yellow and Allura Red, by assessing the physiological, histopathological and ultrastructural changes in the liver and kidney. Also, we investigated the genotoxic effect of both dyes on white blood cells. Thirty adult male albino rats were divided into three groups of 10 animals each: control (received water), Sunset Yellow-treated (2.5 mg/kg body weight) and Allura Red-treated (seven mg/kg body weight). The doses were orally applied for 4 weeks. Our results indicated an increase in the biochemical markers of hepatic and renal function (Aspartate aminotransferase, alanine aminotransferase, urea, uric acid and creatinine) in animals administered with the azo dyes. We also observed a noticeable increase in MDA and a marked decrease in total antioxidant levels in azo dye-treated animals compared to controls. Conversely, both dyes adversely affected the liver and kidney of albino rats and altered their histological and fine structure, with downregulation of Bcl2 and upregulation of COX2 expression. Our comet assay results showed a significant elevation in the fold change of tail moment in response to application of Sunset Yellow but not Allura Red. Collectively, we show that Sunset Yellow and Allura Red cause histopathological and physiological aberrations in the liver and kidney of male Wistar albino rats. Moreover, Sunset Yellow but not Allura Red induces a potential genotoxic effect. creator: Latifa I. Khayyat creator: Amina E. Essawy creator: Jehan M. Sorour creator: Ahmed Soffar uri: https://doi.org/10.7717/peerj.5689 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Khayyat et al. title: Modeled larval connectivity of a multi-species reef fish and invertebrate assemblage off the coast of Moloka‘i, Hawai‘i link: https://peerj.com/articles/5688 last-modified: 2018-09-28 description: We use a novel individual-based model (IBM) to simulate larval dispersal around the island of Moloka‘i in the Hawaiian Archipelago. Our model uses ocean current output from the Massachusetts Institute of Technology general circulation model (MITgcm) as well as biological data on four invertebrate and seven fish species of management relevance to produce connectivity maps among sites around the island of Moloka‘i. These 11 species span the range of life history characteristics of Hawaiian coral reef species and show different spatial and temporal patterns of connectivity as a result. As expected, the longer the pelagic larval duration (PLD), the greater the proportion of larvae that disperse longer distances, but regardless of PLD (3–270 d) most successful dispersal occurs either over short distances within an island (<30 km) or to adjacent islands (50–125 km). Again, regardless of PLD, around the island of Moloka‘i, connectivity tends to be greatest among sites along the same coastline and exchange between northward, southward, eastward and westward-facing shores is limited. Using a graph-theoretic approach to visualize the data, we highlight that the eastern side of the island tends to show the greatest out-degree and betweenness centrality, which indicate important larval sources and connectivity pathways for the rest of the island. The marine protected area surrounding Kalaupapa National Historical Park emerges as a potential source for between-island larval connections, and the west coast of the Park is one of the few regions on Moloka‘i that acts as a net larval source across all species. Using this IBM and visualization approach reveals patterns of exchange between habitat regions and highlights critical larval sources and multi-generational pathways to indicate priority areas for marine resource managers. creator: Emily E. Conklin creator: Anna B. Neuheimer creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.5688 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Conklin et al. title: Functions of Candida albicans cell wall glycosidases Dfg5p and Dcw1p in biofilm formation and HOG MAPK pathway link: https://peerj.com/articles/5685 last-modified: 2018-09-28 description: BackgroundCandida albicans is a commensal fungus that inhabits the oral mucosal surface and causes oral and systemic candidiasis. Oral candidiasis most commonly occurs in patients with AIDS, denture wearers and newborn children. Systemic candidiasis occurs mainly in immunocompromised patients and patients admitted to hospitals for prolonged periods. C. albicans homologous genes, DFG5 and DCW1, encode for two closely related cell wall proteins with putative glycosyltransferase enzyme activity and C-terminal GPI-anchors. Past studies have shown that individual DFG5 and DCW1 mutations are viable but simultaneous deletion of DFG5 and DCW1 in C. albicans results in lethality. However, the exact functions of these cell wall based enzymes, which represent potential drug targets, are not understood.MethodsC. albicans DFG5/DCW1 heterologous and conditional double mutant strains were assessed for growth and biofilm formation in comparison to wild type and parental strains. Cell wall and heat stress susceptibility of the mutant and control strains were assessed using agar spotting assays. Growth was assessed under normal and osmotic stress conditions along with light microscopy imaging. Biofilm dry weight and microscopic imaging analysis of biofilms was performed. Hypha formation in response to serum was analyzed using light microscopy imaging. Western blot analysis of mutant strains and control strains was performed to assess Hog1 basal levels and phosphorylation status.ResultsAnalysis of the heterologous mutants indicated that Dfg5p is more important for growth while Dcw1p appeared to play a role in cell wall integrity response. The conditional double mutant was observed to be less resistant to cell wall stress. However, growth of the mutants was similar under control and osmotic stress conditions. The mutants were also able to grow similar to wild type under heat stress. Biofilm formation was reduced in the mutants where DFG5 was deleted or suppressed. Hyphal morphogenesis was reduced although germ tube formation was observed in the biofilms of the mutant strains. Basal Hog1 protein levels were reduced or absent in the DFG5 and DCW1 mutants. However, osmotic stress was able to induce Hog1 protein levels comparable to wild type. Hog1 phosphorylation appeared to be slightly reduced although not significantly. In addition to biofilm assays, serum dose response imaging analysis indicated that hyphae formation in DFG5 and DCW1 mutants was defective.ConclusionsThese data indicate that DFG5 and DCW1 are required for hyphal morphogenesis and biofilm formation in C. albicans. These functions may be regulated via basal Hog1 MAPK which is required for transcriptional regulation of chitin synthesis. creator: Ryan Mancuso creator: Jennifer Chinnici creator: Charlene Tsou creator: Sujay Busarajan creator: Raveena Munnangi creator: Abhiram Maddi uri: https://doi.org/10.7717/peerj.5685 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mancuso et al. title: Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions link: https://peerj.com/articles/5684 last-modified: 2018-09-28 description: BackgroundComparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM).MethodsA literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner.ResultsMitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM.ConclusionThis study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic. creator: Tom L. Jenkins creator: Rita Castilho creator: Jamie R. Stevens uri: https://doi.org/10.7717/peerj.5684 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jenkins et al. title: Cellular production of a counterfeit viral protein confers immunity to infection by a related virus link: https://peerj.com/articles/5679 last-modified: 2018-09-28 description: DNA copies of many non-retroviral RNA virus genes or portions thereof (NIRVs) are present in the nuclear genomes of many eukaryotes. These have often been preserved for millions of years of evolution, suggesting that they play an important cellular function. One possible function is resistance to infection by related viruses. In some cases, this appears to occur through the piRNA system, but in others by way of counterfeit viral proteins encoded by NIRVs. In the fungi, NIRVs may be as long as 1,400 uninterrupted codons. In one such case in the yeast Debaryomyces hansenii, one of these genes provides immunity to a related virus by virtue of expression of a counterfeit viral capsid protein, which interferes with assembly of viral capsids by negative complementation. The widespread occurrence of non-retroviral RNA virus genes in eukaryotes may reflect an underappreciated method of host resistance to infection. This work demonstrates for the first time that an endogenous host protein encoded by a gene that has been naturally acquired from a virus and fixed in a eukaryote can interfere with the replication of a related virus and do so by negative complementation. creator: Benjamin E. Warner creator: Matthew J. Ballinger creator: Pradeep Yerramsetty creator: Jennifer Reed creator: Derek J. Taylor creator: Thomas J. Smith creator: Jeremy A. Bruenn uri: https://doi.org/10.7717/peerj.5679 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Warner et al. title: Distinguishing between enduring and dynamic concussion symptoms: applying Generalisability Theory to the Rivermead Post Concussion Symptoms Questionnaire (RPQ) link: https://peerj.com/articles/5676 last-modified: 2018-09-28 description: BackgroundThe Rivermead Post Concussion Symptoms Questionnaire (RPQ) is a widely-used, 16-item measure of concussion symptoms yet its ability to assess change in the symptom experience over time has come under criticism. We applied Generalisability theory to differentiate between dynamic and enduring aspects of post-concussion symptoms and to examine sources of measurement error in the RPQ.Materials and MethodsGeneralisability theory was applied using the longitudinal design with persons as the object of measurement. Patients with a traumatic brain injury (n = 145; aged ≥16 years) were assessed at three time occasions (1, 6 and 12 months post-injury) using the RPQ.ResultsThe RPQ showed overall strong generalisability of scores (G = .98) across persons and occasions with a minor proportion of variance attributed to the dynamic aspect of symptoms reflected by interaction between person and occasion. Items measuring concentration, fatigue, restlessness and irritability reflected more dynamic patterns compared to more enduring patterns of sensitivity to noise, impatience, nausea and sleep disturbance.ConclusionThe RPQ demonstrated strong reliability in assessing enduring post-concussion symptoms but its ability to assess dynamic symptoms is limited. Clinicians should exercise caution in use of the RPQ to track dynamic symptom change over time. Further investigation is necessary to enhance the RPQ’s ability to assess dynamic symptoms and to address measurement error associated with individual items. creator: Oleg N. Medvedev creator: Alice Theadom creator: Suzanne Barker-Collo creator: Valery Feigin uri: https://doi.org/10.7717/peerj.5676 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Medvedev et al. title: Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses link: https://peerj.com/articles/5674 last-modified: 2018-09-28 description: Fine scale sexual segregation outside of the mating season is common in sexually dimorphic and polygamous species, particularly in ungulates. A number of hypotheses predict sexual segregation but these are often contradictory with no agreement as to a common cause, perhaps because they are species specific. We explicitly tested three of these hypotheses which are commonly linked by a dependence on sexual dimorphism for animals which exhibit fine-scale sexual segregation; the Predation Risk Hypothesis, the Forage Selection Hypothesis, and the Activity Budget Hypothesis, in a single system the pheasant, Phasianus colchicus; a large, sedentary bird that is predominantly terrestrial and therefore analogous to ungulates rather than many avian species which sexually segregate. Over four years we reared 2,400 individually tagged pheasants from one day old and after a period of 8–10 weeks we released them into the wild. We then followed the birds for 7 months, during the period that they sexually segregate, determined their fate and collected behavioural and morphological measures pertinent to the hypotheses. Pheasants are sexually dimorphic during the entire period that they sexually segregate in the wild; males are larger than females in both body size and gut measurements. However, this did not influence predation risk and predation rates (as predicted by the Predation Risk Hypothesis), diet choice (as predicted by the Forage Selection Hypothesis), or the amount of time spent foraging, resting or walking (as predicted by the Activity Budget Hypothesis). We conclude that adult sexual size dimorphism is not responsible for sexual segregation in the pheasant in the wild. Instead, we consider that segregation may be mediated by other, perhaps social, factors. We highlight the importance of studies on a wide range of taxa to help further the knowledge of sexual segregation. creator: Mark A. Whiteside creator: Jayden O. van Horik creator: Ellis J.G. Langley creator: Christine E. Beardsworth creator: Joah R. Madden uri: https://doi.org/10.7717/peerj.5674 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Whiteside et al. title: Biosorption potential of natural, pyrolysed and acid-assisted pyrolysed sugarcane bagasse for the removal of lead from contaminated water link: https://peerj.com/articles/5672 last-modified: 2018-09-28 description: Lead (Pb) is a ubiquitous pollutant which poses serious threats to plants, animals and humans once entered into the food chain via contaminated industrial effluents on their discharge into the surface of water bodies and/or geological materials. This study aimed to examine and compare the biosorption potential of natural sugarcane bagasse (NB), pyrolysed sugarcane bagasse (PB) and acid assisted pyrolysed sugarcane bagasse (APB) for the removal of Pb from contaminated water. To explore this objective, a series of batch experiments were conducted at various adsorbent mass (0.25, 0.5, 0.75, 1.0 g per 100 ml contaminated water), initial Pb concentration (7, 15, 30, 60 and 120 ppm), and contact time (7, 15, 30, 60 and 120 min). Results revealed that all the tested bio-sorbents have potential to adsorb and remove Pb ions from the contaminated water. In this regard, APB proved more effective since it removed 98% of Pb from aqueous solution at initial Pb concentration of 7 ppm and mass of 0.25 g per 100 ml of aqueous solution. The respective values in case of NB and PB were 90 and 95%. For a given adsorbent type, Pb adsorption decreased by increasing the mass from 0.25 to 1.0 g per 100 ml of aqueous solution. However, the greatest Pb removal occurred at adsorbent mass of 1.0 g per 100 ml of aqueous solution. Initial Pb concentration had a great impact on Pb adsorption and removal by adsorbent. The former increased and the latter decreased with the increase in initial Pb concentration from seven to 120 ppm. At seven ppm Pb concentration, maximum Pb removal took place irrespective to the adsorbent type. Out of the total Pb adsorption and removal, maximum contribution occurred within 15 min of contact time between the adsorbate and adsorbent, which slightly increased till 30 min, thereafter, it reached to equilibrium. Application of equilibrium isotherm models revealed that our results were better fitted with Freundlich adsorption isotherm model. Overall, and for the reasons detailed above, it is concluded that sugarcane bagasse has capabilities to adsorb and remove Pb ions from contaminated water. Its bio-sorption potential was considerably increased after pyrolysis and acid treatment. creator: Ghulam Mustafa Shah creator: Muhammad Nasir creator: Muhammad Imran creator: Hafiz Faiq Bakhat creator: Faiz Rabbani creator: Muhammad Sajjad creator: Abu Bakr Umer Farooq creator: Sajjad Ahmad creator: Lifen Song uri: https://doi.org/10.7717/peerj.5672 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shah et al. title: New mud dragons from Svalbard: three new species of Cristaphyes and the first Arctic species of Pycnophyes (Kinorhyncha: Allomalorhagida: Pycnophyidae) link: https://peerj.com/articles/5653 last-modified: 2018-09-28 description: BackgroundKinorhynchs are marine, microscopic invertebrates inhabiting the seafloors. Their segmented trunk equipped with spines and processes has inspired scientists to give them the common name “mud dragons.” Even though kinorhynchs have been known since the 19th century, less than 300 species are known to science, and it is still considered a largely understudied animal group—in particular in the Arctic, from which only 23 species are known so far.MethodsSamples were collected at eight stations around Svalbard and in the fjords of Spitsbergen. Meiofauna was extracted from the sediment cores with LUDOX centrifugation method, and kinorhynchs were picked up and mounted for light- and scanning electron microscopy.ResultsFour new species of the kinorhynch family Pycnophyidae are described from Svalbard: Cristaphyes dordaidelosensis sp. nov., C. glaurung sp. nov., C. scatha sp. nov., and Pycnophyes ancalagon sp. nov. The new species are generally recognized by their distribution of setae along the trunk segments.DiscussionAfter the discovery of the new species, Pycnophyidae becomes with 14 species the most diverse kinorhynch genus in the Arctic, closely followed by Echinoderidae with 13 species. So far, these are the only kinorhynch families with an Arctic distribution. creator: Martin Vinther Sørensen creator: Katarzyna Grzelak uri: https://doi.org/10.7717/peerj.5653 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sørensen and Grzelak title: Closing the gap: mixed stock analysis of three foraging populations of green turtles (Chelonia mydas) on the Great Barrier Reef link: https://peerj.com/articles/5651 last-modified: 2018-09-28 description: A solid understanding of the spatial ecology of green turtles (Chelonia mydas) is fundamental to their effective conservation. Yet this species, like many marine migratory species, is challenging to monitor and manage because they utilise a variety of habitats that span wide spatio-temporal scales. To further elucidate the connectivity between green turtle rookeries and foraging populations, we sequenced the mtDNA control region of 278 turtles across three foraging sites from the northern Great Barrier Reef (GBR) spanning more than 330 km: Cockle Bay, Green Island and Low Isles. This was performed with a newly developed assay, which targets a longer fragment of mtDNA than previous studies. We used a mixed stock analysis (MSA), which utilises genetic data to estimate the relative proportion of genetically distinct breeding populations found at a given foraging ground. Haplotype and nucleotide diversity was also assessed. A total of 35 haplotypes were identified across all sites, 13 of which had not been found previously in any rookery. The MSA showed that the northern GBR (nGBR), Coral Sea (CS), southern GBR (sGBR) and New Caledonia (NC) stocks supplied the bulk of the turtles at all three sites, with small contributions from other rookeries in the region. Stock contribution shifted gradually from north to south, although sGBR/CS stock dominated at all three sites. The major change in composition occured between Cockle Bay and Low Isles. Our findings, together with other recent studies in this field, show that stock composition shifts with latitude as a natural progression along a coastal gradient. This phenomenon is likely to be the result of ocean currents influencing both post-hatchling dispersal and subsequent juvenile recruitment to diverse coastal foraging sites. creator: Karina Jones creator: Michael Jensen creator: Graham Burgess creator: Johanna Leonhardt creator: Lynne van Herwerden creator: Julia Hazel creator: Mark Hamann creator: Ian Bell creator: Ellen Ariel uri: https://doi.org/10.7717/peerj.5651 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jones et al. title: Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets link: https://peerj.com/articles/5650 last-modified: 2018-09-28 description: Xeno-miRNAs are microRNAs originating from exogenous species detected in host biofluids. A growing number of studies have suggested that many of these xeno-miRNAs may be involved in cross-species interactions and manipulations. To date, hundreds of xeno-miRNAs have been reported in different hosts at various abundance levels. Based on computational predictions, many more miRNAs could be potentially transferred to human circulation system. There is a clear need for bioinformatics resources and tools dedicated to xeno-miRNA annotations and their potential functions. To address this need, we have systematically curated xeno-miRNAs from multiple sources, performed target predictions using well-established algorithms, and developed a user-friendly web-based tool—Xeno-miRNet—to allow researchers to search and explore xeno-miRNAs and their potential targets within different host species. Xeno-miRNet currently contains 1,702 (including both detected and predicted) xeno-miRNAs from 54 species and 98,053 potential gene targets in six hosts. The web application is freely available at http://xeno.mirnet.ca. creator: Yannan Fan creator: Maria Habib creator: Jianguo Xia uri: https://doi.org/10.7717/peerj.5650 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fan et al. title: Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing link: https://peerj.com/articles/5649 last-modified: 2018-09-28 description: BackgroundThe objective of this study was to characterize the oral microflora profile of primary Sjögren’s syndrome (pSS) patients, thereby revealing the connection between oral bacterial composition and dental caries, and to identify the “core microbiome” in the oral cavities of pSS patients and systemic healthy individuals by using a high-throughput sequencing technique.MethodsTwenty-two pSS patients and 23 healthy controls were enrolled in this study. Their clinical data and oral rinse samples were collected. The V3–V4 hypervariable regions of the bacterial 16S rRNA gene of samples were amplified and analyzed by high-throughput sequencing on the Illumina Miseq PE300 platform.ResultsBoth two groups were age- and sex-matched. There were significantly higher decayed, missing and filled teeth (DMFT) and decayed, missing and filled surfaces (DMFS) in the pSS group than in the control group (p < 0.01). Alpha diversity was depleted in pSS patients, compared with healthy controls (p < 0.01), while beta diversity between the two groups was not significantly different. Seven discriminative genera (LDA > 4) were found between the two groups in LEfSe (LDA Effect Size) analysis. The relative abundance of Veillonella in pSS patients was fourfold higher, while Actinomyces, Haemophilus, Neisseria, Rothia, Porphyromonas and Peptostreptococcus were significantly lower in pSS patients than in healthy controls. However, the correlation between Veillonella and DMFT/DMFS was not significant (p > 0.05). In Venn diagram analysis, nine genera shared by all samples of two groups, which comprised 71.88% and 67.64% in pSS patients and controls, respectively.DiscussionThese findings indicate a microbial dysbiosis in pSS patients; notably, Veillonella might be recognized as a biomarker in pSS patients. The core microbiome in pSS patients was similar to the systemic healthy population. These provide insight regarding advanced microbial prevention and treatment of severe dental caries in pSS patients. This study also provides basic data regarding microbiology in pSS. creator: Zhifang Zhou creator: Guanghui Ling creator: Ning Ding creator: Zhe Xun creator: Ce Zhu creator: Hong Hua creator: Xiaochi Chen uri: https://doi.org/10.7717/peerj.5649 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhou et al. title: Dynamics of nitrogen and active nitrogen components across seasons under varying stand densities in a Larix principis-rupprechtii (Pinaceae) plantation link: https://peerj.com/articles/5647 last-modified: 2018-09-28 description: Changes in the concentration of soil nitrogen (N) or its components may directly affect ecosystem functioning in forestry. Thinning of forest stands, a widely used forestry management practice, may transform soil nutrients directly by altering the soil environment, or indirectly by changing above- or belowground plant biomass. The study objectives were to determine how tree stem density affects the soil N pool and what mechanisms drive any potential changes. In this study, N and its active components were measured in the soil of a Larix principis-rupprechtii plantation across two full growing seasons, in 12 (25 × 25 m) plots: (low thinning, removal of 15% of the trees, three plot repetitions), moderate thinning (MT) (35% removal) and heavy thinning (HT) (50% removal) and no thinning control. Environmental indices, like the light condition, soil respiration, soil temperatures, and prescription, were measured in the plots also. Results indicated that soil total nitrogen (STN) was affected by tree stem density adjustments in the short-term; STN generally increased with decreasing tree stem density, reaching its highest concentration in the MT treatment before decreasing in HT. This pattern was echoed by the DON/STN ratio dissolved organic nitrogen (DON) under MT. A lower DON/STN was measured across the seasons. Microbial biomass nitrogen (MBN) and the SOC/STN (soil organic carbon (SOC)) ratio and density treatments influenced MBN concentration and inhibited SOC/STN. MT tended to accumulate more STN, produce lower DON/STN and had a generally higher microbial activity, which may be partly ascribed to the higher MBN value, MBN/STN ratio and lower DON/STN. The water conditions (soil moisture), light and soil temperatures could partly be responsible for the N pool dynamic in the different density treatments. creator: Junyong Ma creator: Hairong Han creator: Wenwen Zhang creator: Xiaoqin Cheng uri: https://doi.org/10.7717/peerj.5647 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ma et al. title: Functional responses of a cosmopolitan invader demonstrate intraspecific variability in consumer-resource dynamics link: https://peerj.com/articles/5634 last-modified: 2018-09-28 description: BackgroundVariability in the ecological impacts of invasive species across their geographical ranges may decrease the accuracy of risk assessments. Comparative functional response analysis can be used to estimate invasive consumer-resource dynamics, explain impact variability, and thus potentially inform impact predictions. The European green crab (Carcinus maenas) has been introduced on multiple continents beyond its native range, although its ecological impacts appear to vary among populations and regions. Our aim was to test whether consumer-resource dynamics under standardized conditions are similarly variable across the current geographic distribution of green crab, and to identify correlated morphological features.MethodsCrabs were collected from multiple populations within both native (Northern Ireland) and invasive regions (South Africa and Canada). Their functional responses to local mussels (Mytilus spp.) were tested. Attack rates and handling times were compared among green crab populations within each region, and among regions (Pacific Canada, Atlantic Canada, South Africa, and Northern Ireland). The effect of predator and prey morphology on prey consumption was investigated.ResultsAcross regions, green crabs consumed prey according to a Type II (hyperbolic) functional response curve. Attack rates (i.e., the rate at which a predator finds and attacks prey), handling times and maximum feeding rates differed among regions. There was a trend toward higher attack rates in invasive than in native populations. Green crabs from Canada had lower handling times and thus higher maximum feeding rates than those from South Africa and Northern Ireland. Canadian and Northern Ireland crabs had significantly larger claws than South African crabs. Claw size was a more important predictor of the proportion of mussels killed than prey shell strength.DiscussionThe differences in functional response between regions reflect observed impacts of green crabs in the wild. This suggests that an understanding of consumer–resource dynamics (e.g., the per capita measure of predation), derived from simple, standardized experiments, might yield useful predictions of invader impacts across geographical ranges. creator: Brett R. Howard creator: Daniel Barrios-O’Neill creator: Mhairi E. Alexander creator: Jaimie T.A. Dick creator: Thomas W. Therriault creator: Tamara B. Robinson creator: Isabelle M. Côté uri: https://doi.org/10.7717/peerj.5634 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: Finding wolf homesites: improving the efficacy of howl surveys to study wolves link: https://peerj.com/articles/5629 last-modified: 2018-09-28 description: Locating wolf (Canis lupus) homesites is valuable for understanding the foraging behavior, population dynamics, and reproductive ecology of wolves during summer. During this period wolf pack members (adults and pups) readily respond to simulated wolf howls (i.e., howl surveys), which allows researchers to estimate the location of the homesite via triangulation. Confirming the actual locations of homesites via ground truthing is labor intensive because of the error surrounding estimated locations. Our objectives were (1) to quantify observer error during howl surveys and compare amongst experience levels, (2) provide a simple method for locating homesites in the field by incorporating observer error, and (3) further document the value of this method for monitoring wolf packs throughout the summer. We located 17 homesites by howl surveys during 2015–2017 in the Greater Voyageurs Ecosystem, Minnesota, USA. Of 62 bearings taken by observers during howl surveys, bearings erred by an average of 7.6° ± 6.3° (SD). There was no difference in observer error between novice and experienced observers. A simple way to increase efficiency when searching for homesites is to search concentric areas (bands) based on estimated observer error, specifically by: (1) adding ±10° error bands around howl survey bearings when ≥3 bearings can be obtained, (2) ±10° and ±20° error bands when 2 bearings are obtained, and (3) ±10° and ±26° error bands when 1 bearing is obtained. By incorporating observer error and understanding how frequently and how far wolves move homesites, it is possible to monitor wolf packs and confirm most, if not all, homesites used by a pack from at least June until August without having a collared individual in a pack. creator: Thomas D. Gable creator: Steve K. Windels creator: Joseph K. Bump uri: https://doi.org/10.7717/peerj.5629 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gable et al. title: E-cigarettes versus nicotine patches for perioperative smoking cessation: a pilot randomized trial link: https://peerj.com/articles/5609 last-modified: 2018-09-28 description: IntroductionCigarette smoking by surgical patients is associated with increased complications. E-cigarettes have emerged as a potential smoking cessation tool. We sought to determine the feasibility and acceptability of e-cigarettes, compared to nicotine patch, for perioperative smoking cessation in veterans.MethodsPreoperative patients were randomized to either the nicotine patch group (n = 10) or the e-cigarette group (n = 20). Both groups were given a free 6-week supply in a tapering dose. All patients received brief counseling, a brochure on perioperative smoking cessation, and referral to the California Smokers’ Helpline. The primary outcome was rate of smoking cessation on day of surgery confirmed by exhaled carbon monoxide. Secondary outcomes included smoking habits, pulmonary function, adverse events, and satisfaction with the products on day of surgery and at 8-weeks follow-up.ResultsBiochemically verified smoking cessation on day of surgery was similar in both groups. Change in forced expiratory volume in one second (FEV1) was 592 ml greater in the e-cigarette group (95% CI [153–1,031] ml, p = 0.01) and change in forced expiratory volume in one second to forced vital capacity ratio (FEV1/FVC ratio) was 40.1% greater in the e-cigarette group (95% CI [18.2%–78.4%], p = 0.04). Satisfaction with the product was similar in both groups.DiscussionE-cigarettes are a feasible tool for perioperative smoking cessation in veterans with quit rates comparable to nicotine replacement patch. Spirometry appears to be improved 8-weeks after initiating e-cigarettes compared to nicotine patch, possibly due to worse baseline spirometry and more smoking reduction in the e-cigarette group. An adequately powered study is recommended to determine if these results can be duplicated. creator: Susan M. Lee creator: Rachel Tenney creator: Arthur W. Wallace creator: Mehrdad Arjomandi uri: https://doi.org/10.7717/peerj.5609 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lee et al. title: First record of Holothuria (Metriatyla) scabra Jaeger, 1833 (Echinodermata: Holothuroidea) from the coastal waters of the United Arab Emirates link: https://peerj.com/articles/5555 last-modified: 2018-09-28 description: The presence of an endangered and economically valuable species of sea cucumber, Holothuria (Metriatyla) scabra Jaeger, 1833, was investigated in the Alqurm Wa Lehhfaiiah Protected Area near the city of Kalba in the Emirate of Sharjah. Sea cucumber specimens were collected, and identification was first conducted using morphological keys. H. scabra identification was confirmed through microscopic observation of ossicles. Though this species is known to occur in other regions along the Gulf of Oman, this paper represents the first published record of H. scabra, in the coastal waters of the United Arab Emirates. creator: Fadi Yaghmour creator: Brendan Whittington-Jones uri: https://doi.org/10.7717/peerj.5555 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yaghmour and Whittington-Jones title: Leaf photosynthetic function duration during yield formation of large-spike wheat in rainfed cropping systems link: https://peerj.com/articles/5532 last-modified: 2018-09-28 description: Improving photosynthetic capacity significantly affects the yield of wheat (Triticum aestivum L.) in rainfed regions. In this study, the physiological characteristics of eight large-spike wheat lines were compared with a multiple-spike cultivar as a control (CK) in a field over two consecutive seasons: 2010–2012. The tillering peak was 7–21 d after returning green for line 2040, the average rate of decline of relative water content was slower, and the average duration time of photosynthetic rate was longer than CK in vitro. There was a strong linear and positive correlation between photosynthetic rate and root activity at jointing, flowering, and grain-filling stages. In addition, average yields were higher in large-spike lines than CK (multiple-spike cultivar). The results suggest that large-spike lines might have greater water retaining capacity during yield formation under rainfed conditions. creator: Lifang Wang creator: Jutao Sun creator: Chenyang Wang creator: Zhouping Shangguan uri: https://doi.org/10.7717/peerj.5532 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Crystal structure and functional analysis of human C1ORF123 link: https://peerj.com/articles/5377 last-modified: 2018-09-28 description: Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation. creator: Siti Nurulnabila A. Rahaman creator: Jastina Mat Yusop creator: Zeti-Azura Mohamed-Hussein creator: Wan Mohd Aizat creator: Kok Lian Ho creator: Aik-Hong Teh creator: Jitka Waterman creator: Boon Keat Tan creator: Hwei Ling Tan creator: Adelicia Yongling Li creator: Ee Sin Chen creator: Chyan Leong Ng uri: https://doi.org/10.7717/peerj.5377 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 A. Rahaman et al. title: New records of the archaic dolphin Agorophius (Mammalia: Cetacea) from the upper Oligocene Chandler Bridge Formation of South Carolina, USA link: https://peerj.com/articles/5290 last-modified: 2018-09-28 description: The stem odontocete Agorophius pygmaeus (Ashley Formation, lower Oligocene, South Carolina; 29.0–26.57 Ma) has been a critical point of comparison for studies of early neocete evolution owing to its early discovery as well as its transitional anatomy relative to archaeocete whales and modern odontocetes. Some time during the late nineteenth century the holotype skull went missing and has never been relocated; supplementary reference specimens have since been recently referred to the species from the Ashley Formation and the overlying Chandler Bridge Formation (upper Oligocene; 24.7–23.5). New crania referable to Agorophius sp. are identifiable to the genus based on several features of the intertemporal region. Furthermore, all published specimens from the Chandler Bridge Formation consistently share larger absolute size and a proportionally shorter exposure of the parietal in the skull roof than specimens from the Ashley Formation (including the holotype). Furthermore, these specimens include well-preserved ethmoid labyrinths and cribriform plates, indicating that Agorophius primitively retained a strong olfactory sense. These new crania suggest that at least two species of Agorophius are present in the Oligocene of South Carolina, revealing a somewhat more complicated taxonomic perspective. creator: Robert W. Boessenecker creator: Jonathan H. Geisler uri: https://doi.org/10.7717/peerj.5290 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Boessenecker and Geisler title: Investigating the relationship between intergroup physical contact and attitudes towards foreigners: the mediating role of quality of intergroup contact link: https://peerj.com/articles/5680 last-modified: 2018-09-27 description: Recent research has shown that a brief, casual touch administered by an outgroup member reduces prejudice towards the group to which the toucher belongs. In this study, we take the research on physical contact and prejudice a step further by addressing the relation between individuals’ amount of Experienced Intergroup Physical Contact (EIPC), across distinct contexts and involving different body parts, and attitudes towards foreign people. Specifically, we hypothesized that the amount of EIPC would be positively associated with both quantity and quality of intergroup contact, but that only quality would mediate the relationship between the amount of EIPC and outgroup attitudes, quality being more directly linked to the evaluative component of outgroup attitudes. To attain this aim, we asked participants to self-report the amount of EIPC, the quantity and quality of their intergroup contact and their attitudes towards foreign people. Consistent with our hypothesis: (1) as EIPC increased, positive attitudes towards foreign people increased; (2) higher levels of EIPC were associated with better quality and higher quantity of intergroup contact; (3) only quality of intergroup contact mediated the relationship between the amount of EIPC and attitudes towards foreign people. Results were discussed in relation to research on intergroup contact and physical contact. creator: Soraya E. Shamloo creator: Andrea Carnaghi creator: Carlo Fantoni uri: https://doi.org/10.7717/peerj.5680 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shamloo et al. title: Growth and feeding of deep-sea coral Lophelia pertusa from the California margin under simulated ocean acidification conditions link: https://peerj.com/articles/5671 last-modified: 2018-09-27 description: The global decrease in seawater pH known as ocean acidification has important ecological consequences and is an imminent threat for numerous marine organisms. Even though the deep sea is generally considered to be a stable environment, it can be dynamic and vulnerable to anthropogenic disturbances including increasing temperature, deoxygenation, ocean acidification and pollution. Lophelia pertusa is among the better-studied cold-water corals but was only recently documented along the US West Coast, growing in acidified conditions. In the present study, coral fragments were collected at ∼300 m depth along the southern California margin and kept in recirculating tanks simulating conditions normally found in the natural environment for this species. At the collection site, waters exhibited persistently low pH and aragonite saturation states (Ωarag) with average values for pH of 7.66 ± 0.01 and Ωarag of 0.81 ± 0.07. In the laboratory, fragments were grown for three weeks in “favorable” pH/Ωarag of 7.9/1.47 (aragonite saturated) and “unfavorable” pH/Ωarag of 7.6/0.84 (aragonite undersaturated) conditions. There was a highly significant treatment effect (P < 0.001) with an average% net