title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2019-08 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Serine protease inhibitors and human wellbeing interplay: new insights for old friends link: https://peerj.com/articles/7224 last-modified: 2019-08-30 description: Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches. creator: Héla Mkaouar creator: Nizar Akermi creator: Aicha Kriaa creator: Anne-Laure Abraham creator: Amin Jablaoui creator: Souha Soussou creator: Raja Mokdad-Gargouri creator: Emmanuelle Maguin creator: Moez Rhimi uri: https://doi.org/10.7717/peerj.7224 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mkaouar et al. title: Post-fledging habitat use in a declining songbird link: https://peerj.com/articles/7358 last-modified: 2019-08-30 description: BackgroundFledglings of many mature forest-dependent Neotropical songbirds move from mature forest habitats into areas of thick vegetation such as regenerating clearcuts. The Cerulean Warbler (Setophaga cerulea), a Neotropical migratory songbird, is a species of conservation concern across its range and it is listed as endangered in Indiana. This species has declined faster than any other species of wood-warbler in North America. Most prior research on Cerulean Warblers has examined the breeding biology, but there are no data on habitat use by fledgling Cerulean Warblers. Our research aimed to determine where fledgling Cerulean Warblers dispersed after they left their nest, but before they migrated to their wintering grounds.MethodsSince 2007, Cerulean Warbler breeding populations have been monitored in Yellowwood and Morgan–Monroe state forests in southern Indiana as part of a 100-year study called the Hardwood Ecosystem Experiment. To identify habitats used by fledgling Cerulean Warblers, we captured by hand or mist-nets, adult and juvenile Cerulean Warblers once young had fledged from a nest. We attached radio-transmitters to individuals and tracked each bird daily using radio-telemetry. Radio-telemetry data were collected from May to July 2015–2017, and microhabitat data on fledgling locations and random locations were collected during the same years in the month of July.ResultsFledgling presence, when compared to random non-use sites, was positively correlated to presence of grapevines, greater vertical vegetation density, and greater ground and canopy cover. Fledgling presence was negatively correlated with white oak abundance, aspect, basal area, and the abundance of mature trees that Cerulean Warbler adults use for nesting.ConclusionsOur study is the first to demonstrate that Cerulean Warbler fledglings occupy habitats that are characterized by specific habitat components. Fledgling sites were located in areas with high vegetation density, such as clusters of grapevine, which provided cover from predators. Identifying Cerulean Warbler habitats throughout the breeding season can better inform natural resource personnel on how to manage forests to meet the habitat needs of this rapidly declining migratory songbird. creator: Clayton D. Delancey creator: Kamal Islam uri: https://doi.org/10.7717/peerj.7358 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Delancey and Islam title: Echinoids from the Tesero Member (Werfen Formation) of the Dolomites (Italy): implications for extinction and survival of echinoids in the aftermath of the end-Permian mass extinction link: https://peerj.com/articles/7361 last-modified: 2019-08-30 description: The end-Permian mass extinction (∼252 Ma) was responsible for high rates of extinction and evolutionary bottlenecks in a number of animal groups. Echinoids, or sea urchins, were no exception, and the Permian to Triassic represents one of the most significant intervals of time in their macroevolutionary history. The extinction event was responsible for significant turnover, with the Permian–Triassic representing the transition from stem group echinoid-dominated faunas in the Palaeozoic to Mesozoic faunas dominated by crown group echinoids. This turnover is well-known, however, the environmental and taxonomic distribution of echinoids during the latest Permian and Early Triassic is not. Here we report on an echinoid fauna from the Tesero Member, Werfen Formation (latest Permian to Early Triassic) of the Dolomites (northern Italy). The fauna is largely known from disarticulated ossicles, but consists of both stem group taxa, and a new species of crown group echinoid, Eotiaris teseroensis n. sp. That these stem group echinoids were present in the Tesero Member indicates that stem group echinoids did not go extinct in the Dolomites coincident with the onset of extinction, further supporting other recent work indicating that stem group echinoids survived the end-Permian extinction. Furthermore, the presence of Eotiaris across a number of differing palaeoenvironments in the Early Triassic may have had implications for the survival of cidaroid echinoids during the extinction event. creator: Jeffrey R. Thompson creator: Renato Posenato creator: David J. Bottjer creator: Elizabeth Petsios uri: https://doi.org/10.7717/peerj.7361 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Thompson et al. title: Age, growth, reproduction and management of Southwestern Atlantic’s largest and endangered herbivorous reef fish, Scarus trispinosus Valenciennes, 1840 link: https://peerj.com/articles/7459 last-modified: 2019-08-30 description: The Brazilian-endemic greenbeack parrotfish, Scarus trispinosus Valenciennes, 1840, is the largest herbivorous reef fish in the South Atlantic. Following the sharp decline of large carnivorous reef fishes, parrotfishes (Labridae: Scarinae) were progressively targeted by commercial fisheries in Brazil, resulting in a global population decline of 50% for S. trispinosus. Most of its remnant population is concentrated in the Abrolhos Bank, where the present study was conducted. We present novel information on age, growth and the reproductive cycle of S. trispinosus, based on 814 individuals obtained from commercial fisheries’ landings and scientific collections, between 2010 and 2013. Sex ratio was biased toward females (1:8), and spawning occurred year-round with discrete peaks in February-March and June-December. Increment analysis indicated annual deposition of growth rings in otoliths, which presented 1–22 rings. The asymptotic length at which growth is zero (L∞) was estimated from a Bayesian logistic regression at 85.28 cm, growth rate (K) at 0.14 year−1, and the theoretical age at zero size (t0) at 0.16. Subregional demographic structuring was detected, with predominance of slower-growing individuals in shallower inshore reefs and predominance of faster-growing and older individuals in deeper offshore sites. We demonstrate that S. trispinosus is highly vulnerable to over-exploitation due to its large size, long live and slow-growth, and review the management measures proposed since its Red List assessment in 2012. creator: Matheus O. Freitas creator: Marília Previero creator: Jonas R. Leite creator: Ronaldo B. Francini-Filho creator: Carolina V. Minte-Vera creator: Rodrigo L. Moura uri: https://doi.org/10.7717/peerj.7459 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Freitas et al. title: The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor link: https://peerj.com/articles/7514 last-modified: 2019-08-30 description: BackgroundNeuropeptides exert their activity through binding to G protein-coupled receptors (GPCRs). GPCRs are well-known drug targets in the pharmaceutical industry and are currently discussed as targets to control pest insects. Here, we investigate the neuropeptide adipokinetic hormone (AKH) system of the desert locust Schistocerca gregaria. The desert locust is known for its high reproduction, and for forming devastating swarms consisting of billions of individual insects. It is also known that S. gregaria produces three different AKHs as ligands but has only one AKH receptor (AKHR). The AKH system is known to be essential for metabolic regulation, which is necessary for reproduction and flight activity.MethodsNuclear magnetic resonance techniques (NMR) in a dodecylphosphocholin (DPC) micelle solution were used to determine the structure of the three AKHs. The primary sequence of the S. gregaria AKHR was used to construct a 3D molecular model. Next, the three AKHs were individually docked to the receptor, and dynamic simulation of the whole ligand–receptor complex in a model membrane was performed.ResultsAlthough the three endogenous AKHs of S. gregaria have quite different amino acids sequences and chain length (two octa- and one decapeptide), NMR experiments assigned a turn structure in DPC micelle solution for all. The GPCR-ModSim program identified human kappa opioid receptor to be the best template after which the S. gregaria AKHR was modeled. All three AKHs were found to have the same binding site on this receptor, interact with similar residues of the receptor and have comparable binding constants. Molecular switches were also identified; the movement of the receptor could be visually shown when ligands (AKHs) were docked and the receptor was activated.ConclusionsThe study proposes a model of binding of the three endogenous ligands to the one existing AKHR in the desert locust and paves the way to use such a model for the design of peptide analogs and finally, peptide mimetics, in the search for novel species-specific insecticides based on receptor–ligand interaction. creator: Graham E. Jackson creator: Elumalai Pavadai creator: Gerd Gäde creator: Niels H. Andersen uri: https://doi.org/10.7717/peerj.7514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jackson et al. title: Expansion of sandhill cranes (Grus canadensis) in east Asia during the non-breeding period link: https://peerj.com/articles/7545 last-modified: 2019-08-30 description: AimHistorically, the distribution of Sandhill Cranes included much of North America and extending in summer into northeast Russia. In recent years, observations of sandhill cranes in Asia during the non-breeding period have been frequently reported. However, the distribution and abundance of sandhill cranes during the non-breeding period in Asia have rarely been summarized and studied. Our study aimed to analyze the status of sandhill cranes that have spread south into East Asia during the non-breeding period and to assess the possible impacts of their potential spread.MethodsBased on opportunistic data collected in the field and occurrence data collected online over the past half century, we used Geographic Information System to visualize the spatial distribution changes and regression analysis to analyze and visualize the changes in the amount of individuals over time.ResultsIn the last 50 years, the distribution of sandhill cranes during the non-breeding season in Asia spanned 31 degrees in longitude to the west and 15 degrees in latitude to the south. Their distribution in Asia has expanded to 17 provinces and municipalities in China, Japan and South Korea. The amount of cranes in the non-breeding period in Asia increased significantly from 1963 to 2017. According to the historical records in East Asia, sandhill cranes were mixed with five other species of crane groups.Main conclusionsThese results indicate that the range and amount of sandhill cranes have expanded. Sandhill cranes were mixed with five other crane species, which indicate their adaptability to a range of habitat types and food resources. The implications of these trends in sandhill cranes in East Asia for this and other crane species warrants further research. creator: Linqiang Gao creator: Chunrong Mi creator: Yumin Guo uri: https://doi.org/10.7717/peerj.7545 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gao et al. title: Sargassum blooms in the Caribbean alter the trophic structure of the sea urchin Diadema antillarum link: https://peerj.com/articles/7589 last-modified: 2019-08-30 description: The arrival of large masses of drifting Sargassum since 2011 has caused changes in the natural dynamics of Caribbean coastal ecosystems. In the summer of 2015, unprecedented and massive mats of S. fluitans and S. natans have been observed throughout the Mexican Caribbean including exceptional accumulations ashore. This study uses stable isotopes to assess the impact of Sargassum blooms on the trophic dynamics of the Diadema antillarum sea urchin, a keystone herbivore on many Caribbean reefs. Bayesian models were used to estimate the variations in the relative proportions of carbon and nitrogen of assimilated algal resources. At three lagoon reef sites, the niche breadth of D. antillarum was analysed and compared under massive influx of drifting Sargassum spp. vs. no influx of Sargassum blooms. The effects of the leachates generated by the decomposition of Sargassum led to hypoxic conditions on these reefs and reduced the taxonomic diversity of macroalgal food sources available to D. antillarum. Our trophic data support the hypothesis that processes of assimilation of carbon and nitrogen were modified under Sargassum effect. Isotopic signatures of macroalgae associated with the reef sites exhibited significantly lower values of δ15N altering the natural herbivory of D. antillarum. The Stable Isotopes Analysis in R (SIAR) indicated that, under the influence of Sargassum blooms, certain algal resources (Dictyota, Halimeda and Udotea) were more assimilated due to a reduction in available algal resources. Despite being an abundant available resource, pelagic Sargassum was a negligible contributor to sea urchin diet. The Stable Isotope Bayesian Ellipses in R (SIBER) analysis displayed differences between sites, and suggests a reduction in trophic niche breadth, particularly in a protected reef lagoon. Our findings reveal that Sargassum blooms caused changes in trophic characteristics of D. antillarum with a negative impact by hypoxic conditions. These dynamics, coupled with the increase in organic matter in an oligotrophic system could lead to reduce coral reef ecosystem function. creator: Nancy Cabanillas-Terán creator: Héctor A. Hernández-Arana creator: Miguel-Ángel Ruiz-Zárate creator: Alejandro Vega-Zepeda creator: Alberto Sanchez-Gonzalez uri: https://doi.org/10.7717/peerj.7589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cabanillas-Terán et al. title: The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene link: https://peerj.com/articles/7596 last-modified: 2019-08-30 description: Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that H. petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family and provide significant sequencing information for the genetic improvement of Jerusalem artichoke. creator: Qiwen Zhong creator: Shipeng Yang creator: Xuemei Sun creator: Lihui Wang creator: Yi Li uri: https://doi.org/10.7717/peerj.7596 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhong et al. title: Two salamander species respond differently to timber harvests in a managed New England forest link: https://peerj.com/articles/7604 last-modified: 2019-08-30 description: BackgroundManaging forests for timber while protecting wildlife habitat is of increasing concern. Amphibians may be particularly sensitive to forest management practices due to their unique biology; however, it is not clear how different species respond to timber harvest practices—particularly over longer time scales.MethodsHere we report on the differential responses of two salamander species—the eastern red-backed salamander (Plethodon cinereus Green) and the eastern newt (Notophthalmus viridescens Rafinesque)—to forest harvesting, by examining communities across a 25-year chronosequence of regenerating shelterwood harvests.ResultsPopulations of both species were lowest immediately after harvest, but increased at substantially different rates. Red-backed salamander populations were highest in 20–25 year-old shelterwoods—significantly higher than in mature, unharvested, control (100–120 year old) stands. Eastern newt populations, however, were greatest in unharvested control stands and still had not recovered to population levels found in mature stands in the 25 years since harvest. Red-backed salamander abundances were strongly tied to stand age as well as abundance of decayed coarse woody debris, suggesting that timber harvests influence some wildlife species by affecting a suite of interacting habitat variables that change over time. In contrast, newt abundances were not directly related to stand age but were more related to downed wood and vegetation characteristics. Our results highlight markedly variable responses by two common salamander species to forest harvesting—species with markedly different life histories and reproductive patterns—and that time since harvest may be useful in predicting abundance. creator: Angus Mossman creator: Max R. Lambert creator: Mark S. Ashton creator: Jessica Wikle creator: Marlyse C. Duguid uri: https://doi.org/10.7717/peerj.7604 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mossman et al. title: Comparative and evolutionary analysis of the reptilian hedgehog gene family (Shh, Dhh, and Ihh) link: https://peerj.com/articles/7613 last-modified: 2019-08-30 description: The hedgehog signaling pathway plays a vital role in human and animal patterning and cell proliferation during the developmental process. The hedgehog gene family of vertebrate species includes three genes, Shh, Dhh, and Ihh, which possess different functions and expression patterns. Despite the importance of hedgehog genes, genomic evidence of this gene family in reptiles is lacking. In this study, the available genomes of a number of representative reptile species were explored by utilizing adaptive evolutionary analysis methods to characterize the evolutionary patterns of the hedgehog gene family. Altogether, 33 sonic hedgehog (Shh), 25 desert hedgehog (Dhh), and 20 Indian hedgehog (Ihh) genes were obtained from reptiles, and six avian and five mammalian sequences were added to the analysis. The phylogenetic maximum likelihood (ML) tree of the Shh, Dhh, and Ihh genes revealed a similar topology, which is approximately consistent with the traditional taxonomic group. No shared positive selection site was identified by the PAML site model or the three methods in the Data Monkey Server. Branch model and Clade model C analyses revealed that the Dhh and Ihh genes experienced different evolutionary forces in reptiles and other vertebrates, while the Shh gene was not significantly different in terms of selection pressure. The different evolutionary rates of the Dhh and Ihh genes suggest that these genes may be potential contributors to the discrepant sperm and body development of different clades. The different adaptive evolutionary history of the Shh, Dhh, and Ihh genes among reptiles may be due to their different functions in regulating cellular events of development from the embryonic stages to adulthood. Overall, this study has provided meaningful information regarding the evolution of the hedgehog gene family in reptiles and a theoretical foundation for further analyses on the functional and molecular mechanisms that have shaped the reptilian hedgehog genes. creator: Tian Xia creator: Honghai Zhang creator: Lei Zhang creator: Xiufeng Yang creator: Guolei Sun creator: Jun Chen creator: Dajie Xu creator: Chao Zhao uri: https://doi.org/10.7717/peerj.7613 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xia et al. title: Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR) link: https://peerj.com/articles/7152 last-modified: 2019-08-29 description: Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance of Acinetobacter reached 70.8%. At the start of the granulation phase the relative abundance of Agrobacterium reached 35.9% and that of Dipodascus 89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation. creator: Fabiola Gómez-Basurto creator: Miguel Vital-Jácome creator: Elizabeth Selene Gómez-Acata creator: Frederic Thalasso creator: Marco Luna-Guido creator: Luc Dendooven uri: https://doi.org/10.7717/peerj.7152 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gómez-Basurto et al. title: Postural control in girls with adolescent idiopathic scoliosis while wearing a Chêneau brace or performing active self-correction: a pilot study link: https://peerj.com/articles/7513 last-modified: 2019-08-29 description: BackgroundIt is known that adolescent idiopathic scoliosis (AIS) is often accompanied by balance deficits. This reciprocal relationship must be taken into account when prescribing new therapeutic modalities because these may differently affect postural control, interacting with therapy and influencing its results.ObjectiveThe purpose was to compare postural control in girls with AIS while wearing the Chêneau brace (BRA) or performing active self-correction (ASC) with their postural control in a quiet comfortable stance.MethodsNine subjects were evaluated on a force plate in three series of two 20-s quiet standing trials with eyes open or closed; three blocks were randomly arranged: normal quiet stance (QST), quiet stance with BRA, and quiet stance with ASC. On the basis of centre-of-pressure (COP) recordings, the spatial and temporal COP parameters were computed.Results and DiscussionPerforming ASC was associated with a significant backward excursion of the COP mean position with eyes open and closed (ES = 0.56 and 0.65, respectively; p < 0.05). This excursion was accompanied by an increase in the COP fractal dimension (ES = 1.05 and 0.98; p < 0.05) and frequency (ES = 0.78; p = 0.10 and ES = 1.14; p < 0.05) in the mediolateral (ML) plane. Finally, both therapeutic modalities decreased COP sample entropy with eyes closed in the anteroposterior (AP) plane. Wearing BRA resulted in ES = 1.45 (p < 0.05) while performing ASC in ES = 0.76 (p = 0.13).ConclusionThe observed changes in the fractal dimension (complexity) and frequency caused by ASC account for better adaptability of patients to environmental demands and for their adequate resources of available postural strategies in the ML plane. These changes in sway structure were accompanied by a significant (around 25 mm) backward excursion of the mean COP position. However, this improvement was achieved at the cost of lower automaticity, i.e. higher attentional involvement in postural control in the AP plane. Wearing BRA may have an undesirable effect on some aspects of body balance. creator: Elżbieta Piątek creator: Michał Kuczyński creator: Bożena Ostrowska uri: https://doi.org/10.7717/peerj.7513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Piątek et al. title: Effects of shading on the growth and leaf photosynthetic characteristics of three forages in an apple orchard on the Loess Plateau of eastern Gansu, China link: https://peerj.com/articles/7594 last-modified: 2019-08-29 description: BackgroundInclusion of forage into the orchard is of great help in promoting the use efficiency of resources, while shading from trees restricts forage growth and production in the Loess Plateau of China. This study was aimed to investigate how tree shading affected leaf trait, photosynthetic gas exchange and chlorophyll feature of forages under the tree in the orchard-forage system.MethodsThe shading treatments were set as partially cutting branches (reduced shading), normal fruit tree shading (normal shading) and normal tree shading plus sun-shading net (enhanced shading) in an apple orchard. Leaf trait, photosynthesis, chlorophyll component and fluorescence related parameters were measured with lucerne (Medicago sativa), white clover (Trifolium repens) and cocksfoot (Dactylis glomerata) which were sown under apple trees.ResultsShading imposed significant impacts on the growth and leaf photosynthetic characteristics, while there were differences among species. Enhanced shading decreased leaf thickness, leaf dry matter content (LDMC) and leaf mass per unit area (LMA). Biomass accumulation decreased with enhanced shading in cocksfoot, but did not change in white clover and lucerne which had much lower biomass accumulation than cocksfoot. Enhanced shading reduced net photosynthetic rate (Pn) of white clover and lucerne, but rarely affected cocksfoot, while it decreased instantaneous water use efficiency (WUEi) of cocksfoot but had few effects on the other forages. Enhanced shading reduced leaf dark respiration rate (Rd), light compensation point (LCP) and maximum assimilation rate. The Rd and LCP of cocksfoot were much lower than those of white clover and lucerne. Chlorophyll contents and chlorophyll a/b changed little with shading. Cocksfoot had the highest contents but lowest ratio. Maximum photochemical rate of photosystem II increased and non-photochemical quenching decreased with enhanced shading in cocksfoot, while did not change in the other forages.DiscussionLeaf trait, photosynthetic gas exchange and chlorophyll feature were variously affected by species, shading and their interaction. Cocksfoot was more efficient than the other two forages in use of weakened light and more tolerant to tree shading. In the apple orchard, we recommend that reducing the density of apple tree or partially cutting branches together with selecting some shading-tolerant forages, i.e., cocksfoot, would be a practical option for the orchard-forage system in the Loess Plateau of China. creator: Mei Yang creator: Minguo Liu creator: Jiaoyun Lu creator: Huimin Yang uri: https://doi.org/10.7717/peerj.7594 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: Comparative transcriptome analysis of panicle development under heat stress in two rice (Oryza sativa L.) cultivars differing in heat tolerance link: https://peerj.com/articles/7595 last-modified: 2019-08-29 description: Heat stress inhibits rice panicle development and reduces the spikelet number per panicle. This study investigated the mechanism involved in heat-induced damage to panicle development and spikelet formation in rice cultivars that differ in heat tolerance. Transcriptome data from developing panicles grown at 40 °C or 32 °C were compared for two rice cultivars: heat-tolerant Huanghuazhan and heat-susceptible IR36. Of the differentially expressed genes (DEGs), 4,070 heat stress-responsive genes were identified, including 1,688 heat-resistant-cultivar-related genes (RHR), 707 heat-susceptible-cultivar-related genes (SHR), and 1,675 common heat stress-responsive genes (CHR). A Gene Ontology (GO) analysis showed that the DEGs in the RHR category were significantly enriched in 54 gene ontology terms, some of which improved heat tolerance, including those in the WRKY, HD-ZIP, ERF, and MADS transcription factor families. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs in the RHR and SHR categories were enriched in 15 and 11 significant metabolic pathways, respectively. Improved signal transduction capabilities of endogenous hormones under high temperature seemed to promote heat tolerance, while impaired starch and sucrose metabolism under high temperature might have inhibited young panicle development. Our transcriptome analysis provides insights into the different molecular mechanisms of heat stress tolerance in developing rice. creator: Yaliang Wang creator: Yikai Zhang creator: Qiang Zhang creator: Yongtao Cui creator: Jing Xiang creator: Huizhe Chen creator: Guohui Hu creator: Yanhua Chen creator: Xiaodan Wang creator: Defeng Zhu creator: Yuping Zhang uri: https://doi.org/10.7717/peerj.7595 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Mapping research trends of retinal vein occlusion from 2009 to 2018: a bibliometric analysis link: https://peerj.com/articles/7603 last-modified: 2019-08-29 description: ObjectivesTo map publication trends and explore research hotspots of retinal vein occlusion (RVO) study.MethodsBased on Web of Science Core Collection (WoSCC), a bibliometric analysis was carried out. The knowledge map was constructed by VOSviewer v.1.6.10 to visualize the annual publication number, the distribution of countries, international collaborations, author productivity, source journals, cited reference and keywords in this field.ResultsA total of 2,135 peer-reviewed papers were retrieved on RVO from 2009 to 2018. The United States ranks highest among countries with the most publications and the most active institution was Kyoto University. Noma H contributed the most publications in this field. Retina—The Journal of Retinal and Vitreous Disease was the most prolific journal in RVO research. The top cited references mainly presented anti-VEGF medications on the management of RVO. The keywords formed six clusters: (1) Risk factors and pathogenesis of RVO; (2) Metabolismof RVO; (3) Therapeutic use of corticosteroids on RVO; (4) Diagnostic methodsof RVO; (5) Management of macular edema secondary to RVO (6) Anti-VEGFtreatment of RVO.ConclusionsThe six major research hotspots could provide an insight into RVO research and valuable information for researchers to identify potential collaborators and partner institutions. creator: Fangkun Zhao creator: Fengkun Du creator: Dong Shi creator: Wenkai Zhou creator: Youhong Jiang creator: Liwei Ma uri: https://doi.org/10.7717/peerj.7603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza link: https://peerj.com/articles/7605 last-modified: 2019-08-29 description: Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza. creator: Caili Li creator: Dongqiao Li creator: Hong Zhou creator: Jiang Li creator: Shanfa Lu uri: https://doi.org/10.7717/peerj.7605 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny link: https://peerj.com/articles/7162 last-modified: 2019-08-28 description: The phylogeny of the Pseudosubhimalus were investigated using of two different data sets, including 91 taxa and 3853 aligned nucleotide positions from the histone H3, 28S rDNA (D2 & D9–10 region). The results suggest the placement of genus in the tribe Ciacadulini, as it was clustered with Cicadulini genera. Relationships between genera of the Cicadulini were strongly supported and leads placement to tribe Cicadulini from Athysanini. Along with this, genus Pseudosubhimalus Ghauri is revised, and P. trilobatus sp. nov. (Himachal Pradesh: Katrain) is added, described from Indian subcontinent and deposited to National Pusa Collection, IARI, New Delhi, with repository number RRS1. creator: GN Niranjana creator: Naresh M. Meshram creator: Pathour R. Shashank creator: Stuti creator: Tahseen Raza Hashmi uri: https://doi.org/10.7717/peerj.7162 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Niranjana et al. title: Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation link: https://peerj.com/articles/7494 last-modified: 2019-08-28 description: BackgroundPseudomonas aeruginosa is an opportunistic and pathogenic bacterium with the ability to produce cyclodipeptides (CDPs), which belong to a large family of molecules with important biological activities. Excessive amounts of CDPs produced by Pseudomonas strains can activate an auxin response in Arabidopsis thaliana and promote plant growth. Target of rapamycin (TOR) is an evolutionarily conserved eukaryotic protein kinase that coordinates cell growth and metabolic processes in response to environmental and nutritional signals. Target of rapamycin kinase phosphorylates various substrates, of which S6 ribosomal protein kinase (S6K) is particularly well known. The PI3K/Akt/mTOR/S6K signaling pathway has been studied extensively in mammals because of its association with fundamental biological processes including cell differentiation. However, evidences suggest that this pathway also has specific and conserved functions in plants and may thus be conserved, as are several of its components like TOR complex 1 and S6K proteins. In plants, TOR-S6K signaling has been shown to be modulated in response to plant growth promoters or stressors.MethodsIn this study, we evaluated the effects of P. aeruginosa CDPs on the growth and root development of maize plants (Zea mays L.) by adding different CDPs concentrations on culture plant media, as well as the effect on the phosphorylation of the maize S6K protein (ZmS6K) by protein electrophoresis and western blot.ResultsOur results showed that P. aeruginosa CDPs promoted maize growth and development, including modifications in the root system architecture, correlating with the increased ZmS6K phosphorylation and changes induced in electrophoretic mobility, suggesting post-translational modifications on ZmS6K. These findings suggest that the plant growth-promoting effect of the Pseudomonas genus, associated with the CDPs production, involves the TOR/S6K signaling pathway as a mechanism of plant growth and root development in plant–microorganism interaction. creator: Iván Corona-Sánchez creator: Cesar Arturo Peña-Uribe creator: Omar González-López creator: Javier Villegas creator: Jesus Campos-Garcia creator: Homero Reyes de la Cruz uri: https://doi.org/10.7717/peerj.7494 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Corona-Sánchez et al. title: Early Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratherium link: https://peerj.com/articles/7517 last-modified: 2019-08-28 description: BackgroundWischberg is a Swiss locality in Bern Canton which has yielded numerous vertebrates remains from the earliest Miocene (= MN1). It has a very rich faunal diversity, one of the richest in Switzerland for this age. Among all the mammals reported in the original faunal list 70 years ago, three rhinocerotid species were identified. The material consists of two fragmentary skulls, cranial fragments, several mandibles, teeth and postcranial bones, in a rather good state of preservation.ResultsAfter reexamination of the material from this locality (curated in three different Swiss museums) and comparison with holotype specimens, we show that all rhinocerotid specimens from Wischberg can be referred to two species only. Most of the material can be attributed to the large-sized teleoceratine Diaceratherium lemanense, while only a few specimens, including a skull and mandible, belong to the much smaller sized Pleuroceros pleuroceros. We describe and illustrate for the first time most of these fossil remains. However, the systematics of the genus Diaceratherium is currently controversial, and based on our new observations we consider seven species as valid, though a large-scale phylogenetic study should be done in the future to resolve it. The rhinocerotid association found in Wischberg is nonetheless typical of the MN1 biozone, which results from a faunal renewal occurring just before the end of the Oligocene. creator: Claire Jame creator: Jérémy Tissier creator: Olivier Maridet creator: Damien Becker uri: https://doi.org/10.7717/peerj.7517 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jame et al. title: Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents link: https://peerj.com/articles/7528 last-modified: 2019-08-28 description: In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents. creator: Jianzhou Qu creator: Shutu Xu creator: Xiaokang Tian creator: Ting Li creator: Licheng Wang creator: Yuyue Zhong creator: Jiquan Xue creator: Dongwei Guo uri: https://doi.org/10.7717/peerj.7528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qu et al. title: The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803 link: https://peerj.com/articles/7529 last-modified: 2019-08-28 description: Synthetic metabolism allows new metabolic capabilities to be introduced into strains for biotechnology applications. Such engineered metabolic pathways are unlikely to function optimally as initially designed and native metabolism may not efficiently support the introduced pathway without further intervention. To develop our understanding of optimal metabolic engineering strategies, a two-enzyme ethanol pathway consisting of pyruvate decarboxylase and acetaldehyde reductase was introduced into Synechocystis sp. PCC 6803. We characteriseda new set of ribosome binding site sequences in Synechocystis sp. PCC 6803 providing a range of translation strengths for different genes under test. The effect of ribosome-bindingsite sequence, operon design and modifications to native metabolism on pathway flux was analysed by HPLC. The accumulation of all introduced proteins was also quantified using selected reaction monitoring mass spectrometry. Pathway productivity was more strongly dependent on the accumulation of pyruvate decarboxylase than acetaldehyde reductase. In fact, abolishment of reductase over-expression resulted in the greatest ethanol productivity, most likely because strains harbouringsingle-gene constructs accumulated more pyruvate decarboxylase than strains carrying any of the multi-gene constructs. Overall, several lessons were learned. Firstly, the expression level of the first gene in anyoperon influenced the expression level of subsequent genes, demonstrating that translational coupling can also occur in cyanobacteria. Longer operons resulted in lower protein abundance for proximally-encoded cistrons. And, implementation of metabolic engineering strategies that have previously been shown to enhance the growth or yield of pyruvate dependent products, through co-expression with pyruvate kinase and/or fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase, indicated that other factors had greater control over growth and metabolic flux under the tested conditions. creator: Paulina Bartasun creator: Nicole Prandi creator: Marko Storch creator: Yarin Aknin creator: Mark Bennett creator: Arianna Palma creator: Geoff Baldwin creator: Yumiko Sakuragi creator: Patrik R. Jones creator: John Rowland uri: https://doi.org/10.7717/peerj.7529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bartasun et al. title: Endogenous testosterone correlates with parochial altruism in relation to costly punishment in different social settings link: https://peerj.com/articles/7537 last-modified: 2019-08-28 description: Testosterone plays a key role in shaping human social behavior. Recent findings have linked testosterone to altruistic behavior in economic decision tasks depending on group membership and intergroup competition. The preferential treatment of ingroup members, while aggression and discrimination is directed towards outgroup members, has been referred to as parochial altruism. Here we investigated in two consecutive studies, whether testosterone is associated with parochial altruism depending on individual tendency for costly punishment. In the first study, 61 men performed a single-shot ultimatum game (UG) in a minimal group context, in which they interacted with members of an ingroup and outgroup. In the second study, 34 men performed a single-shot UG in a more realistic group context, in which they responded to the proposals of supporters of six political parties during the German election year 2017. Political parties varied in their social distance to the participants’ favorite party as indicated by an individual ranking. Participants of study 2 also performed a cued recall task, in which they had to decide whether they had already encountered a face during the previous UG (old-new decision). In order to make the UG data of study 2 most comparable to the data of study 1, the rejection rates of several parties were combined according to the social distance ranking they achieved. Parties ranked 1 to 3 formed the relatively close and favored ‘ingroup’ that shared similar political values with the participant (e.g., left wing parties), while the ‘outgroup’ consisted of parties ranked from 4 to 6 with more distant or even antagonistic political views (e.g., conservative to right wing parties). In both studies, results showed a parochial pattern with higher rejection rates made in response to outgroup compared to ingroup offers. Interestingly, across studies higher salivary testosterone was associated with higher rejection rates related to unfair outgroup offers in comparison to the unfair offers made by ingroup members. The present findings suggest that latent intergroup biases during decision-making may be positively related to endogenous testosterone. Similar to previous evidence that already indicated a role of testosterone in shaping male parochial altruism in male soccer fans, these data underscore the general, yet rather subtle role of male testosterone also in other social settings. creator: Luise Reimers creator: Eli Kappo creator: Lucas Stadler creator: Mostafa Yaqubi creator: Esther K. Diekhof uri: https://doi.org/10.7717/peerj.7537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Reimers et al. title: A real-world study on clinical predictors of relapse after hospitalized detoxification in a Chinese cohort with alcohol dependence link: https://peerj.com/articles/7547 last-modified: 2019-08-28 description: BackgroundThe relapse rate of alcohol dependence (AD) after detoxification is high, but few studies have investigated the clinical predictors of relapse after hospitalized detoxification in real-world clinical practice, especially among Chinese patients.MethodsThis longitudinal cohort study followed up 122 AD patients who were discharged from January 1, 2016 to January 30, 2018 from their most recent hospitalization for detoxification. These patients were interviewed by telephone from May 20, 2017, to June 30, 2018, at least 6 months after discharge. During the interview, the relapse were assessed by using a revised Chinese version of the Alcohol Use Disorder Identification Test. Candidate predictors, such as therapeutic modalities during hospitalization and at discharge, medical history data related to alcohol use, and demographic information, were obtained from the medical records in the hospital information system.ResultsDuring the 6–24 months (with a median of 9 months) follow-up period, the relapse rate was 53.3%. Individuals with a college education level and those who had not been treated with the brief comprehensive cognitive-motivational-behavioural intervention (CCMBI) were more likely than their counterparts to relapse after hospitalized detoxification, and their adjusted HRs (95% CIs) were 1.85 (1.09, 3.16) and 2.00 (1.16, 3.46), respectively. The CCMBI use predicted a reduction in the relapse rate by approximately one-fifth.ConclusionUndergoing the CCMBI during detoxification hospitalization and having less than a college-level education could predict a reduced risk of AD relapse. These findings provide useful information both for further clinical research and for real-world practice. creator: Yu-Jie Tao creator: Li Hu creator: Ying He creator: Bing-Rong Cao creator: Juan Chen creator: Ying-Hua Ye creator: Ting Chen creator: Xia Yang creator: Jia-Jun Xu creator: Jing Li creator: Ya-Jing Meng creator: Tao Li creator: Wan-Jun Guo uri: https://doi.org/10.7717/peerj.7547 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tao et al. title: HiLDA: a statistical approach to investigate differences in mutational signatures link: https://peerj.com/articles/7557 last-modified: 2019-08-28 description: We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs and to compare the estimated frequencies between tumor sets. We apply our method to two datasets, one containing somatic mutations in colon cancer by the time of occurrence, before or after tumor initiation, and the second containing somatic mutations in esophageal cancer by sex, age, smoking status, and tumor site. In colon cancer, the relative frequencies of mutational patterns were found significantly associated with the time of occurrence of mutations. In esophageal cancer, the relative frequencies were significantly associated with the tumor site. Our novel method provides higher statistical power for detecting differences in mutational signatures. creator: Zhi Yang creator: Priyatama Pandey creator: Darryl Shibata creator: David V. Conti creator: Paul Marjoram creator: Kimberly D. Siegmund uri: https://doi.org/10.7717/peerj.7557 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: Nicotinamide riboside exerts protective effect against aging-induced NAFLD-like hepatic dysfunction in mice link: https://peerj.com/articles/7568 last-modified: 2019-08-28 description: Background & AimsAging is one of the risk factors of non-alcoholic fatty liver disease (NAFLD). Yet, the mechanism underlying the aging-associated NAFLD-like syndrome is not fully understood. Nicotinamide adenine dinucleotide (NAD), a ubiquitous coenzyme, has protective effects against aging. Here, we investigated the actions of NAD precursors