title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2019-07 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Taxonomic, biological and geographical traits of species in a coastal dune flora in the southeastern Cape Floristic Region: regional and global comparisons link: https://peerj.com/articles/7336 last-modified: 2019-07-31 description: In Mediterranean-Climate Ecosystems (MCEs), Holocene coastal dunes comprise small, fragmented and dynamic features which have nutritionally imbalanced and excessively drained, droughty, sandy soils. These characteristics, along with summer drought and salt-laden winds, pose many challenges for plant colonization and persistence. Consequently, MCE dune floras are likely to be distinctive with a high proportion of habitat specialists and strong convergence in growth form mixes. Very little research has compared the species traits of dune floras within and across MCEs. This paper contributes to filling that gap. Here, we analyze the taxonomic, biological and geographical traits for all 402 species in a flora from a dune landscape (Cape St Francis) in the southeastern Cape Floristic Region (CFR) and compare patterns with the trait profiles of other dune floras at a regional (CFR) and global (MCE) scale. Within the CFR, the southeastern (all-year-rainfall) flora at Cape St Francis had a similar trait profile to western (winter-rainfall) dune floras, except for having a lower representation of species belonging to CFR-endemic clades, and higher number of species associated with tropical lineages. The St Francis flora, in common with other CFR and MCE floras, was dominated by members of the Asteraceae, Fabaceae and Poaceae. Some 40% of the St Francis flora was endemic to the CFR, typical of the high rate of MCE-level endemism elsewhere in the CFR, and in other MCEs. About 30% of the flora was confined to calcareous sand, a value typical for many other MCE sites. The St Francis flora, as well as other CFR dune floras, differs from those of other MCEs by having many species associated with shrubby lineages, and by the relatively high incidence of species associated with tropical lineages. The growth form profile of the St Francis and other CFR floras shows strongest similarity with that of Australian MCE dunes in that in both regions, evergreen hemicryptophytes and shrubs share dominance, and annuals are floristically and ecologically subordinate. The least similar of MCEs to the St Francis trait profile is the Mediterranean Basin where annuals are the most frequent growth form while shrubs are subordinate. California and Chile dune floras appear to occupy an intermediate position, in terms of growth form mix, between the Cape and Australia on the one hand, where dune floras have retained features typical of nutrient-poor soils, and the Mediterranean Basin, where dwarf, deciduous shrubs and annuals dominate the life form spectrum. All MCE dunes are threatened by alien plants, infrastructure development, tourism demands and rising sea levels. The high incidence of species of conservation concern in CFR dune floras underestimates the exponentially increasing threats to their habitats, which are already historically at a much-reduced extent. All remaining coastal dune habitat in the CFR, and probably in other MCEs, should be conserved in their entirety. creator: Richard M. Cowling creator: Caryl Logie creator: Joan Brady creator: Margie Middleton creator: B. Adriaan Grobler uri: https://doi.org/10.7717/peerj.7336 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cowling et al. title: Discovery of novel astrovirus genotype species in small ruminants link: https://peerj.com/articles/7338 last-modified: 2019-07-31 description: Astroviruses (AstV) are single-stranded, positive-sense RNA viruses, best known for causing diarrhea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic AstV showed associations with encephalitis in humans as well as in other mammals. In Switzerland, two different neurotropic AstV were identified in cattle, as well as one in a sheep. The high genetic similarity between the ovine and one of the bovine AstV strengthens the hypothesis of an interspecies transmission. In humans, AstV associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aims of this study were (1) the investigation of the potential occurrence of neurotropic AstV in feces samples, (2) the discovery and analysis of so far unknown AstV in small ruminants and other ruminant species’ fecal samples and (3) the examination of a potential interspecies transmission of AstV. To achieve these aims, RNA extraction out of 164 fecal samples from different ruminant species was performed and all samples were screened for known neurotropic AstV occurring in Switzerland, as well as for various AstV using RT-PCR. Positive tested samples were submitted to next generation sequencing. The generated sequences were compared to nucleotide- and amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed. The excretion of neurotropic AstV in small ruminants’ feces could not be demonstrated, but this work suggests the first identification of AstV in goats as well as the discovery of multiple and highly diverse new genetic variants in small ruminants, which lead to a classification into novel genotype-species. Additionally, the prediction of multiple recombination events in four of five newly discovered full or almost full-length genome sequences suggests a plausible interspecies transmission. The findings point out the occurrence and fecal shedding of previously unknown AstV in sheep and goats and pave the way towards a better understanding of the diversity and transmission of AstV in small ruminants. creator: Ronja V. Kauer creator: Michel C. Koch creator: Melanie M. Hierweger creator: Simea Werder creator: Céline L. Boujon creator: Torsten Seuberlich uri: https://doi.org/10.7717/peerj.7338 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kauer et al. title: TLR2 polymorphism (rs650082970) is associated with somatic cell count in goat milk link: https://peerj.com/articles/7340 last-modified: 2019-07-31 description: Pathogens invading the mammary gland are recognized through a range of pattern recognition receptors (PRRs), residing on the plasma membrane of mammary epithelial cells. Toll-like receptor 2 (TLR2) signalling is responsible for recognition of Gram-positive bacteria, which are the most common mastitis-causing pathogens in goats. Somatic cell counts (SCC) in milk are routinely determined in goat dairy flocks and serve as an indicator of milk quality, which is highly correlated to intramammary infections. Recently, a single nucleotide polymorphism of the TLR2 was suggested to be associated with SCC in goat milk. To further test the suggested association, we genotyped 61 Slovenian Alpine goats included in the dataset. The effect of the genotype was analysed using the general linear model (GLM) procedure of SAS/STAT software. We found the TLR2 genotypes significantly (p = 0.0007) associated with milk SCC. Animals with the A/G genotype had significantly (p ≤ 0.05) lower SCC value in milk compared to the G/G genotype. Our data suggest that the A allele is the minor one and is associated with lower milk SCC. In the current study, we provide a validated PCR-RFLP based genotyping assay for the TLR2 SNP (rs650082970) and confirm its association with milk SCC. Further studies to confirm the association on a larger number of animals of different breeds and to explain functional consequences of the polymorphism in relation to SCC are encouraged. creator: Jernej Ogorevc creator: Mojca Simčič creator: Minja Zorc creator: Monika Škrjanc creator: Peter Dovč uri: https://doi.org/10.7717/peerj.7340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ogorevc et al. title: Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail link: https://peerj.com/articles/7342 last-modified: 2019-07-31 description: Ampullariids are freshwater gastropods bearing a gill and a lung, thus showing different degrees of amphibiousness. In particular, Pomacea canaliculata (Caenogastropoda, Ampullariidae) is an obligate air-breather that relies mainly or solely on the lung for dwelling in poorly oxygenated water, for avoiding predators, while burying in the mud during aestivation, and for oviposition above water level. In this paper, we studied the morphological peculiarities of the gill in this species. We found (1) the gill and lung vasculature and innervation are intimately related, allowing alternation between water and air respiration; (2) the gill epithelium has features typical of a transporting rather than a respiratory epithelium; and (3) the gill has resident granulocytes within intraepithelial spaces that may serve a role for immune defence. Thus, the role in oxygen uptake may be less significant than the roles in ionic/osmotic regulation and immunity. Also, our results provide a morphological background to understand the dependence on aerial respiration of Pomacea canaliculata. Finally, we consider these findings from a functional perspective in the light of the evolution of amphibiousness in the Ampullariidae, and discuss that master regulators may explain the phenotypic convergence of gill structures amongst this molluscan species and those in other phyla. creator: Cristian Rodriguez creator: Guido I. Prieto creator: Israel A. Vega creator: Alfredo Castro-Vazquez uri: https://doi.org/10.7717/peerj.7342 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rodriguez et al. title: A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma link: https://peerj.com/articles/7360 last-modified: 2019-07-31 description: BackgroundOral squamous cell carcinoma (OSCC) is the most common type of head and neck squamous cell carcinoma with an unsatisfactory prognosis. The aim of this study was to identify potential prognostic mRNA biomarkers of OSCC based on analysis of The Cancer Genome Atlas (TCGA).MethodsExpression profiles and clinical data of OSCC patients were collected from TCGA database. Univariate Cox analysis and the least absolute shrinkage and selection operator Cox (LASSO Cox) regression were used to primarily screen prognostic biomarkers. Then multivariate Cox analysis was performed to build a prognostic model based on the selected prognostic mRNAs. Nomograms were generated to predict the individual’s overall survival at 3 and 5 years. The model performance was assessed by the time-dependent receiver operating characteristic (ROC) curve and calibration plot in both training cohort and validation cohort (GSE41613 from NCBI GEO databases). In addition, machine learning was used to assess the importance of risk factors of OSCC. Finally, in order to explore the potential mechanisms of OSCC, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was completed.ResultsThree mRNAs (CLEC3B, C6 and CLCN1) were finally identified as a prognostic biomarker pattern. The risk score was imputed as: (−0.38602 × expression level of CLEC3B) + (−0.20632 × expression level of CLCN1) + (0.31541 × expression level of C6). In the TCGA training cohort, the area under the curve (AUC) was 0.705 and 0.711 for 3- and 5-year survival, respectively. In the validation cohort, AUC was 0.718 and 0.717 for 3- and 5-year survival. A satisfactory agreement between predictive values and observation values was demonstrated by the calibration curve in the probabilities of 3- and 5- year survival in both cohorts. Furthermore, machine learning identified the 3-mRNA signature as the most important risk factor to survival of OSCC. Neuroactive ligand-receptor interaction was most enriched mostly in KEGG pathway analysis.ConclusionA 3-mRNA signature (CLEC3B, C6 and CLCN1) successfully predicted the survival of OSCC patients in both training and test cohort. In addition, this signature was an independent and the most important risk factor of OSCC. creator: Ruoyan Cao creator: Qiqi Wu creator: Qiulan Li creator: Mianfeng Yao creator: Hongbo Zhou uri: https://doi.org/10.7717/peerj.7360 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cao et al. title: The use of biochar in animal feeding link: https://peerj.com/articles/7373 last-modified: 2019-07-31 description: Biochar, that is, carbonized biomass similar to charcoal, has been used in acute medical treatment of animals for many centuries. Since 2010, livestock farmers increasingly use biochar as a regular feed supplement to improve animal health, increase nutrient intake efficiency and thus productivity. As biochar gets enriched with nitrogen-rich organic compounds during the digestion process, the excreted biochar-manure becomes a more valuable organic fertilizer causing lower nutrient losses and greenhouse gas emissions during storage and soil application. Scientists only recently started to investigate the mechanisms of biochar in the different stages of animal digestion and thus most published results on biochar feeding are based so far on empirical studies. This review summarizes the state of knowledge up to the year 2019 by evaluating 112 relevant scientific publications on the topic to derive initial insights, discuss potential mechanisms behind observations and identify important knowledge gaps and future research needs. The literature analysis shows that in most studies and for all investigated farm animal species, positive effects on different parameters such as toxin adsorption, digestion, blood values, feed efficiency, meat quality and/or greenhouse gas emissions could be found when biochar was added to feed. A considerable number of studies provided statistically non-significant results, though tendencies were mostly positive. Rare negative effects were identified in regard to the immobilization of liposoluble feed ingredients (e.g., vitamin E or Carotenoids) which may limit long-term biochar feeding. We found that most of the studies did not systematically investigate biochar properties (which may vastly differ) and dosage, which is a major drawback for generalizing results. Our review demonstrates that the use of biochar as a feed additive has the potential to improve animal health, feed efficiency and livestock housing climate, to reduce nutrient losses and greenhouse gas emissions, and to increase the soil organic matter content and thus soil fertility when eventually applied to soil. In combination with other good practices, co-feeding of biochar may thus have the potential to improve the sustainability of animal husbandry. However, more systematic multi-disciplinary research is definitely needed to arrive at generalizable recommendations. creator: Hans-Peter Schmidt creator: Nikolas Hagemann creator: Kathleen Draper creator: Claudia Kammann uri: https://doi.org/10.7717/peerj.7373 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Schmidt et al. title: Long-term warming results in species-specific shifts in seed mass in alpine communities link: https://peerj.com/articles/7416 last-modified: 2019-07-31 description: BackgroundGlobal warming can cause variation in plant functional traits due to phenotypic plasticity or rapid microevolutionary change. Seed mass represents a fundamental axis of trait variation in plants, from an individual to a community scale. Here, we hypothesize that long-term warming can shift the mean seed mass of species.MethodsWe tested our hypothesis in plots that had been warmed over 18 years in alpine meadow communities with a history of light grazing (LG) and heavy grazing (HG) on the Qinghai-Tibet plateau. In this study, seeds were collected during the growing season of 2015.ResultsWe found that warming increased the mean seed mass of 4 (n = 19) species in the LG meadow and 6 (n = 20) species in the HG meadow, while decreasing the mean seed mass of 6 species in the LG and HG meadows, respectively. For 7 species, grazing history modified the effect of warming on seed mass. Therefore, we concluded that long-term warming can shift the mean seed mass at the species level. However, the direction of this variation is species-specific. Our study suggests that mean seed mass of alpine plant species appears to decrease in warmer (less stressful) habitats based on life-history theory, but it also suggests there may be an underlying trade-off in which mean seed mass may increase due to greater thermal energy inputs into seed development. Furthermore, the physical and biotic environment modulating this trade-off result in complex patterns of variation in mean seed mass of alpine plant species facing global warming. creator: Chunhui Zhang creator: Zhen Ma creator: Huakun Zhou creator: Xinquan Zhao uri: https://doi.org/10.7717/peerj.7416 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples link: https://peerj.com/articles/7295 last-modified: 2019-07-30 description: BackgroundBiological invasions are major drivers of environmental change that can significantly alter ecosystem function and diversity. In plants, soil microbes play an important role in plant establishment and growth; however, relatively little is known about the role they might play in biological invasions. A first step to assess whether root microbes may be playing a role in the invasion process is to find out if invasive plants host different microbes than neighbouring native plant species.MethodsIn this study we investigated differences in root associated microbes of native sugar maple (Acer saccharum Marsh.) and exotic Norway maple (A. platanoides L.) collected from a forested reserve in eastern Canada. We used microscopy to examine root fungi and high-throughput sequencing to characterize the bacterial, fungal and arbuscular mycorrhizal communities of both maple species over one growing season.ResultsWe found differences in root associated bacterial and fungal communities between host species. Norway maple had a higher bacterial and fungal OTU (operational taxonomic units) richness compared to sugar maple, and the indicator species analysis revealed that nine fungal OTUs and three bacterial OTUs had a significant preference for sugar maple. The dominant bacterial phyla found on the roots of both maple species were Actinobacteria and Proteobacteria. The most common fungal orders associated with the Norway maple roots (in descending order) were Helotiales, Agaricales, Pleosporales, Hypocreales, Trechisporales while the Agaricales, Pleosporales, Helotiales, Capnodiales and Hypocreales were the dominant orders present in the sugar maple roots. Dark septate fungi colonization levels were higher in the sugar maple, but no differences in arbuscular mycorrhizal fungal communities and colonization rates were detected between maple species.DiscussionOur findings show that two congeneric plant species grown in close proximity can harbor distinct root microbial communities. These findings provide further support for the importance of plant species in structuring root associated microbe communities. The high colonization levels observed in Norway maple demonstrates its compatibility with arbuscular mycorrhizal fungi in the introduced range. Plant-associated microbial communities can affect host fitness and function in many ways; therefore, the observed differences suggest a possibility that biotic interactions can influence the dynamics between native and invasive species. creator: Tonia DeBellis creator: Steven W. Kembel creator: Jean-Philippe Lessard uri: https://doi.org/10.7717/peerj.7295 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 DeBellis et al. title: Three-dimensional facial development of children with unilateral cleft lip and palate during the first year of life in comparison with normative average faces link: https://peerj.com/articles/7302 last-modified: 2019-07-30 description: BackgroundStereophotogrammetry can be used to study facial morphology in both healthy individuals as well as subjects with orofacial clefts because it shows good reliability, ability to capture images rapidly, archival capabilities, and high resolution, and does not require ionizing radiation. This study aimed to compare the three-dimensional (3D) facial morphology of infants born with unilateral cleft lip and palate (UCLP) with an age-matched normative 3D average face before and after primary closure of the lip and soft palate.MethodsThirty infants with a non-syndromic complete unilateral cleft lip, alveolus, and palate participated in the study. Three-dimensional images were acquired at 3, 6, 9, and 12 months of age. All subjects were treated according to the primary surgical protocol consisting of surgical closure of the lip and the soft palate at 6 months of age. Three-dimensional images of UCLP patients at 3, 6 (pre-treatment), 9, and 12 months of age were superimposed on normative datasets of average facial morphology using the children’s reference frame. Distance maps of the complete 3D facial surface and the nose, upper lip, chin, forehead, and cheek regions were developed.ResultsAssessments of the facial morphology of UCLP and control subjects by using color-distance maps showed large differences in the upper lip region at the location of the cleft defect and an asymmetry at the nostrils at 3 and 6 months of age. At 9 months of age, the labial symmetry was completely restored although the tip of the nose towards the unaffected side showed some remnant asymmetry. At 12 months of age, the symmetry of the nose improved, with only some remnant asymmetry noted on both sides of the nasal tip. At all ages, the mandibular and chin regions of the UCLP patients were 2.5–5 mm posterior to those in the average controls.ConclusionIn patients with UCLP deviations from the normative average 3D facial morphology of age-matched control subjects existed for the upper lip, nose, and even the forehead before lip and soft palate closure was performed. Compared to the controls symmetry in the upper lip was restored, and the shape of the upper lip showed less variation after primary lip and soft palate closure. At this early age, retrusion of the soft-tissue mandible and chin, however, seems to be developing already. creator: Sander Brons creator: Jene W. Meulstee creator: Tom G.J. Loonen creator: Rania M. Nada creator: Mette A.R. Kuijpers creator: Ewald M. Bronkhorst creator: Stefaan J. Bergé creator: Thomas J.J. Maal creator: Anne Marie Kuijpers-Jagtman uri: https://doi.org/10.7717/peerj.7302 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Brons et al. title: Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead Craterocephalus amniculus (Atheriniformes, Teleostei) link: https://peerj.com/articles/7347 last-modified: 2019-07-30 description: Belonging to the order Atheriniformes, Craterocephalus is one of the most widespread genera of freshwater fishes in Australia, spanning along the northern coast from central Western Australia to central New South Wales and across the Murray-Darling and Lake Eyre basins. In this study, both conventional cytogenetic techniques (Giemsa, C-banding, CMA3/DAPI staining), and fluorescence in situ hybridization (FISH) with telomeric DNA and rDNA probes were used to examine the karyotypes and other chromosomal characteristics of Darling hardyhead (Craterocephalus amniculus) from New South Wales, Australia. We identified a diploid chromosome number 2n = 48 (NF = 58) in all studied individuals. FISH with rDNA probes showed a nonsyntenic pattern, with signals on one pair of subtelocentric chromosomes for 5S rDNA and one pair of submetacentric chromosomes for 28S rDNA. C-banding displayed the accumulation of constitutive heterochromatin in the centromeric regions of approximately 40 chromosomes. CMA3/DAPI fluorescence staining revealed extremely GC-rich signals in the pericentromeric region of one submetacentric chromosomal pair with size polymorphism. We detected telomeric signals at the end of all chromosomes and no interstitial signals. creator: Zuzana Majtánová creator: Karl G. Moy creator: Peter J. Unmack creator: Petr Ráb creator: Tariq Ezaz uri: https://doi.org/10.7717/peerj.7347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Majtánová et al. title: Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis) link: https://peerj.com/articles/7384 last-modified: 2019-07-30 description: Species delimitation is challenging in sibling species/cryptic lineages because of the absence of clear diagnostic traits. However, integration of different approaches such as phylogeography and ecological niche comparison offers one potential approach to tease apart recently diverged lineages. In this study, we estimate the ecological niche divergence among lineages in Chromis viridis in a broad-scale phylogeographic framework to test whether the combination of these two approaches can effectively distinguish recently diverged lineages. Results from Cytb and Rag2 analyses identified two cryptic lineages (C. viridis A and C. viridis B) that diverged ∼3 Myr ago. Estimates of ecological niche divergence with 11 environmental parameters across the broad geographic range of these lineages showed overlapping ecological niches and niche conservatism. However, regardless of the incongruence between genetic and ecological niche divergence, the substantial genetic divergence between the two clades of C. viridis in both mtDNA and nuclear loci strong suggest that they are cryptic taxa. creator: Shang Yin Vanson Liu creator: Mao-Ning Tuanmu creator: Rita Rachmawati creator: Gusti Ngurah Mahardika creator: Paul H. Barber uri: https://doi.org/10.7717/peerj.7384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Identification of significant gene and pathways involved in HBV-related hepatocellular carcinoma by bioinformatics analysis link: https://peerj.com/articles/7408 last-modified: 2019-07-30 description: BackgroundHepatocellular carcinoma (HCC) is a common malignant tumor affecting the digestive system and causes serious financial burden worldwide. Hepatitis B virus (HBV) is the main causative agent of HCC in China. The present study aimed to investigate the potential mechanisms underlying HBV-related HCC and to identify core biomarkers by integrated bioinformatics analyses.MethodsIn the present study, HBV-related HCC GSE19665, GSE55092, GSE94660 and GSE121248 expression profiles were downloaded from the Gene Expression Omnibus database. These databases contain data for 299 samples, including 145 HBV-related HCC tissues and 154 non-cancerous tissues (from patients with chronic hepatitis B). The differentially expressed genes (DEGs) from each dataset were integrated and analyzed using the RobustRankAggreg (RRA) method and R software, and the integrated DEGs were identified. Subsequently, the gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID online tool, and the protein–protein interaction (PPI) network was constructed using STRING and visualized using Cytoscape software. Finally, hub genes were identified, and the cBioPortal online platform was used to analyze the association between the expression of hub genes and prognosis in HCC.ResultsFirst, 341 DEGs (117 upregulated and 224 downregulated) were identified from the four datasets. Next, GO analysis showed that the upregulated genes were mainly involved in cell cycle, mitotic spindle, and adenosine triphosphate binding. The majority of the downregulated genes were involved in oxidation reduction, extracellular region, and electron carrier activity. Signaling pathway analysis showed that the integrated DEGs shared common pathways in retinol metabolism, drug metabolism, tryptophan metabolism, caffeine metabolism, and metabolism of xenobiotics by cytochrome P450. The integrated DEG PPI network complex comprised 288 nodes, and two important modules with high degree were detected using the MCODE plug-in. The top ten hub genes identified from the PPI network were SHCBP1, FOXM1, KIF4A, ANLN, KIF15, KIF18A, FANCI, NEK2, ECT2, and RAD51AP1. Finally, survival analysis revealed that patients with HCC showing altered ANLN and KIF18A expression profiles showed worse disease-free survival. Nonetheless, patients with FOXM1, NEK2, RAD51AP1, ANLN, and KIF18A alterations showed worse overall survival.ConclusionsThe present study identified key genes and pathways involved in HBV-related HCC, which improved our understanding of the mechanisms underlying the development and recurrence of HCC and identified candidate targets for the diagnosis and treatment of HBV-related HCC. creator: Shucai Xie creator: Xili Jiang creator: Jianquan Zhang creator: Shaowei Xie creator: Yongyong Hua creator: Rui Wang creator: Yijun Yang uri: https://doi.org/10.7717/peerj.7408 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xie et al. title: Increasing perceived hand size improves motor performance in individuals with stroke: a home-based training study link: https://peerj.com/articles/7114 last-modified: 2019-07-29 description: BackgroundIncreasing perceived hand size with magnifying lenses improves tactile discrimination and induces changes in action performance. We previously demonstrated that motor skills (tested with grip force, finger tapping, and a reach to grasp tasks) improved when actions were performed with magnified compared to normal vision; twenty-eight percent of 25 participants with stroke exhibited significant improvement on a composite measure of motor performance with magnification as compared to a session without magnification.MethodsTo investigate the potential implications of magnification of vision for motor rehabilitation, we