calcification for favorable conditions of 0.023 ± 0.009% d−1 and net dissolution of −0.010 ± 0.014% d-1 for unfavorable conditions. We did not find any treatment effect on feeding rates, which suggests that corals did not depress feeding in low pH/ Ωarag in an attempt to conserve energy. However, these results suggest that the suboptimal conditions for L. pertusa from the California margin could potentially threaten the persistence of this cold-water coral with negative consequences for the future stability of this already fragile ecosystem. creator: Carlos E. Gómez creator: Leslie Wickes creator: Dan Deegan creator: Peter J. Etnoyer creator: Erik E. Cordes uri: https://doi.org/10.7717/peerj.5671 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gómez et al. title: Distribution, habitat associations, and conservation status updates for the pilose crayfish Pacifastacus gambelii (Girard, 1852) and Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) of the western United States link: https://peerj.com/articles/5668 last-modified: 2018-09-27 description: Our study evaluates the distribution, habitat associations, and current conservation status of the Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) and pilose crayfish Pacifastacus gambelii (Girard, 1852), two little-studied and data-deficient species endemic to the western United States. We first developed a species distribution model (SDM) for the pilose crayfishes based on their historical occurrence records using boosted regression trees and freshwater GIS data layers. We then sampled 163 sites in the summers of 2016 and 2017 within the distribution of these crayfishes, including 50 where these species were observed historically. We next compared our field results to modeled predictions of suitable habitat from the SDM. Our SDM predicted 73 sites (45%) we sampled as suitable for the pilose crayfishes, with a moderate AUC value of 0.824. The pilose crayfishes were generally predicted to occur in larger streams and rivers with less extreme upstream temperature and precipitation seasonality. We found the pilose crayfishes at only 20 (12%) of the 163 total sites we sampled, 14 (20%) of the 73 sites predicted as suitable for them by our SDM, and 12 (24%) of 50 historical sites that we sampled. We found the invasive virile crayfish Faxonius virilis (Hagen, 1870) at 22 sites total and 12 (24%) historical sites for the pilose crayfishes, and we found the “native invader” signal crayfish Pacifastacus leniusculus (Dana, 1852) at 29 sites total and 6 (12%) historical sites for the pilose crayfishes. We subsequently used a single classification tree to identify factors associated with our high rate of false positives for contemporary pilose crayfish distributions relative to our SDM. This classification tree identified the presence of invasive crayfishes, impairment of the benthic community, and sampling method as some of the factors differentiating false positives relative to true positives for the pilose crayfishes. Our study identified the historical distribution and habitat associations for P. connectens and P. gambelii using an SDM and contrasted this prediction to results of contemporary field sampling. We found that the pilose crayfishes have seemingly experienced substantial range declines, attributable to apparent displacement by invasive crayfishes and impairment or change to stream communities and habitat. We recommend increased conservation and management attention to P. connectens and P. gambelii in response to these findings. creator: Rachel M. Egly creator: Eric R. Larson uri: https://doi.org/10.7717/peerj.5668 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Egly and Larson title: Assessing the role of dispersed floral resources for managed bees in providing supporting ecosystem services for crop pollination link: https://peerj.com/articles/5654 last-modified: 2018-09-27 description: Most pollination ecosystem services studies have focussed on wild pollinators and their dependence on natural floral resources adjacent to crop fields. However, managed pollinators depend on a mixture of floral resources that are spatially separated from the crop field. Here, we consider the supporting role these resources play as an ecosystem services provider to quantify the use and availability of floral resources, and to estimate their relative contribution to support pollination services of managed honeybees. Beekeepers supplying pollination services to the Western Cape deciduous fruit industry were interviewed to obtain information on their use of floral resources. For 120 apiary sites, we also analysed floral resources within a two km radius of each site based on geographic data. The relative availability of floral resources at sites was compared to regional availability. The relative contribution of floral resources-types to sustain managed honeybees was estimated. Beekeepers showed a strong preference for eucalypts and canola. Beekeepers selectively placed more hives at sites with eucalypt and canola and less with natural vegetation. However, at the landscape-scale, eucalypt was the least available resource, whereas natural vegetation was most common. Based on analysis of apiary sites, we estimated that 700,818 ha of natural vegetation, 73,910 ha of canola fields, and 10,485 ha of eucalypt are used to support the managed honeybee industry in the Western Cape. Whereas the Cape managed honeybee system uses a bee native to the region, alien plant species appear disproportionately important among the floral resources being exploited. We suggest that an integrated approach, including evidence from interview and landscape data, and fine-scale biological data is needed to study floral resources supporting managed honeybees. creator: Annalie Melin creator: Mathieu Rouget creator: Jonathan F. Colville creator: Jeremy J. Midgley creator: John S. Donaldson uri: https://doi.org/10.7717/peerj.5654 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Melin et al. title: Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model link: https://peerj.com/articles/5643 last-modified: 2018-09-27 description: Ecologists often analyze relative abundances, which are an example of compositional data. However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We fit a quadratic multivariate regression model with multinomial observations to point count data obtained from video transects. As well as being an appropriate observation model in this case, the multinomial deals with the problem of zeros, which often makes compositional data analysis difficult. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data. creator: Fiona Chong creator: Matthew Spencer uri: https://doi.org/10.7717/peerj.5643 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chong and Spencer title: Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species link: https://peerj.com/articles/5605 last-modified: 2018-09-27 description: The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions. creator: Joshua M. Copus creator: W. L. Montgomery creator: Zac H. Forsman creator: Brian W. Bowen creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.5605 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Copus et al. title: Pre-imaginal conditioning alters adult sex pheromone response in Drosophila link: https://peerj.com/articles/5585 last-modified: 2018-09-27 description: Pheromones are chemical signals that induce innate responses in individuals of the same species that may vary with physiological and developmental state. In Drosophila melanogaster, the most intensively studied pheromone is 11-cis-vaccenyl acetate (cVA), which is synthezised in the male ejaculatory bulb and is transferred to the female during copulation. Among other effects, cVA inhibits male courtship of mated females. We found that male courtship inhibition depends on the amount of cVA and this effect is reduced in male flies derived from eggs covered with low to zero levels of cVA. This effect is not observed if the eggs are washed, or if the eggs are laid several days after copulation. This suggests that courtship suppression involves a form of pre-imaginal conditioning, which we show occurs during the early larval stage. The conditioning effect could not be rescued by synthetic cVA, indicating that it largely depends on conditioning by cVA and other maternally-transmitted factor(s). These experiments suggest that one of the primary behavioral effects of cVA is more plastic and less stereotypical than had hitherto been realised. creator: Claude Everaerts creator: Laurie Cazalé-Debat creator: Alexis Louis creator: Emilie Pereira creator: Jean-Pierre Farine creator: Matthew Cobb creator: Jean-François Ferveur uri: https://doi.org/10.7717/peerj.5585 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Everaerts et al. title: Assessing bird avoidance of high-contrast lights using a choice test approach: implications for reducing human-induced avian mortality link: https://peerj.com/articles/5404 last-modified: 2018-09-26 description: BackgroundAvian collisions with man-made objects and vehicles (e.g., buildings, cars, airplanes, power lines) have increased recently. Lights have been proposed to alert birds and minimize the chances of collisions, but it is challenging to choose lights that are tuned to the avian eye and can also lead to avoidance given the differences between human and avian vision. We propose a choice test to address this problem by first identifying wavelengths of light that would over-stimulate the retina using species-specific perceptual models and by then assessing the avoidance/attraction responses of brown-headed cowbirds to these lights during daytime using a behavioral assay.MethodsWe used perceptual models to estimate wavelength-specific light emitting diode (LED) lights with high chromatic contrast. The behavioral assay consisted of an arena where the bird moved in a single direction and was forced to make a choice (right/left) using a single-choice design (one side with the light on, the other with the light off) under diurnal light conditions.ResultsFirst, we identified lights with high saliency from the cowbird visual perspective: LED lights with peaks at 380 nm (ultraviolet), 470 nm (blue), 525 nm (green), 630 nm (red), and broad-spectrum (white) LED lights. Second, we found that cowbirds significantly avoided LED lights with peaks at 470 and 630 nm, but did not avoid or prefer LED lights with peaks at 380 and 525 nm or white lights.DiscussionThe two lights avoided had the highest chromatic contrast but relatively lower levels of achromatic contrast. Our approach can optimize limited resources to narrow down wavelengths of light with high visual saliency for a target species leading to avoidance. These lights can be used as candidates for visual deterrents to reduce collisions with man-made objects and vehicles. creator: Benjamin Goller creator: Bradley F. Blackwell creator: Travis L. DeVault creator: Patrice E. Baumhardt creator: Esteban Fernández-Juricic uri: https://doi.org/10.7717/peerj.5404 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Goller et al. title: De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis link: https://peerj.com/articles/5681 last-modified: 2018-09-26 description: Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis. creator: Li Li creator: Mimi Li creator: Xiwu Qi creator: Xingli Tang creator: Yifeng Zhou uri: https://doi.org/10.7717/peerj.5681 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific link: https://peerj.com/articles/5673 last-modified: 2018-09-26 description: BackgroundGastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific.MethodsWe investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene.ResultsWe found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P.  clathrata).DiscussionEnvironmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities. creator: Tomomi Ogura creator: Hiromi Kayama Watanabe creator: Chong Chen creator: Takenori Sasaki creator: Shigeaki Kojima creator: Jun-ichiro Ishibashi creator: Katsunori Fujikura uri: https://doi.org/10.7717/peerj.5673 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ogura et al. title: Tumor-preventing activity of aspirin in multiple cancers based on bioinformatic analyses link: https://peerj.com/articles/5667 last-modified: 2018-09-26 description: BackgroundAcetylsalicylic acid was renamed aspirin in 1899, and it has been widely used for its multiple biological actions. Because of the diversity of the cellular processes and diseases that aspirin reportedly affects and benefits, uncertainty remains regarding its mechanism in different biological systems.MethodsThe Drugbank and STITCH databases were used to find direct protein targets (DPTs) of aspirin. The Mentha database was used to analyze protein–protein interactions (PPIs) to find DPT-associated genes. DAVID was used for the GO and KEGG enrichment analyses. The cBio Cancer Genomics Portal database was used to mine genetic alterations and networks of aspirin-associated genes in cancer.ResultsEighteen direct protein targets (DPT) and 961 DPT-associated genes were identified for aspirin. This enrichment analysis resulted in eight identified KEGG pathways that were associated with cancers. Analysis using the cBio portal indicated that aspirin might have effects on multiple tumor suppressors, such as TP53, PTEN, and RB1 and that TP53 might play a central role in aspirin-associated genes.DiscussionThe results not only suggest that aspirin might have anti-tumor actions against multiple cancers but could also provide new directions for further research on aspirin using a bioinformatics analysis approach. creator: Diangeng Li creator: Peng Wang creator: Yi Yu creator: Bing Huang creator: Xuelin Zhang creator: Chou Xu creator: Xian Zhao creator: Zhiwei Yin creator: Zheng He creator: Meiling Jin creator: Changting Liu uri: https://doi.org/10.7717/peerj.5667 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Wind-driven spume droplet production and the transport of Pseudomonas syringae from aquatic environments link: https://peerj.com/articles/5663 last-modified: 2018-09-26 description: Natural aquatic environments such as oceans, lakes, and rivers are home to a tremendous diversity of microorganisms. Some may cross the air-water interface within droplets and become airborne, with the potential to impact the Earth’s radiation budget, precipitation processes, and spread of disease. Larger droplets are likely to return to the water or adjacent land, but smaller droplets may be suspended in the atmosphere for transport over long distances. Here, we report on a series of controlled laboratory experiments to quantify wind-driven droplet production from a freshwater source for low wind speeds. The rate of droplet production increased quadratically with wind speed above a critical value (10-m equivalent 5.7 m/s) where droplet production initiated. Droplet diameter and ejection speeds were fit by a gamma distribution. The droplet mass flux and momentum flux increased with wind speed. Two mechanisms of droplet production, bubble bursting and fragmentation, yielded different distributions for diameter, speed, and angle. At a wind speed of about 3.5 m/s, aqueous suspensions of the ice-nucleating bacterium Pseudomonas syringae were collected at rates of 283 cells m−2 s−1 at 5 cm above the water surface, and at 14 cells m−2 s−1 at 10 cm above the water surface. At a wind speed of about 4.0 m/s, aqueous suspensions of P. syringae were collected at rates of 509 cells m−2 s−1 at 5 cm above the water surface, and at 81 cells m−2 s−1 at 10 cm above the water surface. The potential for microbial flux into the atmosphere from aquatic environments was calculated using known concentrations of bacteria in natural freshwater systems. Up to 3.1 × 104 cells m−2 s−1 of water surface were estimated to leave the water in potentially suspended droplets (diameters <100 µm). Understanding the sources and mechanisms for bacteria to aerosolize from freshwater aquatic sources may aid in designing management strategies for pathogenic bacteria, and could shed light on how bacteria are involved in mesoscale atmospheric processes. creator: Renee B. Pietsch creator: Hinrich Grothe creator: Regina Hanlon creator: Craig W. Powers creator: Sunghwan Jung creator: Shane D. Ross creator: David G. Schmale III uri: https://doi.org/10.7717/peerj.5663 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Pietsch et al. title: Effect of changes in the fractal structure of a littoral zone in the course of lake succession on the abundance, body size sequence and biomass of beetles link: https://peerj.com/articles/5662 last-modified: 2018-09-26 description: Dystrophic lakes undergo natural disharmonic succession, in the course of which an increasingly complex and diverse, mosaic-like pattern of habitats evolves. In the final seral stage, the most important role is played by a spreading Sphagnum mat, which gradually reduces the lake’s open water surface area. Long-term transformations in the primary structure of lakes cause changes in the structure of lake-dwelling fauna assemblages. Knowledge of the succession mechanisms in lake fauna is essential for proper lake management. The use of fractal concepts helps to explain the character of fauna in relation to other aspects of the changing complexity of habitats. Our 12-year-long study into the succession of water beetles has covered habitats of 40 selected lakes which are diverse in terms of the fractal dimension. The taxonomic diversity and density of lake beetles increase parallel to an increase in the fractal dimension. An in-depth analysis of the fractal structure proved to be helpful in explaining the directional changes in fauna induced by the natural succession of lakes. Negative correlations appear between the body size and abundance. An increase in the density of beetles within the higher dimension fractals is counterbalanced by a change in the size of individual organisms. As a result, the biomass is constant, regardless of the fractal dimension. creator: Joanna Pakulnicka creator: Andrzej Zawal uri: https://doi.org/10.7717/peerj.5662 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Pakulnicka and Zawal title: Human dimensions of wildfires in NW Spain: causes, value of the burned vegetation and administrative measures link: https://peerj.com/articles/5657 last-modified: 2018-09-26 description: Exploring the human dimensions of forest fires is a crucial, although often overlooked, aspect of wildfire research, since wildfires often have important socio-economic impacts and humans are nowadays the main cause of wildfires in many areas of the world. We carried out a telephone survey (N = 345 interviews) in one of the most fire-prone areas in Europe (NW Spain) in order to assess citizens’ awareness about wildfire causes and risks, their perception of the value of the vegetation and of administrative measures to fight against fires. Perceptions of respondents about fire causes were in general realistic although fires caused by pyromaniacs and for profit were overestimated, while vegetation management was comparatively underestimated. Citizens were broadly aware of the fire risk associated with different vegetation types, rightly considering native oak forests and agricultural fields as less risky than shrublands and pine and eucalypt plantations. Tree-dominated vegetation was more valued than treeless formations, and native forests more than tree plantations, which seems related to a preference for ecological value over utilitarian considerations. In addition, the value of eucalypt plantations was clearly affected by the education level of respondents, being less valued as the education level increased. Most citizens considered that the administration was not doing enough to fight against fires. The law that compels landowners to reduce fuels in wildland-urban interfaces was considered effective by most respondents (72%), but 50% considered it difficult to implement by landowners. This may explain the poor degree of compliance of this law. creator: María Calviño-Cancela creator: Nuria Cañizo-Novelle uri: https://doi.org/10.7717/peerj.5657 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Calviño-Cancela and Cañizo-Novelle title: In silico study of medical decision-making for rare diseases: heterogeneity of decision-makers in a population improves overall benefit link: https://peerj.com/articles/5677 last-modified: 2018-09-25 description: BackgroundMedical decision-making is difficult when information is limited due to its rareness. For example, there are two treatment options for patients affected by a rare disease with high lethality. The information about both treatment effects is unavailable or very limited. Patients are inclined to accept one of the interventions rather than waiting for death, but they are reluctant to be assigned the inferior one. While a single patient selects one treatment that seems better based on the limited information, he or she loses the chance to select the other treatment, which may be the better option. This is the so-called dilemma between exploitation (enjoying the benefits of using current knowledge) and exploration (taking the risk to obtain new knowledge). In clinical settings, the statistical advice for individual patients seems to be the maximum expected success rate or something equivalent and patients’ selections tend to be homogeneous, which does not solve the dilemma. In this study, our aim is to investigate the effects of the heterogeneity of decision-makers in the decision process.MethodsHere, we proposed a decision strategy that introduced the heterogeneity of decision-makers by considering patients’ self-decisions where the patients’ heterogeneous attitudes towards the treatment are integrated into the probabilistic utility function based on the Beta Bayesian posterior. Based on the context of two-armed bandit treatment options with limited information, we compared the overall success rate of treatment between our heterogeneous decision strategy and a homogeneous decision strategy that is defined to select the treatment with the largest posterior mean.ResultsThe heterogeneity of decision-makers in a population improved the overall benefit of treatment under some conditions.DiscussionIn clinical settings, there exists heterogeneity of decision-making among patients. Our study investigated a targeting strategy by respecting the self-decision of all individuals and found that the heterogeneity of decision-making can improve the overall benefit under some conditions. In addition, this outperformance may suggest that heterogeneity of decision-making is of importance to human beings. Besides the ethical merit, our findings provide meaningful ideas for better strategies towards decision-making dilemmas in clinical settings for rare diseases or cases where only limited information is available. Furthermore, it is suggested to investigate the effects of heterogeneity of decision-making in other fashions, such as genetic heterogeneity and phenotypic heterogeneity. creator: Juan Wang creator: Ryo Yamada uri: https://doi.org/10.7717/peerj.5677 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang and Yamada title: High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia link: https://peerj.com/articles/5661 last-modified: 2018-09-25 description: BackgroundKnowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.MethodsWe used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.ResultsSoil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).DiscussionIn spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world’s largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity. creator: Camila D. Ritter creator: Alexander Zizka creator: Fabian Roger creator: Hanna Tuomisto creator: Christopher Barnes creator: R. Henrik Nilsson creator: Alexandre Antonelli uri: https://doi.org/10.7717/peerj.5661 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ritter et al. title: An adaptive scale Gaussian filter to explain White’s illusion from the viewpoint of lightness assimilation for a large range of variation in spatial frequency of the grating and aspect ratio of the targets link: https://peerj.com/articles/5626 last-modified: 2018-09-25 description: The variation between the actual and perceived lightness of a stimulus has strong dependency on its background, a phenomena commonly known as lightness induction in the literature of visual neuroscience and psychology. For instance, a gray patch may perceptually appear to be darker in a background while it looks brighter when the background is reversed. In the literature it is further reported that such variation can take place in two possible ways. In case of stimulus like the Simultaneous Brightness Contrast (SBC), the apparent lightness changes in the direction opposite to that of the background lightness, a phenomenon often referred to as lightness contrast, while in the others like neon colour spreading or checkerboard illusion it occurs opposite to that, and known as lightness assimilation. The White’s illusion is a typical one which according to many, does not completely conform to any of these two processes. This paper presents the result of quantification of the perceptual strength of the White’s illusion as a function of the width of the background square grating as well as the length of the gray patch. A linear filter model is further proposed to simulate the possible neurophysiological phenomena responsible for this particular visual experience. The model assumes that for the White’s illusion, where the edges are strong and quite a few, i.e., the spectrum is rich in high frequency components, the inhibitory surround in the classical Difference-of-Gaussians (DoG) filter gets suppressed, and the filter essentially reduces to an adaptive scale Gaussian kernel that brings about lightness assimilation. The linear filter model with a Gaussian kernel is used to simulate the White’s illusion phenomena with wide variation of spatial frequency of the background grating as well as the length of the gray patch. The appropriateness of the model is presented through simulation results, which are highly tuned to the present as well as earlier psychometric results. creator: Soma Mitra creator: Debasis Mazumdar creator: Kuntal Ghosh creator: Kamales Bhaumik uri: https://doi.org/10.7717/peerj.5626 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mitra et al. title: Effectiveness of winter temperatures for satisfying chilling requirements for reproductive budburst of red alder (Alnus rubra) link: https://peerj.com/articles/5221 last-modified: 2018-09-25 description: BackgroundExperiencing an adequate amount of cold temperatures over winter is necessary for many temperate tree species to break dormancy and flower in spring. Thus, changes in winter and spring temperatures associated with climate change may influence when trees break dormancy and flower in the future. There have been several experimental studies that have quantified the effectiveness of cold temperatures for chilling requirements for vegetative budburst of temperate trees; however, there are few experimental studies addressing the chilling requirements for reproductive budburst of trees, as it is difficult to place reproductively mature trees in temperature-controlled environments.MethodsTo identify how changing temperatures associated with climate change may impact reproductive phenology, we completed a temperature-controlled growth chamber experiment using cuttings of reproductive branches of red alder (Alnus rubra), one of the most widespread hardwood tree species of the Pacific Northwest, USA. The purpose of this study was to examine how colder (4 °C) and warmer (9 °C) winter temperature regimes influenced the timing of reproductive budburst of red alder cuttings in spring. We also compared the date of budburst of cuttings to that of branches from intact trees.ResultsWe found that cuttings flowered earlier after pretreatment with a 4 °C winter temperature regime than after a 9 °C winter temperature regime. We found no significant differences between the timing of male budburst of cuttings exposed to ambient conditions compared to male budburst of branches from intact trees. We used our experimental data to estimate a “possibility-line” that shows the accumulated chilling and forcing temperatures necessary prior to reproductive budburst of red alder.DiscussionThis study provides a preliminary indication that warmer winters with climate change may not be as effective as colder winters for satisfying chilling temperature requirements of a Northwest hardwood tree species. creator: Janet S. Prevéy creator: Constance A. Harrington uri: https://doi.org/10.7717/peerj.5221 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors link: https://peerj.com/articles/5068 last-modified: 2018-09-25 description: BackgroundDengue fever has rapidly manifested into a serious global health concern. The emergence of various viral serotypes has prompted the urgent need for innovative drug design techniques. Of the viral non-structural enzymes, the NS5 RNA-dependent RNA polymerase has been established as a promising target due to its lack of an enzymatic counterpart in mammalian cells and its conserved structure amongst all serotypes. The onus is now on scientists to probe further into understanding this enzyme and its mechanism of action. The field of bioinformatics has evolved greatly over recent decades, with updated drug design tools now being publically available.MethodsIn this study, bioinformatics tools were used to provide a comprehensive sequence and structural analysis of the two most prominent serotypes of Dengue RNA-dependent RNA polymerase. A list of popular flavivirus inhibitors were also chosen to dock to the active site of the enzyme. The best docked compound was then used as a template to generate a pharmacophore model that may assist in the design of target-specific Dengue virus inhibitors.ResultsComparative sequence alignment exhibited similarity between all three domains of serotype 2 and 3.Sequence analysis revealed highly conserved regions at residues Meth530, Thr543 Asp597, Glu616, Arg659 and Pro671. Mapping of the active site demonstrated two highly conserved residues: Ser710 and Arg729. Of the active site interacting residues, Ser796 was common amongst all ten docked compounds, indicating its importance in the drug design process. Of the ten docked flavivirus inhibitors, NITD-203 showed the best binding affinity to the active site. Further pharmacophore modeling of NITD-203 depicted significant pharmacophoric elements that are necessary for stable binding to the active site.DiscussionThis study utilized publically available bioinformatics tools to provide a comprehensive framework on Dengue RNA-dependent RNA polymerase. Based on docking studies, a pharmacophore model was also designed to unveil the crucial pharmacophoric elements that are required when constructing an efficacious DENV inhibitor. We believe that this study will be a cornerstone in paving the road toward the design of target-specific inhibitors against DENV RdRp. creator: Nomagugu B. Nncube creator: Pritika Ramharack creator: Mahmoud E.S. Soliman uri: https://doi.org/10.7717/peerj.5068 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Nncube et al. title: Plurality in multi-disciplinary research: multiple institutional affiliations are associated with increased citations link: https://peerj.com/articles/5664 last-modified: 2018-09-24 description: BackgroundThe institutional affiliations and associated collaborative networks that scientists foster during their research careers are salient in the production of high-quality science. The phenomenon of multiple institutional affiliations and its relationship to research output remains relatively unexplored in the literature.MethodsWe examined 27,612 scientific articles, modelling the normalized citation counts received against the number of authors and affiliations held.ResultsIn agreement with previous research, we found that teamwork is an important factor in high impact papers, with average citations received increasing concordant with the number of co-authors listed. For articles with more than five co-authors, we noted an increase in average citations received when authors with more than one institutional affiliation contributed to the research.DiscussionMultiple author affiliations may play a positive role in the production of high-impact science. This increased researcher mobility should be viewed by institutional boards as meritorious in the pursuit of scientific discovery. creator: Paul Sanfilippo creator: Alex W. Hewitt creator: David A. Mackey uri: https://doi.org/10.7717/peerj.5664 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sanfilippo et al. title: Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation link: https://peerj.com/articles/5648 last-modified: 2018-09-24 description: Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems. creator: Jiayu Li creator: Jiayi Lin creator: Chenyu Pei creator: Kaitao Lai creator: Thomas C. Jeffries creator: Guangda Tang uri: https://doi.org/10.7717/peerj.5648 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Successful transplantation of guinea pig gut microbiota in mice and its effect on pneumonic plague sensitivity link: https://peerj.com/articles/5637 last-modified: 2018-09-24 description: Microbiota-driven variations in the inflammatory response are predicted to regulate host responses to infection. Increasing evidence indicates that the gastrointestinal and respiratory tracts have an intimate relationship with each other. Gut microbiota can influence lung immunity whereby gut-derived injurious factors can reach the lungs and systemic circulation via the intestinal lymphatics. The intestinal microbiota’s ability to resist colonization can be extended to systemic infections or to pathogens infecting distant sites such as the lungs. Unlike the situation with large mammals, the microtus Yersinia pestis 201 strain exhibits strong virulence in mice, but nearly no virulence to large mammals (such as guinea pigs). Hence, to assess whether the intestinal microbiota from guinea pigs was able to affect the sensitivity of mice to challenge infection with the Y. pestis 201 strain, we fed mice with guinea pig diets for two months, after which they were administered 0.5 ml of guinea pig fecal suspension for 30 days by oral gavage. The stools from each mouse were collected on days 0, 15, and 30, DNA was extracted from them, and 16S rRNA sequencing was performed to assess the diversity and composition of the gut microbiota. We found that the intestinal microbiota transplants from the guinea pigs were able to colonize the mouse intestines. The mice were then infected with Yersinia pestis 201 by lung invasion, but no statistical difference was found in the survival rates of the mice that were colonized with the guinea pig’s gut microbiota and the control mice. This indicates that the intestinal microbiota transplantation from the guinea pigs did not affect the sensitivity of the mice to pneumonic plague. creator: Xiang Li creator: Zhengchao Li creator: Yuxiao Chang creator: Fengyi Hou creator: Zongyu Huang creator: Han Ni creator: Ruifu Yang creator: Yujing Bi uri: https://doi.org/10.7717/peerj.5637 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Different environmental gradients affect different measures of snake β-diversity in the Amazon rainforests link: https://peerj.com/articles/5628 last-modified: 2018-09-24 description: Mechanisms generating and maintaining biodiversity at regional scales may be evaluated by quantifying β-diversity along environmental gradients. Differences in assemblages result in biotic complementarities and redundancies among sites, which may be quantified through multi-dimensional approaches incorporating taxonomic β-diversity (TBD), functional β-diversity (FBD) and phylogenetic β-diversity (PBD). Here we test the hypothesis that snake TBD, FBD and PBD are influenced by environmental gradients, independently of geographic distance. The gradients tested are expected to affect snake assemblages indirectly, such as clay content in the soil determining primary production and height above the nearest drainage determining prey availability, or directly, such as percentage of tree cover determining availability of resting and nesting sites, and climate (temperature and precipitation) causing physiological filtering. We sampled snakes in 21 sampling plots, each covering five km2, distributed over 880 km in the central-southern Amazon Basin. We used dissimilarities between sampling sites to quantify TBD, FBD and PBD, which were response variables in multiple-linear-regression and redundancy analysis models. We show that patterns of snake community composition based on TBD, FBD and PBD are associated with environmental heterogeneity in the Amazon. Despite positive correlations between all β-diversity measures, TBD responded to different environmental gradients compared to FBD and PBD. Our findings suggest that multi-dimensional approaches are more informative for ecological studies and conservation actions compared to a single diversity measure. creator: Rafael de Fraga creator: Miquéias Ferrão creator: Adam J. Stow creator: William E. Magnusson creator: Albertina P. Lima uri: https://doi.org/10.7717/peerj.5628 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 de Fraga et al. title: Identification of an aquaculture poriferan “Pest with Potential” and its phylogenetic implications link: https://peerj.com/articles/5586 last-modified: 2018-09-24 description: Correct identification and classification of sponges is challenging due to ambiguous or misleading morphological features. A particular case is a blue keratose sponge occasionally referred to as the “Blue Photo Sponge” among aquarists, which appears frequently (and in several cases unintended) in private aquaria. This spicule-less species, occasionally specified as Collospongia auris Bergquist, Cambie & Kernan 1990, not only displays a high phenotypic plasticity in growth form and colour, it also proliferates in aquacultures under standard conditions unlike most other sponges. Therefore, this species is regarded as a pest for most aquarists. In turn, the ease of cultivation and propagation in aquacultures qualifies this species as a model organism for a wide array of scientific applications. For these purposes, correct identification and classification are indispensable. We reconstructed ribosomal gene trees and determined this species as Lendenfeldia chondrodes (De Laubenfels, 1954) (Phyllospongiinae), distant to Collospongia auris, and corroborated by skeletal features. Additionally, the resulting phylogeny corroborated major shortcomings of the current Phyllospongiinae classification—its consequences are discussed. creator: Adrian Galitz creator: Steve de C. Cook creator: Merrick Ekins creator: John N. A. Hooper creator: Peter T. Naumann creator: Nicole J. de Voogd creator: Muhammad Abdul Wahab creator: Gert Wörheide creator: Dirk Erpenbeck uri: https://doi.org/10.7717/peerj.5586 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Galitz et al. title: Morphometric traits in the fine-leaved fescues depend on ploidy level: the case of Festuca amethystina L. link: https://peerj.com/articles/5576 last-modified: 2018-09-24 description: BackgroundPolyploid specimens are usually characterized by greater exuberance: they reach larger sizes and/or have a larger number of some organs. Festuca amethystina L. belongs to the section Aulaxyper. Based on morphological features, four subspecies of F. amethystina have been already identified. On the other hand, it has two cytotypes: diploid and tetraploid. The main aim of our study was to distinguish morphological differences between the cytotypes of F. amethystina, assuming that its phenotype differs significantly.MethodsThe nuclear DNA content was measured by flow cytometry in dry leaves from specimens originating from 13 populations of F. amethystina. Several macrometric and micrometric traits of stems, spikelets and leaf blades were taken into account in the comparative analysis of two cytotypes.ResultsIn the case of cytotypes, specimens of tetraploids were larger than diploids. The conducted morphometric analysis of leaf cross-sections showed significant differences between the cytotypes.DiscussionThe research has confirmed for the first time that in the case of F. amethystina the principle of greater exuberance of polyploids is true. Differences between the cytotypes are statistically significant, however, they are not enough to make easy the distinction of cytotypes on the basis of the measurements themselves. Our findings favor the rule known in Festuca taxonomy as a whole, i.e. that the ploidy level can be one of the main classification criteria. creator: Agnieszka Rewicz creator: Przemysław Piotr Tomczyk creator: Marcin Kiedrzyński creator: Katarzyna Maria Zielińska creator: Iwona Jędrzejczyk creator: Monika Rewers creator: Edyta Kiedrzyńska creator: Tomasz Rewicz uri: https://doi.org/10.7717/peerj.5576 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rewicz et al. title: Population genetics of the main population of brown bears in southwest Asia link: https://peerj.com/articles/5660 last-modified: 2018-09-21 description: Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kaçkar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroductions in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus. creator: Hüseyin Ambarlı creator: Deniz Mengüllüoğlu creator: Jörns Fickel creator: Daniel W. Förster uri: https://doi.org/10.7717/peerj.5660 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ambarlı et al. title: A secretory hexokinase plays an active role in the proliferation of Nosema bombycis link: https://peerj.com/articles/5658 last-modified: 2018-09-21 description: The microsporidian Nosema bombycis is an obligate intracellular parasite of Bombyx mori, that lost its intact tricarboxylic acid cycle and mitochondria during evolution but retained its intact glycolysis pathway. N. bombycis hexokinase (NbHK) is not only a rate-limiting enzyme of glycolysis but also a secretory protein. Indirect immunofluorescence assays and recombinant HK overexpressed in BmN cells showed that NbHK localized in the nucleus and cytoplasm of host cell during the meront stage. When N. bombycis matured, NbHK tended to concentrate at the nuclei of host cells. Furthermore, the transcriptional profile of NbHK implied it functioned during N. bombycis’ proliferation stages. A knock-down of NbHK effectively suppressed the proliferation of N. bombycis indicating that NbHK is an important protein for parasite to control its host. creator: Yukang Huang creator: Shiyi Zheng creator: Xionge Mei creator: Bin Yu creator: Bin Sun creator: Boning Li creator: Junhong Wei creator: Jie Chen creator: Tian Li creator: Guoqing Pan creator: Zeyang Zhou creator: Chunfeng Li uri: https://doi.org/10.7717/peerj.5658 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Huang et al. title: Does Twitter language reliably predict heart disease? A commentary on Eichstaedt et al. (2015a) link: https://peerj.com/articles/5656 last-modified: 2018-09-21 description: We comment on Eichstaedt et al.’s (2015a) claim to have shown that language patterns among Twitter users, aggregated at the level of US counties, predicted county-level mortality rates from atherosclerotic heart disease (AHD), with “negative” language being associated with higher rates of death from AHD and “positive” language associated with lower rates. First, we examine some of Eichstaedt et al.’s apparent assumptions about the nature of AHD, as well as some issues related to the secondary analysis of online data and to considering counties as communities. Next, using the data files supplied by Eichstaedt et al., we reproduce their regression- and correlation-based models, substituting mortality from an alternative cause of death—namely, suicide—as the outcome variable, and observe that the purported associations between “negative” and “positive” language and mortality are reversed when suicide is used as the outcome variable. We identify numerous other conceptual and methodological limitations that call into question the robustness and generalizability of Eichstaedt et al.’s claims, even when these are based on the results of their ridge regression/machine learning model. We conclude that there is no good evidence that analyzing Twitter data in bulk in this way can add anything useful to our ability to understand geographical variation in AHD mortality rates. creator: Nicholas J.L. Brown creator: James C. Coyne uri: https://doi.org/10.7717/peerj.5656 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brown and Coyne title: How much genetic variation is stored in the endangered and fragmented shrub Tetraena mongolica Maxim? link: https://peerj.com/articles/5645 last-modified: 2018-09-21 description: Tetraena mongolica Maxim (Zygophyllaceae) is an endangered species endemic to western Inner Mongolia and China, and is currently threatened by habitat loss and human over-exploitation. We explored the genetic background, its genetic diversity, population structure, and demographic history, based on 12 polymorphic nuclear microsatellite loci. Our results indicated high genetic diversity in extant populations, but no distinguishable gene cluster corresponding with a specific biogeography. Population demography analysis using a MSVAR indicated a strong, recent population decline approximately 5,455 years ago. These results suggest that the Yellow River and Zhuozi Mountain range may not prevent pollination between populations. Finally, we surmised that the population demography of T. mongolica was likely to have been affected by early mankind activities. creator: Yingbiao Zhi creator: Zhonglou Sun creator: Ping Sun creator: Kai Zhao creator: Yangnan Guo creator: Dejian Zhang creator: Baowei Zhang uri: https://doi.org/10.7717/peerj.5645 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhi et al. title: Short-tailed mice with a long fossil record: the genus Leggadina (Rodentia: Muridae) from the Quaternary of Queensland, Australia link: https://peerj.com/articles/5639 last-modified: 2018-09-21 description: The genus Leggadina (colloquially known as ‘short-tailed mice’) is a common component of Quaternary faunas of northeastern Australia. They represent a member of the Australian old endemic murid radiation that arrived on the continent sometime during the late Cenozoic. Here we describe two new species of extinct Leggadina from Quaternary cave deposits as well as additional material of the extinct Leggadina macrodonta. Leggadina irvini sp. nov. recovered from Middle-Upper (late) Pleistocene cave deposits near Chillagoe, northeastern Queensland, is the biggest member of the genus, being substantially larger than any other species so far described. Leggadina webbi sp. nov. from Middle Pleistocene cave deposits at Mount Etna, central eastern Queensland, shares features with the oldest species of the genus, the Early Pleistocene L. gregoriensis. Based on the current palaeoecological interpretation of the type locality, L. webbi, represents the only member of the genus that inhabited rainforest. The succession of Leggadina species through the late Quaternary suggests an ecological replacement of the extinct large-bodied L. irvini with the extant, small-bodied L. lakedownesis at Chillagoe. At Mt. Etna, the extinct rainforest species L. webbi is replaced with the extant xeric-adapted L. forresti during the latest Middle Pleistocene. This replacement is associated with a mid-Pleistocene shift towards progressive intensifying seasonal and arid climates. Our study adds to the growing list of small-bodied faunal extinctions during the late Quaternary of northern Australia. creator: Jonathan Cramb creator: Gilbert J. Price creator: Scott A. Hocknull uri: https://doi.org/10.7717/peerj.5639 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cramb et al. title: Interleukin 35 induced Th2 and Tregs bias under normal conditions in mice link: https://peerj.com/articles/5638 last-modified: 2018-09-21 description: ObjectiveThe benefits of IL-35 treatment have been verified in multiple animal models of diseases, while its influence on T cells immunity under normal condition still needs to be elucidated. The present study was designed to investigate the effects modulating IL-35 levels in vivo and in vitro on T cells, response and also the effects on T cells subsets in normal mice.MethodsA plasmid pMSCV-IL-35-GFP carrying mouse linear IL-35 fragment with two subunits joint together was constructed and the heterodimer expression was confirmed. Normal mice were randomly divided into three groups and received an intravenous injection of PBS, pMSCV-GFP and pMSCV-IL-35-GFP respectively. After 72 h, spleen tissues and peripheral blood were harvested for following analysis. Meanwhile, splenic T cells were isolated and incubated with 10, 30, or 50 ng/mL recombinant IL-35 factor for 24 h with the addition of anti-CD3/CD28 in vitro. T-cell subsets were assessed by Fluorescence activated cell sorting (FACS) and related cytokines together with effector molecules were determined by real time PCR.ResultsWestern blotting confirmed a 52 kDa band in the cell lysate of HEK 293T transducted with pMSCV-IL-35-GFP plasmid, indicating a successful expression of IL-35. Ebi3 and IL-12A, two subunits of IL-35, could be identified 72 h post DNA injection. IL-35 upregulation in vivo effectively inhibit CD4+ and CD8+ T cell proliferation and Th1 cytokine secretion. Effector molecules of CD8+ T cells were also remarkably suppressed. On the contrary, high level of IL-35 significantly induced CD4+ CD25+ Tregs and Th2 enhancement. The in vitro study provided similar results.ConclusionThe results indicated Th1 and CD8+ T cell inhibition and Th2 and Tregs bias in the presence of IL-35 under a normal state which partly contributed to its therapeutic potential. creator: Xiaoning Zhang creator: Zhiqiang Zhang creator: Zhiqiang He creator: Mingyan Ju creator: Jiaci Li creator: Jinghua Yuan creator: Yaqing Jing creator: Keqiu Li creator: Yi Liu creator: Guang Li uri: https://doi.org/10.7717/peerj.5638 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Plant dominance in a subalpine montane meadow: biotic vs. abiotic controls of subordinate diversity within and across sites link: https://peerj.com/articles/5619 last-modified: 2018-09-21 description: BackgroundUnderstanding the underlying factors that determine the relative abundance of plant species is critical to predict both biodiversity and ecosystem function. Biotic and abiotic factors can shape the distribution and the relative abundance of species across natural communities, greatly influencing local biodiversity.MethodsUsing a combination of an observational study and a five-year plant removal experiment we: (1) documented how plant diversity and composition of montane meadow assemblages vary along a plant dominance gradient using an observational study; (2) tracked above- and belowground functional traits of co-dominant plant species Potentilla and Festuca along a plant dominance gradient in an observational study; (3) determined whether plant species diversity and composition was directly influenced by commonly occurring species Potentilla and Festuca with the use of a randomized plot design, 5-year plant removal experiment (no removal control, Potentilla removed, Festuca removed, n = 10).ResultsWe found that subordinate species diversity and compositional dissimilarity were greatest in Potentilla and Festuca co-dominated sites, where neither Potentilla nor Festuca dominated, rather than at sites where either species became dominant. Further, while above- and belowground plant functional traits varied along a dominance gradient, they did so in a way that inconsistently predicted plant species relative abundance. Also, neither variation in plant functional traits of Festuca and Potentilla nor variation in resources and conditions (such as soil nitrogen and temperature) explained our subordinate diversity patterns. Finally, neither Potentilla nor Festuca influenced subordinate diversity or composition when we directly tested for their impacts in a plant removal experiment.DiscussionTaken together, patterns of subordinate diversity and composition were likely driven by abiotic factors rather than biotic interactions. As a result, the role of abiotic factors influencing local-level species interactions can be just as important as biotic interactions themselves in structuring plant communities. creator: Erika LaPlante creator: Lara Souza uri: https://doi.org/10.7717/peerj.5619 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 LaPlante and Souza title: Improving remote estimation of winter crops gross ecosystem production by inclusion of leaf area index in a spectral model link: https://peerj.com/articles/5613 last-modified: 2018-09-21 description: The hysteresis of the seasonal relationships between vegetation indices (VIs) and gross ecosystem production (GEP) results in differences between these relationships during vegetative and reproductive phases of plant development cycle and may limit their applicability for estimation of croplands productivity over the entire season. To mitigate this problem and to increase the accuracy of remote sensing-based models for GEP estimation we developed a simple empirical model where greenness-related VIs are multiplied by the leaf area index (LAI). The product of this multiplication has the same seasonality as GEP, and specifically for vegetative periods of winter crops, it allowed the accuracy of GEP estimations to increase and resulted in a significant reduction of the hysteresis of VIs vs. GEP. Our objective was to test the multiyear relationships between VIs and daily GEP in order to develop more general models maintaining reliable performance when applied to years characterized by different climatic conditions. The general model parametrized with NDVI and LAI product allowed to estimate daily GEP of winter and spring crops with an error smaller than 14%, and the rate of GEP over- (for spring barley) or underestimation (for winter crops and potato) was smaller than 25%. The proposed approach may increase the accuracy of crop productivity estimation when greenness VIs are saturating early in the growing season. creator: Radosław Juszczak creator: Bogna Uździcka creator: Marcin Stróżecki creator: Karolina Sakowska uri: https://doi.org/10.7717/peerj.5613 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Juszczak et al. title: Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes link: https://peerj.com/articles/5603 last-modified: 2018-09-21 description: BackgroundDenitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab.MethodsBioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5.ResultsThe bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h).DiscussionM. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments. creator: Cíntia Carreira creator: Olga Mestre creator: Rute F. Nunes creator: Isabel Moura creator: Sofia R. Pauleta uri: https://doi.org/10.7717/peerj.5603 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Carreira et al. title: The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies link: https://peerj.com/articles/5152 last-modified: 2018-09-21 description: BackgroundAnalyses of the control region sequences of European brown trout populations’ mitrochondrial DNA have revealed five main evolutionary lineages (Atlantic, Danubian, Mediterranean, Adriatic, Marble) mostly relating to the main water basins; however, the hybridization between lineages were increasingly reported. Due to the hydrogeography of Hungary, wild populations should theoretically belong to the Danubian lineage, however, this has not been verified by genetic studies.MethodsIn our study multiple molecular marker sets (mitochondrial sequence, microsatellites, PCR-RFLP of nuclear markers and sex marker) were used to investigate the genetic composition and population genetics of the brown trout populations in two broodstocks, six wild streams in Hungary and one Serbian population.ResultsThe admixture of Atlantic and Danubian lineages in these populations, except the Serbian population with pure Danubian origin, was observed by control region sequences of mitochondrial DNA and PCR-RFLP markers in the nuclear genome, and one unpublished Danubian haplotype was found in Hungarian populations. A sex-specific marker revealed equal gender ratio in broodstocks and Kemence stream, whereas in other wild streams the proportion of female individuals were less than 50%. Structure and principal component analyses based on the alleles of microsatellite loci also revealed overlapping populations, however the populations were still significantly different from each other and were mostly in Hardy-Weinberg equilibrium.DiscussionStocking and migration can have a significant genetic impact on trout populations of wild streams, however there are no guidelines or common practices for stocking of small streams in Hungary, thus the genetic background of these populations should be considered when developing conservation actions. creator: Ágnes Ősz creator: Ákos Horváth creator: György Hoitsy creator: Dóra Kánainé Sipos creator: Szilvia Keszte creator: Anna Júlia Sáfrány creator: Saša Marić creator: Csaba Palkó creator: Balázs Tóth creator: Béla Urbányi creator: Balázs Kovács uri: https://doi.org/10.7717/peerj.5152 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ősz et al. title: Characterization of retinal regeneration in adult zebrafish following multiple rounds of phototoxic lesion link: https://peerj.com/articles/5646 last-modified: 2018-09-20 description: Müller glia in the zebrafish retina respond to retinal damage by re-entering the cell cycle, which generates large numbers of retinal progenitors that ultimately replace the lost neurons. In this study we compared the regenerative outcomes of adult zebrafish exposed to one round of phototoxic treatment with adult zebrafish exposed to six consecutive rounds of phototoxic treatment. We observed that Müller glia continued to re-enter the cell cycle to produce clusters of retinal progenitors in zebrafish exposed to multiple rounds of phototoxic light. Some abnormalities were noted, however. First, we found that retinas exposed to multiple rounds of damage exhibited a greater loss of photoreceptors at 36 hours of light damage than retinas that were exposed to their first round of light damage. In addition, we found that Müller glia appeared to have an increase in the acute gliotic response in retinas exposed to multiple rounds of light treatment. This was evidenced by cellular hypertrophy, changes in GFAP cellular localization, and transient increases in stat3 and gfap expression. Finally, following the sixth round of phototoxic lesion, we observed a significant increase in mis-localized HuC/D-positive amacrine and ganglion cells in the inner plexiform layer and outer retina, and a decreased number of regenerated blue cone photoreceptors. These data add to recent findings that retinal regeneration in adult zebrafish occurs concomitant with Müller glia reactivity and can result in the generation of aberrant neurons. These data are also the first to demonstrate that Müller glia appear to modify their phenotype in response to multiple rounds of phototoxic lesion, exhibiting an increase in acute gliosis while maintaining a remarkable capacity for long-term regeneration of photoreceptors. creator: Alexandra H. Ranski creator: Ashley C. Kramer creator: Gregory W. Morgan creator: Jennifer L. Perez creator: Ryan Thummel uri: https://doi.org/10.7717/peerj.5646 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ranski et al. title: Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding link: https://peerj.com/articles/5641 last-modified: 2018-09-20 description: Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor. creator: Aimee L. van der Reis creator: Olivier Laroche creator: Andrew G. Jeffs creator: Shane D. Lavery uri: https://doi.org/10.7717/peerj.5641 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 van der Reis et al. title: An examination of the Devonian fishes of Michigan link: https://peerj.com/articles/5636 last-modified: 2018-09-20 description: We surveyed the taxa, ecosystems, and localities of the Devonian fishes of Michigan to provide a framework for renewed study, to learn about the diversity and number of these fishes, and to investigate their connection to other North American faunas. Nineteen genera of fishes have been found in the Middle and Late Devonian deposits of Michigan, of which thirteen are ‘placoderms’ represented by material ranging from articulated head shields to ichthyoliths. As expected from the marine nature of these deposits, ‘placoderms’ are overwhelmingly arthrodire in nature, but two genera of ptyctodonts have been reported along with less common petalichthyid material. The remaining fish fauna consists of fin-spines attributed to ‘acanthodians’, two genera of potential crown chondrichthyans, an isolated dipnoan, and onychodont teeth/jaw material. There was an apparent drop in fish diversity and fossil abundance between Middle and Late Devonian sediments. This pattern may be attributed to a paucity of Late Devonian sites, along with a relative lack of recent collection efforts at existing outcrops. It may also be due to a shift towards open water pelagic environments at Late Devonian localities, as opposed to the nearshore reef fauna preserved in the more numerous Middle Devonian localities. The Middle Devonian vertebrate fauna in Michigan shows strong connections with same-age assemblages from Ohio and New York. Finally, we document the presence of partially articulated vertebrate remains associated with benthic invertebrates, an uncommon occurrence in Devonian strata outside of North America. We anticipate this new survey will guide future field work efforts in an undersampled yet highly accessible region that preserves an abundance of fishes from a critical interval in marine vertebrate evolution. creator: Jack Stack creator: Lauren Sallan uri: https://doi.org/10.7717/peerj.5636 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Stack and Sallan title: Gαq and Phospholipase Cβ signaling regulate nociceptor sensitivity in Drosophila melanogaster larvae link: https://peerj.com/articles/5632 last-modified: 2018-09-20 description: Drosophila melanogaster larvae detect noxious thermal and mechanical stimuli in their environment using polymodal nociceptor neurons whose dendrites tile the larval body wall. Activation of these nociceptors by potentially tissue-damaging stimuli elicits a stereotyped escape locomotion response. The cellular and molecular mechanisms that regulate nociceptor function are increasingly well understood, but gaps remain in our knowledge of the broad mechanisms that control nociceptor sensitivity. In this study, we use cell-specific knockdown and overexpression to show that nociceptor sensitivity to noxious thermal and mechanical stimuli is correlated with levels of Gαq and phospholipase Cβ signaling. Genetic manipulation of these signaling mechanisms does not result in changes in nociceptor morphology, suggesting that changes in nociceptor function do not arise from changes in nociceptor development, but instead from changes in nociceptor activity. These results demonstrate roles for Gαq and phospholipase Cβ signaling in facilitating the basal sensitivity of the larval nociceptors to noxious thermal and mechanical stimuli and suggest future studies to investigate how these signaling mechanisms may participate in neuromodulation of sensory function. creator: Joshua A. Herman creator: Adam B. Willits creator: Andrew Bellemer uri: https://doi.org/10.7717/peerj.5632 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Herman et al. title: Gap analysis and implications for seasonal management on a local scale link: https://peerj.com/articles/5622 last-modified: 2018-09-20 description: BackgroundIdentifying biodiversity hotspots on a local scale, using multiple data sources, and ecological niche modeling, has the potential to contribute to more effective nature reserve management.MethodsIn this study, we used infrared-triggered camera trapping, field surveys, and interviews to create a dataset on the distribution of species (mammals and birds) in Hebei Wulingshan Nature Reserve (Hebei Province, China).ResultsWe identified 101 species (14 orders, 38 families), 64 of which (2,142 effective records) were selected for environmental niche modeling. All results were reclassified into three groups: “priority areas” (areas including the potential distributions of over 80% of species), “important areas” (those with 50% of species), and “normal areas” (all other areas). Our results show that priority areas (1.31–1.82 km2) and important areas (7.73–21.44 km2) for conservation were mainly covered by the core and experimental zones of the reserve; additionally, a kilometer-wide margin around the outside of the nature reserve seems to be important to maintaining biodiversity.DiscussionWe close by suggesting some actions for enhancing conservation of biodiversity in the reserve, including monitoring, strengthen law enforcements, introducing popular science, and co-operating with local people. creator: Li Yang creator: Baofeng Zhang creator: Xinrui Wang creator: Yueheng Ren creator: Jinlin Chen creator: Chao Zhang creator: Yongpeng Xia creator: Yuankun Li creator: Jianguo Sun creator: Jiangang Guo creator: Weijia Wang creator: XiaoFeng Luan uri: https://doi.org/10.7717/peerj.5622 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yang et al. title: Effect of floods on the δ13C values in plant leaves: a study of willows in Northeastern Siberia link: https://peerj.com/articles/5374 last-modified: 2018-09-20 description: Although stable carbon isotopic composition (δ13C) of plants has been widely used to indicate different water regimes in terrestrial ecosystems over the past four decades, the changes in the plant δ13C value under waterlogging have not been sufficiently clarified. With the enhanced global warming in recent years, the increasing frequency and severity of river floods in Arctic regions lead to more waterlogging on willows that are widely distributed in river lowland. To investigate the δ13C changes in plants under different water conditions (including waterlogging), we measured the δ13C values in the leaves of willows with three species, Salix boganidensis, S. glauca, and S. pulchra, and also monitored changes in plant physiology, under several major flooding conditions in Northeastern Siberia. The foliar δ13C values of willows varied, ranging from −31.6 to −25.7‰ under the different hydrological status, which can be explained by: (i) under normal conditions, the foliar δ13C values decrease from dry (far from a river) to wet (along a river bank) areas; (ii) the δ13C values increase in frequently waterlogged areas owing to stomatal closure; and (iii) after prolonged flooding periods, the δ13C values again decrease, probably owing to the effects of not only the closure of stomata but also the reduction of foliar photosynthetic ability under long period of waterlogging. Based on these results, we predict that plant δ13C values are strongly influenced by plant physiological responses to diverse hydrological conditions, particularly the long periods of flooding, as occurs in Arctic regions. creator: Rong Fan creator: Tomoki Morozumi creator: Trofim C. Maximov creator: Atsuko Sugimoto uri: https://doi.org/10.7717/peerj.5374 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Fan et al. title: Spatial and temporal variations of aridity shape dung beetle assemblages towards the Sahara desert link: https://peerj.com/articles/5210 last-modified: 2018-09-20 description: BackgroundAssemblage responses to environmental gradients are key to understand the general principles behind the assembly and functioning of communities. The spatially and temporally uneven distribution of water availability in drylands creates strong aridity gradients. While the effects of spatial variations of aridity are relatively well known, the influence of the highly-unpredictable seasonal and inter-annual precipitations on dryland communities has been seldom addressed.AimsHere, we study the seasonal and inter-annual responses of dung beetle (Coleoptera, Scarabaeidae) communities to the variations of water availability along a semiarid region of the Mediterranean.MethodsWe surveyed a 400 km linear transect along a strong aridity gradient from the Mediterranean coast to the Sahara (Eastern Morocco), during four sampling campaigns: two in the wet season and two in the dry season. We measured species richness, abundance and evenness. Variations in community composition between sites, seasons and years were assessed through beta diversity partitioning of dissimiliarity metrics based on species occurrences and abundances. The effects of climate, soil, vegetation and dung availability were evaluated using Spearman-rank correlations, general linear regressions and partial least-squares generalized linear regressions for community structure, and non-metric multi-dimensional scaling, Permutational Analysis of Variance (PERMANOVA) and distance-based RDA variation partitioning for compositional variations.ResultsDung beetle abundance and species richness showed large seasonal variations, but remained relatively similar between years. Indeed, aridity and its interaction with season and year were the strongest correlates of variations in species richness and composition. Increasing aridity resulted in decreasing species richness and an ordered replacement of species, namely the substitution of the Mediterranean fauna by desert assemblages dominated by saprophagous and generalist species both in space towards the Sahara and in the dry season.DiscussionOur study shows that aridity determines composition in dung beetle communities, filtering species both in space and time. Besides the expected decrease in species richness, such environmental filtering promotes a shift towards generalist and saprophagous species in arid conditions, probably related to changes in resource quality along the transect and through the year. Our results highlight the importance of considering the effects of the highly-unpredictable seasonal and inter-annual variations in precipitation when studying dryland communities. creator: Indradatta deCastro-Arrazola creator: Joaquín Hortal creator: Marco Moretti creator: Francisco Sánchez-Piñero uri: https://doi.org/10.7717/peerj.5210 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 deCastro-Arrazola et al. title: Inflammation-based prognostic scores predict the prognosis of locally advanced cervical esophageal squamous cell carcinoma patients receiving curative concurrent chemoradiotherapy: a propensity score-matched analysis link: https://peerj.com/articles/5655 last-modified: 2018-09-19 description: IntroductionThe present study investigated the crucial role of inflammation-based prognostic scores in locally advanced cervical esophageal squamous cell carcinoma (ESCC) patients who underwent curative concurrent chemoradiotherapy (CCRT).MethodsThere were 411 ESCC patients enrolled, including 63 cervical ESCC patients. Using the propensity score matching method, 63 thoracic ESCC patients were matched to the 63 cervical ESCC patients. The inflammation-based prognostic scores included the neutrophil lymphocyte ratio (NLR), platelet lymphocyte ratio (PLR), albumin level, c-reactive protein (CRP) level, modified Glasgow prognostic score (mGPS), and CRP/albumin ratio. The chi-square test and Kaplan–Meier method were used for categorical variable data and overall survival, respectively. A Cox regression model was performed for univariate and multivariable analyses.ResultsWith respect to cervical ESCC, NLR ≥ 2.5 (P = 0.019), PLR ≥ 103 (P = 0.013), CRP value >10 mg/l (P = 0.040), mGPS ≥ 1 (P = 0.040), and CRP/albumin ratio ≥ 9.5 (P = 0.033) were significant predictors of worse overall survival (OS) in the univariate analysis. In a multivariable analysis, PLR ≥ 103 (P = 0.010, HR: 2.66, 95% CI [1.27–5.58]) and mGPS ≥ 1 (P = 0.030, HR: 2.03, 95% CI [1.07–3.86]) were the independent prognostic parameters of worse OS. The prognostic value of these biomarkers in the matched thoracic ESCC patients was similar and compatible with the results in the cervical ESCC group in the univariate and multivariable analyses.ConclusionsOur study suggests that these inflammation-based prognostic scores are helpful in clinical practice, and PLR and mGPS may predict the prognosis for locally advanced cervical ESCC patients who receive curative CCRT. creator: Chia-Che Wu creator: Shau-Hsuan Li creator: Hung-I Lu creator: Chien-Ming Lo creator: Yu-Ming Wang creator: Shang-Yu Chou creator: Yen-Hao Chen uri: https://doi.org/10.7717/peerj.5655 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wu et al. title: Discovery of two skin-derived dermaseptins and design of a TAT-fusion analogue with broad-spectrum antimicrobial activity and low cytotoxicity on healthy cells link: https://peerj.com/articles/5635 last-modified: 2018-09-19 description: Two novel peptides belonging to the dermaseptin family, namely DRS-CA-1 and DRS-DU-1, were encoded from cDNA libraries derived from the skin secretions of Phyllomedusa camba and Callimedusa (Phyllomedusa) duellmani. Both natural peptides are highly-conserved and exhibited high potency against wild-type Gram-positive, Gram-negative bacteria, yeast and antibiotic-resistant bacteria (MRSA and Pseudomonas aeruginosa) (MICs 4–8 µM) with no obvious hemolytic activity. Collectively these results suggest that both peptides may have potential as novel antibiotics. Additionally, DRS-DU-1 exhibited selective cytotoxicity to tumor cells. The truncated analogue, DP-1 and TAT-fused DP-1 (namely DP-2) were subsequently synthesised. It showed that DP-1 had low antimicrobial activity, no hemolytic and cytotoxicity to tumor cells. However, DP-2 possessed strong antimicrobial activity and the similar selective, no obvious hemolytic activity and cytotoxicity on normal human cells, but enhanced cytotoxicity to tumor cells of DRS-DU-1. These findings indicate that the N-terminus of the dermaseptins may contribute to their bioactivity, and that addition of the TAT peptide can improve biological activity. The results provide a new insight for designing novel peptide-based antimicrobial or anticancer agents with low hemolytic activity and cytotoxicity. creator: Haohao Zhu creator: Xiyan Ding creator: Wei Li creator: Tulin Lu creator: Chengbang Ma creator: Xinping Xi creator: Lei Wang creator: Mei Zhou creator: Roberta Burden creator: Tianbao Chen uri: https://doi.org/10.7717/peerj.5635 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhu et al. title: Evaluation of potential reference genes for quantitative RT-PCR analysis in spotted sea bass (Lateolabrax maculatus) under normal and salinity stress conditions link: https://peerj.com/articles/5631 last-modified: 2018-09-19 description: The aim of this study was to select the most suitable reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) of spotted sea bass (Lateolabrax maculatus), an important commercial marine fish in Pacific Asia, under normal physiological and salinity stress conditions. A total of 9 candidate reference genes (HPRT, GAPDH, EF1A, TUBA, RPL7, RNAPol II, B2M, ACTB and 18S rRNA) were analyzed by qRT-PCR in 10 tissues (intestine, muscle, stomach, brain, heart, liver, gill, kidney, pectoral fins and spleen) of L. maculatus. Four algorithms, geNorm, NormFinder, BestKeeper, and comparative ΔCt method, were used to evaluate the expression stability of the candidate reference genes. The results showed the 18S rRNA was most stable in different tissues under normal conditions. During salinity stress, RPL7 was the most stable gene according to overall ranking and the best combination of reference genes was RPL7 and RNAPol II. In contrast, GAPDH was the least stable gene which was not suitable as reference genes. The study showed that different algorithms might generate inconsistent results. Therefore, the combination of several reference genes should be selected to accurately calibrate system errors. The present study was the first to select reference genes of L. maculatus by qRT-PCR and provides a useful basis for selecting the appropriate reference gene in L. maculatus. The present study also has important implications for gene expression and functional genomics research in this species or other teleost species. creator: Haolong Wang creator: Haishen Wen creator: Yun Li creator: Kaiqiang Zhang creator: Yang Liu uri: https://doi.org/10.7717/peerj.5631 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: European population trends and current conservation status of an endangered steppe-bird species: the Dupont’s lark Chersophilus duponti link: https://peerj.com/articles/5627 last-modified: 2018-09-19 description: BackgroundSteppe-birds face drastic population declines throughout Europe. The Dupont’s lark Chersophilus duponti is an endangered steppe-bird species whose European distribution is restricted to Spain. This scarce passerine bird could be considered an ‘umbrella species’, since its population trends may reveal the conservation status of shrub-steppes. However, trends for the Spanish, and thus European, population of Dupont’s lark are unknown. In this work, we evaluated Dupont’s lark population trends in Europe employing the most recent and largest compiled database to date (92 populations over 12 years). In addition, we assessed the species threat category according to current applicable criteria (approved in March 2017) in the Spanish catalogue of threatened species (SCTS), which have never been applied to the Dupont’s lark nor to any other Spanish species. Finally, we compared the resulting threat categories with the current conservation status at European, national and regional levels.MethodsWe fitted switching linear trend models (software TRIM—Trends and Indices for Monitoring data) to evaluate population trends at national and regional scale (i.e. per Autonomous Community) during the period 2004–2015. In addition, the average finite annual rate of change ($\overline \lambda $λ¯) obtained from the TRIM analysis was employed to estimate the percentage of population size change in a 10-year period. A threat category was assigned following A1 and A2 criteria applicable in the SCTS.ResultsTrends showed an overall 3.9% annual decline rate for the Spanish population (moderate decline, following TRIM). Regional analyses showed high inter-regional variability. We forecasted a 32.8% average decline over the next 10 years. According to these results, the species should be listed as ‘Vulnerable’ at a national scale (SCTS). At the regional level, the conservation status of the species is of particular concern in Andalusia and Castile-Leon, where the species qualifies for listing as ‘Endangered’.DiscussionOur results highlight the concerning conservation status of the European Dupont’s lark population, undergoing a 3.9% annual decline rate. Under this scenario, the implementation of a wide-ranging conservation plan is urgently needed and is vital to ensuring the conservation of this steppe-bird species. The role of administrations in matters of nature protection and the cataloguing of endangered species is crucial to reverse declining population trends of this and other endangered taxa. creator: Julia Gómez-Catasús creator: Cristian Pérez-Granados creator: Adrián Barrero creator: Gerard Bota creator: David Giralt creator: Germán M. López-Iborra creator: David Serrano creator: Juan Traba uri: https://doi.org/10.7717/peerj.5627 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Gómez-Catasús et al. title: Potential changes in the distribution of Carnegiea gigantea under future scenarios link: https://peerj.com/articles/5623 last-modified: 2018-09-19 description: Over the last decades several studies have identified that the directional changes in climate induced by anthropogenic emissions of greenhouse gases are affecting the ecology of desert ecosystems. In the Southwest United States, the impacts of climate change to plant abundance and distribution have already been reported, including in the Sonoran Desert ecosystem, home of the iconic Saguaro (Carnegiea gigantea). Hence, there is an urgent need to assess the potential impacts of climate change on the saguaro. The goals of this study are to provide a map of actual habitat suitability (1), describe the relationships between abiotic predictors and the saguaro distribution at regional extents (2), and describe the potential effect of climate change on the spatial distribution of the saguaro (3). Species Distribution Modeling (SDM) was used to investigate the relationships between abiotic variables and the Saguaro distribution. SDMs were calibrated using presence records, 2,000 randomly-generated pseudo absences, and ten abiotic variables. Of these, annual precipitation and max temperature of the warmest month was found to have the greatest relative influence on saguaro distribution. SDMs indicated that 6.9% and 8.1% of the current suitable habitat is predicted to be lost by 2050 and 2070, respectively. Therefore, predicted changes in climate may result in a substantial contraction of the suitable habitat for saguaro over the next century. By identifying the drivers of saguaro distribution and assessing potential changes in habitat suitability due to climate change, this study will help practitioners to design more comprehensive strategies to conserve the saguaro in the face of climate change. creator: Fabio Albuquerque creator: Blas Benito creator: Miguel Ángel Macias Rodriguez creator: Caitlin Gray uri: https://doi.org/10.7717/peerj.5623 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Albuquerque