nicotinamide riboside (NR) on the development of aging-induced NAFLD.MethodsNR supplemented food (2.5 g/kg food) was applied to aged mice for three months while normal chow to the other groups. Body weight, food intake, liver weight and fat pat mass were measured. The serum concentrations of lipid content, alanine aminotransferase (ALT), aspartate aminotransferase (AST) and NAD were determined by biochemical assays. Pathological assessment and immunohistochemistry analysis of hepatic tissues were used to evaluate the effect of NR on NAFLD development and inflammatory infiltration.ResultsNR repletion significantly reduced fat pat mass in aged mice, while not altered the body weight, food intake, and liver weight. NR repletion significantly rescued the NAD reduction in aged mice. The total cholesterol and triglyceride levels could be lowered by NR repletion in aged mice. The AST level was also significantly reduced by NR repletion in aged group, while the ALT level lowered but without significance. Notably, moderate NAFLD phenotypes, including steatosis and hepatic fibrosis could be markedly corrected by NR repletion. In addition, Kupffer cells accumulated and inflammatory infiltration could also be remarkably reversed by NR repletion in aged mice.ConclusionAging was associated with NAFLD-like phenotypes in mice, which could be reversed by oral NR repletion. Therefore, oral NR uptake might be a promising strategy to halt the progression of NAFLD. creator: Xue Han creator: Xiaogang Bao creator: Qi Lou creator: Xian Xie creator: Meng Zhang creator: Shasang Zhou creator: Honggang Guo creator: Guojun Jiang creator: Qiaojuan Shi uri: https://doi.org/10.7717/peerj.7568 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Han et al. title: Testing the function of dromaeosaurid (Dinosauria, Theropoda) ‘sickle claws’ through musculoskeletal modelling and optimization link: https://peerj.com/articles/7577 last-modified: 2019-08-28 description: Dromaeosaurids were a clade of bird-like, carnivorous dinosaurs that are well known for their characteristic morphology of pedal digit II, which bore an enlarged, sickle-shaped claw and permitted an extreme range of flexion–extension. Proposed functions for the claw often revolve around predation, but the exact manner of use varies widely. Musculoskeletal modelling provides an avenue to quantitatively investigate the biomechanics of this enigmatic system, and thereby test different behavioural hypotheses. Here, a musculoskeletal model of the hindlimb and pes of Deinonychus was developed, and mathematical optimization was used to assess the factors that maximize production of force at the claw tip. Optimization revealed that more crouched hindlimb postures (i.e., more flexed knees and ankles) and larger flexor muscle volumes consistently increased claw forces, although the optimal degree of digit flexion or extension depended on assumptions of muscle activity and fibre operating range. Interestingly, the magnitude of force capable of being produced at the claw tip was relatively small, arguing against regular transmission of a large proportion of body weight into a substrate principally via the claw tip. Such transmission would therefore likely have needed to occur via more proximal parts of the foot. Collectively, the results best support a grasping function for digit II (e.g., restraint of prey smaller than the dromaeosaurid’s own body size), although other behaviours involving flexed hindlimbs cannot be excluded. creator: Peter J. Bishop uri: https://doi.org/10.7717/peerj.7577 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bishop title: The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices link: https://peerj.com/articles/7599 last-modified: 2019-08-28 description: BackgroundWrist circumference (WrC) is an easily obtained measure in estimating the body frame and regional fat distribution, and has increasingly used as an obesity index. The aim of our study is to estimate the association of WrC with elevated blood pressure (BP) among northeastern Chinese community-dwelling residents, and compare the strength of this association to other anthropometric obesity indices.MethodsA total of 2,331 adult participants (761 male participants, and 1,570 female participants) were included. WrC and other five generally used obesity indices, including body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and neck circumference (NC) were measured. Hypertension was defined as systolic blood pressure (SBP)/diastolic blood pressure (DBP) ≥140/90 mmHg or anti-hypertensive medication use. Multivariable linear and logistic regression models were performed to identify associations of BP and hypertension with per standard deviation (SD) increase of obesity indices. Areas under receiver operative characteristic curves (AUC) were calculated to compare the predicting capacity of WrC and other obesity indices on hypertension.ResultsAll of the six obesity indices were positively associated with both SBP and DBP after adjustment for age and gender (P-values of associations of SBP with obesity indices were 0.043 for WrC, and <0.001 for other five indices; P-values of associations of DBP with obesity indices were 0.011 for WrC, 0.031 for WHR, and <0.001 for other four indices), while the association between SBP and WrC showed no statistically significant after further adjusted for life-style and metabolic risk factors (P-value was 0.062). The increases of both SBP and DBP per SD increase of BMI were the largest. The positive associations of five obesity indices but WHR with hypertension were observed after adjustment for all risk factors (P-values were 0.024 for WrC, 0.064 for WHR and <0.001 for other four indices). However, the odd ratios (OR) of WrC was the smallest, while BMI was the largest. Consistently, the AUC of BMI was the largest and statistically larger than that observed for WrC (P-value <0.001).ConclusionsWrC was associated with hypertension among northeastern Chinese populations. However, the association was not stronger than the other generally used indices, particularly BMI. creator: Yongfang Li creator: Yuyan Liu creator: Jing He creator: Ping Ma creator: Luyang Yu creator: Guifan Sun uri: https://doi.org/10.7717/peerj.7599 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling link: https://peerj.com/articles/7600 last-modified: 2019-08-28 description: With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS. creator: Ming-Hsin Tsai creator: Yen-Yi Liu creator: Chih-Chieh Chen uri: https://doi.org/10.7717/peerj.7600 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tsai et al. title: Healthy eating promoting in a Brazilian sports-oriented school: a pilot study link: https://peerj.com/articles/7601 last-modified: 2019-08-28 description: BackgroundAdolescents, particularly athletes, have high exposure to ultra-processed foods, which could be harmful to their health and physical performance. School environments are capable of improving eating patterns. Our study is aimed at capturing changes in students’ food consumption three years after they enrolled at an experimental school, considered a model of health promotion in Rio de Janeiro city. We also aimed to depict the promising nature of the healthy eating promotion program implemented in the school and share the learnings from its implementation.MethodsOur pilot study was a follow-up on the implementation of a school garden, experimental kitchen activities, and health promotion classes. We evaluated 83 adolescent athletes’ food consumption twice during the study: at its beginning (2013) and end (2016), by administering a food frequency questionnaire (FFQ) that inquired about the frequency of foods consumed in the past week. To evaluate how effectively the activities were established, integrated, and sustained in schools, the Garden Resources, Education, and Environment Nexus (GREEN) tool was used, and the school’s adherence to the school garden program was classified as high (scored 47 points out of 57).ResultsIn 2013, 89 adolescents (mean ± SD 11.9 ± 0.4 years, 54% male) participated in the study, of which 83 continued until 2016 (14.8 ± 0.5 years, 55% male). In 2013, the mean frequency of raw salad and fruits consumption was 1.4 (CI [1.0–1.9]) and 4.3 (CI [3.8–4.9]) days per week, respectively. Three years later, the frequency of raw salad and fruits consumption was 2.2 (CI [1.6–2.7]) and 5.0 (4.5–5.5), respectively. Considering that five meals were offered at school (five days/week), it may be possible to assume that the program raised awareness on the importance of healthy eating.ConclusionOur results suggest that such integrated healthy eating promotion programs may improve adolescent athletes’ eating habits, by increasing the frequency of their consumption of unprocessed foods. This pilot study’s results inspired us to implement an expanded project at the municipal level. Since 2018, teachers who participated in this program are working with Rio de Janeiro’s Municipal Secretary of Education for Coordination of Curricular Projects. Some learnings from this pilot study on implementing the garden/experimental kitchen project in this school are being applied in 65 schools of the municipal network: joint activities must be fostered among students, teachers, and parents; healthy eating needs to be a respected value among adolescent athletes and become an example for parents and teachers. creator: Fábia Albernaz Massarani creator: Marta Citelli creator: Daniela Silva Canella creator: Josely Correa Koury uri: https://doi.org/10.7717/peerj.7601 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Massarani et al. title: Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement link: https://peerj.com/articles/7628 last-modified: 2019-08-28 description: Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL. creator: Hao Zhang creator: Juan Cheng creator: Zijian Li creator: Yaming Xi uri: https://doi.org/10.7717/peerj.7628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies link: https://peerj.com/articles/7386 last-modified: 2019-08-27 description: Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of “slender-bodied Oenochrominae” that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively. creator: Leidys Murillo-Ramos creator: Gunnar Brehm creator: Pasi Sihvonen creator: Axel Hausmann creator: Sille Holm creator: Hamid Reza Ghanavi creator: Erki Õunap creator: Andro Truuverk creator: Hermann Staude creator: Egbert Friedrich creator: Toomas Tammaru creator: Niklas Wahlberg uri: https://doi.org/10.7717/peerj.7386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Murillo-Ramos et al. title: Effect of adjuvant radioactive iodine therapy on survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma) link: https://peerj.com/articles/7458 last-modified: 2019-08-27 description: PurposeRadioactive iodine (RAI) is widely used for adjuvant therapy after thyroidectomy, while its value for thyroid cancer has been controversial recently. The primary objectives of this study were to clarify the influence of Radioactive iodine (RAI) on the survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma, HCC).MethodsPatients diagnosed with oxyphilic thyroid carcinoma from 2004 to 2015 were extracted from the Surveillance, Epidemiology, and End Results Program database. The Kaplan-Meier method was used to compare overall survival (OS) and cancer-specific survival (CSS) among patients who had adjuvant RAI use or not. Univariate and multivariate Cox proportional hazard models were performed for survival analysis, and subsequently visualized by nomogram.ResultsIn all, 2,799 patients were identified, of which 1529 patients had adjuvant RAI use while 1,270 patients had not. Based on multivariate Cox analysis, the RAI therapy confers an improved OS for HCC patients (HR = 0.57, 95% CI [0.44–0.72], P < 0.001), whereas it has no significant benefit in the survival analysis regarding CSS (HR = 0.79, 95% CI [[0.47–1.34], P = 0.382). In a subgroup analysis, the same survival benefit of RAI treatment on OS, but not CSS was observed among patients stratified by AJCC stage and tumor extension. Nevertheless, patients with regional lymph node metastasis benefited from RAI therapy both in OS and CSS (P < 0.001, respectively). Furthermore, nomograms used for predicting long term survival of HCC patients exhibited a better prediction power for OS compared with traditional tumor, nodal and metastatic (TNM) stage made by American Joint Committee on Cancer (AJCC) (C-index = 0.833 of the nomogram model vs. 0.696 of the AJCC system).ConclusionsThis study suggests that RAI therapy is significantly associated with improved OS in patients with Hürthle cell carcinoma. However, there was no association between treatment with radioiodine and CSS, possibly due to small number of deaths that were related to HCC. creator: Qiong Yang creator: Zhongsheng Zhao creator: Guansheng Zhong creator: Aixiang Jin creator: Kun Yu uri: https://doi.org/10.7717/peerj.7458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells link: https://peerj.com/articles/7524 last-modified: 2019-08-27 description: BackgroundAluminum (Al) is toxic to animals and humans. The most common sources of human exposure to Al are food and beverages. The intestinal epithelium is the first barrier against Al-induced toxicity. In this study, HT-29, a human colon cancer cell line, was selected as an in vitro model to evaluate the Al-induced alteration in metabolomic profiles and explore the possible mechanisms of Al toxicity.MethodsMTT assay was performed to determine the half-maximal inhibitory concentration of Al ions. Liquid chromatography-mass spectrometry (LC-MS) was used for metabolomic analysis, and its results were further confirmed using quantitative reverse transcription polymerase chain reaction (RT-qPCR) of nine selected genes.ResultsAl inhibited the growth of the HT-29 cells, and its half-maximal dose for the inhibition of cell proliferation was found to be four mM. This dose was selected for further metabolomic analysis, which revealed that 81 metabolites, such glutathione (GSH), phosphatidylcholines, phosphatidylethanolamines, and creatine, and 17 metabolic pathways, such as the tricarboxylic acid cycle, pyruvate metabolism, and GSH metabolism, were significantly altered after Al exposure. The RT-qPCR results further confirmed these findings.ConclusionThe metabolomics and RT-qPCR results indicate that the mechanisms of Al-induced cytotoxicity in HT-29 cells include cellular apoptosis, oxidative stress, and alteration of lipid, energy, and amino acid metabolism. creator: Leilei Yu creator: Jiangping Wu creator: Qixiao Zhai creator: Fengwei Tian creator: Jianxin Zhao creator: Hao Zhang creator: Wei Chen uri: https://doi.org/10.7717/peerj.7524 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yu et al. title: Determination of nucleotide and enzyme degradation in haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) after high pressure processing link: https://peerj.com/articles/7527 last-modified: 2019-08-27 description: BackgroundThe degradation of nucleotides and their enzymes had been widely used to evaluate fish freshness. Immediately after fish death, adenosine triphosphate (ATP) degrades into inosine-5-monophosphate (IMP) via adenosine-5-diphosphate (ADP) and adenosine-5-monophosphate (AMP). IMP degradation continues to produce inosine (ino) and hypoxanthine (Hx) and further deteriorates the fish by producing xanthine and uric acid. The dephosphorylation of IMP to Ino is carried out by the enzyme 5′-nucleotidase (5′-NT), whereas the degradation of Ino to Hx is carried out by the enzyme nucleoside phosphorylase (NP). This study assesses the application of high pressure processing (HPP) in two species of fishes; haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) as a means to extend the shelf-life by slowing down the rate of nucleotides degradation.MethodsHaddock (Melanogrammus aeglefinus) and herring (Clupea harengus) fillets were subjected to HPP at 200, 250 and 300 MPa for 1 and 3 min before being stored for 14 days. In addition, 5′-NT and NP enzyme activities were determined on both fish species that were subjected to 100–600 MPa for 1 and 3 min.ResultsAdenosine triphosphate, ADP and AMP in both haddock and herring were lower at higher pressure levels. Inosine (Ino) increased (p < 0.05) after treatment at higher pressures in both species. Hx in herring decreased significantly (p < 0.05) at higher pressures but not in haddock. K values are the ratio of Ino and Hx to all nucleotides. K values in haddock were not significantly (p > 0.05) affected by the pressure treatment. H values are ratio of Hx to the sum of IMP, Ino and Hx. H values in haddock were significantly decreased (p < 0.05) with increasing pressure level. F values are ratio of IMP to the sum of IMP, Ino and Hx. F values showed no significant effects (p > 0.05) after pressure treatment. Furthermore, K values in control herring were significantly higher (p < 0.05) than those of the pressure-treated samples. H values in herring decreased significantly (p < 0.05) with increasing pressure level. F values in herring showed no significant effects (p > 0.05) after pressure treatment. Pressure treatment brought a significant decrease (p < 0.05) in protein content in both haddock and herring. 5′-NT activity was 20–35 fold higher compared to NP activity in haddock and 15–44 fold higher than NP activity in herring. 5′-NT and NP activities decreased significantly with increasing pressure level in both species.DiscussionHigh pressure processing effectively slows down the conversion of Ino to Hx, delaying the undesirable flavour that develops in spoiling fish. The autolytic conversion of IMP to Ino by endogenous 5′-NT predominates in the earliest stages of storage is an autolytic process. However, both bacterial and endogenous NP enzymes are probably responsible for the gradual accumulation of Hx in fish. K values are recommended as a useful measurement of fish freshness. creator: Nurul Ulfah Karim creator: James Terence Kennedy creator: Mark Linton creator: Margaret Patterson creator: Sally Watson creator: Norman Gault uri: https://doi.org/10.7717/peerj.7527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Karim et al. title: Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus) link: https://peerj.com/articles/7548 last-modified: 2019-08-27 description: Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies. creator: Carl J. Yeoman creator: Laura M. Brutscher creator: Özcan C. Esen creator: Furkan Ibaoglu creator: Curtis Fowler creator: A. Murat Eren creator: Kevin Wanner creator: David K. Weaver uri: https://doi.org/10.7717/peerj.7548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yeoman et al. title: Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum link: https://peerj.com/articles/7553 last-modified: 2019-08-27 description: This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture. creator: Md Javed Foysal creator: Thi Thu Thuy Nguyen creator: Md Reaz Chaklader creator: Muhammad A.B. Siddik creator: Chin-Yen Tay creator: Ravi Fotedar creator: Sanjay Kumar Gupta uri: https://doi.org/10.7717/peerj.7553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Foysal et al. title: Prevalence of near-death experiences in people with and without REM sleep intrusion link: https://peerj.com/articles/7585 last-modified: 2019-08-27 description: BackgroundThe origin and prevalence of near-death experiences are unknown. A recent study suggested a link with REM sleep intrusion but was criticized for its selection of control participants. We therefore assessed the association of REM intrusion and near-death experiences with different methods.MethodsUsing a crowd-sourcing platform, we recruited 1,034 lay people from 35 countries to investigate the prevalence of near-death experiences and self-reported REM sleep intrusion. Reports were validated using the Greyson Near-Death Experiences Scale (GNDES) with ≥7 points as cut-off for near-death experiences.ResultsNear-death experiences were reported by 106 of 1,034 participants (10%; 95% CI [8.5–12%]). Evidence of REM intrusion was more common in people with near-death experiences (n = 50∕106; 47%) than in people with experiences with 6 points or less on the GNDES (n = 47∕183; 26%) or in those without such experiences (n = 107∕744; 14%; p =  < 0.0001). Following multivariate regression analysis to adjust for age, gender, place of residence, employment and perceived danger, this association remained highly significant; people with REM intrusion were more likely to exhibit near-death experiences than those without (OR 2.85; 95% CI [1.68–4.88]; p = 0.0001).DiscussionUsing a crowd-sourcing approach, we found a prevalence of near-death experiences of 10%. While age, gender, place of residence, employment status and perceived threat do not seem to influence the prevalence of near-death experiences, we confirmed a possible association with REM sleep intrusion. creator: Daniel Kondziella creator: Jens P. Dreier creator: Markus Harboe Olsen uri: https://doi.org/10.7717/peerj.7585 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kondziella et al. title: Insights from the proteome profile of Phytophthora capsici in response to the novel fungicide SYP-14288 link: https://peerj.com/articles/7626 last-modified: 2019-08-27 description: Phytophthora capsica is a destructive oomycete plant pathogen that causes huge losses to crop production worldwide. However, the novel fungicide SYP-14288 has shown excellent activity against various stages of the oomycete life cycle as well against fungal plant pathogens. The current study utilized isobaric tags for relative and absolute quantitation technology to generate proteome profiles of P. capsici in the presence or absence of SYP-14288 in order to gain a greater understanding of the SYP-14288 mode of action. A total of 1,443 individual proteins were identified during the investigation, of which 599 were considered to have significantly altered expression. Further investigation using Cluster of Orthologous Groups of proteins analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated most of the proteins with altered expression were associated with carbohydrate metabolism, energy metabolism and their downstream biological functions, especially with regard to oxidoreductase activity and subsequent adenosine triphosphate (ATP) production associated pathways. Quantitative expression analysis using qRT-PCR validated the proteomic data. These results seem to indicate that SYP-14288 treatment caused a shift in energy metabolism that resulted in the activation of compensatory mechanisms affecting carbohydrate and lipid metabolism. The study also found evidence that the up-regulation of transmembrane transporters and proteins associated with stress response might also be coopted to compensate for the disrupted proton gradient and other downstream effects. Taken together these results provide strong evidence that SYP-14288 has a similar mode of action to the oxidative phosphorylation uncoupler Fluazinam but further investigation, including molecular studies, is required to completely characterize the SYP-14288 mode of action in P. capsici. However, the proteomic data collected in the current study does provide important insight into the overall effect of SYP-14288 in P. capsici, which could be useful for the registration and application of this novel fungicide. creator: Meng Cai creator: Zhiwen Wang creator: Xiaoxia Ni creator: Yanhua Hou creator: Qin Peng creator: Xiang Gao creator: Xili Liu uri: https://doi.org/10.7717/peerj.7626 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cai et al. title: Filter feeding in Late Jurassic pterosaurs supported by coprolite contents link: https://peerj.com/articles/7375 last-modified: 2019-08-26 description: Diets of pterosaurs have mainly been inferred from indirect evidence such as comparative anatomy, associations of co-occurring fossils, and functional morphology. Gut contents are rare, and until now there is only a single coprolite (fossil dropping), with unidentified inclusions, known. Here we describe three coprolites collected from a palaeosurface with numerous pterosaur tracks found in early Kimmeridgian (Hypselocyclum Zone) intertidal deposits of the Wierzbica Quarry, Poland. The specimens’ morphology and association to the tracks suggest a pterosaur producer. Synchrotron scans reveal numerous small inclusions, with foraminifera making up the majority of the identifiable ones. Other small remains include shells/carapaces (of bivalves, ostracods, and other crustaceans/arthropods) and bristles (some possibly of polychaete worms). The high density of the small shelly inclusions suggest that they were not accidently ingested, but constituted an important food source for the pterosaur(s), perhaps together with unpreserved soft-bodied animals. The combined evidence from the tracks and coprolites suggest a filter-feeding ctenochasmatid as the most likely tracemaker. If true, this significantly expands the bromalite record for this pterosaur group, which was previously only known from gastroliths. Moreover, this study also provides the first direct evidence of filter feeding in Jurassic pterosaurs and shows that they had a similar diet to the recent Chilean flamingo (Phoenicopterus chilensis). creator: Martin Qvarnström creator: Erik Elgh creator: Krzysztof Owocki creator: Per E. Ahlberg creator: Grzegorz Niedźwiedzki uri: https://doi.org/10.7717/peerj.7375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qvarnström et al. title: The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations link: https://peerj.com/articles/7447 last-modified: 2019-08-26 description: BackgroundThe RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes.ResultsWe demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses.ConclusionThis software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses. creator: Stephanie van Wyk creator: Christopher H. Harrison creator: Brenda D. Wingfield creator: Lieschen De Vos creator: Nicolaas A. van der Merwe creator: Emma T. Steenkamp uri: https://doi.org/10.7717/peerj.7447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 van Wyk et al. title: Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer link: https://peerj.com/articles/7451 last-modified: 2019-08-26 description: BackgroundBecause of the increasing dysplasia rate in the lifelong course of inflammatory bowel disease (IBD) patients, it is imperative to characterize the crosstalk between IBD and colorectal cancer (CRC). However, there have been no reports revealing the occurrence of the ceRNA network in IBD-related CRC.MethodsIn this study, we conducted gene expression profile studies of databases and performed an integrated analysis to detect the potential of lncRNA-miRNA-mRNA ceRNA in regulating disease transformation. R packages were used to screen differentially expressed mRNA, lncRNA and miRNA among CRC, IBD and normal tissue. The lncRNA-miRNA-mRNA network was constructed based on predicted miRNA-targeted lncRNAs and miRNA-targeted mRNAs. Functional analyses were then conducted to identify genes involved in the ceRNA network, and key lncRNAs were evaluated based on several clinical outcomes.ResultsA total of three lncRNAs, 15 miRNAs, and 138 mRNAs were identified as potential mediators in the pathophysiological processes of IBD-related CRC. Gene Ontology annotation enrichment analysis confirmed that the dysplasia process was strongly associated with immune response, response to lipopolysaccharide, and inflammatory response. Survival analysis showed that LINC01106 (HR = 1.7; p < 0.05) were strongly associated with overall survival of colorectal cancer patients. The current study identified a series of IBD-related mRNAs, miRNA, and lncRNAs, and highlighted the important role of ceRNAs in the pathogenesis of IBD-related CRC. Among them, the LINC01106-miRNA-mRNA axis was identified as vital targets for further research. creator: Fangfang Sun creator: Weiwei Liang creator: Kejun Tang creator: Mengying Hong creator: Jing Qian uri: https://doi.org/10.7717/peerj.7451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sun et al. title: Effectiveness of small road tunnels and fences in reducing amphibian roadkill and barrier effects at retrofitted roads in Sweden link: https://peerj.com/articles/7518 last-modified: 2019-08-26 description: Schemes to reduce road impacts on amphibians have been implemented for decades in Europe, yet, several aspects on the effectiveness of such schemes remain poorly understood. Particularly in northern Europe, including Sweden, there is a lack of available information on road mitigation for amphibians, which is hampering implementation progress and cost-effectiveness analyses of mitigation options. Here, we present data derived from systematic counts of amphibians during spring migration at three previous hot-spots for amphibian roadkill in Sweden, where amphibian tunnels with guiding fences have been installed. We used the data in combination with a risk model to estimate the number of roadkills and successful crossings before vs. after mitigation and mitigated vs. adjacent non-mitigated road sections. In mitigated road sections, the estimated number of amphibians killed or at risk of being killed by car traffic decreased by 85–100% and the estimated number successfully crossing the road increased by 25–340%. Data, however, suggested fence-end effects that may moderate the reduction in roadkill. We discuss possible explanations for the observed differences between sites and construction types, and implications for amphibian conservation. We show how effectiveness estimates can be used for prioritizing amphibian passages along the existing road network. Finally, we emphasize the importance of careful monitoring of amphibian roadkill and successful crossings before and after amphibian passages are constructed. creator: Jan Olof Helldin creator: Silviu O. Petrovan uri: https://doi.org/10.7717/peerj.7518 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Helldin and Petrovan title: Detecting the impact of land cover change on observed rainfall link: https://peerj.com/articles/7523 last-modified: 2019-08-26 description: Analysis of observational data to pinpoint impact of land cover change on local rainfall is difficult due to multiple environmental factors that cannot be strictly controlled. In this study we use a statistical approach to identify the relationship between removal of tree cover and rainfall with data from best available sources for two large areas in Australia. Gridded rainfall data between 1979 and 2015 was used for the areas, while large scale (exogenous) effects were represented by mean rainfall across a much larger area and climatic indicators, such as Southern Oscillation Index and Indian Ocean Dipole. Both generalised additive modelling and step trend tests were used for the analysis. For a region in south central Queensland, the reported change in tree clearing between 2002–2005 did not result in strong statistically significant precipitation changes. On the other hand, results from a bushfire affected region on the border of New South Wales and Victoria suggest significant changes in the rainfall due to changes in tree cover. This indicates the method works better when an abrupt change in the data can be clearly identified. The results from the step trend test also mainly identified a positive relationship between the tree cover and the rainfall at p < 0.1 at the NSW/Victoria region. High rainfall variability and possible regrowth could have impacted the results in the Queensland region. creator: Chun Xia Liang creator: Floris F. van Ogtrop creator: R. Willem Vervoort uri: https://doi.org/10.7717/peerj.7523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liang et al. title: Three new species, one new genus and subfamily of Dorylaimida (de Man, 1876) Pearse, 1942, and revisions on the families Tylencholaimellidae Jairajpuri, 1964 and Mydonomidae Thorne, 1964 (Nematoda: Dorylaimida) link: https://peerj.com/articles/7541 last-modified: 2019-08-26 description: Three new species of the order Dorylaimida (de Man, 1876) Pearse, 1942 were identified and described. Paratylencholaimus sanshaensis gen. nov. sp. nov. from Hainan is proposed as a new member of the family Tylencholaimellidae Jairajpuri, 1964. Paratylencholaimus gen. nov. is close to Phellonema Thorne, 1964 and Goferus Jairajpuri & Ahmad, 1992 but can be differentiated mainly by having basal part of odontophore rod-like and without knobs, and basal part of pharynx expanded gradually. Tylencholaimus zhongshanensis sp. nov. from Guangdong and Dorylaimoides shapotouensis sp. nov. from the Ningxia Hui Autonomous Region are also described herein. Phylogenetic analyses based on the 18S rDNA and the D2–D3 region of the 28S rDNA support that the three new species are valid. The classifications of the families Tylencholaimellidae and Mydonomidae Thorne, 1964 are revised mainly based on the analysis of the morphology of odontostyle and odontophore. After these revisions, Paratylencholaiminae subfam. nov. including Paratylencholaimus gen. nov. and Goferus is proposed. Athernema and Agmodorus of Tylencholaimellidae are transferred into Mydonomidae, and the subfamily Athernematinae of Tylencholaimellidae is dismissed. The main characteristics of the family Mydonomidae and Tylencholaimellidae are revised. Keys to the genera of Mydomonidae and Tylencholaimellidae are included. creator: Wen-Jia Wu creator: Chun-Ling Xu creator: Hui Xie creator: Dong-Wei Wang uri: https://doi.org/10.7717/peerj.7541 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wu et al. title: Cell-free supernatants from cultures of lactic acid bacteria isolated from fermented grape as biocontrol against Salmonella Typhi and Salmonella Typhimurium virulence via autoinducer-2 and biofilm interference link: https://peerj.com/articles/7555 last-modified: 2019-08-26 description: BackgroundSalmonella Typhi and Salmonella Typhimurium are the causative pathogens of salmonellosis, and they are mostly found in animal source foods (ASF). The inappropriate use of antibiotics enhances the possibility for the emergence of antibiotic resistance in pathogens and antibiotic residue in ASF. One promising alternative to antibiotics in animal farming is the use of lactic acid bacteria (LAB).MethodsThe present study was carried out the cells and/or the cell-free culture supernatants (CFCS) from beneficial LAB against S. Typhi and S. Typhimurium. The antibacterial mechanisms of LAB-CFCS as biocontrol agents against both Salmonella serovars were investigated through the analysis of anti-salmonella growth activity, biofilm inhibition and quorum quenching activity.ResultsAmong 146 LAB strains isolated from 110 fermented food samples, the 2 strong inhibitory effect strains (WM33 and WM36) from fermented grapes against both Salmonella serovars were selected. Out of the selected strains, WM36 was the most effective inhibitor, which indicated S. Typhi by showing 95.68% biofilm inhibition at 20% biofilm inhibition concentration (BIC) and reduced 99.84% of AI-2 signaling interference. The WM33 was the best to control S. Typhimurium by producing 66.46% biofilm inhibition at only 15% BIC and 99.99% AI-2 signaling a reduction. The 16S rDNA was amplified by a polymerase chain reaction (PCR). The selected isolates were identified as Weissella viridescens WM33 and Weissella confusa WM36 based on nucleotide homology and phylogenetic analysis.ConclusionThe metabolic extracts from Weissella spp. inhibit Salmonella serovars with the potential to be used as biocontrol agents to improve microbiological safety in the production of ASF. creator: Wattana Pelyuntha creator: Chaiyavat Chaiyasut creator: Duangporn Kantachote creator: Sasithorn Sirilun uri: https://doi.org/10.7717/peerj.7555 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pelyuntha et al. title: Association between serum uric acid and nonalcoholic fatty liver disease in community patients with type 2 diabetes mellitus link: https://peerj.com/articles/7563 last-modified: 2019-08-26 description: BackgroundTo investigate whether SUA is associated with NAFLD in men and women with T2DM.MethodsThis cross-sectional study enrolled patients with T2DM at Shanxi High-Tech Development Zone Central Hospital (June 2011 to September 2017). Patients were stratified according to gender and presence/absence of NAFLD. Parameters associated with NAFLD were identified using multivariate stepwise linear regression and univariate/multivariate logistic regression.ResultsAmong 597 patients (325 males) enrolled, 352 had NAFLD. SUA was higher in the NAFLD group than in the non-NAFLD group for both men and women (P < 0.001). Multiple linear regression showed that body mass index (positively), triglycerides (positively) and estimated glomerular filtration rate (negatively) were independently related to SUA (P < 0.001). Univariate logistic regression revealed increased odds of NAFLD for SUA tertiles 2 (P = 0.022) and 3 (P = 0.001) in women and tertile 3 (P = 0.039) in men. After adjustment for multiple clinical parameters, SUA tertiles were significantly associated with NAFLD for tertile 3 in women (P = 0.014), although there were trends toward associations for tertile 2 in women (P = 0.074) and tertiles 2 and 3 in men (P = 0.085 and 0.054, respectively).ConclusionSUA is not independently associated with NAFLD in men or women with T2DM after rigorous adjustment for other metabolic parameters. creator: Linxin Xu creator: Ting Li creator: Jianhong Yin creator: Gang Lin creator: Yali Xu creator: Yi Ren creator: Yan Wang creator: Jing Yang creator: Liming Chen uri: https://doi.org/10.7717/peerj.7563 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu et al. title: Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data link: https://peerj.com/articles/7564 last-modified: 2019-08-26 description: BackgroundMycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low- and middle-income high TB-burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance.MethodsWe developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs—Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data.ResultsThe MTBGT tool correctly transformed the single nucleotide polymorphism (SNP) data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin-susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda.ConclusionOverall, the MTBGT tool allows low- and middle-income countries to make sense of the increasingly generated WGS in light of the readily available RDT results, and assess whether currently implemented RDTs adequately detect RR-TB in their setting. With its feature to transform WGS to RDT results and facilitate continuous RR-TB data analysis, the MTBGT tool may bridge the gap between and among data from periodic surveys, continuous surveillance, research, and routine tests, and may be integrated within the national information system for use by the NTP and epidemiologists to improve setting-specific RR-TB control. The MTBGT source code and accompanying documentation are available at https://github.com/KamelaNg/MTBGT. creator: Kamela C. S. Ng creator: Jean Claude S. Ngabonziza creator: Pauline Lempens creator: Bouke C. de Jong creator: Frank van Leth creator: Conor J. Meehan uri: https://doi.org/10.7717/peerj.7564 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ng et al. title: The association between evidence of a predator threat and responsiveness to alarm calls in Western Australian magpies (Cracticus tibicen dorsalis) link: https://peerj.com/articles/7572 last-modified: 2019-08-26 description: Alarm calls are a widespread form of antipredator defence and being alerted to the presence of predators by the alarm calls of conspecifics is considered one of the benefits of group living. However, while social information can allow an individual to gain additional information, it can also at times be inaccurate or irrelevant. Such variation in the accuracy of social information is predicted to select for receivers to discriminate between sources of social information. In this study, we used playback experiments to determine whether Western Australian magpies (Cracticus tibicen dorsalis) respond to the predator information associated with alarm calls. Magpies were exposed to the alarm calls of two group members that differed in the threat associated with the alarm call: one call was played in the presence of a predator model while the other was not—in order to establish differences in the predator information provided by each caller. We then played back the alarm calls of the same group members in the absence of the predator model to determine whether magpies responded differently to signallers in response to the previous association between the alarm call and a predator threat. We found that receivers showed significantly greater levels of responsiveness to signallers that previously gave alarm calls in the appropriate context. Thus, the accuracy of threat-based information influenced subsequent receiver response. creator: Annabel Silvestri creator: Kate Morgan creator: Amanda R. Ridley uri: https://doi.org/10.7717/peerj.7572 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Silvestri et al. title: Cell proliferation controls body size growth, tentacle morphogenesis, and regeneration in hydrozoan jellyfish Cladonema pacificum link: https://peerj.com/articles/7579 last-modified: 2019-08-26 description: Jellyfish have existed on the earth for around 600 million years and have evolved in response to environmental changes. Hydrozoan jellyfish, members of phylum Cnidaria, exist in multiple life stages, including planula larvae, vegetatively-propagating polyps, and sexually-reproducing medusae. Although free-swimming medusae display complex morphology and exhibit increase in body size and regenerative ability, their underlying cellular mechanisms are poorly understood. Here, we investigate the roles of cell proliferation in body-size growth, appendage morphogenesis, and regeneration using Cladonema pacificum as a hydrozoan jellyfish model. By examining the distribution of S phase cells and mitotic cells, we revealed spatially distinct proliferating cell populations in medusae, uniform cell proliferation in the umbrella, and clustered cell proliferation in tentacles. Blocking cell proliferation by hydroxyurea caused inhibition of body size growth and defects in tentacle branching, nematocyte differentiation, and regeneration. Local cell proliferation in tentacle bulbs is observed in medusae of two other hydrozoan species, Cytaeis uchidae and Rathkea octopunctata, indicating that it may be a conserved feature among hydrozoan jellyfish. Altogether, our results suggest that hydrozoan medusae possess actively proliferating cells and provide experimental evidence regarding the role of cell proliferation in body-size control, tentacle morphogenesis, and regeneration. creator: Sosuke Fujita creator: Erina Kuranaga creator: Yu-ichiro Nakajima uri: https://doi.org/10.7717/peerj.7579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fujita et al. title: Transgenerational effects of UV-B radiation on egg size, fertilization, hatching and larval size of sea urchins Strongylocentrotus intermedius link: https://peerj.com/articles/7598 last-modified: 2019-08-26 description: Transgenerational effects are important for phenotypic plasticity and adaptation of marine invertebrates in the changing ocean. Ultraviolet-B (UV-B) radiation is an increasing threat to marine invertebrates. For the first time, we reported positive and negative transgenerational effects of UV-B radiation on egg size, fertilization, hatchability and larval size of a marine invertebrate. Strongylocentrotus intermedius exposed to UV-B radiation showed positive transgenerational effects and adaptation on egg size, hatching rate and post-oral arm length of larvae. Negative transgenerational effects were found in body length, stomach length and stomach width of larvae whose parents were exposed to UV-B radiation. Sires probably play important roles in transgenerational effects of UV-B. The present study provides valuable information into transgenerational effects of UV-B radiation on fitness related traits of sea urchins (at least Strongylocentrotus intermedius). creator: Jingyun Ding creator: Lingling Zhang creator: Jiangnan Sun creator: Dongtao Shi creator: Xiaomei Chi creator: Mingfang Yang creator: Yaqing Chang creator: Chong Zhao uri: https://doi.org/10.7717/peerj.7598 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ding et al. title: Metabolic alterations in pea leaves during arbuscular mycorrhiza development link: https://peerj.com/articles/7495 last-modified: 2019-08-23 description: Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90–110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies. creator: Oksana Y. Shtark creator: Roman K. Puzanskiy creator: Galina S. Avdeeva creator: Andrey P. Yurkov creator: Galina N. Smolikova creator: Vladislav V. Yemelyanov creator: Marina S. Kliukova creator: Alexey L. Shavarda creator: Anastasiia A. Kirpichnikova creator: Aleksandr I. Zhernakov creator: Alexey M. Afonin creator: Igor A. Tikhonovich creator: Vladimir A. Zhukov creator: Maria F. Shishova uri: https://doi.org/10.7717/peerj.7495 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Shtark et al. title: The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs link: https://peerj.com/articles/7532 last-modified: 2019-08-23 description: The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu(UAG), tRNALeu(UUR), tRNAThr, tRNAPro, tRNAPhe, tRNAVal, tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae). creator: Yin-Yin Cai creator: Shi-Qi Shen creator: Li-Xu Lu creator: Kenneth B. Storey creator: Dan-Na Yu creator: Jia-Yong Zhang uri: https://doi.org/10.7717/peerj.7532 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cai et al. title: Identification of a native Bacillus thuringiensis strain from Sri Lanka active against Dipel-resistant Plutella xylostella link: https://peerj.com/articles/7535 last-modified: 2019-08-23 description: BackgroundBiopesticides based on strains of the bacterium Bacillus thuringiensis (Bt) are used globally for effective and environmentally friendly pest control. The most serious threat to the sustainable use of these microbial pesticides is the development of resistance on targeted pests. Populations of Plutella xylostella (diamondback moth) have evolved field resistance to Bt pesticides at diverse locations worldwide. Discovery of novel Bt strains with varied toxin profiles that overcome resistance is one of the strategies to increase sustainability of Bt pesticides against P. xylostella. In this study, we report isolation and characterization of a Bt strain named AB1 from Sri Lanka displaying toxicity towards larvae of P. xylostella resistant to the commercial Bt pesticide Dipel.MethodsStrains of Bt from diverse environments in Sri Lanka were evaluated for protein crystal production through Differential Interference Contrast (DIC) microscopic examination, and for insecticidal activity against P. xylostella in bioassays. The genome of the AB1 strain was sequenced by Hiseq Illumina sequencing to identify the insecticidal genes present in the genome and nano liquid chromatography followed by tandem mass spectrometry (nanoLC/MS/MS) of purified crystal proteins of AB1 was performed to identify the expressed insecticidal proteins. Multilocus sequence typing and Gyrase B gene sequence analyses were performed to identify the phylogenetic origin of the AB1 strain.ResultsThe AB1 strain was identified as producing high levels of bipyramidal crystals and displaying insecticidal activity against susceptible and Dipel-resistant strains of P. xylostella. Multilocus sequence typing and phylogenetic analysis of the Gyrase B gene identified that AB1 belongs to the B. thuringiensis subsp. aizawai serotype. Comparative analysis of genomic and proteomic data showed that among the insecticidal protein coding genes annotated from the AB1 genome (cry1Aa, cry1Ca, cry1Da, cry1Ia, cry2Ab and cry9), Cry1Ca and Cry1Da toxins represented most of the toxin fraction in parasporal crystals from AB1. Overall findings warrant further development of B. thuringiensis subsp. aizawai AB1 strain as a pesticide to control P. xylostella. creator: Rashini Yasara Baragamaarachchi creator: Jayanetti Koralage Ramani Radhika Samarasekera creator: Ovitigala Vithanage Don Sisira Jagathpriya Weerasena creator: Kurt Lamour creator: Juan Luis Jurat-Fuentes uri: https://doi.org/10.7717/peerj.7535 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Baragamaarachchi et al. title: RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat link: https://peerj.com/articles/7540 last-modified: 2019-08-23 description: The hypothalamic neuropeptide RFRP3 can suppress hypothalamic GnRH neuron activation and inhibit gonadotropin release from the anterior pituitary. RFRP3 is also produced locally in the ovary and can inhibit steroidogenesis and follicle development in many vertebrates. However, almost nothing is known about the presence and regulatory action of RFRP3 in gonads of any carnivore species. Such knowledge is important for developing captive breeding programs for endangered carnivores and for inhibiting reproduction in feral species. Using the domestic cat as a model, our objectives were to (1) demonstrate the expression of feline RFRP3 (fRFRP3) and its receptor in the cat ovary and (2) assess the influence of fRFRP3 on ovarian follicle integrity, survival, and steroidogenesis in vitro. We first confirmed that fRFRP3 and its receptors (NPFFR1 and NPFFR2) were expressed in cat ovaries by sequencing PCR products from ovarian RNA. We then isolated and cultured preantral ovarian follicles in the presence of 10 or 1 µM fRFRP3 + FSH (1 µg/mL). We recorded the percentage of morphologically viable follicles (basal lamina integrity) over 8 days and calculated percentage survival of follicles on Day 8 (using fluorescent markers for cell survival and death). Last, we quantified progesterone accumulation in media. 