recruited individuals with stroke from the original cohort who exhibited an improvement of at least 10% in grip force and/or finger tapping for a home training protocol. Six individuals with stroke completed a two-week home-based training program in which they performed a range of activities while looking at their hand magnified. Motor skills were measured before, immediately after, and two weeks after the training.ResultsFive of the six participants showed an improvement on motor tasks when tested after the training. In two participants the improvement was evident immediately after the training and persisted in time, while it occurred at two-weeks post-training in the other participants. These results suggest that the magnification of vision is a potential tool for the rehabilitation of post-stroke motor deficits. creator: Elisabetta Ambron creator: Steven Jax creator: Luis Schettino creator: H. Branch Coslett uri: https://doi.org/10.7717/peerj.7114 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ambron et al. title: Altitudinal gradients in Magellanic sub-Antarctic lagoons: the effect of elevation on freshwater macroinvertebrate diversity and distribution link: https://peerj.com/articles/7128 last-modified: 2019-07-29 description: BackgroundThe study of altitudinal gradients provides insights about species diversity, distribution patterns and related drivers. The Magellanic sub-Antarctic ecoregion has a steep elevational gradient, peaking at around 1,000 m a.s.l., and marked changes in temperature and landscape composition can be observed over relatively short distances.MethodsThis study assessed freshwater macroinvertebrate diversity associated with lakes and ponds along the altitudinal gradient of a Magellanic sub-Antarctic watershed.ResultsA monotonic decline in species richness was observed with increasing elevation, with simpler and more even community composition at higher altitude. This pattern differs from the mid-peak trend found in streams of the same watershed. Functional feeding group structure also diminished with increasing elevation.DiscussionThe study provides a descriptive baseline of macroinvertebrate community structure associated with lentic freshwater ecosystems in the Magellanic sub-Antarctic ecoregion, and confirms that elevation has substantial effects on community structure, function and environmental features, even in these relatively low elevation mountain ranges. The harsh environmental conditions of this ecoregion increase freshwater macroinvertebrate development time, as well as decreasing habitat availability and food supply, supporting simple but well adapted communities. In conjunction with previous research, this study provides a watershed-scale platform of information underpinning future long-term research in the region. creator: Javier Rendoll Cárcamo creator: Tamara Contador creator: Melisa Gañán creator: Carolina Pérez Troncoso creator: Alan Maldonado Márquez creator: Peter Convey creator: James Kennedy creator: Ricardo Rozzi uri: https://doi.org/10.7717/peerj.7128 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rendoll Cárcamo et al. title: Neutrophil–lymphocyte ratio is prognostic in early stage resected small-cell lung cancer link: https://peerj.com/articles/7232 last-modified: 2019-07-29 description: BackgroundFor selected early stage small cell lung cancer (SCLC), curative intent surgery is often performed. Previous studies, predominantly from East Asia, reported that high neutrophil to lymphocyte ratio (NLR), and platelet–lymphocyte ratio (PLR) correlate with poor prognosis in several types of tumors including SCLC. Our aim was to investigate the prognostic value of NLR and PLR in Caucasian patients with resected SCLC, as potential tool to select patients for multimodal treatment including surgery.MethodsConsecutive patients evaluated at three centers between 2000 and 2013 with histologically confirmed and surgically resected SCLC were retrospectively analyzed. NLR and PLR at diagnosis was used to categorize patients into “high” and “low” groups based on receiver operating curve analysis. Univariate and multivariate analyses were used to evaluate the impact of clinical and pathological characteristics on outcome.ResultsThere were a total of 189 patients with a median age of 58 years, and the majority had stage I or II disease. We found a significant correlation between NLR and tumor stage (p = 0.007) and age (p = 0.038). Low NLR (LNLR) was associated with significantly longer overall survival, while PLR had no prognostic impact. There were significant associations between NLR and PLR but not with gender, vascular involvement, tumor necrosis, peritumoral inflammation, or tumor grade.ConclusionPre-operative LNLR may be a favorable prognostic factor in stage I–II SCLCs. PLR is not prognostic in this population. LNLR is easy to assess and can be integrated into routine clinical practice. Further prospective studies are needed to confirm these observations. creator: Zoltan Lohinai creator: Laura Bonanno creator: Aleksei Aksarin creator: Alberto Pavan creator: Zsolt Megyesfalvi creator: Balazs Santa creator: Virag Hollosi creator: Balazs Hegedus creator: Judit Moldvay creator: PierFranco Conte creator: Mikhail Ter-Ovanesov creator: Evgeniy Bilan creator: Balazs Dome creator: Glen J. Weiss uri: https://doi.org/10.7717/peerj.7232 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lohinai et al. title: Identification of cecum time-location in a colonoscopy video by deep learning analysis of colonoscope movement link: https://peerj.com/articles/7256 last-modified: 2019-07-29 description: BackgroundCecal intubation time is an important component for quality colonoscopy. Cecum is the turning point that determines the insertion and withdrawal phase of the colonoscope. For this reason, obtaining information related with location of the cecum in the endoscopic procedure is very useful. Also, it is necessary to detect the direction of colonoscope’s movement and time-location of the cecum.MethodsIn order to analysis the direction of scope’s movement, the Horn–Schunck algorithm was used to compute the pixel’s motion change between consecutive frames. Horn–Schunk-algorithm applied images were trained and tested through convolutional neural network deep learning methods, and classified to the insertion, withdrawal and stop movements. Based on the scope’s movement, the graph was drawn with a value of +1 for insertion, −1 for withdrawal, and 0 for stop. We regarded the turning point as a cecum candidate point when the total graph area sum in a certain section recorded the lowest.ResultsA total of 328,927 frame images were obtained from 112 patients. The overall accuracy, drawn from 5-fold cross-validation, was 95.6%. When the value of “t” was 30 s, accuracy of cecum discovery was 96.7%. In order to increase visibility, the movement of the scope was added to summary report of colonoscopy video. Insertion, withdrawal, and stop movements were mapped to each color and expressed with various scale. As the scale increased, the distinction between the insertion phase and the withdrawal phase became clearer.ConclusionInformation obtained in this study can be utilized as metadata for proficiency assessment. Since insertion and withdrawal are technically different movements, data of scope’s movement and phase can be quantified and utilized to express pattern unique to the colonoscopist and to assess proficiency. Also, we hope that the findings of this study can contribute to the informatics field of medical records so that medical charts can be transmitted graphically and effectively in the field of colonoscopy. creator: Minwoo Cho creator: Jee Hyun Kim creator: Kyoung Sup Hong creator: Joo Sung Kim creator: Hyoun-Joong Kong creator: Sungwan Kim uri: https://doi.org/10.7717/peerj.7256 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cho et al. title: First molecular approach to the octopus fauna from the southern Caribbean link: https://peerj.com/articles/7300 last-modified: 2019-07-29 description: The octopus fauna from the southern Caribbean is an understudied field. However, recent taxonomic work in the Colombian Caribbean has led to the discovery of several new species in the family Octopodidae. To provide molecular evidence for recent descriptions in the area (i.e., Octopus taganga, O. tayrona and Macrotritopus beatrixi) and contribute to the systematics of the family, we reconstructed the first molecular phylogenies of the family including Colombian Caribbean octopus species. Using cytochrome c oxidase subunit I and rhodopsin sequences from specimens collected in three sites (Santa Marta, Old Providence and San Andrés Islands) we inferred maximum-likelihood trees and delimited species with PTP. Our mitochondrial analysis supported the monophyly of species found in the area (i.e., O. taganga, O. hummelincki and O. briareus). The genetic distinction of the species O. tayrona and O. insularis was not resolved, as these were found in one clade together with Caribbean O. vulgaris and O. aff. tayrona species (O. spB) and delimited as a single species. Additionally, our results suggest a distant relationship of the Type I O. vulgaris group (Caribbean region) from the other forms of the species complex (Old World and Brazil). Lastly, the third newly described species M. beatrixi emerged as an independent lineage and was delimited as a single species. However, its relationship to other species of its genus remains unknown due to the lack of sequences in databases. Altogether, our molecular approach to the octopus fauna from the southern Caribbean adds on information to the relationship of Octopodidae species world-wide by providing sequences from recently described species from an understudied region. Further studies employing higher taxon sampling and more molecular information are needed to fill taxonomic gaps in the area and account for single-locus resolution on the systematics of this group. creator: Elena A. Ritschard creator: Jürgen Guerrero-Kommritz creator: Juan A. Sanchez uri: https://doi.org/10.7717/peerj.7300 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ritschard et al. title: Genetic diversity in natural populations of noble crayfish (Astacus astacus L.) in north-western Poland on the basis of combined SSR and AFLP data link: https://peerj.com/articles/7301 last-modified: 2019-07-29 description: BackgroundConservation of noble crayfish (Astacus astacus) populations is becoming particularly important since the number of individuals is rapidly declining across the distribution range of the species in Europe. Five crayfish populations in northwestern Poland have been constantly monitored for two decades. However, the genetic structure of these populations has not been analysed, although this information is important to devise effective conservation strategies.MethodsNoble crayfish were collected in the autumn of 2014 by scuba diving in Lakes Graniczne, Babinki, Biwakowe, Sęki and Kwisno, all of which are situated in the Bytów Lakeland of northwestern Poland. Genetic diversity of the five populations was assessed based on allele variability in nine SSR regions and six AFLP primer combinations.ResultsMicrosatellite results analysed with AMOVA showed that the diversity between populations corresponds to 18% of total variability, which was confirmed by similar results obtained using AFLP. Additionally, significant genetic diversity was revealed by high average FST values. All of the studied crayfish populations significantly deviated from the expected Hardy–Weinberg genetic equilibrium and were characterised by negative values of inbreeding coefficient (FIS).DiscussionThe invariably negative inbreeding coefficients (FIS) suggest a low number of mating individuals, a possible consequence of the phenomenon known as genetic bottleneck. However, additional comprehensive analyses are needed to assess the genetic structure, origin and vulnerability of the remaining populations of noble crayfish in the Bytów Lakeland of northwestern Poland, which have high conservation value and are particularly important as a live genetic bank for breeding and restitution purposes. creator: Remigiusz Panicz creator: Łukasz Napora-Rutkowski creator: Sławomir Keszka creator: Lidia Skuza creator: Magdalena Szenejko creator: Przemysław Śmietana uri: https://doi.org/10.7717/peerj.7301 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Panicz et al. title: Genome-wide identification and classification of the Hsf and sHsp gene families in Prunus mume, and transcriptional analysis under heat stress link: https://peerj.com/articles/7312 last-modified: 2019-07-29 description: The transcriptional activation of heat shock proteins (Hsps) by heat shock transcription factors (Hsfs) is presumed to have a pivotal role in plant heat stress (HS) response. Prunus mume is an ornamental woody plant with distinctive features, including rich varieties and colors. In this study, 18 Hsfs and 24 small Hsps (sHsps) were identified in P. mume. Their chromosomal locations, protein domains, conserved motifs, phylogenetic relationships, and exon–intron structures were analyzed and compared with Arabidopsis thaliana Hsfs or sHsps. A total of 18 PmHsf members were classified into three major classes, A, B, and C. A total of 24 PmsHsps were grouped into eight subfamilies (CI to CIII, P, endoplasmic reticulum, M, and CI- or P-related). Quantitative reverse transcription PCR analysis revealed that members of the A2, A7, and A9 groups became the prominent Hsfs after heat shock, suggesting their involvement in a key regulatory role of heat tolerance. Most of the PmsHsp genes were up-regulated upon exposure to HS. Overall, our data contribute to an improved understanding of the complexity of the P. mume Hsf and sHsp gene families, and provide a basis for directing future systematic studies investigating the roles of the Hsf and sHsp gene families. creator: Xueli Wan creator: Jie Yang creator: Cong Guo creator: Manzhu Bao creator: Junwei Zhang uri: https://doi.org/10.7717/peerj.7312 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wan et al. title: Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls link: https://peerj.com/articles/7315 last-modified: 2019-07-29 description: The human gut microbiota plays a major role in maintaining human health and was recently recognized as a promising target for disease prevention and treatment. Many diseases are traceable to microbiota dysbiosis, implicating altered gut microbial ecosystems, or, in many cases, disrupted microbial enzymes carrying out essential physio-biochemical reactions. Thus, the changes of essential microbial enzyme levels may predict human disorders. With the rapid development of high-throughput sequencing technologies, metagenomics analysis has emerged as an important method to explore the microbial communities in the human body, as well as their functionalities. In this study, we analyzed 156 gut metagenomics samples from patients with colorectal cancer (CRC) and adenoma, as well as that from healthy controls. We estimated the abundance of microbial enzymes using the HMP Unified Metabolic Analysis Network method and identified the differentially abundant enzymes between CRCs and controls. We constructed enzymatic association networks using the extended local similarity analysis algorithm. We identified CRC-associated enzymic changes by analyzing the topological features of the enzymatic association networks, including the clustering coefficient, the betweenness centrality, and the closeness centrality of network nodes. The network topology of enzymatic association network exhibited a difference between the healthy and the CRC environments. The ABC (ATP binding cassette) transporter and small subunit ribosomal protein S19 enzymes, had the highest clustering coefficient in the healthy enzymatic networks. In contrast, the Adenosylhomocysteinase enzyme had the highest clustering coefficient in the CRC enzymatic networks. These enzymic and metabolic differences may serve as risk predictors for CRCs and are worthy of further research. creator: Dongmei Ai creator: Hongfei Pan creator: Xiaoxin Li creator: Min Wu creator: Li C. Xia uri: https://doi.org/10.7717/peerj.7315 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ai et al. title: Cardioprotective effects of Prolame and SNAP are related with nitric oxide production and with diminution of caspases and calpain-1 activities in reperfused rat hearts link: https://peerj.com/articles/7348 last-modified: 2019-07-29 description: Cardiac tissue undergoes changes during ischemia-reperfusion (I-R) that compromise its normal function. Cell death is one of the consequences of such damage, as well as diminution in nitric oxide (NO) content. This signaling molecule regulates the function of the cardiovascular system through dependent and independent effects of cyclic guanosine monophosphate (cGMP). The independent cGMP pathway involves post-translational modification of proteins by S-nitrosylation. Studies in vitro have shown that NO inhibits the activity of caspases and calpains through S-nitrosylation of a cysteine located in their catalytic site, so we propose to elucidate if the regulatory mechanisms of NO are related with changes in S-nitrosylation of cell death proteins in the ischemic-reperfused myocardium. We used two compounds that increase the levels of NO by different mechanisms: Prolame, an amino-estrogenic compound with antiplatelet and anticoagulant effects that induces the increase of NO levels in vivo by activating the endothelial nitric oxide synthase (eNOS) and that has not been tested as a potential inhibitor of apoptosis. On the other hand, S-Nitroso-N-acetylpenicillamine (SNAP), a synthetic NO donor that has been shown to decrease cell death after inducing hypoxia-reoxygenation in cell cultures. Main experimental groups were Control, I-R, I-R+Prolame and I-R+SNAP. Additional groups were used to evaluate the NO action pathways. Contractile function represented as heart rate and ventricular pressure was evaluated in a Langendorff system. Infarct size was measured with 2,3,5-triphenyltetrazolium chloride stain. NO content was determined indirectly by measuring nitrite levels with the Griess reaction and cGMP content was measured by Enzyme-Linked ImmunoSorbent Assay. DNA integrity was evaluated by DNA laddering visualized on an agarose gel and by Terminal deoxynucleotidyl transferase dUTP Nick-End Labeling assay. Activities of caspase-3, caspase-8, caspase-9 and calpain-1 were evaluated spectrophotometrically and the content of caspase-3 and calpain-1 by western blot. S-nitrosylation of caspase-3 and calpain-1 was evaluated by labeling S-nitrosylated cysteines. Our results show that both Prolame and SNAP increased NO content and improved functional recovery in post-ischemic hearts. cGMP-dependent and S-nitrosylation pathways were activated in both groups, but the cGMP-independent pathway was preferentially activated by SNAP, which induced higher levels of NO than Prolame. Although SNAP effectively diminished the activity of all the proteases, a correlative link between the activity of these proteases and S-nitrosylation was not fully established. creator: Nadia Giovanna Román-Anguiano creator: Francisco Correa creator: Agustina Cano-Martínez creator: Aurora de la Peña-Díaz creator: Cecilia Zazueta uri: https://doi.org/10.7717/peerj.7348 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Román-Anguiano et al. title: Manifestations of muscle fatigue in baseball pitchers: a systematic review link: https://peerj.com/articles/7390 last-modified: 2019-07-29 description: BackgroundFatigue in baseball pitchers is a process linked to lowered physical and mental performance, injury, and changes in kinematics. Numerous studies have associated fatigue with overuse, high ball velocities, lack of rest time, poor mechanics, and degree of self-satisfaction. The aim of this study was to systematically review the literature to identify a theoretical framework for the relationship between outcomes and the manifestation of fatigue on baseball pitching. The synthesized data may identify areas requiring further research.MethodologyThis protocol was registered with PROSPERO (ID: CRD42018114194). SPORTDiscus, Medline, PubMed, Cochrane Database of Systematic Reviews, and Google Scholar were searched, using keywords such as fatigue in pitchers and changes in kinematics (e.g., pitching mechanics, valgus elbow torque), performance (e.g., pitch count, pitch type), and injury (e.g., pain, elbow, and shoulder soreness). Three reviewers independently screened the articles, selected relevant literature based on abstract eligibility, and assessed the methods described therein for final inclusion.ResultsA total of 31,860 articles were screened for eligibility and 25 articles were included for the review. The selected articles included epidemiological, longitudinal, experimental, conference papers, and crossover laboratory studies. Evidence extracted from the 25 studies demonstrates a relationship between fatigue in baseball pitching, and three overarching outcomes: changes in kinematics, a decrease in performance, and an increase in injury risk.ConclusionsFindings show that a co-dependence between changes in kinematics and a decrease in performance, which stems from central and peripheral fatigue, is a contributing factor of injury in baseball pitchers. A large percentage of baseball pitchers exhibit pain or soreness in either their elbow or shoulder, or both at some point in a season. Initially, kinematic changes occur that could maintain performance, but may increase joint and tissue loading. Performance decreased with elevated pitch counts and innings thrown, and pitching further into games or the season. Evidence was found to be consistent across all studies; however, more work is needed in the area of fatigue as an injury mechanism during pitching. With a proof of concept established, the prevention of negative outcomes associated with fatigue must be the focus of future research and performance should not be the only criteria. creator: Richard Birfer creator: Michael WL Sonne creator: Michael WR Holmes uri: https://doi.org/10.7717/peerj.7390 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Birfer et al. title: Mobile learning in dentistry: usage habits, attitudes and perceptions of undergraduate students link: https://peerj.com/articles/7391 last-modified: 2019-07-29 description: IntroductionThe aim of this study was to evaluate usage habits, attitudes and perceptions towards mobile learning (m-learning), as well as to identify variables related to those attitudes amongst undergraduate dental students.Materials and MethodsThe study consists of 81 dental undergraduate students who who volunteered to participate. The data collection tool consists of an m-learning attitude scale, a questionnaire, and open-ended questions. To compare the total scores and factors of m-learning attitude scale for demographic information and mobile technology usage habits of the students; the Mann–Whitney U test was used for two independent groups such as gender, presence of electronic devices, and places of Internet usage. The Kruskal–Wallis test was also used to compare the total scores and factors of m-learning attitude scale for more than two independent groups including internet usage purposes and opinions. Spearman’s correlation coefficient was performed, and linear regression analysis was used to predict the change in total score according to the purposes of Internet usage.ResultsThe majority of students thought that the use of mobile devices in dentistry courses was useful and their attitudes towards m-learning were high. The students generally use the Internet for online shopping, connecting to social networks, and communication. They tend to use mobile technologies for personal use, followed by educational purposes. There were significant differences found in the m-learning attitudes for gender, having a portable power supply and use of mobile devices in dentistry courses. Communication was found significant in predicting the change in total score for the m-learning attitude scale according to the purpose of Internet usage.ConclusionDental students have generally positive attitudes towards m-learning. Students raise awareness towards the promise of m-learning in order to apply their individual technology use and learning behaviours. Designing learning materials and applications for mobile devices may increase students’ performances. creator: Aslı Suner creator: Yusuf Yilmaz creator: Beyser Pişkin uri: https://doi.org/10.7717/peerj.7391 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Suner et al. title: Self-efficacy and enjoyment of physical activity in children: factorial validity of two pictorial scales link: https://peerj.com/articles/7402 last-modified: 2019-07-29 description: BackgroundSelf-efficacy and enjoyment are two main constructs proposed within many motivational theories in any human endeavor, sport and physical activity included.MethodsThe purpose of this study was to examine the factor structure of two pictorial scales measuring self-efficacy and enjoyment levels in a sample of 14,035 Italian schoolchildren (7,075 boys and 6,960 girls, 6- to 7-year-olds). An important feature of the two scales is that they are in a pictorial format in order to prompt a straightforward understanding in children. The whole sample was randomly split in two subsamples according to gender and age and the factor structure of the measures was examined across subsamples.ResultsData were subjected to confirmatory factor analysis, which yielded satisfactory fit indices on the measures of both subsamples. Overall findings supported the single factor structure of the scales, which can be easily administered to 6- to 7-year-old children to assess two relevant psychological constructs in physical education. creator: Milena Morano creator: Laura Bortoli creator: Montse C. Ruiz creator: Francesca Vitali creator: Claudio Robazza uri: https://doi.org/10.7717/peerj.7402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Morano et al. title: Integrative analysis of transcriptome-wide association study and gene expression profiling identifies candidate genes associated with stroke link: https://peerj.com/articles/7435 last-modified: 2019-07-29 description: BackgroundStroke is a major public health burden worldwide. Although genetic variation is known to play a role in the pathogenesis of stroke, the specific pathogenic mechanisms are still unclear. Transcriptome-wide association studies (TWAS) is a powerful approach to prioritize candidate risk genes underlying complex traits. However, this approach has not been applied in stroke.MethodsWe conducted an integrative analysis of TWAS using data from the MEGASTROKE Consortium and gene expression profiling to identify candidate genes for the pathogenesis of stroke. Gene ontology (GO) enrichment analysis was also conducted to detect functional gene sets.ResultsThe TWAS identified 515 transcriptome-wide significant tissue-specific genes, among which SLC25A44 (P = 5.46E−10) and LRCH1 (P = 1.54E−6) were significant by Bonferroni test for stroke. After validation with gene expression profiling, 19 unique genes were recognized. GO enrichment analysis identified eight significant GO functional gene sets, including regulation of cell shape (P = 0.0059), face morphogenesis (P = 0.0247), and positive regulation of ATPase activity (P = 0.0256).ConclusionsOur study identified multiple stroke-associated genes and gene sets, and this analysis provided novel insights into the genetic mechanisms underlying stroke. creator: Jian Yang creator: Bin Yan creator: Yajuan Fan creator: Lihong Yang creator: Binbin Zhao creator: Xiaoyan He creator: Qingyan Ma creator: Wei Wang creator: Ling Bai creator: Feng Zhang creator: Xiancang Ma uri: https://doi.org/10.7717/peerj.7435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: The disappearing hand: vestibular stimulation does not improve hand localisation link: https://peerj.com/articles/7201 last-modified: 2019-07-26 description: BackgroundBodily self-consciousness depends on the coherent integration of sensory information. In addition to visual and somatosensory information processing, vestibular contributions have been proposed and investigated. Vestibular information seems especially important for self-location, but remains difficult to study.MethodsThis randomised controlled experiment used the MIRAGE multisensory illusion box to induce a conflict between the visually- and proprioceptively-encoded position of one hand. Over time, the perceived location of the hand slowly shifts, due to the fact that proprioceptive input is progressively weighted more heavily than the visual input. We hypothesised that left cold caloric vestibular stimulation (CVS) augments this shift in hand localisation.ResultsThe results from 24 healthy participants do not support our hypothesis: CVS had no effect on the estimations with which the perceived position of the hand shifted from the visually- to the proprioceptively-encoded position. Participants were more likely to report that their hand was ‘no longer there’ after CVS. Taken together, neither the physical nor the subjective data provide evidence for vestibular enhanced