et al. title: Function matters: a review of terminological differences in applied and basic clicker training research link: https://peerj.com/articles/5621 last-modified: 2018-09-19 description: In clicker training, animal trainers pair a small device (a “clicker”) with a reward when teaching or maintaining responding. Animal trainers often assume clicker training is a “science-based” way to train animals. But, the few studies that have compared clicker training to a control have not provided evidence that adding a clicker is beneficial to training. This may be because research on clicker training has studied only one of several potential functions of the clicker stimulus that have been discussed by animal trainers. A systematic approach to researching the function of the clicker in clicker training would benefit from collaboration between applied and basic researchers. However, this will require that terminological differences between animal trainers and basic researchers are reconciled. This paper reviews the few studies that have compared clicker training to a control group and then discusses how trainers and basic researchers use the same terminology in functionally different ways—suggesting the empirical support for mechanisms underlying clicker training is less robust than previously assumed. These differences highlight many opportunities to answer basic and applied research questions relative to clicker training methods. Advancements in clicker training methods will benefit animal trainers who have been using clicker training for decades as well as applied practitioners who have extended clicker training to humans in educational and clinical settings. creator: Nicole R. Dorey creator: David J. Cox uri: https://doi.org/10.7717/peerj.5621 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dorey and Cox title: Foraging dynamics are associated with social status and context in mouse social hierarchies link: https://peerj.com/articles/5617 last-modified: 2018-09-19 description: Living in social hierarchies requires individuals to adapt their behavior and physiology. We have previously shown that male mice living in groups of 12 form linear and stable hierarchies with alpha males producing the highest daily level of major urinary proteins and urine. These findings suggest that maintaining alpha status in a social group requires higher food and water intake to generate energetic resources and produce more urine. To investigate whether social status affects eating and drinking behaviors, we measured the frequency of these behaviors in each individual mouse living in a social hierarchy with non-stop video recording for 24 h following the initiation of group housing and after social ranks were stabilized. We show alpha males eat and drink most frequently among all individuals in the hierarchy and had reduced quiescence of foraging both at the start of social housing and after hierarchies were established. Subdominants displayed a similar pattern of behavior following hierarchy formation relative to subordinates. The association strength of foraging behavior was negatively associated with that of agonistic behavior corrected for gregariousness (HWIG), suggesting animals modify foraging behavior to avoid others they engaged with aggressively. Overall, this study provides evidence that animals with different social status adapt their eating and drinking behaviors according to their physiological needs and current social environment. creator: Won Lee creator: Eilene Yang creator: James P. Curley uri: https://doi.org/10.7717/peerj.5617 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lee et al. title: Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree link: https://peerj.com/articles/5606 last-modified: 2018-09-19 description: Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis. creator: Jun Zeng creator: Jie Chen creator: Yixuan Kou creator: Yujin Wang uri: https://doi.org/10.7717/peerj.5606 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zeng et al. title: The metabolic response of the Bradypus sloth to temperature link: https://peerj.com/articles/5600 last-modified: 2018-09-19 description: Poikilotherms and homeotherms have different, well-defined metabolic responses to ambient temperature (Ta), but both groups have high power costs at high temperatures. Sloths (Bradypus) are critically limited by rates of energy acquisition and it has previously been suggested that their unusual departure from homeothermy mitigates the associated costs. No studies, however, have examined how sloth body temperature and metabolic rate vary with Ta. Here we measured the oxygen consumption (VO2) of eight brown-throated sloths (B. variegatus) at variable Ta’s and found that VO2 indeed varied in an unusual manner with what appeared to be a reversal of the standard homeotherm pattern. Sloth VO2 increased with Ta, peaking in a metabolic plateau (nominal ‘thermally-active zone’ (TAZ)) before decreasing again at higher Ta values. We suggest that this pattern enables sloths to minimise energy expenditure over a wide range of conditions, which is likely to be crucial for survival in an animal that operates under severe energetic constraints. To our knowledge, this is the first evidence of a mammal provisionally invoking metabolic depression in response to increasing Ta’s, without entering into a state of torpor, aestivation or hibernation. creator: Rebecca Naomi Cliffe creator: David Michael Scantlebury creator: Sarah Jane Kennedy creator: Judy Avey-Arroyo creator: Daniel Mindich creator: Rory Paul Wilson uri: https://doi.org/10.7717/peerj.5600 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cliffe et al. title: Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus link: https://peerj.com/articles/5598 last-modified: 2018-09-19 description: Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9–CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway. creator: Jonathan I. Watkinson creator: Peter A. Bowerman creator: Kevin C. Crosby creator: Sherry B. Hildreth creator: Richard F. Helm creator: Brenda S.J. Winkel uri: https://doi.org/10.7717/peerj.5598 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Watkinson et al. title: Transkingdom network reveals bacterial players associated with cervical cancer gene expression program link: https://peerj.com/articles/5590 last-modified: 2018-09-19 description: Cervical cancer is the fourth most common cancer in women worldwide with human papillomavirus (HPV) being the main cause the disease. Chromosomal amplifications have been identified as a source of upregulation for cervical cancer driver genes but cannot fully explain increased expression of immune genes in invasive carcinoma. Insight into additional factors that may tip the balance from immune tolerance of HPV to the elimination of the virus may lead to better diagnosis markers. We investigated whether microbiota affect molecular pathways in cervical carcinogenesis by performing microbiome analysis via sequencing 16S rRNA in tumor biopsies from 121 patients. While we detected a large number of intra-tumor taxa (289 operational taxonomic units (OTUs)), we focused on the 38 most abundantly represented microbes. To search for microbes and host genes potentially involved in the interaction, we reconstructed a transkingdom network by integrating a previously discovered cervical cancer gene expression network with our bacterial co-abundance network and employed bipartite betweenness centrality. The top ranked microbes were represented by the families Bacillaceae, Halobacteriaceae, and Prevotellaceae. While we could not define the first two families to the species level, Prevotellaceae was assigned to Prevotella bivia. By co-culturing a cervical cancer cell line with P. bivia, we confirmed that three out of the ten top predicted genes in the transkingdom network (lysosomal associated membrane protein 3 (LAMP3), STAT1, TAP1), all regulators of immunological pathways, were upregulated by this microorganism. Therefore, we propose that intra-tumor microbiota may contribute to cervical carcinogenesis through the induction of immune response drivers, including the well-known cancer gene LAMP3. creator: Khiem Chi Lam creator: Dariia Vyshenska creator: Jialu Hu creator: Richard Rosario Rodrigues creator: Anja Nilsen creator: Ryszard A. Zielke creator: Nicholas Samuel Brown creator: Eva-Katrine Aarnes creator: Aleksandra E. Sikora creator: Natalia Shulzhenko creator: Heidi Lyng creator: Andrey Morgun uri: https://doi.org/10.7717/peerj.5590 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lam et al. title: A phylogenetic taxonomy of the Cyrtodactylus peguensis group (Reptilia: Squamata: Gekkonidae) with descriptions of two new species from Myanmar link: https://peerj.com/articles/5575 last-modified: 2018-09-19 description: A phylogenetic taxonomy of species in the Cyrtodactylus peguensis group from the Ayeyarwady Basin of Myanmar is constructed based on color pattern, morphology, and molecular systematic analyses using the mitochondrial gene NADH dehydrogenase subunit 2. Newly collected samples from the type locality of C. peguensis and other localities indicate that this clade is endemic to central Myanmar and contains at least seven species, four of which are undescribed. Three species, including C. peguensis occur in the low hills of the Bago Yoma Range within the central portion of the Ayeyarwady Basin. Two of these, C. myintkyawthurai sp. nov. from the northern and central Bago Yoma and C. meersi sp. nov. which is syntopic with C. peguensis in the southern Bago Yoma are described herein. As more lowland hilly areas bordering, and within the Ayeyarwady Basin are surveyed, more new species of this group are likely to be discovered. These discoveries continue the recent surge of descriptions of new species of Cyrtodactylus that are being discovered in Myanmar. creator: L. Lee Grismer creator: Perry L. Wood creator: Evan S.H. Quah creator: Matthew L. Murdoch creator: Marta S. Grismer creator: Mark W. Herr creator: Robert E. Espinoza creator: Rafe M. Brown creator: Aung Lin uri: https://doi.org/10.7717/peerj.5575 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Grismer et al. title: Colour vision of green turtle (Chelonia mydas) hatchlings: do they still prefer blue under water? link: https://peerj.com/articles/5572 last-modified: 2018-09-19 description: BackgroundSeveral anatomical studies provide evidence that green turtles (Chelonia mydas) possess the necessary anatomy for colour vision. Behavioural experiments have previously been conducted with newly emerged hatchlings, concluding that they are attracted to shorter wavelengths compared to longer wavelengths within a terrestrial environment, suggesting a possible attraction towards blue. This paper assessed the colour vision of hatchlings within an aquatic environment, and investigated whether the attraction for shorter wavelengths remains consistent within water, whether the colour saturation of the chromatic stimuli was an important factor, and whether rearing and testing individual animals in different coloured housing tanks has an impact on their visual choices.MethodsForty-one hatchling green turtles were presented with a three-choice experiment where food was attached to three different coloured plates. The plates (blue, yellow, and red) were randomly arranged in the turtle’s tank and four different colour saturations were tested (100, 75, 50, and 25%). Turtles were individually placed into their housing tanks (coloured either red, white, blue or grey) with three different colour plates in front of them, from the same saturation level. The colour of the plate with food first approached and bitten by the turtle was recorded.ResultsThe colour of the tank in which an individual was reared, and where experiments were conducted, significantly influenced which food item was selected on the different coloured plates. While individual turtles preferred to select the food items associated with blue plates across the entire experiment (66.1% of the time compared to 18.2% and 15.7% for yellow and red plates respectively), the preference for blue plates was influenced by the colour of the rearing/experimental tank. Individuals raised in red, white or blue tanks appeared to consistently prefer food on blue plates, but there appeared to be no plate colour preference by turtles in grey tanks. There was no significant effect of either colour saturation or the spatial arrangement of the three colours within an experimental tank on colour choice, and no significant interaction between tank colour and colour saturation.DiscussionThesefindings confirm that the terrestrial preference towards shorter wavelength colours, such as blue, compared to longer wavelength colours remains consistent within an aquatic environment. This preference for blue continues even as the colour saturation reduces from 100% down to 25%, and the colours become darker. Thus, it is suggested that green turtle hatchlings have a strong attraction towards blue. This attraction, however, is influenced by the colour of the tank the turtles were raised in. While this supports the notion that environmental colour may influence individual turtle visual capabilities, it suggests that this relationship is more complicated, and requires further investigation. creator: Rebecca Jehne Hall creator: Simon K.A. Robson creator: Ellen Ariel uri: https://doi.org/10.7717/peerj.5572 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hall et al. title: Population trend inferred from aural surveys for calling anurans in Korea link: https://peerj.com/articles/5568 last-modified: 2018-09-19 description: Amphibian populations fluctuate naturally in size and range and large datasets are required to establish trends in species dynamics. To determine population trends for the endangered Suweon Treefrog (Dryophytes suweonensis), we conducted aural surveys in 2015, 2016, and 2017 at each of 122 sites where the species was known to occur in the Republic of Korea. Despite being based on individual counts, the focus of this study was to establish population trends rather than population size estimates, and we found both environmental and landscape variables to be significant factors. Encroachment was also a key factor that influenced both the decreasing number of calling individuals and the negative population dynamics, represented here by the difference in the number of calling individuals between years. Generally, most sites displayed minimal differences in the number of calling males between years, although there was a large fluctuation in the number of individuals at some sites. Finally, when adjusted for the overall population size difference between years, we found the population size to be decreasing between 2015 and 2017, with a significant decrease in the number of calling individuals at specific sites. High rate of encroachment was the principal explanatory factor behind these marked negative peaks in population dynamics. creator: Amaël Borzée creator: Desiree Andersen creator: Yikweon Jang uri: https://doi.org/10.7717/peerj.5568 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Borzée et al. title: Parvalbumin expression and gamma oscillation occurrence increase over time in a neurodevelopmental model of NMDA receptor dysfunction link: https://peerj.com/articles/5543 last-modified: 2018-09-19 description: Dysfunction of the N-methyl-d-aspartate receptor (NMDAR) is thought to play a role in the pathophysiology of neurodevelopmental diseases like schizophrenia. To study the effects of NMDAR dysfunction on synaptic transmission and network oscillations, we used hippocampal tissue of NMDAR subunit GluN2A knockout (KO) mice. Field excitatory postsynaptic potentials were recorded in acute hippocampal slices of adult animals. Synaptic transmission was impaired in GluN2A KO slices compared to wild-type (WT) slices. Further, to investigate whether NMDAR dysfunction would alter neurodevelopment in vitro, we used organotypic hippocampal slice cultures of WT and GluN2A KO mice. Immunostaining performed with cultures kept two, seven, 14, 25 days in vitro (DIV) revealed an increasing expression of parvalbumin (PV) over time. As a functional readout, oscillatory activity induced by the cholinergic agonist carbachol was recorded in cultures kept seven, 13, and 26 DIV using microelectrode arrays. Initial analysis focused on the occurrence of delta, theta, beta and gamma oscillations over genotype, DIV and hippocampal area (CA1, CA3, dentate gyrus (DG)). In a follow-up analysis, we studied the peak frequency and the peak power of each of the four oscillation bands per condition. The occurrence of gamma oscillations displayed an increase by DIV similar to the PV immunostaining. Unlike gamma occurrence, delta, theta, and beta occurrence did not change over time in culture. The peak frequency and peak power in the different bands of the oscillations were not different in slices of WT and GluN2A KO mice. However, the level of PV expression was lower in GluN2A KO compared to WT mice. Given the role of PV-containing fast-spiking basket cells in generation of oscillations and the decreased PV expression in subjects with schizophrenia, the study of gamma oscillations in organotypic hippocampal slices represents a potentially valuable tool for the characterization of novel therapeutic drugs. creator: Ben van Lier creator: Andreas Hierlemann creator: Frédéric Knoflach uri: https://doi.org/10.7717/peerj.5543 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 van Lier et al. title: High definition video loggers provide new insights into behaviour, physiology, and the oceanic habitat of a marine predator, the yellow-eyed penguin link: https://peerj.com/articles/5459 last-modified: 2018-09-19 description: Camera loggers are increasingly used to examine behavioural aspects of free-ranging animals. However, often video loggers are deployed with a focus on specific behavioural traits utilizing small cameras with a limited field of view, poor light performance and video quality. Yet rapid developments in consumer electronics provide new devices with much improved visual data allowing a wider scope for studies employing this novel methodology. We developed a camera logger that records full HD video through a wide-angle lens, providing high resolution footage with a greater field of view than other camera loggers. The main goal was to assess the suitability of this type of camera for the analysis of various aspects of the foraging ecology of a marine predator, the yellow-eyed penguin in New Zealand. Frame-by-frame analysis allowed accurate timing of prey pursuits and time spent over certain seafloor types. The recorded video footage showed that prey species were associated with certain seafloor types, revealed different predator evasion strategies by benthic fishes, and highlighted varying energetic consequences for penguins pursuing certain types of prey. Other aspects that could be analysed were the timing of breathing intervals between dives and observe exhalation events during prey pursuits, a previously undescribed behaviour. Screen overlays facilitated analysis of flipper angles and beat frequencies throughout various stages of the dive cycle. Flipper movement analysis confirmed decreasing effort during descent phases as the bird gained depth, and that ascent was principally passive. Breathing episodes between dives were short (<1 s) while the majority of the time was devoted to subsurface scanning with a submerged head. Video data recorded on free-ranging animals not only provide a wealth of information recorded from a single deployment but also necessitate new approaches with regards to analysis of visual data. Here, we demonstrate the diversity of information that can be gleaned from video logger data, if devices with high video resolution and wide field of view are utilized. creator: Thomas Mattern creator: Michael D. McPherson creator: Ursula Ellenberg creator: Yolanda van Heezik creator: Philipp J. Seddon uri: https://doi.org/10.7717/peerj.5459 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mattern et al. title: Neural processing of working memory in adults with ADHD in a visuospatial change detection task with distractors link: https://peerj.com/articles/5601 last-modified: 2018-09-18 description: Individuals with Attention-Deficit Hyperactivity Disorder (ADHD) are often characterized by deficits in working memory (WM), which manifest in academic, professional, and mental health difficulties. To better understand the underlying mechanisms of these presumed WM deficits, we compared adults with ADHD to their peers on behavioral and neural indices of WM. We used a visuospatial change detection task with distractors which was designed to assess the brain’s ability to effectively filter out distractors from WM, in addition to testing for effects of WM load. Twenty-seven unmedicated adults with ADHD were compared to 27 matched peers on event-related potential (ERP) measures of WM, i.e., the contralateral delay activity (CDA). Despite severe impairments in everyday life functioning, findings showed no difference in deficits in behavioral tests of working memory for adults with ADHD compared to their peers. Interestingly, there were differences in neural activity between individuals with ADHD and their peers showing that the CDA of individuals with ADHD did not distinguish between high, distractor, and low memory load conditions. These data suggest, in the face of comparable behavioral performance, a difference in neural processing efficiency, wherein the brains of individuals with ADHD may not be as selective in the allocation of neural resources to perform a WM task. creator: Chao Gu creator: Zhong-Xu Liu creator: Rosemary Tannock creator: Steven Woltering uri: https://doi.org/10.7717/peerj.5601 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gu et al. title: Local-scale determinants of arboreal spider beta diversity in a temperate forest: roles of tree architecture, spatial distance, and dispersal capacity link: https://peerj.com/articles/5596 last-modified: 2018-09-18 description: Spiders are a functionally important taxon in forest ecosystems, but the determinants of arboreal spider beta diversity are poorly understood at the local scale. We examined spider assemblages in 324 European beech (Fagus sylvatica) trees of varying sizes across three forest stands in Würzburg (Germany) to disentangle the roles of tree architecture, spatial distance, and dispersal capacity on spider turnover across individual trees. A large proportion of tree pairs (66%) showed higher compositional dissimilarity in spider assemblages than expected by chance, suggesting prominent roles of habitat specialization and/or dispersal limitation. Trees with higher dissimilarity in DBH and canopy volume, and to a lesser extent in foliage cover, supported more dissimilar spider assemblages, suggesting that tree architecture comprised a relevant environmental gradient of sorting spider species. Variation partitioning revealed that 28.4% of the variation in beta diversity was jointly explained by tree architecture, spatial distance (measured by principal coordinates of neighbor matrices) and dispersal capacity (quantified by ballooning propensity). Among these, dispersal capacity accounted for a comparable proportion as spatial distance did (6.8% vs. 5.9%). Beta diversity did not significantly differ between high- and low-vagility groups, but beta diversity in species with high vagility was more strongly determined by spatially structured environmental variation. Altogether, both niche specialization, along the environmental gradient defined by tree architecture, and dispersal limitation are responsible for structuring arboreal spider assemblages. High dispersal capacity of spiders appears to reinforce the role of niche-related processes. creator: Qiongdao Zhang creator: Dong He creator: Hua Wu creator: Wei Shi creator: Cong Chen uri: https://doi.org/10.7717/peerj.5596 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Mitogenomics of Perumytilus purpuratus (Bivalvia: Mytilidae) and its implications for doubly uniparental inheritance of mitochondria link: https://peerj.com/articles/5593 last-modified: 2018-09-18 description: Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research. creator: Beata Śmietanka creator: Marek Lubośny creator: Aleksandra Przyłucka creator: Karin Gérard creator: Artur Burzyński uri: https://doi.org/10.7717/peerj.5593 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Śmietanka et al. title: Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses link: https://peerj.com/articles/5560 last-modified: 2018-09-18 description: BackgroundThe unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs.MethodsThe phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses.ResultsNo spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years.DiscussionThe comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers. creator: Alice Ferrari creator: Fausto Tinti creator: Victoria Bertucci Maresca creator: Alessandro Velonà creator: Rita Cannas creator: Ioannis Thasitis creator: Filipe Oliveira Costa creator: Maria Cristina Follesa creator: Daniel Golani creator: Farid Hemida creator: Sarah J. Helyar creator: Cecilia Mancusi creator: Antonello Mulas creator: Fabrizio Serena creator: Letizia Sion creator: Marco Stagioni creator: Alessia Cariani uri: https://doi.org/10.7717/peerj.5560 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ferrari et al. title: Functional significance of cuckoo Cuculus canorus calls: responses of conspecifics, hosts and non-hosts link: https://peerj.com/articles/5302 last-modified: 2018-09-18 description: Male cuckoos Cuculus canorus produce calls that differ in number of syllables depending on environmental conditions and presence of male and female conspecifics. Why different males produce so repeatable calls that vary greatly in duration among males remains an open question. We used playback of cuckoo calls with few or many syllables (hereafter short and long calls), and woodpigeon calls (a control that also produces few or many syllables), predicting that playback of longer cuckoo calls should attract more male cuckoos (if males with such calls are dominant and successfully out-compete other males due to intraspecific competition), and attract more hosts mobbing male cuckoos (cuckoos with such calls and their females attract more hosts because of an increased risk of parasitism). Because cuckoos differentially parasitize hosts away from human habitation, we also tested whether the number of syllables in cuckoo calls differed with distance from buildings. Playback showed significant effects of number of syllables in cuckoo calls, but not woodpigeon Columba palumbus calls, with an additional effect of distance from human habitation decreasing the response to playback. These findings are consistent with the hypothesis that longer cuckoo calls, especially played back near human habitation, attract more conspecifics and hosts than shorter calls. To the best of knowledge this is the first study showing that cuckoo call response modified both other cuckoo individuals, as well as hosts response. creator: Piotr Tryjanowski creator: Federico Morelli creator: Tomasz S. Osiejuk creator: Anders Pape Møller uri: https://doi.org/10.7717/peerj.5302 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tryjanowski et al. title: Neuroblastomas in Eastern China: a retrospective series study of 275 cases in a regional center link: https://peerj.com/articles/5665 last-modified: 2018-09-17 description: PurposeMost studies on neuroblastoma (NB) have been conducted in Western countries or Japan. The objective of our study was to analyze clinical and pathological features, MYCN status, surgical methods, and prognosis in Chinese NB patients.MethodsA retrospective, single-center case series study of 275 NBs was implemented. Clinical manifestations, pathological features, MYCN status, and surgical treatment were analyzed. Log-rank test and Cox hazards models were used to assess overall survivals (OSs).ResultsThe cohort consisted of 105 females and 170 males, with an age range of five days to 15 years. MYCN amplification was detected in 21.5% of all cases. The median OS was 15.0 months for MYCN amplified group. The five-year OS rates were 70.8% and 18.3% for MYCN unamplified and amplified groups, respectively, and the comparison of Kaplan–Meier curves for these two groups showed statistical significance (P < .001 by log-rank test). Gross total resection (GTR, n = 111) and subtotal resection (STR, n = 58) were administered in 169 patients at stages 3 and 4 who received chemotherapy and the comparison of Kaplan–Meier curves for different groups in these patients had statistical significance (STR vs. GTR, P = .009; MYCN unamplified vs. amplified, P < .001 by log-rank test, respectively).The multivariate survival analyses showed statistical significance (STR vs. GTR, P = .047; MYCN unamplified vs. amplified, P = .001 by Cox regression model).ConclusionsMYCN amplification is an independently adverse prognostic factor in Chinese NB patients at stages 3 and 4 and GTR is associated with improved OS compared with STR in these patients. creator: Yangyang Ma creator: Jicui Zheng creator: Jiayan Feng creator: Lian Chen creator: Kuiran Dong creator: Xianmin Xiao uri: https://doi.org/10.7717/peerj.5665 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ma et al. title: 60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3 link: https://peerj.com/articles/5620 last-modified: 2018-09-17 description: The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome. creator: Sergey Levitskii creator: Ksenia Derbikova creator: Maria V. Baleva creator: Anton Kuzmenko creator: Andrey V. Golovin creator: Ivan Chicherin creator: Igor A. Krasheninnikov creator: Piotr Kamenski uri: https://doi.org/10.7717/peerj.5620 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Levitskii et al. title: Zooming into plant-flower visitor networks: an individual trait-based approach link: https://peerj.com/articles/5618 last-modified: 2018-09-17 description: Understanding how ecological communities are structured is a major goal in ecology. Ecological networks representing interaction patterns among species have become a powerful tool to capture the mechanisms underlying plant-animal assemblages. However, these networks largely do not account for inter-individual variability and thus may be limiting our development of a clear mechanistic understanding of community structure. In this study, we develop a new individual-trait based approach to examine the importance of individual plant and pollinator functional size traits (pollinator thorax width and plant nectar holder depth) in mutualistic networks. We performed hierarchical cluster analyses to group interacting individuals into classes, according to their similarity in functional size. We then compared the structure of bee-flower networks where nodes represented either species identity or trait sets. The individual trait-based network was almost twice as nested as its species-based equivalent and it had a more symmetric linkage pattern resulting from of a high degree of size-matching. In conclusion, we show that by constructing individual trait-based networks we can reveal important patterns otherwise difficult to observe in species-based networks and thus improve our understanding of community structure. We therefore recommend using both trait-based and species-based approaches together to develop a clearer understanding of the properties of ecological networks. creator: Beatriz Rumeu creator: Danny J. Sheath creator: Joseph E. Hawes creator: Thomas C. Ings uri: https://doi.org/10.7717/peerj.5618 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rumeu et al. title: Insomnia and intellect mask the positive link between schizotypal traits and creativity link: https://peerj.com/articles/5615 last-modified: 2018-09-17 description: BackgroundSchizotypy is a set of personality traits that resemble the signs and symptoms of schizophrenia in the general population, and it is associated with various subclinical mental health problems, including sleep disturbances. Additionally, dimensions of schizotypy show specific but weak associations with creativity. Given that creativity demands cognitive control and mental health, and that sleep disturbances negatively impact cognitive control, we predicted that positive, impulsive and disorganised schizotypy will demonstrate stronger associations with indicators of creativity, if the effect of mental health, insomnia, and intellect are statistically controlled.MethodsUniversity students (N = 182) took part in the study. Schizotypy was assessed with the shortened Oxford-Liverpool Inventory of Feelings and Experiences (sO-LIFE). Creative achievements were measured with the Creative Achievement Questionnaire (CAQ), divergent thinking was assessed with the ‘Just suppose’ task, and remote association problem solving was tested with Compound Remote Associate (CRA) problems. Mental health was assessed with the 12-item version of the General Health Questionnaire (GHQ-12), and insomnia was examined with the Athens Insomnia Scale (AIS). Verbal short term memory was measured with the forward digit span task, and intellect was assessed with the Rational-Experiential Inventory (REI). Multiple linear regressions were performed to examine the relationship between creativity and schizotypy. Indicators of creativity were the dependent variables. In the first block, dimensions of schizotypy, age, gender and smoking were entered, and in the second block, the models were extended with mental health, insomnia, verbal short term memory, and intellect.ResultsPositive schizotypy positively predicted real-life creative achievements, independently from the positive effect of intellect. Follow-up analyses revealed that positive schizotypy predicted creative achievements in art, while higher disorganised schizotypy was associated with creative achievements in science (when intellect was controlled for). Furthermore, disorganised schizotypy positively predicted remote association problem solving performance, if insomnia and verbal short term memory were statistically controlled. No dimension of schizotypy was significantly associated with divergent thinking.DiscussionIn line with previous findings, positive schizotypy predicted real-life creative achievements. The positive effects of disorganised schizotypy might be explained in terms of the simultaneous involvement of enhanced semantic priming and cognitive control in problem solving. We speculate that the lack of associations between divergent thinking and schizotypy might be related to instruction effects. Our study underscores the relevance of sleep impairment to the psychosis-spectrum, and refines our knowledge about the adaptive aspects of schizotypy in the general population. creator: Bertalan Polner creator: Péter Simor creator: Szabolcs Kéri uri: https://doi.org/10.7717/peerj.5615 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Polner et al. title: Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales link: https://peerj.com/articles/5614 last-modified: 2018-09-17 description: Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects. creator: Daan R. Speth creator: Victoria J. Orphan uri: https://doi.org/10.7717/peerj.5614 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Speth and Orphan title: Effects of income and residential area on survival of patients with head and neck cancers following radiotherapy: working age individuals in Taiwan link: https://peerj.com/articles/5591 last-modified: 2018-09-17 description: ObjectivesThe five-year survival rate of head and neck cancer (HNC) after radiotherapy (RT) varies widely from 35% to 89%. Many studies have addressed the effect of socioeconomic status and urban dwelling on the survival of HNC, but a limited number of studies have focused on the survival rate of HNC patients after RT.Materials and methodsDuring the period of 2000–2013, 40,985 working age individuals (20 < age < 65 years) with HNC patients treated with RT were included in this study from a registry of patients with catastrophic illnesses maintained by the Taiwan National Health Insurance Research Database (NHIRD).ResultsThe cumulative survival rate of HNC following RT in Taiwan was 53.2% (mean follow-up period, 3.75 ± 3.31 years). The combined effects of income and geographic effect on cumulative survival rates were as follows: high income group > medium income group > low income group and northern > central > southern > eastern Taiwan. Patients with moderate income levels had a 36.9% higher risk of mortality as compared with patients with high income levels (hazard ratio (HR) = 1.369; p < 0.001). Patients with low income levels had a 51.4% greater risk of mortality than patients with high income levels (HR = 1.514, p < 0.001).ConclusionIn Taiwan, income and residential area significantly affected the survival rate of HNC patients receiving RT. The highest income level group had the best survival rate, regardless of the geographic area. The difference in survival between the low and high income groups was still pronounced in more deprived areas. creator: Yu Cheng Lai creator: Pei Ling Tang creator: Chi Hsiang Chu creator: Tsu Jen Kuo uri: https://doi.org/10.7717/peerj.5591 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lai et al. title: The influence of sample distribution on growth model output for a highly-exploited marine fish, the Gulf Corvina (Cynoscion othonopterus) link: https://peerj.com/articles/5582 last-modified: 2018-09-17 description: Estimating the growth of fishes is critical to understanding their life history and conducting fisheries assessments. It is imperative to sufficiently sample each size and age class of fishes to construct models that accurately reflect biological growth patterns, but this may be a challenging endeavor for highly-exploited species in which older fish are rare. Here, we use the Gulf Corvina (Cynoscion othonopterus), a vulnerable marine fish that has been persistently overfished for two decades, as a model species to compare the performance of several growth models. We fit the von Bertalanffy, Gompertz, logistic, Schnute, and Schnute–Richards growth models to length-at-age data by nonlinear least squares regression and used simple indicators to reveal biased data and ensure our results were biologically feasible. We then explored the consequences of selecting a biased growth model with a per-recruit model that estimated female spawning-stock-biomass-per-recruit and yield-per-recruit. Based on statistics alone, we found that the Schnute–Richards model described our data best. However, it was evident that our data were biased by a bimodal distribution of samples and underrepresentation of large, old individuals, and we found the Schnute–Richards model output to be biologically implausible. By simulating an equal distribution of samples across all age classes, we found that sample distribution distinctly influenced model output for all growth models tested. Consequently, we determined that the growth pattern of the Gulf Corvina was best described by the von Bertalanffy growth model, which was the most robust to biased data, comparable across studies, and statistically comparable to the Schnute–Richards model. Growth model selection had important consequences for assessment, as the per-recruit model employing the Schnute–Richards model fit to raw data predicted the stock to be in a much healthier state than per-recruit models employing other growth models. Our results serve as a reminder of the importance of complete sampling of all size and age classes when possible and transparent identification of biased data when complete sampling is not possible. creator: Derek G. Bolser creator: Arnaud Grüss creator: Mark A. Lopez creator: Erin M. Reed creator: Ismael Mascareñas-Osorio creator: Brad E. Erisman uri: https://doi.org/10.7717/peerj.5582 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bolser et al. title: The role of miRNAs 34a, 146a, 320a and 542 in the synergistic anticancer effects of methyl 2-(5-fluoro-2-hydroxyphenyl)-1H- benzo[d]imidazole-5-carboxylate (MBIC) with doxorubicin in breast cancer cells link: https://peerj.com/articles/5577 last-modified: 2018-09-17 description: Combination Index (CI) analysis suggested that MBIC and doxorubicin synergistically inhibited up to 97% of cell proliferation in ER+/PR+MCF-7 and triple negative MDA-MB-231 breast cancer cell lines. Moreover, treatment of the breast cancer cells with the combined drugs resulted in lower IC50 values in contrast to the individual drug treatment. Small noncoding microRNAs (miRNA) may function as non-mutational gene regulators at post-transcriptional level of protein synthesis. In the present study, the effect of the combined treatment of MBIC and doxorubicin on the expression level of several miRNAs including miR-34a, miR-146a, miR-320a