10 µM fRFRP3 had no observable effect on viability, survival, or steroid production compared to follicles exposed to only FSH. However, 1 µM fRFRP3 decreased the percentage of morphologically viable follicles and the percentage of surviving follicles on Day 8. At the same time, 1 µM fRFRP3 increased the accumulation of progesterone in media. Our study shows, for the first time, direct action of RFRP3 on the follicle as a functional unit, and it is the first in a carnivore species. More broadly, our results support a conserved, inhibitory action of RFRP3 on ovarian follicle development and underscore the importance of comparative functional studies. creator: Kathryn Wilsterman creator: George E. Bentley creator: Pierre Comizzoli uri: https://doi.org/10.7717/peerj.7540 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wilsterman et al. title: Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia link: https://peerj.com/articles/7567 last-modified: 2019-08-23 description: Intersex is an intermediate stage of sexual differentiation in insects. Determining intersex morphology and the cause of its production will aid in the understanding of the mechanism of sexual differentiation in insects. In this paper, Wolbachia-infected Trichogramma pretiosum (T. preW+) that shows thelytokous parthenogenesis were used as subjects. In order to determine the causes of the T. preW+ intersex and the influence of parental generation temperature on gradual changes in secondary masculinization in intersex offspring, we examined the occurrence of intersex offspring (F1 and F2 generation) after the parental generations were treated with high temperature (27, 29, 31, and 33 °C) and described the external morphology of the intersexes. The results showed that the T. preW+ parental generation temperature is positively correlated with the probability of intersex offspring. The probability of F1 intersex is significantly higher than that of F2 intersex in different high temperature. The degree of secondary masculinization in T. preW+ intersexes increases as parental generation temperature increases. In addition, our study first identified 11 intersex types in T. preW+ and found that the primary and secondary sexual characteristics showed a regular distribution. We also found that the D type and H type of intersex have the highest frequency of appearance. The external genitalia of most intersexes were female, and only three intersex types have male external genitalia. Conclusions were ultimately obtained: Wolbachia is a direct factor that causes the occurrence of intersexes, while high temperature is an indirect factor that determines the external morphology of intersexes. The effects of high temperature on T. preW+ intersexes is passed through the parental generation to offspring, and this maternal effect weakens as the number of generations increases. In T. preW+ intersex individuals, most exhibit female primary sexual characteristics, and secondary sexual characteristics exhibit signs of masculinization. creator: Su-fang Ning creator: Jin-cheng Zhou creator: Quan-quan Liu creator: Qian Zhao creator: Hui Dong uri: https://doi.org/10.7717/peerj.7567 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ning et al. title: Visual search characteristics of precise map reading by orienteers link: https://peerj.com/articles/7592 last-modified: 2019-08-23 description: This article compares the differences in eye movements between orienteers of different skill levels on map information searches and explores the visual search patterns of orienteers during precise map reading so as to explore the cognitive characteristics of orienteers’ visual search. We recruited 44 orienteers at different skill levels (experts, advanced beginners, and novices), and recorded their behavioral responses and eye movement data when reading maps of different complexities. We found that the complexity of map (complex vs. simple) affects the quality of orienteers’ route planning during precise map reading. Specifically, when observing complex maps, orienteers of higher competency tend to have a better quality of route planning (i.e., a shorter route planning time, a longer gaze time, and a more concentrate distribution of gazes). Expert orienteers demonstrated obvious cognitive advantages in the ability to find key information. We also found that in the stage of route planning, expert orienteers and advanced beginners first pay attention to the checkpoint description table. The expert group extracted information faster, and their attention was more concentrated, whereas the novice group paid less attention to the checkpoint description table, and their gaze was scattered. We found that experts regarded the information in the checkpoint description table as the key to the problem and they give priority to this area in route decision making. These results advance our understanding of professional knowledge and problem solving in orienteering. creator: Yang Liu uri: https://doi.org/10.7717/peerj.7592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu title: Revision of the Tanzanian dicynodont Dicynodon huenei (Therapsida: Anomodontia) from the Permian Usili Formation link: https://peerj.com/articles/7420 last-modified: 2019-08-22 description: A single species of the dicynodontoid dicynodont Dicynodon is currently recognized from the late Permian Usili Formation of Tanzania: Dicynodon hueneiHaughton, 1932. Restudy of the known Tanzanian materials of D. huenei demonstrates that they represent two distinct morphotypes, here considered separate taxa. The holotype of D. huenei is not referable to Dicynodon and instead is transferred to the genus Daptocephalus (but retained as a valid species, Daptocephalus huenei comb. nov.). A number of published dicynodontoid specimens from the Usili Formation, however, are referable to Dicynodon, and are here recognized as a new species (Dicynodon angielczyki sp. nov.) Dicynodon angielczyki can be distinguished from its South African congener Dicynodon lacerticeps by the presence of an expansion of the squamosal and jugal beneath the postorbital bar and a curved, posterolateral expansion of the squamosal behind the temporal fenestra. Inclusion of Dicynodon angielczyki and D. huenei in a phylogenetic analysis supports their referral to Dicynodon and Daptocephalus (respectively). These results indicate higher basinal endemism in large late Permian dicynodonts than previously thought, a sharp contrast to the cosmopolitanism in the group in the earliest Triassic. creator: Christian F. Kammerer uri: https://doi.org/10.7717/peerj.7420 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kammerer title: Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods link: https://peerj.com/articles/7476 last-modified: 2019-08-22 description: BackgroundIn the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods.MethodsWe digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure.ResultsWhatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony. creator: Eduardo Ascarrunz creator: Julien Claude creator: Walter G. Joyce uri: https://doi.org/10.7717/peerj.7476 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ascarrunz et al. title: Characterisation of bacteria isolated from the stingless bee, Heterotrigona itama, honey, bee bread and propolis link: https://peerj.com/articles/7478 last-modified: 2019-08-22 description: Bacteria are present in stingless bee nest products. However, detailed information on their characteristics is scarce. Thus, this study aims to investigate the characteristics of bacterial species isolated from Malaysian stingless bee, Heterotrigona itama, nest products. Honey, bee bread and propolis were collected aseptically from four geographical localities of Malaysia. Total plate count (TPC), bacterial identification, phenotypic profile and enzymatic and antibacterial activities were studied. The results indicated that the number of TPC varies from one location to another. A total of 41 different bacterial isolates from the phyla Firmicutes, Proteobacteria and Actinobacteria were identified. Bacillus species were the major bacteria found. Therein, Bacillus cereus was the most frequently isolated species followed by Bacillus aryabhattai, Bacillus oleronius, Bacillus stratosphericus, Bacillus altitudinis, Bacillus amyloliquefaciens, Bacillus nealsonii, Bacillus toyonensis, Bacillus subtilis, Bacillus safensis, Bacillus pseudomycoides, Enterobacter asburiae, Enterobacter cloacae, Pantoea dispersa and Streptomyces kunmingensis. Phenotypic profile of 15 bacterial isolates using GEN III MicroPlate™ system revealed most of the isolates as capable to utilise carbohydrates as well as amino acids and carboxylic acids and derivatives. Proteolytic, lipolytic and cellulolytic activities as determined by enzymatic assays were detected in Bacillus stratosphericus PD6, Bacillus amyloliquefaciens PD9, Bacillus subtilis BD3 and Bacillus safensis BD9. Bacillus amyloliquefaciens PD9 showed broad-spectrum of antimicrobial activity against Gram-positive and Gram-negative bacteria in vitro. The multienzymes and antimicrobial activities exhibited by the bacterial isolates from H. itama nest products could provide potential sources of enzymes and antimicrobial compounds for biotechnological applications. creator: Mohamad Syazwan Ngalimat creator: Raja Noor Zaliha Raja Abd. Rahman creator: Mohd Termizi Yusof creator: Amir Syahir creator: Suriana Sabri uri: https://doi.org/10.7717/peerj.7478 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ngalimat et al. title: Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage link: https://peerj.com/articles/7484 last-modified: 2019-08-22 description: The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system. creator: Amanda E. Haponski creator: Diarmaid Ó Foighil uri: https://doi.org/10.7717/peerj.7484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Haponski and Ó Foighil title: Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China link: https://peerj.com/articles/7526 last-modified: 2019-08-22 description: The seasonal dynamics of microbial diversity within the rhizosphere of Ulmus pumila L. var. sabulosa in the hinterland of the Otindag Sandy Land of China were investigated using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences. A significant level of bacterial and fungal diversity was observed overall, with detection of 7,676 bacterial Operational Taxonomic Units (OTUs) belonging to 40 bacteria phyla and 3,582 fungal OTUs belonging to six phyla. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla among communities, while Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla of fungal communities. Seasonal changes influenced the α-diversity and β-diversity of bacterial communities within elm rhizospheres more than for fungal communities. Inferred functional analysis of the bacterial communities identified evidence for 41 level two KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology groups, while guild-based analysis of the fungal communities identified eight ecological guilds. Metabolism was the most prevalent bacterial functional group, while saprotrophs prevailed among the identified fungal ecological guilds. Soil moisture and soil nutrient content were important factors that affected the microbial community structures of elm rhizospheres across seasons. The present pilot study provides an important baseline investigation of elm rhizosphere microbial communities. creator: Tianyu Liang creator: Guang Yang creator: Yunxia Ma creator: Qingzhi Yao creator: Yuan Ma creator: Hui Ma creator: Yang Hu creator: Ying Yang creator: Shaoxiong Wang creator: Yiyong Pan creator: Gangtie Li uri: https://doi.org/10.7717/peerj.7526 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liang et al. title: Root tolerance and biochemical response of Chinese lettuce (Lactuca sativa L.) genotypes to cadmium stress link: https://peerj.com/articles/7530 last-modified: 2019-08-22 description: This study was conducted to determine the root tolerance and biochemical responses of four Chinese Lactuca sativa L. genotypes (Lüsu, Lümeng, Yidali and Anyan) to cadmium (Cd2+) stress. Twenty-eight days old seedlings were exposed to Hoagland’s nutrient solution supplied with or without 100 µM CdCl2 and monitored for seven days in a climate controlled room. The 100 µM CdCl2 significantly (P < 0.001) decreased all the root morphological indexes of the four genotypes. However, Yidali, which possessed the smallest root system, exhibited greater root tolerance to Cd2+ by having the highest tolerance indexes for root volume (46%), surface area (61%), projected area (74%) and numbers of root forks (63%) and root tips (58%). Moreover, Cd2+ stress also caused increases in H2O2 contents in the roots but the increase was least in Yidali which showed greater root tolerance to Cd2+stress. The effect of Cd2+ stress on the contents of hormones in the roots depended on the genotypes. Under Cd2+ stress, abscisic acid correlated positively with indole-3-acetic acid (r = 0.669*), gibberellic acid (r = 0.630*) and cytokinin (r = 0.785**). The antioxidant enzyme activities and proline responses of the four genotypes to Cd2+ stress were similar. The SOD activity was decreased whiles the CAT and POD activities, as well as the contents of proline increased in all the genotypes under the stress condition. These results suggest that lettuce genotypes with smaller root systems could be more tolerant to Cd2+ stress compared to those with larger root systems. creator: Mohammed Mujitaba Dawuda creator: Weibiao Liao creator: Linli Hu creator: Jihua Yu creator: Jianming Xie creator: Alejandro Calderón-Urrea creator: Xin Jin creator: Yue Wu uri: https://doi.org/10.7717/peerj.7530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dawuda et al. title: Development of a multiplex RT-PCR assay for simultaneous detection of Cucumber green mottle mosaic virus and Acidovorax citrulli in watermelon link: https://peerj.com/articles/7539 last-modified: 2019-08-22 description: Watermelon (Citrullus lanatus Thunb.) is considered as a popular and nutritious fruit crop worldwide. Watermelon blood flesh disease caused by Cucumber green mottle mosaic virus (CGMMV) and bacterial fruit blotch caused by Acidovorax citrulli, are two major quarantine diseases of watermelon and result in considerable losses to global watermelon production. In this study, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) method was developed for simultaneous detection of CGMMV and A. citrulli in both watermelon leaves and seeds. Two pairs of specific primers were designed based on the conserved sequences of the genomic RNA of CGMMV and the internal transcribed spacer of A. citrulli, respectively. Transcriptional elongation factor-1α from watermelon was added as an internal reference gene to prevent false negatives. No cross-reactivity was detected with other viral or bacterial pathogens infecting watermelon. Moreover, the multiplex RT-PCR showed high sensitivity and could simultaneously detect CGMMV and A. citrulli as little as 102 copies of plasmid DNA. This method was successfully applied to test field-collected watermelon leaves and stored seeds of cucurbitaceous crops. These results suggested that the developed multiplex RT-PCR technique is a rapid, efficient, and sensitive method for simultaneous detection of CGMMV and A. citrulli, providing technical support for monitoring, predicting, and preventing these two quarantine diseases. To our knowledge, this is the first report on simultaneous detection of a virus and a bacterium by multiplex RT-PCR in watermelon. creator: Xinyue Bi creator: Xiaodong Li creator: Haibo Yu creator: Mengnan An creator: Rui Li creator: Zihao Xia creator: Yuanhua Wu uri: https://doi.org/10.7717/peerj.7539 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bi et al. title: Perceptual load modulates contour integration in conscious and unconscious states link: https://peerj.com/articles/7550 last-modified: 2019-08-22 description: Previous research has documented that contour detection and integration may either be affected by local features such as the distances between elements or by high-level cognitive factors such as attention in our visual system. Less is known about how low and high level factors interact to influence contour integration. In this paper, we investigated how attention modulates contour integration through saliency (different element spacing) and topological propert ies (circle or S-shaped) when the state of conscious awareness is manipulated. A modified inattentional blindness (IB) combined with the Posner cuing paradigm was adopted in our three-phased experiment (unconscious-training-conscious). Attention was manipulated with high or low perceptual load for a foveal go/no-go task. Cuing effects were utilized to assess the covert processing of contours prior to a peripheral orientation discrimination task. We found that (1) salient circles and S-contours induced different cuing effects under low perceptual load but not with high load; (2) no consistent pattern of cuing effects was found for non-salient contours in all the conditions; (3) a positive cuing effect was observed for salient circles either consciously or unconsciously while a negative cuing effect occurred for salient S-contours only consciously. These results suggest that conscious awareness plays a pivotal role in coordinating a closure effect with the level of perceptual load. Only salient circles can be successfully integrated in an unconscious state under low perceptual load although both salient circles and S-contours can be done consciously. Our findings support a bi-directional mechanism that low-level sensory features interact with high-level cognitive factors in contour integration. creator: Kaiwen Cheng creator: Keyu Yang creator: Long Qin creator: Yixuan Zhuo creator: Hongmei Yan uri: https://doi.org/10.7717/peerj.7550 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cheng et al. title: Middle East Respiratory Syndrome Coronavirus and the One Health concept link: https://peerj.com/articles/7556 last-modified: 2019-08-22 description: Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is one of the major threats to the healthcare systems in some countries, especially in the Arabian Peninsula. MERS-CoV is considered an ideal example of the One Health concept. This is due to the animals, especially dromedary camels, play important roles in the transmission and sustainability of the virus, and the virus can be transmitted through aerosols of infected patients into the environment. However, there is some debate regarding the origin of MERS-CoV either from bats or other unknown reservoirs. The dromedary camel is the only identified animal reservoir to date. These animals play important roles in sustaining the virus in certain communities and may act as an amplifier of the virus by secreting it in their body fluids, especially in nasal and rectal discharges. MERS-CoV has been detected in the nasal and rectal secretions of infected camels, and MERS-CoV of this origin has full capacity to infect human airway epithelium in both in vitro and in vivo models. Other evidence confirms the direct transmission of MERS-CoV from camels to humans, though the role of camel meat and milk products has yet to be well studied. Human-to-human transmission is well documented through contact with an active infected patient or some silently infected persons. Furthermore, there are some significant risk factors of individuals in close contact with a positive MERS-CoV patient, including sleeping in the same patient room, removing patient waste (urine, stool, and sputum), and touching respiratory secretions from the index case. Outbreaks within family clusters have been reported, whereby some blood relative patients were infected through their wives in the same house were not infected. Some predisposing genetic factors favor MERS-CoV infection in some patients, which is worth investigating in the near future. The presence of other comorbidities may be another factor. Overall, there are many unknown/confirmed aspects of the virus/human/animal network. Here, the most recent advances in this context are discussed, and the possible reasons behind the emergence and sustainability of MERS-CoV in certain regions are presented. Identification of the exact mechanism of transmission of MERS-CoV from camels to humans and searching for new reservoir/s are of high priority. This will reduce the shedding of the virus into the environment, and thus the risk of human infection can be mitigated. creator: Maged Gomaa Hemida uri: https://doi.org/10.7717/peerj.7556 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hemida title: Therapeutic effect of Bacillus Calmette–Guerin polysaccharide nucleic acid on mast cell at the transcriptional level link: https://peerj.com/articles/7404 last-modified: 2019-08-21 description: BackgroundChronic spontaneous urticaria (CSU) is a common and recurrent autoimmune-related disease with unclear pathogenesis. Dysfunction of immune cells, such as T cells, mast cells, and basophils, is involved. Bacillus Calmette–Guerin polysaccharide nucleic acid (BCG–PSN), an immunomodulator partially extracted from BCG, can be used in the combined treatment of CSU with an unknown mechanism.MethodsTo study the therapeutic effect and mechanism of BCG–PSN on CSU, we initially assessed the clinical efficacy in 110 enrolled CSU patients of 4-week antihistamine monotherapy vs. antihistamine plus BCG–PSN combined therapy. Subsequently, to explore the further mechanism of BCG-PSN, the mast cell line RBL-2H3 pretreated with BCG-PSN was used to evaluate the transcriptional expression profiles via lncRNA sequencing. Real time PCR was conducted to validate the candidate gene expression.ResultsWe found no significant difference in treatment efficacy between the BCG–PSN group (71.7%) and the monotherapy group (71.9%). However, the average time of complete relief in the BCG–PSN group was significantly shorter than that in the monotherapy group (36.77 ± 17.33 vs. 51.27 ± 16.80, p = 0.026). In vitro experiments showed that BCG-PSN inhibited β-hexosaminidase release rates in IgE-sensitized RBL-2H3 cells (p < 0.001). Sequencing data revealed the expression profiles of functional genes, including a significant decrease in Erb-B2 receptor tyrosine kinase 4, which can be regulated by the nuclear factor kappa B (NF-κB) pathway.DiscussionCSU is a chronic, recurrent disease with complex pathogenesis. Mast cells and basophils are the primary target cells of the disease. BCG–PSN decrease the β-HEX release rates and regulated IgE-mediated mast cell activation in RBL-2H3 cells by mediating immune-related gene expression including ERBB4. These findings suggest that BCG–PSN may mediate ERBB4 expression via the NF-κB pathway and may have value in the treatment of CSU. creator: Siyu Yan creator: Runqiu Liu creator: Manyun Mao creator: Zhaoqian Liu creator: Wei Zhang creator: Yi Zhang creator: Jie Li creator: Cong Peng creator: Xiang Chen uri: https://doi.org/10.7717/peerj.7404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yan et al. title: Diet and wild ungulate preferences of wolves in northwestern Anatolia during winter link: https://peerj.com/articles/7446 last-modified: 2019-08-21 description: The gray wolf (Canis lupus) is making a comeback in many habitats in central Europe, where it has been once extirpated. Although densities are still low to moderate, this comeback already raises management concerns. In Anatolia, the gray wolf is one of the most common predator species occupying almost all kind of habitats. Although its numbers were reduced in some parts of the country, it has never been extirpated and lived in sympatry with humans. In this study we investigated, for the first time, the winter diet of wolves in north-west Anatolia, where a multispecies wild ungulate community occurs in sympatry with high density livestock. We selected two geographically close but different habitats (steppe and forest) with different wild prey availabilities and compositions. In both areas ungulate contribution to winter diet biomass was more than 90%. Wolf pack size (four to eight wolves) were higher in the study area where livestock numbers and human disturbance were lower and wild prey were more available. In both study areas, wild boar (Sus scrofa) was the main and most preferred food item (Chesson’s α = 0.7 − 0.9) and it occurred at higher density where wolf pack size was smaller. We could not find a high preference (Chesson’s α = 0.3) and high winter predation pressure on the reintroduced Anatolian wild sheep (Ovis gmelinii anatolica) population that occurs in the study area covered by steppe vegetation. Contribution of livestock and food categories other than wild ungulates to wolf diet stayed low. Wolves can help mitigate human-wildlife conflict regulating wild boar numbers, the most common conflict-causing ungulate species in Anatolia. Instead of managing wolf numbers in human dominated landscapes, we recommend reintroduction of wild ungulates to the areas where they became locally extinct and replaced by livestock. creator: Deniz Mengüllüoğlu creator: Eylül İlaslan creator: Hasan Emir creator: Anne Berger uri: https://doi.org/10.7717/peerj.7446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mengüllüoğlu et al. title: Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes link: https://peerj.com/articles/7480 last-modified: 2019-08-21 description: Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships. creator: Qi Chen creator: Xiaobo Wu creator: Dequan Zhang uri: https://doi.org/10.7717/peerj.7480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max) link: https://peerj.com/articles/7509 last-modified: 2019-08-21 description: BackgroundVQ proteins, the plant-specific transcription factors, are involved in plant development and multiple stresses; however, only few articles systematic reported the VQ genes in soybean.MethodsIn total, we identified 75 GmVQ genes, which were classified into 7 groups (I-VII). Conserved domain analysis indicated that VQ gene family members all contain the VQ domains. VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed that cis-elements related to stress responses, phytohormone responses and controlling physical as well as reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were showed expressing in nine tissues, suggesting their putative function in many aspects of plant growth and development as well as response to stress in Glycine max.ResultsThis study aims to understand the roles of VQ genes in various development processes and their expression patterns in responses to stimuli. Our results provide basic information in identification and classification of GmVQ genes. Further experimental analysis will allows us to know the functions of GmVQs participation in plant growth and stress responses. creator: Yongbin Wang creator: Zhenfeng Jiang creator: Zhenxiang Li creator: Yuanling Zhao creator: Weiwei Tan creator: Zhaojun Liu creator: Shaobin Cui creator: Xiaoguang Yu creator: Jun Ma creator: Guangjin Wang creator: Wenbin Li uri: https://doi.org/10.7717/peerj.7509 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Delivery of targeted gene therapies using a hybrid cryogel-coated prosthetic vascular graft link: https://peerj.com/articles/7377 last-modified: 2019-08-20 description: ObjectivesThe success of prosthetic vascular grafts in the management of peripheral arterial disease is frequently limited by the development of anastomotic neointimal hyperplasia (ANIH), with the host response to prosthetic grafts beginning soon after implantation. To address this, we combine a platform of polyethylene terephthalate (PET) fabric with an applied cryogel layer containing biologic agents to create a bioactive prosthetic graft system, with the ability to deliver therapeutics targeting modulators of the ANIH-associated transcriptome response, along with antithrombotic agents.MethodsHybrid graft materials were synthesized by cryopolymerization of methacrylated alginate and heparin onto electrospun (ePET), knitted PET (kPET), or woven PET (wPET). Arg-Gly-Asp (RGD) peptides were added to increase cell adhesion. Scanning electron microscopy (SEM) was used to study the microstructure at 1 day, and 2, 4, and 8 weeks. Physical properties such as swelling ratio, pore connectivity, shape recovery, and stiffness were evaluated. Human aortic endothelial cell (HAoEC) adherence was visualized using confocal microscopy after 24 hours and proliferation was evaluated with a resazurin-based assay for 7 days. Confocal microscopy was used to assess delivery of adeno-associated virus (AAV-GFP) after incubation of hybrid grafts with HAoECs. Heparin activity of the materials was measured using an anti-Xa assay.ResultsSEM demonstrated large interconnected pores throughout the entire structure for all graft types, with minimal degradation of the cryogel after 8 weeks. Hybrid materials showed a trend towards increased shape recovery, increased stiffness, decreased swelling ratio, and no difference in pore connectivity. HAoECs incorporated, adhered, and proliferated over 7 days on all materials. HAoECs were successfully transduced with AAV-GFP from the hybrid graft materials. Anti-Xa assay confirmed continued activity of heparin from all materials for over 7 days.ConclusionsWe have developed a bioactive prosthetic graft system with a cryogel coating capable of delivering biologic agents with antithrombotic activity. By applying the cryogel and selected agents onto PET prior to graft implantation, this study sets the stage for the system to be individualized and tailored to the patient, with bioengineering and targeted gene therapy strategies dovetailing to create an improved prosthetic graft adaptable to emerging knowledge and technologies. creator: Cindy Huynh creator: Ting-Yu Shih creator: Alexander Mammoo creator: Amruta Samant creator: Saif Pathan creator: David W. Nelson creator: Christiane Ferran creator: David Mooney creator: Frank LoGerfo creator: Leena Pradhan-Nabzdyk uri: https://doi.org/10.7717/peerj.7377 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huynh et al. title: Twisted tale of the tiger: the case of inappropriate data and deficient science link: https://peerj.com/articles/7482 last-modified: 2019-08-20 description: Publications in peer-reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer-review process. We review a recent publication by Gopalaswamy et al. (10.1111/2041-210X.12351) that challenges the use of “double sampling” in large-scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large-scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. (10.1111/2041-210X.12351) to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index-Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, the paper of Gopalaswamy et al. could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences. creator: Qamar Qureshi creator: Rajesh Gopal creator: Yadvendradev Jhala uri: https://doi.org/10.7717/peerj.7482 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Qureshi et al. title: Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA link: https://peerj.com/articles/7490 last-modified: 2019-08-20 description: BackgroundThe safety of vaccines is a critical factor in maintaining public trust in national vaccination programs. This study aimed to evaluate the safety profiles of human papillomavirus (HPV) vaccines with regard to the distribution of adverse events (AE) across gender and age, and the correlations across various AEs using the Food and Drug Administration/Centers for Disease Control and Prevention Vaccine Adverse Event Reporting System (VAERS).MethodsFor analyses, 27,348 patients aged between 9 and 25 years old with at least one AE reported in VAERS between the year of 2006 and 2017 were included. AEs were summarized into two levels: the lower level preferred term (PT) and higher level system organ classes (SOCs) based on the structure of Medical Dictionary for Regulatory Activities (MedDRA). A series of statistical analyses were applied on both levels of AEs. Zero-truncated Poisson regression and multivariate logistic regression models were first developed to assess the rate and risk of SOCs across age groups and genders. Pairwise Pearson correlation analyses and hierarchical clustering analyses were then conducted to explore the interrelationships and clustering pattern among AEs.ResultsWe identified 27,337 unique HPV vaccine reports between 2006 and 2017. Disproportional reporting of AEs was observed across age and gender in 21 SOCs (p < 0.05). The correlation analyses found most SOCs demonstrate weak positive correlations except for five pairs which were negatively correlated: skin and subcutaneous tissue disorders + injury poisoning and procedural complications; skin and subcutaneous tissue disorders + nervous system disorders; Skin and subcutaneous tissue disorders + pregnancy, puerperium and perinatal conditions; nervous system disorders + pregnancy, puerperium and perinatal conditions; pregnancy, puerperium and perinatal conditions + general disorders and administration site conditions. Nervous system disorders had the most AEs which contributed to 12,448 (46%) cases. In the further analyses of correlations between PT in nervous system disorders, the three most strongly correlated AEs were psychiatric disorders (r = 0.35), gastrointestinal disorders (r = 0.215), and musculoskeletal and connective tissue disorders (r = 0.261). We observed an inter-SOCs correlation of the PTs among AE pairs by nervous system disorders/psychiatric disorders/gastrointestinal disorders/musculoskeletal and connective tissue disorders.ConclusionsThe analyses revealed a different distribution pattern of AEs across gender and age subgroups in 21 SOC level AEs. Correlation analyses and hierarchical clustering analyses further revealed several correlated patterns across various AEs. However, findings from this study should be interpreted with caution. Further clinical studies are needed to understand the heterogeneity of AEs reporting across subgroups and the biological pathways among the statistically correlated AEs. creator: Yuxi Jia creator: Cong Zhu creator: Jingcheng Du creator: Yang Xiang creator: Yong Chen creator: Wei Wang creator: Cui Tao uri: https://doi.org/10.7717/peerj.7490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jia et al. title: Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland link: https://peerj.com/articles/7506 last-modified: 2019-08-20 description: Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong (Bettongia gaimardi) and that of the exotic European rabbit (Oryctolagus cuniculus). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas. creator: Catherine E. Ross creator: Nicola T. Munro creator: Philip S. Barton creator: Maldwyn J. Evans creator: John Gillen creator: Ben C.T. Macdonald creator: Sue McIntyre creator: Saul A. Cunningham creator: Adrian D. Manning uri: https://doi.org/10.7717/peerj.7506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ross et al. title: Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors link: https://peerj.com/articles/7511 last-modified: 2019-08-20 description: Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions. creator: Ziwei Liang creator: Mengdi Li creator: Zhengyi Liu creator: Jianbo Wang uri: https://doi.org/10.7717/peerj.7511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liang et al. title: Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women link: https://peerj.com/articles/7533 last-modified: 2019-08-20 description: BackgroundMovement velocity has been proposed as an effective tool to prescribe the load during resistance training in young healthy adults. This study aimed to elucidate whether movement velocity could also be used to estimate the relative load (i.e., % of the one-repetition maximum (1RM)) in older women.MethodsA total of 22 older women (age = 68.2 ± 3.6 years, bench press 1RM = 22.3 ± 4.7 kg, leg press 1RM = 114.6 ± 15.9 kg) performed an incremental loading test during the free-weight bench press and the leg press exercises on two separate sessions. The mean velocity (MV) was collected with a linear position transducer.ResultsA strong linear relationship between MV and the relative load was observed for the bench press (%1RM = −130.4 MV + 119.3; r2 = 0.827, standard error of the estimate (SEE) = 6.10%1RM, p < 0.001) and leg press exercises (%1RM = −158.3 MV + 131.4; r2 = 0.913, SEE = 5.63%1RM, p < 0.001). No significant differences were observed between the bench press and leg press exercises for the MV attained against light-medium relative loads (≤70%1RM), while the MV associated with heavy loads (≥80%1RM) was significantly higher for the leg press.ConclusionsThese results suggest that the monitoring of MV could be useful to prescribe the loads during resistance training in older women. However, it should be noted that the MV associated with a given %1RM is significantly lower in older women compared to young healthy individuals. creator: Pablo Jorge Marcos-Pardo creator: Jorge Miguel González-Hernández creator: Amador García-Ramos creator: Abraham López-Vivancos creator: Pedro Jiménez-Reyes uri: https://doi.org/10.7717/peerj.7533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Marcos-Pardo et al. title: Anxiety-like behavior and whole-body cortisol responses to components of energy drinks in zebrafish (Danio rerio) link: https://peerj.com/articles/7546 last-modified: 2019-08-20 description: The current study investigated the independent and combined effects of caffeine and taurine on anxiety-like behavior and neuroendocrine responses in adult zebrafish (Danio rerio). Caffeine (1,3,7-trimethylpurine-2,6-dione), the world’s most commonly used psychoactive drug, acts as an adenosine receptor blocker and a mild central nervous system stimulant. However, excessive use of caffeine is associated with heightened anxiety levels. Taurine (2-aminoethanesulfonic acid), a semi-essential amino acid synthesized within the human brain, has been hypothesized to play a role in regulating anxiolytic behavior. Caffeine and taurine are two common additives in energy drinks and are often found in high concentrations in these beverages. However, few studies have investigated the interaction of these two chemicals with regards to anxiety measures. A suitable vertebrate to examine anxiety-like behavior and physiological stress responses is the zebrafish, which has shown promise due to substantial physiological and genetic homology with humans. Anxiety-like behavior in zebrafish can be determined by analyzing habituation to novelty when fish are placed into a novel tank and scototaxis (light avoidance) behavior in the light-dark test. Stress-related neuroendocrine responses can be measured in zebrafish by analyzing whole-body cortisol levels. The goal of this study was to determine if exposure to caffeine, taurine, or a combination of the two compounds altered anxiety-like behavior and whole-body cortisol levels in zebrafish relative to control. Zebrafish were individually exposed to either caffeine (100 mg/L), taurine (400 mg/L), or both for 15 min. Zebrafish in the control group were handled in the same manner but were only exposed to system tank water. After treatment, fish were transferred to the novel tank test or the light-dark test. Behavior was tracked for the first 6 min in the novel tank and 15 min in the light-tark test. Fifteen min after introduction to the behavioral task, fish were euthanized for the analysis of whole-body cortisol levels. The results demonstrate that caffeine treatment decreased the amount of exploration in the top of the novel tank and increased scototaxis behavior in the light-dark test, which supports the established anxiogenic effect of acute exposure to caffeine. Taurine alone did not alter basal levels of anxiety-like behavioral responses nor ameliorated the anxiogenic effects of caffeine on behavior when the two compounds were administered concurrently. None of the drug treatments altered basal levels of whole-body cortisol. The current results of this study suggest that, at least at this dose and time of exposure, taurine does not mitigate the anxiety-producing effects of caffeine when administered in combination, such as with energy drink consumption. creator: Alia O. Alia creator: Maureen L. Petrunich-Rutherford uri: https://doi.org/10.7717/peerj.7546 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Alia and Petrunich-Rutherford title: A revision of the Neotropical caddisfly genus Ascotrichia Flint, 1983 (Trichoptera, Hydroptilidae) link: https://peerj.com/articles/7560 last-modified: 2019-08-20 description: A revision of the microcaddisfly genus Ascotrichia (Trichoptera, Hydroptilidae) is provided, including a generic diagnosis, illustrations, and descriptions of males. This genus is endemic to the Neotropical region and has been recorded from countries in northern South America. Adults of the genus are notable within the family for the contrasting black and green hairs on the forewings. A total of six species are treated, three described as new: Ascotrichia adirecta sp. n. (Brazil), A. hystricosa sp. n. (Brazil), and A. simoma sp. n. (Brazil). creator: Robin E. Thomson uri: https://doi.org/10.7717/peerj.7560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Thomson title: Assessment of complementary and alternative medicine use among patients admitted to the emergency room: a descriptive study from a Turkish hospital link: https://peerj.com/articles/7584 last-modified: 2019-08-20 description: BackgroundThe main aim of this study was to assess the frequency of use of complementary and alternative medicine (CAM) in patients admitted to the emergency room (ER). Additionally, we aimed to evaluate the socio-demographic and clinical factors associated with CAM use.MethodsThis was a descriptive study. A total of 951 patients who were admitted to the ER of a tertiary hospital between October 2018 and November 2018 were enrolled. Data were obtained using a questionnaire that was prepared by the researchers considering the literature data.ResultsThe mean age of the patients was 37.98 ± 15.65 years. Of the 951 patients, 48.4% (n = 460) were female and 51.6% (n = 491) were male. The rate of patients who used CAM at least once was 47.3% (n = 450). The most frequently used CAM methods were herbal therapy (68.9%), massage (40.7%), dietary supplements (24.7%), and hijama (24.2%). Being aged 64 years or younger (p = 0.001), having an education level of university or higher (p = 0.006), having an income more than minimum wage (p = 0.016), and having a chronic disease (p = 0.003) were found to be associated with CAM use in this study.DiscussionCAM methods were used by a considerable proportion of patients admitted to the ER. Physicians should incorporate CAM use history in their patient assessments and should provide accurate and unbiased information about CAM methods. creator: Hakan Hakkoymaz creator: Burhan Fatih Koçyiğit uri: https://doi.org/10.7717/peerj.7584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hakkoymaz et al. title: Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies link: https://peerj.com/articles/7410 last-modified: 2019-08-19 description: Information on taxa distribution is a prerequisite for many research fields, and biological records are a major source of data contributing to biogeographic studies. The Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS) are important infrastructures facilitating free and open access to classical biological data from several sources in both temporal and spatial scales. Over the last ten years, high throughput sequencing (HTS) metabarcoding data have become available, which constitute a great source of detailed occurrence data. Among the global sampling projects that have contributed to such data are Tara Oceans and the Ocean Sampling Day (OSD). Integration of classical and metabarcoding data may aid a more comprehensive assessment of the geographic range of species, especially of microscopic ones such as protists. Rare, small and cryptic species are often ignored in surveys or mis-assigned with the classical approaches. Here we show how integration of data from various sources can contribute to insight in the biogeography and diversity at the genus- and species-level using Chaetoceros as study system, one of the most diverse and abundant genera among marine planktonic diatoms. Chaetoceros records were extracted from GBIF and OBIS and literature data were collected by means of a Google Scholar search. Chaetoceros references barcodes where mapped against the metabarcode datasets of Tara Oceans (210 sites) and OSD (144 sites). We compared the resolution of different data sources in determining the global distribution of the genus and provided examples, at the species level, of detection of cryptic species, endemism and cosmopolitan or restricted distributions. Our results highlighted at genus level a comparable picture from the different sources but a more complete assessment when data were integrated. Both the importance of the integration but also the challenges related to it were illustrated. Chaetoceros data collected in this study are organised and available in the form of tables and maps, providing a powerful tool and a baseline for further research in e.g., ecology, conservation and evolutionary biology. creator: Daniele De Luca creator: Wiebe H.C.F. Kooistra creator: Diana Sarno creator: Chetan C. Gaonkar creator: Roberta Piredda uri: https://doi.org/10.7717/peerj.7410 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 De Luca et al. title: A comparative study of root canal shaping using protaper universal and protaper next rotary files in preclinical dental education link: https://peerj.com/articles/7419 last-modified: 2019-08-19 description: BackgroundDentistry has undergone an evolution in endodontics practice caused by the advancement of rotary techniques for root canal preparation and their subsequent incorporation into the teaching of dentistry undergraduates. This research aimed to evaluate the shaping ability of third-year dental students as their first experience in rotary instrumentation using ProTaper Universal (PTU) and ProTaper Next (PTN) (Dentsply Maillefer) rotary instruments in simulated curved canals.MethodsForty students instrumented 200 simulated canals with a 40° curvature in resin blocks according to the manufacturer’s instructions with PTU and 39 students and 195 canals with PTN files. The canals were prepared at a speed of 300 rpm using a 16:1 reduction hand-piece powered by an electric motor (Xsmart; Dentsply Maillefer). The final apical preparation was set to F2 for the PTU and X2 for the PTN group. The change in canal curvature was evaluated based on Schneider technique using the AutoCAD 2007 software on post-digital photographs. The incidence of instrument fracture and deformation, the incidence of ledge, the change in working length (WL), and the working time were noted. The data were analyzed with Student’s t-test and Chi-Square test at a significance level of 0.05 using SPSS.ResultsPTN maintained the original canal curvature better, resulting in fewer fractures and ledges, and shaped the canals faster than the PTU (P < 0.05). The mean curves of the resin canals after the instrumentation for the PTU and PTN groups were 24.03° ± 3.14° and 25.64° ± 2.72°, respectively. Thirty-three (17.4%) PTU and 18 (9.3%) PTN files fractured (p < 0.05). Nine (4.5%) PTU and 2 (2.6%) PTN deformed (p > 0.05). The change in WL after instrumentation was 0.97 mm ± 0.95 mm in PTU and 0.96 mm ± 0.80 mm in PTN (p < 0.05). The mean times were 627 s ± 18 s for PTU and 379 s ± 18 s for PTN (p < 0.000).DiscussionPTN can be recommended in severely curved root canals in terms of maintenance of the original canal curvature, superior instrument fracture and fewer ledges. Even if training before preparation provides an acceptable level of canal shaping for preclinical students, the use of NiTi rotary instruments should be included in the undergraduate dental curriculum, contributing to an increase in the quality of root canal shaping and, consequently, to an improvement of the clinical experience of students. creator: Gül Çelik creator: Feyza Özdemir Kısacık creator: Emir Faruk Yılmaz creator: Arife Mersinlioğlu creator: İhsan Furkan Ertuğrul creator: Hikmet Orhan uri: https://doi.org/10.7717/peerj.7419 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Çelik et al. title: Redescription of Hargeria rapax (Harger, 1879) and description of H. chetumalensis a new species from the Mexican Caribbean (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) based upon morphological and molecular evidence link: https://peerj.com/articles/7472 last-modified: 2019-08-19 description: Until now, Hargeria was considered a monospecific leptocheliid genus, with the species Hargeria rapax considered a taxon with a wide distribution, from the Northwestern Atlantic to the Mexican Caribbean. Herein, after a detailed revision of type and topotype materials and specimens collected from the Mexican Caribbean, a new species H. chetumalensis sp. nov. is described, and the redescription of H. rapax is provided. Also, we found a significant genetic divergence between the two species based on the nucleotide sequences of cytochrome oxidase subunit I, which support the morphological data. The morphological features used to recognize both species are also adequate to link males, females, and juvenile stages, although these species have a high intraspecific polymorphism. creator: Jani Jarquín-González creator: Luis F. Carrera-Parra uri: https://doi.org/10.7717/peerj.7472 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jarquín-González and Carrera-Parra title: Serological evidence of hepatitis A, B, and C virus infection in older adults in Khon Kaen, Thailand and the estimated rates of chronic hepatitis B and C virus infection in Thais, 2017 link: https://peerj.com/articles/7492 last-modified: 2019-08-19 description: Hepatitis A (HAV), hepatitis B (HBV), and hepatitis C (HCV) viruses are hepatotropic viruses responsible for acute/chronic hepatitis associated with liver failure, cirrhosis, and hepatocellular carcinoma. Due to the limited data on the prevalence of hepatitis in the older population in Thailand, this study aimed to evaluate the seroprevalence of these viruses in elderly Thais. Using an automated immunoassay, serum samples from individuals older than 60 years of age in Chum Phae district of Khon Kaen province in northeast Thailand were analyzed for anti-HAV (n = 93), HBV markers (n = 460, HBsAg, anti-HBs, and anti-HBc), and anti-HCV (n = 460). Samples were classified into five age groups (61–65, 66–70, 71–75, 76–80, and >80 years). The overall seroprevalence of anti-HAV, HBsAg, anti-HBc, anti-HBs, and anti-HCV was 98.9%, 4.6%, 51.5%, 32.4%, and 1.3%, respectively. When samples were stratified into three groups representing three generations (children/young adults aged 6 months-30 years and middle-aged adults between 31–60 years old from a previous survey, and older adults aged >60 years from the current study), the highest levels of anti-HAV and anti-HBc were found in older adults. Children/young adults had the lowest levels of HBsAg and anti-HCV, and the highest level of anti-HBs. These findings are consistent with the integration of HBV vaccination into the Expanded Program on Immunization (EPI) in 1992 and coincide with increased awareness of blood-borne viral transmission in Thailand. Extrapolating from our data, the estimated numbers of cases of chronic HBV and HCV infection in Thailand in 2017 were 2.2 and 0.79 million, respectively. Thus, effective treatments for viral hepatitis B and C for middle-aged and elderly Thais are needed. This seroprevalence survey could be used to help formulate policies and possible guidelines for treatment and prevention in specific age groups, which is recommended to facilitate the elimination of viral hepatitis by 2030. creator: Nawarat Posuwan creator: Viboonsak Vuthitanachot creator: Teeraporn Chinchai creator: Rujipat Wasitthankasem creator: Nasamon Wanlapakorn creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.7492 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Posuwan et al. title: Improvement of subsoil physicochemical and microbial properties by short-term fallow practices link: https://peerj.com/articles/7501 last-modified: 2019-08-19 description: Fallow management can improve the soil nutrients in the topsoil and upper subsoil. However, little is known about the effects of short-term (one year) fallowing with different treatments, such as vegetation and fertilization, on subsoil (20–40 cm) properties. We conducted field trials to explore the changes in subsoil properties in response to such treatments in the Yellow River Delta region in China. Different vegetation and fertilization treatments were applied, and we measured the carbon and nitrogen contents, microbial biomass and microbial community structure in the subsoil. Fallowing without manure resulted in the storage of more total nitrogen (16.38%) than fallowing with manure, and meadow vegetation improved the ammonium nitrogen content (45.71%) relative to spontaneous vegetation. Spontaneous vegetation with manure improved the microbial biomass nitrogen (P < 0.05). Although the impact of short-term fallowing on microbial community structure was low, an effect of management was observed for some genera. Blastopirellula, Lysobacter, and Acidobacteria Gp6 showed significant differences among fallow treatments by the end of the year (P < 0.05). Blastopirellula abundance was related to the microbial biomass nitrogen and nitrogen mineralization rate in the subsoil. Manure retained a high abundance of Lysobacter, which may strengthen soil-borne disease resistance. The response of Acidobacteria Gp6 showed that meadow vegetation without manure may not benefit future crops. Although the treatments did not significantly improve microbial community structure in the one-year period, annual fallowing improved certain subsoil properties and increased the number of functional genera, which may enhance crop productivity in the future. creator: Guangyu Li creator: Walter Timo de Vries creator: Cifang Wu creator: Hongyu Zheng uri: https://doi.org/10.7717/peerj.7501 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Monitoring and analysis of the expansion of the Ajmr Port, Davao City, Philippines using multi-source remote sensing data link: https://peerj.com/articles/7512 last-modified: 2019-08-19 description: Ports have been built or expanded in a number of countries to cater to increasing maritime trade in the 21st century. Port expansion is associated with economic and environmental impacts on the local and regional scales, and these impacts can be studied using remote sensing. The present study presents new results from multi-source remote sensing monitoring of the Ajmr Port expansion. An analysis of land use and vegetation coverage at the port is used to monitor the impact of port construction on the local ecology, while changes in roads, buildings, and lights are used to monitor the economic impact. The results show that: (1) After nine years of expansion, the port area has gradually expanded from the central to the southern coastal area, with an increase of 21.68 hectares during the expansion period. After the expansion, the area of builidings and construction in the study area increased significantly, while the area of water and green areas decreased significantly, indicating that the port construction changed the land use structure of the area. (2) From the perspective of vegetation coverage, the vegetation coverage within 5 km from the port is in good condition. After 9 years, the vegetation coverage in the region between 0.6 and 1 increased from 43.71% to 44.25%, reflecting the higher overall greening level in the region. (3) By analyzing the increase in roads and buildings, it can be seen that the port’s comprehensive transportation capacity has improved, the population of the region has increased significantly. As the scale of construction has been continuously expanded , the prosperity as increased. (4) By analyzing the changes in the light index, the light data from the northeast to the southwest in the region is very obvious, and it is clearly located along the coast, indicating that the economic development of the coastal zone is faster than other regions, and the coastal region has promoted the development of the inland region. creator: Humei Li creator: Mingquan Wu creator: Dinghui Tian creator: Lianxi Wu creator: Zheng Niu uri: https://doi.org/10.7717/peerj.7512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Trophic upgrading and mobilization of wax esters in microzooplankton link: https://peerj.com/articles/7549 last-modified: 2019-08-19 description: Heterotrophic protists play pivotal roles in aquatic ecosystems by transferring matter and energy, including lipids, from primary producers to higher trophic predators. Using Oxyrrhis marina as a model organism, changes to the non-saponifiable protist lipids were investigated under satiation and starvation conditions. During active feeding on the alga Cryptomonas sp., the O. marina hexane soluble non-saponifiable fraction lipid profile reflected its food source with the observed presence of long chain mono-unsaturated fatty alcohols up to C25:1. Evidence of trophic upgrading in O. marina was observed with long chain mono-unsaturated fatty alcohol accumulation of up to C35:1. To the best of our knowledge, this is the first evidence that heterotrophic dinoflagellates are capable of producing ester derived alcohols and that dinoflagellates like O. marina are capable of synthesizing fatty alcohols up to C35. Additionally, we show evidence of trophic upgrading of lipids. During a 20-day resource deprivation, the lipid profile remained constant. During starvation, the mobilization of wax esters as energy stores was observed with long chain fatty alcohols mobilized first. Changes in lipid class profile and utilization of wax esters in O. marina provides insight into the types of lipids available for energy demand, the transfer of lipids through the base of marine food webs, and the catabolic response induced by resource deprivation. creator: Keyana Roohani creator: Brad A. Haubrich creator: Kai-Lou Yue creator: Nigel D’Souza creator: Amanda Montalbano creator: Tatiana Rynearson creator: Susanne Menden-Deuer creator: Christopher W. Reid uri: https://doi.org/10.7717/peerj.7549 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Roohani et al. title: Modest dose anti-thymocyte globulin administered intraoperatively is safe and effective in kidney transplantations: a retrospective study link: https://peerj.com/articles/7274 last-modified: 2019-08-16 description: BackgroundAnti-thymocyte globulin (ATG) as induction therapy in renal transplantation is facing the dilemma of reducing the incidence of acute rejection (AR) and delayed graft function (DGF) or increasing risks of infection and malignancy. The purpose of this study was to delineate the safety and efficiency of the optimal ATG dosage.MethodsWe retrospectively evaluated 91 deceased donor kidney transplant recipients (KTRs) in our institution between March 2011 and January 2019. The patients were classified into three groups based on induction therapy: (1) Group 1: modest-dose ATG (three mg/kg) intraoperatively (N = 21); (2) Group 2: low-dose ATG (1–1.5 mg/kg) intraoperatively (N = 23); (3) Group 3: basiliximab 20 mg both on day 0 and 4 (N = 47). In Groups 1 and 2, all patients received a daily low-dose program (1–1.5 mg/kg each day) with target dosage of six mg/kg. Induction therapy was combined with standard immunosuppressive regimen consisting of calcineurin inhibitors, mycophenolate/the mammalian target of rapamycin inhibitors and corticosteroids.ResultsThere was no significant difference in patient characteristics among groups. The outcomes of infection rate, biopsy-proven acute rejection, post-transplant diabetes mellitus, graft survival, and patient survival were similar among groups. Compared to the daily low-dose ATG regimen, the intraoperative modest-dose regimen did not cause more dose interruption and hence was more likely to reach the target ATG dosage. The intraoperative modest-dose regimen also seemed to reduce the rate of DGF.DiscussionIn recent years, a trend of using a “lower” dose of ATG has seemed to emerge. Our results suggest intraoperative modest-dose ATG followed by daily low-dose ATG regimen was safe and effective in cadaveric renal transplantations for preventing DGF, AR, and graft loss. creator: Hui-Ying Liu creator: Yuan-Tso Cheng creator: Hao Lun Luo creator: Chiang-Chi Huang creator: Chien Hsu Chen creator: Yuan-Chi Shen creator: Wen-Chin Lee uri: https://doi.org/10.7717/peerj.7274 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Differential expression of AtWAKL10 in response to nitric oxide suggests a putative role in biotic and abiotic stress responses link: https://peerj.com/articles/7383 last-modified: 2019-08-16 description: Plant defense against pathogens and abiotic stresses is regulated differentially by communicating signal transduction pathways in which nitric oxide (NO) plays a key role. Here, we show the biological role of Arabidopsis thaliana wall-associated kinase (AtWAK) Like10 (AtWAKL10) that exhibits greater than a 100-fold change in transcript accumulation in response to the NO donor S-nitroso-L-cysteine (CysNO), identified from high throughput RNA-seq based transcriptome analysis. Loss of AtWAKL10 function showed a similar phenotype to wild type (WT) with, however, less branching. The growth of atwakl10 on media supplemented with oxidative or nitrosative stress resulted in differential results with improved growth following treatment with CysNO but reduced growth in response to S-nitrosoglutatione (GSNO) and methyl-viologen. Further, atwakl10 plants exhibited increased susceptibility to virulent Pseudomonas syringae pv tomato (Pst) DC3000 with a significant increase in pathogen growth and decrease in PR1 transcript accumulation compared to WT overtime. Similar results were found in response to Pst DC3000 avrB, resulting in increased cell death as shown by increased electrolyte leakage in atwakl10. Furthermore, atwakl10 also showed increased reactive oxygen species accumulation following Pst DC3000 avrB inoculation. Promoter analysis of AtWAKL10 showed transcription factor (TF) binding sites for biotic and abiotic stress-related TFs. Further investigation into the role of AtWAKL10 in abiotic stresses showed that following two weeks water-withholding drought condition most of the atwakl10 plants got wilted; however, the majority (60%) of these plants recovered following re-watering. In contrast, in response to salinity stress, atwakl10 showed reduced germination under 150 mM salt stress compared to WT, suggesting that NO-induced AtWAKL10 differentially regulates different abiotic stresses. Taken together, this study further elucidates the importance of NO-induced changes in gene expression and their role in plant biotic and abiotic stress tolerance. creator: Phearom Bot creator: Bong-Gyu Mun creator: Qari Muhammad Imran creator: Adil Hussain creator: Sang-Uk Lee creator: Gary Loake creator: Byung-Wook Yun uri: https://doi.org/10.7717/peerj.7383 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bot et al. title: Towards a barnacle tree of life: integrating diverse phylogenetic efforts into a comprehensive hypothesis of thecostracan evolution link: https://peerj.com/articles/7387 last-modified: 2019-08-16 description: Barnacles and their allies (Thecostraca) are a biologically diverse, monophyletic crustacean group, which includes both intensely studied taxa, such as the acorn and stalked barnacles, as well as cryptic taxa, for example, Facetotecta. Recent efforts have clarified phylogenetic relationships in many different parts of the barnacle tree, but the outcomes of these phylogenetic studies have not yet been combined into a single hypothesis for all barnacles. In the present study, we applied a new “synthesis” tree approach to estimate the first working Barnacle Tree of Life. Using this approach, we integrated phylogenetic hypotheses from 27 studies, which did not necessarily include the same taxa or used the same characters, with hierarchical taxonomic information for all recognized species. This first synthesis tree contains 2,070 barnacle species and subspecies, including 239 barnacle species with phylogenetic information and 198 undescribed or unidentified species. The tree had 442 bifurcating nodes, indicating that 79.3% of all nodes are still unresolved. We found that the acorn and stalked barnacles, the Thoracica, and the parasitic Rhizocephala have the largest amount of published phylogenetic information. About half of the thecostracan families for which phylogenetic information was available were polyphyletic. We queried publicly available geographic occurrence databases for the group, gaining a sense of geographic gaps and hotspots in our phylogenetic knowledge. Phylogenetic information is especially lacking for deep sea and Arctic taxa, but even coastal species are not fully incorporated into phylogenetic studies. creator: Christine Ewers-Saucedo creator: Christopher L. Owen creator: Marcos Pérez-Losada creator: Jens T. Høeg creator: Henrik Glenner creator: Benny K.K. Chan creator: Keith A. Crandall uri: https://doi.org/10.7717/peerj.7387 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ewers-Saucedo et al. title: Paranoia and conspiracy: group cohesion increases harmful intent attribution in the Trust Game link: https://peerj.com/articles/7403 last-modified: 2019-08-16 description: Current theories argue that hyper-sensitisation of social threat perception is central to paranoia. Affected people often also report misperceptions of group cohesion (conspiracy) but little is known about the cognitive mechanisms underpinning this conspiracy thinking in live interactions. In a pre-registered experimental study, we used a large-scale game theory approach (N > 1,000) to test whether the social cohesion of an opposing group affects paranoid attributions in a mixed online and lab-based sample. Participants spanning the full population distribution of paranoia played as proposers in a modified Trust Game: they were allocated a bonus and chose how much money to send to a pair of responders which was quadrupled before reaching these responders. Responders decided how much to return to the proposers through the same process. Participants played in one of two conditions: against a cohesive group who communicated and arrived at a joint decision, or a non-cohesive group who made independent decisions. After the exchange, proposers rated the extent to which the responders’ decisions were driven by (i) self-interest and (ii) intent to harm. Although the true motives are ambiguous, cohesive responders were reliably rated by participants as being more strongly motivated by intent to harm, indicating that group cohesion affects social threat perception. Highly paranoid participants attributed harmful intent more strongly overall but were equally reactive to social cohesion as other participants. This suggests that paranoia involves a generally lowered threshold for social threat detection but with an intact sensitivity for cohesion-related group characteristics. creator: Anna Greenburgh creator: Vaughan Bell creator: Nichola Raihani uri: https://doi.org/10.7717/peerj.7403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Greenburgh et al. title: Random allogeneic blood transfusion in pigs: characterisation of a novel experimental model link: https://peerj.com/articles/7439 last-modified: 2019-08-16 description: BackgroundOrgan cross-talk describes interactions between a primary affected organ and a secondarily injured remote organ, particularly in lung-brain interactions. A common theory is the systemic distribution of inflammatory mediators that are released by the affected organ and transferred through the bloodstream. The present study characterises the baseline immunogenic effects of a novel experimental model of random allogeneic blood transfusion in pigs designed to analyse the role of the bloodstream in organ cross-talk.MethodsAfter approval of the State and Institutional Animal Care Committee, 20 anesthetized pig were randomized in a donor and an acceptor (each n = 8): the acceptor animals each received high-volume whole blood transfusion from the donor (35–40 ml kg−1). Four animals received balanced electrolyte solution instead of blood transfusion (control group; n = 4). Afterwards the animals underwent extended cardiorespiratory monitoring for eight hours. Post mortem assessment included pulmonary, cerebral and systemic mediators of early inflammatory response (IL-6, TNF-alpha, iNOS), wet to dry ratio, and lung histology.ResultsNo adverse events or incompatibilities occurred during the blood transfusion procedures. Systemic cytokine levels and pulmonary function were unaffected. Lung histopathology scoring did not display relevant intergroup differences. Neither within the lung nor within the brain an up-regulation of inflammatory mediators was detected. High volume random allogeneic blood transfusion in pigs neither impaired pulmonary integrity nor induced systemic, lung, or brain inflammatory response.ConclusionThis approach can represent a novel experimental model to characterize the blood-bound transmission in remote organ injury. creator: Alexander Ziebart creator: Moritz M. Schaefer creator: Rainer Thomas creator: Jens Kamuf creator: Andreas Garcia-Bardon creator: Christian Möllmann creator: Robert Ruemmler creator: Florian Heid creator: Arno Schad creator: Erik K. Hartmann uri: https://doi.org/10.7717/peerj.7439 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ziebart et al. title: Group B Streptococcus colonization induces Prevotella and Megasphaera abundance-featured vaginal microbiome compositional change in non-pregnant women link: https://peerj.com/articles/7474 last-modified: 2019-08-16 description: BackgroundPrevious studies have indicated that variations in the vaginal microbiome result in symptomatic conditions. Group B Streptococcus (GBS) is a significant neonatal pathogen and maternal vaginal colonization has been recognized as an important risk factor for neonatal disease. Therefore, it is important to discover the relationship between the composition of the vaginal microbiome and GBS colonization. This study explores the potential relationship between the composition of the vaginal microbiome and GBS colonization in non-pregnant Chinese women.MethodsA total of 22 GBS-positive, non-pregnant women and 44 matched GBS-negative women were recruited for the current study. The composition of the vaginal microbiome was profiled by sequencing the 16S rRNA genes. The microbiome diversity and variation were then evaluated.ResultsThe vaginal microbiome of the 66 subjects enrolled in the current study were compared and the results showed that GBS-positive women exhibited significant vaginal microbial differences compared with the GBS-negative women based on the analysis of similarities (r = 0.306, p < 0.01). The relative abundance of the bacterial genus Lactobacillus (p < 0.01) was significantly lower in the GBS-positive group, while the abundances of the bacterial genera Prevotella (p < 0.01), Megasphaera (p < 0.01), and Streptococcus (p < 0.01) were significantly higher in the GBS-positive group.DiscussionThe current study addressed significant variations across the communities of the vaginal microbiome in GBS-positive and GBS-negative women in a Chinese cohort, which paves the way for a larger cohort-based clinical validation study and the development of therapeutic probiotics in the future. creator: Xiaofeng Mu creator: Changying Zhao creator: Junjie Yang creator: Xiaofang Wei creator: Jiaming Zhang creator: Cheng Liang creator: Zhongtao Gai creator: Chunling Zhang creator: Dequan Zhu creator: Ye Wang creator: Lei Zhang uri: https://doi.org/10.7717/peerj.7474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mu et al. title: Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci link: https://peerj.com/articles/7477 last-modified: 2019-08-16 description: BackgroundBacterial symbiosis is widespread in arthropods, especially in insects. Some of the symbionts undergo a long-term co-evolution with the host, resulting in massive genome decay. One particular consequence of genome decay is thought to be the elimination of transcriptional elements within both the coding region and intergenic sequences. In the whitefly Bemisia tabaci species complex, the obligate symbiont Candidatus Portiera aleyrodidarum is of vital importance in nutrient provision, and yet little is known about the regulatory capacities of it.MethodsPortiera genomes of two whitefly species in China were sequenced and assembled. Gene content of these two Portiera genomes was predicted, and then subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis. Together with two other Portiera genomes from whitefly species available previously, four Portiera genomes were utilized to investigate regulatory capacities of Portiera, focusing on transcriptional elements, including genes related with transcription and functional elements within the intergenic spacers.ResultsComparative analyses of the four Portiera genomes of whitefly B. tabaci indicate that the obligate symbionts Portiera is similar in different species of whiteflies, in terms of general genome features and possible functions in the biosynthesis of essential amino acids. The screening of transcriptional factors suggests compromised ability of Portiera to regulate the essential amino acid biosynthesis pathways. Meanwhile, thermal tolerance ability of Portiera is indicated with the detection of a σ32 factor, as well as two predicted σ32 binding sites. Within intergenic spacers, functional elements are predicted, including 37 Shine-Dalgarno sequences and 34 putative small RNAs. creator: Dan-Tong Zhu creator: Chi Zou creator: Fei-Xue Ban creator: Hua-Ling Wang creator: Xiao-Wei Wang creator: Yin-Quan Liu uri: https://doi.org/10.7717/peerj.7477 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhu et al. title: Risk and prognostic nomograms for hepatocellular carcinoma with newly-diagnosed pulmonary metastasis using SEER data link: https://peerj.com/articles/7496 last-modified: 2019-08-16 description: PurposeThis research aimed to identify risk factors of pulmonary metastasis (PM) from hepatocellular carcinoma (HCC) and prognostic factors of patients with PM from HCC at initial diagnosis.MethodsPatients diagnosed with HCC between 2010 and 2015 were reviewed retrospectively in the Surveillance, Epidemiology, and End Results (SEER) database. Patients with PM from HCC at initial diagnosis were identified from the entire cohort. Predictors for PM from HCC were identified by multivariate logistic regression analysis. Independent prognostic factors for patients with PM were determined by univariate and multivariate Cox regression analysis. Nomograms were also constructed for quantifying risk of metastasis and overall survival estimation visually.ResultsOur research included 30,641 patients diagnosed with HCC, of whom 1,732 cases were with PM from HCC at initial diagnosis. The risk factors causing PM from HCC were age (P = 0.001), race (P < 0.001), primary tumor size (P < 0.001), T stage (P < 0.001), N stage (P < 0.001), alpha-fetoprotein (P < 0.001), bone metastasis (P < 0.001), brain metastasis (P < 0.001), and intrahepatic metastasis (P < 0.001). The significantly prognostic factors for overall survival were age (P = 0.014), T stage (P = 0.009), surgical approach (P < 0.001), and chemotherapy (P < 0.001). Harrell’s C-index statistics of two nomograms were 0.768 and 0.687 respectively, indicating satisfactory predictive power.ConclusionsThis research provided evaluation of risk factors and prognosis for patients with PM from HCC. Two nomograms we developed can be convenient individualized tools to facilitate clinical decision-making. creator: Guanzhi Ye creator: Lin Wang creator: Zhengyang Hu creator: Jiaqi Liang creator: Yunyi Bian creator: Cheng Zhan creator: Zongwu Lin uri: https://doi.org/10.7717/peerj.7496 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ye et al. title: Factors affecting the composition of the gut microbiota, and its modulation link: https://peerj.com/articles/7502 last-modified: 2019-08-16 description: Gut microbiota have important functions in the body, and imbalances in the composition and diversity of those microbiota can cause several diseases. The host fosters favorable microbiota by releasing specific factors, such as microRNAs, and nonspecific factors, such as antimicrobial peptides, mucus and immunoglobulin A that encourage the growth of specific types of bacteria and inhibit the growth of others. Diet, antibiotics, and age can change gut microbiota, and many studies have shown the relationship between disorders of the microbiota and several diseases and reported some ways to modulate that balance. In this review, we highlight how the host shapes its gut microbiota via specific and nonspecific factors, how environmental and nutritional factors affect it, and how to modulate it using prebiotics, probiotics, and fecal microbiota transplantation. creator: Nihal Hasan creator: Hongyi Yang uri: https://doi.org/10.7717/peerj.7502 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hasan and Yang title: Exploring the potential of deep-blue autofluorescence for monitoring amyloid fibril formation and dissociation link: https://peerj.com/articles/7554 last-modified: 2019-08-16 description: Protein aggregation into amyloid fibrils has been linked to multiple neurodegenerative disorders. Determining the kinetics of fibril formation, as well as their structural stability are important for the mechanistic understanding of amyloid aggregation. Tracking both fibril association and dissociation is usually performed by measuring light scattering of the solution or fluorescence of amyloid specific dyes, such as thioflavin-T. A possible addition to these methods is the recently discovered deep-blue autofluorescence (dbAF), which is linked to amyloid formation. In this work we explore the potential of this phenomenon to monitor amyloid fibril formation and dissociation, as well as show its possible relation to fibril size rather than amyloid structure. creator: Mantas Ziaunys creator: Tomas Sneideris creator: Vytautas Smirnovas uri: https://doi.org/10.7717/peerj.7554 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ziaunys et al. title: Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle link: https://peerj.com/articles/7444 last-modified: 2019-08-15 description: The red-eared slider turtle (Trachemys scripta elegans; RES) is often considered one of the world’s most invasive species. Results from laboratory and mesocosm experiments suggest that introduced RES outcompete native turtles for key ecological resources, but such experiments can overestimate the strength of competition. We report on the first field experiment with a wild turtle community, involving introduced RES and a declining native species of conservation concern, the western pond turtle (Emys marmorata; WPT). Using a before/after experimental design, we show that after removing most of an introduced RES population, the remaining RES dramatically shifted their spatial basking distribution in a manner consistent with strong intraspecific competition. WPT also altered their spatial basking distribution after the RES removal, but in ways inconsistent with strong interspecific competition. However, we documented reduced levels of WPT basking post-removal, which may reflect a behavioral shift attributable to the lower density of the turtle community. WPT body condition also increased after we removed RES, consistent with either indirect or direct competition between WPT and RES and providing the first evidence that RES can compete with a native turtle in the wild. We conclude that the negative impacts on WPT basking by RES in natural contexts are more limited than suggested by experiments with captive turtles, although wild WPT do appear to compete for food with introduced RES. Our results highlight the importance of manipulative field experiments when studying biological invasions, and the potential value of RES removal as a management strategy for WPT. creator: Max R. Lambert creator: Jennifer M. McKenzie creator: Robyn M. Screen creator: Adam G. Clause creator: Benjamin B. Johnson creator: Genevieve G. Mount creator: H Bradley Shaffer creator: Gregory B. Pauly uri: https://doi.org/10.7717/peerj.7444 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lambert et al. title: Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study link: https://peerj.com/articles/7488 last-modified: 2019-08-15 description: BackgroundLactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a “healthy” cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants’ metadata.MethodsThe cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants’ metadata were assessed using GraphPad Prism, R packages and an in-house script.ResultsThe cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p = 0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6–17.2]); p = 0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2–1.9) versus 2.3 (0.6–2.3); p = 0.025) and beta (permutational multivariate analysis of variance (PERMANOVA) pseudo-F statistic =4.31, p = 0.019) diversity compared to non-users. There was no significant difference in the alpha (Shannon indices: 1.0 (0.3–2.2) versus 1.9 (0.3–2.2); p = 0.483) and beta (PERMANOVA pseudo-F statistic = 0.89, p = 0.373) diversity in women with versus without human papillomavirus infection.ConclusionsThe majority of Black women in our study had non-Lactobacillus-dominated cervical microbiota. Additional studies are needed to examine whether such microbiota represent abnormal, intermediate or variant states of health. Lastly, the association of hormonal contraception with L. iners dominance requires further in-depth research to confirm this association, determine its biological mechanism and whether it has a beneficial effect on the cervicovaginal health. creator: Harris Onywera creator: Anna-Lise Williamson creator: Zizipho Z.A. Mbulawa creator: David Coetzee creator: Tracy L. Meiring uri: https://doi.org/10.7717/peerj.7488 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Onywera et al. title: Assessment of the factors influencing primary care physicians’ approach to vaccination of adult risk groups in Istanbul, Turkey link: https://peerj.com/articles/7516 last-modified: 2019-08-15 description: BackgroundWe aimed to assess the factors influencing primary care physicians’ (PCPs) approach to adult vaccination in specific risk groups and evaluate the compliance to adult immunization guidelines.MethodsThis cross-sectional study performed between January 2016 and