self-location. creator: Luzia Grabherr creator: Leslie N. Russek creator: Valeria Bellan creator: Mohammad Shohag creator: Danny Camfferman creator: G. Lorimer Moseley uri: https://doi.org/10.7717/peerj.7201 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Grabherr et al. title: Comparison of physiological responses of Arabian striped hyaena (Hyaena hyaena sultana) to effective immobilisations with ketamine-medetomidine and ketamine-xylazine in (semi-) captive conditions link: https://peerj.com/articles/7326 last-modified: 2019-07-26 description: Chemical immobilisation is an integral component for the conservation of wild animals and can be stressful if proper protocols are not administered. References on the immobilisation of Arabian striped hyaena (Hyaena hyaena sultana) are scarce. The current study was designed to evaluate the physiological and clinical responses of Arabian striped hyaena, immobilised with ketamine-medetomidine (KM) and ketamine-xylazine (KX); and to compare immobilisation effectiveness of the two combinations in a cross-sectional clinical study. A total of 15 (six males, nine females) (semi-) captive and adult Arabian striped hyaena with an average weight of 31.39 ± 0.36 kg were immobilised 50 times for annual vaccination and translocation purposes from January 2014 till March 2018 on Sir Bani Yas Island, United Arab Emirates. A total of 34 immobilisations were executed with (Mean ± SE) 2.27 ± 0.044 mg/kg ketamine and 0.04 ± 0.001 mg/kg medetomidine; while 16 with 4.95 ± 0.115 mg/kg ketamine and 0.99 ± 0.023 mg/kg xylazine. The drugs were remotely delivered intramuscular. The evaluation of physiological and clinical parameters included monitoring of vital signs through pulse oximetry, blood gas analysis of arterial blood through Istat blood gas analyser, and blood biochemistry and haematology. The quality of induction, anaesthesia and recovery was also assessed. Atipamezole (0.21 ± 0.003 mg/kg) was used to antagonise the effects of KM and 0.09 ± 0.003 mg/kg atipamezole or by 0.23 ± 0.006 mg/kg yohimbine for KX. Data were analysed using the general linear model and inferential statistics. KM was more effective in induction (scores; KM = 1.41 ± 0.10; KX = 1.31 ± 0.12), anaesthesia (KM = 1.00 ± 0.00; KX = 2.0 ± 0.0) and recovery (KM = 1.76 ± 0.15; KX = 2.69 ± 0.12) phases as compared to KX. There was a significant difference (P < 0.05) amongst the two combinations for anaesthesia time (KM = 59.5 ± 2.41; KX = 49.25 ± 1.31 min.), time to stand after reversal (KM = 4.91 ± 0.60; KX = 10.38 ± 1.48 min.) and full loss of the signs of anaesthetics (KM = 12.32 ± 1.37; KX = 21.25 ± 2.16 min.) along with rectal temperature (KM = 37.58 ± 0.29; KX = 36.00 ± 0.68 °C), pulse rate (KM = 50.46 ± 1.90; KX = 61.14 ± 2.79 beats/min), respiration rate (KM = 29.44 ± 0.99; KX = 23.80 ± 1.57 breaths/min.) and partial pressure of oxygen (KM = 89.59 ± 1.34; KX = 82.06 ± 3.92%). The blood oxygen saturation by oximeter indicated hypoxaemia in KX (82.06 ± 3.92), supported by the data from blood gas analyser. KM combination was more suitable for the immobilisation of Arabian striped hyaena, providing a better quality of induction, anaesthesia and recovery compared to KX. However, we strongly suggest further investigation to see the effects of oxygen supplementation for the compensation of hypoxaemia. creator: Abid Mehmood creator: Sadia Abid creator: Pavla Hejcmanová creator: Muhammad Arslan Asadi creator: Bilal Kabeer creator: Muhammad Jawad Jilani creator: Sadaf Bilal creator: Muhammad Waseem Ashraf uri: https://doi.org/10.7717/peerj.7326 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mehmood et al. title: Observations on carapace color change in the juvenile big-headed turtle (Platysternon megacephalum) link: https://peerj.com/articles/7331 last-modified: 2019-07-26 description: The carapace color of newborn big-headed turtles (Platysternon megacephalum) is polymorphic and usually consists of two phenotypes: yellowish brown and olive green. As the turtles grew, over the first year of life, its carapace gradually turned from yellowish brown to chestnut brown, or from olive green to dark brown, depending on the phenotype. Meanwhile, the turtle’s plastron remained an orange and black pattern and did not change much. In this study, we primarily used HE staining to observe the carapace color change with age in big-headed turtle juveniles. We took the carapace marginal scute tissues twice from the same turtles before and after the carapace color change. Histological observations show that in the marginal scutes of the four tested turtles with different carapace color phenotypes, melanin granules are all concentrated in the dermal layer underneath the dorsal corneous layer, but rarely on the ventral side. Melanin deposits in the dorsal corneous layer were found to increase as the corneous layers thickened, while the melanin deposits in the ventral corneous layer did not change significantly. However, there was no significant difference in melanin deposition in the epidermis and dermis of the carapace among the yellowish brown, chestnut brown, olive green, and dark brown big-headed turtles. The results of our study indicate that the carapace color darkening in big-headed turtles may not be due to changes in melanin content of the carapace, but is the result of melanin accumulation and superposition in the dorsal corneous layer. creator: Dainan Cao creator: Yan Ge creator: Yufeng Wei creator: Haoran Duan creator: Shiping Gong uri: https://doi.org/10.7717/peerj.7331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cao et al. title: The effects of spatial and temporal replicate sampling on eDNA metabarcoding link: https://peerj.com/articles/7335 last-modified: 2019-07-26 description: BackgroundThe heterogeneous nature of environmental DNA (eDNA) and its effects on species detection and community composition estimates has been highlighted in several studies in the past decades. Mostly in the context of spatial distribution over large areas, in fewer occasions looking at spatial distribution within a single body of water. Temporal variation of eDNA, similarly, has mostly been studied as seasonality, observing changes over large periods of time, and often only for small groups of organisms such as fish and amphibians.MethodsWe analyzed and compared small-scale spatial and temporal variation by sampling eDNA from two small, isolated dune lakes for 20 consecutive weeks. Metabarcoding was performed on the samples using generic COI primers. Molecular operational taxonomic unit (MOTUs) were used to assess dissimilarities between spatial and temporal replicates.ResultsOur results show large differences between samples taken within one lake at one point in time, but also expose the large differences between temporal replicates, even those taken only 1 week apart. Furthermore, between-site dissimilarities showed a linear correlation with time frame, indicating that between-site differences will be inflated when samples are taken over a period of time. We also assessed the effects of PCR replicates and processing strategies on general patterns of dissimilarity between samples. While more inclusive PCR replicate strategies lead to higher richness estimations, dissimilarity patterns between samples did not significantly change.ConclusionsWe conclude that the dissimilarity of temporal replicates at a 1 week interval is comparable to that of spatial replicate samples. It increases, however, for larger time intervals, which suggests that population turnover effects can be stronger than community heterogeneity. Spatial replicates alone may not be enough for optimal recovery of taxonomic diversity, and cross-comparisons of different locations are susceptible to inflated dissimilarities when performed over larger time intervals. Many of the observed MOTUs could be classified as either phyto- or zooplankton, two groups that have gained traction in recent years as potential novel bio-indicator species. Our results, however, indicate that these groups might be susceptible to large community shifts in relatively short periods of time, highlighting the need to take temporal variations into consideration when assessing their usability as water quality indicators. creator: Kevin K. Beentjes creator: Arjen G. C. L. Speksnijder creator: Menno Schilthuizen creator: Marten Hoogeveen creator: Berry B. van der Hoorn uri: https://doi.org/10.7717/peerj.7335 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Beentjes et al. title: The effects of a 4-week mesocycle of barbell back squat or barbell hip thrust strength training upon isolated lumbar extension strength link: https://peerj.com/articles/7337 last-modified: 2019-07-26 description: ObjectivesCommon exercises such as the barbell back squat (BBS) and barbell hip thrust (BHT) are perceived to provide a training stimulus to the lumbar extensors. However, to date there have been no empirical studies considering changes in lumbar extension strength as a result of BBS or BHT resistance training (RT) interventions.PurposeTo consider the effects of BBS and BHT RT programmes upon isolated lumbar extension (ILEX) strength.MethodsTrained male subjects (n = 14; 22.07 ± 0.62 years; 179.31 ± 6.96 cm; 79.77 ± 13.81 kg) were randomised in to either BBS (n = 7) or BHT (n = 7) groups and performed two training sessions per week during a 4-week mesocycle using 80% of their 1RM. All subjects were tested pre- and post-intervention for BBS and BHT 1RM as well as isometric ILEX strength.ResultsAnalyses revealed that both BBS and BHT groups significantly improved both their BBS and BHT 1RM, suggesting a degree of transferability. However, the BBS group improved their BBS 1RM to a greater degree than the BHT group (p = 0.050; ∼11.8 kg/10.2% vs. ∼8.6 kg/7.7%, respectively). And the BHT group improved their BHT 1RM to a greater degree than the BBS group (p = 0.034; ∼27.5 kg/24.8% vs. ∼20.3 kg/13.3%, respectively). Neither BBS nor BHT groups significantly improved their isometric ILEX strength.ConclusionsThe present study supports the concept of specificity, particularly in relation to the movement mechanics between trunk extension (including pelvic rotation) and ILEX. Our data suggest that strength coaches, personal trainers, and trainees can self-select multi-joint lower-body trunk extension exercises based on preference or variety. However, evidence suggests that neither the BBS nor BHT exercises can meaningfully increase ILEX strength. Since strengthening these muscles might enhance physical and sporting performance we encourage strength coaches and personal trainers to prescribe ILEX exercise. creator: Alexander Hammond creator: Craig Perrin creator: James Steele creator: Jürgen Giessing creator: Paulo Gentil creator: James P. Fisher uri: https://doi.org/10.7717/peerj.7337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hammond et al. title: MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies link: https://peerj.com/articles/7359 last-modified: 2019-07-26 description: We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat. creator: Dongwan D. Kang creator: Feng Li creator: Edward Kirton creator: Ashleigh Thomas creator: Rob Egan creator: Hong An creator: Zhong Wang uri: https://doi.org/10.7717/peerj.7359 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Asexual reproduction of a few genotypes favored the invasion of the cereal aphid Rhopalosiphum padi in Chile link: https://peerj.com/articles/7366 last-modified: 2019-07-26 description: BackgroundAphids (Hemiptera: Aphididae) are insects with one of the highest potentials for invasion. Several aphid species are present globally due to introduction events; they represent important pests of agroecosystems. The bird cherry-oat aphid Rhopalosiphum padi (Linnaeus) is a major pest of cereals and pasture grasses worldwide. Here, we report the genetic features of populations of R. padi that colonize different cereal crops in central Chile.MethodsRhopalosiphum padi individuals were collected in central Chile and genotyped at six microsatellite loci. The most frequent multilocus genotype (MLG) was then studied further to assess its reproductive performance across cereal hosts under laboratory conditions.ResultsPopulations of R. padi in Chile are characterized by a low clonal diversity (G/N = 62/377 = 0.16) and the overrepresentation of a few widely distributed MLGs. One of the MLGs constituted roughly half of the sample and was observed in all sampled populations at high frequencies. Furthermore, this putative aphid “superclone” exhibited variations in its reproductive performance on cereals most commonly cultivated in Chile. The sampled populations also exhibited weak signs of genetic differentiation among hosts and localities. Our findings suggest that (1) obligate parthenogenesis is the primary reproductive mode of R. padi in Chile in the sampled range and (2) its introduction involved the arrival of a few genotypes that multiplied asexually. creator: María E. Rubio-Meléndez creator: Joceline Barrios-SanMartin creator: Felipe E. Pina-Castro creator: Christian C. Figueroa creator: Claudio C. Ramirez uri: https://doi.org/10.7717/peerj.7366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rubio-Meléndez et al. title: Rapid response to anthropogenic climate change by Thuja occidentalis: implications for past climate reconstructions and future climate predictions link: https://peerj.com/articles/7378 last-modified: 2019-07-26 description: Carbon isotope values of leaves (δ13Cleaf) from meta-analyses and growth chamber studies of C3 plants have been used to propose generalized relationships between δ13Cleaf and climate variables such as mean annual precipitation (MAP), atmospheric concentration of carbon dioxide ([CO2]), and other climate variables. These generalized relationships are frequently applied to the fossil record to create paleoclimate reconstructions. Although plant evolution influences biochemistry and response to environmental stress, few studies have assessed species-specific carbon assimilation as it relates to climate outside of a laboratory. We measured δ13Cleaf values and C:N ratios of a wide-ranging evergreen conifer with a long fossil record, Thuja occidentalis (Cupressaceae) collected 1804–2017, in order to maximize potential paleo-applications of our focal species. This high-resolution record represents a natural experiment from pre-Industrial to Industrial times, which spans a range of geologically meaningful [CO2] and δ13Catm values. Δleaf values (carbon isotope discrimination between δ13Catm and δ13Cleaf) remain constant across climate conditions, indicating limited response to environmental stress. Only δ13Cleaf and δ13Catm values showed a strong relationship (linear), thus, δ13Cleaf is an excellent record of carbon isotopic changes in the atmosphere during Industrialization. In contrast with previous free-air concentration enrichment experiments, no relationship was found between C:N ratios and increasing [CO2]. Simultaneously static C:N ratios and Δleaf in light of increasing CO2 highlights plants’ inability to match rapid climate change with increased carbon assimilation as previously expected; Δleaf values are not reliable tools to reconstruct MAP and [CO2], and δ13Cleaf values only decrease with [CO2] in line with atmospheric carbon isotope changes. creator: Rebekah A. Stein creator: Nathan D. Sheldon creator: Selena Smith uri: https://doi.org/10.7717/peerj.7378 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Stein et al. title: Short-term effects of thinning on the understory natural environment of mixed broadleaf-conifer forest in Changbai Mountain area, Northeast China link: https://peerj.com/articles/7400 last-modified: 2019-07-26 description: BackgroundThe understory natural environment is critical in affecting the succession and recovery process of vegetation, stand structure, and species composition of forest. The thinning intensity could significantly change the forest microclimates and soil properties, therefore, to analyze the effects of thinning intensity on the understory natural environment of forest is of important significance for promoting the ecological benefits of thinning.MethodsA total of 16 fixed sample plots with different thinning intensities were established in the mixed broadleaf-conifer forest in Jiaohe, situated in Changbai Mountain area, Northeast China, and the forest microclimates and soil properties were investigated after 4 years since the establishment of the sample plots.ResultsThe results showed that the high intensity thinning significantly decreased the leaf area index from 4.13 (unthinned plot) to 2.21 (high intensity thinned plot), and the air temperature was increased by thinning from May to July. Comparing with the unthinned plot, thinning caused a rise of temperature (ranging from 2.11 to 6.74 °C, depending on the intensity of thinning) in May. However, it showed cooling effect in September and October. Besides, the air moisture of thinning plots was lower than the control plot in May and October, when the density of leaves is lower in the forest, and it even decreased 20.27% after thinning. The thinning intensity had no significantly effect on water content and organic carbon in forest soils, and only the bulk density in the top-layer soils in high intensity thinning plot was remarkably increased. Total nitrogen in soil was increased by different intensities of thinning, and the availability of nutrients for nitrogen, phosphorus and potassium in some soils were also affected. creator: Qiang Liu creator: Yue Sun creator: Gerong Wang creator: Fushan Cheng creator: Fucai Xia uri: https://doi.org/10.7717/peerj.7400 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: TiO2 nanoparticles affect the bacterial community structure and Eisenia fetida (Savigny, 1826) in an arable soil link: https://peerj.com/articles/6939 last-modified: 2019-07-25 description: The amount of nanoparticles (NP), such as TiO2, has increased substantially in the environment. It is still largely unknown, however, how NP might interact with earthworms and organic material and how this might affect the bacterial community structure and their functionality. Therefore, an arable soil was amended with TiO2 NP at 0, 150 or 300 mg kg−1 and subjected to different treatments. Treatments were soil amended with ten earthworms (Eisenia fetida (Savigny, 1826)) with fully developed clitellum and an average fresh mass of 0.5 to 500 g dry soil, 1.75 g tyndallized Quaker® oat seeds Avena sativa (L.) kg−1, or earthworms plus oat seeds, or left unamended. The bacterial community structure was monitored throughout the incubation period. The bacterial community in the unamended soil changed over time and application of oats, earthworm and a combination of both even further, with the largest change found in the latter. Application of NP to the unamended soil and the earthworm-amended soil altered the bacterial community, but combining it by adding oats negated that effect. It was found that the application of organic material, that is, oats, reduced the effect of the NP applied to soil. However, as the organic material applied was mineralized by the soil microorganisms, the effect of NP increased again over time. creator: Katia Berenice Sánchez-López creator: Francisco J. De los Santos-Ramos creator: Elizabeth Selene Gómez-Acata creator: Marco Luna-Guido creator: Yendi E. Navarro-Noya creator: Fabián Fernández-Luqueño creator: Luc Dendooven uri: https://doi.org/10.7717/peerj.6939 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sánchez-López et al. title: The Munduruku marmoset: a new monkey species from southern Amazonia link: https://peerj.com/articles/7019 last-modified: 2019-07-25 description: Although the Atlantic Forest marmosets (Callithrix spp.) are among the best studied Neotropical primates, the Amazonian marmosets (Callibella humilis, Cebuella spp. and Mico spp.) are much less well-known. Even species diversity and distributions are yet to be properly determined because field data and materials currently available in scientific collections do not allow comprehensive taxonomic studies of Amazonian marmosets. From 2015 to 2018, we conducted 10 expeditions in key-areas within southern Amazonia where little or no information on marmosets was available. In one such region—the Tapajós–Jamanxim interfluve—we recorded marmosets with a distinctive pelage pigmentation pattern suggesting they could represent a new species. We tested this hypothesis using an integrative taxonomic framework that included phylogenomic data (ddRAD sequences), pelage pigmentation characters, and distribution records. We found that the marmosets of the northern Tapajós–Jamanxim interfluve have unique states in pelage pigmentation characters, form a clade (100% support) in our Bayesian and Maximum-Likelihood phylogenies, and occur in an area isolated from other taxa by rivers. The integration of these lines of evidence leads us to describe a new marmoset species in the genus Mico, named after the Munduruku Amerindians of the Tapajós–Jamanxim interfluve, southwest of Pará State, Brazil. creator: Rodrigo Costa-Araújo creator: Fabiano R. de Melo creator: Gustavo Rodrigues Canale creator: Sandra M. Hernández-Rangel creator: Mariluce Rezende Messias creator: Rogério Vieira Rossi creator: Felipe E. Silva creator: Maria Nazareth Ferreira da Silva creator: Stephen D. Nash creator: Jean P. Boubli creator: Izeni Pires Farias creator: Tomas Hrbek uri: https://doi.org/10.7717/peerj.7019 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Costa-Araújo et al. title: Detection of human Metapneumovirus infection in children under 18 years old hospitalized in Lima-Peru link: https://peerj.com/articles/7266 last-modified: 2019-07-25 description: BackgroundHuman Metapneumovirus (hMPV) is a negative single-stranded RNA virus. Infection by hMPV mainly affects the pediatric population and can cause upper or lower respiratory tract pathologies which can develop life threating complications. This study was carried out between 2009 and 2010 in a high complexity national hospital in Lima, Peru. The time frame corresponds to the pandemic of influenza A H1N1.MethodsA prospective study was performed between September 2009 and September 2010. Patients with a clinical diagnosis suggestive of an acute respiratory infection were included. RT-PCR was utilized to attain the amplification and identification of the hMPV.ResultsA total of 539 samples were analyzed from patients with a clinical context suggestive of an acute respiratory tract infection. Of these samples 73, (13.54%) were positive for hMPV. Out of the positive cases, 63% were under one year old, and increased to nearly 80% when considering children younger than two years old. Cough was the most frequent symptom presented by our population with a number of 62 cases (84.93%). Viral seasonality was also established, noting its predominance during the months of summer in the southern hemisphere. The infection by hMPV has an important prevalence in Peru. It mainly affects children under one year old and should be considered an important differential diagnosis in a patient with an acute respiratory infection. creator: Juana del Valle-Mendoza creator: Fiorella Orellana-Peralta creator: Luis J. del Valle creator: Eduardo Verne creator: Claudia Ugarte creator: Claudia Weilg creator: Wilmer Silva-Caso creator: Jorge Valverde-Ezeta creator: Hugo Carrillo-Ng creator: Isaac Peña-Tuesta creator: Carlos Palomares-Reyes creator: Angela Cornejo-Tapia creator: Miguel Angel Aguilar-Luis uri: https://doi.org/10.7717/peerj.7266 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 del Valle-Mendoza et al. title: Exploring spatial nonstationary environmental effects on Yellow Perch distribution in Lake Erie link: https://peerj.com/articles/7350 last-modified: 2019-07-25 description: BackgroundGlobal regression models under an implicit assumption of spatial stationarity were commonly applied to estimate the environmental effects on aquatic species distribution. However, the relationships between species distribution and environmental variables may change among spatial locations, especially at large spatial scales with complicated habitat. Local regression models are appropriate supplementary tools to explore species-environment relationships at finer scales.MethodWe applied geographically weighted regression (GWR) models on Yellow Perch in Lake Erie to estimate spatially-varying environmental effects on the presence probabilities of this species. Outputs from GWR were compared with those from generalized additive models (GAMs) in exploring the Yellow Perch distribution. Local regression coefficients from the GWR were mapped to visualize spatially-varying species-environment relationships. K-means cluster analyses based on the t-values of GWR local regression coefficients were used to characterize the distinct zones of ecological relationships.ResultsGeographically weighted regression resulted in a significant improvement over the GAM in goodness-of-fit and accuracy of model prediction. Results from the GWR revealed the magnitude and direction of environmental effects on Yellow Perch distribution changed among spatial locations. Consistent species-environment relationships were found in the west and east basins for adults. The different kinds of species-environment relationships found in the central management unit (MU) implied the variation of relationships at a scale finer than the MU.ConclusionsThis study draws attention to the importance of accounting for spatial nonstationarity in exploring species-environment relationships. The GWR results can provide support for identification of unique stocks and potential refinement of the current jurisdictional MU structure toward more ecologically relevant MUs for the sustainable management of Yellow Perch in Lake Erie. creator: Changdong Liu creator: Junchao Liu creator: Yan Jiao creator: Yanli Tang creator: Kevin B. Reid uri: https://doi.org/10.7717/peerj.7350 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Comprehensive map and functional annotation of the mouse white adipose tissue proteome link: https://peerj.com/articles/7352 last-modified: 2019-07-25 description: White adipose tissue (WAT) plays a significant role in energy metabolism and the obesity epidemic. In this study, we sought to (1) profile the mouse WAT proteome with advanced 2DLC/MS/MS approach, (2) provide insight into WAT function based on protein functional annotation, and (3) predict potentially secreted proteins. A label-free 2DLC/MS/MS proteomic approach was used to identify the WAT proteome from female mouse WAT. A total of 6,039 proteins in WAT were identified, among which 5,160 were quantified (spanning a magnitude of 106) using an intensity-based absolute quantification algorithm, and 3,117 proteins were reported by proteomics technology for the first time in WAT. To comprehensively analyze the function of WAT, the proteins were divided into three quantiles based on abundance and we found that proteins of different abundance performed different functions. High-abundance proteins (the top 90%, 1,219 proteins) were involved in energy metabolism; middle-abundance proteins (90–99%, 2,273 proteins) were involved in the regulation of protein synthesis; and low-abundance proteins (99–100%, 1,668 proteins) were associated with lipid metabolism and WAT beiging. Furthermore, 800 proteins were predicted by SignalP4.0 to have signal peptides, 265 proteins had never been reported, and five have been reported as adipokines. The above results provide a large dataset of the normal mouse WAT proteome, which might be useful for WAT function research. creator: Xiaoyue Tang creator: Juan Li creator: Wei-gang Zhao creator: Haidan Sun creator: Zhengguang Guo creator: Li Jing creator: Zhufang She creator: Tao Yuan creator: Shuai-nan Liu creator: Quan Liu creator: Yong Fu creator: Wei Sun uri: https://doi.org/10.7717/peerj.7352 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tang et al. title: A six-microRNA signature can better predict overall survival of patients with esophagus adenocarcinoma link: https://peerj.com/articles/7353 last-modified: 2019-07-25 description: BackgroundThe microRNAs (miRNAs) have been validated as prognostic markers in many cancers. Here, we aimed at developing a miRNA-based signature for predicting the prognosis of esophagus adenocarcinoma (EAC).MethodsThe RNA-sequencing data set of EAC was downloaded from The Cancer Genome Atlas (TCGA). Eighty-four patients with EAC were classified into a training set and a test set randomly. Using univariate Cox regression analysis and the least absolute shrinkage and selection operator (LASSO), we identified prognostic factors and constructed a prognostic miRNA signature. The accuracy of the signature was evaluated by the receiver operating characteristic (ROC) curve.ResultIn general, in the training set, six miRNAs (hsa-mir-425, hsa-let-7b, hsa-mir-23a, hsa-mir-3074, hsa-mir-424 and hsa-mir-505) displayed good prognostic power as markers of overall survival for EAC patients. Relative to patients in the low-risk group, those assigned to the high-risk group according to their risk scores of the designed miRNA model displayed reduced overall survival. This 6-miRNA model was validated in test and entire