and miR-542 were evaluated in MCF-7 and MDA-MB-231 breast cancer cell lines. These miRNAs have the potential to alter the protein level of survivin, the anti-apoptotic protein and reduce the metastatic activity in human breast cancer cell lines by interfering with the nuclear accumulation of NF-κB. Our results demonstrated the several fold changes in expression of miRNAs, which is drug and cell line dependent. This finding demonstrated a functional synergistic network between miR-34a, miR-320a and miR-542 that are negatively involved in post-transcriptional regulation of survivin in MCF-7 cells. While in MDA-MB-231 cells, changes in expression level of miR-146a was correlated with inhibition of the nuclear translocation of NF-κB. The overall result suggested that alteration in protein level and location of survivin and NF-κB by miR-34a, miR-320a, miR-146a and miR-542, remarkably influenced the synergistic enhancement of combined MBIC and doxorubicin in treatment of aggressive and less aggressive human breast cancer cell lines. creator: Mohadeseh Hasanpourghadi creator: Nazia Abdul Majid creator: Mohd Rais Mustafa uri: https://doi.org/10.7717/peerj.5577 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hasanpourghadi et al. title: Nonspecific stress response to temperature increase in Gammarus lacustris Sars with respect to oxygen-limited thermal tolerance concept link: https://peerj.com/articles/5571 last-modified: 2018-09-17 description: The previously undescribed dynamics of the heat shock protein HSP70 and subsequent lipid peroxidation products have been assessed alongside lactate dehydrogenase activity for Gammarus lacustris Sars, an amphipod species from the saltwater Lake Shira (Republic of Khakassia). Individuals were exposed to a gradual temperature increase of 1 °C/hour (total exposure duration of 26 hours) starting from the mean annual temperature of their habitat (7 °C) up to 33 °C. A complex of biochemical reactions occurred when saltwater G. lactustris was exposed to the gradual changes in temperature. This was characterized by a decrease in lactate dehydrogenase activity and the launching of lipid peroxidation. The HSP70 level did not change significantly during the entire experiment. In agreement with the concept of oxygen-limited thermal tolerance, an accumulation of the most toxic lipid peroxides (triene conjugates and Schiff bases) in phospholipids occurred at the same time and temperature as the accumulation of lactate. The main criterion overriding the temperature threshold was, therefore, the transition to anaerobiosis, confirmed by the elevated lactate levels as observed in our previous associated study, and by the development of cellular stress, which was expressed by an accumulation of lipid peroxidation products. An earlier hypothesis, based on freshwater individuals of the same species, has been confirmed whereby the increased thermotolerance of G. lacustris from the saltwater lake was caused by differences in energy metabolism and energy supply of nonspecific cellular stress-response mechanisms. With the development of global climate change, these reactions could be advantageous for saltwater G. lacustris. The studied biochemical reactions can be used as biomarkers for the stress status of aquatic organisms when their habitat temperature changes. creator: Kseniya Vereshchagina creator: Elizaveta Kondrateva creator: Denis Axenov-Gribanov creator: Zhanna Shatilina creator: Andrey Khomich creator: Daria Bedulina creator: Egor Zadereev creator: Maxim Timofeyev uri: https://doi.org/10.7717/peerj.5571 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vereshchagina et al. title: Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013 link: https://peerj.com/articles/5566 last-modified: 2018-09-17 description: This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs, Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 257 monthly environmental variables and performing stepwise multiple regression analyses. Crab densities in a given year were best explained by potential settlement during the summer and the maximum sea-surface temperature during March of the same year. However, potential roles of other factors (e.g., autumn winds, summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the area, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region. creator: Brady K. Quinn uri: https://doi.org/10.7717/peerj.5566 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Quinn title: Exome sequencing study of 20 patients with high myopia link: https://peerj.com/articles/5552 last-modified: 2018-09-17 description: BackgroundHigh myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations.MethodsA total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses. Network and enrichment analysis were employed to examine the biological pathways involved in the candidate genes.ResultsIn 16 out of 20 patients, we identified 20 potential pathogenic gene variants for high myopia. A total of 18 variants were located in myopia-associated chromosomal regions. In addition to the novel mutations found in five known myopia genes (ADAMTS18, CSMD1, P3H2, RPGR, and SLC39A5), we also identified pathogenic variants in seven ocular disease genes (ABCA4, CEP290, HSPG2, PCDH15, SAG, SEMA4A, and USH2A) as novel candidate genes. The biological processes associated with vision were significantly enriched in our candidate genes, including visual perception, photoreceptor cell maintenance, retinoid metabolic process, and cellular response to zinc ion starvation.DiscussionSystematic mutation analysis of candidate genes was performed using WES data, functional interaction (FI) network, Gene Ontology and pathway enrichment. FI network analysis revealed important network modules and regulator linker genes (EP300, CTNNB1) potentially related to high myopia development. Our study expanded the list of candidate genes associated with high myopia, which increased the genetic screening performance and provided implications for future studies on the molecular genetics of myopia. creator: Ling Wan creator: Boling Deng creator: Zhengzheng Wu creator: Xiaoming Chen uri: https://doi.org/10.7717/peerj.5552 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wan et al. title: Phylogeography of Swertia perennis in Europe based on cpDNA markers link: https://peerj.com/articles/5512 last-modified: 2018-09-17 description: BackgroundSwertia perennis(Gentianaceae) is a perennial diploid and clonal plant species that is discontinuously distributed in peat bogs in the mountains of Europe, Asia and North America as well as in the lowlands of Europe. The current geographical dispersion of S. perennis is probably the result of quaternary climatic changes that have played an important role in determining the distribution of Swertia and other plant and animal species.MethodsIn this study we used molecular techniques and combined data from chloroplast DNA markers (trnLF region and trnH-psbA spacer) to elucidate the phylogeography of S. perennis in Europe. Plants were collected from 28 populations in different locations in the lowlands and mountainous areas of Europe (e.g., the Carpathians, Sudetes, Bohemian Forest and Alps). cDNA was analysed to detect the genetic relationship between specimens from different locations.ResultsA total of 20 haplotypes were identified across the dataset. They were characterised by a high level of genetic variability but showed a lack of phylogeographical structure. This pattern may be the result of repeated recolonization and expansion from several areas. Such genetic differentiation may also be attributed to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, which resulted in independent separation of different cpDNA phylogenetic lineages and variation in the nucleotide composition of cpDNA.DiscussionThe lack of strong phylogeographical structure makes it impossible to indicate the centre of haplotype diversity; however, refugia located in the Carpathians, Sudetes or Alps are the most probable sites where S. perennis existed in Europe. This lack of structure may also indicate a high level of gene flow in times when the landscape and fen systems were not fragmented in numerous geographically-isolated populations. This makes it difficult to speculate about the relationships between Asiatic and European plant populations and the origin and distribution of this species in Europe. Today, it seems to be restricted due to the occurrence of plants which clearly reflects the genetic variability from the ancient period. creator: Jacek Urbaniak creator: Paweł Kwiatkowski creator: Paweł Pawlikowski uri: https://doi.org/10.7717/peerj.5512 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Urbaniak et al. title: Th2 cytokine bias induced by silver nanoparticles in peripheral blood mononuclear cells of common bottlenose dolphins (Tursiops truncatus) link: https://peerj.com/articles/5432 last-modified: 2018-09-17 description: BackgroundSilver nanoparticles (AgNPs) have been widely used in many commercial products due to their excellent antibacterial ability. The AgNPs are released into the environment, gradually accumulate in the ocean, and may affect animals at high trophic levels, such as cetaceans and humans, via the food chain. Hence, the negative health impacts caused by AgNPs in cetaceans are of concern. Cytokines play a major role in the modulation of immune system and can be classified into two types: Th1 and Th2. Th1/Th2 balance can be evaluated by the ratios of their polarizing cytokines (i.e., interferon [IFN]-γ/Interleukin [IL]-4), and animals with imbalanced Th1/Th2 response may become more susceptible to certain kinds of infection. Therefore, the present study evaluated the in vitro cytokine responses of cetacean peripheral blood mononuclear cells (cPBMCs) to 20 nm citrate-AgNPs (C-AgNP20) by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR).MethodsBlood samples were collected from six captive common bottlenose dolphins (Tursiops truncatus). The cPBMCs were isolated and utilized for evaluating the in vitro cytokine responses. The cytokines evaluated included IL-2, IL-4, IL-10, IL-12, interferon (IFN)-γ, and tumor necrosis factor (TNF)-α. The geometric means of two housekeeping genes (HKGs), glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and β2-microglobulin (B2M), of each sample were determined and used to normalize the mRNA expression levels of target genes.ResultsThe ratio of late apoptotic/necrotic cells of cPBMCs significantly increased with or without concanavalin A (ConA) stimulation after 24 h of 10 µg/ml C-AgNP20 treatment. At 4 h of culture, the mRNA expression level of IL-10 was significantly decreased with 1 µg/ml C-AgNP20 treatment. At 24 h of culture with 1 µg/ml C-AgNP20, the mRNA expression levels of all cytokines were significantly decreased, with the exceptions of IL-4 and IL-10. The IFN-γ/IL-4 ratio was significantly decreased at 24 h of culture with 1 µg/ml C-AgNP20 treatment, and the IL-12/IL-4 ratio was significantly decreased at 4 or 24 h of culture with 0.1 or 1 µg/ml C-AgNP20 treatment, respectively. Furthermore, the mRNA expression level of TNF-α was significantly decreased by 1 µg/ml C-AgNP20 after 24 h of culture.DiscussionThe present study demonstrated that the sublethal dose of C-AgNP20 (≤1 µg/ml) had an inhibitory effect on the cytokine mRNA expression levels of cPBMCs with the evidence of Th2 cytokine bias and significantly decreased the mRNA expression level of TNF-α. Th2 cytokine bias is associated with enhanced immunity against parasites but decreased immunity to intracellular microorganisms. TNF-α is a contributing factor for the inflammatory response against the infection of intracellular pathogens. In summary, our data indicate that C-AgNP20 suppresses the cellular immune response and thereby increases the susceptibility of cetaceans to infection by intracellular microorganisms. creator: Wen-Ta Li creator: Lei-Ya Wang creator: Hui-Wen Chang creator: Wei-Cheng Yang creator: Chieh Lo creator: Victor Fei Pang creator: Meng-Hsien Chen creator: Chian-Ren Jeng uri: https://doi.org/10.7717/peerj.5432 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Lessepsian migration and parasitism: richness, prevalence and intensity of parasites in the invasive fish Sphyraena chrysotaenia compared to its native congener Sphyraena sphyraena in Tunisian coastal waters link: https://peerj.com/articles/5558 last-modified: 2018-09-14 description: BackgroundParasites can play various roles in the invasion of non-native species, but these are still understudied in marine ecosystems. This also applies to invasions from the Red Sea to the Mediterranean Sea via the Suez Canal, the so-called Lessepsian migration. In this study, we investigated the role of parasites in the invasion of the Lessepsian migrant Sphyraena chrysotaenia in the Tunisian Mediterranean Sea.MethodsWe compared metazoan parasite richness, prevalence and intensity of S. chrysotaenia (Perciformes: Sphyraenidae) with infections in its native congener Sphyraena sphyraena by sampling these fish species at seven locations along the Tunisian coast. Additionally, we reviewed the literature to identify native and invasive parasite species recorded in these two hosts.ResultsOur results suggest the loss of at least two parasite species of the invasive fish. At the same time, the Lessepsian migrant has co-introduced three parasite species during the initial migration to the Mediterranean Sea, that are assumed to originate from the Red Sea of which only one parasite species has been reported during the spread to Tunisian waters. In addition, we found that the invasive fish has acquired six parasite species that are native in the Mediterranean Sea. However, parasite richness, prevalence and intensity were overall much lower in the invasive compared to the native fish host in the Mediterranean Sea.DiscussionThese results suggest that the Lessepsian migrant may affect native fish hosts by potentially altering the dynamics of native and invasive parasite-host interactions via parasite release, parasite co-introduction and parasite acquisition. They further suggest that the lower infection levels in the invasive fish may result in a competitive advantage over native fish hosts (enemy release hypothesis). This study demonstrates that cross-species comparisons of parasite infection levels are a valuable tool to identify the different roles of parasites in the course of Lessepsian migrations. creator: Wiem Boussellaa creator: Lassad Neifar creator: M. Anouk Goedknegt creator: David W. Thieltges uri: https://doi.org/10.7717/peerj.5558 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Boussellaa et al. title: Luciferin production and luciferase transcription in the bioluminescent copepod Metridia lucens link: https://peerj.com/articles/5506 last-modified: 2018-09-14 description: Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in oceanic food webs. Metridia copepods exhibit particularly bright bioluminescence, and the molecular basis of their light production has just recently begun to be explored. Here we add to this body of work by transcriptomically profiling Metridia lucens, a common species found in temperate, northern, and southern latitudes. In this previously molecularly-uncharacterized species, we find the typical luciferase paralog gene set found in Metridia. More surprisingly, we recover noteworthy putative luciferase sequences that had not been described from Metridia species, indicating that bioluminescence produced by these copepods may be more complex than previously known. This includes another copepod luciferase, as well as one from a shrimp. Furthermore, feeding experiments using mass spectrometry and 13C labelled L-tyrosine and L-phenylalanine firmly establish that M. lucens produces its own coelenterazine luciferin rather than acquiring it through diet. This coelenterazine synthesis has only been directly confirmed in one other copepod species. creator: Michael Tessler creator: Jean P. Gaffney creator: Jason M. Crawford creator: Eric Trautman creator: Nehaben A. Gujarati creator: Philip Alatalo creator: Vincent A. Pieribone creator: David F. Gruber uri: https://doi.org/10.7717/peerj.5506 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tessler et al. title: Urban waste disposal explains the distribution of Black Vultures (Coragyps atratus) in an Amazonian metropolis: management implications for birdstrikes and urban planning link: https://peerj.com/articles/5491 last-modified: 2018-09-14 description: Collision rates between aircraft and birds have been rising worldwide. The increases in both air traffic and population sizes of large-bodied birds in cities lacking urban planning result in human-wildlife conflicts, economic loss and even lethal casualties. Black Vultures (Coragyps atratus) represent the most hazardous bird to Brazilian civil and military aviation on the basis of their flight behavior, body mass and consequently physical damage to aircraft following collisions. This study investigated how storage apparatus and type of organic residue discarded in public street markets modulate the spatial distribution and abundance of urban Black Vultures in the largest city in the Amazon (Manaus, Brazil). We estimated Black Vulture abundance in relation to the type of solid human waste (animal or plant), the type of waste storage containers and market sizes in terms of the number of vendor stalls at 20 public markets. We also visually quantified the abundance of Black Vultures in urban markets in relation to air traffic. Our results suggest that urban solid waste storage procedures currently used (or the lack thereof) are related to the occurrence and abundance of Black Vultures. Moreover, storage type and the proportion of animal protein (red meat and fish) within rubbish bins directly affects foraging aggregations in vultures. We recommend that policymakers should invest more efforts in building larger and more resistant closable waste containers to avoid organic solid waste exposure. We also identified five outdoor markets as urgent priorities to improve waste disposal. Finally, our waste management guidelines would not only reduce aviation collision risks but also benefit human health and well-being in most cities. creator: Giase M. de Araujo creator: Carlos A. Peres creator: Fabricio B. Baccaro creator: Rafael S. Guerta uri: https://doi.org/10.7717/peerj.5491 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Araujo et al. title: Economic value of trees in the estate of the Harewood House stately home in the United Kingdom link: https://peerj.com/articles/5411 last-modified: 2018-09-14 description: The estates of stately homes or manor houses are an untapped resource for assessing the ecosystem services provided by trees. Many of these estates have large collections of trees with clear value in terms of carbon storage, runoff prevention, and pollution removal along with additional benefits to biodiversity and human health. The estate of Harewood House in North Yorkshire represents an ideal example of such a stately home with a mixture of parkland and more formally planted gardens. The trees in each type of garden were analysed for height, diameter at breast height and light exposure. The data were then processed in iTrees software to generate economic benefits for each tree in both gardens. The analysis found that the larger North Front parkland garden had greater total benefits but the more densely planted formal West Garden had the greater per hectare value. In total, the trees on Harewood House estate are estimated to provide approximately £29 million in ecosystem service benefits. This study is the first to analyse the trees of stately homes for economic benefits and highlights that the trees are a valuable commodity for the estates. This should be considered in future planning and management of such estates. creator: Julie Peacock creator: Joey Ting creator: Karen L. Bacon uri: https://doi.org/10.7717/peerj.5411 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Peacock et al. title: Maxent estimation of aquatic Escherichia coli stream impairment link: https://peerj.com/articles/5610 last-modified: 2018-09-13 description: BackgroundThe leading cause of surface water impairment in United States’ rivers and streams is pathogen contamination. Although use of fecal indicators has reduced human health risk, current approaches to identify and reduce exposure can be improved. One important knowledge gap within exposure assessment is characterization of complex fate and transport processes of fecal pollution. Novel modeling processes can inform watershed decision-making to improve exposure assessment.MethodsWe used the ecological model, Maxent, and the fecal indicator bacterium Escherichia coli to identify environmental factors associated with surface water impairment. Samples were collected August, November, February, and May for 8 years on Sinking Creek in Northeast Tennessee and analyzed for 10 water quality parameters and E. coli concentrations. Univariate and multivariate models estimated probability of impairment given the water quality parameters. Model performance was assessed using area under the receiving operating characteristic (AUC) and prediction accuracy, defined as the model’s ability to predict both true positives (impairment) and true negatives (compliance). Univariate models generated action values, or environmental thresholds, to indicate potential E. coli impairment based on a single parameter. Multivariate models predicted probability of impairment given a suite of environmental variables, and jack-knife sensitivity analysis removed unresponsive variables to elicit a set of the most responsive parameters.ResultsWater temperature univariate models performed best as indicated by AUC, but alkalinity models were the most accurate at correctly classifying impairment. Sensitivity analysis revealed that models were most sensitive to removal of specific conductance. Other sensitive variables included water temperature, dissolved oxygen, discharge, and NO3. The removal of dissolved oxygen improved model performance based on testing AUC, justifying development of two optimized multivariate models; a 5-variable model including all sensitive parameters, and a 4-variable model that excluded dissolved oxygen.DiscussionResults suggest that E. coli impairment in Sinking Creek is influenced by seasonality and agricultural run-off, stressing the need for multi-month sampling along a stream continuum. Although discharge was not predictive of E. coli impairment alone, its interactive effect stresses the importance of both flow dependent and independent processes associated with E. coli impairment. This research also highlights the interactions between nutrient and fecal pollution, a key consideration for watersheds with multiple synergistic impairments. Although one indicator cannot mimic theplethora of existing pathogens in water, incorporating modeling can fine tune an indicator’s utility, providing information concerning fate, transport, and source of fecal pollution while prioritizing resources and increasing confidence in decision making. creator: Dennis Gilfillan creator: Timothy A. Joyner creator: Phillip Scheuerman uri: https://doi.org/10.7717/peerj.5610 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gilfillan et al. title: Mass fluctuation in breeding females, males, and helpers of the Florida scrub-jay Aphelocoma coerulescens link: https://peerj.com/articles/5607 last-modified: 2018-09-13 description: Much evidence suggests that birds actively regulate their body mass reserves relative to their energy needs. Energy requirements during reproduction may differ in relation to sex-specific behavioural roles or, in the case of cooperative breeders, breeders relative to helpers. We measured body mass of free-living Florida scrub-jays throughout the nesting season by training them to land on an electronic balance. Jays exhibited a pattern of diurnal linear mass gain, from morning to afternoon. Day-to-day mass fluctuations, defined as the difference between mass on two consecutive days, were small (>80% were within 2 g, less than 3% of the mass of an adult bird) for all classes of jays: female breeders, male breeders and prebreeding helpers. The jays, which live in subtropical south-central Florida, did not exhibit changes in day-to-day mass fluctuation relative to weather or climate variables or calendar date. Day-to-day mass fluctuations influenced mass fluctuation between the following third and fourth days. These changes were usually compensatory, indicating that jays are able to regulate their body mass on a short-term basis, despite strong differences in their roles in reproduction. During reproduction, jays have a relatively predictable and abundant food supply, thus the appropriate strategy may be to maintain a stable body mass that balances some energy reserves against maintaining a low body mass for efficient flight, as required during reproduction. creator: Marco Cucco creator: Reed Bowman uri: https://doi.org/10.7717/peerj.5607 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cucco and Bowman title: Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico link: https://peerj.com/articles/5583 last-modified: 2018-09-13 description: The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88; H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2; H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded to Kordiimonadales, Rhodospirillales, Desulfobacterales (Desulfococcus), Syntrophobacterales and Nitrospirales (GOUTA 19, BD2-6, LCP-6), whilst Chromatiales, Oceanospirillales (Amphritea, Alcanivorax), Methylococcales, Flavobacteriales, Alteromonadales (Shewanella, ZD0117) and Rhodobacterales were the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM. creator: Ma. Fernanda Sánchez-Soto Jiménez creator: Daniel Cerqueda-García creator: Jorge L. Montero-Muñoz creator: Ma. Leopoldina Aguirre-Macedo creator: José Q. García-Maldonado uri: https://doi.org/10.7717/peerj.5583 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sánchez-Soto Jiménez et al. title: An integrative and citizen science based approach to the rediscovery and redescription of the only known high-altitude endemic Pill Millipede, Glomeris aurita Koch (Diplopoda, Glomerida) link: https://peerj.com/articles/5569 last-modified: 2018-09-13 description: The pill millipede species Glomeris auritaKoch, 1847 remained of relative unknown origin and appearance until its recent rediscovery in samples from the Bergamasque Alps, northern Italy. In order to provide an integrative redescription and accurate identification of the high-altitude microendemic G. aurita, COI barcode sequences from three individuals coming from two different localities were obtained. These sequences are compared with those of the syntopic endemic G. oblongoguttataVerhoeff, 1894, the widespread black morph of G. romanaVerhoeff, 1900, as well as several widespread species including G. marginataVillers, 1789, G. connexaKoch, 1847, and G. klugiiBrandt, 1833, which have rare colour morphs that exhibit some similarity to G. aurita. To rule-out any identity confusion of G. aurita with other high-altitude or little-known Italian Glomeris, specimens of G. transalpinaKoch, 1836, G. oropensisVerhoeff, 1934, and G. primordialisVerhoeff, 1932 were also added to the dataset. Altogether, 24 sequences were compared. Morphologically, the specimens of G. aurita were studied utilizing scanning electron microscopy as well as non-invasive micro-CT technology. The distribution of both Bergamasque endemics, G. aurita and G. oblongoguttata, could be mapped and compared utilizing samples from the Museo civico di Scienze Naturali di Bergamo, as well as photographic evidence from an Italian naturalist forum. G. aurita has a very short active period and is the first known pill millipede species restricted to mountain tops and cold places, possibly representing a Nunatak survivor. creator: Thomas Wesener uri: https://doi.org/10.7717/peerj.5569 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wesener title: Cytokine and microRNA levels during different periods of paradoxical sleep deprivation and sleep recovery in rats link: https://peerj.com/articles/5567 last-modified: 2018-09-13 description: BackgroundSleep has a fundamental role in the regulation of homeostasis. The aim of this study was to assess the effect of different periods of paradoxical sleep deprivation (PSD) and recovery on serum levels of cytokines and miRNAs related to inflammatory responses.MethodsMale Wistar rats were submitted to a PSD of 24, 96, or 192 h, or of 192 h followed by 20 days of recovery (192 h PSD+R). The concentrations of corticosterone, cytokines (IL-6, TNF, IL-10, Adiponectin) and miRNAs (miR-146a, miR-155, miR-223, miR-16, miR-126, miR-21) in serum were evaluated.ResultsAt PSD 24 h a significant increase of IL-6 and decrease of IL-10 were observed. At PSD 96h adiponectin increased. At 192 h of PSD IL-6 increased significantly again, accompanied by a threefold increase of IL-10 and an increase of serum corticosterone. After 20 days of recovery (192 h PSD+R) corticosterone, IL-6 and TNF levels increased significantly, while IL-10 decreased also significantly. Regarding the miRNAs at 24 h of PSD serum miR-146a, miR-155, miR-223, and miR-16 levels all increased. At 96 h of PSD miR-223 decreased. At 192 h of PSD decreases in miR-16 and miR-126 were observed. After recovery serum miR-21 increased and miR-16 decreased.ConclusionPSD induces a dynamic response likely reflecting the induced cellular stress and manifested as variating hormonal and inflammatory responses. Sleep deprivation disturbed corticosterone, cytokine and miRNA levels in serum related to the duration of sleep deprivation, as short-term PSD produced effects similar to those of an acute inflammatory response and long-term PSD induced long-lasting disturbances of biological mediators. creator: Malinalli Brianza-Padilla creator: Fausto Sánchez-Muñoz creator: Gonzalo Vázquez-Palacios creator: Fengyang Huang creator: Julio César Almanza-Pérez creator: Rafael Bojalil creator: Herlinda Bonilla-Jaime uri: https://doi.org/10.7717/peerj.5567 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brianza-Padilla et al. title: Differential expression of NF-κB heterodimer RelA/p50 in human urothelial carcinoma link: https://peerj.com/articles/5563 last-modified: 2018-09-13 description: BackgroundUrothelial carcinoma (UC) is the fifth most common malignancy that accounts for 5% of all cancers. Diagnostic markers that predict UC progressions are inadequate. NF-κB contributes towards disease progression upon constitutive activation in many solid tumors. The nuclear localization of NF-κB indicates increased transcriptional activity while cytoplasmic localization indicates the inactive protein repository that can be utilized readily by a malignant cell. This study delineates the nuclear and cytoplasmic differential expression of NF-κB heterodimers in UC progression.MethodsThe involvement of the NF-κB proteins in UC was analyzed in silico using cytoscape. The expression of NF-κB heterodimers was analyzed by immunohistochemistry.ResultsPINA4MS app in cytoscape revealed over expression of RelA and suppression of NF-κB1 (p50 precursor) in UC whereas the expression of NF-κB target proteins remained unhindered. Immunohistochemical localization showed nuclear RelA/p50 in low grade UC whereas in high grade only RelA expression was observed. Conversely, cytoplasmic expression of RelA/p50 remained extensive across high and low grade UC tissues (p < 0.005). RelA nuclear and cytoplasmic expression (p < 0.005) was directly proportional to the disease progression. In our study, some of the high-grade UC tissues with squamous differentiation and muscle invasion had extensive nuclear p50 localization. The phenomenon of RelA/p50 expression seen increased in low-grade UC than high grade UC might be due to their interaction with other members of NF-κB family of proteins. Thus, NF-κB RelA/p50 differential expression may play a unique role in UC pathogenesis and can serve as a biomarker for diagnosis. creator: Sankari Durairajan creator: Charles Emmanuel Jebaraj Walter creator: Mary Divya Samuel creator: Dinesh Palani creator: Dicky John Davis G creator: George Priya Doss C creator: Sneha Pasupati creator: Thanka Johnson uri: https://doi.org/10.7717/peerj.5563 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Durairajan et al. title: Balanced and positively worded personality short-forms: Mini-IPIP validity and cross-cultural invariance link: https://peerj.com/articles/5542 last-modified: 2018-09-13 description: BackgroundThe Mini-IPIP scales (Donellan et al., 2006) are possibly one of the most commonly used short inventories for measuring the Big Five Factors of personality. In this study, we aimed to investigate the psychometric properties of two Mini-IPIP Spanish short forms, one balanced and one positively wording (PW).MethodTwo samples, one from native Spanish speakers and another from native English speakers, made up a total of 940 participants in this study. The short forms were translated and adapted based on international guidelines. Reliability (internal and composite) and validity analyses (construct ESEM, concurrent, predictive and cross-cultural invariance through multi-group factorial models) were performed.ResultsFor both the balanced scale and the PW one, modeling a method factor was not relevant. The reliability and validity indices of both forms were according to theory and prior studies’ findings: (a) personality factors were medium-high related to affective factors; (b) personality factors were less related to life satisfaction than affective factors; (c) life satisfaction was medium-high related to affective factors; (d) neuroticism appeared mainly related to all criteria variables; and (e) an acceptable level of invariance was achieved with regard to the English version.DiscussionThis study contributes to research on personality assessment by providing the first evidence regarding the psychometric properties of a PW short measure. These results suggest that PW short scales of personality used after data screening techniques may be appropriate for future studies (e.g., cross-cultural, content validity). creator: Agustín Martínez-Molina creator: Víctor B. Arias uri: https://doi.org/10.7717/peerj.5542 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Martínez-Molina and Arias title: Autonomic dysfunction and white matter microstructural changes in drug-naïve patients with Parkinson’s disease link: https://peerj.com/articles/5539 last-modified: 2018-09-13 description: BackgroundAutonomic dysfunction (AD) is one of the non-motor features of Parkinson’s disease (PD). Some symptoms tend to occur in the early stages of PD. AD also has a great impact on patient’s quality of life. In this study, we aimed to discover the association between AD (Scales for Outcomes in Parkinson’s disease-Autonomic, SCOPA-AUT) and microstructural changes in white matter tracts in drug-naïve early PD patients to elucidate the central effects of autonomic nervous system impairments.MethodIn total, this study included 85 subjects with PD recruited from the Parkinson’s Progression Markers Initiative (PPMI) database. Among the 85 PD patients, 38 were in Hoehn & Yahr stage 1 (HY1PD) and 47 were in stage 2 (HY2PD). Diffusion magnetic resonance imaging (DMRI) data were reconstructed in the MNI space using q-space diffeomorphic reconstruction to obtain the spin distribution function. The spin distribution function (SDF) values were used in DMRI connectometry analysis. We investigated through diffusion MRI connectometry the structural correlates of white matter tracts with SCOPA-AUT subscores and total score.ResultsConnectometry analysis also revealed positive association with white matter density in bilateral corticospinal tract in HY1PD patients and negative association in genu of corpus callosum (CC) and, bilateral cingulum in both groups. In addition, there were associations between gastrointestinal, sexual, thermoregulatory and urinary items and structural brain connectivity in PD.ConclusionOur study reveals positive correlation, suggesting neural compensations in early PD. Cingulum and CC tracts have well-known roles in PD pathology, compatible with our findings that bring new insights to specific areas of AD and its role in central nervous system (CNS) neurodegeneration, paving the way for using prodromal makers in the diagnosis and treatment of PD. creator: Amir Ashraf-Ganjouei creator: Alireza Majd creator: Ali Javinani creator: Mohammad Hadi Aarabi uri: https://doi.org/10.7717/peerj.5539 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ashraf-Ganjouei et al. title: The ability of magnetic field sensors to monitor feeding in three domestic herbivores link: https://peerj.com/articles/5489 last-modified: 2018-09-13 description: The rate at which animals ingest food is a fundamental part of animal ecology although it is rarely quantified, with recently-developed animal-attached tags providing a potentially viable approach. However, to date, these methods lack clarity in differentiating various eating behaviours, such as ‘chewing’ from ‘biting’. The aims of this study were to examine the use of inter-mandibular angle sensors (IMASENs), to quantify grazing behaviour in herbivores including cattle (Bos taurus), sheep (Ovis aries) and pygmy goats (Capra aegagrus hircus) eating different foodstuffs. Specifically, we aimed to: (1) quantify jaw movements of each species and determine differences between biting and chewing; (2) assess whether different food types can be discerned from jaw movements; and (3) determine whether species-specific differences in jaw movements can be detected. Subjects were filmed while consuming concentrate, hay, grass and browse to allow comparison of observed and IMASEN-recorded jaw movements. This study shows that IMASENs can accurately detect jaw movements of feeding herbivores, and, based on the rate of jaw movements, can classify biting (taking new material into the mouth) from chewing (masticating material already in the mouth). The biting behaviours associated with concentrate pellets could be identified easily as these occurred at the fastest rate for all species. However, the rates of chewing different food items were more difficult to discern from one another. Comparison of chew:bite ratios of the various food types eaten by each species showed no differences. Species differences could be identified using bite and chew rates. Cattle consistently displayed slower bite and chew rates to sheep and pygmy goats when feeding, while sheep and pygmy goats showed similar bite and chew rates when feeding on concentrate pellets. Species-specific differences in chew:bite ratios were not identified. Magnetometry has the potential to record quantitative aspects of foraging such as the feeding duration, food handling time and food type. This is of major importance for researchers interested in both captive (e.g., agricultural productivity) and wild animal foraging dynamics as it can provide quantitative data with minimal observer interference. creator: Christina C. Mulvenna creator: Rory P. Wilson creator: Nikki J. Marks creator: Aaron G. Maule creator: David M. Scantlebury uri: https://doi.org/10.7717/peerj.5489 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mulvenna et al. title: TNFRSF10C methylation is a new epigenetic biomarker for colorectal cancer link: https://peerj.com/articles/5336 last-modified: 2018-09-13 description: BackgroundAbnormal methylation of TNFRSF10C was found to be associated with different types of cancers, excluding colorectal cancer (CRC). In this paper, the performance of TNFRSF10C methylation in CRC was studied in two stages.MethodThe discovery stage was involved with 38 pairs of CRC tumor and paired adjacent non-tumor tissues, and 69 pairs of CRC tumor and paired adjacent non-tumor tissues were used for the validation stage. Quantitative methylation specific PCR (qMSP) method and percentage of methylated reference (PMR) were used to test and represent the methylation level of TNFRSF10C, respectively. A dual-luciferase reporter gene experiment was conducted to evaluate the promoter activity of TNFRSF10C fragment.ResultsA significant association of TNFRSF10C promoter hypermethylation with CRC was found and validated (discovery stage: 24.67 ± 7.52 vs. 3.36 ± 0.89; P = 0.003; validation stage: 31.21 ± 12.48 vs. 4.52 ± 1.47; P = 0.0005). Subsequent analyses of TCGA data among 46 pairs of CRC samples further confirmed our findings (cg23965061: P = 4E − 6; cg14015044: P = 1E − 7). Dual-luciferase reporter gene assay revealed that TNFRSF10C fragment was able to significantly promote gene expression (Fold change = 2.375, P = 0.013). Our data confirmed that TNFRSF10C promoter hypermethylation can predict shorter overall survival of CRC patients (P = 0.032). Additionally, bioinformatics analyses indicated that TNFRSF10C hypermethylation