April 2016 in İstanbul, Turkey. A questionnaire designed to obtain physicians’ demographical data, experience, immunization status, and attitude on prescribing or recommending vaccines for adults in the risk group. Healthy individuals older than 65 and patients suffer from chronic diseases or had splenectomy before are considered as a risk group. The questionnaire was sent via email to a randomly selected group of 1,500 PCPs. The data of 221 physicians who responded emails were recorded for statistical analysis.ResultsOf the 221 participants (123 women, 98 men), the majority were aged 31–40 years. Their vaccination rates were 74.2% for hepatitis B, 54.3% for seasonal influenza, and 47.1% for tetanus. Among participants, the highest recommendation and prescription rate of adult vaccines was recorded in PCPs aged 31–40 years. In addition, PCPs with <10 years occupational experience were found to prescribe adult vaccines more frequently than PCPs with longer occupational experience.ConclusionsPrimary care physicians with lower age and relatively less experience are more intent to prescribe adult vaccines to patients that are in risk groups. This result may be due to increased awareness of adult immunization among PCPs who had more recent medical training. However, many other factors could have caused this difference, including physicians’ approach to primary medical care. creator: Fatma Yılmaz Karadağ creator: Zuhal Aydan Sağlam uri: https://doi.org/10.7717/peerj.7516 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yılmaz Karadağ and Sağlam title: Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species link: https://peerj.com/articles/7531 last-modified: 2019-08-15 description: Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages. creator: Carlos A. Santamaria uri: https://doi.org/10.7717/peerj.7531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Santamaria title: Modeling tree diversity, stand structure and productivity of northern temperate coniferous forests of Mexico link: https://peerj.com/articles/7051 last-modified: 2019-08-14 description: There is increasing evidence complex forest structure and tree diversity correlates positively with the productivity of forest ecosystems. However, there is little quantitative information regarding the effect of these factors on stand productivity of northern temperate coniferous forests of Mexico. This study aimed to test the hypothesis tree diversity and canopy structure positively associates with forest productivity. Parameterization of tree diversity, stand structure and productivity were carried out on dasometric data from 36 permanent sampling plots re-measured in 1982, 1993, and 2004. Statistical analysis of stand parameters tested the null hypothesis. Statistical relationships revealed well-balanced canopy strata and imbalanced diameter structures positively correlated with stand productivity. Tree diversity was also positively linked with stand productivity, but the effect appeared to be most important in the early to intermediate stages of succession. Further research is required to understand the long-term effects of tree diversity and canopy structure on stand productivity. These preliminary observations stress the importance of prescribing silvicultural practices that maintain the three-dimensional structure of stands and diversity of forest canopies that aim to preserve ecosystem function, diversity, and productivity. creator: José Návar uri: https://doi.org/10.7717/peerj.7051 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Návar title: Ontogenetic braincase development in Psittacosaurus lujiatunensis (Dinosauria: Ceratopsia) using micro-computed tomography link: https://peerj.com/articles/7217 last-modified: 2019-08-14 description: Ontogenetic sequences are relatively rare among dinosaurs, with Ceratopsia being one of the better represented clades, and especially among geologically earlier forms, such as Psittacosaurus. Psittacosaurus is a small, bipedal basal ceratopsian abundant in the Lower Cretaceous deposits of Asia, whose cranial and endocranial morphology has been well studied, but only cursory details have been published on the bones surrounding the brain. Using reconstructions created from micro-computed tomography scans of well-preserved skulls from the Barremian–Aptian Yixian Formation, China, we document morphological changes in the braincase of Psittacosaurus lujiatunensis through three growth stages, hatchling, juvenile, and adult, thus providing the first detailed study of ceratopsian braincase morphology through ontogeny. Notable ontogenetic changes in the braincase of P. lujiatunensis include a dramatic relative reduction in size of the supraoccipital, an increase in the lateral expansion of the paroccipital processes and a decrease in the angle between the lateral semicircular canal and the palatal plane. These ontogenetic morphological changes in the braincase relate to expansion of the cranium and brain through growth, as well as reflecting the switch from quadrupedal juveniles to bipedal adults as documented in the changing orientation of the horizontal semicircular canal through ontogeny. Recognition of these patterns in a basal ceratopsian has implications for understanding key events in later ceratopsian evolution, such as the development of the parieto-squamosal frill in derived neoceratopsians. creator: Claire M. Bullar creator: Qi Zhao creator: Michael J. Benton creator: Michael J. Ryan uri: https://doi.org/10.7717/peerj.7217 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bullar et al. title: Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China link: https://peerj.com/articles/7356 last-modified: 2019-08-14 description: BackgroundThe Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years).MethodsThe diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR).ResultsnosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis). creator: Yan Bai creator: Xiying Huang creator: Xiangrui Zhou creator: Quanju Xiang creator: Ke Zhao creator: Xiumei Yu creator: Qiang Chen creator: Hao Jiang creator: Tashi Nyima creator: Xue Gao creator: Yunfu Gu uri: https://doi.org/10.7717/peerj.7356 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bai et al. title: Application of the Ostrom framework in the analysis of a social-ecological system with multiple resources in a marine protected area link: https://peerj.com/articles/7374 last-modified: 2019-08-14 description: The framework proposed by Ostrom (2009) has become one of the most utilized tools to address the complexity of social-ecological systems. Most cases use this framework to analyze the systems from the perspective of a single resource unit. However, the livelihoods in several coastal communities are diverse, so that the users interact with multiple common-pool resources, which makes their analysis difficult. In this sense, it is important to identify the key elements of management to achieve the sustainable use of the resources. In this study, we were able to do this in a coastal community where commercial fishing, ecotourism, and recreational fishing coexist. The system of interest, located in the state of Quintana Roo, Mexico, was subdivided by resource type using a multi-method approach to data collection including surveys, interviews, and records review. A conceptual map was developed that shows how the second-tier variables are integrated through the governance and actors with the biophysical system. The actors involved in lobster fishing achieved a more complex governance system, followed by the ecotourism and recreational fishing; the complexity of the governance was related with the equity level of the actors. The analysis revealed the research gaps to develop management strategies and improve the sustainability of the system. creator: Leopoldo E. Palomo creator: Alvaro Hernández-Flores uri: https://doi.org/10.7717/peerj.7374 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Palomo and Hernández-Flores title: Latitudinal variation in phlorotannin contents from Southwestern Atlantic brown seaweeds link: https://peerj.com/articles/7379 last-modified: 2019-08-14 description: Phlorotannins are primary and/or secondary metabolites found exclusively in brown seaweeds, but their geographic distribution and abundance dynamic are not very well understood. In this study we evaluated the phlorotannin concentrations among and within-species of brown seaweeds in a broad latitudinal context (range of 21°) along the Brazilian coast (Southwestern Atlantic), using the Folin-Ciocalteau colorimetric method. In almost all species (16 out of 17) very low phlorotannin concentrations were found (<2.0%, dry weight for the species), confirming reports of the typical amounts of these chemicals in tropical brown seaweeds, but with significantly distinct values among seven different and probably highly structured populations. In all 17 seaweed species (but a total of 25 populations) analyzed there were significant differences on the amount of phlorotannins in different individuals (t-test, p < 0.01), with coefficients of variation (CV) ranging from 5.2% to 65.3%. The CV, but not the total amount of phlorotannins, was significantly correlated with latitude, and higher values of both these variables were found in brown seaweeds collected at higher latitudes. These results suggest that brown seaweeds from higher latitudes can produce phlorotannins in a wider range of amounts and probably as response to environmental variables or stimuli, compared to low latitude algae. creator: Glaucia Ank creator: Bernardo Antônio Perez da Gama creator: Renato Crespo Pereira uri: https://doi.org/10.7717/peerj.7379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ank et al. title: Borneo coral reefs subject to high sediment loads show evidence of resilience to various environmental stressors link: https://peerj.com/articles/7382 last-modified: 2019-08-14 description: For reefs in South East Asia the synergistic effects of rapid land development, insufficient environmental policies and a lack of enforcement has led to poor water quality and compromised coral health from increased sediment and pollution. Those inshore turbid coral reefs, subject to significant sediment inputs, may also inherit some resilience to the effects of thermal stress and coral bleaching. We studied the inshore turbid reefs near Miri, in northwest Borneo through a comprehensive assessment of coral cover and health in addition to quantifying sediment-related parameters. Although Miri’s Reefs had comparatively low coral species diversity, dominated by massive and encrusting forms of Diploastrea, Porites, Montipora, Favites, Dipsastrea and Pachyseris, they were characterized by a healthy cover ranging from 22 to 39%. We found a strong inshore to offshore gradient in hard coral cover, diversity and community composition as a direct result of spatial differences in sediment at distances <10 km. As well as distance to shore, we included other environmental variables like reef depth and sediment trap accumulation and particle size that explained 62.5% of variation in benthic composition among sites. Miri’s reefs showed little evidence of coral disease and relatively low prevalence of compromised health signs including bleaching (6.7%), bioerosion (6.6%), pigmentation response (2.2%), scars (1.1%) and excessive mucus production (0.5%). Tagged colonies of Diploastrea and Pachyseris suffering partial bleaching in 2016 had fully (90–100%) recovered the following year. There were, however, seasonal differences in bioerosion rates, which increased five-fold after the 2017 wet season. Differences in measures of coral physiology, like that of symbiont density and chlorophyll a for Montipora, Pachyseris and Acropora, were not detected among sites. We conclude that Miri’s reefs may be in a temporally stable state given minimal recently dead coral and a limited decline in coral cover over the last two decades. This study provides further evidence that turbid coral reefs exposed to seasonally elevated sediment loads can exhibit relatively high coral cover and be resilient to disease and elevated sea surface temperatures. creator: Nicola Browne creator: Christina Braoun creator: Jennifer McIlwain creator: Ramasamy Nagarajan creator: Jens Zinke uri: https://doi.org/10.7717/peerj.7382 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Browne et al. title: Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence–structure–function analysis link: https://peerj.com/articles/7504 last-modified: 2019-08-14 description: BackgroundNon-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences—and counting—have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues. Deciphering their functions means collecting and analyzing a variety of data from gene sequence to protein structure, from cellular localization to the physiological role. As a huge and growing number of new protein sequences are available nowadays, extracting meaningful knowledge from sequence–structure–function relationships calls for the development of new tools and approaches. As nsLTPs show high evolutionary divergence, but a conserved common right handed superhelix structural fold, and as they are involved in a large number of key roles in plant development and defense, they are a stimulating case study for validating such an approach.MethodsIn this study, we comprehensively investigated 797 nsLTP protein sequences, including a phylogenetic analysis on canonical protein sequences, three-dimensional structure modeling and functional annotation using several well-established bioinformatics programs. Additionally, two integrative methodologies using original tools were developed. The first was a new method for the detection of (i) conserved amino acid residues involved in structure stabilization and (ii) residues potentially involved in ligand interaction. The second was a structure–function classification based on the evolutionary trace display method using a new tree visualization interface. We also present a new tool for visualizing phylogenetic trees.ResultsFollowing this new protocol, an updated classification of the nsLTP superfamily was established and a new functional hypothesis for key residues is suggested. Lastly, this work allows a better representation of the diversity of plant nsLTPs in terms of sequence, structure and function. creator: Cécile Fleury creator: Jérôme Gracy creator: Marie-Françoise Gautier creator: Jean-Luc Pons creator: Jean-François Dufayard creator: Gilles Labesse creator: Manuel Ruiz creator: Frédéric de Lamotte uri: https://doi.org/10.7717/peerj.7504 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fleury et al. title: Conspicuous colours reduce predation rates in fossorial uropeltid snakes link: https://peerj.com/articles/7508 last-modified: 2019-08-14 description: Uropeltid snakes (Family Uropeltidae) are non-venomous, fossorial snakes that are found above ground occasionally, during which time they are exposed to predation. Many species are brightly coloured, mostly on the ventral surface, but these colours are expected to have no function below the ground. Observations have shown that the cephalic resemblance (resemblance to heads) of uropeltid tails may direct attacks of predators towards the hardened tails, thereby potentially increasing handling times for predators. Experiments have also shown that predators learn to avoid prey that are non-toxic and palatable but are difficult to capture, hard to process or require long handling time when such prey advertise their unprofitability through conspicuous colours. We here postulate that uropeltid snakes use their bright colours to signal long handling times associated with attack deflection to the tails, thereby securing reduced predation from predators that can learn to associate colour with handling time. Captive chicken experiments with dough models mimicking uropeltids indicate that attacks were more common on the tail than on the head. Field experiments with uropeltid clay models show that the conspicuous colours of these snakes decrease predation rates compared to cryptic models, but a novel conspicuous colour did not confer such a benefit. Overall, our experiments provide support for our hypothesis that the conspicuous colours of these snakes reduce predation, possibly because these colours advertise unprofitability due to long handling times. creator: Vivek Philip Cyriac creator: Ullasa Kodandaramaiah uri: https://doi.org/10.7717/peerj.7508 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cyriac and Kodandaramaiah title: Dynamics of a methanol-fed marine denitrifying biofilm: 1-Impact of environmental changes on the denitrification and the co-occurrence of Methylophaga nitratireducenticrescens and Hyphomicrobium nitrativorans link: https://peerj.com/articles/7497 last-modified: 2019-08-13 description: BackgroundThe biofilm of a methanol-fed denitrification system that treated a marine effluent is composed of multi-species microorganisms, among which Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities. Here, we report the capacity of the denitrifying biofilm to sustain environmental changes, and the impact of these changes on the co-occurrence of H. nitrativorans and M. nitratireducenticrescens.MethodsIn a first set of assays, the original biofilm (OB) was cultivated in an artificial seawater (ASW) medium under anoxic conditions to colonize new carriers. The new formed biofilm was then subjected to short exposures (1–5 days) of a range of NaCl, methanol, nitrate (NO3−) and nitrite (NO2−) concentrations, and to different pHs and temperatures. In a second set of assays, the OB was cultivated in ASW medium for five weeks with (i) a range of NaCl concentrations, (ii) four combinations of NO3−/methanol concentrations and temperatures, (iii) NO2−, and (iv) under oxic conditions. Finally, the OB was cultivated for five weeks in the commercial Instant Ocean (IO) seawater. The growth of the biofilm and the dynamics of NO3− and NO2− were determined. The levels of M. nitratireducenticrescens and H. nitrativorans were measured by qPCR.ResultsIn the first set of assays, the biofilm cultures had the capacity to sustain denitrifying activities in most of the tested conditions. Inhibition occurred when they were exposed to high pH (10) or to high methanol concentration (1.5%). In the second set of assays, the highest specific denitrification rates occurred with the biofilm cultures cultivated at 64.3 mM NO3− and 0.45% methanol, and at 30 °C. Poor biofilm development occurred with the biofilm cultures cultivated at 5% and 8% NaCl. In all biofilm cultures cultivated in ASW at 2.75% NaCl, H. nitrativorans strain NL23 decreased by three orders of magnitude in concentrations compared to that found in OB. This decrease coincided with the increase of the same magnitude of a subpopulation of M. nitratireducenticrescens (strain GP59 as representative). In the biofilm cultures cultivated at low NaCl concentrations (0% to 1.0%), persistence of H. nitrativorans strain NL23 was observed, with the gradual increase in concentrations of M. nitratireducenticrescens strain GP59. High levels of H. nitrativorans strain NL23 were found in the IO biofilm cultures. The concentrations of M. nitratireducenticrescens strain JAM1 were lower in most of the biofilms cultures than in OB.ConclusionsThese results demonstrate the plasticity of the marine methylotrophic denitrifying biofilm in adapting to different environmental changes. The NaCl concentration is a crucial factor in the dynamics of H. nitrativorans strain NL23, for which growth was impaired above 1% NaCl in the ASW-based biofilm cultures in favor of M. nitratireducenticrescens strain GP59. creator: Geneviève Payette creator: Valérie Geoffroy creator: Christine Martineau creator: Richard Villemur uri: https://doi.org/10.7717/peerj.7497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Payette et al. title: Grazing effects on woody and herbaceous plant biodiversity on a limestone mountain in northern Tunisia link: https://peerj.com/articles/7296 last-modified: 2019-08-13 description: Mediterranean maquis vegetation is highly biodiverse, but widespread grazing poses a challenge for management and conservation. We sampled woody and herbaceous plants separately on a limestone mountain with strong mesic-xeric gradients in Tunisia’s Parc National de L’Ichkeul, assessed grazing pressure (on a scale of 1–3), and asked whether grazing had a significant effect on plant compositional abundance before and after controlling for environmental covariates. Sites on the more mesic lakeside face of the mountain were most compositionally unique, and forbs contributed most to the herbaceous beta-diversity on the mountain. We used variance partitioning to separate the collective and individual effects of the abiotic environment, grazing, human activity, and space on herbaceous and woody beta-diversity. However, the individual effect of grazing on overall plant community composition was confounded with space, due to the spatially autocorrelated grazing pressure on the mountain. Importantly, we found that herbaceous and woody communities responded differently to increasing levels of grazing intensity: herbaceous beta-diversity was highest between sites with no grazing pressure, while woody beta-diversity peaked under light grazing. Herbaceous community composition was sensitive to any intensity of grazing pressure, and biotic homogenization occured under moderate-to-high grazing pressure. On the other hand, woody community composition remained relatively similar under no to light grazing pressure, but differed under moderate-to-heavy grazing. Using a one-way permutational analysis of variance analysis, we showed that grazing had a significant effect when controlling for abiotic and spatial covariates. Our findings offer insight into the effects of grazing on maquis vegetation at Jebel Ichkeul, acting as a microcosm of similar conservation and management issues elsewhere in the Mediterranean. We suggest that a combination of monitoring and carefully controlled grazing may enhance plant diversity and maintain the region’s biodiverse maquis vegetation, potentially maintaining a key climate refugium for vulnerable endemic species. Importantly, our study provides a useful baseline of the plant assemblages at Jebel Ichkeul with which to compare future vegetation changes. creator: David Anthony Kirk creator: Katherine Hébert creator: Frank Barrie Goldsmith uri: https://doi.org/10.7717/peerj.7296 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kirk et al. title: Mitochondrial DNA in human identification: a review link: https://peerj.com/articles/7314 last-modified: 2019-08-13 description: Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics. creator: António Amorim creator: Teresa Fernandes creator: Nuno Taveira uri: https://doi.org/10.7717/peerj.7314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Amorim et al. title: Developing sport expertise in youth sport: a decision training program in basketball link: https://peerj.com/articles/7392 last-modified: 2019-08-13 description: BackgroundThis study has analyzed the impact of applying a decision training program, in which video-feedback and questioning were used, on the development of decision-making, skill execution and procedural knowledge in basketball players.MethodsParticipants were eleven male players aged between 12 and 13 years old (Mage = 12.75, SDage = .65), who were assigned to an experimental or control group within a pre-test/intervention test/retention test quasi-experimental design. The decision training program was applied over 11 weeks. Throughout this intervention, players had to analyze the causes and reasons for the decision made, using video feedback and questioning to this end. Decision-making and skill execution variables were analyzed using the French & Thomas (1987) observation instrument, while a validated questionnaire was used to assess procedural knowledge in basketball.ResultsThe results reported that sport expertise improved in players from the experimental group, who had significantly higher intervention test scores for successful decisions and skill executions when compared to players in the control group. In the intra-group analysis, the experimental group significantly improved in the intervention test compared to the pre-test, in terms of some of the variables of decision-making, skill execution and procedural knowledge.DiscussionThese results reinforce the idea of including cognitive tools in training, such as video-feedback and questioning, to improve sport expertise in players’ formative stages, and presumably to improve their performance whilst maintaining decision training throughout time. creator: Alexander Gil-Arias creator: Luis Garcia-Gonzalez creator: Fernando Del Villar Alvarez creator: Damián Iglesias Gallego uri: https://doi.org/10.7717/peerj.7392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gil-Arias et al. title: The effects of detraining and retraining periods on fat-mass and fat-free mass in elite male soccer players link: https://peerj.com/articles/7466 last-modified: 2019-08-13 description: The aim of the study was to examine the effects of a detraining period (DTP) (i.e., off-season) with an individually prescribed training program, and a retraining period (RTP) (i.e., pre-season) combining soccer and flywheel-based strength training on fat-free mass (FFM) and fat-mass (FM) in 10 elite professional male soccer players. The present study used a controlled repeated-measures research design to investigate the changes in FFM and FM using dual-energy X-ray absorptiometry. Whole body %FM increased (effect size (ES) = 0.87 ± 0.46) and FFM reduced after DTP (ES = −0.30 ± 0.19), returning to values comparable to the end of the previous season after RTP. At regional levels, arms, legs, and trunk %FM increased (ES = from 0.42 to 1.29) while trunk-FFM was reduced (ES = −0.40 ± 0.26) after DTP, returning to the values observed at the end of the previous season after RTP. Legs-FFM did not change after DTP, with a substantial increase after RTP in comparison with pre-season values (ES = 0.34 ± 0.29 and 0.53 ± 0.36 for the right and left leg, respectively). Despite the small sample size of the present study, the findings indicate that elite soccer players can be allowed 2 weeks of rest during a five-week DTP, since the changes in %FM and FFM were relatively small, and FM and FFM returned to the optimal initial values for competition after the proposed RTP during the pre-season. creator: Luis Suarez-Arrones creator: Pilar Lara-Lopez creator: Rafael Maldonado creator: Nacho Torreno creator: Moises De Hoyo creator: Fabio Yuzo Nakamura creator: Valter Di Salvo creator: Alberto Mendez-Villanueva uri: https://doi.org/10.7717/peerj.7466 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Suarez-Arrones et al. title: Dynamics of a methanol-fed marine denitrifying biofilm: 2—impact of environmental changes on the microbial community link: https://peerj.com/articles/7467 last-modified: 2019-08-13 description: BackgroundThe biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of H. nitrativorans strain NL23 and M. nitratireducenticrescens in the biofilm cultures. Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm.MethodsThe original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures. The OB was also cultivated in the commercial Instant Ocean seawater (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences. Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans strain NL23 and M. nitratireducenticrescens strain GP59.ResultsHigh proportions of M. nitratireducenticrescens occurred in the biofilm cultures. H. nitrativorans strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl. It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0–1% NaCl and in the IO biofilm cultures. Denitrifying bacterial isolates affiliated to Marinobacter spp. and Paracoccus spp. were isolated. Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the Stappia spp. were metabolically active in the biofilm cultures.ConclusionsThese results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures. Up regulation of the denitrification genes of M. nitratireducenticrescens strain GP59 and H. nitrativorans strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm. Other denitrifying heterotrophic bacteria are present in low proportions, suggesting that the biofilm has the potential to adapt to heterotrophic, non-methylotrophic environments. creator: Richard Villemur creator: Geneviève Payette creator: Valérie Geoffroy creator: Florian Mauffrey creator: Christine Martineau uri: https://doi.org/10.7717/peerj.7467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Villemur et al. title: Vulnerability of small-scale fishers to benzene exposure and the current knowledge gap on benzene-exposure in Brazilian fishers link: https://peerj.com/articles/7483 last-modified: 2019-08-13 description: Fishers are a particularly vulnerable population, chronically exposed to many stresses, injuries and health conditions directly linked to their fishing activities. This includes benzene exposure through gasoline and diesel exhaust fumes. Benzene is a known carcinogen, and has been assessed in many worker groups, but reports on fisher benzene exposure are extremely scarce in the literature. This paper discusses benzene exposure in small-scale fishers and reflects on the current knowledge gap on benzene-exposure in Brazilian fishers. creator: Rachel Ann Hauser-Davis uri: https://doi.org/10.7717/peerj.7483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hauser-Davis title: The effect of mangrove restoration on avian assemblages of a coastal lagoon in southern Mexico link: https://peerj.com/articles/7493 last-modified: 2019-08-13 description: BackgroundMangrove forests provide many ecosystem services, including the provision of habitat that supports avian biodiversity. However, hurricanes can knock down trees, alter hydrologic connectivity, and affect avian habitat. In 1995, Hurricanes Opal and Roxanne destroyed approximately 1,700 ha of mangrove forest in Laguna de Términos, Mexico. Since then, hydrological restoration has been implemented to protect the mangrove forest and its biodiversity.MethodsSince avian communities are often considered biological indicators of ecosystem quality, avian diversity and species relative abundance were evaluated as indicators of mangrove restoration success by comparing undisturbed mangrove patches with those affected by the hurricanes. Using bird surveys, similarity analyses, and generalized linear models, we evaluated the effects of water quality variables and forest structure on the relative abundance and diversity of the avian community in disturbed, restored, and undisturbed mangrove patches.ResultsHigher bird species richness and relative abundances were found in disturbed and restored sites compared to the undisturbed site. After restoration, values of frequency of flooding, water temperature, tree density, and the number of tree species were more similar to that of the undisturbed site than to the values of the disturbed one. Such variables influenced the relative abundance of bird guilds in the different habitat conditions. Furthermore, some insectivorous bird species, such as the Yellow Warbler and Tropical Kingbird, were found to be similarly abundant in both undisturbed and restored sites, but absent or very low in occurrence at the disturbed site.ConclusionsCollectively, our results strongly suggest that hydrologic restoration helps to enhance niche availability for different bird guilds, including water and canopy bird species. Our work can help inform management strategies that benefit avian communities in mangrove forests and wetland systems. creator: Julio Cesar Canales-Delgadillo creator: Rosela Perez-Ceballos creator: Mario Arturo Zaldivar-Jimenez creator: Martin Merino-Ibarra creator: Gabriela Cardoza creator: Jose-Gilberto Cardoso-Mohedano uri: https://doi.org/10.7717/peerj.7493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Canales-Delgadillo et al. title: Identification and functional analysis of LecRLK genes in Taxodium ‘Zhongshanshan’ link: https://peerj.com/articles/7498 last-modified: 2019-08-13 description: BackgroundLectin receptor-like protein kinases (LecRLKs) can transform external stimuli into intracellular signals and play important regulatory roles in plant development and response to environmental stressors. However, research on the LecRLK gene family of conifers has seldom been reported.MethodsPutative LecRLK genes were identified in the transcriptome of Taxodium ‘Zhongshanshan’. The classification, domain structures, subcellular localization prediction, and expression patterns of LecRLK genes, as well as co-expressed genes, were analyzed using bioinformatics methods. Fifteen representative genes were further selected for qRT-PCR analysis in six tissues and under five different environmental stressor conditions.ResultsIn total, 297 LecRLK genes were identified, including 155 G-type, 140 L-type, and 2 C-type. According to the classification, G-type and L-type LecRLK genes both can be organized into seven groups. The domain architecture of G-type proteins were more complex compared with that of L- and C-type proteins. Conservative motifs were found in G-type and L-type diverse lectin domains. Prediction and transient expression experiments to determine subcellular localization showed that LecRLKs were mainly concentrated in the cell membrane system, and some members were located at multiple sites at the same time. RNA-seq-based transcriptomics analysis suggested functional redundancy and divergence within each group. Unigenes co-expressed with LecRLKs in the transcriptome were found to be enriched in pathways related to signal transduction and environmental adaptation. Furthermore, qRT-PCR analysis of representative genes showed evidence of functional divergence between different groups.ConclusionsThis is the first study to conduct an identification and expression analysis of the LecRLK gene family in Taxodium. These results provide a basis for future studies on the evolution and function of this important gene family in Taxodium. creator: Jinbo Guo creator: Hao Duan creator: Lei Xuan creator: Ziyang Wang creator: Jianfeng Hua creator: Chaoguang Yu creator: Yunlong Yin creator: Mingzhi Li creator: Ying Yang uri: https://doi.org/10.7717/peerj.7498 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guo et al. title: Evaluation of the socially evaluated cold-pressor group test (SECPT-G) in the general population link: https://peerj.com/articles/7521 last-modified: 2019-08-13 description: BackgroundIn stress research, economic instruments for introducing acute stress responses are needed. In this study, we investigated whether the socially evaluated cold-pressor group test (SECPT-G) induces salivary alpha-amylase (sAA) and/or cortisol responses in the general population and whether this is associated with anthropometric, experimental, and lifestyle factors.MethodsA sample of 91 participants from the general population was recruited. Salivary cortisol and sAA levels were assessed prior to (t0), immediately after (t1), and 10 min after the SECPT-G (t2).ResultsA robust cortisol increase was found immediately after the SECPT-G, which further increased between t1 and t2. This was independent of most of the control variables. However, men showed a trend toward higher cortisol increases than women (p = 0.005). No sAA responses were found at all. However, sAA levels were dependent on measurement time point with highest levels between 9 pm and 9:30 pm. Participants who immersed their hands into the ice water for the maximally allowed time of 3 min showed higher sAA levels at all time points than participants who removed their hands from the water earlier.ConclusionsWe conclude that the SECPT-G is a good means of an acute stress test when cortisol—but not necessarily sAA—responses are intended. creator: Linda Becker creator: Ursula Schade creator: Nicolas Rohleder uri: https://doi.org/10.7717/peerj.7521 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Becker et al. title: No evidence for negative impacts of acute sulfoxaflor exposure on bee olfactory conditioning or working memory link: https://peerj.com/articles/7208 last-modified: 2019-08-12 description: Systemic insecticides such as neonicotinoids and sulfoximines can be present in the nectar and pollen of treated crops, through which foraging bees can become acutely exposed. Research has shown that acute, field realistic dosages of neonicotinoids can negatively influence bee learning and memory, with potential consequences for bee behaviour. As legislative reassessment of neonicotinoid use occurs globally, there is an urgent need to understand the potential risk of other systemic insecticides. Sulfoxaflor, the first branded sulfoximine-based insecticide, has the same mode of action as neonicotinoids, and may potentially replace them over large geographical ranges. Here we assessed the impact of acute sulfoxaflor exposure on performance in two paradigms that have previously been used to illustrate negative impacts of neonicotinoid pesticides on bee learning and memory. We assayed whether acute sulfoxaflor exposure influences (a) olfactory conditioning performance in both bumblebees (Bombus terrestris) and honeybees (Apis mellifera), using a proboscis extension reflex assay, and (b) working memory performance of bumblebees, using a radial-arm maze. We found no evidence to suggest that sulfoxaflor influenced performance in either paradigm. Our results suggest that despite a shared mode of action between sulfoxaflor and neonicotinoid-based insecticides, widely-documented effects of neonicotinoids on bee cognition may not be observed with sulfoxaflor, at least at acute exposure regimes. creator: Harry Siviter creator: Alfie Scott creator: Grégoire Pasquier creator: Christopher D. Pull creator: Mark J.F. Brown creator: Ellouise Leadbeater uri: https://doi.org/10.7717/peerj.7208 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Siviter et al. title: Pollen report: quantitative review of pollen crude protein concentrations offered by bee pollinated flowers in agricultural and non-agricultural landscapes link: https://peerj.com/articles/7394 last-modified: 2019-08-12 description: To ease nutritional stress on managed as well as native bee populations in agricultural habitats, agro-environmental protection schemes aim to provide alternative nutritional resources for bee populations during times of need. However, such efforts have so far focused on quantity (supply of flowering plants) and timing (flower-scarce periods) while ignoring the quality of the two main bee relevant flower-derived resources (pollen and nectar). As a first step to address this issue we have compiled one geographically explicit dataset focusing on pollen crude protein concentration, one measurement traditionally associated with pollen quality for bees. We attempt to provide a robust baseline for protein levels bees can collect in- (crop and weed species) and off-field (wild plants) in agricultural habitats around the globe. Using this dataset we identify crops which provide sub-optimal pollen resources in terms of crude protein concentration for bees and suggest potential plant genera that could serve as alternative resources for protein. This information could be used by scientists, regulators, bee keepers, NGOs and farmers to compare the pollen quality currently offered in alternative foraging habitats and identify opportunities to improve them. In the long run, we hope that additional markers of pollen quality will be added to the database in order to get a more complete picture of flower resources offered to bees and foster a data-informed discussion about pollinator conservation in modern agricultural landscapes. creator: Tobias Pamminger creator: Roland Becker creator: Sophie Himmelreich creator: Christof W. Schneider creator: Matthias Bergtold uri: https://doi.org/10.7717/peerj.7394 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pamminger et al. title: A new species of terrestrial frog of the genus Noblella Barbour, 1930 (Amphibia: Strabomantidae) from the Llanganates-Sangay Ecological Corridor, Tungurahua, Ecuador link: https://peerj.com/articles/7405 last-modified: 2019-08-12 description: We describe a new species of terrestrial frog of the genus Noblella from the eastern versants of the Ecuadorian Andes in the upper Pastaza watershed. Noblella naturetrekii sp. n. differs from its Ecuadorian congeners by the presence of a differentiated tympanic membrane and a weakly defined tympanic annulus, and eyelids with rounded tubercles. In addition, the new species is characterized by its blackish–dark brown ventral coloration scattered with little white dots and the absence of papillae at the tip of the fingers and toes. We provide a detailed description of the call and osteology of the new species. Finally, we present the most complete phylogeny of the genus, which confirms that Noblella is a non-monophyletic group. creator: Juan Pablo Reyes-Puig creator: Carolina Reyes-Puig creator: Santiago Ron creator: Jhael A. Ortega creator: Juan M. Guayasamin creator: Mindee Goodrum creator: Fausto Recalde creator: Jose J. Vieira creator: Claudia Koch creator: Mario H. Yánez-Muñoz uri: https://doi.org/10.7717/peerj.7405 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Reyes-Puig et al. title: Phosphorylation/dephosphorylation response to light stimuli of Symbiodinium proteins: specific light-induced dephosphorylation of an HSP-like 75 kDa protein from S. microadriaticum link: https://peerj.com/articles/7406 last-modified: 2019-08-12 description: BackgroundSome genera of the family Symbiodiniaceae establish mutualistic endosymbioses with various marine invertebrates, with coral being the most important ecologically. Little is known about the biochemical communication of this association and the perception and translation of signals from the environment in the symbiont. However, specific phosphorylation/dephosphorylation processes are fundamental for the transmission of external signals to activate physiological responses. In this work, we searched phosphorylatable proteins in amino acids of Ser, Thr and Tyr from three species of the family Symbiodiniaceae, Symbiodinium kawagutii, Symbiodinium sp. Mf11 and Symbiodinium microadriaticum.MethodsWe used specific antibodies to the phosphorylated aminoacids pSer, pThr and pTyr to identify proteins harboring them in total extracts from three species of Symbiodinium in culture. Extractions were carried out on logarithmic phase growing cultures under a 12 h light/dark photoperiod. Various light/dark, nutritional and other stimuli were applied to the cultures prior to the extractions, and proteins were subjected to SDS-PAGE and western immunoblotting. Partial peptide sequencing was carried out by MALDI-TOF on specific protein spots separated by 2D electrophoresis.ResultsAt 4 h of the light cycle, several Thr-phosphorylated proteins were consistently detected in the three species suggesting a genus-dependent expression; however, most Ser- and Tyr-phosphorylated proteins were species-specific. Analysis of protein extracts of S. microadriaticum cultures demonstrated that the level of phosphorylation of two Thr-phosphorylated proteins with molecular weights of 43 and 75 kDa, responded inversely to a light stimulus. The 43 kDa protein, originally weakly Thr-phosphorylated when the cells were previously adapted to their 12 h dark cycle, underwent an increase in Thr phosphorylation when stimulated for 30 min with light. On the other hand, the 75 kDa protein, which was significantly Thr-phosphorylated in the dark, underwent dephosphorylation in Thr after 30 min of the light stimulus. The phosphorylation response of the 43 kDa protein only occurred in S. microadriaticum, whereas the dephosphorylation of the 75 kDa protein occurred in the three species studied suggesting a general response. The 75 kDa protein was separated on 2D gels as two isoforms and the sequenced spots corresponded to a BiP-like protein of the HSP70 protein family. The presence of differential phosphorylations on these proteins after a light stimulus imply important light-regulated physiological processes in these organisms. creator: Raúl E. Castillo-Medina creator: Tania Islas-Flores creator: Marco A. Villanueva uri: https://doi.org/10.7717/peerj.7406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Castillo-Medina et al. title: An enigmatic decoupling between heat stress and coral bleaching on the Great Barrier Reef link: https://peerj.com/articles/7473 last-modified: 2019-08-12 description: Ocean warming threatens the functioning of coral reef ecosystems by inducing mass coral bleaching and mortality events. The link between temperature and coral bleaching is now well-established based on observations that mass bleaching events usually occur when seawater temperatures are anomalously high. However, times of high heat stress but without coral bleaching are equally important because they can inform an understanding of factors that regulate temperature-induced bleaching. Here, we investigate the absence of mass coral bleaching on the Great Barrier Reef (GBR) during austral summer 2004. Using four gridded sea surface temperature data products, validated with in situ temperature loggers, we demonstrate that the summer of 2004 was among the warmest summers of the satellite era (1982–2017) on the GBR. At least half of the GBR experienced temperatures that were high enough to initiate bleaching in other years, yet mass bleaching was not reported during 2004. The absence of bleaching is not fully explained by wind speed or cloud cover. Rather, 2004 is clearly differentiated from bleaching years by the slow speed of the East Australian Current (EAC) offshore of the GBR. An anomalously slow EAC during summer 2004 may have dampened the upwelling of nutrient-rich waters onto the GBR shelf, potentially mitigating bleaching due to the lower susceptibility of corals to heat stress in low-nutrient conditions. Although other factors such as irradiance or acclimatization may have played a role in the absence of mass bleaching, 2004 remains a key case study for demonstrating the dynamic nature of coral responses to marine heatwaves. creator: Thomas M. DeCarlo creator: Hugo B. Harrison uri: https://doi.org/10.7717/peerj.7473 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 DeCarlo and Harrison title: Efficient virus-induced gene silencing in Hibiscus hamabo Sieb. et Zucc. using tobacco rattle virus link: https://peerj.com/articles/7505 last-modified: 2019-08-12 description: BackgroundHibiscus hamabo Sieb. et Zucc. is a semi-mangrove plant used for the ecological restoration of saline-alkali land, coastal afforestation and urban landscaping. The genetic transformation H. hamabo is currently inefficient and laborious, restricting gene functional studies on this species. In plants, virus-induced gene silencing provides a pathway to rapidly and effectively create targeted gene knockouts for gene functional studies.MethodsIn this study, we tested the efficiency of a tobacco rattle virus vector in silencing the cloroplastos alterados 1 (CLA1) gene through agroinfiltration.ResultsThe leaves of H. hamabo showed white streaks typical of CLA1 gene silencing three weeks after agroinfiltration. In agroinfiltrated H. hamabo plants, the CLA1 expression levels in leaves with white streaks were all significantly lower than those in leaves from mock-infected and control plants.ConclusionsThe system presented here can efficiently silence genes in H. hamabo and may be a powerful tool for large-scale reverse-genetic analyses of gene functions in H. hamabo. creator: Zhiquan Wang creator: Xiaoyang Xu creator: Longjie Ni creator: Jinbo Guo creator: Chunsun Gu uri: https://doi.org/10.7717/peerj.7505 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Transplantation of adipose-derived stem cells overexpressing inducible nitric oxide synthase ameliorates diabetes mellitus-induced erectile dysfunction in rats link: https://peerj.com/articles/7507 last-modified: 2019-08-12 description: BackgroundErectile dysfunction is a major complication of diabetes mellitus. Adipose-derived stem cells (ADSCs) have attracted much attention as a promising tool for the treatment of diabetes mellitus-induced erectile dysfunction (DMED). Inducible nitric oxide synthase (iNOS) plays an important role in protecting penile tissues from fibrosis. The aim of this study was to determine the efficacy of ADSCs overexpressing iNOS on DMED in rats.MethodsADSCs were isolated and infected with adenovirus overexpressing iNOS (named as ADSCs-iNOS). The expression of iNOS was detected using western blot analysis and real-time PCR. Rats were randomly assigned into five groups: control group, DMED group, ADSCs group, ADSCs-EGFP group and ADSCs-iNOS group. 