set. The area under curve (AUC) for ROC at 3 years was 0.959, 0.840, and 0.868 in training, test, and entire set, respectively. Molecular functional analysis and pathway enrichment analysis indicated that the target messenger RNAs associated with 6-miRNA signature were closely related to several pathways involved in carcinogenesis, especially cell cycle.ConclusionIn summary, a novel 6-miRNA expression-based prognostic signature derived from the EAC data of TCGA was constructed and validated for predicting the prognosis of EAC. creator: Tian Lan creator: Yunyan Lu creator: Zunqiang Xiao creator: Haibin Xu creator: Junling He creator: Zujian Hu creator: Weimin Mao uri: https://doi.org/10.7717/peerj.7353 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lan et al. title: Monensin may inhibit melanoma by regulating the selection between differentiation and stemness of melanoma stem cells link: https://peerj.com/articles/7354 last-modified: 2019-07-25 description: Melanoma is the most lethal cutaneous malignancy that threatens human lives. Poor sensitivity to chemotherapy drugs and the high rate of resistance are the bottlenecks of melanoma treatment. Thus, new chemotherapy drugs are needed. Drug repurposing is a safe, economical and timesaving way to explore new chemotherapy for diseases. Here, we investigated the possibility of repurposing the antibiotic monensin as an anti-melanoma agent. Using three human melanoma cells and two nomal human cell lines as cell models, we found that monensin is obviously toxic to human melanoma cells while safe to nomal human cells. It effectively inhibited cell proliferation and viability, while promoted apoptosis and differentiation of human melanoma cells in vitro. By establishment of an animal model of transplanted human melanoma in nude mice, we demonstrated that monensin suppressed the growth of xenografts in vivo. At the same time, we found that melanogenesis increased and the ability of sphere and cloning forming of melanoma decreased under the treatment of monensin. Further detection about differentiation and pluripotent regulations were executed. Our results suggest that monensin is a potent inhibitor of melanoma, and its anti-tumor mechanism may be through promoting the final differentiation of melanoma stem cells and inhibiting their stemness maintenance. creator: Haoran Xin creator: Jie Li creator: Hao Zhang creator: Yuhong Li creator: Shuo Zeng creator: Zhi Wang creator: Zhihui Zhang creator: Fang Deng uri: https://doi.org/10.7717/peerj.7354 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xin et al. title: DeepBindRG: a deep learning based method for estimating effective protein–ligand affinity link: https://peerj.com/articles/7362 last-modified: 2019-07-25 description: Proteins interact with small molecules to modulate several important cellular functions. Many acute diseases were cured by small molecule binding in the active site of protein either by inhibition or activation. Currently, there are several docking programs to estimate the binding position and the binding orientation of protein–ligand complex. Many scoring functions were developed to estimate the binding strength and predict the effective protein–ligand binding. While the accuracy of current scoring function is limited by several aspects, the solvent effect, entropy effect, and multibody effect are largely ignored in traditional machine learning methods. In this paper, we proposed a new deep neural network-based model named DeepBindRG to predict the binding affinity of protein–ligand complex, which learns all the effects, binding mode, and specificity implicitly by learning protein–ligand interface contact information from a large protein–ligand dataset. During the initial data processing step, the critical interface information was preserved to make sure the input is suitable for the proposed deep learning model. While validating our model on three independent datasets, DeepBindRG achieves root mean squared error (RMSE) value of pKa (−logKd or −logKi) about 1.6–1.8 and R value around 0.5–0.6, which is better than the autodock vina whose RMSE value is about 2.2–2.4 and R value is 0.42–0.57. We also explored the detailed reasons for the performance of DeepBindRG, especially for several failed cases by vina. Furthermore, DeepBindRG performed better for four challenging datasets from DUD.E database with no experimental protein–ligand complexes. The better performance of DeepBindRG than autodock vina in predicting protein–ligand binding affinity indicates that deep learning approach can greatly help with the drug discovery process. We also compare the performance of DeepBindRG with a 4D based deep learning method “pafnucy”, the advantage and limitation of both methods have provided clues for improving the deep learning based protein–ligand prediction model in the future. creator: Haiping Zhang creator: Linbu Liao creator: Konda Mani Saravanan creator: Peng Yin creator: Yanjie Wei uri: https://doi.org/10.7717/peerj.7362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Seazzadactylus venieri gen. et sp. nov., a new pterosaur (Diapsida: Pterosauria) from the Upper Triassic (Norian) of northeastern Italy link: https://peerj.com/articles/7363 last-modified: 2019-07-25 description: A new non-monofenestratan pterosaur with multicusped dentition, Seazzadactylus venieri, is described from the Upper Triassic (middle-upper Norian) of the Carnian Prealps (northeastern Italy). The holotype of S. venieri preserves a complete mandibular and maxillary dentition, along with a nearly complete premaxillary one, showing unique features. Furthermore, the arrangement of the premaxillary teeth and the shape of jugal, pterygoid, ectopterygoid, scapula and pteroid are unique within non-monofenestratan pterosaurs. S. venieri is similar and closely related to Carniadactylus rosenfeldi and Austriadraco dallavecchiai, which are also from the Alpine middle-upper Norian of Italy and Austria, respectively. In a parsimony-based phylogenetic analysis, S. venieri is found to nest within a clade of Triassic pterosaurs composed of Arcticodactylus cromptonellus, Austriadraco dallavecchiai, Carniadactylus rosenfeldi and a trichotomy of Raeticodactylus filisurensis, Caviramus schesaplanensis and MCSNB 8950. This unnamed clade is basal within the Pterosauria, but is not the basalmost clade. Eudimorphodon ranzii lies outside this clade and is more derived, making the Eudimorphodontidae paraphyletic. S. venieri increases the diversity of Triassic pterosaurs and brings the number of pterosaur genera and species in the Dolomia di Forni Formation to four. creator: Fabio Marco Dalla Vecchia uri: https://doi.org/10.7717/peerj.7363 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dalla Vecchia title: Studying the impact of young age on prognosis and treatment in laryngeal squamous cell carcinomas using the SEER database link: https://peerj.com/articles/7368 last-modified: 2019-07-25 description: BackgroundLaryngeal squamous cell carcinoma (LSCC) in young patients was reported to be more aggressive and associated with poorer survival than in older patients. However, very few studies contained sufficient cases to permit meaningful statistical analysis. It is still unknown whether less aggressive method like radical radiotherapy (RT) is comparable to total laryngectomy (TL) in survival rate among young patients.MethodsThis study extracted patient data from the surveillance, epidemiology, and end results database from 2004 to 2015. The findings for 304 patients (1.2%) below the age of 40 were compared with those for 24,827 patients (98.8%) aged 40 or older.ResultsThe younger cohorts contained a higher proportion of female patients (33.6% vs. 19.1%, respectively), had more cases of glottic involvement (64.5% vs. 53.1%), and were less likely to have distant metastasis (0.7% vs.3.2%). A total of 5-year overall survival and cancer-specific survival rates (CSS) in the younger patients were 86.3% and 88.8%, respectively, significantly better than for older patients (53.8% and 67.6%). Significant differences were still observed when stratified for tumor stage (stage I–IV). The negative independent prognostic factors in younger patients were advanced tumor stage, degree of nodal involvement, and status of distant metastasis. Treatment with surgery and/or RT all produced excellent outcomes in stage I–IV diseases, and radical RT resulted in survival rates equal to those for TL in locally advanced LSCC among young patients (5-year CSS: 90% vs. 91.5%, p = 0.99).ConclusionLSCC is less aggressive and has significantly better survival in younger patients. For younger patients, advanced nodal involvement is the most important independent prognostic factor, and larynx preservation is comparable to TL in survival rate. creator: Ruichen Li creator: Shitong Yu creator: Wenjia Zhu creator: Shengzi Wang creator: Li Yan uri: https://doi.org/10.7717/peerj.7368 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Osteokines and the vasculature: a review of the in vitro effects of osteocalcin, fibroblast growth factor-23 and lipocalin-2 link: https://peerj.com/articles/7139 last-modified: 2019-07-24 description: Bone-derived factors that demonstrate extra-skeletal functions, also termed osteokines, are fast becoming a highly interesting and focused area of cross-disciplinary endocrine research. Osteocalcin (OCN), fibroblast growth factor-23 (FGF23) and lipocalin-2 (LCN-2), produced in bone, comprise an important endocrine system that is finely tuned with other organs to ensure homeostatic balance and health. This review aims to evaluate in vitro evidence of the direct involvement of these proteins in vascular cells and whether any causal roles in cardiovascular disease or inflammation can be supported. PubMed, Medline, Embase and Google Scholar were searched for relevant research articles investigating the exogenous addition of OCN, FGF23 or LCN-2 to vascular smooth muscle or endothelial cells. Overall, these osteokines are directly vasoactive across a range of human and animal vascular cells. Both OCN and FGF23 have anti-apoptotic properties and increase eNOS phosphorylation and nitric oxide production through Akt signalling in human endothelial cells. OCN improves intracellular insulin signalling and demonstrates protective effects against endoplasmic reticulum stress in murine and human endothelial cells. OCN may be involved in calcification but further research is warranted, while there is no evidence for a pro-calcific effect of FGF23 in vitro. FGF23 and LCN-2 increase proliferation in some cell types and increase and decrease reactive oxygen species generation, respectively. LCN-2 also has anti-apoptotic effects but may increase endoplasmic reticulum stress as well as have pro-inflammatory and pro-angiogenic properties in human vascular endothelial and smooth muscle cells. There is no strong evidence to support a pathological role of OCN or FGF23 in the vasculature based on these findings. In contrast, they may in fact support normal endothelial functioning, vascular homeostasis and vasodilation. No studies examined whether OCN or FGF23 may have a role in vascular inflammation. Limited studies with LCN-2 indicate a pro-inflammatory and possible pathological role in the vasculature but further mechanistic data is required. Overall, these osteokines pose intriguing functions which should be investigated comprehensively to assess their relevance to cardiovascular disease and health in humans. creator: Sophie A. Millar creator: Susan I. Anderson creator: Saoirse E. O’Sullivan uri: https://doi.org/10.7717/peerj.7139 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Millar et al. title: Spawning stock recruitment creates misleading dynamics under predation release in ecosystem and multi-species models link: https://peerj.com/articles/7308 last-modified: 2019-07-24 description: Ecosystem and multi-species models are used to understand ecosystem-wide effects of fishing, such as population expansion due to predation release, and further cascading effects. Many are based on fisheries models that focus on a single, depleted population, and may not always behave as expected in a multi-species context. The spawning stock recruitment (SSR) relationship, a curve linking the number of juvenile fish to the existing adult biomass, can produce dynamics that are counter-intuitive and change scenario outcomes. We analysed the Beverton–Holt SSR curve and found a population with low resilience when depleted becomes very productive under persistent predation release. To avoid implausible increases in biomass, we propose limiting recruitment to its unfished level. This allows for specification of resilience when a population is depleted, without sudden and excessive increase when the population expands. We demonstrate this dynamic and solution within an end-to-end ecosystem model, focusing on myctophids under fishing-induced predation release. We present one possible solution, but the specification of stock-recruitment models should continue to be a topic of discussion amongst multi-species and ecosystem modellers and empiricists going forward. creator: Vidette L. McGregor creator: Elizabeth A. Fulton creator: Matthew R. Dunn uri: https://doi.org/10.7717/peerj.7308 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 McGregor et al. title: Development of a short questionnaire based on the Practice Environment Scale-Nursing Work Index in primary health care link: https://peerj.com/articles/7369 last-modified: 2019-07-24 description: BackgroundProfessional nursing environments determine the quality of care and patient outcomes. Assessing the quality of environments is essential to improve and obtain better health outcomes. Simplifying and shortening the way to evaluate environments reliably is also important to help nurses better understand the strengths and weaknesses of their environments. In that sense, identifying essential elements of nursing environments would allow the construction of short assessment tools to improve such environments.ObjectiveTo construct a short tool to assess primary health care (PHC) nursing environments based on the Practice Environment Scale-Nursing Work Index (PES-NWI) questionnaire.MethodsObservational, cross-sectional, analytical study (data collection February–April 2015). Tool: PES-NWI (31 items). Population: PHC nurses (three health districts in Valencia, Spain) with more than 3 months in the organization. The nurses were asked to select the 10 elements of the questionnaire (items) that they considered key to facilitate and improve professional care, establishing as a final selection criterion that they obtain a global election >40%. Variables: sociodemographic and 31 questionnaire items. Analysis: descriptive statistics, reliability, multidimensional scaling (ALSCAL), factor analysis, multiple linear regression. Finally, we have analyzed the concordance between both measurements (TOP10 score on the full scale score) using the Bland–Altman method.ResultsStudy sample = 269 (Response rate = 80.29%). A total of 10 elements were identified based on selection frequency of the questionnaire PES-NWI. A factorial analysis explained 62.1% of variance, internal structure of three dimensions: (1) Participation in leadership and management, (2) Nursing foundations for quality of care, (3) Adequacy of resources, with Accumulate Variance explained: Component (1): 24%; Component (2): 43.1%; Component (3): 62.1%. Reliability (Cronbach’s Alpha) was 0.816 for short questionnaire, and >0.8 for all measurements. Stress = 0.184 and RSQ = 0.793. Bland–Altman method: the scaling tends to be 1.92 points higher (equivalent to a maximum deviation of 1.54%) than the full-scale PES-NWI score (max score on PES-NWI = 124 points).ConclusionsIt is possible to identify essential elements of environments to construct a short tool that simplifies the study of PHC environments. Conducting rapid studies of environments will provide managers with information about specific elements that require prioritization to enhance quality of care and safety. creator: Vicente Gea-Caballero creator: Raúl Juárez-Vela creator: Miguel-Ángel Díaz-Herrera creator: María-Isabel Mármol-López creator: Ruben Alfaro Blazquez creator: José Ramón Martínez-Riera uri: https://doi.org/10.7717/peerj.7369 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gea-Caballero et al. title: Investigating the physiological responses of Pacific white shrimp Litopenaeus vannamei to acute cold-stress link: https://peerj.com/articles/7381 last-modified: 2019-07-24 description: BackgroundLitopenaeus vannamei is one of the most important aquaculture shrimps in the world and low temperatures present a serious challenge to its survival, growth, and distribution.MethodsTo investigate their physiological responses during acute cold-stress, L. vannamei were treated under acute cooling conditions from 28 to 13 °C with a cooling rate of 2.5 °C/2 h and were maintained at 13 °C for 12 h. Plasma metabolite concentrations, histological changes, and relative gene expression related to the unfolded protein response (UPR) pathway and apoptosis in the hepatopancreas and the hemocytes of L. vannamei were investigated.ResultsThe results revealed that the concentrations of triglycerides, total cholesterol, and total protein in plasma reached their peaks at 23 °C, and then decreased to their minimum values at 13 °C for 12 h. The activity of alkaline phosphatase in the plasma decreased to its lowest level while the activity of alanine aminotransferase increased to its highest level at 13 °C for 12 h. The hepatic tubules became necrotic and the basement membranes were ruptured at 13 °C for 12 h. The gene expression related to UPR and apoptosis in the hepatopancreas and hemocytes was significantly altered by the decrease in the temperature.DiscussionThe results revealed that acute cold-stress caused histological damage in the hepatopancreas of L. vannamei, reducing its immunity. The three UPR pathways were involved in the process of acute cold-stress and the response of activating transcription factor 6 to UPR may be faster and more directthan the IRE1 and PERK pathways. creator: Zhenlu Wang creator: Yuexin Qu creator: Xiaolei Zhuo creator: Junyi Li creator: Jixing Zou creator: Lanfen Fan uri: https://doi.org/10.7717/peerj.7381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Characterization and localization of cyclin B3 transcript in both oocyte and spermatocyte of the rainbow trout (Oncorhynchus mykiss) link: https://peerj.com/articles/7396 last-modified: 2019-07-24 description: B-type cyclins are regulatory subunits with distinct roles in the cell cycle. To date, at least three subtypes of B-type cyclins (B1, B2, and B3) have been identified in vertebrates. Previously, we reported the characterization and expression profiles of cyclin B1 and B2 during gametogenesis in the rainbow trout (Oncorhynchus mykiss). In this paper, we isolated another subtype of cyclin B, cyclin B3 (CB3), from a cDNA library of the rainbow trout oocyte. The full-length CB3 cDNA (2,093 bp) has an open reading frame (1,248 bp) that encodes a protein of 416 amino acid residues. The CB3 transcript was widely distributed in all the examined tissues, namely, eye, gill, spleen, brain, heart, kidney, stomach, skin, muscle, and, especially, gonad. Northern blot analysis indicated only one form of the CB3 transcript in the testis and ovary. In situ hybridization revealed that, in contrast to cyclin B1 and B2 transcripts, CB3 transcripts were localized in the oocytes, spermatocytes, and spermatogonia. These findings strongly suggest that CB3 plays a role not only as a mitotic cyclin in spermatogonial proliferation during early spermatogenesis but also during meiotic maturation of the spermatocyte and oocyte in the rainbow trout. creator: Wenzhi Guan creator: Liangjie Qiu creator: Bo Zhang creator: Jianbo Yao creator: Qing Xiao creator: Gaofeng Qiu uri: https://doi.org/10.7717/peerj.7396 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guan et al. title: Peptide-based NTA(Ni)-nanodiscs for studying membrane enhanced FGFR1 kinase activities link: https://peerj.com/articles/7234 last-modified: 2019-07-23 description: Tyrosine autophosphorylation plays a crucial regulatory role in the kinase activities of fibroblast growth factor receptors (FGFRs), and in the recruitment and activation of downstream intracellular signaling pathways. Biophysical and biochemical investigations of FGFR kinase domains in membrane environments offer key insights into phosphorylation mechanisms. Hence, we constructed nickel chelating nanodiscs based on a 22-residue peptide. The spontaneous anchoring of N-terminal His6-tagged FGFR1c kinase domain (FGFR1K) onto peptide nanodiscs grants FGFR1K orientations occurring on native plasma membranes. Following membrane incorporation, the autophosphorylation of FGFR1K, as exemplified by Y653 and Y654 in the A-loop and the total tyrosine phosphorylation, increase significantly. This in vitro reconstitution system may be applicable to studies of other membrane associated phenomena. creator: Juanjuan Liu creator: Lei Zhu creator: Xueli Zhang creator: Bo Wu creator: Ping Zhu creator: Hongxin Zhao creator: Junfeng Wang uri: https://doi.org/10.7717/peerj.7234 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Bacillus spp.: potent microfactories of bacterial IAA link: https://peerj.com/articles/7258 last-modified: 2019-07-23 description: BackgroundAuxin production by bacteria is one of the most important direct mechanisms utilized by plant growth-promoting bacteria (PGPB) for the betterment of plants naturally because auxin is a plant friendly secondary metabolite synthesized naturally by bacteria, and hence improves the growth of associated plants. So, the current study focuses on bacterial synthesis of Indole-3-acetic acid (IAA) for plant growth improvement.MethodsIn the current study, the PGPB were selected on the basis of their auxin production potential and their growth promoting attributes were evaluated. Indole-3-acetic acid producing potential of two selected bacterial isolates was observed by varying different growth conditions i.e., media composition, carbon sources (glucose, sucrose and lactose) and different concentrations of precursor. Influence of various physiological factors (temperature and incubation time period) on IAA production potential was also evaluated.ResultsBoth the bacterial strains Bacillus cereus (So3II) and B. subtilis (Mt3b) showed variable potential for the production of bacterial IAA under different set of growth and environmental conditions. Hence, the IAA production potential of the bacterial isolates can be enhanced by affecting optimum growth conditions for bacterial isolates and can be used for the optimal production of bacterial IAA and its utilization for plant growth improvement can lead to better yield in an eco-friendly manner. creator: Shabana Wagi creator: Ambreen Ahmed uri: https://doi.org/10.7717/peerj.7258 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wagi and Ahmed title: Growth and development of soybean under changing light environments in relay intercropping system link: https://peerj.com/articles/7262 last-modified: 2019-07-23 description: BackgroundMaize-soybean relay-intercropping (MSR) is a famous system of crop production in developing countries. However, maize shading under this system directly affects the light quality and intensity of soybean canopy. This is a challenging scenario in which to implement the MSR system, in terms of varieties selection, planting pattern, and crop management since the duration of crop resource utilization clearly differs.MethodsTherefore, this experiment aimed to elucidate the effect of leaf excising treatments from maize top to fully clarify the needs and balance of light quality and intensity of intercrop-soybean under MSR in field conditions. The effects of different leaf excising treatments (T0, no removal of leaves; T2, removal of two topmost leaves; T4, removal of four topmost leaves; T6, removal of six topmost leaves from maize plants were applied at first-trifoliate stage (V1) of soybean) on photosynthetically active radiation transmittance (PART), red to far-red ratio (R:FR), morphological and photosynthetic characteristics and total biomass production at second-trifoliate stage (V2), fifth-trifoliate stage (V5), and flowering-stage (R1) of soybean were investigated through field experiments for 2-years under MSR.ResultsAs compared to T0, treatment T6 increased the PART and R:FR ratio at soybean canopy by 77% and 37% (V2), 70% and 34% (V5), and 41% and 36% (R1), respectively. This improved light environment in T6 considerably enhanced the leaf area index, SPAD values and photosynthetic rate of soybean plants by 66%, 25% and 49% at R1, respectively than T0. Similarly, relative to control, T6 also increased the stem diameter (by 29%) but decreased the plant height (by 23%) which in turn significantly increased stem breaking strength (by 87%) by reducing the lodging rate (by 59%) of soybean plants. Overall, under T6, relay-cropped soybean produced 78% of sole soybean seed-yield, and relay-cropped maize produced 81% of sole maize seed-yield. Our findings implied that by maintaining the optimum level of PART (from 60% to 80%) and R:FR ratio (0.9 to 1.1), we can improve morphological and photosynthetic characteristics of soybean plants in MSR. Therefore, more attention should be paid to the light environment when considering the sustainability of MSR via appropriate planting pattern selection. creator: Muhammad Ali Raza creator: Ling Yang Feng creator: Nasir Iqbal creator: Mukhtar Ahmed creator: Yuan Kai Chen creator: Muhammad Hayder Bin Khalid creator: Atta Mohi Ud Din creator: Ahsin Khan creator: Waqas Ijaz creator: Anwaar Hussain creator: Muhammad Atif Jamil creator: Muhammd Naeem creator: Sadam Hussain Bhutto creator: Muhammad Ansar creator: Feng Yang creator: Wenyu Yang uri: https://doi.org/10.7717/peerj.7262 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Raza et al. title: Mitochondrial phylogeny and comparative mitogenomics of closely related pine moth pests (Lepidoptera: Dendrolimus) link: https://peerj.com/articles/7317 last-modified: 2019-07-23 description: BackgroundPine moths, Dendrolimus spp. (Lasiocampidae), are serious economic pests of conifer forests. Six closely related species (Dendrolimus punctatus, D. tabulaeformis, D. spectabilis, D. superans, D. houi, and D. kikuchii) occur in China and cause serious damage to coniferophyte. The complete mito genomes of Dendrolimus genus are significant to resolve the phylogenetic relationship and provide theoretical support in pest control.MethodsThe complete mitogenomes of three species (D. superans, D. houi, and D. kikuchii) were sequenced based on PCR-amplified with universal primers, which were used to amplify initial fragments. Phylogenetic analyses were carried out with 78 complete mitogenomes of lepidopteran species from 10 superfamilies.ResultsThe complete mitochondrial genomes of these three species were 15,417, 15,381, and 15,377 bp in length, separately. The phylogenetic analyses produced consistent results for six Dendrolimus species based on complete mitogenomes, two major clades were formed, one containing D. spectabilis clustered with D. punctatus + D. tabulaeformis, and D. superans as the sister group to this three-taxon clade, the other containing D. kikuchii and D. houi. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that non-coding regions were more variable than the A+T rich region. The mitochondrial nucleotide diversity was more variable when compared within than among genus, and the concatenated tRNA region was the most conserved and the nd6 genes was the most variable. creator: Jie Qin creator: Jing Li creator: Qiang Gao creator: John-James Wilson creator: Ai-bing Zhang uri: https://doi.org/10.7717/peerj.7317 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Qin et al. title: Children’s attitudes towards animals are similar across suburban, exurban, and rural areas link: https://peerj.com/articles/7328 last-modified: 2019-07-23 description: The decline in the number of hours Americans spend outdoors, exacerbated by urbanization, has affected people’s familiarity with local wildlife. This is concerning to conservationists, as people tend to care about and invest in what they know. Children represent the future supporters of conservation, such that their knowledge about and feelings toward wildlife have the potential to influence conservation for many years to come. Yet, little research has been conducted on children’s attitudes toward wildlife, particularly across zones of urbanization. We surveyed 2,759 4–8th grade children across 22 suburban, exurban, and rural schools in North Carolina to determine their attitudes toward local, domestic, and exotic animals. We predicted that children who live in rural or exurban areas, where they may have more direct access to more wildlife species, would list more local animals as “liked” and fewer as “scary” compared to children in suburban areas. However, children, regardless of where they lived, provided mostly non-native mammals for open-ended responses, and were more likely to list local animals as scary than as liked. We found urbanization to have little effect on the number of local animals children listed, and the rankings of “liked” animals were correlated across zones of urbanization. Promising for conservation was that half of the top “liked” animals included species or taxonomic groups containing threatened or endangered species. Despite different levels of urbanization, children had either an unfamiliarity with and/or low preference for local animals, suggesting that a disconnect between children and local biodiversity is already well-established, even in more rural areas where many wildlife species can be found. creator: Stephanie G. Schuttler creator: Kathryn Stevenson creator: Roland Kays creator: Robert R. Dunn uri: https://doi.org/10.7717/peerj.7328 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Schuttler et al. title: Epidemiological analysis of respiratory and intestinal infectious diseases in three counties of Sichuan: the baseline survey of Disaster Mitigation Demonstration Area in western China link: https://peerj.com/articles/7341 last-modified: 2019-07-23 description: BackgroundNatural disasters can indirectly induce epidemics of infectious diseases through air and water pollution, accelerated pathogen reproduction, and population migration. This study aimed to explore the epidemiological characteristics of the main infectious diseases in Sichuan, a province with a high frequency of natural disasters.MethodsData were collected from the local Centers for Disease Control infectious disease reports from Lu, Shifang and Yuexi counties from 2011 to 2015 and from the baseline survey of the Disaster Mitigation Demonstration Area in Western China in 2016. Principal component regression was used to explore the main influencing factors of respiratory infectious diseases (RIDs).ResultsThe incidence rates of RIDs and intestinal infectious diseases (IIDs) in 2015 were 78.99/100,000, 125.53/100,000, 190.32/100,000 and 51.70/100,000, 206.00/100,000, 69.16/100,000 in Lu, Shifang and Yuexi respectively. The incidence rates of pulmonary tuberculosis (TB) was the highest among RIDs in the three counties. The main IIDs in Lu and Shifang were hand-foot-mouth disease (HFMD) and other infectious diarrhea; however, the main IIDs in Yuexi was bacillary dysentery. The proportions of illiterate and ethnic minorities and per capita disposable income were the top three influencing factors of RIDs.ConclusionsTB was the key point of RIDs prevention among the three counties. The key preventable IIDs in Lu and Shifang were HFMD and other infectious diarrhea, and bacillary dysentery was the major IIDs in Yuexi. The incidence rates of RIDs was associated with the population composition, the economy and personal hygiene habits. creator: Zhiqiang Xue creator: Zhenbo Yang creator: Hui Sun creator: Jinghuan Ren creator: Mengzi Sun creator: Jiagen Li creator: Anning Zhang creator: Pingping Zheng creator: Pan Pan creator: Jing Dou creator: Li Shen creator: Yang Chen creator: Kexin Li creator: Tianyu Feng creator: Yaogai Lv creator: Chunli Bi creator: Lina Jin creator: Zhe Wang creator: Yan Yao uri: https://doi.org/10.7717/peerj.7341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xue et al. title: Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions link: https://peerj.com/articles/7355 last-modified: 2019-07-23 description: The cochlea and semicircular canals (SCCs) of the inner ear are vital neurosensory devices. There are associations between the anatomy of these sensorineural structures, their function, and the function of related biological systems, for example, hearing ability, gaze stabilization, locomotor agility, and posture. The endosseous labyrinth is frequently used as a proxy to infer the performance of the hearing and vestibular systems, locomotor abilities, and ecology of extinct species. Such fossil inferences are often based on single specimens or even a single ear, representing an entire species. To address whether a single ear is representative of a population, we used geometric morphometrics to quantitatively assess the variation in shape and symmetry in a sample of endosseous labyrinths of wild turkeys Meleagris gallopavo of southern Ohio. We predicted that ears would be symmetrical both within individuals and across the sample; that labyrinth shape and size would covary; that labyrinth shape would vary with the size of the brain, measured as width of the endocranium at the cerebellum; and that labyrinths would be morphologically integrated. To test these predictions, we microCT-scanned the heads of 26 cadaveric turkeys, digitally segmented their endosseous labyrinths in Avizo, and assigned 15 manual landmarks and 20 sliding semilandmarks to each digital model. Following Procrustes alignment, we conducted an analysis of bilateral symmetry, a Procrustes regression analysis for allometry and other covariates including side and replicate, and analyses of global integration and modularity. Based on Procrustes distances, no individual’s left and right ears were clearly different from each other. When comparing the ears of different specimens, statistically clear differences in shape were found in only 66 of more than 1,300 contrasts. Moreover, effects of both directional and fluctuating asymmetry were very small—generally, two orders of magnitude smaller than the variance explained by individual variation. Statistical tests disagreed on whether these asymmetric effects crossed the threshold of significance, possibly due to non-isotropic variation among landmarks. Regardless, labyrinths appeared to primarily vary in shape symmetrically. Neither labyrinth size nor endocranial width was correlated with labyrinth shape, contrary to our expectations. Finally, labyrinths were found to be moderately integrated in a global sense, but four weakly separated modules—the three SCCs and cochlea—were recovered using a maximum-likelihood analysis. The results show that both fluctuating and directional asymmetry play a larger role in shape variation than expected—but nonetheless, endosseous labyrinths are symmetrical within individuals and at the level of the population, and their shape varies symmetrically. Thus, inferences about populations, and very possibly species, may be confidently made when only a single specimen, or even a single ear, is available for study. creator: Donald G. Cerio creator: Lawrence M. Witmer uri: https://doi.org/10.7717/peerj.7355 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cerio and Witmer title: Cloning, purification, and characterization of GH3 β-glucosidase, MtBgl85, from Microbulbifer thermotolerans DAU221 link: https://peerj.com/articles/7106 last-modified: 2019-07-22 description: Backgroundβ-Glucosidases have attracted considerable attention due to their important roles in various biotechnological processes such as cellulose degradation to make energy and hydrolysis of isoflavone. Microbulbifer thermotolerans (M. thermotolerans) is isolated from deep-sea sediment and has not been researched much yet. As a potential candidate for a variety of biotechnological industries, β-glucosidases from the novel bacterial species should be researched extensively.Methodsβ-Glucosidase, MtBgl85, from M. thermotolerans DAU221 was purified by His-tag affinity chromatography and confirmed by SDS-PAGE and zymogram. Its biochemical and physiological properties, such as effects of temperature, pH, metal ions, and organic solvents, substrate specificity, and isoflavone hydrolysis, were investigated.ResultsM. thermotolerans DAU221 showed β-glucosidase activity in a marine broth plate containing 0.1% esculin and 0.25% ammonium iron (III) citrate. The β-glucosidase gene, mtbgl85, was isolated from the whole genome sequence of M. thermotolerans DAU221. The β-glucosidase gene was 2,319 bp and encoded 772 amino acids. The deduced amino acid sequence had a 43% identity with OaBGL84 from Olleya aquimaris and 35% and 32% identity with to CfBgl3A and CfBgl3C from Cellulomonas fimi among bacterial glycosyl hydrolase family 3, respectively. The optimal temperature of MtBgl85 was 50 °C and the optimum pH was 7.0. MtBgl85 activity was strongly reduced in the presence of Hg2+ and Cu2+ ions. As a result of measuring the activity at various concentrations of NaCl, it was confirmed that the activity was maintained up to the concentration of 1 M, but gradually decreased with increasing concentration. MtBgl85 showed higher enzyme stability at non-polar solvents (high Log Pow) than polar solvents (low Log Pow). The hydrolyzed products of isoflavone glycosides and arbutin were analyzed by HPLC. creator: Hyo-Min Pyeon creator: Yong-Suk Lee creator: Yong-Lark Choi uri: https://doi.org/10.7717/peerj.7106 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pyeon et al. title: Thermal conditions and age structure determine the spawning regularities and condition of Baltic herring (Clupea harengus membras) in the NE of the Baltic Sea link: https://peerj.com/articles/7345 last-modified: 2019-07-22 description: Baltic herring (Clupea harengus membras) is a total spawner with a group-synchronous ovarian organization. Age polymodality in total spawners is considered an important factor in assuring that a strong population is sustainable under an intensive harvesting regime and different climatic conditions. In the present study, we investigated the seasonal and inter-annual variation in spawner age structure and the effect of preceding winter thermal conditions on the start of the herring spawning and larvae retention period. Herring spawning season in the Gulf of Riga starts up to six weeks later after colder winters compared to milder winters. Significantly older individuals dominated at the beginning of the spawning season, and thus herring mean age gradually decreased towards the end of the spawning season from 1999–2015. On an annual scale, this pattern was obvious after cold winters, while after mild winters the pattern did not continue, indicating a more homogenous maturation cycle and spawning period, despite the age and size of the herring population in mild winters. Further, herring condition factor was studied in relation to age and spawning season following different winter thermal conditions. Young, 2- and 3- year old first-spawning herring experienced significantly lower conditions after cold winters compared to older ages, indicating an age-dependent effect of preceding winter on herring maturation cycle, condition and spawning time. creator: Timo Arula creator: Heli Shpilev creator: Tiit Raid creator: Elor Sepp uri: https://doi.org/10.7717/peerj.7345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Arula et al. title: SLCV–a supervised learning—computer vision combined strategy for automated muscle fibre detection in cross-sectional images link: https://peerj.com/articles/7053 last-modified: 2019-07-22 description: Muscle fibre cross-sectional area (CSA) is an important biomedical measure used to determine the structural composition of skeletal muscle, and it is relevant for tackling research questions in many different fields of research. To date, time consuming and tedious manual delineation of muscle fibres is often used to determine the CSA. Few methods are able to automatically detect muscle fibres in muscle fibre cross-sections to quantify CSA due to challenges posed by variation of brightness and noise in the staining images. In this paper, we introduce the supervised learning-computer vision combined pipeline (SLCV), a robust semi-automatic pipeline for muscle fibre detection, which combines supervised learning (SL) with computer vision (CV). SLCV is adaptable to different staining methods and is quickly and intuitively tunable by the user. We are the first to perform an error analysis with respect to cell count and area, based on which we compare SLCV to the best purely CV-based pipeline in order to identify the contribution of SL and CV steps to muscle fibre detection. Our results obtained on 27 fluorescence-stained cross-sectional images of varying staining quality suggest that combining SL and CV performs significantly better than both SL-based and CV-based methods with regards to both the cell separation- and the area reconstruction error. Furthermore, applying SLCV to our test set images yielded fibre detection results of very high quality, with average sensitivity values of 0.93 or higher on different cluster sizes and an average Dice similarity coefficient of 0.9778. creator: Anika Rettig creator: Tobias Haase creator: Alexandr Pletnyov creator: Benjamin Kohl creator: Wolfgang Ertel creator: Max von Kleist creator: Vikram Sunkara uri: https://doi.org/10.7717/peerj.7053 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rettig et al. title: Main histological parameters to be evaluated in an experimental model of myocardial infarct treated by stem cells on pigs link: https://peerj.com/articles/7160 last-modified: 2019-07-22 description: Myocardial infarction has been carefully studied in numerous experimental models. Most of these models are based on electrophysiological and functional data, and pay less attention to histological discoveries. During the last decade, treatment using advanced therapies, mainly cell therapy, has prevailed from among all the options to be studied for treating myocardial infarction. In our study we wanted to show the fundamental histological parameters to be evaluated during the development of an infarction on an experimental model as well as treatment with mesenchymal stem cells derived from adipose tissue applied intra-lesionally. The fundamental parameters to study in infarcted tissue at the histological level are the cells involved in the inflammatory process (lymphocytes, macrophages and M2, neutrophils, mast cells and plasma cells), neovascularization processes (capillaries and arterioles) and cardiac cells (cardiomyocytes and Purkinje fibers). In our study, we used intramyocardial injection of mesenchymal stem cells into the myocardial infarction area 1 hour after arterial occlusion and allowed 1 month of evolution before analyzing the modifications on the normal tissue inflammatory infiltrate. Acute inflammation was shortened, leading to chronic inflammation with abundant plasma cells and mast cells and complete disappearance of neutrophils. Another benefit was an increase in the number of vessels formed. Cardiomyocytes and Purkinje fibers were better conserved, both from a structural and metabolic point of view, possibly leading to reduced morbidity in the long term. With this study we present the main histological aspects to be evaluated in future assays, complementing or explaining the electrophysiological and functional findings. creator: Soledad García Gómez-Heras creator: Carlota Largo creator: Jose Luis Larrea creator: Luz Vega-Clemente creator: Miguel Calderón Flores creator: Daniel Ruiz-Pérez creator: Damián García-Olmo creator: Mariano García-Arranz uri: https://doi.org/10.7717/peerj.7160 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 García Gómez-Heras et al. title: Differences in biomass and silica content in typical plant communities with ecotones in the Min River estuary of southeast China link: https://peerj.com/articles/7218 last-modified: 2019-07-22 description: Silica (Si) is a basic nutrient requirement for many aquatic organisms and its biogeochemical cycle plays an important role in estuarine coastal ecosystems. However, little is known about the role Si plays during plant–plant interactive processes in the marsh ecosystems. Here, variations in biomass, biogenic silica (BSi) content, and available Si content of Cyperus malaccensis-dominated marshes, Phragmites australis-dominated marshes, and their ecotonal marshes were studied in the Shanyutan marsh in the Min River estuary, China. Results showed that C. malaccensis and P. australis biomass in ecotones was lower than those in typical communities by 46.4% and 46.3%, respectively. BSi content in aboveground organs of C. malaccensis and culms and roots of P. australis was lower in ecotones than in typical communities, whereas BSi content in other organs showed the opposite trend. Biomass allocation in C. malaccensis and P. australis roots in ecotones was higher by 56.9% and 19.5%, respectively, and BSi stock in C. malaccensis and P. australis roots was higher than that in typical communities by 120.9% and 18.9%, respectively. Available Si content in ecotonal marsh soils was 12.6% greater than that in typical communities. Thus, the two plant species may use different strategies for Si accumulation and allocation in ecotones to adapt to the competitive environment. P. australis may expand primarily via occupation of wider aboveground space, thereby increasing the Si accumulation capacity in aboveground organs. Meanwhile, C. malaccensis may increase the Si allocation capacity of its roots to withstand the pressure from P. australis. This study will provide new insights into marsh plant competition from the perspective of Si, which can also benefit plant management in marsh ecosystems. creator: Hui Gao creator: Shuijing Zhai creator: Zhigao Sun creator: Juan Liu creator: Chuan Tong uri: https://doi.org/10.7717/peerj.7218 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gao et al. title: First ex situ outplanting of the habitat-forming seaweed Cystoseira amentacea var. stricta from a restoration perspective link: https://peerj.com/articles/7290 last-modified: 2019-07-22 description: In the Mediterranean Sea, brown algae belonging to the Cystoseira genus play a valuable role as foundation species. Due to evidences of regression/loss of the habitats of these species caused by the interplay of human and climatic disturbances, active restoration measures have been encouraged by EU regulations. In particular, nondestructive restoration techniques, which avoid the depletion of threatened species in donor populations, are strongly recommended. In the framework of the EU project ROCPOP-Life, the first ex situ outplanting experience of Cystoseira amentacea var. stricta has been implemented in the Cinque Terre Marine Protected Area (northwestern Mediterranean). A total of 400 clay tiles, hosting approximately three mm-long germlings of C. amentacea, were fixed to the rocky shore with screws: the tiles were monitored for the next 2 months by photographic sampling, and survival (presence/absence of juveniles on the tiles), cover and growth were assessed. Additional sampling was performed 6 months after tile deployment, after which an unprecedented storm surge severely affected the restoration performance. After 2 months, over 40% of the tiles were covered with Cystoseira juveniles, which reached approximately eight mm in total length. The tiles that survived the storm hosted three to six cm-long juveniles. The high cover (≥25%), assuring moisture and shading, and the appropriate size of the juveniles, to avert micro-grazing, at time of deployment were key to the survival and growth of the outplanted juveniles, increasing the potential for restoration success. Our findings show that outplanting of midlittoral canopy-forming species is a feasible approach for restoration efforts, with particular attention given to the early phases: (i) laboratory culture, (ii) transport, and (iii) juvenile densities. These results are strongly encouraging for the implementation of restoration actions for C. amentacea on a large scale, in light of EU guidelines. creator: Gina De La Fuente creator: Mariachiara Chiantore creator: Valentina Asnaghi creator: Sara Kaleb creator: Annalisa Falace uri: https://doi.org/10.7717/peerj.7290 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 De La Fuente et al. title: Patterned progression of gut microbiota associated with necrotizing enterocolitis and late onset sepsis in preterm infants: a prospective study in a Chinese neonatal intensive care unit link: https://peerj.com/articles/7310 last-modified: 2019-07-22 description: Necrotizing enterocolitis (NEC) and late-onset sepsis (LOS) are two common premature birth complications with high morbidity and mortality. Recent studies in Europe and America have linked gut microbiota dysbiosis to their etiology. However, similar studies in Asian populations remain scant. In this pilot study, we profiled gut microbiota of 24 Chinese preterm infants from birth till death or discharge from NICU. Four of them developed NEC and three developed LOS. Unexpectedly, we detected highly-diversified microbiota with similar compositions in all patients shortly after birth. However, as patients aged, the microbial diversities in case groups differed significantly from that of the control group. These differences emerged after the third day of life and persisted throughout the course of both NEC and LOS. Using a Zero-Inflated Beta Regression Model with Random Effects (ZIBR), we detected higher Bacillus (p = 0.032) and Solibacillus (p = 0.047) before the onset of NEC and LOS. During NEC progression, Enterococcus, Streptococcus and Peptoclostridium were the dominant genera while during LOS progression; Klebsiella was the only dominant genus that was also detected by the diagnostic hemoculture. These results warrant further studies to identify causative microbial patterns and underlying mechanisms. creator: Jiayi Liu creator: Yuqing Li creator: Yi Feng creator: Liya Pan creator: Zhoulonglong Xie creator: Zhilong Yan creator: Li Zhang creator: Mingkun Li creator: Jianhua Zhao creator: Jianhua Sun creator: Li Hong uri: https://doi.org/10.7717/peerj.7310 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Increased expression of caspase 1 during active phase of connective tissue disease link: https://peerj.com/articles/7321 last-modified: 2019-07-22 description: Key factors of pyroptosis play an important role in the inflammatory response to connective tissue disease (CTD). However, information on active and stable stages of CTD is scarce. To distinguish the differences of concentrations of C-reactive protein (CRP), caspase 1, caspase 4, caspase 5 and sCD14 in plasma between the patients with active and stable stages of CTD. A cohort study was conducted to recruit patients diagnosed with CTD of active phase and stable phase as well as health control. These data included the analysis of the concentration of sCD14, caspase 1, caspase 4 and caspase 5 in peripheral plasma by ELISA. The Wilcoxon rank-sum test was used to compare the two groups. The sex ratio and ages of the three groups were not different statistically. The concentrations of sCD14, caspase4 and caspase5 of plasma in the CTD of active phase and the stable phase as well as the health control. The concentration of caspase 1 in active phase of CTD (470.19 [422.33–513.14] pmol/L) was significantly higher than that in stable group (203.95 [160.94–236.12] pmol/L) and healthy control (201.65 [191.11–240.35] pmol/L] pmol/L) (p < 0.001, both), but there was no significant difference between stable group and healthy control (p = 0.2312). Similarly, the concentration of CRP in the active phase of CTD (8.96 [3.06–20.28] mg/L) was significantly higher than that in the stable group (3.00 [1.30–11.40] mg/L) and the healthy control (3.70 [2.30–4.73] mg/L) (p = 0.0013, p = 0.0006, respectively), but there was no significant difference between the stable group and the healthy control (p = 0.3205). However, there were no significant differences in the concentration of sCD14, caspase 4 and caspase 5 in the active phase of CTD and the stable group as well as the health group. Consequently, the patients of the active phase of CTD showed increased expression of caspase 1. creator: Rentian Cai creator: Qiongqiong Wang creator: Gongmin Zhu creator: Liying Zhu creator: Zhen Tao uri: https://doi.org/10.7717/peerj.7321 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cai et al. title: Appendicular skeleton of Protoceratops andrewsi (Dinosauria, Ornithischia): comparative morphology, ontogenetic changes, and the implications for non-ceratopsid ceratopsian locomotion link: https://peerj.com/articles/7324 last-modified: 2019-07-22 description: Protoceratops andrewsi is a well-known ceratopsian dinosaur from the Djadokhta Formation (Upper Cretaceous, Mongolia). Since the 1920s, numerous skeletons of different ontogenetic stages from hatchlings to adults, including fully articulated specimens, have been discovered, but the postcranial anatomy of Protoceratops has not been studied in detail. A new, mostly articulated subadult individual provides an excellent opportunity for us to comprehensively describe the anatomy of the limb skeleton, to compare to other ceratopsian dinosaurs, and to study the ontogenetic and intraspecific variation in this species. New data provided by the specimen shed light on the lifestyle of P. andrewsi. The young subadult individuals present an array of morphological characters intermediate between the bipedal Psittacosaurus and fully quadrupedal adult P. andrewsi. We compare these observations with a broad range of non-ceratopsid Neoceratopsia (of various locomotor adaptations) and Psittacosauridae (obligate bipeds), which gives us insight into the evolution of the skeletal characters informative for the postural change in ceratopsian dinosaurs. creator: Justyna Słowiak creator: Victor S. Tereshchenko creator: Łucja Fostowicz-Frelik uri: https://doi.org/10.7717/peerj.7324 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Słowiak et al. title: Extinction risk of narrowly distributed species of seed plants in Brazil due to habitat loss and climate change link: https://peerj.com/articles/7333 last-modified: 2019-07-22 description: In a world where changes in land cover and climate happen faster than ever due to the expansion of human activities, narrowly distributed species are predicted to be the first to go extinct. Studies projecting species extinction in tropical regions consider either habitat loss or climate change as drivers of biodiversity loss but rarely evaluate them together. Here, the contribution of these two factors to the extinction risk of narrowly distributed species (with ranges smaller than 10,000 km2) of seed plants endemic to a fifth-order watershed in Brazil (microendemics) is assessed. We estimated the Regional Climate Change Index (RCCI) of these watersheds (areas with microendemics) and projected three scenarios of land use up to the year 2100 based on the average annual rates of habitat loss in these watersheds from 2000 to 2014. These scenarios correspond to immediate conservation action (scenario 1), long-term conservation action (scenario 2), and no conservation action (scenario 3). In each scenario, areas with microendemics were classified into four classes: (1) areas with low risk, (2) areas threatened by habitat loss, (3) areas threatened by climate change, and (4) areas threatened by climate change and habitat loss. We found 2,354 microendemic species of seed plants in 776 areas that altogether cover 17.5% of Brazil. Almost 70% (1,597) of these species are projected to be under high extinction risk by the end of the century due to habitat loss, climate change, or both, assuming that these areas will not lose habitat in the future due to land use. However, if habitat loss in these areas continues at the prevailing annual rates, the number of threatened species is projected to increase to more than 85% (2,054). The importance of climate change and habitat loss as drivers of species extinction varies across phytogeographic domains, and this variation requires the adoption of retrospective and prospective conservation strategies that are context specific. We suggest that tropical countries, such as Brazil, should integrate biodiversity conservation and climate change policies (both mitigation and adaptation) to achieve win-win social and environmental gains while halting species extinction. creator: José Maria Cardoso da Silva creator: Alessandro Rapini creator: Luis Cláudio F. Barbosa creator: Roger R. Torres uri: https://doi.org/10.7717/peerj.7333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Silva et al. title: Measuring the dispersion of rainfall using Bayesian confidence intervals for coefficient of variation of delta-lognormal distribution: a study from Thailand link: https://peerj.com/articles/7344 last-modified: 2019-07-22 description: Since rainfall data series often contain zero values and thus follow a delta-lognormal distribution, the coefficient of variation is often used to illustrate the dispersion of rainfall in a number of areas and so is an important tool in statistical inference for a rainfall data series. Therefore, the aim in this paper is to establish new confidence intervals for a single coefficient of variation for delta-lognormal distributions using Bayesian methods based on the independent Jeffreys’, the Jeffreys’ Rule, and the uniform priors compared with the fiducial generalized confidence interval. The Bayesian methods are constructed with either equitailed confidence intervals or the highest posterior density interval. The performance of the proposed confidence intervals was evaluated using coverage probabilities and expected lengths via Monte Carlo simulations. The results indicate that the Bayesian equitailed confidence interval based on the independent Jeffreys’ prior outperformed the other methods. Rainfall data recorded in national parks in July 2015 and in precipitation stations in August 2018 