was significantly associated with lower TNFRSF10C expression.ConclusionOur work suggested that TNFRSF10C hypermethylation was significantly associated with the risk of CRC. creator: Cong Zhou creator: Ranran Pan creator: Haochang Hu creator: Bin Li creator: Jie Dai creator: Xiuru Ying creator: Hang Yu creator: Jie Zhong creator: Yiyi Mao creator: Yihan Zhang creator: Dongping Wu creator: Shiwei Duan uri: https://doi.org/10.7717/peerj.5336 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhou et al. title: Distraction of cyclists: how does it influence their risky behaviors and traffic crashes? link: https://peerj.com/articles/5616 last-modified: 2018-09-12 description: BackgroundUndisputedly, traffic crashes constitute a public health concern whose impact and importance have been increasing during the past few decades. Specifically, road safety data have systematically shown how cyclists are highly vulnerable to suffering traffic crashes and severe injuries derived from them. Furthermore, although the empirical evidence is still very limited in this regard, in addition to other human factors involved in cycling crashes, distractions while cycling appear to be a major contributor to the road risk of cyclists.ObjectivesThe main objectives of this study were, first, to explore the prevalence and trends of cycling distractions within an international sample of bike users, and second, to determine the influence of such distractions on road crashes suffered by cyclists, simultaneously considering the explanatory role of risky behaviors (errors and traffic violations) as potentially mediating variables between cycling distractions and traffic crashes.MethodsFor this cross-sectional study, we analyzed the data obtained from 1,064 cyclists—61.2% male and 38.8% female—from 20 different countries, who answered an on-line questionnaire on cycling-related features, habits, behaviors and accidents.ResultsThe prevalence of different cycling distractions oscillated between 34.7% and 83.6%. The most common distractions were those related to the behavior of other users, physical elements of the road, weather conditions and phone calls. Age trends and differences were also found, thus establishing a positive association between age and distractibility during cycling. Furthermore, the effect of distractions on traffic crashes of cyclists was significant when tested together with age, risk perception and risky behaviors on the road.ConclusionThe results of this study support the hypotheses that distractions have a major prevalence among bike users, and that they play a significant role in the prediction of the traffic crash rates of cyclists, through the mediation of risky behaviors. creator: Sergio A. Useche creator: Francisco Alonso creator: Luis Montoro creator: Cristina Esteban uri: https://doi.org/10.7717/peerj.5616 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Useche et al. title: Molecular typing and profiling of topoisomerase mutations causing resistance to ciprofloxacin and levofloxacin in Elizabethkingia species link: https://peerj.com/articles/5608 last-modified: 2018-09-12 description: ObjectivesSeveral Elizabethkingia species often exhibit extensive antibiotic resistance, causing infections associated with severe morbidity and high mortality rates worldwide. In this study, we determined fluoroquinolone susceptibility profiles of clinical Elizabethkingia spp. isolates and investigated the resistance mechanisms.MethodsIn 2017–2018, 131 Elizabethkingia spp. isolates were recovered from specimens collected at tertiary care centers in northern Taiwan. Initial species identification using the Vitek MS system and subsequent verification by 16S rRNA sequencing confirmed the presence of Elizabethkingia anophelis (n = 111), E. miricola (n = 11), and E. meningoseptica (n = 9). Fluoroquinolone susceptibility was determined using the microbroth dilution method, and fluoroquinolone resistance genes were analyzed by sequencing.ResultsAmong Elizabethkingia spp. isolates, 91% and 77% were resistant to ciprofloxacin and levofloxacin, respectively. The most prevalent alterations were two single mutations in GyrA, Ser83Ile, and Ser83Arg, detected in 76% of the isolates exhibiting fluoroquinolone MIC between 8 and 128 μg/ml. Another GyrA single mutation, Asp87Asn, was identified in two quinolone-resistant E. miricola strains. None of the isolates had alterations in GyrB, ParC, or ParE. We developed a high-resolution melting assay for rapid identification of the prevalent gyrA gene mutations. The genetic relationship between the isolates was evaluated by random amplified polymorphic DNA PCR that yielded diverse pulsotypes, indicating the absence of any temporal or spatial overlap among the patients during hospitalization.ConclusionOur analysis of fluoroquinolone-resistant Elizabethkingia spp. isolates provides information for further research on the variations of the resistance mechanism and potential clinical guidance for infection management. creator: Ming-Jr Jian creator: Yun-Hsiang Cheng creator: Cherng-Lih Perng creator: Hung-Sheng Shang uri: https://doi.org/10.7717/peerj.5608 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Jian et al. title: Explanation of observational data engenders a causal belief about smoking and cancer link: https://peerj.com/articles/5597 last-modified: 2018-09-12 description: Most researchers do not deliberately claim causal results in an observational study. But do we lead our readers to draw a causal conclusion unintentionally by explaining why significant correlations and relationships may exist? Here we perform a randomized controlled experiment in a massive open online course run in 2013 that teaches data analysis concepts to test the hypothesis that explaining an analysis will lead readers to interpret an inferential analysis as causal. We test this hypothesis with a single example of an observational study on the relationship between smoking and cancer. We show that adding an explanation to the description of an inferential analysis leads to a 15.2% increase in readers interpreting the analysis as causal (95% confidence interval for difference in two proportions: 12.8%–17.5%). We then replicate this finding in a second large scale massive open online course. Nearly every scientific study, regardless of the study design, includes an explanation for observed effects. Our results suggest that these explanations may be misleading to the audience of these data analyses and that qualification of explanations could be a useful avenue of exploration in future research to counteract the problem. Our results invite many opportunities for further research to broaden the scope of these findings beyond the single smoking-cancer example examined here. creator: Leslie Myint creator: Jeffrey T. Leek creator: Leah R. Jager uri: https://doi.org/10.7717/peerj.5597 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Myint et al. title: A close relative of the Amazon river dolphin in marine deposits: a new Iniidae from the late Miocene of Angola link: https://peerj.com/articles/5556 last-modified: 2018-09-12 description: BackgroundA few odontocetes (echolocating toothed cetaceans) have been able to independently colonize freshwater ecosystems. Although some extant species of delphinids (true dolphins) and phocoenids (porpoises) at least occasionally migrate upstream of large river systems, they have close relatives in fully marine regions. This contrasts with the three odontocete families only containing extant species with a strictly freshwater habitat (Iniidae in South America, the recently extinct Lipotidae in China, and Platanistidae in southeast Asia). Among those, the fossil record of Iniidae includes taxa from freshwater deposits of South America, partly overlapping geographically with the extant Amazon river dolphin Inia geoffrensis, whereas a few marine species from the Americas were only tentatively referred to the family, leaving the transition from a marine to freshwater environment poorly understood.MethodsBased on a partial odontocete skeleton including the cranium, discovered in late Miocene (Tortonian-Messinian) marine deposits near the estuary of the Cuanza River, Angola, we describe a new large iniid genus and species. The new taxon is compared to other extinct and extant iniids, and its phylogenetic relationships with the latter are investigated through cladistic analysis.Results and DiscussionThe new genus and species Kwanzacetus khoisani shares a series of morphological features with Inia geoffrensis, including the combination of a frontal boss with nasals being lower on the anterior wall of the vertex, the laterally directed postorbital process of the frontal, the anteroposterior thickening of the nuchal crest, and robust teeth with wrinkled enamel. As confirmed (although with a low support) with the phylogenetic analysis, this makes the new taxon the closest relative of I. geoffrensis found in marine deposits. The geographic provenance of K. khoisani, on the eastern coast of South Atlantic, suggests that the transition from the marine environment to a freshwater, Amazonian habitat may have occurred on the Atlantic side of South America. This new record further increases the inioid diversity during the late Miocene, a time interval confirmed here as the heyday for this superfamily. Finally, this first description of a Neogene cetacean from inland deposits of western sub-Saharan Africa reveals the potential of this large coastal area for deciphering key steps of the evolutionary history of modern cetaceans in the South Atlantic. creator: Olivier Lambert creator: Camille Auclair creator: Cirilo Cauxeiro creator: Michel Lopez creator: Sylvain Adnet uri: https://doi.org/10.7717/peerj.5556 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lambert et al. title: Children are not like other loads: a cross-cultural perspective on the influence of burdens and companionship on human walking link: https://peerj.com/articles/5547 last-modified: 2018-09-12 description: A major portion of humans’ activity-based energy expenditure is taken up by locomotion, particularly walking. Walking behaviors have energetic outcomes and as such can be important windows into how populations and groups adjust to different environmental and task constraints. While sex differences in the speed of paired walkers have been established by others, the dynamics of how walkers adjust their speed in more varied groups and in groups containing children remains unexplored. Furthermore, little ecological data exists to illustrate the relationships between walking speed and child-carrying. Here, we aim to determine how culture impacts the effects of group composition and infant-carrying on walking speed. Because the determinants of group dynamics and parental investment are partially cultural, we examine walking behavior in the Northwestern United States and in Central Uganda. Using an observational method, we recorded the speed, load carriage, and group composition of pedestrians in a single naturalistic urban environment within each country. Our data suggest that children are treated fundamentally differently than other loads or the presence of walking partners, and that major speed adjustments are child-dependent. Our data furthermore indicate that Ugandans walk more slowly in groups than when alone, while Americans walk more quickly in groups. Clear distinctions between the groups make large generalizations about walking behavior difficult, and highlight the importance of culturally specific contexts. creator: Leah Bouterse creator: Cara Wall-Scheffler uri: https://doi.org/10.7717/peerj.5547 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bouterse and Wall-Scheffler title: Interaction of guidance types and the Need for Cognitive Closure in wiki-based learning link: https://peerj.com/articles/5541 last-modified: 2018-09-12 description: One purpose of wikis is the collaborative generation of content. During creation processes, controversies between authors emerge that they discuss on the article’s talk page. Research suggests that controversies based on opposing points of view and contradictory evidence can be fruitful to trigger individual elaboration processes. However, previous research also showed that many wikis are not necessarily suited to identify relevant discussion contents and thus users need additional support as guidance. In an experimental laboratory study (N = 181) on wiki talk pages, we investigated two guidance measures in conjunction with the need for cognitive closure: (1) visual markers to highlight controversy status (implicit guidance) and (2) a collaboration script that directs users towards discussions (explicit guidance). Effects on wiki processes and learning outcomes were analysed. The results show that both guidance types can affect user behaviours, but in interaction with the individual Need for Cognitive Closure there were no meaningful effects. With respect to learning outcomes, we found an anticipated pattern for the interaction of the Need for Cognitive Closure with both guidance principles. The data provides support for differences in the learning success depending on the provided guidance type and the individual Need for Cognitive Closure. creator: Sven Heimbuch creator: Daniel Bodemer uri: https://doi.org/10.7717/peerj.5541 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Heimbuch and Bodemer title: Effects of macroalgae loss in an Antarctic marine food web: applying extinction thresholds to food web studies link: https://peerj.com/articles/5531 last-modified: 2018-09-12 description: Antarctica is seriously affected by climate change, particularly at the Western Antarctic Peninsula (WAP) where a rapid regional warming is observed. Potter Cove is a WAP fjord at Shetland Islands that constitutes a biodiversity hotspot where over the last years, Potter Cove annual air temperatures averages increased by 0.66 °C, coastal glaciers declined, and suspended particulate matter increased due to ice melting. Macroalgae are the main energy source for all consumers and detritivores of Potter Cove. Some effects of climate change favor pioneer macroalgae species that exploit new ice-free areas and can also decline rates of photosynthesis and intensify competition between species due to the increase of suspended particulate matter. In this study, we evaluated possible consequences of climate change at Potter Cove food web by simulating the extinction of macroalgae and detritus using a topological approach with thresholds of extinction. Thresholds represent the minimum number of incoming links necessary for species’ survival. When we simulated the extinctions of macroalgae species at random, a threshold of extinction beyond 50% was necessary to obtain a significant number of secondary extinctions, while with a 75% threshold a real collapse of the food web occurred. Our results indicate that Potter Cove food web is relative robust to macroalgae extinction. This is dramatically different from what has been found in other food webs, where the reduction of 10% in prey intake caused a disproportionate increase of secondary extinctions. Robustness of the Potter Cove food web was mediated by omnivory and redundancy, which had an important relevance in this food web. When we eliminated larger-biomass species more secondary extinctions occurred, a similar response was observed when more connected species were deleted, yet there was no correlation between species of larger-biomass and high-degree. This similarity could be explained because both criteria involved key species that produced an emerging effect on the food web. In this way, large-biomass and high-degree species could be acting as source for species with few trophic interactions or low redundancy. Based on this work, we expect the Potter Cove food web to be robust to changes in macroalgae species caused by climate change until a high threshold of stress is reached, and then negative effects are expected to spread through the entire food web leading to its collapse. creator: Georgina Cordone creator: Tomás I. Marina creator: Vanesa Salinas creator: Santiago R. Doyle creator: Leonardo A. Saravia creator: Fernando R. Momo uri: https://doi.org/10.7717/peerj.5531 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cordone et al. title: An overview report on the application of heteropoly acids on supporting materials in the photocatalytic degradation of organic pollutants from aqueous solutions link: https://peerj.com/articles/5501 last-modified: 2018-09-12 description: Organic pollutants contaminate water resources and the environment when discharged into water streams. Also, the presence of these materials in incompletely treated or untreated wastewater leads to serious environmental hazards. The hydroxyl radicals and holes are regarded as the most oxidant species in the degradation of organic pollutants using the studied composites. The results of this review show that heteropoly acids on supporting materials could be considered as appropriate photocatalysts in the removal of organic pollutant from aqueous solutions. creator: Ali Nikoonahad creator: Babak Djahed creator: Samira Norzaee creator: Hadi Eslami creator: Zahra Derakhshan creator: Mohammad Miri creator: Yadolah Fakhri creator: Edris Hoseinzadeh creator: Seyed Mehdi Ghasemi creator: Davoud Balarak creator: Reza Ali Fallahzadeh creator: Mansur Zarrabi creator: Mahmoud Taghavi uri: https://doi.org/10.7717/peerj.5501 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Nikoonahad et al. title: Deep divergence of Red-crowned Ant Tanager (Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica link: https://peerj.com/articles/5496 last-modified: 2018-09-12 description: Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species’ distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation “diagonal” (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species. creator: Sandra M. Ramírez-Barrera creator: Blanca E. Hernández-Baños creator: Juan P. Jaramillo-Correa creator: John Klicka uri: https://doi.org/10.7717/peerj.5496 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ramírez-Barrera et al. title: The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome link: https://peerj.com/articles/5494 last-modified: 2018-09-12 description: Chemerin is an adipocyte derived signalling molecule (adipokine) that serves as a ligand activator of Chemokine-like receptor 1(CMKLR1). Chemerin/CMKLR1 signalling is well established to regulate fundamental processes in metabolism and inflammation. The composition and function of gut microbiota has also been shown to impact the development of metabolic and inflammatory diseases such as obesity, diabetes and inflammatory bowel disease. In this study, we assessed the microbiome composition of fecal samples isolated from wildtype, chemerin, or CMKLR1 knockout mice using Illumina-based sequencing. Moreover, the knockout mice and respective wildtype mice used in this study were housed at different universities allowing us to compare facility-dependent effects on microbiome composition. While there was no difference in alpha diversity within samples when compared by either facility or genotype, we observed a dramatic difference in the presence and abundance of numerous taxa between facilities. There were minor differences in bacterial abundance between wildtype and chemerin knockout mice, but significantly more differences in taxa abundance between wildtype and CMKLR1 knockout mice. Specifically, CMKLR1 knockout mice exhibited decreased abundance of Akkermansia and Prevotella, which correlated with body weight in CMKLR1 knockout, but not wildtype mice. This is the first study to investigate a linkage between chemerin/CMKLR1 signaling and microbiome composition. The results of our study suggest that chemerin/CMKLR1 signaling influences metabolic processes through effects on the gut microbiome. Furthermore, the dramatic difference in microbiome composition between facilities might contribute to discrepancies in the metabolic phenotype of CMKLR1 knockout mice reported by independent groups. Considered altogether, these findings establish a foundation for future studies to investigate the relationship between chemerin signaling and the gut microbiome on the development and progression of metabolic and inflammatory disease. creator: Helen J. Dranse creator: Ashlee Zheng creator: André M. Comeau creator: Morgan G.I. Langille creator: Brian A. Zabel creator: Christopher J. Sinal uri: https://doi.org/10.7717/peerj.5494 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dranse et al. title: Antiviral therapy effectively improves liver hemodynamics as evidenced by serum biomarker and contrast-enhanced ultrasound examinations in patients with hepatitis B cirrhosis link: https://peerj.com/articles/5484 last-modified: 2018-09-12 description: Background and AimsTo prospectively evaluate the effects of antiviral therapy on liver hemodynamics in patients with hepatitis B cirrhosis.MethodsSeventy consecutive eligible HBV-related cirrhotic inpatients were enrolled in the prospective study. Fifty-two received different nucleoside analogs monotherapy and 18 denied antiviral therapy. Their liver biochemistry profiles and HBV-DNA were measured at the baseline and every 3 months. Peripheral blood vWF and sCD163, as well as liver ultrasound Doppler parameters including portal vein diameter (PVD), portal vein velocity (PVV), portal vein congestion index (PV-CI), hepatic vein damping index (HV-DI), hepatic arterial arrival time (HAAT), hepatic vein arrival time (HVAT) and intrahepatic cycle time (HV-HA), were measured at the baseline and the follow-up periods.ResultsIn the antiviral group, all patients achieved complete virologic and liver biochemical responses after 3-month antiviral treatment. Furthermore, the response states were maintained till the follow-up endpoint. However, in the non-antiviral group, HBV DNA replication resulted in higher levels of ALT and AST compared to the baseline values (P < 0.05). In the antiviral group, PVD, PV-CI, HV-DI, vWF-Ag and sCD163 were all significantly reduced than the baseline values (P < 0.05), and PVV was significantly increased than the baseline value (P < 0.05).ConclusionsAntiviral therapy could effectively suppress hepatocyte inflammation and alleviate the dysfunction of intrahepatic vascular endothelial and hepatic macrophages, which might improve hepatic hemodynamic function in HBV-related cirrhosis. creator: Xiaoyong Xu creator: Chaoxue Zhang creator: Chen Shi creator: Naizhong Hu creator: Bin Sun creator: Derun Kong creator: Jianming Xu uri: https://doi.org/10.7717/peerj.5484 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Xu et al. title: Trust and distrust in information systems at the workplace link: https://peerj.com/articles/5483 last-modified: 2018-09-12 description: Digitalization of work processes is advancing, and this is increasingly supported by complex information systems (IS). However, whether such systems are used by employees largely depends on users’ trust in these IS. Because there are few systematic studies on this topic, this research provides an initial exploration and validation of preconditions for trust in work-related IS. In Study 1, N = 30 professionals were asked to describe occupational incidents in which they had highly trusted or distrusted an IS. Content analysis of 111 critical incidents described in the in-depth interviews led to 12 predictors of trust and distrust in IS, which partly correspond to the structure of the established IS success model (Delone & McLean, 2003) but also exceed this structure. The resulting integrative model of trust in IS at work was validated in Study 2 using an online questionnaire with N = 179 professionals. Based on regression analyses, reliability (system quality) and credibility (information quality) of IS were identified as the most important predictors for both trust and distrust in IS at work. Contrasting analyses revealed diverging qualities of trust and distrust in IS : whereas well-being and performance were rated higher in trust events, experienced strain was rated higher in distrust events. Together, this study offers a first comprehensive model of trust in IS at work based on systematic empirical research. In addition to implications for theory advancement, we suggest practical implications for how to support trust and to avoid distrust in IS at work. creator: Meinald T. Thielsch creator: Sarah M. Meeßen creator: Guido Hertel uri: https://doi.org/10.7717/peerj.5483 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Thielsch et al. title: Multielement analysis of plant extracts with potential use in the treatment of peptic ulcers by synchrotron radiation total reflection X-ray fluorescence link: https://peerj.com/articles/5375 last-modified: 2018-09-12 description: Some plants popularly employed for the treatment of peptic ulcers have proved to be attractive sources of new drugs. Despite extensive research, the pharmacological and toxicological potentials of these plants are not fully understood. In this context, the aim of this work was to analyze the multielemental composition of the methanolic extracts of three of those plants, Alchornea glandulosa (AG), Davilla elliptica (DE) and Davilla nitida (DN), with the intention of contributing to the understanding of the mechanisms of action of these extracts. For this purpose, we used the analytical technique of total reflection X-ray fluorescence (TXRF) by synchrotron radiation at the Brazilian Synchrotron Light Source (LNLS/CNPEM). It was possible to determine the concentrations of the elements: P, S, Cl, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, Rb and Br in all of the samples. Selenium (Se) was detected only in the DN extract. An inverse relationship between the concentrations of elements with proven effectiveness and the gastroprotective activity of extracts considering induction protocols with ethanol and non-steroidal anti-inflammatory drugs (NSAIDs) was obtained. This data suggests that the function of the extract is not only associated with providing the elements for restoring the gastric mucosa but that it also promotes the displacement of these elements from other parts of the mucosa to the damaged area. Correlations between the concentrations of the elements were also obtained. In the DE extract, which is the most effective extract for both induction protocols, the obtained correlations were above 70% among almost all of the elements, and no anticorrelations were found. For the other two extracts, in the less effective extract (AG) anticorrelations above 70% were predominantly found. Meanwhile, in the DN extract, a few high anticorrelations were found, which may explain its intermediate stage of effectiveness. creator: Leticia Diniz Vieira creator: Káthia Takeda da Silva creator: Rodrigo Sanchez Giarola creator: Guilherme Franco Inocente creator: Hélio Kushima creator: Clelia Akiko Hiruma Lima creator: Joel Mesa Hormaza uri: https://doi.org/10.7717/peerj.5375 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vieira et al. title: Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae) link: https://peerj.com/articles/5573 last-modified: 2018-09-11 description: Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent. creator: Artur Burzyński creator: Marianna Soroka uri: https://doi.org/10.7717/peerj.5573 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Burzyński and Soroka title: Data challenges of biomedical researchers in the age of omics link: https://peerj.com/articles/5553 last-modified: 2018-09-11 description: BackgroundHigh-throughput technologies are rapidly generating large amounts of diverse omics data. Although this offers a great opportunity, it also poses great challenges as data analysis becomes more complex. The purpose of this study was to identify the main challenges researchers face in analyzing data, and how academic libraries can support them in this endeavor.MethodsA multimodal needs assessment analysis combined an online survey sent to 860 Yale-affiliated researchers (176 responded) and 15 in-depth one-on-one semi-structured interviews. Interviews were recorded, transcribed, and analyzed using NVivo 10 software according to the thematic analysis approach.ResultsThe survey response rate was 20%. Most respondents (78%) identified lack of adequate data analysis training (e.g., R, Python) as a main challenge, in addition to not having the proper database or software (54%) to expedite analysis. Two main themes emerged from the interviews: personnel and training needs. Researchers feel they could improve data analyses practices by having better access to the appropriate bioinformatics expertise, and/or training in data analyses tools. They also reported lack of time to acquire expertise in using bioinformatics tools and poor understanding of the resources available to facilitate analysis.ConclusionsThe main challenges identified by our study are: lack of adequate training for data analysis (including need to learn scripting language), need for more personnel at the University to provide data analysis and training, and inadequate communication between bioinformaticians and researchers. The authors identified the positive impact of medical and/or science libraries by establishing bioinformatics support to researchers. creator: Rolando Garcia-Milian creator: Denise Hersey creator: Milica Vukmirovic creator: Fanny Duprilot uri: https://doi.org/10.7717/peerj.5553 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Garcia-Milian et al. title: Tibia functionality and Division II female and male collegiate athletes from multiple sports link: https://peerj.com/articles/5550 last-modified: 2018-09-11 description: BackgroundBone strength is developed through a combination of the size and shape (architecture) of a bone as well as the bone’s material properties; and therefore, no one outcome variable can measure a positive or negative adaptation in bone. Skeletal robusticity (total area/ bone length) a measure of bones external size varies within the population and is independent of body size, but robusticity has been associated with bone strength. Athletes may have similar variability in robusticity values as the general population and thus have a wide range of bone strengths based on the robustness of their bones. Therefore, the purpose of this study was to determine if an athlete’s bone strength and cortical area relative to body size was dependent on robusticity. The second aim was to determine if anthropometry or muscle function measurements were associated with bone robusticity.MethodsBone variables contributing to bone strength were measured in collegiate athletes and a reference group using peripheral quantitative computed tomography (pQCT) at the 50% tibial site. Bone functionality was assessed by plotting bone strength and cortical area vs body size (body weight x tibial length) and robustness (total area/length) vs body size. Bone strength was measured using the polar strength-strain index (SSIp). Based on the residuals from the regression, an athlete’s individual functionality was determined, and two groups were formed “weaker for size” (WS) and “stronger for size” (SS). Grip strength, leg extensor strength and lower body power were also measured.ResultsDivision II athletes exhibited a natural variation in (SSIp) relative to robusticity consistent with previous studies. Bone strength (SSIp) was dependent on the robusticity of the tibia. The bone traits that comprise bone strength (SSIp) were significantly different between the SS and WS groups, yet there were minimal differences in the anthropometric data and muscle function measures between groups. A lower percentage of athletes from ball sports were “weaker for size” (WS group) and a higher percentage of swimmers were in the WS group.DiscussionA range of strength values based on robusticity occurs in athletes similar to general populations. Bones with lower robusticity (slender) were constructed with less bone tissue and had less strength. The athletes with slender bones were from all sports including track and field and ball sports but the majority were swimmers.ConclusionsAthletes, even after optimal training for their sport, may have weaker bones based on robusticity. Slender bones may therefore be at a higher risk for fracture under extreme loading events but also yield benefits to some athletes (swimmers) due to their lower bone mass. creator: Vanessa R. Yingling creator: Benjamin Ferrari-Church creator: Ariana Strickland uri: https://doi.org/10.7717/peerj.5550 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yingling et al. title: A short, robust brain activation control task optimised for pharmacological fMRI studies link: https://peerj.com/articles/5540 last-modified: 2018-09-11 description: BackgroundFunctional magnetic resonance imaging (fMRI) is a popular method for examining pharmacological effects on the brain; however, the BOLD response is dependent on intact neurovascular coupling, and potentially modulated by a number of physiological factors. Pharmacological fMRI is therefore vulnerable to confounding effects of pharmacological probes on general physiology or neurovascular coupling. Controlling for such non-specific effects in pharmacological fMRI studies is therefore an important consideration, and there is an additional need for well-validated fMRI task paradigms that could be used to control for such effects, or for general testing purposes.MethodsWe have developed two variants of a standardized control task that are short (5 minutes duration) simple (for both the subject and experimenter), widely applicable, and yield a number of readouts in a spatially diverse set of brain networks. The tasks consist of four functionally discrete three-second trial types (plus additional null trials) and contain visual, auditory, motor and cognitive (eye-movements, and working memory tasks in the two task variants) stimuli. Performance of the tasks was assessed in a group of 15 subjects scanned on two separate occasions, with test-retest reliability explicitly assessed using intra-class correlation coefficients.ResultsBoth tasks produced robust patterns of brain activation in the expected brain regions, and region of interest-derived reliability coefficients for the tasks were generally high, with four out of eight task conditions rated as ‘excellent’ or ‘good’, and only one out of eight rated as ‘poor’. Median values in the voxel-wise reliability measures were also >0.7 for all task conditions, and therefore classed as ‘excellent’ or ‘good’. The spatial concordance between the most highly activated voxels and those with the highest reliability coefficients was greater for the sensory (auditory, visual) conditions than the other (motor, cognitive) conditions.DiscussionEither of the two task variants would be suitable for use as a control task in future pharmacological fMRI studies or for any other investigation where a short, reliable, basic task paradigm is required. Stimulus code is available online for re-use by the scientific community. creator: Jessica-Lily Harvey creator: Lysia Demetriou creator: John McGonigle creator: Matthew B. Wall uri: https://doi.org/10.7717/peerj.5540 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Harvey et al. title: DNA mismatch repair and CD133-marked cancer stem cells in colorectal carcinoma link: https://peerj.com/articles/5530 last-modified: 2018-09-11 description: BackgroundExcept for a few studies with contradictory observations, information is lacking on the possibility of association between DNA mismatch repair (MMR) status and the presence of cancer stem cells in colorectal carcinoma (CRC), two important aspects in colorectal carcinogenesis.MethodsEighty (40 right-sided and 40 left-sided) formalin-fixed, paraffin-embedded primary CRC were immunohistochemically studied for CD133, a putative CRC stem cell marker, and MMR proteins MLH1, MSH2, MSH6 and PMS2. CD133 expression was semi-quantitated for proportion of tumor immunopositivity on a scale of 0–5 and staining intensity on a scale of 0–3 with a final score (units) being the product of proportion and intensity of tumor staining. The tumor was considered immunopositive only when the tumor demonstrated moderate to strong intensity of CD133 staining (a decision made after analysis of CD133 expression in normal colon). Deficient MMR (dMMR) was interpreted as unequivocal loss of tumor nuclear staining for any MMR protein despite immunoreactivity in the internal positive controls.ResultsCD133 was expressed in 36 (90.0%) left-sided and 28 (70.0%) right-sided tumors (p < 0.05) and CD133 score was significantly higher in left- (mean ± SD = 9.6 ± 5.3 units) compared with right-sided tumors (mean ± SD = 6.8 ± 5.6 units) p < 0.05). dMMR was noted in 14 (35%) right-sided and no (0%) left-sided CRC. When stratified according to MMR status, dMMR cases showed a lower frequency of CD133 expression (42.9%) and CD133 score (mean ± SD = 2.5 ± 3.6 units) compared with pMMR tumors on the right (frequency = 84.6%; mean score ± SD = 9.2 ± 5.0 units) as well as pMMR tumors on the left (frequency = 90.0%; mean score ± SD = 9.6 ± 5.3 units) (p < 0.05). Interestingly, frequencies of CD133 immunoreactivity and CD133 scores did not differ between pMMR CRC on the right versus the left (p > 0.05).ConclusionProficient MMR correlated with high levels of CD133-marked putative cancer stem cells in both right- and left-sided tumors, whereas significantly lower levels of CD133-marked putative cancer stem cells were associated with deficient MMR status in colorectal carcinomas found on the right. creator: Phaik-Leng Cheah creator: Jing Li creator: Lai-Meng Looi creator: Kean-Hooi Teoh creator: Diana Bee-Lan Ong creator: Mark J. Arends uri: https://doi.org/10.7717/peerj.5530 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cheah et al. title: Growth under cold conditions in a wide perennial ryegrass panel is under tight physiological control link: https://peerj.com/articles/5520 last-modified: 2018-09-11 description: BackgroundPerennial ryegrass is a cool-season grass species from the family Poaceae and is widely cultivated in temperate regions because it exhibits rapid growth and establishment, and possesses high forage quality. The extension of the growing season in Ireland in spring and autumn is a breeding target to make farming more profitable since a grass-fed diet based on grazing is the cheapest way of nutrition for ruminants.MethodsFifty-seven perennial ryegrass accessions were screened for their ability to grow under typical Irish spring conditions as taken from long term temperature records in controlled climate chambers. They were grown in low temperature (8 °C/2 °C day/night) and control conditions (15 °C/8 °C day/night) in three consecutive independent experiments. Fresh weight, height, chlorophyll content and electrolyte leakage were measured, and these parameters were used to rank plant performance under low temperature growth conditions.ResultsThe results showed that height, yield and electrolyte leakage are excellent measures for the impact of cold stress tolerance. Little variation in growth was seen under cold stress, but a wide variety of responses were observed under control conditions.DiscussionOur results suggest that cold stress is under tight physiological control. Interestingly, the various genotypes responded differentially to more amenable control conditions, indicating that a quick response to more amenable growth conditions is a better target for breeding programmes. creator: Lena Förster creator: Jim Grant creator: Thibauld Michel creator: Carl Ng creator: Susanne Barth uri: https://doi.org/10.7717/peerj.5520 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Förster et al. title: A comparison of perceptions of nuts between the general public, dietitians, general practitioners, and nurses link: https://peerj.com/articles/5500 last-modified: 2018-09-11 description: BackgroundNut consumption at the population level remains low despite the well-documented benefits of their consumption, including their cardioprotective effects. Studies have suggested that advice from health professionals may be a means to increase nut consumption levels. Understanding how nuts are perceived by the public and health professionals, along with understanding the public’s perceptions of motivators of and deterrents to consuming nuts, may inform the development of initiatives to improve on these low levels of consumption. The aim of this cross-sectional study was to compare perceptions of nuts among three groups of health professionals (dietitians, general practioners, and practice nurses) and the general public in New Zealand (NZ), along with motivators of and deterrents to consuming nuts amongst the general public and their experiences of receiving advice around nut consumption.MethodsThe NZ electoral roll was used to identify dietitians, general practitioners (GPs), and practice nurses, based on their free-text occupation descriptions, who were then invited to complete a questionnaire with 318, 292, and 149 respondents respectively. 