5 × 105 cells were given once via the intracorporal route. Two weeks after treatment, erectile function was assessed by electrical stimulation of the cavernous nerve. Penile tissues were obtained and evaluated at histology level.ResultsWe found that ADSCs-iNOS had significantly higher expression of iNOS at mRNA and protein levels and generated more nitric oxide (NO). ADSCs-iNOS reduced collagen I and collagen IV expression of corpus cavernosum smooth muscle cells (CCSMCs) in cell co-culture model. Transforming growth factor-β1 expression in CCSMCs reduced following co-culture with ADSCs-iNOS. Injection of ADSCs-iNOS significantly ameliorated DMED in rats and decreased collagen/smooth muscle cell ratio of penile tissues. Moreover, elevated NO and cyclic guanosine monophosphate concentrations were detected in penile tissues of ADSCs-iNOS group.ConclusionTaken together, ADSCs-iNOS significantly improved erectile function of DMED rats. The therapeutic effect may be achieved by increased NO generation and the suppression of collagen I and collagen IV expression in the CCSMCs to decrease penile fibrosis. creator: Yan Zhang creator: Jun Yang creator: Li Zhuan creator: Guanghui Zang creator: Tao Wang creator: Jihong Liu uri: https://doi.org/10.7717/peerj.7507 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: The effects of high versus low talker variability and individual aptitude on phonetic training of Mandarin lexical tones link: https://peerj.com/articles/7191 last-modified: 2019-08-09 description: High variability (HV) training has been found to be more effective than low variability (LV) training when learning various non-native phonetic contrasts. However, little research has considered whether this applies to the learning of tone contrasts. The only two relevant studies suggested that the effect of HV training depends on the perceptual aptitude of participants (Perrachione et al., 2011; Sadakata & McQueen, 2014). The present study extends these findings by examining the interaction between individual aptitude and input variability using natural, meaningful second language input (both previous studies used pseudowords). A total of 60 English speakers took part in an eight session phonetic training paradigm. They were assigned to high/low/high-blocked variability training groups and learned real Mandarin tones and words. Individual aptitude was measured following previous work. Learning was measured using one discrimination task, one identification task and two production tasks. All tasks assessed generalization. All groups improved in both the production and perception of tones which transferred to untrained voices and items, demonstrating the effectiveness of training despite the increased complexity compared with previous research. Although the LV group exhibited an advantage with the training stimuli, there was no evidence for a benefit of high-variability in any of the tests of generalisation. Moreover, although aptitude significantly predicted performance in discrimination, identification and training tasks, no interaction between individual aptitude and variability was revealed. Additional Bayes Factor analyses indicated substantial evidence for the null for the hypotheses of a benefit of high-variability in generalisation, however the evidence regarding the interaction was ambiguous. We discuss these results in light of previous findings. creator: Hanyu Dong creator: Meghan Clayards creator: Helen Brown creator: Elizabeth Wonnacott uri: https://doi.org/10.7717/peerj.7191 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dong et al. title: Taxonomic revision of the genus Cranichis (Orchidaceae, Cranichideae) in Colombia link: https://peerj.com/articles/7385 last-modified: 2019-08-09 description: The geographical range of the orchid genus Cranichis extends from USA, Central America, and the Caribbean to Bolivia and Argentina—with the greatest diversity observed in the Andean region. This taxon embraces herbs with the scape and basal leaves developing from a single, terminal bud and having the scape enclosed in several sheaths. The small, non-resupinate, flowers are arranged in a racemose inflorescence. The petals and lip are free from the column part and their gynostemium is short and massive. In this paper, the synopsis of Cranichis in Colombia is presented. Each species occurring in the country is characterized and illustrated. The information about habitat and distribution of national genus representatives are provided. Several groups of species that are very similar in their morphology are delineated to facilitate process of species identification. A total of 10 species are described here as new. Lectotypes for the six species Cranichis ciliata, C. fendleri, C. mandonii, C. tenuis, C. viereckii, and C. wageneri have been selected. Additionally, two new nomenclatorial combinations within Ocampoa are proposed. creator: Dariusz L. Szlachetko creator: Marta Kolanowska uri: https://doi.org/10.7717/peerj.7385 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Szlachetko and Kolanowska title: Functional group based marine ecosystem assessment for the Bay of Biscay via elasticity analysis link: https://peerj.com/articles/7422 last-modified: 2019-08-09 description: The transitory and long-term elasticities of the Bay of Biscay ecosystem to density-independent and density-dependent influences were estimated within a state space model that accounted for both process and observation uncertainties. A functional group based model for the Bay of Biscay fish ecosystem was fit to time series obtained from scientific survey and commercial catch and effort data. The observation model parameters correspond to the unknown catchabilities and observation error variances that vary across the commercial fisheries and fishery-independent scientific surveys. The process model used a Gompertz form of density dependence, which is commonly used for the analysis of multivariate ecological time series, with unknown time-varying fishing mortalities. Elasticity analysis showed that the process model parameters are directly interpretable in terms of one-year look-ahead prediction elasticities, which measure the proportional response of a functional group in the next year given a proportional change to a variable or parameter in the current year. The density dependent parameters were also shown to define the elasticities of the long term means or quantiles of the functional groups to changes in fishing pressure. Evidence for the importance of indirect effects, mediated by density dependence, in determining the ecosystem response of the Bay of Biscay to changes in fishing pressure is presented. The state space model performed favourably in an assessment of model adequacy that compared observations of catch per unit effort against cross-validation predictive densities blocked by year. creator: Geoffrey R. Hosack creator: Verena M. Trenkel uri: https://doi.org/10.7717/peerj.7422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hosack and Trenkel title: Potential benefits from global warming to the thermal biology and locomotor performance of an endangered Patagonian lizard link: https://peerj.com/articles/7437 last-modified: 2019-08-09 description: Global warming can significantly affect many aspects of the biology of animal species, including their thermal physiology and physiological performance. Thermal performance curves provide a heuristic model to evaluate the impacts of temperature on the ecophysiology of ectotherms. When integrated with other thermal biology parameters, they can be used to predict the impacts of climate change on individual fitness and population viability. In this study, we combine holistic measures of thermal physiology and the thermal sensitivity of locomotor performance with environmental temperatures measured at fine scale to estimate the vulnerability to global warming of the endangered Patagonian lizard Phymaturus tenebrosus. Our results indicate that this lizard exhibits its preferred temperatures and maximum locomotor performance at higher temperatures than the mean temperature it currently experiences in its habitat. In addition, it exhibits a low effectiveness of thermoregulation, being a poor thermoregulator. In view of the results obtained, we suggest that the climatic conditions of Patagonia may be advantageous for P. tenebrosus to survive future global warming, since its thermal physiology and locomotor performance may improve under increasing in environmental temperatures in its habitat. creator: Facundo Cabezas-Cartes creator: Jimena B. Fernández creator: Fernando Duran creator: Erika L. Kubisch uri: https://doi.org/10.7717/peerj.7437 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cabezas-Cartes et al. title: Horse phenotyping based on video image analysis of jumping performance for conservation breeding link: https://peerj.com/articles/7450 last-modified: 2019-08-09 description: BackgroundMany horse breeds in the world are reserved as genetic resources; however, their characteristics seem to be insufficiently clarified, especially in terms of horse performance. Two jumping ability evaluation methods have been used to compare different types of performance breeds and on this basis their applicability for precision phenotyping has been determined.MethodsJumping data of 186 young Polish Warmblood stallions (27 with an endangered status) bred for sport and multipurpose use was collected during their performance tests organised under identical environmental conditions following the same guidelines. Jumping data consisted of objective measurements of free jumping parameters and the marks for jumping. Video recordings of 514 jumps (73 records for 27 stallions with an endangered status) were collected using a digital Panasonic AG-EZ 35 camera (25 fr/sec). Filming was recorded during a free jumping test in the line on a doublebarre obstacle (100–120 cm × 100 cm). Spatial and temporal variables of the jump were measured. The analysis of variance was performed (SAS, General Linear Model and Mixed procedures) using the statistical model, which included the random effect of the horse and fixed effects of the year of test, breeding status, height of jump and the successive number of the jump for objective kinematic data. The fixed effects of the year of test and breeding status were included in the model for subjective performance test data.ResultsPerformance marks for free jumping were lower in the endangered group of stallions in the trainers’ opinion (p ≤ 0.05), while no statistically significant differences were found in the judges’ opinions. Statistically significant differences in jumping variables were measured for the bascule points—the elevations of the withers and croup were higher in the endangered group (p ≤ 0.001) and the take-off time was prolonged (p ≤ 0.05), which explained the subjective evaluation.DiscussionThe use of objective evaluation methods provides important information for practice, as phenotypic differences between horses may be unclear in the subjective evaluation. The objective evaluation should be used to characterise the performance potential of different breeds, because the information from the evaluators might not be consistent. Such characteristics should be recorded at least for every new population. creator: Dorota Lewczuk creator: Ewa Metera-Zarzycka uri: https://doi.org/10.7717/peerj.7450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lewczuk and Metera-Zarzycka title: Musculoskeletal models of a human and bonobo finger: parameter identification and comparison to in vitro experiments link: https://peerj.com/articles/7470 last-modified: 2019-08-09 description: IntroductionKnowledge of internal finger loading during human and non-human primate activities such as tool use or knuckle-walking has become increasingly important to reconstruct the behaviour of fossil hominins based on bone morphology. Musculoskeletal models have proven useful for predicting these internal loads during human activities, but load predictions for non-human primate activities are missing due to a lack of suitable finger models. The main goal of this study was to implement both a human and a representative non-human primate finger model to facilitate comparative studies on metacarpal bone loading. To ensure that the model predictions are sufficiently accurate, the specific goals were: (1) to identify species-specific model parameters based on in vitro measured fingertip forces resulting from single tendon loading and (2) to evaluate the model accuracy of predicted fingertip forces and net metacarpal bone loading in a different loading scenario.Materials & MethodsThree human and one bonobo (Pan paniscus) fingers were tested in vitro using a previously developed experimental setup. The cadaveric fingers were positioned in four static postures and load was applied by attaching weights to the tendons of the finger muscles. For parameter identification, fingertip forces were measured by loading each tendon individually in each posture. For the evaluation of model accuracy, the extrinsic flexor muscles were loaded simultaneously and both the fingertip force and net metacarpal bone force were measured. The finger models were implemented using custom Python scripts. Initial parameters were taken from literature for the human model and own dissection data for the bonobo model. Optimized model parameters were identified by minimizing the error between predicted and experimentally measured fingertip forces. Fingertip forces and net metacarpal bone loading in the combined loading scenario were predicted using the optimized models and the remaining error with respect to the experimental data was evaluated.ResultsThe parameter identification procedure led to minor model adjustments but considerably reduced the error in the predicted fingertip forces (root mean square error reduced from 0.53/0.69 N to 0.11/0.20 N for the human/bonobo model). Both models remained physiologically plausible after the parameter identification. In the combined loading scenario, fingertip and net metacarpal forces were predicted with average directional errors below 6° and magnitude errors below 12%.ConclusionsThis study presents the first attempt to implement both a human and non-human primate finger model for comparative palaeoanthropological studies. The good agreement between predicted and experimental forces involving the action of extrinsic flexors—which are most relevant for forceful grasping—shows that the models are likely sufficiently accurate for comparisons of internal loads occurring during human and non-human primate manual activities. creator: Alexander Synek creator: Szu-Ching Lu creator: Evie E. Vereecke creator: Sandra Nauwelaerts creator: Tracy L. Kivell creator: Dieter H. Pahr uri: https://doi.org/10.7717/peerj.7470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Synek et al. title: Test-retest reliability of a smartphone app for measuring core stability for two dynamic exercises link: https://peerj.com/articles/7485 last-modified: 2019-08-09 description: BackgroundRecently, there has been growing interest in using smartphone applications to assess gait speed and quantify isometric core stability exercise intensity. The purpose of this study was to investigate the between-session reliability and minimal detectable change of a smartphone app for two dynamic exercise tests of the lumbopelvic complex.MethodsThirty-three healthy young and active students (age: 22.3 ± 5.9 years, body weight: 66.9 ± 11.3 kg, height: 167.8 ± 10.3 cm) participated in this study. Intraclass correlation coefficient (ICC), coefficient of variation (%CV), and Bland–Altman plots were used to verify the reliability of the test. The standard error of measurement (SEM) and the minimum detectable difference (MDD) were calculated for clinical applicability.ResultsThe ICCs ranged from 0.73 to 0.96, with low variation (0.9% to 4.8%) between days of assessments. The Bland–Altman plots and one-sample t-tests (p > 0.05) indicated that no dynamic exercise tests changed systematically. Our analyses showed that SEM 0.6 to 1.5 mm/s-2) and MDD (2.1 to 3.5 mm/s-2).ConclusionThe OCTOcore app is a reliable tool to assess core stability for two dynamic exercises. A minimal change of 3.5 mm/s-2 is needed to be confident that the change is not a measurement error between two sessions. creator: Paloma Guillén-Rogel creator: Cristina Franco-Escudero creator: Pedro J. Marín uri: https://doi.org/10.7717/peerj.7485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guillén-Rogel et al. title: Association between motor competence and Functional Movement Screen scores link: https://peerj.com/articles/7270 last-modified: 2019-08-08 description: BackgroundMotor competence (MC) is generally used to describe a person’s proficiency in a variety of motor skills and is the basis for one’s performance in sports and recreational activities. Functional Movement Screen (FMSTM) is one of the most used screening systems to provide interpretable measure of movement quality. Both FMSTM and MC constructs share three components: locomotor, manipulative and stabilizing movements. In the present study, it was hypothesized that MC scores can explain FMSTM variables. It was also predicted that better MC leads to better functional movement patterns in young adults.MethodsA sample of 92 young adults (73.9% men) with a mean age of 21.2 years participated in this study. All participants were evaluated on anthropometric measurements, dual x-ray absorptiometry; FMSTM and MC.ResultsMen showed better MC scores and fat mass composition than women. Regarding specific tests, women scored higher in the FMSTMactive straight leg raise test, whereas men performed better in the FMSTM trunk stability push-up (TSP) test. Manipulative tasks and construct presents’ significant and positive associations with FMSTM composite score (r ≥ 0.303). The significant negative correlation were more related to FMSTM TSP and MC shuttle run and FMSTM in-line lunge and MC manipulative. The FMSTM TSP presents significant associations with all MC constructs and tasks. Meanwhile, the FMSTM composite score is associated with all components of MC Stability (p < 0.05). In young adults, and independent of gender, the FMSTMexplains fundamental movements based on motor control according to the stability construct. Moreover, the FMSTM TSP is associated with better performance in the all MC constructs and MC tasks. The FMSTM, on its own, is linked to objective MC stability measures. creator: Bruno Silva creator: Luis Paulo Rodrigues creator: Filipe Manuel Clemente creator: José M. Cancela creator: Pedro Bezerra uri: https://doi.org/10.7717/peerj.7270 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Silva et al. title: Image based quantitative comparisons indicate heightened megabenthos diversity and abundance at a site of weak hydrocarbon seepage in the southwestern Barents Sea link: https://peerj.com/articles/7398 last-modified: 2019-08-08 description: BackgroundHigh primary productivity in the midst of high toxicity defines hydrocarbon seeps; this feature usually results in significantly higher biomass, but in lower diversity communities at seeps rather than in the surrounding non-seep benthos. Qualitative estimates indicate that this dichotomy does not necessarily hold true in high latitude regions with respect to megafauna. Instead, high latitude seeps appear to function as local hotspots of both megafaunal diversity and abundance, although quantitative studies do not exist. In this study, we tested this hypothesis quantitatively by comparing georeferenced seafloor mosaics of a seep in the southwestern Barents Sea with the adjacent non-seep seafloor.MethodsSeafloor images of the Svanefjell seep site and the adjacent non seep-influenced background seabed in the southwestern Barents Sea were used to construct georeferenced mosaics. All megafauna were enumerated and mapped on these mosaics and comparisons of the communities at the seep site and the non-seep background site were compared. Sediment push cores were taken in order to assess the sediment geochemical environment.ResultsTaxonomic richness and abundance were both considerably higher at the seep site than the non-seep location. However, taxa were fewer at the seep site compared to other seeps in the Barents Sea or the Arctic, which is likely due to the Svanefjell seep site exhibiting relatively low seepage rates (and correspondingly less chemosynthesis based primary production). Crusts of seep carbonates account for the higher diversity of the seep site compared to the background site, since most animals were either colonizing crust surfaces or using them for shelter or coverage. Our results indicate that seeps in northern latitudes can enhance local benthic diversity and this effect can take place even with weak seepage. Since crusts of seep carbonates account for most of the aggregating effect of sites experiencing moderate/weak seepage such as the study site, this means that the ability of seep sites to attract benthic species extends well beyond the life cycle of the seep itself, which has important implications for the larger marine ecosystem and its management policies. creator: Arunima Sen creator: Cheshtaa Chitkara creator: Wei-Li Hong creator: Aivo Lepland creator: Sabine Cochrane creator: Rolando di Primio creator: Harald Brunstad uri: https://doi.org/10.7717/peerj.7398 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sen et al. title: A century of waiting: description of a new Epictia Gray, 1845 (Serpentes: Leptotyphlopidae) based on specimens housed for more than 100 years in the collection of the Natural History Museum Vienna (NMW) link: https://peerj.com/articles/7411 last-modified: 2019-08-08 description: We describe a new species of Epictia based on eight specimens from Nicaragua collected and housed in the collection of the Natural History Museum Vienna for more than a century. The species differs from the congeners by the combination of external morphological characters: midtail scale rows 10; supralabials two, anterior one large and in broad contact with supraocular; infralabials four; subcaudals 14–19; middorsal scale rows 250–267; supraocular scales present; frontal scale distinct; striped dorsal color pattern with more or less triangular dark blotches on each scale; small white blotch in anterior part of dorsal surface of rostral present in five out of six specimens (two further specimens are lacking their heads); terminal spine and adjacent scales white. Eidonomic species separation from other Epictia spp. is also supported by a few qualitative and quantitative differences in vertebrae count and morphology. The new species is putatively assigned to the Epictia phenops species group based on external morphological characters and distribution. creator: Claudia Koch creator: Angele Martins creator: Silke Schweiger uri: https://doi.org/10.7717/peerj.7411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Koch et al. title: Identification of crucial genes based on expression profiles of hepatocellular carcinomas by bioinformatics analysis link: https://peerj.com/articles/7436 last-modified: 2019-08-08 description: Hepatocellular carcinoma (HCC) is one of the most heterogeneous malignant cancers with no effective targets and treatments. However, the molecular pathogenesis of HCC remains largely uncertain. The aims of our study were to find crucial genes involved in HCC through multidimensional methods and revealed potential molecular mechanisms. Here, we reported the gene expression profile GSE121248 findings from 70 HCC and 37 adjacent normal tissues, all of which had chronic hepatitis B virus (HBV) infection, we were seeking to identify the dysregulated pathways, crucial genes and therapeutic targets implicated in HBV-associated HCC. We found 164 differentially expressed genes (DEGs) (92 downregulated genes and 72 upregulated genes). Gene ontology (GO) analysis of DEGs revealed significant functional enrichment of mitotic nuclear division, cell division, and the epoxygenase P450 pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were mainly enriched in metabolism, cell cycle regulation and the p53 signaling pathway. The Mcode plugin was calculated to construct a module complex of DEGs, and the module was mainly enriched in cell cycle checkpoints, RHO GTPase effectors and cytochrome P450. Considering a weak contribution of each gene, gene set enrichment analysis (GSEA) was performed, revealing results consistent with those described above. Six crucial proteins were selected based on the degree of centrality, including NDC80, ESR1, ZWINT, NCAPG, ENO3 and CENPF. Real-time quantitative PCR analysis validated the six crucial genes had the same expression trend as predicted. Furthermore, the methylation data of The Cancer Genome Atlas (TCGA) with HCC showed that mRNA expression of crucial genes was negatively correlated with methylation levels of their promoter region. The overall survival reflected that high expression of NDC80, CENPF, ZWINT, and NCAPG significantly predicted poor prognosis, whereas ESR1 high expression exhibited a favorable prognosis. The identification of the crucial genes and pathways would contribute to the development of novel molecular targets and biomarker-driven treatments for HCC. creator: Ze-Kun Liu creator: Ren-Yu Zhang creator: Yu-Le Yong creator: Zhi-Yun Zhang creator: Can Li creator: Zhi-Nan Chen creator: Huijie Bian uri: https://doi.org/10.7717/peerj.7436 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Communities of oil palm flower-visiting insects: investigating the covariation of Elaeidobius kamerunicus and other dominant species link: https://peerj.com/articles/7464 last-modified: 2019-08-08 description: Insects visit flowers not only to forage for nectar or pollen but also to search for hosts or prey, and to look for suitable habitats for breeding sites. In oil palm flowers, it has been documented that not all flower-visiting insects are pollinators, but some insects are recognized as predators, parasitoids or saprophages, which may affect the abundance and persistence of the weevil pollinating oil palm, Elaeidobius kamerunicus. We studied the community of oil palm flower-visiting insects and investigated the covariation between the abundance E. kamerunicus and that of other dominant species. Ecological research was conducted in oil palm plantations with different tree ages in Central Borneo. Our results found that tree age and flower type of oil palm did not influence the abundance and species richness of flower-visiting insects, but significantly affected their species composition. There was a significant positive relationship between the abundance of E. kamerunicus and the fly Scaptodrosophila sp, indicating that these species covariate in oil palm flowers. These findings suggest that understanding the covariation between E. kamerunicus and Scaptodrosophila sp may help develop the conservation strategies for E. kamerunicus to support the sustainable production of oil palm. creator: Akhmad Rizali creator: Bambang Tri Rahardjo creator: Sri Karindah creator: Fatma Ramadhani Wahyuningtyas creator: Nurindah creator: Bandung Sahari creator: Yann Clough uri: https://doi.org/10.7717/peerj.7464 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rizali et al. title: The effect of platelet lysate in culture of PDLSCs: an in vitro comparative study link: https://peerj.com/articles/7465 last-modified: 2019-08-08 description: BackgroundCellular therapy clinical applications require large-scale production of stem cells. Therefore, abundance, ease of isolation, and proliferative potential are the most important factors in choosing the appropriate source of cells for transplantation studies. Multipotent stem cells obtained from periodontal ligament (PDL) can be used in periodontal tissue regeneration. In this study, we aimed to evaluate and compare the characteristics of periodontal ligament stem cells (PDLSCs), extracted by either enzymatic digestion or explant methods, and expanded using two different serum types: fetal bovine serum (FBS) and xeno-free platelet lysate (PL).MethodsExpanded PDLSCs were assessed for their proliferation capacity, surface markers expression, colony formation, differentiation potential and ability to self-renewal. Most importantly, PDLSCs were evaluated for their ability to produce osteoblasts in vitro.ResultsPDLSCs isolated by explant method and expanded in PL serve as a promising source of stem cells for osteoblasts regeneration. These cells showed higher proliferation capacity, they retained their stemness characteristics throughout the passages and they revealed an increase in the expression level of osteogenic markers, without showing any karyotypic abnormalities after cell expansion.ConclusionsPDLSCs produced using explant extraction method and expanded in cell culture media supplemented with PL provide an excellent source of xeno-free cells for the generation of functional osteoblasts. creator: Duaa A. Abuarqoub creator: Nazneen Aslam creator: Raghda B. Barham creator: Nidaa A. Ababneh creator: Diana A. Shahin creator: Abdallah A. Al-oweidi creator: Hanan D. Jafar creator: Mazin A. Al-Salihi creator: Abdalla S. Awidi uri: https://doi.org/10.7717/peerj.7465 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Abuarqoub et al. title: Cortisol, progesterone, 17α-hydroxyprogesterone, and TSH responses in dogs injected with low-dose lipopolysaccharide link: https://peerj.com/articles/7468 last-modified: 2019-08-08 description: BackgroundStress and diseases such as endotoxemia induce cortisol synthesis through a complex biosynthetic pathway involving intermediates (progesterone, and 17α-hydroxyprogesterone (17α-OHP)) and suppression of the hypothalamus-pituitary-thyroid axis.ObjectiveTo measure plasma concentrations of cortisol, progesterone, 17α-OHP, and thyroid stimulating hormone (TSH) in dogs experimentally injected with intravenous low-dose lipopolysaccharide (LPS). Our hypothesis was that LPS treatment would elicit a significant increase in cortisol and its precursors, and a significant decrease in TSH concentration.MethodsHormone measurements were performed on blood samples left over from a previous investigation (2011) on the effect of low-dose LPS on hematological measurands. Five sexually intact female dogs, none in estrous at the time of the study, were administered saline treatment two weeks prior to LPS treatment. LPS was administered intravenously at a dose of 0.1 µg/kg. Blood was collected before (baseline, time -24 hours) and 3-, 6- and 24-hours post-injection. Mixed model analysis for repeated measures was used, with both treatment and time as the repeated factors. Ranked transformation were applied when diagnostic analysis exhibited violation of normality and equal variance assumptions. Post hoc multiple comparisons were performed with Tukey’s adjustment. Statistical significance was defined as p < 0.05.ResultsSignificant differences relative to baseline values were detected following both treatments. Compared to baseline, dogs had significantly higher cortisol and 17α-OHP at 3-hours, and significantly lower TSH at 3- and 6-hours following LPS treatment. Dogs had significantly lower TSH at 6- and 24- following saline treatment. Though not statistically significant, the trend in progesterone concentrations was similar to cortisol and 17α-OHP, with an increase at 3-hours post-injection followed by a decrease close to baseline following both LPS and saline. Cortisol and 17α-OHP concentrations were higher after LPS treatment than after saline treatment at 3- and 6-hours post-injection, but differences were not statistically significant, and no significant differences between treatments were detected for any other hormone or timepoint.Discussion and conclusionCortisol and its adrenal precursors are released in the bloodstream following a low dose of LPS, while TSH appears to decrease. Similar changes occurred following saline treatment, suggesting that even routine handling and saline injection in conditioned dogs can elicit alterations in the internal equilibrium with subsequent modification of both hypothalamus-pituitary-adrenal and thyroid axes. Changes to adrenal and thyroid hormone concentrations must be interpreted in light of clinical information. Further studies are needed to elucidate mechanisms of adrenal steroidal hormone synthesis and secretion in response to various stressful stimuli in both neutered and intact animals. creator: Nicole L.B. Corder-Ramos creator: Bente Flatland creator: Michael M. Fry creator: Xiaocun Sun creator: Kellie Fecteau creator: Luca Giori uri: https://doi.org/10.7717/peerj.7468 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Corder-Ramos et al. title: Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume link: https://peerj.com/articles/7499 last-modified: 2019-08-08 description: The homeodomain-leucine zipper (HD-Zip) gene family, a group of plant-specific transcriptional factors (TFs), participates in regulating growth, development, and environmental responses. However, the characteristics and biological functions of HD-Zip genes in Prunus mume, which blooms in late winter or early spring, have not been reported. In this study, 32 HD-Zip genes, named PmHB1–PmHB32 based on their chromosomal positions, were identified in the genome of P. mume. These genes are distributed among seven chromosomes and are phylogenetically clustered into four major groups. Gene structure and motif composition were mostly conserved in each group. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolution of the genes, which maintained the function of this family. MicroRNA target site prediction indicated that the genes of the HD-Zip III subfamily may be regulated by miR165/166. Expression pattern analysis showed that the 32 genes were differentially expressed across five different tissues (leaf, flower bud, stem, fruit, and root) and at different stages of stem and leaf-bud development, suggesting that 10 of the genes may play important roles in stem development. Protein–protein interaction predictions showed that the subfamily III genes may regulate vascular development and shoot apical meristem (SAM) maintenance. Promoter analysis showed that the HD-Zip III genes might be involved in responses to light, hormones, and abiotic stressors and stem development. Taken together, our results provide an overview of the HD-Zip family in P. mume and lay the foundation for the molecular breeding of woody ornamental plants. creator: Lulu Li creator: Tangchun Zheng creator: Xiaokang Zhuo creator: Suzhen Li creator: Like Qiu creator: Jia Wang creator: Tangren Cheng creator: Qixiang Zhang uri: https://doi.org/10.7717/peerj.7499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Gaining insights in the nutritional metabolism of amphibians: analyzing body nutrient profiles of the African clawed frog, Xenopus laevis link: https://peerj.com/articles/7365 last-modified: 2019-08-07 description: Whole bodies of Xenopus laevis (n = 19) were analysed for chemical composition and morphometrics. The nutrient profile (macronutrients, amino acids, fatty acids and minerals) was evaluated by sex; interactions among variables with body weights and lengths, and comparisons made with different species of marine and fresh water fish. Significant differences were found in morphometric measurements, water content, several minerals and fatty acids between sexes of X. laevis. Amino acid profiles differed in methionine, proline and cysteine, which could underlie different metabolic pathways in frogs when compared to fish. In addition, fatty acid profiles revealed more monounsaturated and n − 6 polyunsaturated fatty acids in frogs than in fish, more similar to values reported for terrestrial than aquatic vertebrates. Important interactions were also found between body measurements and fat, calcium, and phosphorus, as well as between essential and non-essential amino acids. The results indicate that frogs might have particular biochemical pathways for several nutrients, dependent on sex and linked to body weight, which ultimately could reflect specific nutrient needs. creator: Andrea Brenes-Soto creator: Ellen S. Dierenfeld creator: Guido Bosch creator: Wouter H. Hendriks creator: Geert P.J. Janssens uri: https://doi.org/10.7717/peerj.7365 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Brenes-Soto et al. title: Validity of the iLOAD® app for resistance training monitoring link: https://peerj.com/articles/7372 last-modified: 2019-08-07 description: BackgroundThis study aimed (I) to assess the inter-rater agreement for measuring the mean velocity (MV) of the barbell with the iLOAD® app, and (II) to compare the magnitude of the MV and total work of a training session between the iLOAD® app and a linear encoder (reference method).MethodSixteen young healthy individuals (four women and 12 men) were tested in two sessions separated by 48 h. The 10 repetition maximum (RM) load was determined in the first testing session in the half squat exercise. The second testing session consisted of 3 sets of 10 repetitions during the half squat exercise performed against the 10RM load. Both the iLOAD® app and a linear encoder were used to calculate the MV and total work of each training set. MV was recorded with the iLOAD® app by two independent researchers to evaluate the inter-rater agreement.ResultsTrivial differences and nearly perfect correlations were observed between raters for the MV values collected under individual sets (effect size [ES] ≤ 0.02, r ≥ 0.987), as well as for the whole training session (ES = 0.01, r = 0.997). Trivial-small differences and nearly perfect correlations were observed between the iLOAD® app and the linear encoder (Chronojump, Barcelona, Spain) for MV (EV ≤ 0.25, r ≥ 0.903) and total work (ES ≤ 0.05, r ≥ 0.973). Bland-Altman plots did not reveal heteroscedasticity of the errors between the iLOAD® app and the linear encoder for MV (r2 = 0.010) and total work (r2 < 0.001).ConclusionsiLOAD® is a valid smartphone app which can provide real-time feedback of the MV and total work completed in a set of multiple repetitions in the half squat exercise. creator: Evandro Claudino de Sá creator: André Ricarte Medeiros creator: André Santana Ferreira creator: Amador García Ramos creator: Danica Janicijevic creator: Daniel Boullosa uri: https://doi.org/10.7717/peerj.7372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 de Sá et al. title: The clinical value of carcinoembryonic antigen for tumor metastasis assessment in lung cancer link: https://peerj.com/articles/7433 last-modified: 2019-08-07 description: BackgroundCarcinoembryonic antigen (CEA) as a diagnostic or prognostic marker has been widely studied in patients with lung cancer. However, the relationship between serum CEA and tumor metastasis in lung cancer remains controversial. This study aimed to investigate the ability of serum CEA to assess tumor metastasis in lung cancer patients.MethodsWe performed a retrospective analysis of 238 patients diagnosed with lung cancer from January to December 2016 at pneumology department of Dazhou Central Hospital (Dazhou, China). Serum CEA levels were quantified in each patient at the time of diagnosis of lung cancer. Metastasis was confirmed by computed tomography (CT), and/or positron emission tomography (PET) and/or surgery or other necessary detecting methods.ResultsOf the 213 patients eligible for final analysis, 128 were diagnosed with metastasis and 85 were diagnosed without metastasis. Compared to non-metastatic patients, the serum CEA was markedly higher in patients with metastasis (p < 0.001), and the area under the curve (AUC) was 0.724 (95% CI [0.654–0.793]). Subsequent analyses regarding the number and location of tumor metastases showed that CEA also had clinical value for multiple metastases versus single metastasis (AUC = 0.780, 95% CI [0.699–0.862]) and distant metastasis versus non-distant metastasis (AUC = 0.815, 95% CI [0.733–0.897]). In addition, we found that tumor size, histology diagnosis, age and gender had no impact on the assessment performance of CEA.ConclusionOur study suggested the serum CEA as a valuable marker for tumor metastases assessment in newly diagnosed lung cancer patients, which could have some implications in clinical application. creator: Jiasi Wang creator: Yanpeng Chu creator: Jie Li creator: Tingjie Wang creator: Liangli Sun creator: Pingfei Wang creator: Xiangdong Fang creator: Fanwei Zeng creator: Junfeng Wang creator: Fanxin Zeng uri: https://doi.org/10.7717/peerj.7433 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Patient-reported outcomes measured with and without dizziness associated with non-specific chronic neck pain: implications for primary care link: https://peerj.com/articles/7449 last-modified: 2019-08-07 description: BackgroundThe aim of this study was to compare health-related quality of life (HRQoL) and disability and fear of movement in patients with non-specific chronic neck pain (NSCNP) associated with dizziness with respect to patients with isolated NSCNP in primary care settings.MethodsA cross-sectional study was carried out in a primary care center. A total of 120 patients were divided into two groups and analyzed in this study. One group of patients reported dizziness combined with NSCNP (n = 60), and the other reported no dizziness with their NSCNP (n = 60). Patient-reported outcome measurements were HRQoL (primary outcome) and disability and kinesiophobia (secondary outcomes) assessed by the EuroQoL Five Dimensions and Five Levels (EQ-5D-5L), neck disability index (NDI) and Tampa Scale of Kinesiophobia (TSK-11), respectively.ResultsStatistically significant differences (P < 0.05) for a 95% confidence interval (CI) with a large effect size (Cohen d) were found between both groups with greater values of disability (mean difference = 6.30 points; 95% CI [3.84–8.75]; d = 0.94) and kinesiophobia (mean difference = 8.36 points; 95% CI [6.07–10.65]; d = 1.33), and an impairment of HRQoL (mean difference = 16.16 points; 95% CI [11.09–21.23]; d = 1.16), for patients with NSCNP associated with dizziness with respect to patients with isolated NSCNP.ConclusionsPatients with NSCNP in conjunction with dizziness present higher HRQoL impairment and higher disability and kinesiophobia compared to patients with isolated NSCNP. creator: Raúl Ferrer-Peña creator: Gonzalo Vicente-de-Frutos creator: Diego Flandez-Santos creator: Carlos Martín-Gómez creator: Carolina Roncero-Jorge creator: César Calvo-Lobo uri: https://doi.org/10.7717/peerj.7449 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ferrer-Peña et al. title: Acute net stress of young adult zebrafish (Danio rerio) is not sufficient to increase anxiety-like behavior and whole-body cortisol link: https://peerj.com/articles/7469 last-modified: 2019-08-07 description: In recent years, the zebrafish (Danio rerio) has become a popular model to study the mechanisms of physiological and behavioral effects of stress, due to the similarity in neural structures and biochemical pathways between zebrafish and mammals. Previous research in this vertebrate animal model has demonstrated an increase in whole-body cortisol resulting from an acute (30-second) net handling stress, but it remains unclear whether such a stressor will concomitantly increase anxiety-like behavior. In addition, as the previous study examined the effects of this acute stressor in adult zebrafish after a brief period of isolation, it is unclear whether this stressor would be effective in eliciting cortisol increases in younger aged subjects without isolation. In the current study, young adult zebrafish (approximately 90 days post-fertilization) were briefly exposed to a net handling stressor and were subsequently subjected to either the novel tank test or the light/dark preference test. The novel tank test was used to measure exploration and habituation in response to a novel environment, and the light/dark preference test was used to measure locomotor activity and scototaxis behavior. All subjects were sacrificed 15 minutes post-stressor and were analyzed for whole-body levels of cortisol. Contrary to expectations, there was no effect of acute net handling on cortisol levels. Similarly, acute net handling did not significantly induce anxiety-like behavior during the novel tank test or the light/dark preference test. Our findings demonstrate that there are possible developmental differences in response to an acute net handling stress, as we did not observe alterations in hormonal or behavioral measures of anxiety in young adult zebrafish. Alternatively, if zebrafish are not isolated before the stressor, they may be more resilient to a brief acute stressor. These results suggest the need for a different or more intense acute stressor in order further explore neuroendocrine mechanisms and anxiety-like behavior at this developmental stage in the zebrafish animal model. creator: Amy Aponte creator: Maureen L. Petrunich-Rutherford uri: https://doi.org/10.7717/peerj.7469 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Aponte and Petrunich-Rutherford title: Muscle quality index and isometric strength in older adults with hip osteoarthritis link: https://peerj.com/articles/7471 last-modified: 2019-08-07 description: BackgroundOlder adults with hip osteoarthritis (OA) suffer a progressive loss of muscle quality and strength, affecting their daily activities and quality of life. The purpose of this study is to compare the levels of isometric strength among older adults with and without hip OA and healthy young adults, and to determine the relationship between muscle quality index (MQI) and isometric strength.MethodsFourteen subjects with hip OA (65.6 ± 3.0 years), 18 healthy older adults (66.6 ± 6.5 years) and 32 young adults (20.7 ± 2.0 years) participated in the study. MQI, isometric muscle strength of the hip, ten time sit-to-stand tests, and body composition were measured.ResultsThe MQI was lower in subjects with hip OA, with no significant differences between groups (p > 0.054). Subjects with OA produced significantly less isometric strength in hip extension (p < 0.001), flexion (p < 0.001), abduction (p < 0.05), adduction (p < 0.001), external (p < 0.05) and internal rotation (p < 0.05). Subjects with OA demonstrated longer time in the execution of the sit-to-stand test (p < 0.001) in comparison with healthy older and young adults. High correlations between MQI, sit-to-stand (r =  − 0.76, p < 0.01) and peak force during hip abduction (r = 0.78, p < 0.01) where found in subjects with OA. Moderate correlation between MQI and peak force during hip flexion (r = 0.55, p < 0.05) and external rotation (r = 0.61, p < 0.05) were found in the OA group.ConclusionsSubjects with OA have lower MQI than old and young healthy controls. In subjects with OA, there was a significant relationship between isometric strength of hip muscles and performance on the sit-to-stand test and the MQI. creator: Daniel Jerez-Mayorga creator: Luis Javier Chirosa Ríos creator: Alvaro Reyes creator: Pedro Delgado-Floody creator: Ramon Machado Payer creator: Isabel María Guisado Requena uri: https://doi.org/10.7717/peerj.7471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jerez-Mayorga et al. title: Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species link: https://peerj.com/articles/7479 last-modified: 2019-08-07 description: BackgroundLicorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb in European and Asian countries. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated species. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species.MethodsIn the present study, we developed polymorphic SSR markers based on whole-genomesequence data of Glycyrrhiza lepidota. Then, based on the sequence information, the polymorphic SSR markers were developed. The SSR markers were applied to 23 Glycyrrhiza individual plants. We also evaluated the phylogenetic relationships and interspecies transferability among samples.ResultsThe genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The reported markers represent a valuable resource for the genetic characteri z ation of Glycyrrhiza spp. for theanalysis of its genetic variability, and as a tool for licorice transferability. This is the first intraspecific study in a collection of Glycyrrhiza spp. germplasm using SSR markers. creator: Jun Hyoung Bang creator: Chi Eun Hong creator: Sebastin Raveendar creator: Kyong Hwan Bang creator: Kyung Ho Ma creator: Soon Wook Kwon creator: Hojin Ryu creator: Ick Hyun Jo creator: Jong-Wook Chung uri: https://doi.org/10.7717/peerj.7479 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bang et al. title: Pangenomic type III effector database of the plant pathogenic Ralstonia spp. link: https://peerj.com/articles/7346 last-modified: 2019-08-06 description: BackgroundThe bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex” gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. Type III-secreted effectors (T3Es) are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology).MethodsExpert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors.ResultsWe curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires. creator: Cyrus Raja Rubenstein Sabbagh creator: Sebastien Carrere creator: Fabien Lonjon creator: Fabienne Vailleau creator: Alberto P. Macho creator: Stephane Genin creator: Nemo Peeters uri: https://doi.org/10.7717/peerj.7346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sabbagh et al. title: 262 Voyages Beneath the Sea: a global assessment of macro- and megafaunal biodiversity and research effort at deep-sea hydrothermal vents link: https://peerj.com/articles/7397 last-modified: 2019-08-06 description: For over 40 years, hydrothermal vents and the communities that thrive on them have been a source of profound discovery for deep-sea ecologists. These ecosystems are found throughout the world on active plate margins as well as other geologically active features. In addition to their ecologic interest, hydrothermal vent fields are comprised of metallic ores, sparking a nascent industry that aims to mine these metal-rich deposits for their mineral wealth. Here, we provide the first systematic assessment of macrofaunal and megafaunal biodiversity at hydrothermal vents normalized against research effort. Cruise reports from scientific expeditions as well as other literature were used to characterize the extent of exploration, determine the relative biodiversity of different biogeographic provinces, identify knowledge gaps related to the distribution of research effort, and prioritize targets for additional sampling to establish biodiversity baselines ahead of potential commercial exploitation. The Northwest Pacific, Southwest Pacific, and Southern Ocean biogeographic provinces were identified as high biodiversity using rarefaction of family-level incidence data, whereas the North East Pacific Rise, Northern East Pacific, Mid-Atlantic Ridge, and Indian Ocean provinces had medium biodiversity, and the Mid-Cayman Spreading Center was identified as a province of relatively low biodiversity. A North/South divide in the extent of biological research and the targets of hydrothermal vent mining prospects was also identified. Finally, we provide an estimate of sampling completeness for each province to inform scientific and stewardship priorities. creator: Andrew D. Thaler creator: Diva Amon uri: https://doi.org/10.7717/peerj.7397 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Thaler and Amon title: Genetic structure of two sympatric gudgeon fishes (Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin link: https://peerj.com/articles/7393 last-modified: 2019-08-06 description: BackgroundXenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions.MethodsIn the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa. Microsatellite DNA data, jointly with traditional summary statistics including FST and Fis, were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history.ResultsXenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa.DiscussionThe genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity. creator: Weiwei Dong creator: Dengqiang Wang creator: Huiwu Tian creator: Yan Pu creator: Lixiong Yu creator: Xinbin Duan creator: Shaoping Liu creator: Daqing Chen uri: https://doi.org/10.7717/peerj.7393 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dong et al. title: Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage link: https://peerj.com/articles/7388 last-modified: 2019-08-06 description: We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered shallow, but significant, levels of divergence among O. celata populations across the species range. Our results suggest that island isolation, subspecies (delineation by morphology, ecological, and life-history characteristics), and isolation-by-distance, in that order, are the variables that best explain the geographic structure detected across the range of O. celata. Populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters. creator: Zachary R. Hanna creator: Carla Cicero creator: Rauri C.K. Bowie uri: https://doi.org/10.7717/peerj.7388 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hanna et al. title: Large pelvic tubercle in orangutans relates to the adductor longus muscle link: https://peerj.com/articles/7273 last-modified: 2019-08-06 description: Orangutan pelves commonly exhibit a large, projecting tubercle in the iliopubic region, historically assumed to homologous to the pubic tubercle in humans. However, it is not clear whether this tubercle is a unique feature of Pongo, or if it is anatomically homologous with the human pubic tubercle when considered as a soft tissue attachment point. To clarify this issue, we dissected orangutan and other ape cadaveric specimens to evaluate the pelvic brim soft tissues and how they may relate to the tubercle (when present). We additionally conducted a broad osteological survey of pelvic brim morphology across 28 primate genera (n = 294 specimens) to document the presence of the tubercle in primate pelves. Cadaveric dissections revealed that the tubercle is exclusively associated with the proximal attachment of the adductor longus muscle tendon in orangutans. Our osteological survey confirms that the tubercle is both constantly present and very prominent in orangutans. We observed that the tubercle is consistently situated along the pectineal line, lateral to where the pubic tubercle in humans is found, thereby making its structural homology unlikely. The osteological survey documented the tubercle at polymorphic frequencies in all hominoid taxa, though generally less protuberant than observed in Pongo. We argue that this further excludes its possibility of homology with the pubic tubercle, and that it may therefore be more appropriately be considered an adductor longus tubercle. We discuss possible functional and phylogenetic implications for this feature. creator: Brian M. Shearer creator: Magdalena Muchlinski creator: Ashley S. Hammond uri: https://doi.org/10.7717/peerj.7273 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Shearer et al. title: miRDRN—miRNA disease regulatory network: a tool for exploring disease and tissue-specific microRNA regulatory networks link: https://peerj.com/articles/7309 last-modified: 2019-08-06 description: BackgroundMicroRNA (miRNA) regulates cellular processes by acting on specific target genes, and cellular processes proceed through multiple interactions often organized into pathways among genes and gene products. Hundreds of miRNAs and their target genes have been identified, as are many miRNA-disease associations. These, together with huge amounts of data on gene annotation, biological pathways, and protein–protein interactions are available in public databases. Here, using such data we built a database and web service platform, miRNA disease regulatory network (miRDRN), for users to construct disease and tissue-specific miRNA-protein regulatory networks, with which they may explore disease related molecular and pathway associations, or find new ones, and possibly discover new modes of drug action.MethodsData on disease-miRNA association, miRNA-target association and validation, gene-tissue association, gene-tumor association, biological pathways, human protein interaction, gene ID, gene ontology, gene annotation, and product were collected from publicly available databases and integrated. A large set of miRNA target-specific regulatory sub-pathways (RSPs) having the form (T, G1, G2) was built from the integrated data and stored, where T is a miRNA-associated target gene, G1 (G2) is a gene/protein interacting with T (G1). Each sequence (T, G1, G2) was assigned a p-value weighted by the participation of the three genes in molecular interactions and reaction pathways.ResultsA web service platform, miRDRN (http://mirdrn.ncu.edu.tw/mirdrn/), was built. The database part of miRDRN currently stores 6,973,875 p-valued RSPs associated with 116 diseases in 78 tissue types built from 207 diseases-associated miRNA regulating 389 genes. miRDRN also provides facilities for the user to construct disease and tissue-specific miRNA regulatory networks from RSPs it stores, and to download and/or visualize parts or all of the product. User may use miRDRN to explore a single disease, or a disease-pair to gain insights on comorbidity. As demonstrations, miRDRN was applied: to explore the single disease colorectal cancer (CRC), in which 26 novel potential CRC target genes were identified; to study the comorbidity of the disease-pair Alzheimer’s disease-Type 2 diabetes, in which 18 novel potential comorbid genes were identified; and, to explore possible causes that may shed light on recent failures of late-phase trials of anti-AD, BACE1 inhibitor drugs, in which genes downstream to BACE1 whose suppression may affect signal transduction were identified. creator: Hsueh-Chuan Liu creator: Yi-Shian Peng creator: Hoong-Chien Lee uri: https://doi.org/10.7717/peerj.7309 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: First report of cestode infection in the crustacean Artemia persimilis from Southern Chilean Patagonia and its relation with the Neotropical aquatic birds link: https://peerj.com/articles/7395 last-modified: 2019-08-06 description: The brine shrimp genus Artemia Leach (Crustacea, Branchiopoda), a keystone group in hipersaline wetlands all over the world, offers an excellent model to study species interactions (parasitism) and to explore “hidden fauna” (avian endoparasites). The present study is the first report on the parasite infection of the South American species Artemia persimilis from the Southern Chilean Patagonia (50°S–53°S). Samples were collected in Los Cisnes and Amarga lagoons, the two most austral populations of this crustacean described to date, during two seasons (spring and autumn). A total of 98 larvae of cestodes of the family Hymenolepididae (Cestoda, Cyclophyllidea) were found and identified as belonging to the following taxa: Confluaria podicipina (adult parasitic in grebes), Flamingolepis sp. (a cestode parasite of flamingos), Fimbriarioides (?) sp. (adults of the species of this genus infect waterfowl and shorebirds) and Wardium sp. (definitive host unknown, most probably charadriiform birds). This is a new geographical record of C. podicipina and the genus Fimbriarioides for the Neotropical Region, the latter being the most widely distributed species at both localities and seasons surveyed, and the only species recorded in autumn (April). Cestode community composition in Los Cisnes population was characterised by dominance of Flamingolepis sp., representing more than 65% of the total cestode species recorded, whereas in the Amarga population the most abundant parasite (>83%) was Fimbriarioides (?) sp. Significant seasonal variations were detected in Los Cisnes lagoon for Flamingolepis sp. and C. podicipina, with exclusive presence of them in spring (November). Besides providing novel information on cestodes infection in A. persimilis, this study provides new data on the life cycle of cestodes of Neotropical aquatic birds such as South American flamingos and grebes. Our finding expands the knowledge on the biodiversity and population dynamics of extreme and unique environments from high latitudes (Patagonia) and makes evident the need of further taxonomical and ecological studies for better understanding the life cycles of avian helminth parasites in the Neotropics and the role of aquatic invertebrates in them. creator: Stella Redón creator: Gergana P. Vasileva creator: Boyko B. Georgiev creator: Gonzalo Gajardo uri: https://doi.org/10.7717/peerj.7395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Redón et al. title: Road traffic injuries in China from 2007 to 2016: the epidemiological characteristics, trends and influencing factors link: https://peerj.com/articles/7423 last-modified: 2019-08-06 description: BackgroundRoad traffic accidents are one of the serious disasters that cause public injury, fatality and great economic loss. They are a growing public health problem around the world.ObjectivesThe aim of this study was to determine epidemiological characteristics, tendency and possible influencing factors of road traffic injuries (RTIs) in China, so as to give target suggestions on preventative measures.MethodsRoad traffic accident data were obtained from National Bureau of Statistics of China and Ministry of Transport of the People’s Republic of China. Descriptive statistic such as RTIs frequency, trends of different accident types from 2007 to 2016; the RTIs difference between different regions and road surfaces were compared; and the possible influencing factors of RTIs were also explored.ResultsOver the past decade, with the mileage of constructed highway increased, the frequency of road traffic accidents have declined substantially in China, and the death toll from road traffic accidents with motor vehicles has declined from 2007 to 2015, Conversely, the number of deaths from non-motor vehicle accidents has risen rapidly since 2012. Our study showed that the traffic accident related mortality in Guizhou province was different from the level of the whole nation, and the Eastern, Central and Western areas of China were all significantly different (P < 0.001). Linear regression suggested a significant affected of gross domestic product (GDP)-per-capita, education level, the number of health institutions, populations, and car ownership status on traffic accident death tolls (P < 0.001). Moreover, cement concrete pavement roads were associated with the highest occurrence rates of RTI, and RTIs was statistically significant (P < 0.001) on different road surfaces.ConclusionEven though the frequency of road traffic accidents has declined, RTIs remain an urgent public health problem in China. Thus, the government should give some target preventative measures to reduce RTIs, aiming at different regions, the increasing trend of the death toll related to non-motor vehicles and the highest occurrence on cement concrete pavement roads. creator: Xue Wang creator: Huiting Yu creator: Chan Nie creator: Yanna Zhou creator: Haiyan Wang creator: Xiuquan Shi uri: https://doi.org/10.7717/peerj.7423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions link: https://peerj.com/articles/7426 last-modified: 2019-08-06 description: It is an important issue whether microorganisms can live harmoniously with normal cells in the cardiovascular system. The answer to the question will have enormous impact on medical microbiology. To address the issue, it is essential to identify and characterize the bloodborne microbes in an efficient and comprehensive manner. Due to microbial sequence complexity and the composition of significant number of unknown microbial species in the circulatory system, traditional approaches using cell culture, PCR, or microarray are not suitable for the purpose. Recent reports indicate that cell-free DNA (cfDNA) sequencing using next-generation sequencing (NGS) or single-molecule sequencing (SMS), together with bioinformatics approaches, possesses a strong potential enabling us to distinguish microbial species at the nucleotide level. Multiple studies using microbial cfDNA sequencing to identify microbes for septic patients have shown strong agreement with cell culture. Similar approaches have also been applied to reveal previously unidentified microorganisms or to demonstrate the feasibility of comprehensive assessment of bloodborne microorganisms for healthy and/or diseased individuals. SMS using either SMRT (single-molecule real-time) sequencing or Nanopore sequencing are providing new momentum to reinforce this line of investigation. Taken together, microbial cfDNA sequencing provides a novel opportunity allowing us to further understand the involvement of bloodborne microbes in development of diseases. Similar approaches should also be applicable to the study of metagenomics for sufficient and comprehensive analysis of microbial species living in various environments. This article reviews this line of research and discuss the methodological approaches that have been developed, or are likely to be developed in the future, which may have strong potential to facilitate cfDNA- and cfRNA-based studies of cancer and acute/chronic diseases, in the hope that a better understanding of the hidden microbes in the circulatory system will improve diagnosis, prevention and treatment of problematic diseases. creator: Kuo-Ping Chiu creator: Alice L. Yu uri: https://doi.org/10.7717/peerj.7426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chiu and Yu title: Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river link: https://peerj.com/articles/7455 last-modified: 2019-08-06 description: BackgroundIn the United States, an estimated 14,748 wastewater treatment plants (WWTPs) provide wastewater collection, treatment, and disposal service to more than 230 million people. The quality of treated wastewater is often assessed by the presence or absence of fecal indicator bacteria. UV disinfection of wastewater is a common final treatment step used by many wastewater treatment plants in order to reduce fecal coliform bacteria and other pathogens; however, its potential impacts on the total effluent bacterial community are seemingly varied. This is especially important given that urban WWTPs typically return treated effluent to coastal and riverine environments and thus are a major source of microorganisms, genes, and chemical compounds to these systems. Following rainfall, stormflow conditions can result in substantial increases to effluent flow into combined systems.MethodsHere, we conducted a lab-scale UV disinfection on WWTP effluent using UV dosage of 100 mJ/cm2 and monitored the active microbiome in UV-treated effluent and untreated effluent over the course of 48 h post-exposure using 16S rRNA sequencing. In addition, we simulated stormflow conditions with effluent UV-treated and untreated effluent additions to river water and compared the microbial communities to those in baseflow river water. We also tracked the functional profiles of genes involved in tetracycline resistance (tetW) and nitrification (amoA) in these microcosms using RT-qPCR.ResultsWe showed that while some organisms, such as members of the Bacteroidetes, are inhibited by UV disinfection and overall diversity of the microbial community decreases following treatment, many organisms not only survive, but remain active. These include common WWTP-derived organisms such as Comamonadaceae and Pseudomonas. When combined with river water to mimic stormflow conditions, these organisms can persist in the environment and potentially enhance microbial functions such as nitrification and antibiotic resistance. creator: Imrose Kauser creator: Mark Ciesielski creator: Rachel S. Poretsky uri: https://doi.org/10.7717/peerj.7455 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kauser et al. title: Ngwevu intloko: a new early sauropodomorph dinosaur from the Lower Jurassic Elliot Formation of South Africa and comments on cranial ontogeny in Massospondylus carinatus link: https://peerj.com/articles/7240 last-modified: 2019-08-05 description: Our knowledge of Early Jurassic palaeobiodiversity in the upper Elliot Formation of South Africa has increased markedly in recent years with the discovery of new fossils, re-assessments of previously collected material and a better understanding of Stormberg Group stratigraphy. Here, Ngwevu intloko, a new genus of upper Elliot basal sauropodomorph is named on the basis of a complete skull and partial skeleton (BP/1/4779) previously assigned to Massospondylus carinatus. It can be distinguished from all other basal sauropodomorphs by a combination of 16 cranial and six postcranial characters. The new species is compared to a small ontogenetic series of M. carinatus as well as to a range of closely related taxa. Taphonomic deformation, sexual dimorphism and ontogeny are rejected as possible explanations for the morphological differences present between BP/1/4779 and other taxa. Osteohistological examination reveals that BP/1/4779 had nearly reached adult size at the time of its death at a minimum age of 10 years. creator: Kimberley E.J. Chapelle creator: Paul M. Barrett creator: Jennifer Botha creator: Jonah N. Choiniere uri: https://doi.org/10.7717/peerj.7240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chapelle et al. title: Taxonomic reassessment of the genus Dichotomius (Coleoptera: Scarabaeinae) through integrative taxonomy link: https://peerj.com/articles/7332 last-modified: 2019-08-05 description: Dung beetles of the subfamily Scarabaeinae are widely recognised as important providers of multiple ecosystem services and are currently experiencing revisions that have improved our understanding of higher-level relationships in the subfamily. However, the study of phylogenetic relationships at the level of genus or species is still lagging behind. In this study we investigated the New World beetle genus Dichotomius, one of the richest within the New World Scarabaeinae, using the most comprehensive molecular and morphological dataset for the genus to date (in terms of number of species and individuals). Besides evaluating phylogenetic relationships, we also assessed species delimitation through a novel Bayesian approach (iBPP) that enables morphological and molecular data to be combined. Our findings support the monophyly of the genus Dichotomius but not that of the subgenera Selenocopris and Dichotomius sensu stricto (s.s). Also, our results do not support the recent synonymy of Selenocopris with Luederwaldtinia. Some species-groups within the genus were recovered, and seem associated with elevational distribution. Our species delimitation analyses were largely congruent irrespective of the set of parameters applied, but the most robust results were obtained when molecular and morphological data were combined. Although our current sampling and analyses were not powerful enough to make definite interpretations on the validity of all species evaluated, we can confidently recognise D. nisus, D. belus and D. mamillatus as valid and well differentiated species. Overall, our study provides new insights into the phylogenetic relationships and classification of dung beetles and has broad implications for their systematics and evolutionary analyses. creator: Carolina Pardo-Diaz creator: Alejandro Lopera Toro creator: Sergio Andrés Peña Tovar creator: Rodrigo Sarmiento-Garcés creator: Melissa Sanchez Herrera creator: Camilo Salazar uri: https://doi.org/10.7717/peerj.7332 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pardo-Diaz et al. title: Elevated frequencies of total and MAIT cell subsets in patients with knee osteoarthritis link: https://peerj.com/articles/7443 last-modified: 2019-08-05 description: BackgroundOsteoarthritis (OA) is characterized by the degeneration of joint cartilage, with concomitant changes in the synovium and subchondral bone. Recently, the inflammatory response and involvement of several types of T-cells has been implicated in the development of OA. This study investigated the frequency of MR1-restricted mucosal-associated invariant T (MAIT) cells in patients with knee OA.MethodsForty-five patients recently diagnosed with knee OA and 21 age- and gender-matched healthy controls were recruited for this study. Percentages of circulating MAIT cells were assessed by flow cytometry. Plasma cytokine levels were measured using cytometric bead arrays. Associations between the percentages of MAIT cells, plasma cytokine levels, and clinical parameters of OA (erythrocyte sedimentation rate [ESR] and the Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC]) were analyzed using the Spearman correlation test.ResultsThe percentages of total, CD8αα, and CD8αβ MAIT cells were higher in patients with OA compared to healthy controls. The percentages of total and CD8αα MAIT cells were higher in patients with multi-joint OA (MOA) compared to patients with knee-only OA (KOA). Plasma IFN-γ and TNF-α levels were elevated in patients with OA compared to healthy controls, and there was a positive correlation between plasma IFN-γ levels and the percentages of total, CD8αα, and CD8αβ MAIT cells. Plasma IFN-γ and IL-17 levels were higher in patients with MOA compared to healthy controls or patients with KOA. There were positive correlations between the percentages of total and CD8αα MAIT cells and clinical parameters (ESR and WOMAC scores) in patients with OA or MOA. Binary logistic regression analysis shown the frequency of MAIT cells was associated with the risk of OA.ConclusionsMAIT cells and their subpopulations were significantly increased in patients with OA and have potential as biological markers of OA disease severity, especially in patients with MOA. creator: Ding Zhao creator: Wei Zhong creator: Dongfeng Han creator: Yingbo Li creator: Yanfang Jiang creator: Guishan Gu uri: https://doi.org/10.7717/peerj.7443 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Sex differences in the response to angiotensin II receptor blockade in a rat model of eccentric cardiac hypertrophy link: https://peerj.com/articles/7461 last-modified: 2019-08-05 description: Background. Men and women differ in their susceptibility to cardiovascular disease, though the underlying mechanism has remained elusive. Heart disease symptoms, evolution and response to treatment are often sex-specific. This has been studied in animal models of hypertension or myocardial infarction in the past but has received less attention in the context of heart valve regurgitation. The aim of the study was to evaluate the development of cardiac hypertrophy (CH) in response to left ventricle (LV) volume overload (VO) caused by chronic aortic valve regurgitation (AR) in male and female rats treated or not with angiotensin II receptor blocker (ARB), valsartan. We studied eight groups of Wistar rats: male or female, AR or sham-operated (sham) and treated or not with valsartan (30 mg/kg/day) for 9 weeks starting one week before AR surgical induction.Results. As expected, VO from AR resulted for both male and female rats in significant LV dilation (39% vs. 40% end-diastolic LV diameter increase, respectively; p < 0.0001) and CH (53% vs. 64% heart weight increase, respectively; p < 0.0001) compared to sham. Sex differences were observed in LV wall thickening in response to VO. In untreated AR males, relative LV wall thickness (a ratio of wall thickness to end-diastolic diameter) was reduced compared to sham, whereas this ratio in females remained unchanged. ARB treatment did not prevent LV dilation in both male and female animals but reversed LV wall thickening in females. Systolic and diastolic functions in AR animals were altered similarly for both sexes. ARB treatment did not improve systolic function but helped normalizing diastolic parameters such as left atrial mass and E wave slope in female AR rats. Increased LV gene expression of Anp and Bnp was normalized by ARB treatment in AR females but not in males. Other hypertrophy gene markers (Fos, Trpc6, Klf15, Myh6 and Myh7) were not modulated by ARB treatment. The same was true for genes related to LV extracellular matrix remodeling (Col1a1, Col3a1, Fn1, Mmp2, Timp1 and Lox). In summary, ARB treatment of rats with severe AR blocked the female-specific hypertrophic response characterized by LV chamber wall thickening. LV dilation, on the other hand, was not significantly decreased by ARB treatment. This also indicates that activation of the angiotensin II receptor is probably more involved in the early steps of LV remodeling caused by AR in females than in males. creator: Élisabeth Walsh-Wilkinson creator: Marie-Claude Drolet creator: Charlie Le Houillier creator: Ève-Marie Roy creator: Marie Arsenault creator: Jacques Couet uri: https://doi.org/10.7717/peerj.7461 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Walsh-Wilkinson et al. title: Effect of dietary concentrate to forage ratio on growth performance, rumen fermentation and bacterial diversity of Tibetan sheep under barn feeding on the Qinghai-Tibetan plateau link: https://peerj.com/articles/7462 last-modified: 2019-08-05 description: This study aimed to research the effects of different dietary concentrate to forage (C:F) ratio on growth performance, rumen fermentation and bacteria diversity of barn feeding Tibetan sheep. The experiment contains fiver treatments (HS1, HS2 HS3, HS4 and HS5; n = 8, respectively) based on dietary C:F ratios 0:100, 15:85, 30:70, 45:55, and 60:40, respectively. The ruminal bacterial community structure was investigated through high-throughput sequencing of 16S rRNA genes in V4 hypervariable region. The results showed that increasing dietary concentrate feed level from 0% to 60% exerted a positive effect on DMI, BW gain, gain rate and feed conversation ratio (FCR) in Tibetan sheep. The increases dietary concentrate feed level elevatedNH3-N, propionate and valerate concentrations, whereas, reduced molar ratio of acetate to propionate (A/P ratio) (P < 0.05). For rumen bacterial diversity, increases in dietary concentrate content contributed to lower alpha diversity indexes including Shannon wiener, Chao1 and observed species, meanwhile, significantly increased the abundances of the phylum Bacteroidetes and the genus Prevotella_1 (P < 0.05). In conclusion, increases dietary concentrate content improved the growth performance and Tibetan sheep fed diets of 45% concentrate obtained a better performance; the inclusion of concentrate in feed changed rumen fermentation from acetate fermentation to propionate fermentation, and improved the energy utilization efficiency of Tibetan sheep; the increased in concentrate content significantly reduced rumen bacteria diversity and changed the abundance of some core bacteria. creator: Hongjin Liu creator: Tianwei Xu creator: Shixiao Xu creator: Li Ma creator: Xueping Han creator: Xungang Wang creator: Xiaoling Zhang creator: Linyong Hu creator: Na Zhao creator: Yongwei Chen creator: Li Pi creator: Xinquan Zhao uri: https://doi.org/10.7717/peerj.7462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study link: https://peerj.com/articles/7329 last-modified: 2019-08-05 description: Epididymal protease inhibitor (EPPIN) that is located on the sperm surface and specific to the male reproductive system is a non-hormonal contraceptive target, since the binding of EPPIN with the seminal plasma protein semenogelin-1 (SEMG1) causes a loss of sperm function. Here, we investigated the binding interactions between EPPIN and SEMG1 by homology modeling, docking and molecular dynamics simulation. Since no crystal structure was reported for EPPIN, its 3D structure was constructed by homology modeling and refined by dynamics simulation, illustrating the C-terminus domain of EPPIN could bind with its N-terminus domain through the residues 30–32 and 113–116. The binding interaction of SEMG110-8 peptide and EPPIN was investigated by Z-DOCK and dynamics simulation. After evaluating the models according to the calculated binding free energies, we demonstrated that C-terminus domain of EPPIN was important for the binding of SEMG1 via residues Tyr107, Gly112, Asn116, Gln118 and Asn122, while residue Arg32 in N-terminus domain also had contribution for their binding interaction. Additionally, the binding pocket of EPPIN was defined according to these key residues and verified by molecular docking with reported inhibitor EP055, suggesting that the pocket formed by Arg32, Asn114, Asn116, Phe117 and Asn122 could be important for the design of new ligands. This study might be helpful for the understanding of biological function of EPPIN and would encourage the discovery of non-hormonal contraceptive leads/drugs in the future. creator: Changyu Shan creator: Hongwei Li creator: Yuping Zhang creator: Yuyan Li creator: Yingchun Chen creator: Wei He uri: https://doi.org/10.7717/peerj.7329 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Shan et al. title: Impact of digital video analytics on accuracy of chemobehavioural phenotyping in aquatic toxicology link: https://peerj.com/articles/7367 last-modified: 2019-08-05 description: Chemobehavioural phenotypic analysis using small aquatic model organisms is becoming an important toolbox in aquatic ecotoxicology and neuroactive drug discovery. The analysis of the organisms’ behavior is usually performed by combining digital video recording with animal tracking software. This software detects the organisms in the video frames, and reconstructs their movement trajectory using image processing algorithms. In this work we investigated the impact of video file characteristics, video optimization techniques and differences in animal tracking algorithms on the accuracy of quantitative neurobehavioural endpoints. We employed larval stages of a free-swimming euryhaline crustacean Artemia franciscana,commonly used for marine ecotoxicity testing, as a proxy modelto assess the effects of video analytics on quantitative behavioural parameters. We evaluated parameters such as data processing speed, tracking precision, capability to perform high-throughput batch processing of video files. Using a model toxicant the software algorithms were also finally benchmarked against one another. Our data indicates that variability in video file parameters; such as resolution, frame rate, file containers types, codecs and compression levels, can be a source of experimental biases in behavioural analysis. Similarly, the variability in data outputs between different tracking algorithms should be taken into account when designing standardized behavioral experiments and conducting chemobehavioural phenotyping. creator: Jason Henry creator: Alvaro Rodriguez creator: Donald Wlodkowic uri: https://doi.org/10.7717/peerj.7367 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Henry et al. title: The role of past experience in development of feeding behavior in common vampire bats link: https://peerj.com/articles/7448 last-modified: 2019-08-05 description: The life history strategy of common vampire bats (Desmodus rotundus) suggests that learning might play a role in development of their foraging skills. We took advantage of 12 captive births in a study colony of vampire bats to test the role of past experience in two aspects of feeding. First, we compared preferences for blood temperature in 32 wild-born vampire bats versus 11 captive-born vampire bats that had only previously fed on blood of ambient temperature or colder. We found no evidence for a preference in either group for blood presented at 4 °C versus 37 °C. Second, we tested whether captive-born vampire bats with no previous experience of feeding on live animals could successfully feed on a live chicken. Five of 12 naïve captive-born bats were able to bite the chicken and draw blood, but only one bat gained more than 5% of body mass. We were unable to reasonably compare their feeding performance with that of wild-born bats because only two of three wild-born, short-term captive bats fed on the chicken and none of the seven wild-born, long-term captive mothers attempted to feed. This unexpected lack of feeding might be due to a previously