in Nan province, Thailand are used to illustrate the efficacy of the proposed methods using a real-life dataset. creator: Noppadon Yosboonruang creator: Sa-aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.7344 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yosboonruang et al. title: Comprehensive assessment of paddy soil quality under land consolidation: a novel perspective of microbiology link: https://peerj.com/articles/7351 last-modified: 2019-07-22 description: Soil quality assessment is an important means to demonstrate how effective land consolidation is. However, the existing assessment system is not sufficient to reflect actual soil quality. So, the purpose of this study is to integrate abiological and biological indicators into a comprehensive assessment to evaluate the paddy soil quality under different land consolidation practices. Soil samples were collected from 35 paddy sites under different land consolidation practices including land merging, land leveling (LL), ditch construction (DC) and application of organic fertilizer (AO). A total of 10 paddy sites were selected under conventional tillage (CT) from non-land consolidation area as a control group in Y county, China. The results indicated that soil organic matter (OM), total nitrogen (TN), available phosphorus, bacterial functional diversity (BFD), bacterial and fungal abundances were significantly improved. Fields under LL, among all the land consolidation practices, might still face the risk of land degradation caused by low TN, OM and microbial diversity. High microbial biomass, BFD and OM were significantly higher in fields under AO in nutrient cycle. According to the results of comprehensive assessment, the samples with severe heavy metal contamination and low microbial diversity were generally concentrated in CT. These results indicated that land consolidation was an efficient technique to improve soil quality and could achieve higher quality of agricultural products. creator: Yaoben Lin creator: Yanmei Ye creator: Cifang Wu creator: Jianhui Yang creator: Yiming Hu creator: Haokun Shi uri: https://doi.org/10.7717/peerj.7351 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lin et al. title: A revision of the diagnosis and affinities of the metriorhynchoids (Crocodylomorpha, Thalattosuchia) from the Rosso Ammonitico Veronese Formation (Jurassic of Italy) using specimen-level analyses link: https://peerj.com/articles/7364 last-modified: 2019-07-22 description: Neptunidraco ammoniticus is a thalattosuchian crocodylomorph from the Rosso Ammonitico Veronese Formation (RAVF, Middle Jurassic) of northern Italy. Erected from one partial specimen, Neptunidraco is pivotal in reconstructing thalattosuchian evolution, being it the oldest known member of Metriorhynchidae. Two additional RAVF thalattosuchians have been referred to Neptunidraco. A revised diagnosis of N. ammoniticus is provided here. Using a well-sampled phylogenetic data set of Crocodylomorpha, the affinities of all three RAVF thalattosuchian specimens are investigated simultaneously for the first time using parsimony tree-search strategies and Bayesian inference using the Fossilized Birth-Death with Sampled Ancestor (FBDSA) model. The results of the alternative analyses are not consistent in the placement of the RAVF specimens. The holotype of N. ammoniticus is consequently referred to Metriorhynchidae incertae sedis. The first referred specimen is recovered in various alternative placements among Metriorhynchoidea. The third and most fragmentary specimen is recovered as a crocodylomorph of uncertain affinities in the parsimony analysis and in the undated Bayesian analysis, and a metriorhynchoid sister taxon of the second RAVF specimen in the tip-dated Bayesian analysis. Only a subset of the results in the parsimony-based analyses supports the referral of the latter two specimens to Neptunidraco. The unusually high rate of morphological divergence for the Neptunidraco branch, inferred in previous iterations of the Bayesian inference analyses but not recovered in the novel analysis, was likely an artifact of the a priori constraint of all RAVF thalattosuchians into a single taxonomic unit, and of the arbitrarily fixed tip-age priors for the terminal taxa. These results confirm the utility of specimen-level morphological analysis and of combined tree-search strategies for inferring the affinities and the inclusiveness of fragmentary but significant fossil taxa, and reinforce the importance of incorporating stratigraphic uncertainty as prior in tip-dated Bayesian inference analyses. creator: Andrea Cau uri: https://doi.org/10.7717/peerj.7364 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cau title: Construction and integrated analysis of crosstalking ceRNAs networks in laryngeal squamous cell carcinoma link: https://peerj.com/articles/7380 last-modified: 2019-07-22 description: BackgroundLaryngeal squamous cell carcinoma (LSCC) is one of the most common malignant tumours of the head and neck. Recent evidence has demonstrated that lncRNAs play important roles in tumour progression and could be used as biomarkers for early diagnosis, prognosis, and potential therapeutic targets. The “competitive endogenous RNA (ceRNA)” hypothesis states that lncRNAs competitively bind to miRNAs through their intramolecular miRNA reaction elements (MREs) to construct a wide range of ceRNA regulatory networks. This study aims to predict the role of ceRNA network in LSCC, for advancing the understanding of underlying mechanisms of tumorigenesis.Material and MethodsIn this study, the functions of lncRNAs as ceRNAs in LSCC and their prognostic significance were investigated via comprehensive integrated expression profiles data of lncRNAs, mRNAs, and miRNAs obtained from The Cancer Genome Atlas (TCGA). Protein–protein interaction, gene ontology, pathway, and Kaplan–Meier curves analysis were used to profile the expression and function of altered RNAs in LSCC.ResultsAs a result, 889 lncRNAs, 55 miRNAs and 1946 mRNAs were found to be differentially expressed in LSCC. These altered mRNAs were mainly involved in extracellular matrix organization, calcium signaling, and metabolic pathways. To study the regulatory function of lncRNAs, an lncRNA-mediated ceRNA network was constructed. This ceRNA network included 61 lncRNAs, seven miRNAs and seven target mRNAs. Of these RNAs, lncRNAs (TSPEAR-AS, CASK-AS1, MIR137HG, PART1, LSAMP-AS1), miRNA (has-mir-210) and mRNAs (HOXC13, STC2, DIO1, FOXD4L1) had a significant effect on the prognosis of LSCC.ConclusionThe results of this study broaden the understanding of the mechanisms by which lncRNAs are involved in tumorigenesis. Furthermore, five lncRNAs (TSPEAR-AS, CASK-AS1, MIR137HG, PART1, LSAMP-AS1) were identified as potential prognostic biomarkers and therapeutic targets for LSCC. These results provide a basis for further experimental and clinical research. creator: Yuehui Liu creator: Fan Ye uri: https://doi.org/10.7717/peerj.7380 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu and Ye title: RITAN: rapid integration of term annotation and network resources link: https://peerj.com/articles/6994 last-modified: 2019-07-19 description: BackgroundIdentifying the biologic functions of groups of genes identified in high-throughput studies currently requires considerable time and/or bioinformatics experience. This is due in part to each resource housed within separate databases, requiring users to know about them, and integrate across them. Time consuming and often repeated for each study, integrating across resources and merging with data under study is an increasingly common bioinformatics task.MethodsWe developed an open-source R software package for assisting researchers in annotating their genesets with functions, pathways, and their interconnectivity across a diversity of network resources.ResultsWe present rapid integration of term annotation and network resources (RITAN) for the rapid and comprehensive annotation of a list of genes using functional term and pathway resources and their relationships among each other using multiple network biology resources. Currently, and to comply with data redistribution policies, RITAN allows rapid access to 16 term annotations spanning gene ontology, biologic pathways, and immunologic modules, and nine network biology resources, with support for user-supplied resources; we provide recommendations for additional resources and scripts to facilitate their addition to RITAN. Having the resources together in the same system allows users to derive novel combinations. RITAN has a growing set of tools to explore the relationships within resources themselves. These tools allow users to merge resources together such that the merged annotations have a minimal overlap with one another. Because we index both function annotation and network interactions, the combination allows users to expand small groups of genes using links from biologic networks—either by adding all neighboring genes or by identifying genes that efficiently connect among input genes—followed by term enrichment to identify functions. That is, users can start from a core set of genes, identify interacting genes from biologic networks, and then identify the functions to which the expanded list of genes contribute.ConclusionWe believe RITAN fills the important niche of bridging the results of high-throughput experiments with the ever-growing corpus of functional annotations and network biology resources.AvailabilityRapid integration of term annotation and network resources is available as an R package at github.com/MTZimmer/RITAN and BioConductor.org. creator: Michael T. Zimmermann creator: Brian Kabat creator: Diane E. Grill creator: Richard B. Kennedy creator: Gregory A. Poland uri: https://doi.org/10.7717/peerj.6994 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zimmermann et al. title: Identification of primary genes in glomeruli compartment of immunoglobulin A nephropathy by bioinformatic analysis link: https://peerj.com/articles/7067 last-modified: 2019-07-19 description: The current study is aimed to explore the specific genes which are responsible for the manifestation of Immunoglobulin A nephropathy (IgAN). Gene expression profiles GSE37460, GSE93798 and GSE104948 were analyzed using biological informatics methods to identify differentially expressed genes (DEGs) in IgAN glomeruli samples which were then compared to normal control samples. Subsequently, the DEGs were overlapped to explore genes with significant expression in at least two profiles. Finally, the enrichment analysis was conducted and the protein-protein interaction (PPI) network was constructed for the overlapping DEGs. A total of 28 genes were up-regulated and 10 genes were down-regulated. The up-regulated genes including CD44 and FN1 were chiefly involved in extracellular matrix receptors interaction pathway. In addition, CX3CR1 and CCL4 were associated with chemokine signaling pathway. ITGB2, PTPRC, FN1, and FCER1G were hub genes with a high degree of interaction in the PPI network. Therefore, this study identified many significant genes associated with extracellular matrix expansion and inflammatory mechanism which may be the novel biomarker and target candidates in IgAN. creator: Mohammed Khamis Miraji creator: Yichun Cheng creator: Shuwang Ge creator: Gang Xu uri: https://doi.org/10.7717/peerj.7067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Miraji et al. title: Evaluating the oestrogenic activities of aqueous root extract of Asparagus africanus Lam in female Sprague-Dawley rats and its phytochemical screening using Gas Chromatography-Mass Spectrometry (GC/MS) link: https://peerj.com/articles/7254 last-modified: 2019-07-19 description: Asparagus africanus Lam. is a plant used traditionally for natal care. This study evaluates the oestrogenic activities of aqueous root extract and screens for possible bioactive phytochemicals. Oestrogenicity of A. africanus was evaluated in ovariectomised rats treated with 50, 200, and 800 mg/kgBW doses twice daily for three days. Ethinyl estradiol (EE)1 mg/kg was used as positive control, and hormonal analysis and gene expression were carried out. The findings demonstrated that the extract produced a dose-dependent increase in the oestrogen levels with a significant increase compared to untreated rats. Pre-treatment with oestrogen receptor antagonist (ORA) prior to A. africanus treatment reversed the trend. Gene expression analysis on rats treated with 200 mg/kgBW A. africanus showed significant (p < 0.005) upregulation of oestrogen receptor alpha (ERα), while pre-treating animals with (ORA) significantly (p < 0.005) increased the expression of calbindin 3 (Calb3) in the EE group as compared to the untreated rats. The GC/MS results showed the presence of steroidal saponins such as stigmasterol and sarsasapogenin. These might be the bioactive constituents that exhibited these activities. The oestrogenic properties of A. africanus revealed in this study could contribute to the antifertility properties of the plant. However, further pharmacological studies are required to confirm the antifertility effect. creator: Abubakar El-Ishaq creator: Mohammed A. Alshawsh creator: Zamri Bin Chik uri: https://doi.org/10.7717/peerj.7254 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 El-Ishaq et al. title: Proximate grassland and shrub-encroached sites show dramatic restructuring of soil bacterial communities link: https://peerj.com/articles/7304 last-modified: 2019-07-19 description: BackgroundChanges in aboveground community composition and diversity following shrub encroachment have been studied extensively. Recently, shrub encroachment was associated with differences in belowground bacterial communities relative to non-encroached grassland sites hundreds of meters away. This spatial distance between grassland and shrub sites left open the question of how soil bacterial communities associated with different vegetation types might differ within the same plot location.MethodsWe examined soil bacterial communities between shrub-encroached and adjacent (one m apart) grassland soils in Chinese Inner Mongolian, using high-throughput sequencing method (Illumina, San Diego, CA, USA).ResultsShrub-encroached sites were associated with dramatic restructuring of soil bacterial community composition and predicted metabolic function, with significant increase in bacterial alpha-diversity. Moreover, bacterial phylogenic structures showed clustering in both shrub-encroached and grassland soils, suggesting that each vegetation type was associated with a unique and defined bacterial community by niche filtering. Finally, soil organic carbon (SOC) was the primary driver varied with shifts in soil bacterial community composition. The encroachment was associated with elevated SOC, suggesting that shrub-mediated shifts in SOC might be responsible for changes in belowground bacterial community.DiscussionThis study demonstrated that shrub-encroached soils were associated with dramatic restructuring of bacterial communities, suggesting that belowground bacterial communities appear to be sensitive indicators of vegetation type. Our study indicates that the increased shrub-encroached intensity in Inner Mongolia will likely trigger large-scale disruptions in both aboveground plant and belowground bacterial communities across the region. creator: Xingjia Xiang creator: Sean M. Gibbons creator: He Li creator: Haihua Shen creator: Haiyan Chu uri: https://doi.org/10.7717/peerj.7304 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xiang et al. title: Manic episode, aggressive behavior and poor insight are significantly associated with involuntary admission in patients with bipolar disorders link: https://peerj.com/articles/7339 last-modified: 2019-07-19 description: Objective(s)Serious mental illnesses, such as bipolar disorders and schizophrenia, are closely associated with involuntary admission. Many studies have focused on involuntary admission in people with schizophrenia, but little is known about the factors associated with involuntary admission in Chinese patients with bipolar disorders. This study aimed to investigate socio-demographic and clinical factors associated with involuntary admission in Chinese patients with bipolar disorders.MethodsIn this multi-center cross-sectional survey in China, a total of 155 newly admitted patients with bipolar disorders were consecutively recruited from 16 psychiatric institutions from 15 March to 14 April, 2013. Patients’ socio-demographic and clinical data were collected from their medical records. The Modified Overt Aggression Scale and the Insight and Treatment Attitudes Questionnaire were used to measure patients’ level of aggression and insight of current psychiatric illness.ResultsThe prevalence of involuntary admission was 52% in this sample of Chinese inpatients with bipolar disorders. In multiple logistic regression, a high level of aggression (odds ratio (OR) = 2.48), diagnosis of manic episode (OR = 3.65), poor insight (OR = 7.52), and a low level of education (OR = 3.13) were significantly associated with involuntary admission.ConclusionManic episode, aggressive behavior, and poor insight were the significant contributing factors to involuntary admission in Chinese patients with bipolar disorders. creator: Chenyuli Luo creator: Hui Chen creator: Shaoling Zhong creator: Huijuan Guo creator: Qiguang Li creator: Weixiong Cai creator: Giovanni de Girolamo creator: Jiansong Zhou creator: Xiaoping Wang uri: https://doi.org/10.7717/peerj.7339 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Luo et al. title: Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location link: https://peerj.com/articles/7376 last-modified: 2019-07-19 description: Previous studies indicate that the plant phenotypic traits eventually shape its microbiota due to the community assembly based on the functional types. If so, the distance-related variations of microbial communities are mostly only in taxonomical composition due to the different seeds pool, and there is no difference in microbial community functional structure if the location associated factors would not cause phenotypical variations in plants. We test this hypothesis by investigating the phyllospheric microbial community from five species of spruce (Picea spp.) trees that planted similarly but at three different locations. Results indicated that the geographical location affected microbial taxonomical compositions and had no effect on the community functional structure. In fact, this actually leads to a spurious difference in the microbial community. Our findings suggest that, within similar host plants, the phyllosphere microbial communities with differing taxonomical compositions might be functionally similar. creator: Yunshi Li creator: Xiukun Wu creator: Wanfu Wang creator: Minghao Wang creator: Changming Zhao creator: Tuo Chen creator: Guangxiu Liu creator: Wei Zhang creator: Shiweng Li creator: Huaizhe Zhou creator: Minghui Wu creator: Ruiqi Yang creator: Gaosen Zhang uri: https://doi.org/10.7717/peerj.7376 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Visual complexity modelling based on image features fusion of multiple kernels link: https://peerj.com/articles/7075 last-modified: 2019-07-18 description: Humans’ perception of visual complexity is often regarded as one of the key principles of aesthetic order, and is intimately related to the physiological, neurological and, possibly, psychological characteristics of the human mind. For these reasons, creating accurate computational models of visual complexity is a demanding task. Building upon on previous work in the field (Forsythe et al., 2011; Machado et al., 2015) we explore the use of Machine Learning techniques to create computational models of visual complexity. For that purpose, we use a dataset composed of 800 visual stimuli divided into five categories, describing each stimulus by 329 features based on edge detection, compression error and Zipf’s law. In an initial stage, a comparative analysis of representative state-of-the-art Machine Learning approaches is performed. Subsequently, we conduct an exhaustive outlier analysis. We analyze the impact of removing the extreme outliers, concluding that Feature Selection Multiple Kernel Learning obtains the best results, yielding an average correlation to humans’ perception of complexity of 0.71 with only twenty-two features. These results outperform the current state-of-the-art, showing the potential of this technique for regression. creator: Carlos Fernandez-Lozano creator: Adrian Carballal creator: Penousal Machado creator: Antonino Santos creator: Juan Romero uri: https://doi.org/10.7717/peerj.7075 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fernandez-Lozano et al. title: Characterization of carbonate fraction of the Atlantic bluefin tuna fin spine bone matrix for stable isotope analysis link: https://peerj.com/articles/7176 last-modified: 2019-07-18 description: The mineral component of fish otoliths (ear bones), which is aragonitic calcium carbonate (CaCO3), makes this structure the preferred sample choice for measuring biological carbon and oxygen-stable isotopes in order to address fundamental questions in fish ecology and fisheries science. The main drawback is that the removal of otoliths requires sacrificing the specimen, which is particularly impractical for endangered and commercially valuable species such as Atlantic bluefin tuna (Thunnus thynnus) (ABFT). This study explores the suitability of using the first dorsal fin spine bone of ABFT as a non-lethal alternative to otolith analysis or as a complementary hard structure. The fin spines of freshly caught ABFT were collected to identify carbonate ions within the mineral matrix (i.e., hydroxyapatite) and to determine the nature of the carbonate substitution within the crystal lattice, knowledge which is crucial for correct measurement and ecological interpretation of oxygen and carbon stable isotopes of carbonates. Fin spine sections were analyzed via X-ray Photoelectron Spectroscopy (XPS), Raman Spectroscopy, and Fourier Transform InfraRed (FTIR). The XPS survey analysis showed signals of Ca, O, and P (three compositional elements that comprise hydroxyapatite). The Raman and FTIR techniques showed evidence of carbonate ions within the hydroxyapatite matrix, with the IR spectra being the most powerful for identifying the type B carbonate substitution as shown by the carbonate band in the v2 CO32− domain at ∼872 cm−1. The results of this study confirmed the presence of carbonate ions within the mineral matrix of the fin spine bone of ABFT, showing the feasibility of using this calcified structure for analysis of stable isotopes. Overall, our findings will facilitate new approaches to safeguarding commercially valuable and endangered/protected fish species and will open new research avenues to improve fisheries management and species conservation strategies. creator: Patricia L. Luque creator: María Belén Sanchez-Ilárduya creator: Alfredo Sarmiento creator: Hilario Murua creator: Haritz Arrizabalaga uri: https://doi.org/10.7717/peerj.7176 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Luque et al. title: An ambiguous N-terminus drives the dual targeting of an antioxidant protein Thioredoxin peroxidase (TgTPx1/2) to endosymbiotic organelles in Toxoplasma gondii link: https://peerj.com/articles/7215 last-modified: 2019-07-18 description: Toxoplasma gondii harbors two endosymbiotic organelles: a relict plastid, the apicoplast, and a mitochondrion. The parasite expresses an antioxidant protein, thioredoxin peroxidase 1/2 (TgTPx1/2), that is dually targeted to these organelles. Nuclear-encoded proteins such as TgTPx1/2 are trafficked to the apicoplast via a secretory route through the endoplasmic reticulum (ER) and to the mitochondrion via a non-secretory pathway comprising of translocon uptake. Given the two distinct trafficking pathways for localization to the two organelles, the signals in TgTPx1/2 for this dual targeting are open areas of investigation. Here we show that the signals for apicoplast and mitochondrial trafficking lie in the N-terminal 50 amino acids of the protein and are overlapping. Interestingly, mutational analysis of the overlapping stretch shows that despite this overlap, the signals for individual organellar uptake can be easily separated. Further, deletions in the N-terminus also reveal a 10 amino acid stretch that is responsible for targeting the protein from punctate structures surrounding the apicoplast into the organelle itself. Collectively, results presented in this report suggest that an ambiguous signal sequence for organellar uptake combined with a hierarchy of recognition by the protein trafficking machinery drives the dual targeting of TgTPx1/2. creator: Pragati Mastud creator: Swati Patankar uri: https://doi.org/10.7717/peerj.7215 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mastud and Patankar title: Depression and sexual risk behavior among long-distance truck drivers at roadside wellness clinics in Kenya link: https://peerj.com/articles/7253 last-modified: 2019-07-18 description: BackgroundTruck drivers in sub-Saharan Africa are at high risk for both mental health disorders and sexually transmitted infections. We sought to determine the prevalence of depression among a sample of long-distance truck drivers seeking services at roadside wellness clinics in Kenya and explore the relationship between depression and sexual risk behavior.MethodsWe used data from an interviewer-administered questionnaire from 284 truck drivers in Kenya who participated in a randomized controlled trial evaluating whether offering oral HIV self-testing could increase HIV test uptake. Depression was categorized based on the Patient Health Questionnaire-9 score, with a score ≥10 indicative of probable major depressive disorder (MDD). Sexual risk behavior was operationalized as the number of condomless sex partners in the past 6 months.ResultsThe mean participant age was 36.9 years, 83.0% were married, and 37.0% had a secondary school education or higher. Overall, 24% of participants had probable MDD, and 58.2% reported having one condomless sex partner in the past 6 months, whereas 27.3% reported having had two or more. In a multivariable Poisson regression model adjusted for demographic and other relevant variables, including number of sex partners, MDD was significantly associated with a greater number of condomless sex partners (adjusted prevalence ratio 1.63, 95% confidence interval [1.25–2.12], p < 0.001). General self-efficacy significantly mediated the association between MDD and number of condomless sex partners.ConclusionsThe high prevalence of depression highlights the need to test the feasibility and acceptability of mental healthcare interventions for this population, possibly integrated with HIV prevention services. Future research is needed to better understand the association between depression and sexual risk behavior, as well as the role of self-efficacy. creator: Matthew L. Romo creator: Gavin George creator: Joanne E. Mantell creator: Eva Mwai creator: Eston Nyaga creator: Michael Strauss creator: Jacob O. Odhiambo creator: Kaymarlin Govender creator: Elizabeth A. Kelvin uri: https://doi.org/10.7717/peerj.7253 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Romo et al. title: Assessing soil compaction and micro-topography impacts of alternative heather cutting as compared to burning as part of grouse moor management on blanket bog link: https://peerj.com/articles/7298 last-modified: 2019-07-18 description: BackgroundOver 25% of the UK land area is covered by uplands, the bulk of which are comprised of blanket bog. This not only contains most of the UK’s terrestrial carbon stocks, but also represents 15% of this globally rare habitat. About 30% of UK blanket bog is managed for red grouse by encouraging ling heather (Calluna vulgaris) with rotational burning, which has been linked to habitat degradation, with reduced carbon storage and negative impacts on water storage and quality. Alternative cutting is currently being pursued as a potential restoration management. However, the often used heavy cutting machinery could cause considerable compaction and damage to the peat surface. Two particular issues are (i) a potential increase in bulk density reducing water storage capacity (i.e., less pore volume and peat depth), and (ii) a possible reduction of the micro-topography due to cutting off the tops of hummocks (i.e., protruding clumps or tussocks of sedges).MethodsWe set up a fully replicated field experiment assessing cutting versus burn management impacts on peat physical and surface properties. Both managements reflected commonly used grouse moor management practice with cutting using heavy tractors fitted with load distributing double wheel and tracks (lowering ground pressure), whilst burning was done manually (setting heather areas alight with flame torches). We assessed management impacts on peat depth, bulk density and peat surface micro-topography which either included pre-management measurements or plot-level data for uncut plots. Total peat depth and bulk density in four 5 cm sections within the top 50 cm was assessed. Micro-topography was determined as