1,600 members of the general public were randomly selected from the roll with 710 respondents. Analyses were performed using chi-squared tests to look at differences in categorical variables and linear regression for differences in other variables between the four survey groups.ResultsAlthough there were significant differences between the four groups regarding the perceptions of nuts, in general there was agreement that nuts are healthy, high in protein and fat, are filling, and some nuts are high in selenium. We noted frequent agreement that the general public participants would consume more if nuts: improved health (67%), were more affordable (60%), or improved the nutrient content (59%) and balance of fats (58%) within their diets. Over half the respondents reported they would eat more nuts if they were advised to do so by a dietitian or doctor, despite less than 4% reporting they had received such advice. The most frequently selected deterrents to increasing nut consumption were: cost (67%), potential weight gain (66%), and leading to eating too much fat (63%).DiscussionIt is concerning that so few among the general public report receiving advice to consume more nuts from health professionals, especially given their apparent responsiveness to such advice. Health professionals could exploit the motivators of nut consumption, while also addressing the deterrents, to promote nut intake. These factors should also be addressed in public health messages to encourage regular nut consumption among the public. Educational initiatives could also be used to improve the nutritional knowledge of GPs and practice nurses with regard to nuts, although even dietitians were unsure of their knowledge in some cases. creator: Rachel Clare Brown creator: Andrew Robert Gray creator: Lee Ching Yong creator: Alex Chisholm creator: Sook Ling Leong creator: Siew Ling Tey uri: https://doi.org/10.7717/peerj.5500 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brown et al. title: A novel experimental design for the measurement of metacarpal bone loading and deformation and fingertip force link: https://peerj.com/articles/5480 last-modified: 2018-09-11 description: BackgroundMusculoskeletal and finite element modelling are often used to predict joint loading and bone strength within the human hand, but there is a lack of in vitro evidence of the force and strain experienced by hand bones.MethodsThis study presents a novel experimental setup that allows the positioning of a cadaveric digit in a variety of postures with the measurement of force and strain experienced by the third metacarpal. The setup allows for the measurement of fingertip force as well. We tested this experimental setup using three cadaveric human third digits in which the flexor tendons were loaded in two tendon pathways: (1) parallel to the metacarpal bone shaft, with bowstringing; (2) a semi-physiological condition in which the tendons were positioned closer to the bone shaft.ResultsThere is substantial variation in metacarpal net force, metacarpal strain and fingertip force between the two tendon pathways. The net force acting on the metacarpal bone is oriented palmarly in the parallel tendon condition, causing tension along the dorsum of the metacarpal shaft, while the force increases and is oriented dorsally in the semi-physiological condition, causing compression of the dorsal metacarpal shaft. Fingertip force is also greater in the semi-physiological condition, implying a more efficient grip function. Inter-individual variation is observed in the radioulnar orientation of the force experienced by the metacarpal bone, the fingertip force, and the strain patterns on the metacarpal shaft.ConclusionThis study demonstrates a new method for measuring force and strain experienced by the metacarpal, and fingertip force in cadaveric digits that can, in turn, inform computation models. Inter-individual variation in loads experienced by the third digit suggest that there are differences in joint contact and/or internal bone structure across individuals that are important to consider in clinical and evolutionary contexts. creator: Szu-Ching Lu creator: Evie E. Vereecke creator: Alexander Synek creator: Dieter H. Pahr creator: Tracy L. Kivell uri: https://doi.org/10.7717/peerj.5480 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lu et al. title: Effects of resveratrol, exercises and their combination on Farnesoid X receptor, Liver X receptor and Sirtuin 1 gene expression and apoptosis in the liver of elderly rats with nonalcoholic fatty liver link: https://peerj.com/articles/5522 last-modified: 2018-09-10 description: BackgroundNon-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder. This study aims to consider effects of resveratrol, exercise and their combination on Farnesoid X receptor (Fxr), the liver X receptor (Lxr) and Sirtuin 1 (Sirt 1) genes expression in the liver of elderly rats with NAFLD.MethodsRats with NAFLD were randomly divided into seven groups including patient, saline, resveratrol (RSV), interval exercise, continuous exercise, interval exercise + RSV and continuous exercise + RSV. Levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP) in the liver tissue were measured using specific ELISA kits. A TUNEL assay kit was used for the assessment of hepatic cells apoptosis. Lipid profiles were considered by measuring the serum triglyceride, cholesterol, LDL, and HDL. Expression of Sirt1, Lxr and Fxr genes was considered using RT-PCR.ResultsResveratrol administration alone or combined with exercise training significantly improved the expression of Sirt1, Lxr and Fxr genes (p < 0.05) in the hepatic tissue of rats with NAFLD, while levels of AST, ALT, ALP enzymes, as well as apoptotic cells were significantly decreased (p < 0.05).DiscussionAlthough resveratrol alone improves the expression of Sirt1, Lxr and Fxr, as well as liver function, combined therapy with exercise training is more effective to improve NAFLD. creator: Amir Hajighasem creator: Parvin Farzanegi creator: Zohreh Mazaheri creator: Marjan Naghizadeh creator: Ghoncheh Salehi uri: https://doi.org/10.7717/peerj.5522 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hajighasem et al. title: Association of burnout with doctor–patient relationship and common stressors among postgraduate trainees and house officers in Lahore—a cross-sectional study link: https://peerj.com/articles/5519 last-modified: 2018-09-10 description: IntroductionBurnout is defined as a prolonged state of physical and psychological exhaustion. Doctors, due to the demanding nature of their job, are susceptible to facing burnout, which has far reaching implications on their productivity and motivation. It affects the quality of care they provide to patients, thus eroding the doctor–patient relationship which embodies patient centeredness and autonomy. The study aims at addressing the stressors leading to burnout and its effect on the doctor–patient relationship.MethodsA descriptive, cross-sectional study design with convenience (non-probability) sampling technique was employed in six major hospitals of Lahore, Pakistan. A total of 600 doctors were approached for the study which included house officers or “HOs” (recent graduates doing their 1 year long internship) and post-graduate trainees or “PGRs” (residents for 4–5 years in their specialties). Burnout was measured using the Copenhagen Burnout Inventor (CBI) while attitudes towards the doctor–patient relationship was measured using the Patient Practitioner Orientation Scale (PPOS), which measures two components of the relationship: power sharing and patient caring. Pearson correlation and linear regression analysis were used to analyze the data via SPSS v.21.ResultsA total of 515 doctors consented to take part in the study (response rate 85.83%). The final sample consisted of 487 doctors. The burnout score was not associated with the total and caring domain scores of PPOS (P > 0.05). However, it was associated with the power sharing sub-scale of PPOS. Multiple linear regression analysis yielded a significant model, by virtue of which CBI scores were positively associated with factors such as female gender, feeling of burn out, scoring high on sharing domain of PPOS and a lack of personal control while CBI scores were negatively associated with private medical college education, having a significant other, accommodation away from home and a sense of never ending competition. Burnout levels varied significantly between house officers and post graduate trainees. Twenty-three percent of the participants (mostly house officers) had high/very high burnout levels on the CBI (Kristenson’s burnout scoring). Both groups showed significant differences with respect to working hours, smoking status and income.ConclusionAlthough burnout showed no significant association with total and caring domain scores of PPOS (scale used to assess doctor–patient relationship), it showed a significant association with the power sharing domain of PPOS suggesting some impact on the overall delivery of patient care. Thus, it necessitates the monitoring of stressors in order to provide an atmosphere where patient autonomy can be practiced. creator: Waqas Ahmad creator: Huma Ashraf creator: Afnan Talat creator: Aleena Ahmad Khan creator: Ammad Anwar Baig creator: Iqra Zia creator: Zohak Sarfraz creator: Hifsa Sajid creator: Marium Tahir creator: Usman Sadiq creator: Hira Imtiaz uri: https://doi.org/10.7717/peerj.5519 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ahmad et al. title: Effects of environmental and anthropogenic landscape features on mule deer harvest in Nebraska link: https://peerj.com/articles/5510 last-modified: 2018-09-10 description: Understanding the habitat use of wildlife species is important for effective management. Nebraska has a variety of habitat types, with the majority being covered by rangeland and cropland. These habitat types likely influence the harvest of mule deer (MD; Odocoileus hemionus) in Nebraska, but their specific effects are unknown, and moreover, harvest may also be influenced by the accessibility of deer habitats for hunters. We modeled which environmental and anthropogenic landscape features influenced harvest densities. Spatial analysis in a Geographic Information System was used to determine the mean values of environmental and anthropogenic landscape features at the county level. We then used a generalized linear model to determine which of those factors influenced MD harvest from 2014–2016. We found that NDVI amplitude, hunter effort, road density, terrain roughness, and canopy cover influence MD harvest in Nebraska. According to our model, MD harvest densities are significantly greater areas with NDVI amplitude ∼38, increasing hunter effort, road densities near 1,750 m/km2, increasing terrain roughness, and decreasing canopy cover. Understanding increased harvest densities of MD can be beneficial for wildlife managers, allowing for more efficient allocation of efforts and expenses by managers for population management. creator: Bryan J. O’Connor creator: Nicolas J. Fryda creator: Dustin H. Ranglack uri: https://doi.org/10.7717/peerj.5510 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 O’Connor et al. title: Unconscious response inhibition differences between table tennis athletes and non-athletes link: https://peerj.com/articles/5548 last-modified: 2018-09-07 description: BackgroundResponse inhibition is associated with successful sporting performance. However, research on response inhibition in athletes from open-skill sports has mainly focused on a consciously triggered variety; little is known about open-skill athletes’ response inhibition elicited by unconscious stimuli.MethodsHere, we explored unconscious response inhibition differences between table tennis athletes (n = 20) and non-athletes (n = 19) using the masked go/no-go task and event-related potentials technique (ERPs).ResultsAt the behavioral level, table tennis athletes displayed shorter go-response times (RTs) than non-athletes in the conscious condition. Furthermore, table tennis athletes exhibited longer response time–slowing (RT-slowing) than non-athletes in the unconscious condition. At the neural level, table tennis athletes displayed shorter event-related potential N2 component latencies than non-athletes for all conditions. More importantly, athletes displayed larger no-go event-related potential P3 component amplitudes than non-athletes at both the conscious and unconscious levels.DiscussionThe present study results suggested that table tennis athletes have superior conscious and unconscious response inhibition compared to non-athletes. creator: Yihong You creator: Yiming Ma creator: Zhiguang Ji creator: Fanying Meng creator: Anmin Li creator: Chunhua Zhang uri: https://doi.org/10.7717/peerj.5548 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 You et al. title: Measurement matters: higher waist-to-hip ratio but not body mass index is associated with deficits in executive functions and episodic memory link: https://peerj.com/articles/5624 last-modified: 2018-09-07 description: BackgroundThe current study aimed to reconcile the inconsistent findings between obesity, executive functions, and episodic memory by addressing major limitations of previous studies, including overreliance on body mass index (BMI), small sample sizes, and failure to control for confounds.MethodsParticipants consisted of 3,712 midlife adults from the Cognitive Project of the National Survey of Midlife Development. Executive functions and episodic memory were measured by a battery of cognitive function tests.ResultsWe found that higher waist-to-hip ratio was associated with deficits in both executive functions and episodic memory, above and beyond the influence of demographics, comorbid health issues, health behaviors, personality traits, and self-perceived obesity. However, higher BMI was not associated with deficits in executive functions and episodic memory. More importantly, these differential associations were robust and stable across adulthood.DiscussionOur findings confirm the association between obesity and episodic memory while highlighting the need for better measures of obesity when examining its associations with individual differences in cognitive functions. creator: Andree Hartanto creator: Jose C. Yong uri: https://doi.org/10.7717/peerj.5624 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hartanto and Yong title: A bathypelagic ostracod Conchoecissa nigromaculatus sp. nov. (Myodocopa, Halocyprididae) from the South China Sea link: https://peerj.com/articles/5557 last-modified: 2018-09-07 description: Pelagic ostracods are one of the main groups of zooplankton and are abundant in marine ecosystems worldwide. The record of marine planktonic ostracod species in the central and southern part of the South China Sea accounts over for one-third of the total recorded marine planktonic ostracods in seas around China. In this study, we examined and compared the specimens from a recent cruise in this region that appeared to be different from previously described species of genus Conchoecissa, and then confirmed them as a new bathypelagic species Conchoecissa nigromaculatus. These specimens clearly differed from the other species of genus Conchoecissa with differences observed in the size, carapace, locations of glands, mandible, maxilla, sixth limb, and furca. In this species, mandibular coxal endite has no ventral finger process, maxilla has prominently large endites and has only two claws on the tip, the sixth limb has very simple endites, and this species has distinctive features not previously observed in the tribe Conchoeciini before. It is therefore necessary to emend the diagnosis of this group. creator: Peng Xiang creator: Yu Wang creator: Ruixiang Chen creator: Liyuan Zhao creator: Chunguang Wang creator: Mao Lin uri: https://doi.org/10.7717/peerj.5557 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Xiang et al. title: Dietary diversity is inversely correlated with pre-pregnancy body mass index among women in a Michigan pregnancy cohort link: https://peerj.com/articles/5526 last-modified: 2018-09-07 description: BackgroundDuring pregnancy, healthy maternal body weight and a nutritionally complete diet provide a favorable environment for fetal development. Yet nearly two-thirds of women of reproductive age in the United States (US) are either overweight or obese. The objective of this research was to investigate the relationship between a measure of dietary diversity and body mass index (BMI) in a sample of women enrolled in a US pregnancy cohort.MethodsDietary data was obtained from one 24-hour dietary recall collected during the third trimester of pregnancy (n = 40). Pre-pregnancy BMI was calculated from pre-pregnancy weight and height self-reported by survey at the time of enrollment. Using the Minimum Dietary Diversity for Women (MDD-W) indicator developed by the Food and Agriculture Organization of the United Nations, dietary data was categorized and scored.ResultsOverall, 35% of participants did not achieve minimum dietary diversity (MDD-W ≥5). In addition, 45% of participants were obese, 35% were normal weight and 20% were overweight. Women with higher BMI had lower MDD-W scores than women with lower BMI (p < 0.05). The median MDD-W for both normal and overweight women was ≥5 indicating that normal and overweight pregnant women tended to consume a diet that was high in micronutrients. Conversely, the median MDD-W for obese women was below 5 meaning these women tended to consume a diet that was low in micronutrient density. The most commonly consumed food group was grain. In addition, 75% of all participants consumed sweetened drinks. Individuals with an MDD-W score ≥5, were more likely to have consumed dark green leafy vegetables, vitamin A-rich fruits or vegetables, other vegetables and other fruits than those with MDD-W scores <5.DiscussionIn this study, we show that a food group diversity indicator that has been shown to reflect adequacy of micronutrient intake in populations from less economically developed countries may also be informative in US populations. Furthermore, these results reflect the importance of encouraging all pregnant women with less varied diets to consume more fruits and vegetables. creator: Breanna M. Kornatowski creator: Sarah S. Comstock uri: https://doi.org/10.7717/peerj.5526 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kornatowski and Comstock title: The palaeoenvironment of the Upper Cretaceous (Cenomanian–Turonian) portion of the Winton Formation, Queensland, Australia link: https://peerj.com/articles/5513 last-modified: 2018-09-07 description: The Winton Formation is increasingly recognised as an important source of information about the Cretaceous of Australia, and, more broadly, the palaeobiogeographic history of eastern Gondwana. With more precise dating and stratigraphic controls starting to provide temporal context to the geological and palaeontological understanding of this formation, it is timely to reassess the palaeoenvironment in which it was deposited. This new understanding helps to further differentiate the upper, most-studied portion of the formation (Cenomanian–Turonian) from the lower portions (Albian–Cenomanian), allowing a coherent picture of the ecosystem to emerge. Temperatures during the deposition of the Upper Cretaceous portion of the Winton Formation were warm, with high, seasonal rainfall, but not as extreme as the modern monsoon. The landscape was heterogeneous, a freshwater alluvial plain bestrode by low energy, meandering rivers, minor lakes and mires. Infrequent, scouring flood events were part of a multi-year cycle of drier and wetter years. The heavily vegetated flood plains supported abundant large herbivores. This was the final infilling of the great Eromanga Basin. creator: Tamara L. Fletcher creator: Patrick T. Moss creator: Steven W. Salisbury uri: https://doi.org/10.7717/peerj.5513 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fletcher et al. title: Primary molt in Gruiforms and simpler molt summary tables link: https://peerj.com/articles/5499 last-modified: 2018-09-07 description: Molt summary tables reveal the sequence and mode of flight-feather replacement and how these feathers are divided into independent replacement series. Tables for summarizing molt are relatively new, and the rules for generating them were first formally illustrated using data from a temperate passerine. However, this first illustration failed to address (i) species with primaries divided into more than one replacement series, (ii) species with stepwise primary replacement, which almost always involves incomplete annual replacement of the primaries, and (iii) species with incomplete annual replacement within molt series characterized by single-wave replacement. Here, we review complications that arise in developing molt summary tables for such cases and we offer solutions that remove ambiguity about the direction that molt proceeds within a replacement series and about the recognition of nodal and terminal feathers that mark the beginning and end of molt series. We use these modified molt summary tables to describe the sequence of primary replacement in four groups of Gruiform birds, a group for which primary replacement has been reported to proceed from the outermost primary toward the body, unlike most other birds. Eighty molting Grey-winged Trumpeters, Psophia crepitans, and 124 molting Limpkins, Aramus guarauna, show the sequence of primary replacement is proximal in both groups; furthermore, the primaries of trumpeters are divided into two replacement series, one beginning at the outermost primary P10, and the other beginning at P3. To further evaluate the extent of this highly unusual direction of replacement in Gruiforms, we cast the data (Stresemann & Stresemann, 1966) on primary replacement in upland rails (Rallidae) and flufftails (Sarothruridae) into molt summary tables; both also replace their primaries proximally, from outermost to innermost, suggesting that this mode of primary replacement may be characteristic of Gruiformes. creator: Sievert Rohwer creator: Vanya G. Rohwer uri: https://doi.org/10.7717/peerj.5499 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rohwer and Rohwer title: Biodiversity surveys reveal eight new species of freshwater crabs (Decapoda: Brachyura: Potamidae) from Yunnan Province, China link: https://peerj.com/articles/5497 last-modified: 2018-09-07 description: Yunnan Province is known to host the highest species diversity of the true freshwater crabs in China; 50 species have been recorded from the province by 2017. In 2004, our team conducted a biodiversity survey of the freshwater crabs in Yunnan Province to determine how well the diversity of crabs in the area has been characterized. We collected a total of 25 species, of which nine species proved to be new to science, and eight of which are described here. These include four species of the genus IndochinamonYeo & Ng, 2007, two species of the genus PotamiscusAlcock, 1909, and one species each of the genera PararangunaDai & Chen, 1985, and ParvuspotamonDai & Bo, 1994. The new species of Pararanguna and Parvuspotamon represent the second species of respective genera, which are here redefined. Detailed comparisons with morphologically allied species are provided. Photographs of the type specimens of their comparative species which are poorly illustrated in the literature are also provided to allow better understanding of their morphology. This study brings the number of the freshwater crabs of Yunnan Province to 58. Since about 13.8% of the number of species (eight out of 58 species) is increased by surveys conducted within a relatively short period, it is most probable that the species diversity of this group is still understudied in Yunnan Province. creator: Tohru Naruse creator: Jing En Chia creator: Xianmin Zhou uri: https://doi.org/10.7717/peerj.5497 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Naruse et al. title: Flower-mediated plant-butterfly interactions in an heterogeneous tropical coastal ecosystem link: https://peerj.com/articles/5493 last-modified: 2018-09-07 description: BackgroundInterspecific interactions play an important role in determining species richness and persistence in a given locality. However at some sites, the studies, especially for interaction networks on adult butterflies are scarce. The present study aimed the following objectives: (1) determine butterfly species richness and diversity that visit flowering plants, (2) compare species richness and diversity in butterfly-plant interactions among six different vegetation types and (3) analyze the structure of butterfly-flowering plant interaction networks mediated by flowers.MethodsThe study was developed in six vegetation types within the natural reserve of La Mancha, located in Veracruz, Mexico. In each vegetation type, we recorded the frequency of flower visits by butterflies monthly in round plots (of radius 5 m) for 12 months. We calculated Shannon diversity for butterfly species and diversity of interactions per vegetation type. We determined the classic Jaccard similarity index among vegetation types and estimated parameters at network and species-level.ResultsWe found 123 species of butterflies belonging to 11 families and 87 genera. The highest number of species belonged to Hesperiidae (46 species), followed by Nymphalidae (28) and Pieridae (14). The highest butterfly diversity and interaction diversity was observed in pioneer dune vegetation (PDV), coastal dune scrub (CDS) and tropical deciduous flooding forest and wetland (TDF-W). The same order of vegetation types was found for interaction diversity. Highest species similarity was found between PDV-CDS and PDV-TDF. The butterfly-plant interaction network showed a nested structure with one module. The species Ascia monuste, Euptoieta hegesia and Leptotes cassius were the most generalist in the network, while Horama oedippus, E. hegesia, and L. cassius were the species with highest dependencies per plant species.DiscussionOur study is important because it constitutes a pioneer study of butterfly-plant interactions in this protected area, at least for adult butterflies; it shows the diversity of interactions among flowering plants and butterflies. Our research constitutes the first approach (at a community level) to explore the functional role of pollination services that butterflies provide to plant communities. We highlighted that open areas show a higher diversity and these areas shared a higher number of species that shaded sites. In the interaction networks parameters, our results highlighted the higher dependence of butterflies by the flowers on which they feed than vice versa. In conclusion, the plant species (as a feeding resource) seem to limit the presence of butterfly species. Thus, this protected area is highly relevant for Lepidoptera diversity and the interaction between these insects and flowering plants. We suggest that studying plant and butterfly diversity in tropical habitats will provide insight into their interspecific interactions and community structure. creator: Cristian A. Martínez-Adriano creator: Cecilia Díaz-Castelazo creator: Armando Aguirre-Jaimes uri: https://doi.org/10.7717/peerj.5493 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Martínez-Adriano et al. title: Genetic variability of Akhal-Teke horses bred in Italy link: https://peerj.com/articles/4889 last-modified: 2018-09-06 description: BackgroundThe Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences.MethodsSeventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences.ResultsNucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy. creator: Maria C. Cozzi creator: Maria G. Strillacci creator: Paolo Valiati creator: Elisa Rogliano creator: Alessandro Bagnato creator: Maria Longeri uri: https://doi.org/10.7717/peerj.4889 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cozzi et al. title: Seasonal changes in the abundance and biomass of copepods in the south-eastern Baltic Sea in 2010 and 2011 link: https://peerj.com/articles/5562 last-modified: 2018-09-06 description: BackgroundCopepods are major secondary producers in the World Ocean. They represent an important link between phytoplankton, microzooplankton and higher trophic levels such as fish. They are an important source of food for many fish species but also a significant producer of detritus. In the terms of the role they play in the marine food web, it is important to know how environmental variability affects the population of copepods.MethodsThe study of the zooplankton community in the south-eastern Baltic Sea conducted during a 24-month survey (from January 2010 to November 2011) resulted in the identification of 24 invertebrate species (10 copepods, seven cladocerans, four rotifers, one ctenophore, one larvacean, and one amphipod). Data were collected at two stations located in the open sea waters of the Gulf of Gdansk: the Gdansk Deep (P1) (54°50′N, 19°19′E) and in the western, inner part of the Gulf of Gdansk (P2) (54°32′N, 18°48.2′E). The vertical hauls were carried out with the use of two kinds of plankton nets with a mesh size of 100 µm: a Copenhagen net (in 2010), and a WP-2 net (in 2011).ResultsThe paper describes the seasonal changes in the abundance and biomass of copepods, taking into account the main Baltic calanoid copepod taxa (Acartia spp., Temora longicornis and Pseudocalanus sp.). They have usually represented the main component of zooplankton. The average number of copepods at the P1 Station during the study period of 2010 was 3,913 ind m−3(SD 2,572) and their number ranged from 1,184 ind m−3 (in winter) to 6,293 ind m−3(in spring). One year later, the average count of copepods was higher, at 11,723 ind m−3(SD 6,980), and it ranged from 2,351 ind m−3(in winter) to 18,307 ind m−3(in summer). Their average count at P2 Station in 2010 was 29,141 ind m−3, ranging from 3,330 ind m−3(in March) to 67,789 ind m−3(in May). The average count of copepods in 2011 was much lower at 17,883 ind m−3, and it ranged from 1,360 ind m−3 (in April) to 39,559 ind m−3 (in May).DiscussionThe environmental conditions of the pelagic habitat change in terms of both depth and distance from the shore. Although the qualitative (taxonomic) structure of zooplankton is almost identical to that of the coastal waters, the quantitative structure (abundance and biomass) changes quite significantly. The maximum values of zooplankton abundance and biomass were observed in the summer season, both in the Gdansk Deep and in the inner part of the Gulf of Gdansk. Copepods dominated in the composition of zooplankton for almost the entire time of the research duration. Quantitative composition of copepods at the P1 Station differed from the one at P2 Station due to the high abundance of Pseudocalanus sp. which prefers colder, more saline waters. creator: Lidia Dzierzbicka-Glowacka creator: Anna Lemieszek creator: Marcin Kalarus creator: Evelina Griniene uri: https://doi.org/10.7717/peerj.5562 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dzierzbicka-Glowacka et al. title: Selecting appropriate variables for detecting grassland to cropland changes using high resolution satellite data link: https://peerj.com/articles/5487 last-modified: 2018-09-06 description: Grassland is one of the most represented, while at the same time, ecologically endangered, land cover categories in the European Union. In view of the global climate change, detecting its change is growing in importance from both an environmental and a socio-economic point of view. A well-recognised tool for Land Use and Land Cover (LULC) Change Detection (CD), including grassland changes, is Remote Sensing (RS). An important aspect affecting the accuracy of change detection is finding the optimal indicators of LULC changes (i.e., variables). Inappropriately selected variables can produce inaccurate results burdened with a number of uncertainties. The aim of our study is to find the most suitable variables for the detection of grassland to cropland change, based on a pair of high resolution images acquired by the Landsat 8 satellite and from the vector database Land Parcel Identification System (LPIS). In total, 59 variables were used to create models using Generalised Linear Models (GLM), the quality of which was verified through multi-temporal object-based change detection. Satisfactory accuracy for the detection of grassland to cropland change was achieved using all of the statistically identified models. However, a three-variable model can be recommended for practical use, namely by combining the Normalised Difference Vegetation Index (NDVI), Wetness and Fifth components of Tasselled Cap. Increasing number of variables did not significantly improve the accuracy of detection, but rather complicated the interpretation of the results and was less accurate than detection based on the original Landsat 8 images. The results obtained using these three variables are applicable in landscape management, agriculture, subsidy policy, or in updating existing LULC databases. Further research implementing these variables in combination with spatial data obtained by other RS techniques is needed. creator: Tomáš Klouček creator: David Moravec creator: Jan Komárek creator: Ondřej Lagner creator: Přemysl Štych uri: https://doi.org/10.7717/peerj.5487 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Klouček et al. title: Episodix: a serious game to detect cognitive impairment in senior adults. A psychometric study link: https://peerj.com/articles/5478 last-modified: 2018-09-05 description: IntroductionAssessment of episodic memory is traditionally used to evaluate potential cognitive impairments in senior adults. The present article discusses the capabilities of Episodix, a game to assess the aforementioned cognitive area, as a valid tool to discriminate among mild cognitive impairment (MCI), Alzheimer’s disease (AD) and healthy individuals (HC); that is, it studies the game’s psychometric validity study to assess cognitive impairment.Materials and MethodsAfter a preliminary study, a new pilot study, statistically significant for the Galician population, was carried out from a cross-sectional sample of senior adults as target users. A total of 64 individuals (28 HC, 16 MCI, 20 AD) completed the experiment from an initial sample of 74. Participants were administered a collection of classical pen-and-paper tests and interacted with the games developed. A total of six machine learning classification techniques were applied and four relevant performance metrics were computed to assess the classification power of the tool according to participants’ cognitive status.ResultsAccording to the classification performance metrics computed, the best classification result is obtained using the Extra Trees Classifier (F1 = 0.97 and Cohen’s kappa coefficient = 0.97). Precision and recall values are also high, above 0.9 for all cognitive groups. Moreover, according to the standard interpretation of Cohen’s kappa index, classification is almost perfect (i.e., 0.81–1.00) for the complete dataset for all algorithms.LimitationsWeaknesses (e.g., accessibility, sample size or speed of stimuli) detected during the preliminary study were addressed and solved. Nevertheless, additional research is needed to improve the resolution of the game for the identification of specific cognitive impairments, as well as to achieve a complete validation of the psychometric properties of the digital game.ConclusionPromising results obtained about psychometric validity of Episodix, represent a relevant step ahead towards the introduction of serious games and machine learning in regular clinical practice for detecting MCI or AD. However, more research is needed to explore the introduction of item response theory in this game and to obtain the required normative data for clinical validity. creator: Sonia Valladares-Rodriguez creator: Manuel J. Fernández-Iglesias creator: Luis Anido-Rifón creator: David Facal creator: Roberto Pérez-Rodríguez uri: https://doi.org/10.7717/peerj.5478 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Valladares-Rodriguez et al. title: The first Caipirasuchus (Mesoeucrocodylia, Notosuchia) from the Late Cretaceous of Minas Gerais, Brazil: new insights on sphagesaurid anatomy and taxonomy link: https://peerj.com/articles/5594 last-modified: 2018-09-05 description: Field work conducted by the staff of the Centro de Pesquisas Paleontológicas Llewellyn Ivor Price of the Universidade Federal do Triângulo Mineiro since 2009 at Campina Verde municipality (MG) have resulted in the discovery of a diverse vertebrate fauna from the Adamantina Formation (Bauru Basin). The baurusuchid Campinasuchus dinizi was described in 2011 from Fazenda Três Antas site and after that, preliminary descriptions of a partial crocodyliform egg, abelisaurid teeth, and fish remains have been done. Recently, the fossil sample has been considerably increased including the discovery of several, partially articulated fish remains referred to Lepisosteiformes and an almost complete and articulated skeleton referred to a new species of Caipirasuchus (Notosuchia, Sphagesauridae), which is the main subject of this contribution. At present, this genus was restricted to the Adamantina Formation cropping out in São Paulo state, with the species Caipirasuchus montealtensis, Caipirasuchus paulistanus, and Caipirasuchus stenognathus. The new material represents the holotype of a new species, Caipirasuchus mineirus n. sp., diferenciated from the previously ones due to the following traits: last two maxillary teeth located posterior to anterior edge of infraorbital fenestra, elongated lateroventral maxillo-jugal suture—about ½ the anteroposterior maxillar length—and contact between posterior crest of quadrate and posterior end of squamosal forming an almost 90° flaring roof of the squamosal, among others. C. mineirus was found in the same outcrop than Campinasuchus but stratigraphically the former occurs in the lower portion of the section with no unambiguous data supporting the coexistance of both taxa. creator: Agustín G. Martinelli creator: Thiago S. Marinho creator: Fabiano V. Iori creator: Luiz Carlos B. Ribeiro uri: https://doi.org/10.7717/peerj.5594 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Martinelli et al. title: Cell-wall-degrading enzymes produced in vitro and in vivo by Rhizoctonia solani, the causative fungus of peanut sheath blight link: https://peerj.com/articles/5580 last-modified: 2018-09-05 description: Rhizoctonia solani causes the disease peanut sheath blight, involving symptoms of maceration and necrosis of infected tissue, mainly caused by cell-wall-degrading enzymes (CWDEs). This study investigated the production of CWDEs including polygalacturonase (PG), polymethyl-galacturonase (PMG), cellulase (Cx) and β-glucosidase by R. solani in vitro (in liquid culture) and in vivo (in peanut plants). Significant PG, PMG, Cx and β-glucosidase activities were detected in infected tissues including stalk and leaves of Baisha and Silihong peanut cultivars. Extracts of healthy tissue showed little or no such activities. In shaken liquid cultures of R. solani in medium containing pectin or pectin plus carboxymethyl cellulose (CMC) as the carbon source(s), PG and PMG were notably active. Significant Cx activity was detected in cultures with CMC or pectin plus CMC as the carbon source(s). However, only a very low level of β-glucosidase activity was observed in cultures with any of the tested carbon sources. An increase of pH was recorded in decayed peanut tissues and liquid culture filtrates; the filtrate pH and fungal growth positively correlated. The fungal growth and/or pH were important factors for the production of PG, PMG and Cx in culture with pectin plus CMC as the carbon source. A single active PG isozyme with isoelectric point around 9.2 was detected in culture filtrates and in infected peanut tissues by the method of isoelectric focusing electrophoresis. The crude enzymes extracted from liquid culture of R. solani induced decay of healthy peanut leaves. creator: Cai Yun Xue creator: Ru Jun Zhou creator: Yuan Jie Li creator: Di Xiao creator: Jun Fan Fu uri: https://doi.org/10.7717/peerj.5580 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Xue et al. title: Early Holocene morphological variation in hunter-gatherer hands and feet link: https://peerj.com/articles/5564 last-modified: 2018-09-05 description: BackgroundThe Windover mortuary pond dates to the Early Archaic period (6,800–5,200 years ago) and constitutes one of the earliest archaeological sites with intact and well-preserved human remains in North America. Unlike many prehistoric egalitarian hunter-gatherers, the Windover people may not have practiced a sex-based division of labor; rather, they may have shared the load. We explore