reported age-dependent neophobia. When six of the captive-born bats were released in the wild, they appeared to feed successfully because they survived for more than three consecutive nights. We suggest further tests that would better clarify the role of learning in the development of foraging in vampire bats. creator: Jineth Berrío-Martínez creator: Samuel Kaiser creator: Michelle Nowak creator: Rachel A. Page creator: Gerald G. Carter uri: https://doi.org/10.7717/peerj.7448 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Berrío-Martínez et al. title: Pruning and dormancy breaking make two sustainable grape-cropping productions in a protected environment possible without overlap in a single year link: https://peerj.com/articles/7412 last-modified: 2019-08-02 description: In table grape production, protected cultivation in a vineyard in different regions and climates is currently a commonly used practice. The aims of this study were to provide key approaches to sustainably produce two crops of grape without overlap under protected environment in a single year. Spraying the degreening chemicals 400 mg/L ethephon +0.4% sulfur at 4 weeks of vine nutrient restoration after the harvest of the summer crop resulted in the highest percentage of sprouting inflorescence. The retention of 7–10 buds in the base shoot results in the high percentage of sprouting inflorescence. Bud breaking chemicals with 2.5% hydrogen cyanamide+2.0% Baoguoliang +0.02% Shenzhonggen significantly led to sprout inflorescence more efficiently. Cluster and fruit weights of the winter crop weighed significantly less than those of the summer crop. However, the contents of total soluble sugar and titratable acidity were higher than those of the summer crop. The anthocyanin content in the peel of the winter fruit was significantly higher than that in the summer fruit. The yield of the winter crop is controlled by the yield of the summer fruit. To maintain the stability of the two crops for one year, the ratio of yield in the winter to the summer should be controlled from 2:5 to 3:5 to ensure the sustainable production of two crops without overlap for ‘Summer Black’ grape. These results may help grape growers to overcome the impacts of rainy and hot climates with the help of protected facilities, and it could enable the use of solar radiation and heat resources in subtropical and tropical areas. creator: Zhipeng Qiu creator: Guangzheng Chen creator: Dongliang Qiu uri: https://doi.org/10.7717/peerj.7412 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qiu et al. title: Influence of acute combined physical and cognitive exercise on cognitive function: an NIRS study link: https://peerj.com/articles/7418 last-modified: 2019-08-02 description: The purpose of this study is to investigate the effects of different types of acute exercise on cognitive function and cerebral oxygenation. A within-subject design was adopted. In total, 20 healthy older adults were enrolled in the study. They came to the laboratory individually on four separate days and completed four conditions of activity. Four conditions were sedentary reading control (RC), cognitive exercise (CE), physical exercise (PE) and cognitive + physical exercise (CE + PE). During these visits, participants completed the Stroop task before and immediately after the experimental condition, which consisted of 15 min of aerobic exercise, verbal fluency task (VFT), and dual task. The Stroop task included the following two conditions: a naming condition and an executive condition. The fNIRS is an optical method using near-infrared light to measure relative changes of oxygenated (O2Hb) and deoxygenated (HHb) hemoglobin in the cortex. The results indicate that acute exercise facilitates performance for executive tasks, not only combined cognition, but also the different results between combined exercise and single exercise. The fNIRS findings showed that acute single exercise influences oxygenation for executive tasks but not for naming tasks. Greater improvement was observed in the post-exercise session of combined exercise during the modified Stroop. These findings demonstrate that acute single exercise, single cognition exercise, and combined exercise enhanced the performance of the inhibition control task. Only acute combined exercise has a general facilitative effect on inhibition control. Combined exercise was shown to be superior to single exercise for task-efficient cerebral oxygenation and improved oxygen utilization during cortical activation in older individuals. Also, to maximize the performance of cognition it may be important for older adults to take part in more cognitive demand exercise or take more kinds of exercise. creator: Zhiguang Ji creator: Tian Feng creator: Lingnan Mei creator: Anmin Li creator: Chunhua Zhang uri: https://doi.org/10.7717/peerj.7418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ji et al. title: Spatiotemporal patterns of urban thermal environment and comfort across 180 cities in summer under China’s rapid urbanization link: https://peerj.com/articles/7424 last-modified: 2019-08-02 description: BackgroundChina is considered as the largest and most rapidly urbanizing nation in the world. However, possible changes of urban thermal environment and comfort under the rapid urbanization in China still remain poorly understood at a national scale.MethodsBased on the data collected from 180 cities in 1990, 2005, and 2015 in China, the spatiotemporal patterns of urban thermal environment and comfort in summer and their relationships with urbanization variables were investigated in this study. ResultsOur results indicate that urban thermal environment has changed greatly during the 25 years. Furthermore, the changes of urban climate in different regions are inconsistent. The Physiological Equivalent Temperature (PET) at most cities (81%) in China increased from 1990 to 2015, which suggested that urban thermal comfort in China was also deteriorating during the 25 years. However, while the PET of some cities in China began to decrease from 2005 to 2015, there were still 33% of cities that had positive trends,which mainly located in North region. Urbanization resulted in a significant influence on urban climate. Compared to southern cities, northern cities were more sensitive to urbanization impact. The most important contribution to increasing of PET for urbanization variables is gross domestic product, followed by urban population. The analysis results reveal changing patterns of urban thermal comfort in China during summer season. It can help urban government and managers improve urban thermal environment and comfort. creator: Zhibin Ren creator: Yao Fu creator: Yunxia Du creator: Hongbo Zhao uri: https://doi.org/10.7717/peerj.7424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ren et al. title: Physiological and immunological responses of sea cucumber Apostichopus japonicus during desiccation and subsequent resubmersion link: https://peerj.com/articles/7427 last-modified: 2019-08-02 description: Desiccation is one of the extremely stressful situations experienced by aquatic animals, and sea cucumber usually suffers from desiccation stress during transportation without water. The present study was conducted to evaluate the effect of desiccation and subsequent resubmersion on physiological stress, oxidative damage, antioxidant status and non-specific immune response of Apostichopus japonicus, providing valuable information on the health management of sea cucumber culturing. Control and desiccation groups were set up, and each group has three replicates. After 1, 3 and 6 h of desiccation, individuals were resubmersed in aerated seawater for a 24 h recovery in three batches, which were represented as D1, D3 and D6, respectively. The results showed that glucose level in coelomic fluid of sea cucumber significantly decreased after desiccation, whereas lactate, cortisol and osmolality showed remarkable ascending trends. Thereafter, all stress parameters gently recovered towards normal levels as control group during 24 h resubmersion. The prolonged desiccation at D6 treatment induced the significant increases of malondialdehyde (MDA) and reactive oxygen species (ROS) contents, as well as relatively lower superoxide dismutase (SOD) and catalase (CAT) activities. During the period of desiccation and subsequent resubmersion, sea cucumber adjusted antioxidant defense to reduce the concentrations of MDA and ROS as a strategy for protecting against oxidative damage. Desiccation also had significant effects on non-specific immune parameters (total coelomocytes counts, TCC; complement C3; total nitric oxide synthase, T-NOS; lysozyme, LSZ; alkaline phosphatase, AKP) of A. japonicus, which could be recovered to some extent during resubmersion. In conclusion, less than 6 h of desiccation did not induce irreparable damage to sea cucumber, and was recommended for handling and shipping live sea cucumbers. creator: Shiying Hou creator: Zewei Jin creator: Wenwen Jiang creator: Liang Chi creator: Bin Xia creator: Jinghua Chen uri: https://doi.org/10.7717/peerj.7427 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hou et al. title: Reconstruction of insect hormone pathways in an aquatic firefly, Sclerotia aquatilis (Coleoptera: Lampyridae), using RNA-seq link: https://peerj.com/articles/7428 last-modified: 2019-08-02 description: Insect hormones: ecdysteroids and juvenile hormones have crucial functions during the regulation of different developmental pathways in insects. Insect metamorphosis is one of the primary pathways regulated by these hormones. The insect hormone biosynthetic pathway is conserved among arthropods, including insects, with some variations in the form of hormones used among each group of insects. In this study, the candidate genes involved in the insect hormone pathways and their functional roles were assessed in an aquatic firefly, Sclerotia aquatilis using a high-throughput RNA sequencing technique. Illumina next-generation sequencing (NGS) was used to generate transcriptome data for the different developmental stages (i.e., larva, pupa, and adult) of S. aquatilis. A total of 82,022 unigenes were generated across all different developmental stages. Functional annotation was performed for each gene, based on multiple biological databases, generating 46,230 unigenes. These unigenes were subsequently mapped using KEGG pathways. Accordingly, 221 protein-encoding genes involved in the insect hormone pathways were identified, including, JHAMT, CYP15A1, JHE, and Halloween family genes. Twenty potential gene candidates associated with the biosynthetic and degradation pathways for insect hormones were subjected to real-time PCR, reverse transcriptase PCR (RT-PCR) and sequencing analyses. The real-time PCR results showed similar expression patterns as those observed for transcriptome expression profiles for most of the examined genes. RT-PCR and Sanger sequencing confirmed the expressed coding sequences of these gene candidates. This study is the first to examine firefly insect hormone pathways, facilitating a better understanding of firefly growth and development. creator: Pornchanan Chanchay creator: Wanwipa Vongsangnak creator: Anchana Thancharoen creator: Ajaraporn Sriboonlert uri: https://doi.org/10.7717/peerj.7428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chanchay et al. title: Age-associated changes of cytochrome P450 and related phase-2 gene/proteins in livers of rats link: https://peerj.com/articles/7429 last-modified: 2019-08-02 description: Cytochrome P450s (CYPs) are phase-I metabolic enzymes playing important roles in drug metabolism, dietary chemicals and endogenous molecules. Age is a key factor influencing P450s expression. Thus, age-related changes of CYP 1–4 families and bile acid homeostasis-related CYPs, the corresponding nuclear receptors and a few phase-II genes were examined. Livers from male Sprague-Dawley rats at fetus (−2 d), neonates (1, 7, and 14 d), weanling (21 d), puberty (28 and 35 d), adulthood (60 and 180 d), and aging (540 and 800 d) were collected and subjected to qPCR analysis. Liver proteins from 14, 28, 60, 180, 540 and 800 days of age were also extracted for selected protein analysis by western blot. In general, there were three patterns of their expression: Some of the drug-metabolizing enzymes and related nuclear receptors were low in fetal and neonatal stage, increased with liver maturation and decreased quickly at aging (AhR, Cyp1a1, Cyp2b1, Cyp2b2, Cyp3a1, Cyp3a2, Ugt1a2); the majority of P450s (Cyp1a2, Cyp2c6, Cyp2c11, Cyp2d2, Cyp2e1, CAR, PXR, FXR, Cyp7a1, Cyp7b1. Cyp8b1, Cyp27a1, Ugt1a1, Sult1a1, Sult1a2) maintained relatively high levels throughout the adulthood, and decreased at 800 days of age; and some had an early peak between 7 and 14 days (CAR, PXR, PPARα, Cyp4a1, Ugt1a2). The protein expression of CYP1A2, CYP2B1, CYP2E1, CYP3A1, CYP4A1, and CYP7A1 corresponded the trend of mRNA changes. In summary, this study characterized three expression patterns of 16 CYPs, five nuclear receptors, and four phase-II genes during development and aging in rat liver, adding to our understanding of age-related CYP expression changes and age-related disorders. creator: Shang-Fu Xu creator: An-Ling Hu creator: Lu Xie creator: Jia-Jia Liu creator: Qin Wu creator: Jie Liu uri: https://doi.org/10.7717/peerj.7429 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu et al. title: Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression link: https://peerj.com/articles/7442 last-modified: 2019-08-02 description: Delta bovine papillomaviruses (δBPVs) mainly infect cattle and cause fibropapillomas. δBPVs encode three oncogenes, E5, E6 and E7. The effect of E6 on microRNA (miRNA) and mRNA expression profiles is not well characterized. In this study, RNA sequencing and small RNA sequencing were used to explore alterations in mRNAs and miRNAs in E6 over-expressing NIH/3T3 cells (NH-E6) compared with control cells (NH-GFP). We found that 350 genes (181 upregulated and 169 downregulated) and 54 miRNAs (26 upregulated and 28 downregulated) were differentially expressed (DE) following E6 expression. The top 20 significantly enriched GO terms in “biological process” included inflammatory response, innate immune response, immune response, immune system process, positive regulation of apoptotic process, cell adhesion, and angiogenesis. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, we selected 19 immune-response related DEGs and 11 DE miRNAs for qPCR validation. Of these, upregulation of 12 genes, Ccl2, Ccl7, Cxcl1, Cxcl5, Tlr2, Nfkbia, Fas, Il1rl1, Ltbp1, Rab32, and Zc3h12a, Dclk1 and downregulation of four genes, Agtr2, Ptx3, Sfrp1, and Thbs1 were confirmed. Ccl2, Ccl7, Cxcl1 and Cxcl5 were upregulated more than ten-fold in NH-E6 compared with NH-GFP. Also, upregulation of three miRNAs, mmu-miR-129-2-3p, mmu-miR-149-5p-R-2 and mmu-miR-222-3p, and downregulation of five miRNAs, mmu-miR-582-3p-R+1, mmu-miR-582-5p, mmu-miR-708-3p, mmu-miR-708-5p and mmu-miR-1197-3p, were confirmed. Our study describes changes in both mRNA and miRNA profiles in response to BPV E6 expression, providing new insights into BPV E6 oncogene functions. creator: Feng Pang creator: Mengmeng Zhang creator: Guohua Li creator: Zhenxing Zhang creator: Haifeng Huang creator: Baobao Li creator: Chengqiang Wang creator: Xiaohong Yang creator: Yiying Zheng creator: Qi An creator: Luyin Zhang creator: Li Du creator: Fengyang Wang uri: https://doi.org/10.7717/peerj.7442 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pang et al. title: Histological evaluation of five suture materials in the telson ligament of the American horseshoe crab (Limulus polyphemus) link: https://peerj.com/articles/7061 last-modified: 2019-08-01 description: An ideal suture material supports healing, minimizes inflammation, and decreases the likelihood of secondary infection. While there are published recommendations for suture materials in some invertebrates, there are no published recommendations for Limulus polyphemus or any chelicerate. This study evaluates the histological reaction of horseshoe crabs to five commonly used suture materials: monofilament nylon, silk, poliglecaprone, polydioxanone, and polyglycolic acid. None of the materials were superior with regards to holding nor was there any dehiscence. Nylon evoked the least amount of tissue reaction. This work also provides a histopathological description of the soft membrane at the hinge area between the opisthosoma and telson (telson ligament) and comments on euthanasia with intracardiac eugenol. creator: Ami E. Krasner creator: Amy Hancock-Ronemus creator: Larry S. Christian creator: Emily H. Griffith creator: Gregory A. Lewbart creator: Jerry M. Law uri: https://doi.org/10.7717/peerj.7061 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Krasner et al. title: Taxonomic revision of black salamanders of the Aneides flavipunctatus complex (Caudata: Plethodontidae) link: https://peerj.com/articles/7370 last-modified: 2019-08-01 description: We present a taxonomic revision of the black salamander (Aneides flavipunctatus) complex of northwestern California and extreme southeastern Oregon. The revision is based on a number of published works as well as new molecular and morphological data presented herein. The subspecies Aneides flavipunctatus niger Myers & Maslin 1948 is raised in rank to a full species. It is isolated far to the south of the main range on the San Francisco Peninsula, south and west of San Francisco Bay. Another geographically isolated set of populations occurs well inland in Shasta County, northern CA, mainly in the vicinity of Shasta Lake. It is raised from synonymy and recognized as Aneides iecanus (Cope 1883). The remaining taxa occur mainly along and inland from the coast from the vicinity of the Russian River and Lake Berryessa/Putah Creek, north to the vicinity of the Smith River near the Oregon border and more inland along the Klamath and Trinity Rivers and tributaries into Oregon. The northern segment of this nearly continuous range is named Aneides klamathensis Reilly and Wake 2019. We use molecular data to provide a detailed examination of a narrow contact zone between the northern A. klamathensis and the more southern A. flavipunctatus in southern Humboldt County in the vicinity of the Van Duzen and main fork of the Eel rivers. To the south is the remnant of the former species and it takes the name Aneides flavipunctatus (Strauch 1870). It is highly diversified morphologically and genetically and requires additional study. creator: Sean B. Reilly creator: David B. Wake uri: https://doi.org/10.7717/peerj.7370 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Reilly and Wake title: Fleas of black rats (Rattus rattus) as reservoir host of Bartonella spp. in Chile link: https://peerj.com/articles/7371 last-modified: 2019-08-01 description: BackgroundRattus rattus is a widely distributed, invasive species that presents an important role in disease transmission, either directly or through vector arthropods such as fleas. These black rats can transmit a wide variety of pathogens, including bacteria of the genus Bartonella, which can cause diseases in humans and animals. In Chile, no data are available identifying fleas from synanthropic rodents as Bartonella vectors. The aim of this study was to investigate the prevalence of Bartonella spp. in the fleas of R. rattus in areas with different climate conditions and featuring different human population densities.MethodsIn all, 174 fleas collected from 261 R. rattus captured from 30 localities with different human densities (cities, villages, and wild areas) across five hydrographic zones of Chile (hyper-arid, arid, semi-arid, sub-humid, and hyper-humid) were examined. Bartonella spp. presence was determined through polymerase chain reaction, using gltA and rpoB genes, which were concatenated to perform a similarity analysis with BLAST and phylogenetic analysis.ResultsOverall, 15 fleas species were identified; Bartonella gltA and rpoB fragments were detected in 21.2% (37/174) and 19.5% (34/174) of fleas, respectively. A total of 10 of the 15 fleas species found were positive for Bartonella DNA. Leptopsylla segnis was the most commonly collected flea species (n = 55), and it also presented a high prevalence of Bartonella DNA (P% = 34.5%). The highest numbers of fleas of this species were collected in villages of the arid zone. There were no seasonal differences in the prevalence of Bartonella DNA. The presence of Bartonella DNA in fleas was recorded in all hydrographic areas, and the arid zone presented the highest prevalence of this species. Regarding areas with different human densities, the highest prevalence was noted in the villages (34.8% gltA and 31.8% rpoB), followed by cities (14.8% gltA and 11.1% rpoB) and wild areas (7.4% gltA and 14.8% rpoB). The BLAST analysis showed a high similitude (>96%) with four uncharacterized Bartonella genotypes and with two species with zoonotic potential: B. mastomydis and B. tribocorum. The phylogenetic analysis showed a close relationship with B. elizabethae and B. tribocorum. This is the first study to provide evidence of the presence of Bartonella in fleas of R. rattus in Chile, indicating that the villages and arid zone correspond to areas with higher infection risk. creator: Lucila Moreno Salas creator: Mario Espinoza-Carniglia creator: Nicol Lizama Schmeisser creator: L. Gonzalo Torres creator: María Carolina Silva-de la Fuente creator: Marcela Lareschi creator: Daniel González-Acuña uri: https://doi.org/10.7717/peerj.7371 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Moreno Salas et al. title: Bioremediation of engine-oil contaminated soil using local residual organic matter link: https://peerj.com/articles/7389 last-modified: 2019-08-01 description: Soil remediation industries continue to seek technologies to speed-up treatment and reduce operating costs. Some processes are energy intensive and, in some cases, transport can be the main source of carbon emissions. Residual fertilizing materials (RFM), such as organic residues, have the potential to be beneficial bioremediation agents. Following a circular economy framework, we investigated the feasibility of sourcing RFMs locally to reduce transport and assess possible bioremediation efficiency gains. RFMs were recruited within 100 km of the treatment site: ramial chipped wood (RCW), horse manure (MANR) and brewer spent grain (BSG). They were added to the land treatment unit’s baseline fertilizer treatment (FERT, “F”) to measure if they improved the remediation efficiency of an engine oil-contaminated soil (7,500 ± 100 mg kg−1). Results indicate that MANR-F was the only amendment more effective than FERT for petroleum hydrocarbons (PHC) reduction, while emitting the least CO2 overall. RCW-F was equivalent to FERT but retained more moisture. Although BSG contributed the most nitrogen to the soil, BSG-F retained excessive moisture, emitted more volatile organic compounds, contained less soil O2, and was less effective than the baseline treatment. Significantly more of the C16–C22 fraction was removed (63% ± 22%) than all other fractions (C22–C28, C28–C34, C34–C40), which were equally removed. Microbial community-level physiological profiling was conducted with Biolog Ecoplates™, and catabolic diversity differed between treatments (utilization rates of 31 carbon sources). MANR-F has the potential to increase PHC-remediation speed and efficiency compared to inorganic fertilizer alone. Other RFM promote moisture retention and diverse microbial catabolic activity. A variety of RFM are present across the globe and some can offer low-cost amendments to boost remediation efficiency, while reducing treatment time compared to traditional fertilizer-only methods. creator: Kawina Robichaud creator: Miriam Lebeau creator: Sylvain Martineau creator: Marc Amyot uri: https://doi.org/10.7717/peerj.7389 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Robichaud et al. title: Association of genetic polymorphisms in SOD2, SOD3, GPX3, and GSTT1 with hypertriglyceridemia and low HDL-C level in subjects with high risk of coronary artery disease link: https://peerj.com/articles/7407 last-modified: 2019-08-01 description: BackgroundOxidative stress modulates insulin resistant-related atherogenic dyslipidemia: hypertriglyceridemia (HTG) and low high-density lipoprotein cholesterol (HDL-C) level. Gene polymorphisms in superoxide dismutase (SOD2 and SOD3), glutathione peroxidase-3 (GPX3), and glutathione S-transferase theta-1 (GSTT1) may enable oxidative stress-related lipid abnormalities and severity of coronary atherosclerosis. The present study investigated the associations of antioxidant-related gene polymorphisms with atherogenic dyslipidemia and atherosclerotic severity in subjects with high risk of coronary artery disease (CAD).MethodsStudy population comprises of 396 subjects with high risk of CAD. Gene polymorphisms: SOD2 rs4880, SOD3 rs2536512 and rs2855262, GPX rs3828599, and GSTT1 (deletion) were evaluated the associations with HTG, low HDL-C, high TG/HDL-C ratio, and severity of coronary atherosclerosis.ResultsSOD2 rs4880-CC, SOD3 rs2536512-AA, rs2855262-CC, and GPX3 rs3828599-AA, but not GSTT1-/- individually increased risk of HTG combined with low HDL-C level. With a combination of five risk-genotypes as a genetic risk score (GRS), GRS ≥ 6 increased risks of low HDL-C, high TG/HDL-C ratio, and HTG combined with low HDL-C, comparing with GRS 0–2 [respective adjusted ORs (95% CI) = 2.70 (1.24–5.85), 3.11 (1.55–6.23), and 5.73 (2.22–14.77)]. Gene polymorphisms, though, were not directly associated with severity of coronary atherosclerosis; high TG/HDL-C ratio was associated with coronary atherosclerotic severity [OR = 2.26 (95% CI [1.17–4.34])].ConclusionCombined polymorphisms in antioxidant-related genes increased the risk of dyslipidemia related to atherosclerotic severity, suggesting the combined antioxidant-related gene polymorphisms as predictor of atherogenic dyslipidemia. creator: Nisa Decharatchakul creator: Chatri Settasatian creator: Nongnuch Settasatian creator: Nantarat Komanasin creator: Upa Kukongviriyapan creator: Phongsak Intharaphet creator: Vichai Senthong uri: https://doi.org/10.7717/peerj.7407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Decharatchakul et al. title: Identification of a novel four-lncRNA signature as a prognostic indicator in cirrhotic hepatocellular carcinoma link: https://peerj.com/articles/7413 last-modified: 2019-08-01 description: BackgroundMany studies have shown that long noncoding RNAs (lncRNA) are closely associated with the occurrence and development of various tumors and have the potential to be prognostic markers. Moreover, cirrhosis is an important prognostic risk factors in patients with liver cancer. Some studies have reported that lncRNA-related prognostic models have been used to predict overall survival (OS) and recurrence-free survival (RFS) in patients with hepatocellular carcinoma (HCC). However, no one has constructed a prognostic lncRNA model only in patients with cirrhotic HCC. Thus, it is necessary to screen novel potential lncRNA markers for improve the prognosis of cirrhotic HCC patients.MethodsThe probe expression profile dataset (GSE14520–GPL3921) from the Gene Expression Omnibus (GEO), which included 204 cirrhotic HCC samples, was reannotated and the lncRNA and mRNA expression dataset was obtained. The patients were randomly assigned to either the training set (n = 103) and testing set (n = 100). Univariate cox regression and the least absolute shrinkage and selection operator (LASSO) model were applied to screen lncRNAs linked to the OS of cirrhotic HCC in the training set. The lncRNAs having significant correlation with OS were then selected and the multivariate Cox regression model was implemented to construct the prognostic score model. Whether or not this model was related to RFS in the training set was simultaneously determined. The testing set was used to validate the lncRNA risk score model. A risk score based on the lncRNA signature was used for stratified analysis of different clinical features to test their prognostic performance. The prognostic lncRNA-related protein genes were identified by the co-expression matrix of lncRNA-mRNA, and the function of these lncRNAs was predicted through the enrichment of these co-expression genes.ResultsThe signature consisted of four lncRNAs:AC093797.1,POLR2J4,AL121748.1 and AL162231.4. The risk model was closely correlated with the OS of cirrhotic HCC in the training cohort, with a hazard ratio (HR) of 3.650 (95% CI [1.761–7.566]) and log-rank P value of 0.0002. Moreover, this model also showed favorable prognostic significance for RFS in the training set (HR: 2.392, 95% CI [1.374–4.164], log-rank P = 0.0015). The predictive performance of the four-lncRNA model for OS and RFS was verified in the testing set. Furthermore, the results of stratified analysis revealed that the four-lncRNA model was an independent factor in the prediction of OS and RFS of patients with clinical characteristics such as TNM (Tumor, Node, Metastasis system) stages I–II, Barcelona Clinic Liver Cancer (BCLC) stages 0–A, and solitary tumors in both the training set and testing set. The results of functional prediction showed that four lncRNAs may be potentially involve in multiple metabolic processes, such as amino acid, lipid, and glucose metabolism in cirrhotic HCC. creator: Linkun Ma creator: Cunliang Deng uri: https://doi.org/10.7717/peerj.7413 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma and Deng title: The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis link: https://peerj.com/articles/7415 last-modified: 2019-08-01 description: The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases. creator: An Huang creator: Shuo Liu creator: Haijun Li creator: Hongdi Luo creator: Qingyong Ni creator: Yongfang Yao creator: Huailiang Xu creator: Bo Zeng creator: Ying Li creator: Zhimin Wei creator: Song Li creator: Mingwang Zhang uri: https://doi.org/10.7717/peerj.7415 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huang et al. title: Complexity of human walking: the attractor complexity index is sensitive to gait synchronization with visual and auditory cues link: https://peerj.com/articles/7417 last-modified: 2019-08-01 description: BackgroundDuring steady walking, gait parameters fluctuate from one stride to another with complex fractal patterns and long-range statistical persistence. When a metronome is used to pace the gait (sensorimotor synchronization), long-range persistence is replaced by stochastic oscillations (anti-persistence). Fractal patterns present in gait fluctuations are most often analyzed using detrended fluctuation analysis (DFA). This method requires the use of a discrete times series, such as intervals between consecutive heel strikes, as an input. Recently, a new nonlinear method, the attractor complexity index (ACI), has been shown to respond to complexity changes like DFA, while being computed from continuous signals without preliminary discretization. Its use would facilitate complexity analysis from a larger variety of gait measures, such as body accelerations. The aim of this study was to further compare DFA and ACI in a treadmill experiment that induced complexity changes through sensorimotor synchronization.MethodsThirty-six healthy adults walked 30 min on an instrumented treadmill under three conditions: no cueing, auditory cueing (metronome walking), and visual cueing (stepping stones). The center-of-pressure trajectory was discretized into time series of gait parameters, after which a complexity index (scaling exponent alpha) was computed via DFA. Continuous pressure position signals were used to compute the ACI. Correlations between ACI and DFA were then analyzed. The predictive ability of DFA and ACI to differentiate between cueing and no-cueing conditions was assessed using regularized logistic regressions and areas under the receiver operating characteristic curves (AUC).ResultsDFA and ACI were both significantly different among the cueing conditions. DFA and ACI were correlated (Pearson’s r = 0.86). Logistic regressions showed that DFA and ACI could differentiate between cueing/no cueing conditions with a high degree of confidence (AUC = 1.00 and 0.97, respectively).ConclusionBoth DFA and ACI responded similarly to changes in cueing conditions and had comparable predictive power. This support the assumption that ACI could be used instead of DFA to assess the long-range complexity of continuous gait signals. However, future studies are needed to investigate the theoretical relationship between DFA and ACI. creator: Philippe Terrier uri: https://doi.org/10.7717/peerj.7417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Terrier title: Downregulated expression of ARHGAP10 correlates with advanced stage and high Ki-67 index in breast cancer link: https://peerj.com/articles/7431 last-modified: 2019-08-01 description: BackgroundRho GTPase-activating protein 10 (ARHGAP10), which catalyzes the conversion of active Rho GTPase to the inactive form, is downregulated in some cancers. However, little is known about ARHGAP10 in breast cancer.MethodsThe transcriptional expression level of ARHGAP10 in breast cancer was analyzed with the data downloaded from The Cancer Genome Atlas (TCGA) and Oncomine, then verified by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) in 30 pairs of breast cancer tissues and the corresponding adjacent normal tissues. ARHGAP10 protein expression was examined by immunohistochemistry (IHC) in 190 breast cancer and 30 corresponding adjacent normal breast tissue samples. The associations between ARHGAP10 expression and clinicopathological characteristics of patients were analyzed, and Kaplan–Meier Plotter was used to assess the relationship between ARHGAP10 and relapse-free survival (RFS). Different expression levels of ARHGAP10 in response to chemotherapy agents were determined by GEO2R online tool. The potential biological functions of ARHGAP10 were analyzed by Gene Set Enrichment Analysis (GSEA) using data downloaded from TCGA.ResultsARHGAP10 mRNA and protein expression was lower in breast cancer tissues than in adjacent normal tissues. Low expression of ARHGAP10 was associated with advanced clinical TNM (cTNM) stage (pb = 0.001) and high Ki-67 index (p = 0.015). Low expression of ARHGAP10 indicated worse RFS (p = 0.0015) and a poor response to chemotherapy (p = 0.006). GSEA results showed that ARHGAP10 was involved in signaling pathways including protein export, nucleotide excision repair, base excision repair, focal adhesion, JAK-STAT pathway and the actin cytoskeleton. creator: Yujing Li creator: Beilei Zeng creator: Yunhai Li creator: Chong Zhang creator: Guosheng Ren uri: https://doi.org/10.7717/peerj.7431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Defining cognitive profiles of depressive patients using the Brief Assessment of Cognition in Affective Disorders link: https://peerj.com/articles/7432 last-modified: 2019-08-01 description: BackgroundCognitive impairments in patients with depressive disorders have a negative impact on their daily skill functioning and quality of life. In this study, we evaluated the cognitive profiles and associated factors of patients with depressive disorders with the Brief Assessment of Cognition in Affective Disorders (BAC-A).MethodsThis cross-sectional study consisted of 75 patients with depressive disorders (56 patients with major depressive disorder (MDD) and 19 patients with depressive disorder NOS or dysthymic disorder (non-MDD)). We evaluated the participants’ cognitive functions at euthymic status using the BAC-A. The BAC-A includes six subtests derived from the Brief Assessment of Cognition in Schizophrenia (BAC-S) and Affective Processing Tests. The current severity of depressive symptoms was assessed with the 17-item Hamilton Depression Rating Scale (HAMD-17), and we recorded any psychotropic drugs being used by the patients.ResultsWe observed no differences in cognitive profiles in the MDD group and non-MDD group after adjusting for educational levels, severity of depression, and psychotropic drugs. Instead, the HAMD-17 scores were negatively correlated to cognitive performance in working memory, motor speed, verbal fluency, attention and processing speed, executive function, composite score, and the six indexes of the Affective Processing Test measured by the BAC-A. A longer illness duration was associated with worse performance of four indexes of the Affective Processing Test. Furthermore, benzodiazepine use was associated with a worse performance of verbal memory, and antidepressant use was associated with better motor speed performance.ConclusionThe current severity of depressive symptoms and psychotropic drugs being taken, not the diagnosis category, are associated with cognitive impairments in patients with depressive disorders. Clinicians should pay particular attention to managing residual depressive symptoms and prescribing adequate psychotropic drugs in order to eliminate depressive patients’ cognitive deficits. creator: Ruei-An Chen creator: Chun-Yi Lee creator: Yu Lee creator: Chi-Fa Hung creator: Yu-Chi Huang creator: Pao-Yen Lin creator: Sheng-Yu Lee creator: Liang-Jen Wang uri: https://doi.org/10.7717/peerj.7432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Use of factor scores in multiple regression analysis for estimation of body weight by certain body measurements in Romanov Lambs link: https://peerj.com/articles/7434 last-modified: 2019-08-01 description: The study investigates the solution of the multicollinearity between certain body measurements of Romanov lambs and prediction of the body weight of Romanov lambs using the thus calculated factor analysis scores and a multiple regression model. For this purpose, the body measurements (wither height (WH), croup height (CH), body length (BL), chest depth (CD), chest circumference (CC), chest width behind shoulders (CWS) and head length (HL)) and body weight (BW) of 6-month-old 50 Romanov lambs born in 2015 were used. The factor analysis scores were used to obtain the prediction equation for the relationship between the investigated traits. The analysis results showed that there was a multicollinearity between the wither and croup height traits used in the prediction equation. Moreover, the results revealed that the variables for the body measurements can be represented by two factors. These factors explained 50.89% and 22.86% of the total variance, respectively. The multicollinearity between the independent variables was eliminated with the use of the factor scores obtained with the factor analysis in the multiple regression model, and thus it was observed that better results can be obtained by using the factor analysis scores in the prediction of the body weight of 6-month-old Romanov lambs. creator: Yalcin Tahtali uri: https://doi.org/10.7717/peerj.7434 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tahtali title: Indirect Doppler flow systolic blood pressure measurements taken with and without headphones in privately-owned, conscious dogs link: https://peerj.com/articles/7440 last-modified: 2019-08-01 description: ObjectiveThe purpose of this study was to assess the effect of headphone use and covariates on indirect radial Doppler flow systolic arterial blood pressure (BP) measurements in dogs.MethodsBetween May and August 2018, 100 privately-owned dogs were enrolled. Blood pressure was measured in lateral recumbency, with and without headphones, using a randomized crossover design. The initial BP, mean of BP 2-6, weight, BCS, MCS, anxiety score, and heart rate were recorded. Mixed effects crossover analyses and Spearman rank correlation coefficients were determined.ResultsEighty-four dogs completed the study. Eleven dogs were removed due to excessive anxiety, 10 of which were in the non-headphone first group. The number of dogs diagnosed as hypertensive did not differ between measurement types (19 vs. 18), with seven dogs categorized as hypertensive during both periods. Significant differences in BP were identified (F[1, 80] = 4.3, P = 0.04) due to higher results for measurements taken without headphones for BP 1, but not BP 2-6. Systolic BP was positively correlated with anxiety score, age, and weight.Conclusions and Clinical RelevanceThough BP 1 was significantly higher when taken without headphones, this pattern did not persist for BP 2-6. Lack of association between BP 2-6 results and measurement type could reflect exclusion of dogs most sensitive to white coat hypertension, acclimation to technique, or improved sound quality of headphones. Given significantly higher BP 1 results and disproportionate exclusion of dogs due to anxiety when measurements first were taken without headphones, use of headphones is recommended to improve accuracy of results. creator: India R. Gill creator: Joshua M. Price creator: Jacqueline C. Whittemore uri: https://doi.org/10.7717/peerj.7440 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gill et al. title: Universal linguistic hierarchies are not innately wired. Evidence from multiple adjectives link: https://peerj.com/articles/7438 last-modified: 2019-08-01 description: BackgroundLinguists and psychologists have explained the remarkable similarities in the orderings of linguistic elements across languages by suggesting that our inborn ability for language makes available certain innately wired primitives. Different types of adjectives, adverbs, and other elements in the functional spine are considered to occupy fixed positions via innate hierarchies that determine orderings such as A>B>C, banning other permutations (*B>C>A). The goal of this research is to tap into the nature and rigidity of such hierarchies by comparing what happens when people process orderings that either comply with them or violate them.MethodN = 170 neurotypical, adult speakers completed a timed forced choice task that featured stimuli showing a combination of two adjectives and a Spelke-object (e.g., ‘I bought a square black table’). Two types of responses were collected: (i) acceptability judgments on a 3-point Likert scale that featured the options ‘correct’, ‘neither correct nor wrong’, and ‘wrong’ and (ii) reaction times. The task featured three conditions: 1. size adjective > nationality adjective, 2. color adjective > shape adjective, 3. subjective comment adjective > material adjective. Each condition had two orders. In the congruent order, the adjective pair was ordered in agreement with what is traditionally accepted as dictated by the universal hierarchy. In the incongruent order, the ordering was reversed, thus the hierarchy was violated.ResultsIn the first experiment, the results of n = 140 monolinguals showed that across conditions, both congruent and incongruent orders were generally accepted as correct. For 2/3 conditions, the difference in acceptability ratings between congruent and incongruent orders did not reach statistical significance. Using time as a window to processing, reaction times showed that incongruent orders do not take longer to process than congruent ones, as should be the case if the former were treated as being licensed under some type of special condition (e.g., contrastive focus) that reverses the unmarked order and legitimizes the violation of the hierarchy. In the second experiment, the results of n = 30 bidialectals, tested in both language varieties, corroborated the findings of the first experiment.ConclusionsOur findings do not provide evidence for an innate hierarchy for adjective ordering that imposes one rigid, unmarked order. We discuss the importance of notions such as subjectivity and inherentness, and show that for some conditions, not only is there no evidence for a hard constraint that bans incongruent orders, but even simple preferences of congruent orders over incongruent ones are hard to discern. Capturing the bigger picture, given that both the hierarchies and their legit permutations have been described as innate, our results reduce the amount of primitives that are cast as innate, eventually offering a deflationist approach to human linguistic cognition. creator: Evelina Leivada creator: Marit Westergaard uri: https://doi.org/10.7717/peerj.7438 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Leivada and Westergaard