the standard deviation of the height offsets measured over several plot transects in relation to the plot peat surface level at the start and end points of each transect.ResultsDespite an anticipated compaction from the heavy machinery used for cutting, the peat showed resilience and there was no lasting plot-level impact on either peat depth or bulk density. Notably, bulk density showed differences prior to, and thus unrelated to, management, and an overall increasing bulk density, even in uncut plots. However, cutting did reduce the plot micro-topography by about 2 cm, mostly due to removing the tops of hummocks, whereas burnt plots did not differ from uncut plots.DiscussionCutting is suggested as a suitable alternative to burning on grouse moors, although compaction issues might be site specific, depending on the nature of the peat, the machinery used and impacts at resting and turning points (which were not assessed). However, any observed bulk density differences could reflect natural changes in relation to changes in peat moisture, requiring adequate experimental comparisons. Moreover, where micro-topography is a priority, cutting equipment might need to consider the specific ground conditions, which could involve adjusting cutting height and the type of cutting machinery used. creator: Andreas Heinemeyer creator: Rebecca Berry creator: Thomas J. Sloan uri: https://doi.org/10.7717/peerj.7298 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Heinemeyer et al. title: Kininogen-1 as a protein biomarker for schizophrenia through mass spectrometry and genetic association analyses link: https://peerj.com/articles/7327 last-modified: 2019-07-18 description: BackgroundSchizophrenia (SCZ) is a complex and severe mental illness. There is a lack of effective biomarkers for SCZ diagnosis. The aim of this study was to explore the possibility of using serum peptides for the diagnosis of SCZ as well as analyze the association of variants in genes coding for these peptides and SCZ.MethodsAfter bead-based fractionation, the matrix-assisted laser desorption ionization/time-of-flight mass spectrometry technique was used to identify peptides that showed different expressions between 166 SCZ patients and 201 healthy controls. Differentially expressed peptides were verified in a second set of samples (81 SCZ patients and 103 healthy controls). The association of SCZ and three tagSNPs selected in genes coding for differentially expressed peptides was performed in 1,126 SCZ patients and 1,168 controls.ResultsThe expression level of peptides with m/z 1,945.07 was significant lower in SCZ patients than in healthy controls (P < 0.000001). The peptide with m/z 1,945.07 was confirmed to be a fragment of Kininogen-1. In the verification tests, Kininogen-1 had a sensitivity of 95.1% and a specificity of 97.1% in SCZ prediction. Among the three tagSNPs (rs13037490, rs2983639, rs2983640) selected in the Cystatin 9 gene (CST9) which encodes peptides including Kininogen-1, tagSNP rs2983640 had its genotype distributions significantly different between SCZ patients and controls under different genetic models (P < 0.05). Haplotypes CG (rs2983639–rs2983640) and TCG (rs13037490–rs2983639–rs2983640) were significantly associated with SCZ (CG: OR = 1.21, 95% CI [1.02–1.44], P = 0.032; TCG: OR = 24.85, 95% CI [5.98–103.17], P < 0.0001).ConclusionsThe present study demonstrated that SCZ patients had decreased expression of Kininogen-1 and genetic variants in Kininogen-1 coding gene CST9 were significantly associated with SCZ. The findings from both protein and genetic association studies suggest that Kininogen-1 could be a biomarker of SCZ. creator: Mingjia Yang creator: Na Zhou creator: Huiping Zhang creator: Guojun Kang creator: Bonan Cao creator: Qi Kang creator: Rixin Li creator: Xiaojing Zhu creator: Wenwang Rao creator: Qiong Yu uri: https://doi.org/10.7717/peerj.7327 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: Nutritional assessment, phytochemical composition and antioxidant analysis of the pulp and seed of medjool date grown in Mexico link: https://peerj.com/articles/6821 last-modified: 2019-07-17 description: The aim of this study was the characterization of fatty acids, antioxidant activity, some physical properties, nutrient content, sugars, and minerals in the pulp and seeds of the date cultivar ‘Medjool’ (Phoenix dactylifera L.) grown in Mexico. The samples were obtained at maturity (Tamar) in the 2017 harvest season in the valleys of San Luis Rio Colorado and Mexicali, Mexico. The following average values were obtained on a % dry weight basis for pulp and seeds, respectively: protein, 3.14% and 4.84%; lipids, 0.75% and 9.94%; fiber, 6.34% and 66.79%; total sugars, 75.32% and 5.88%; reducing sugars, 70.26% and 4.40%; and sucrose, 5.06% and 1.46%. Analysis of the minerals revealed that the most abundant elements for the pulp were: potassium, 851.98 mg/100 g; magnesium, 142.97 mg/100 g; and phosphorus, 139.40 mg/100 g, whereas for the seeds, they were potassium, 413.36 mg/100 g; sulfur, 151.36 mg/100 g; and phosphorus, 92.42 mg/100 g. Gas chromatography-mass spectrometry analysis revealed that the major unsaturated fatty acid was oleic acid, at 52.34% and 45.92%, respectively, for pulp and seeds. The main saturated fatty acids were palmitic acid (6.75%) and lauric acid (17.24%) in pulp and seeds, respectively. The total phenolic content was 1.16 and 13.73 mg GAE/100 g for pulp and seeds, respectively. Finally, the antioxidant activities were: b-carotene, 65.50% and 47.75%; DPPH, 0.079 IC50 g/L and 0.0046 IC50 g/L; and ABTS, 13.72 IC50 g/L and 0.238 IC50 g/L, respectively. The results obtained in this study confirm that the ‘Medjool’ cultivar grown in Mexico has the same quality of nutrients and antioxidants as those grown in the other main date-producing countries. creator: Ricardo Salomón-Torres creator: Noé Ortiz-Uribe creator: Benjamín Valdez-Salas creator: Navor Rosas-González creator: Conrado García-González creator: Daniel Chávez creator: Iván Córdova-Guerrero creator: Laura Díaz-Rubio creator: María del Pilar Haro-Vázquez creator: José Luis Mijangos-Montiel creator: Antonio Morales-Maza creator: Padmanabhan Mahadevan creator: Robert Krueger uri: https://doi.org/10.7717/peerj.6821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Salomón-Torres et al. title: Comparative proteomics analysis reveals the difference during antler regeneration stage between red deer and sika deer link: https://peerj.com/articles/7299 last-modified: 2019-07-17 description: Deer antler, as the only mammalian regenerative appendage, provides an optimal model to study regenerative medicine. Antler harvested from red deer or sika deer were mainly study objects used to disclose the mechanism underlying antler regeneration over past decades. A previous study used proteomic technology to reveal the signaling pathways of antler stem cell derived from red deer. Moreover, transcriptome of antler tip from sika deer provide us with the essential genes, which regulated antler development and regeneration. However, antler comparison between red deer and sika deer has not been well studied. In our current study, proteomics were employed to analyze the biological difference of antler regeneration between sika deer and red deer. The proteomics profile was completed by searching the UniProt database, and differentially expressed proteins were identified by bioinformatic software. Thirty-six proteins were highly expressed in red deer antler, while 144 proteins were abundant in sika deer. GO and KEGG analysis revealed that differentially expressed proteins participated in the regulation of several pathways including oxidative phosphorylation, ribosome, extracellular matrix interaction, and PI3K-Akt pathway. creator: Hang Su creator: Xiaolei Tang creator: Xiaocui Zhang creator: Li Liu creator: Li Jing creator: Daian Pan creator: Weijie Sun creator: Huinan He creator: Chonghui Yang creator: Daqing Zhao creator: He Zhang creator: Bin Qi uri: https://doi.org/10.7717/peerj.7299 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Su et al. title: Intrageneric differences in the effects of acute temperature exposure on competitive behaviour of damselfishes link: https://peerj.com/articles/7320 last-modified: 2019-07-17 description: Projected increases in global temperatures brought on by climate change threaten to disrupt many biological and ecological processes. Tropical ectotherms, like many fishes, can be particularly susceptible to temperature change as they occupy environments with narrow thermal fluctuations. While climate change models predict temperatures to increase over decades, thermal fluctuations are already experienced on a seasonal scale, which may affect the ability to capture and defend resources across a thermal gradient. For coral reef fish, losers of competitive interactions are often more vulnerable to predation, and this pressure is strongest just after settlement. Competitive interactions may determine future success for coral reef fishes, and understanding how temperature experienced during settlement can influence such interactions will give insight to community dynamics in a future warmer world. We tested the effect of increased temperatures on intraspecific competitive interactions of two sympatric species of reef damselfish, the blue damselfish Pomacentrus nagasakiensis, and the whitetail damselfish Pomacentrus chrysurus. Juvenile fishes were exposed to one of four temperature treatments, ranging from 26–32 °C, for seven days then placed into competitive arenas where aggressive interactions were recorded between sized matched individuals within each species. While there was no apparent effect of temperature treatment on aggressive behaviour for P. chrysurus, we observed up to a four-fold increase in aggression scores for P. nagasakiensis with increasing temperature. Results suggest that temperature experienced as juveniles can impact aggressive behaviour; however, species-specific thermal tolerances led to behavioural affects that differ among closely related species. Differential thermal tolerance among species may cause restructuring of the interaction network that underlies the structure of reef assemblages. creator: Donald T. Warren creator: Mark I. McCormick uri: https://doi.org/10.7717/peerj.7320 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Warren and McCormick title: The extent to which genetics and lean grade affect fatty acid profiles and volatile compounds in organic pork link: https://peerj.com/articles/7322 last-modified: 2019-07-17 description: Niche production is intended to produce premium pork, but several husbandry factors may affect the meat fatty acid composition and aroma. Fatty acid profile (by GC-FID) of raw meat and volatile compounds (by SPME-GC–MS) of cooked meat were analysed in loin samples from two pig genetic types-75% Duroc (Du) and 50% Pietrain (Pi) rossbreds that were slaughtered at different weights (90 kg and 105 kg, respectively) to achieve similar target carcass fatness, and the outcome carcasses were balanced for lean grade groups (<60% or ≥60% lean) within genotypes. Genetic type did not affect fatty acids (FA) profile of meat. The leaner meat had lower C12:0 and C20:3n − 3, lower saturated fatty acids (SFA) and higher MUFA/SFA ratio content than the fattier meat. Short-chain alcohols were lower in Pietrain and in leaner pork compared to the samples from Duroc crossbreds and fattier pork. A greater amount of hexane,2,4,4-trimethyl (an aliphatic hydrocarbon) but lower carbon disulphide (sulphur compound) content was detected in pork from leaner compared to fattier pork. Higher aromatics hydrocarbons were exclusively associated with Duroc crossbreds, and lower aliphatic hydrocarbons with pigs classified as fattier. Most of the volatile compounds detected in the present study came from lipid oxidation. creator: Immaculada Argemí-Armengol creator: Daniel Villalba creator: Marc Tor creator: Cristina Pérez-Santaescolástica creator: Laura Purriños creator: José Manuel Lorenzo creator: Javier Álvarez-Rodríguez uri: https://doi.org/10.7717/peerj.7322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Argemí-Armengol et al. title: Effects of reindeer grazing and recovery after cessation of grazing on the ground-dwelling spider assemblage in Finnish Lapland link: https://peerj.com/articles/7330 last-modified: 2019-07-17 description: The effect of reindeer Rangifer tarandus L. grazing on the ground-dwelling spider assemblage in Northern Finland was studied. Changes in species richness, abundance and evenness of spider assemblages were analyzed in relation to changes in vegetation and environmental factors in long term grazed and ungrazed sites as well as sites that had recently switched from grazed to ungrazed and vice versa. Grazing was found to have a significant impact on height and biomass of lichens and other ground vegetation. However, it seemed not to have an impact on the total abundance of spiders. This is likely caused by opposing family and species level responses of spiders to the grazing regime. Lycosid numbers were highest in grazed and linyphiid numbers in ungrazed areas. Lycosidae species richness was highest in ungrazed areas whereas Linyphiidae richness showed no response to grazing. Four Linyphiidae, one Thomisidae and one Lycosidae species showed strong preference for specific treatments. Sites that had recovered from grazing for nine years and the sites that were grazed for the last nine years but were previously ungrazed resembled the long term grazed sites. The results emphasize the importance of reindeer as a modifier of boreal forest ecosystems but the impact of reindeer grazing on spiders seems to be family and species specific. The sites with reversed grazing treatment demonstrate that recovery from strong grazing pressure at these high latitudes is a slow process whereas reindeer can rapidly change the conditions in previously ungrazed sites similar to long term heavily grazed conditions. creator: Teemu Saikkonen creator: Varpu Vahtera creator: Seppo Koponen creator: Otso Suominen uri: https://doi.org/10.7717/peerj.7330 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Saikkonen et al. title: Microbial regulation of soil carbon properties under nitrogen addition and plant inputs removal link: https://peerj.com/articles/7343 last-modified: 2019-07-17 description: BackgroundSoil microbial communities and their associated enzyme activities play key roles in carbon cycling in terrestrial ecosystems. Soil microbial communities are sensitive to resource availability, but the mechanisms of microbial regulation have not been thoroughly investigated. Here, we tested the mechanistic relationships between microbial responses and multiple interacting resources.MethodsWe examined soil carbon properties, soil microbial community structure and carbon-related functions under nitrogen addition and plant inputs removal (litter removal (NL), root trench and litter removal (NRL)) in a pure Larix principis-rupprechtii plantation in northern China.ResultsWe found that nitrogen addition affected the soil microbial community structure, and that microbial biomass increased significantly once 100 kg ha−1 a−1 of nitrogen was added. The interactions between nitrogen addition and plant inputs removal significantly affected soil bacteria and their enzymatic activities (oxidases). The NL treatment enhanced soil microbial biomass under nitrogen addition. We also found that the biomass of gram-negative bacteria and saprotrophic fungi directly affected the soil microbial functions related to carbon turnover. The biomass of gram-negative bacteria and peroxidase activity were key factors controlling soil carbon dynamics. The interactions between nitrogen addition and plant inputs removal strengthened the correlation between the hydrolases and soil carbon.ConclusionsThis study showed that nitrogen addition and plant inputs removal could alter soil enzyme activities and further affect soil carbon turnover via microbial regulation. The increase in soil microbial biomass and the microbial regulation of soil carbon both need to be considered when developing effective sustainable forest management practices for northern China. Moreover, further studies are also needed to exactly understand how the complex interaction between the plant and below-ground processes affects the soil microbial community structure. creator: Ran Wu creator: Xiaoqin Cheng creator: Wensong Zhou creator: Hairong Han uri: https://doi.org/10.7717/peerj.7343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wu et al. title: Internet addiction and poor quality of life are significantly associated with suicidal ideation of senior high school students in Chongqing, China link: https://peerj.com/articles/7357 last-modified: 2019-07-17 description: BackgroundAdolescence is a vulnerable period of life, and many mental health and behavioral problems emerge during this particular period, including depression, internet addiction (IA), and suicidal behaviors. Poor quality of life (QOL) and IA have been found to be significantly associated with suicidal ideation (SI) among Chinese university students, of whom most have been adults. Nevertheless, their associations with SI are rarely studied among Chinese adolescents. The objective of this study was to examine these relationships in a representative adolescent sample of Chinese senior high school students, who are experiencing an enormous transition from childhood to adulthood.MethodsBy using multi-stage sampling, a total of 26,688 students were successfully recruited from 29 senior high schools of a very large City in western China, Chongqing municipality. In this cross-sectional online survey, students’ demographic and lifestyle characteristics were collected with a standardized questionnaire. The Young’s IA Test, the Chinese Six-item QOL questionnaire, and item 15 of the Symptom Checklist-90-R were used to measure IA, QOL, and SI, respectively.ResultsThe 1-month prevalence of SI was 11.5% among students of senior high schools in Chongqing, China. Students with SI had significantly higher QOL scores (17.3 ± 3.7 vs. 13.7 ± 3.8, P < 0.001) and higher prevalence of IA (49.6% vs. 25.6%, P < 0.001) than those without SI. After controlling for demographic, lifestyle, and clinical covariates, IA (odd ratio (OR) = 1.15, P = 0.003) and a high QOL score (OR = 1.09, P < 0.001) remained significantly associated with SI.ConclusionSuicidal ideation is prevalent among Chinese adolescents and it is associated with IA and poor QOL. Measures aimed at reducing IA and improving QOL may help prevent suicidal behaviors among Chinese adolescents. creator: Wo Wang creator: Dong Dong Zhou creator: Ming Ai creator: Xiao Rong Chen creator: Zhen Lv creator: Yan Huang creator: Li Kuang uri: https://doi.org/10.7717/peerj.7357 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Geographic context affects the landscape change and fragmentation caused by wind energy facilities link: https://peerj.com/articles/7129 last-modified: 2019-07-16 description: Wind energy generation affects landscapes as new roads, pads, and transmission lines are constructed. Limiting the landscape change from these facilities likely minimizes impacts to biodiversity and sensitive wildlife species. We examined the effects of wind energy facilities’ geographic context on changes in landscape patterns using three metrics: portion of undeveloped land, core area index, and connectance index. We digitized 39 wind facilities and the surrounding land cover and measured landscape pattern before and after facility construction using the amount, core area, and connectivity of undeveloped land within one km around newly constructed turbines and roads. New facilities decreased the amount of undeveloped land by 1.8% while changes in metrics of landscape pattern ranged from 50 to 140%. Statistical models indicated pre-construction development was a key factor explaining the impact of new wind facilities on landscape metrics, with pre-construction road networks, turbine spacing, and topography having smaller influences. As the proportion of developed land around facilities increased, a higher proportion of the facility utilized pre-construction developed land and a lower density of new roads were built, resulting in smaller impacts to undeveloped landscapes. Building of new road networks was also a predictor of landscape fragmentation. Utilizing existing development and carefully placing turbines may provide opportunities to minimize the impacts of new wind energy facilities. creator: Jay E. Diffendorfer creator: Monica A. Dorning creator: Jolene R. Keen creator: Louisa A. Kramer creator: Robert V. Taylor uri: https://doi.org/10.7717/peerj.7129 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Infectious hematopoietic necrosis virus: advances in diagnosis and vaccine development link: https://peerj.com/articles/7151 last-modified: 2019-07-16 description: The aquaculture of salmonid fishes is a multi-billion dollar industry with production over 3 million tons annually. However, infectious hematopoietic necrosis virus (IHNV), which infects and kills salmon and trout, significantly reduces the revenue of the salmon farming industry. Currently, there is no effective treatment for IHNV infected fishes; therefore, early detection and depopulation of the infected fishes remain the most common practices to contain the spread of IHNV. Apart from hygiene practices in aquaculture and isolation of infected fishes, loss of fishes due to IHNV infection can also be significantly reduced through vaccination programs. In the current review, some of the diagnostic methods for IHNV, spanning from clinical diagnosis to cell culture, serological and molecular methods are discussed in detail. In addition, some of the most significant candidate vaccines for IHNV are also extensively discussed, particularly the DNA vaccines. creator: Chean Yeah Yong creator: Hui Kian Ong creator: Hooi Chia Tang creator: Swee Keong Yeap creator: Abdul Rahman Omar creator: Kok Lian Ho creator: Wen Siang Tan uri: https://doi.org/10.7717/peerj.7151 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yong et al. title: Climate change and forest plagues: assessing current and future impacts of diprionid sawflies on the pine forests of north-western Mexico link: https://peerj.com/articles/7220 last-modified: 2019-07-16 description: The imminent threat of climate change lies in its potential to disrupt the balance of ecosystems, particularly vulnerable areas such as mountain-top remnant forests. An example of such a fragile ecosystem is the Sierra San Pedro Mártir (SSPM) National Park of Mexico’s Baja California state, where high levels of endemism can be found, and which is home to one of the country’s few populations of the emblematic Jeffrey pine (Pinus jeffreyi). Recent outbreaks of pine-feeding sawfly larvae in SSPM increase the vulnerability of this forest ecosystem, calling for immediate assessments of the severity of this threat. Here, we present a thorough study of the sawfly’s biology and distribution, carrying out molecular and morphology-based identification of the species and creating model-based predictions of the species distribution in the area. The sawfly was found to belong to an undescribed species of the genus Zadiprion (family Diprionidae) with a one-year life-cycle. The distribution of this species appears to be restricted to the SSPM national park and it will probably persist for at least another 50 years, even considering the effects of climate change. creator: Víctor M. Aguilera-Molina creator: Khutzy K. Munguía-Ortega creator: Eulogio López-Reyes creator: Andrés Martínez-Aquino creator: F. Sara Ceccarelli uri: https://doi.org/10.7717/peerj.7220 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Aguilera-Molina et al. title: Assessing subspecies status of leopards (Panthera pardus) of northern Pakistan using mitochondrial DNA link: https://peerj.com/articles/7243 last-modified: 2019-07-16 description: Despite being classified as critically endangered, little work has been done on leopard protection in Pakistan. Once widely present throughout this region, leopards are now sparsely distributed, and possibly extinct from much of their previously recorded habitat. While leopards show morphological and genetic variation across their species range worldwide, resulting in the classification of nine different subspecies, the leopard genetic structure across Pakistan is unknown, with previous studies including only a very limited sampling. To clarify the genetic status of leopards in Pakistan we investigated the sequence variation in the subunit 5 of the mitochondrial gene NADH from 43 tissue samples and compared it with 238 sequences available from online databases. Phylogenetic analysis clearly separates the Pakistani leopards from the African and Arabian clades, confirming that leopards from Pakistan are members of the Asian clade. Furthermore, we identified two separate subspecies haplotypes within our dataset: P. p. fusca (N = 23) and P. p. saxicolor (N = 12). creator: Muhammad Asad creator: Francesco Martoni creator: James G. Ross creator: Muhammad Waseem creator: Fakhar-i- Abbas creator: Adrian M. Paterson uri: https://doi.org/10.7717/peerj.7243 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Asad et al. title: Changes of the erythrocyte phenotype and blood biochemistry in dairy calves during the first ten weeks of age link: https://peerj.com/articles/7248 last-modified: 2019-07-16 description: BackgroundBovine erythrocytes undergo important changes in their morphology and chemical composition during the first weeks of age, which must be understood to accurately interpret hematology results in calves. The objectives of this prospective cohort study were to describe physiological changes of calf erythrocytes and to investigate mechanisms potentially causing these changes.MethodsBlood samples from 30 clinically healthy dairy calves were obtained from birth to the tenth week of age in weekly intervals. Hematological and plasma biochemical parameters as well as the mineral electrolyte content of erythrocytes were determined and followed over time. The changes of parameters characterizing the erythrocyte phenotype over time were compared to the changes of plasma and erythrocyte biochemical parameters and possible associations were investigated using correlation and stepwise regression analyses.ResultsAlthough the erythrocyte mean corpuscular volume (MCV) declined from 43.6 ± 3.7 fL to 35.6 ± 3.2 fL between the first and seventh week, the red blood cell count (RBC) increased from 7.2 ± 1.1 × 1012/L to 9.3 ± 1.0 × 1012/L until the fifth week of age. The blood hemoglobin (Hb) concentration increased from 0.96 ± 0.16 g/L to 1.16 ± 0.11 g/L in the first three weeks of age and remained at this level until the end of the study. Changes in MCV were accompanied by a decline of the erythrocyte potassium content (KERY) from 91.9 ± 13.5 to 24.6 ± 7.2 mmol/L and a concomitant increase of the erythrocyte sodium content from 45.0 ± 32.0 to 102.7 ± 26.5 mmol/L. MCV was found to be associated with KERY, the primary determinant of the intra-erythrocyte osmotic pressure from the sixth week of age and with blood hemoglobin, the primary determinant of the intra-erythrocyte oncotic pressure from the eighth week of age, when KERY, blood Hb and MCV already had reached or approached normal levels of adult cattle. The plasma iron concentration was not found to be associated to any of the studied hematological parameters.ConclusionA volume reduction of 20% in bovine neonatal erythrocytes is a physiological change occurring during the first weeks of age and is neither associated with sideropenia nor with anemia in healthy calves. The mechanism driving the observed erythrocyte volume change could not be identified. Results of the correlation and regression analyses indicate that changes in intra-erythrocyte osmotic or oncotic pressure are improbable underlying causes. Results reported here show that KERY is an unreliable indicator for the K homeostasis of the intracellular space in neonatal calves and that a decrease in MCV in early life per-se is an unreliable indicator for the development of microcytic anemia. creator: Lennart Golbeck creator: Imke Cohrs creator: Theresa Scheu creator: Walter Grünberg uri: https://doi.org/10.7717/peerj.7248 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Golbeck et al. title: The relationship between fish abundance and benthic community structure on artificial reefs in the Mid-Atlantic Bight, and the importance of sea whip corals Leptogorgia virgulata link: https://peerj.com/articles/7277 last-modified: 2019-07-16 description: Autogenic engineers (i.e., biogenic structure) add to habitat complexity by altering the environment by their own physical structures. The presence of autogenic engineers is correlated with increases in species abundance and biodiversity. Biogenic structural communities off the coast of Delaware, Maryland, and Virginia (Delmarva) are comprised of multiple species including boring sponge Cliona celata, various hydroids (i.e., Tubularia sp., Obelia sp., Campanular sp.), northern stone coral Astrangia poculata, sea whips Leptogorgia virgulata, and blue mussels Mytilus edulis. Sea