how mobility and subsistence, as reconstructed from archaeological data, influenced hand and foot bone morphology at Windover.MethodsWe took length and width measurements on four carpal bones, four tarsal bones, and load-bearing tarsal areas (calcaneus load arm, trochlea of the talus). We analyzed lateralization using side differences in raw length and width measurements. For other hypothesis testing, we used log transformed length-width ratios to mitigate the confounding effects of sexual dimorphism and trait size variation; we tested between-sex differences in weight-bearing (rear foot) and shock-absorbing (mid foot) tarsal bones and between-sex differences in carpal bones.ResultsWe identified no significant between-sex differences in rear and midfoot areas, suggesting similar biomechanical stresses. We identified no significant between-sex differences in carpal bones but the test was under-powered due to small sample sizes. Finally, despite widespread behavioral evidence on contemporary populations for human hand and foot lateralization, we found no evidence of either handedness or footedness.DiscussionThe lack evidence for footedness was expected due its minimal impact on walking gait but the lack of evidence for handedness was surprising given that ethnographic studies have shown strong handedness in hunter-gatherers during tool and goods manufacture. The reconstructed activity patterns suggested both sexes engaged in heavy load carrying and a shared division of labor. Our results support previous findings—both sexes had stronger weight-bearing bones. Male shock-absorbing bones exhibited a trend towards greater relative width (suggesting greater comparative biomechanical stress) than females which may reflect the typical pattern of male hunter-gatherers engaging in walking greater distances at higher speeds than females. While there were no significant between-sex differences in carpal bones (supporting a shared work load model), females exhibited greater variation in index values, which may reflect a greater variety of and specialization in tasks compared to males. Because carpals and tarsals are so well-preserved at archaeological sites, we had surmised they might be useful proxies for activity in the absence of well-preserved long bones. Tarsals provide a stronger signal of past activity and may be useful in the absence of, or in addition to, preferred bones. Carpals, however, may not be useful as the effect size of biomechanical stress (in this study at least) is low and would require larger samples than may be possible at archaeological sites. creator: Kara C. Hoover creator: J. Colette Berbesque uri: https://doi.org/10.7717/peerj.5564 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hoover and Berbesque title: Lysmata arvoredensis nov. sp. a new species of shrimp from the south coast of Brazil with a key to species of Lysmata (Caridea: Lysmatidae) recorded in the southwestern Atlantic link: https://peerj.com/articles/5561 last-modified: 2018-09-05 description: Lysmata arvoredensis sp. nov. inhabits temperate waters in the south coast of Brazil and is named in tribute to the Marine Protected Area REBIO Arvoredo. This is the fourth species belonging to the genus Lysmata recorded for the region and the ninth for Brazil. L. arvoredensis sp. nov. can be distinguished from other species of Lysmata by the presence of a nearly completely fused accessory branch with a single free unguiform segment on the outer antennular flagellum; a rostrum with seven dorsal (2+5) and three ventral teeth; a stylocerite with a pointed tip bearing mesial setae; a second pereiopod with 22–24 carpal subsegments and 14–16 subsegments in the merus; a merus of the third pereiopod with five ventrolateral and 12 ventral spines on the propodus; and its color pattern, with red bands and patches in pleonites 2–3 that resemble a mask in dorsal view. Molecular characters demonstrate that L. arvoredensis sp. nov. is most closely related to other species of Lysmata belonging to the Neotropical and Cleaner clades. To support future ecological studies in the region, identification keys to the species of Lysmata recorded in the southwestern Atlantic Ocean are provided. creator: Bruno W. Giraldes creator: Thais P. Macedo creator: Manoela C. Brandão creator: J. Antonio Baeza creator: Andrea S. Freire uri: https://doi.org/10.7717/peerj.5561 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Giraldes et al. title: Impacts of climate change on infestations of Dubas bug (Ommatissus lybicus Bergevin) on date palms in Oman link: https://peerj.com/articles/5545 last-modified: 2018-09-05 description: Climate change has determined shifts in distributions of species and is likely to affect species in the future. Our study aimed to (i) demonstrate the linkage between spatial climatic variability and the current and historical Dubas bug (Ommatissus lybicus Bergevin) distribution in Oman and (ii) model areas becoming highly suitable for the pest in the future. The Dubas bug is a pest of date palm trees that can reduce the crop yield by 50% under future climate scenarios in Oman. Projections were made in three species distribution models; generalized linear model, maximum entropy, boosted regression tree using of four global circulation models (GCMs) (a) HadGEM2, (b) CCSM4, (c) MIROC5 and (d) HadGEM2-AO, under four representative concentration pathways (2.6, 4.5, 6.0 and 8.5) for the years 2050 and 2070. We utilized the most commonly used threshold of maximum sensitivity + specificity for classifying outputs. Results indicated that northern Oman is currently at great risk of Dubas bug infestations (highly suitable climatically) and the infestations level will remain high in 2050 and 2070. Other non-climatic integrated pest management methods may be greater value than climatic parameters for monitoring infestation levels, and may provide more effective strategies to manage Dubas bug infestations in Oman. This would ensure the continuing competitiveness of Oman in the global date fruit market and preserve national yields. creator: Farzin Shabani creator: Lalit Kumar creator: Rashid Hamdan Saif al Shidi uri: https://doi.org/10.7717/peerj.5545 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Shabani et al. title: Antithrombin deficiency is associated with mortality and impaired organ function in septic pediatric patients: a retrospective study link: https://peerj.com/articles/5538 last-modified: 2018-09-05 description: BackgroundSepsis remains a major problem in intensive care medicine. It is often accompanied by coagulopathies, leading to thrombotic occlusion of small vessels with subsequent organ damage and even fatal multi-organ failure. Prediction of the clinical course and outcome—especially in the heterogeneous group of pediatric patients—is difficult. Antithrombin, as an endogenous anticoagulant enzyme with anti-inflammatory properties, plays a central role in controling coagulation and infections. We investigated the relationship between antithrombin levels and organ failure as well as mortality in pediatric patients with sepsis.MethodsData from 164 patients under the age of 18, diagnosed with sepsis, were retrospectively reviewed. Antithrombin levels were recorded three days before to three days after peak C-reactive protein to correlate antithrombin levels with inflammatory activity. Using the concept of developmental haemostasis, patients were divided into groups <1 yr and ≥1 yr of age.ResultsIn both age groups, survivors had significantly higher levels of antithrombin than did deceased patients. An optimal threshold level for antithrombin was calculated by ROC analysis for survival: 41.5% (<1 yr) and 67.5% (≥1 yr). The mortality rate above this level was 3.3% (<1 yr) and 9.5% (≥1 yr), and below this level 41.7% (<1 yr) and 32.2% (≥1 yr); OR 18.8 (1.74 to 1005.02), p = 0.0047, and OR 4.46 (1.54 to 14.89), p = 0.003. In children <1 yr with antithrombin levels <41.5% the rate of respiratory failure (66.7%) was significantly higher than in patients with antithrombin levels above this threshold level (23.3%), OR 6.23 (1.23 to 37.81), p = 0.0132. In children ≥1 yr, both liver failure (20.3% vs 1.6%, OR 15.55 (2.16 to 685.01), p = 0.0008) and a dysfunctional intestinal tract (16.9% vs 4.8%, OR 4.04 (0.97 to 24.08), p = 0.0395) occurred more frequently above the antithrombin threshold level of 67.5%.ConclusionIn pediatric septic patients, significantly increased mortality and levels of organ failure were found below an age-dependent antithrombin threshold level. Antithrombin could be useful as a prognostic marker for survival and occurrence of organ failure in pediatric sepsis. creator: Christian Niederwanger creator: Tobias Hell creator: Sophie Hofer creator: Christina Salvador creator: Miriam Michel creator: Bettina Schenk creator: Benedikt Treml creator: Mirjam Bachler uri: https://doi.org/10.7717/peerj.5538 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Niederwanger et al. title: Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP link: https://peerj.com/articles/5505 last-modified: 2018-09-05 description: The ε subunit from ATP synthases acts as an ATP sensor in the bacterial cell to prevent ATP hydrolysis and thus the waste of ATP under conditions of low ATP concentration. However, the ATP binding affinities from various bacterial organisms differ markedly, over several orders of magnitude. For example, the ATP synthases from thermophilic Bacillus PS3 and Escherichia coli exhibit affinities of 4 µM and 22 mM, respectively. The recently reported R103A/R115A double mutant of Bacillus PS3 ATP synthase demonstrated an increased binding affinity by two orders of magnitude with respect to the wild type. Here, we used atomic-resolution molecular dynamics simulations to determine the role of the R103A and R115A single mutations. These lead us to predict that both single mutations also cause an increased ATP binding affinity. Evolutionary analysis reveals R103 and R115 substitutions in the ε subunit from other bacillic organisms, leading us to predict they likely have a higher ATP binding affinity than previously expected. creator: Alexander Krah creator: Peter J. Bond uri: https://doi.org/10.7717/peerj.5505 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Krah and Bond title: Shrub encroachment into grasslands: end of an era? link: https://peerj.com/articles/5474 last-modified: 2018-09-05 description: Shifts in the abundance of grasses and woody plants in drylands have occurred several times during the Holocene. However, our understanding of the rates and dynamics of this state-change in recent decades is limited to scattered studies conducted at disparate spatial and temporal scales; the potential misperceptions of shrub cover change could be remedied using cross spatiotemporal scale analyses that link field observations, repeat ground-level photography and remote sensing perspectives. The study was conducted across a semi-arid landscape in southern Arizona. Local data from long-term transects revealed three distinct chronological phases of shrub cover change: expansion (1961–1991, 0.7% y−1), decline (1992–1997, −2.3% y−1) and stabilization (1998–2012, 22–25% with no net cover change). Twenty-eight years (1984–2011) of broad-scale Landsat Thematic Mapper assessments confirm that shrub cover has been relatively stable in recent decades regardless of grazing regimes and landforms with the exception of the proliferation of succulents at lower elevations (verified by repeat photography acquired in 1987 and 2015) where the physical environment is the harshest, reflecting elevated temperature and winter precipitation deficit. Warmer, drier future climates are predicted to reduce woody plant carrying capacity and promote a shift to xerophytic succulents. creator: Cho-ying Huang creator: Steven R. Archer creator: Mitchel P. McClaran creator: Stuart E. Marsh uri: https://doi.org/10.7717/peerj.5474 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Huang et al. title: Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients link: https://peerj.com/articles/5473 last-modified: 2018-09-05 description: BackgroundAvian influenza viruses (AIVs) have been endemic in Egypt since 2006, and the co-circulation of high-pathogenic avian influenza H5N1 and low-pathogenic avian influenza H9N2 subtypes in poultry has been reported; therefore, Egypt is considered a hotspot for the generation of new subtypes and genotypes. We aimed to characterize AIVs circulating on commercial farms and in live bird markets (LBMs) during the winters of 2015 and 2016 in the study area and to identify H5N1 and H9N2 viruses in respiratory patients.MethodsIn total, 159 samples were collected from ducks, pigeons and quails on farms (n = 59) and in LBMs (n = 100) and screened by real-time RT-PCR for H5N1 and H9N2 subtypes. Clinical and postmortem examination was carried out on birds from the farms. Positive H5N1 samples were sequenced and analysed for mutations. Tracheal swabs were also collected from 89 respiratory patients admitted to respiratory hospitals in the same study area.ResultsOverall, H5N1 was identified in 13.6% of birds from farms, while it was detected in 17% of birds in LBMs. Subtype H9N2 was only identified from pigeons on farms (6.5%) and LBMs (11.4%). Sequencing of the haemagglutination gene (HA) in nine representative H5N1 isolates revealed a multi-basic amino acid motif at the cleavage site (321-PQGEKRRKKR/GLF-333), which is characteristic of highly pathogenic AIV, in five of our isolates, while the other four isolates showed an amino acid substitution (Q322K) at this cleavage site to make it (321-P K GEKRRKKR/GLF-333). All the isolates belonged to clade 2.2.1.2, and a comparison of HA sequences at the amino acid level showed 98.8–100% homology among the nine isolates, while they showed 94.1–96.1% identity with reference strains and the commonly used vaccine strain in Egypt. Out of 89 respiratory patients, 3.4% were positive for H5N1 and no patients were positive for H9N2.DiscussionOur results indicated the circulation of the endemic H5N1 and H9N2 viruses among poultry in 2015 and 2016. Birds on farms and in LBMs are reservoirs playing a role in the dissemination of the virus and producing a public health risk. The application of proper hygienic measures in farms and LBMs to control the exposure of birds and humans to the source of infection along with continuous monitoring of the circulating viruses will provide information on understanding the evolution of the viruses for vaccine studies. creator: Hala M.N. Tolba creator: Rasha M.M. Abou Elez creator: Ibrahim Elsohaby creator: Heba A. Ahmed uri: https://doi.org/10.7717/peerj.5473 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tolba et al. title: Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids link: https://peerj.com/articles/5445 last-modified: 2018-09-05 description: Plant growth-promoting bacteria (PGPB) and humic acids (HA) have been used as biostimulants in field conditions. The complete genomic and proteomic transcription of Herbaspirillum seropedicae and Gluconacetobacter diazotrophicus is available but interpreting and utilizing this information in the field to increase crop performance is challenging. The identification and characterization of metabolites that are induced by genomic changes may be used to improve plant responses to inoculation. The objective of this study was to describe changes in sugarcane metabolic profile that occur when HA and PGPB are used as biostimulants. Inoculum was applied to soil containing 45-day old sugarcane stalks. One week after inoculation, the methanolic extracts from leaves were obtained and analyzed by gas chromatography coupled to time-of-flight mass spectrometry; a total of 1,880 compounds were observed and 280 were identified in all samples. The application of HA significantly decreased the concentration of 15 metabolites, which generally included amino acids. HA increased the levels of 40 compounds, and these included metabolites linked to the stress response (shikimic, caffeic, hydroxycinnamic acids, putrescine, behenic acid, quinoline xylulose, galactose, lactose proline, oxyproline and valeric acid) and cellular growth (adenine and adenosine derivatives, ribose, ribonic acid and citric acid). Similarly, PGPB enhanced the level of metabolites identified in HA-treated soils; e.g., 48 metabolites were elevated and included amino acids, nucleic acids, organic acids, and lipids. Co-inoculation (HA+PGPB) boosted the level of 110 metabolites with respect to non-inoculated controls; these included amino acids, lipids and nitrogenous compounds. Changes in the metabolic profile induced by HA+PGPB influenced both glucose and pentose pathways and resulted in the accumulation of heptuloses and riboses, which are substrates in the nucleoside biosynthesis and shikimic acid pathways. The mevalonate pathway was also activated, thus increasing phytosterol synthesis. The improvement in cellular metabolism observed with PGPB+HA was compatible with high levels of vitamins. Glucuronate and amino sugars were stimulated in addition to the products and intermediary compounds of tricarboxylic acid metabolism. Lipids and amino acids were the main compounds induced by co-inoculation in addition to antioxidants, stress-related metabolites, and compounds involved in cellular redox. The primary compounds observed in each treatment were identified, and the effect of co-inoculation (HA+PGPB) on metabolite levels was discussed. creator: Natalia O. Aguiar creator: Fabio L. Olivares creator: Etelvino H. Novotny creator: Luciano P. Canellas uri: https://doi.org/10.7717/peerj.5445 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Aguiar et al. title: Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis link: https://peerj.com/articles/5239 last-modified: 2018-09-05 description: Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein–protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin–proteasome system—it regulates the proteolysis. P53 is recognized as a central regulator of the cell cycle and apoptosis. These proteins, which have been identified as the most significant hubs, may be involved in aging muscle and sarcopenia. creator: Gita Shafiee creator: Yazdan Asgari creator: Akbar Soltani creator: Bagher Larijani creator: Ramin Heshmat uri: https://doi.org/10.7717/peerj.5239 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shafiee et al. title: Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species link: https://peerj.com/articles/5160 last-modified: 2018-09-05 description: The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different. creator: Jinming Lu creator: Yuan Zhang creator: Hongwei Chen uri: https://doi.org/10.7717/peerj.5160 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lu et al. title: Effect of vineyard soil variability on chlorophyll fluorescence, yield and quality of table grape as influenced by soil moisture, grown under double cropping system in protected condition link: https://peerj.com/articles/5592 last-modified: 2018-09-04 description: Environmental factors greatly influence grape quality. Among them, the effect of within-vineyard variability of soil in relation to soil moisture on table grape under protected condition has rarely been studied. In this present research, we investigated the influence of soil variability, in relation with soil moisture on chlorophyll fluorescence, yield and quality attributes of the “Summer Black” (Vitis vinifera L. × V. labruscana L.) table grape, popularly grown under double cropping system in protected covering in the southern part of China. The vineyard was divided vertically into three sites (lower, middle and upper, 192, 202 and 212 m above sea level, respectively) and data on soil moisture and other yield and quality parameters were recorded. Among the three vineyard sites, middle site resulted in higher yield compared to the upper and lower sites during winter and summer cropping cycles. However, compared to regular summer cycle, winter cycle provided grapevines with higher quality attributes. Polyphasic OJIP fluorescence transient exhibited a considerable increase in fluorescence intensity at J, I and P phase in the upper and middle sites compared to the lower site due to variation in soil moisture in both seasons. Values of fluorescence parameters including minimal fluorescence, relative variable fluorescence at phase J and I, the maximal quantum yield of photosystem II were also influenced by soil moisture in different sites. Different sites also exhibited a significant difference in total phenolics, flavonoid, antioxidant activity and individual anthocyanin which was influenced by available soil moisture. The present study shows that chlorophyll fluorescence OJIP transient can be used as a sensitive indicator to determine the moisture stress in grape grown in a varied soil. Double cropping proved to be a powerful technique to improve the fruit quality. This result may be useful for the table grape growers to better utilize the vineyard soil variability with water management to get higher yield and quality table grape under protected condition. creator: Sangeeta Mitra creator: Muhammad Irshad creator: Biswojit Debnath creator: Xiaocao Lu creator: Min Li creator: Chandra Kanta Dash creator: Hafiz Muhammad Rizwan creator: Zhipeng Qiu creator: Dongliang Qiu uri: https://doi.org/10.7717/peerj.5592 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Mitra et al. title: An LED-based multi-actinic illumination system for the high throughput study of photosynthetic light responses link: https://peerj.com/articles/5589 last-modified: 2018-09-04 description: The responses of photosynthetic organisms to light stress are of interest for both fundamental and applied research. Functional traits related to the photoinhibition, the light-induced loss of photosynthetic efficiency, are particularly interesting as this process is a key limiting factor of photosynthetic productivity in algae and plants. The quantitative characterization of light responses is often time-consuming and calls for cost-effective high throughput approaches that enable the fast screening of multiple samples. Here we present a novel illumination system based on the concept of ‘multi-actinic imaging’ of in vivo chlorophyll fluorescence. The system is based on the combination of an array of individually addressable low power RGBW LEDs and custom-designed well plates, allowing for the independent illumination of 64 samples through the digital manipulation of both exposure duration and light intensity. The illumination system is inexpensive and easily fabricated, based on open source electronics, off-the-shelf components, and 3D-printed parts, and is optimized for imaging of chlorophyll fluorescence. The high-throughput potential of the system is illustrated by assessing the functional diversity in light responses of marine macroalgal species, through the fast and simultaneous determination of kinetic parameters characterizing the response to light stress of multiple samples. Although the presented illumination system was primarily designed for the measurement of phenotypic traits related to photosynthetic activity and photoinhibition, it can be potentially used for a number of alternative applications, including the measurement of chloroplast phototaxis and action spectra, or as the basis for microphotobioreactors. creator: João Serôdio creator: William Schmidt creator: Jörg C. Frommlet creator: Gregor Christa creator: Matthew R. Nitschke uri: https://doi.org/10.7717/peerj.5589 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Serôdio et al. title: Translational effects of robot-mediated therapy in subacute stroke patients: an experimental evaluation of upper limb motor recovery link: https://peerj.com/articles/5544 last-modified: 2018-09-04 description: Robot-mediated therapies enhance the recovery of post-stroke patients with motor deficits. Repetitive and repeatable exercises are essential for rehabilitation following brain damage or other disorders that impact the central nervous system, as plasticity permits to reorganize its neural structure, fostering motor relearning. Despite the fact that so many studies claim the validity of robot-mediated therapy in post-stroke patient rehabilitation, it is still difficult to assess to what extent its adoption improves the efficacy of traditional therapy in daily life, and also because most of the studies involved planar robots. In this paper, we report the effects of a 20-session-rehabilitation project involving the Armeo Power robot, an assistive exoskeleton to perform 3D upper limb movements, in addition to conventional rehabilitation therapy, on 10 subacute stroke survivors. Patients were evaluated through clinical scales and a kinematic assessment of the upper limbs, both pre- and post-treatment. A set of indices based on the patients’ 3D kinematic data, gathered from an optoelectronic system, was calculated. Statistical analysis showed a remarkable difference in most parameters between pre- and post-treatment. Significant correlations between the kinematic parameters and clinical scales were found. Our findings suggest that 3D robot-mediated rehabilitation, in addition to conventional therapy, could represent an effective means for the recovery of upper limb disability. Kinematic assessment may represent a valid tool for objectively evaluating the efficacy of the rehabilitation treatment. creator: Eduardo Palermo creator: Darren Richard Hayes creator: Emanuele Francesco Russo creator: Rocco Salvatore Calabrò creator: Alessandra Pacilli creator: Serena Filoni uri: https://doi.org/10.7717/peerj.5544 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Palermo et al. title: GDF11 induces differentiation and apoptosis and inhibits migration of C17.2 neural stem cells via modulating MAPK signaling pathway link: https://peerj.com/articles/5524 last-modified: 2018-09-04 description: GDF11, a member of TGF-β superfamily, has recently received widespread attention as a novel anti-ageing/rejuvenation factor to reverse age-related dysfunctions in heart and skeletal muscle, and to induce angiogenesis and neurogenesis. However, these positive effects of GDF11 were challenged by several other studies. Furthermore, the mechanism is still not well understood. In the present study, we evaluated the effects of GDF11 on C17.2 neural stem cells. GDF11 induced differentiation and apoptosis, and suppressed migration of C17.2 neural stem cells. In addition, GDF11 slightly increased cell viability after 24 h treatment, showed no effects on proliferation for about 10 days of cultivation, and slightly decreased cumulative population doubling for long-term treatment (p < 0.05). Phospho-proteome profiling array displayed that GDF11 significantly increased the phosphorylation of 13 serine/threonine kinases (p < 0.01), including p-p38, p-ERK and p-Akt, in C17.2 cells, which implied the activation of MAPK pathway. Western blot validated that the results of phospho-proteome profiling array were reliable. Based on functional analysis, we demonstrated that the differentially expressed proteins were mainly involved in signal transduction which was implicated in cellular behavior. Collectively, our findings suggest that, for neurogenesis, GDF11 might not be the desired rejuvenation factor, but a potential target for pharmacological blockade. creator: Zongkui Wang creator: Miaomiao Dou creator: Fengjuan Liu creator: Peng Jiang creator: Shengliang Ye creator: Li Ma creator: Haijun Cao creator: Xi Du creator: Pan Sun creator: Na Su creator: Fangzhao Lin creator: Rong Zhang creator: Changqing Li uri: https://doi.org/10.7717/peerj.5524 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Factors influencing exotic species richness in Argentina’s national parks link: https://peerj.com/articles/5514 last-modified: 2018-09-04 description: Exotic species introductions are a global phenomenon and protected areas are susceptible to them. Understanding the drivers of exotic species richness is vital for prioritizing natural resource management, particularly in developing countries with limited resources. We analyzed the influence of coarse resolution factors on exotic species richness (plants, mammals, and birds) in Argentina’s National Parks System. We collected data on native species richness, year of park formation, park area, region, elevation range, number of rivers crossing area boundaries, roads entering area, mean annual rainfall, mean annual temperature, mean annual number of visitors, and Human Influence Index within and surrounding each park. We compiled 1,688 exotic records in 36 protected areas: 83% plants and 17% animals (9.5% mammals, 5.5% birds, 1.5% fishes, 0% amphibians, 0% reptiles). The five parks with the most exotic species (all taxa combined) were in north Patagonia. Exotic grasses were the most common exotic plants, and within animals, lagomorphs and feral ungulates were remarkably widespread. Exotic plant richness was mostly influenced by temperature and native plant richness, while exotic mammal and bird richness was driven mostly by anthropogenic variables, with models explaining 36–45% of data deviance. Most variables that positively influenced exotic taxa were indirectly related to an increase in spatial heterogeneity (natural or anthropogenic), suggesting greater niche space variability as facilitators of exotic richness increase. Additional data are needed to further investigate the patterns and mechanisms of exotic species richness in protected areas, which will help to prioritize the greatest needs of monitoring and management. creator: Mariela G. Gantchoff creator: Clay M. Wilton creator: Jerrold L. Belant uri: https://doi.org/10.7717/peerj.5514 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gantchoff et al. title: Physical, mechanical and energy characterization of wood pellets obtained from three common tropical species link: https://peerj.com/articles/5504 last-modified: 2018-09-04 description: BackgroundThe need for energy sources with low greenhouse gas emissions and sustainable production encourages the search for alternative biomass sources. However, the use of biomass fuels faces the problem of storage, transport and lower energy densities. Low-density values can negatively affect energy density, leading to an increase in transportation and storage costs. Use of pellets as alternative biomass source is a way to reduce the volume of biomass by densification, which improves their energy quality. They are produced by diverse biomass resources and mainly from wood materials. In all cases, it is important to evaluate the fuel characteristics, to determine their suitability on the heating system and handling properties.MethodsThe present study determines and compares data from proximate analysis, calorific values, physical and mechanical properties of wood pellets produced from the common tropical species Acacia wrightii, Ebenopsis ebano and Havardia pallens. Data were obtained from pellets produced from each species chips collected from an experimental plantation and analyzed through ANOVA and Kruskal–Wallis test at 0.05 significance level.ResultsThe results of diameter, length and length/diameter ratio didn’t show statistical differences (p > 0.05) among species. Acacia wrightii showed the highest density (1.2 g/cm3). Values on weight retained and compression test showed statistical differences (p = 0.05) among species. Havardia pallens was more resistant to compression strength than A. wrightii and Ebenopsis ebano. Statistical differences (p < 0.01) were also observed for the volatile matter and calorific value. E. ebano has the lowest volatile matter (72%), highest calorific value (19.6 MJ/kg) as well as the fixed carbon (21%).DiscussionThe pellets of the species studied have a high energy density, which makes them suitable for both commercial and industrial heating applications.A pellet with low compression resistance tends to disintegrate easily, due to moisture adsorption. The percentages obtained for the resistance index were higher than 97.5%, showing that the pellets studied are high-quality biofuels. Proximate analysis values also indicate good combustion parameters. Pellets of Acacia wrightii and Ebenopsis ebano are the more favorable raw material sources for energy purposes because of their high density, calorific value, low ash content and they also met majority of the international quality parameters. creator: Carrillo Parra Artemio creator: Ngangyo Heya Maginot creator: Colín-Urieta Serafín creator: Foroughbakhch Pournavab Rahim creator: Rutiaga Quiñones José Guadalupe creator: Correa-Méndez Fermín uri: https://doi.org/10.7717/peerj.5504 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Artemio et al. title: Investigating individual and social behaviour of the Northern bald ibis (Geronticus eremita): behavioural variety and welfare link: https://peerj.com/articles/5436 last-modified: 2018-09-04 description: The Northern bald ibis (Geronticus eremita) (NBI) is one of the most threatened birds in the world. Intense conservation efforts have been undertaken and several research projects on the species are being done in Morocco and in Europe. Observing animal behaviour has been proved to be an efficient and non-invasive technique to assess the animal welfare, with the performance of a wide array of natural behaviours being one of the mostly used indicators of good mental and physical well-being. The aim of this study was to investigate the behaviour of a flock of 14 zoo-living NBI of different ages. The study focused on the variety of species-specific individual and social behaviours, in the light of reintroduction of the study juveniles in the wild. Per subject, 20 10-min. sessions were done. A continuous focal animal sampling method was used to collect individual and social behaviours. Behavioural data have been compared between adults and juveniles. Moreover, a Behavioural Variety Index (BVI) has been proposed and calculated based on previous literature describing natural ibis behaviours. The BVI might help in the evaluation of the variety of behaviours performed by each individual and the monitoring of the diversity of the behavioural repertoire of zoo animals. Our results showed that the birds performed species-specific behaviours and no abnormal behaviour was reported. Moreover, the BVI highlighted a good behavioural variety as each bird performed approximately 78% of the natural behaviours described in the Northern bald ibis and in close relative species. Our findings seem to suggest the presence of qualitative and quantitative similarities between the behavioural repertoires of the study ibises and those described in wild conspecifics, suggesting a good welfare of the colony. Finally, the BVI proposed in the current study seems to be a useful and practical tool to test behavioural diversity in zoo animals. creator: Caterina Spiezio creator: Valentina Valsecchi creator: Camillo Sandri creator: Barbara Regaiolli uri: https://doi.org/10.7717/peerj.5436 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Spiezio et al. title: Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments link: https://peerj.com/articles/5578 last-modified: 2018-09-03 description: In single-cell RNA-sequencing, it is important to know the frequency at which the sequenced transcriptomes actually derive from multiple cells. A common method to estimate this multiplet frequency is to mix two different types of cells (e.g., human and mouse), and then determine how often the transcriptomes contain transcripts from both cell types. When the two cell types are mixed in equal proportion, the calculation of the multiplet frequency from the frequency of mixed transcriptomes is straightforward. But surprisingly, there are no published descriptions of how to calculate the multiplet frequency in the general case when the cell types are mixed unequally. Here, I derive equations to analytically calculate the multiplet frequency from the numbers of observed pure and mixed transcriptomes when two cell types are mixed in arbitrary proportions, under the assumption that the loading of cells into droplets or wells is Poisson. creator: Jesse D. Bloom uri: https://doi.org/10.7717/peerj.5578 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bloom title: Development of a Chlamydomonas reinhardtii metabolic network dynamic model to describe distinct phenotypes occurring at different CO2 levels link: https://peerj.com/articles/5528 last-modified: 2018-09-03 description: The increase in atmospheric CO2 due to anthropogenic activities is generating climate change, which has resulted in a subsequent rise in global temperatures with severe environmental impacts. Biological mitigation has been considered as an alternative for environmental remediation and reduction of greenhouse gases in the atmosphere. In fact, the use of easily adapted photosynthetic organisms able to fix CO2 with low-cost operation is revealing its high potential for industry. Among those organism, the algae Chlamydomonas reinhardtii have gain special attention as a model organism for studying CO2 fixation, biomass accumulation and bioenergy production upon exposure to several environmental conditions. In the present study, we studied the Chlamydomonas response to different CO2 levels by comparing metabolomics and transcriptomics data with the predicted results from our new-improved genomic-scale metabolic model. For this, we used in silico methods at steady dynamic state varying the levels of CO2. Our main goal was to improve our capacity for predicting metabolic routes involved in biomass accumulation. The improved genomic-scale metabolic model presented in this study was shown to be phenotypically accurate, predictive, and a significant improvement over previously reported models. Our model consists of 3726 reactions and 2436 metabolites, and lacks any thermodynamically infeasible cycles. It was shown to be highly sensitive to environmental changes under both steady-state and dynamic conditions. As additional constraints, our dynamic model involved kinetic parameters associated with substrate consumption at different growth conditions (i.e., low CO2-heterotrophic and high CO2-mixotrophic). Our results suggest that cells growing at high CO2 (i.e., photoautotrophic and mixotrophic conditions) have an increased capability for biomass production. In addition, we have observed that ATP production also seems to be an important limiting factor for growth under the conditions tested. Our experimental data (metabolomics and transcriptomics) and the results predicted by our model clearly suggest a differential behavior between low CO2-heterotrophic and high CO2-mixotrophic growth conditions. The data presented in the current study contributes to better dissect the biological response of C. reinhardtii, as a dynamic entity, to environmental and genetic changes. These findings are of great interest given the biotechnological potential of this microalga for CO2 fixation, biomass accumulation, and bioenergy production. creator: Daniela Alejandra Mora Salguero creator: Miguel Fernández-Niño creator: Luis Miguel Serrano-Bermúdez creator: David O. Páez Melo creator: Flavia V. Winck creator: Camila Caldana creator: Andrés Fernando González Barrios uri: https://doi.org/10.7717/peerj.5528 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mora Salguero et al. title: A bioinformatics approach to identifying Wolbachia infections in arthropods link: https://peerj.com/articles/5486 last-modified: 2018-09-03 description: Wolbachia is the most widespread endosymbiont, infecting >20% of arthropod species, and capable of drastically manipulating the host’s reproductive mechanisms. Conventionally, diagnosis has relied on PCR amplification; however, PCR is not always a reliable diagnostic technique due to primer specificity, strain diversity, degree of infection and/or tissue sampled. Here, we look for evidence of Wolbachia infection across a wide array of arthropod species using a bioinformatic approach to detect the Wolbachia genes ftsZ, wsp, and the groE operon in next-generation sequencing samples available through the NCBI Sequence Read Archive. For samples showing signs of infection, we attempted to assemble entire Wolbachia genomes, and in order to better understand the relationships between hosts and symbionts, phylogenies were constructed using the assembled gene sequences. Out of the 34 species with positively identified infections, eight species of arthropod had not previously been recorded to harbor Wolbachia infection. All putative infections cluster with known representative strains belonging to supergroup A or B, which are known to only infect arthropods. This study presents an efficient bioinformatic approach for post-sequencing diagnosis and analysis of Wolbachia infection in arthropods. creator: Jane Pascar creator: Christopher H. Chandler uri: https://doi.org/10.7717/peerj.5486 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Pascar and Chandler