whips are soft corals that provide the majority of vertical height to benthic structure off the coast of the Delmarva peninsula. The mid-Atlantic bight is inhabited by several economically valuable fishes; however, data regarding habitat composition, habitat quality, and fish abundance are scarce. We collected quadrat and sea whip images from 12 artificial reef sites (i.e., shipwrecks) ranging from 10 to 24 m depth to determine proportional coverage of biogenic structures and to assess habitat health, respectively. Underwater video surveys were used to estimate fish abundances on the 12 study sites and determine if fish abundance was related to biogenic coverage and habitat health. Our results showed that higher fish abundance was significantly correlated with higher proportional sea whip coral coverage, but showed no significant relationship to other biogenic structure. Assessment of sea whip condition (as a damage index) showed that sea whip corals on artificial reefs off the Delmarva coast exhibited minor signs of degradation that did not differ significantly among study sites. creator: Cara C. Schweitzer creator: Bradley G. Stevens uri: https://doi.org/10.7717/peerj.7277 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Schweitzer and Stevens title: Marine biodiversity from zero to a thousand meters at Clipperton Atoll (Île de La Passion), Tropical Eastern Pacific link: https://peerj.com/articles/7279 last-modified: 2019-07-16 description: Clipperton Atoll (Île de La Passion) is the only atoll in the Tropical Eastern Pacific (TEP) ecoregion and, owing to its isolation, possesses several endemic species and is likely an important stepping stone between Oceania, the remainder of the TEP, including other oceanic islands and the west coast of Central America. We describe the biodiversity at this remote atoll from shallow water to depths greater than one thousand meters using a mixture of technologies (SCUBA, stereo baited remote underwater video stations, manned submersible, and deep-sea drop cameras). Seventy-four unique taxa of invertebrates were identified during our expedition. The majority (70%) of these taxa were confined to the top 400 m and consisted mostly of sessile organisms. Decapod crustaceans and black corals (Antipatharia) had the broadest depth ranges, 100–1,497 m and 58–967 m, respectively. Decapods were correlated with the deepest depths, while hard corals were correlated with the shallow depths. There were 96 different fish taxa from 41 families and 15 orders, of which 70% were restricted to depths <200 m. While there was a decreasing trend in richness for both fish and invertebrate taxa with depth, these declines were not linear across the depth gradient. Instead, peaks in richness at ∼200 m and ∼750 m coincided with high turnover due to the appearance of new taxa and disappearance of other taxa within the community and is likely associated with the strong oxygen minimum zone that occurs within the region. The overall depth effect was stronger for fishes compared with invertebrates, which may reflect ecological preferences or differences in taxonomic resolution among groups. The creation of a no-take marine reserve 12 nautical miles around the atoll in 2016 will help conserve this unique and relatively intact ecosystem, which possesses high predator abundance. creator: Alan M. Friedlander creator: Jonatha Giddens creator: Enric Ballesteros creator: Shmulik Blum creator: Eric K. Brown creator: Jennifer E. Caselle creator: Bradley Henning creator: Christian Jost creator: Pelayo Salinas-de-León creator: Enric Sala uri: https://doi.org/10.7717/peerj.7279 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: UK universities compliance with the Concordat to Support Research Integrity: findings from cross-sectional time-series link: https://peerj.com/articles/7292 last-modified: 2019-07-16 description: BackgroundThe Concordat to Support Research Integrity published in 2012 recommends that UK research institutions should provide a named point of contact to receive concerns about research integrity (RI). The Concordat also requires institutions to publish annual RI statements.ObjectiveTo see whether contact information for a staff member responsible for RI was readily available from UK university websites and to see how many universities published annual RI statements.MethodsUK university websites were searched in mid-2012, mid-2014 and mid-2018. The availability of contact details for RI inquiries, other information about RI and, specifically, an annual RI statement, was recorded.ResultsThe proportion of UK universities publishing an email address for RI inquiries rose from 23% in 2012 (31/134) to 55% in 2018. The same proportion (55%) published at least one annual RI statement in 2018, but only three provided statements for all years from 2012/13. There was great variation in the titles used for the staff member with responsibility for RI which made searching difficult.ConclusionOver 6 years after the publication of the Concordat to Support Research Integrity, nearly half of UK universities are not complying with all its recommendations and do not provide contact details for a staff member with responsibility for RI or an annual statement. creator: Elizabeth Wager uri: https://doi.org/10.7717/peerj.7292 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wager title: Monitoring cyanobacterial toxins in a large reservoir: relationships with water quality parameters link: https://peerj.com/articles/7305 last-modified: 2019-07-16 description: Cyanobacteria are widely distributed in fresh, brackish, and ocean water environments, as well as in soil and on moist surfaces. Changes in the population of cyanobacteria can be an important indicator of alterations in water quality. Metabolites produced by blooms of cyanobacteria can be harmful, so cell counts are frequently monitored to assess the potential risk from cyanobacterial toxins. A frequent uncertainty in these types of assessments is the lack of strong relationships between cell count numbers and algal toxin concentrations. In an effort to use ion concentrations and other water quality parameters to determine the existence of any relationships with cyanobacterial toxin concentrations, we monitored four cyanobacterial toxins and inorganic ions in monthly water samples from a large reservoir over a 2-year period. Toxin concentrations during the study period never exceeded safety limits. In addition, toxin concentrations at levels above the limit of quantitation were infrequent during the 2-year sampling period; non-detects were common. Microcystin-LA was the least frequently detected analyte (86 of 89 samples were ND), followed by the other microcystins (microcystin-RR, microcystin-LR). Cylindrospermopsin and saxitoxin were the most frequently detected analytes. Microcystin and anatoxin concentrations were inversely correlated with Cl−, SO${}_{4}^{-2}$4−2, Na+, and NH${}_{4}^{+}$4+, and directly correlated with turbidity and total P. Cylindrospermopsin and saxitoxin concentrations in water samples were inversely correlated with Mg+2 and directly correlated with water temperature. Results of our study are expected to increase the understanding of potential relationships between human activities and water quality. creator: Seenivasan Subbiah creator: Adcharee Karnjanapiboonwong creator: Jonathan D. Maul creator: Degeng Wang creator: Todd A. Anderson uri: https://doi.org/10.7717/peerj.7305 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Subbiah et al. title: Selection of reliable reference genes for quantitative RT-PCR in garlic under salt stress link: https://peerj.com/articles/7319 last-modified: 2019-07-16 description: Quantitative real-time reverse-transcriptase PCR (qRT-PCR) has been frequently used for detecting gene expression. To obtain reliable results, selection of suitable reference genes is a fundamental and necessary step. Garlic (Allium sativum), a member from Alliaceae family, has been used both as a food flavoring and as a traditional medicine. In the present study, garlic plants were exposed to salt stress (200 mM NaCl) for 0, 1, 4 and 12 h, and garlic roots, bulbs, and leaves were harvested for subsequent analysis. The expression stability of eight candidate reference genes, eukaryotic translation initiation factor 4α (eIF-4α), actin (ACTIN), tubulin β-7 (TUB7), TAP42-interacting protein of 41 kDa (TIP41), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), SAND family protein (SAND), elongation factor 1 alpha (EF-1α), and protein phosphatase 2A (PP2A) were evaluated by geNorm, NormFinder, and BestKeeper. All genes tested displayed variable expression profiles under salt stress. In the leaf and root group, ACTIN was the best reference gene for normalizing gene expression. In garlic clove, ACTIN and SAND were the least variable, and were suitable for gene expression studies under salt stress; these two genes also performed well in all samples tested. Based on our results, we recommend that it is essential to use specific reference genes in different situations to obtain accurate results. Using a combination of multiple stable reference genes, such as ACTIN and SAND, to normalize gene expression is encouraged. The results from the study will be beneficial for accurate determination of gene expression in garlic and other plants. creator: Guanglong Wang creator: Chang Tian creator: Yunpeng Wang creator: Faxiang Wan creator: Laibao Hu creator: Aisheng Xiong creator: Jie Tian uri: https://doi.org/10.7717/peerj.7319 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Herbivore corridors sustain genetic footprint in plant populations: a case for Spanish drove roads link: https://peerj.com/articles/7311 last-modified: 2019-07-15 description: Habitat fragmentation is one of the greatest threats to biodiversity conservation and ecosystem productivity mediated by direct human impact. Its consequences include genetic depauperation, comprising phenomena such as inbreeding depression or reduction in genetic diversity. While the capacity of wild and domestic herbivores to sustain long-distance seed dispersal has been proven, the impact of herbivore corridors in plant population genetics remains to be observed. We conducted this study in the Conquense Drove Road in Spain, where sustained use by livestock over centuries has involved transhumant herds passing twice a year en route to winter and summer pastures. We compared genetic diversity and inbreeding coefficients of Plantago lagopus populations along the drove road with populations in the surrounding agricultural matrix, at varying distances from human settlements. We observed significant differences in coefficients of inbreeding between the drove road and the agricultural matrix, as well as significant trends indicative of higher genetic diversity and population nestedness around human settlements. Trends for higher genetic diversity along drove roads may be present, although they were only marginally significant due to the available sample size. Our results illustrate a functional landscape with human settlements as dispersal hotspots, while the findings along the drove road confirm its role as a pollinator reservoir observed in other studies. Drove roads may possibly also function as linear structures that facilitate long-distance dispersal across the agricultural matrix, while local P. lagopus populations depend rather on short-distance seed dispersal. These results highlight the role of herbivore corridors for conserving the migration capacity of plants, and contribute towards understanding the role of seed dispersal and the spread of invasive species related to human activities. creator: Alfredo García-Fernández creator: Pablo Manzano creator: Javier Seoane creator: Francisco M. Azcárate creator: Jose M. Iriondo creator: Begoña Peco uri: https://doi.org/10.7717/peerj.7311 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 García-Fernández et al. title: Scenarios of availability of water due to overexploitation of the aquifer in the basin of Laguna de Santiaguillo, Durango, Mexico link: https://peerj.com/articles/6814 last-modified: 2019-07-15 description: BackgroundThe importance of water to life is unquestionable. Most of the fresh water we use for daily activities comes from the aquifers, which in many cases due to misuse are overexploited and at risk. This article studies the aquifer that appeared in Laguna de Santiaguillo basin; it should be noted that the most important economic activity in the basin is agriculture.MethodsBy analyzing vector and demographic information, using GIS and with some field trips, the impact and risk on the level of disposition in every micro-basin that forms the basin were determined.ResultsThe different modeling scenarios demonstrate that the basin and sub-basins that conform Santiaguillo are overexploited.DiscussionThe volumes concessioned are of such magnitude that they generate a condition of vulnerability to the activities of the basin and sustain the overexploitation conditions of the aquifer. creator: María de Lourdes Corral-Bermudez creator: Eduardo Sánchez-Ortiz creator: Dioselina Álvarez-Bernal creator: Martín Omar Gutiérrez-Montenegro creator: Erika Cassio-Madrazo uri: https://doi.org/10.7717/peerj.6814 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Corral-Bermudez et al. title: Comparison of integrated PET/MRI with PET/CT in evaluation of endometrial cancer: a retrospective analysis of 81 cases link: https://peerj.com/articles/7081 last-modified: 2019-07-15 description: BackgroundThe objective of this study was to compare the diagnostic value of integrated PET/MRI with PET/CT for assessment of regional lymph node metastasis and deep myometrial invasion detection of endometrial cancer.MethodsEighty-one patients with biopsy-proven endometrial cancer underwent preoperative PET/CT (n = 37) and integrated PET/MRI (n = 44) for initial staging. The diagnostic performance of PET/CT and integrated PET/MRI for assessing the extent of the primary tumor and metastasis to the regional lymph nodes was evaluated by two experienced readers. Histopathological and follow-up imaging results were used as the gold standard. McNemar’s test was employed for statistical analysis.ResultsIntegrated PET/MRI and PET/CT both detected 100% of the primary tumors. Integrated PET/MRI proved significantly more sensitivity and specificity than PET/CT in regional lymph node metastasis detection (P = 0.015 and P < 0.001, respectively). The overall accuracy of myometrial invasion detection for PET/CT and Integrated PET/MRI was 45.9% and 81.8%, respectively. Integrated PET/MRI proved significantly more accurate than PET/CT (P < 0.001).ConclusionIntegrated PET/MRI, which complements the individual advantages of MRI and PET, is a valuable technique for the assessment of the lymph node metastasis and myometrial invasion in patients with endometrial cancer. creator: Li-hua Bian creator: Min Wang creator: Jing Gong creator: Hong-hong Liu creator: Nan Wang creator: Na Wen creator: Wen-sheng Fan creator: Bai-xuan Xu creator: Ming-yang Wang creator: Ming-xia Ye creator: Yuan-guang Meng uri: https://doi.org/10.7717/peerj.7081 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bian et al. title: Trajectories of change after a health-education program in Japan: decay of impact in anxiety, depression, and patient-physician communication link: https://peerj.com/articles/7229 last-modified: 2019-07-15 description: BackgroundHealth education can benefit people with chronic diseases. However, in previous research those benefits were small, and reinforcement to maintain them was not effective. A possible explanation is that the benefits appeared to be small and reinforcement appeared to be ineffective because those analyses mixed data from two latent groups: one group of people who needed reinforcement and one group of people who did not. The hypothesis is that mixing the data from those two different groups caused the true effects to be “diluted.”MethodsTo test that hypothesis we used data from the Chronic Disease Self-Management Program in Japan, focusing on anxiety, depression, and patient-physician communication. To identify latent trajectories of change after the program, we used growth-mixture modeling. Then, to find out which baseline factors were associated with trajectory-group membership, we used logistic regression.ResultsGrowth-mixture modeling revealed two trajectories—two groups that were defined by distinct patterns of change after the program. One of those patterns was improvement followed by backsliding: decay of impact. On anxiety and depression the decay of impact was large enough to be clinically important, and its prevalence was as high as 50%. Next, logistic regression analysis revealed that being in the decay-of-impact group could be predicted from multimorbidity, low self-efficacy, and high scores on anxiety or depression at baseline. In addition, one unexpected finding was an association between multimorbidity and better patient-physician communication.ConclusionsThese results support the hypothesis that previous findings (i.e., apparently small effect sizes and apparently ineffective reinforcement) actually reflect “dilution” of large effects, which was caused by mixing of data from distinct groups. Specifically, there was one group with decay of impact and one without. Thus, evaluations of health education should include analyses of trajectory-defined groups. These results show how the group of people who are most likely to need reinforcement can be identified even before the educational program begins. Extra attention and reinforcement can then be tailored. They can be focused specifically to benefit the people with the greatest need. creator: Min Jeong Park creator: Joseph Green creator: Hun Sik Jung creator: Yoon Soo Park uri: https://doi.org/10.7717/peerj.7229 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Park et al. title: Diversity, ecology and distribution of benthic diatoms in thermo-mineral springs in Auvergne (France) and Sardinia (Italy) link: https://peerj.com/articles/7238 last-modified: 2019-07-15 description: This study investigated and compared the diatom flora from thermo-mineral springs in Auvergne (France) and Sardinia (Italy). Samples were collected from rock/cobbles and fine sediments in 16 springs between January 2015 and March 2017. A total of 207 taxa (59 genera) were found. Multivariate analyses revealed significant differences in species composition and abundance among diatom assemblages both within each geographic region and between Auvergne and Sardinia (global R = 0.516; p = 0.002), suggesting the importance of local and climatic factors in species distribution. Based on abundance and common occurrence in multiple sites, some taxa can be considered more representative of springs in each region: Crenotia thermalis for Auvergne and Lemnicola exigua, Nitzschia amphibia, N. inconspicua and Rhopalodia operculata for Sardinia. pH, conductivity and HCO3− were the most significant environmental variables for diatom assemblages. Our results highlight the high heterogeneity of these spring systems. Future taxonomic insights can be useful to define the identity of some abundant and dominant taxa not identified at the species level in this study. Their identification is a crucial step for a more precise ecological characterization and comparison of these peculiar spring systems. creator: Giuseppina G. Lai creator: Aude Beauger creator: Carlos E. Wetzel creator: Bachisio M. Padedda creator: Olivier Voldoire creator: Antonella Lugliè creator: Elisabeth Allain creator: Luc Ector uri: https://doi.org/10.7717/peerj.7238 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lai et al. title: Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions link: https://peerj.com/articles/7241 last-modified: 2019-07-15 description: Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO3. creator: Ikuko Yuyama creator: Tomihiko Higuchi uri: https://doi.org/10.7717/peerj.7241 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yuyama and Higuchi title: A green garlic (Allium sativum L.) based intercropping system reduces the strain of continuous monocropping in cucumber (Cucumis sativus L.) by adjusting the micro-ecological environment of soil link: https://peerj.com/articles/7267 last-modified: 2019-07-15 description: The continuous cropping obstacle of cucumber (Cucumis sativus L.) under facility cultivation is more prevalent in China. This is associated with an imbalance in soil microbial and ecological environment in long-term monocultures. It was postulated that intercropping with green garlic would relieve the continuous cropping obstacle of cucumber by altering the soil micro-ecology status. A pot-based experiment was conducted to investigate the green garlic-cucumber intercropping and cucumber monocropping systems. The results showed that the cucumber shoot biomass was improved by intercropping with green garlic. However, the population of soil bacteria and actinomycetes increased, while the fungal population decreased. The fatty acid methyl ester (FAME) profiles indicated that soil contained more fungal FAME biomarkers (18:1ω9c, 18:2ω6, 9) and higher fungal:bacterial ratio in the monoculture system, whereas clustering of more bacterial FAME biomarkers (cy17:0, cy19:0, 16:1ω7c10, Me16:0, 10Me17:0, 10Me18:0) was observed under intercropping conditions. Moreover, significantly (P < 0.05) higher soil invertase and alkaline phosphatase activities, organic matter, and available N, P and K contents were observed under intercropping systems. These were high in both bulk and rhizosphere soils in the intercropping system when compared to monocropping system. These findings suggest that intercropping with green garlic can alleviate continuous cropping obstacle of cucumber by improving the diverse composition of soil microbial community, enzyme activities, and nutrient availability. creator: Xuemei Xiao creator: Zhihui Cheng creator: Jian Lv creator: Jianming Xie creator: Ning Ma creator: Jihua Yu uri: https://doi.org/10.7717/peerj.7267 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xiao et al. title: The aridity index governs the variation of vegetation characteristics in alpine grassland, Northern Tibet Plateau link: https://peerj.com/articles/7272 last-modified: 2019-07-15 description: The vegetation dynamic (e.g., community productivity) is an important index used to evaluate the ecosystem function of grassland ecosystem. However, the critical factors that affect vegetation biomass are disputed continuously, and most of the debates focus on mean annual precipitation (MAP) or temperature (MAT). This article integrated these two factors, used the aridity index (AI) to describe the dynamics of MAP and MAT, and tested the hypothesis that vegetation traits are influenced primarily by the AI. We sampled 275 plots at 55 sites (five plots at each site, including alpine steppe and meadow) across an alpine grassland of the northern Tibet Plateau, used correlation analysis and redundancy analysis (RDA) to explore which key factors determine the biomass dynamic, and explained the mechanism by which they affect the vegetation biomass in different vegetation types via structural equation modelling (SEM). The results supported our hypothesis, in all of the environmental factors collected, the AI made the greatest contribution to biomass variations in RDA , and the correlation between the AI and biomass was the largest (R = 0.85, p < 0.05). The final SEM also validated our hypothesis that the AI explained 79.3% and 84.4% of the biomass variations in the alpine steppe and the meadow, respectively. Furthermore, we found that the soils with higher carbon to nitrogen ratio and soil total nitrogen had larger biomass, whereas soil organic carbon had a negative effect on biomass in alpine steppe; however, opposite effects of soil factors on biomass were observed in an alpine meadow. The findings demonstrated that the AI was the most critical factor affecting biomass in the alpine grasslands, and different reaction mechanisms of biomass response to the AI existed in the alpine steppe and alpine meadow. creator: Biying Liu creator: Jian Sun creator: Miao Liu creator: Tao Zeng creator: Juntao Zhu uri: https://doi.org/10.7717/peerj.7272 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Molecular characterization of bacterial leaf streak resistance in hard winter wheat link: https://peerj.com/articles/7276 last-modified: 2019-07-15 description: Bacterial leaf streak (BLS) caused by Xanthomonas campestris pv. translucens is one of the major bacterial diseases threatening wheat production in the United States Northern Great Plains (NGP) region. It is a sporadic but widespread wheat disease that can cause significant loss in grain yield and quality. Identification and characterization of genomic regions in wheat that confer resistance to BLS will help track resistance genes/QTLs in future wheat breeding. In this study, we evaluated a hard winter wheat association mapping panel (HWWAMP) containing 299 hard winter wheat lines from the US hard winter wheat growing region for their reactions to BLS. We observed a range of BLS responses among the lines, importantly, we identified ten genotypes that showed a resistant reaction both in greenhouse and field evaluation. ­Genome-wide association analysis with 15,990 SNPs was conducted using an exponentially compressed mixed linear model. Five genomic regions (p < 0.001) that regulate the resistance to BLS were identified on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS. The QTLs Q.bls.sdsu-1AL, Q.bls.sdsu-1BS, Q.bls.sdsu-3AL, Q.bls.sdsu-4AL, and Q.bls.sdsu-7AS explain a total of 42% of the variation. In silico analysis of sequences in the candidate regions on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS identified 10, 25, 22, eight, and nine genes, respectively with known plant defense-related functions. Comparative analysis with rice showed two syntenic regions in rice that harbor genes for bacterial leaf streak resistance. The ten BLS resistant genotypes and SNP markers linked to the QTLs identified in our study could facilitate breeding for BLS resistance in winter wheat. creator: Sai Mukund Ramakrishnan creator: Jagdeep Singh Sidhu creator: Shaukat Ali creator: Navjot Kaur creator: Jixiang Wu creator: Sunish K. Sehgal uri: https://doi.org/10.7717/peerj.7276 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ramakrishnan et al. title: Multi-scale relationship between land use/land cover types and water quality in different pollution source areas in Fuxian Lake Basin link: https://peerj.com/articles/7283 last-modified: 2019-07-15 description: The spatial-temporal evolution of land use and land cover (LULC) and its multi-scale impact on the water environment is becoming highly significant in the LULC research field. The current research results show that the more significant scale impact on LULC and water quality in the whole basin and the riparian buffer scale is unclear. A consensus has not been reached about the optimal spatial scale problem in the relationship between the LULC and water quality. The typical lake basin of the Fuxian Lake watershed was used as the research area and the scale relationship between the LULC and water quality was taken as the research object. High resolution remote sensing images, archival resources of surveying, mapping and geographic information, and the monitoring data of water quality were utilized as the main data sources. Remote sensing and Geometric Information Technology were applied. A multi-scale object random forest algorithm (MSORF) was used to raise the classification accuracy of the high resolution remote sensing images from 2005 to 2017 in the basin and the multi-scale relationship between the two was discussed using the Pearson correlation analysis method. From 2005 to 2017, the water quality indicators (Chemical Oxygen Demand (COD), Total Phosphorous (TP), Total Nitrogen (TN)) of nine rivers in the lake’s basin and the Fuxian Lake center were used as response variables and the LULC type in the basin was interpreted as the explanation variable. The stepwise selection method was used to establish a relationship model for the water quality of the water entering the lake and the significance of the LULC type was established at p < 0.05.The results show that in the seven spatial scales, including the whole watershed, sub-basin, and the riparian buffer zone (100 m, 300 m, 500 m, 700 m, and 1,000 m): (1) whether it is in the whole basin or buffer zone of different pollution source areas, impervious surface area (ISA), or other land and is positively correlated with the water quality and promotes it; (2) forestry and grass cover is another important factor and is negatively correlated with water quality; (3) cropping land is not a major factor explaining the decline in water quality; (4) the 300 m buffer zone of the river is the strongest spatial scale for the LULC type to affect the Chemical Oxygen Demand (COD). Reasonable planning for the proportion of land types in the riparian zone and control over the development of urban land in the river basin is necessary for the improvement of the urban river water quality. Some studies have found that the relationship between LULC and water quality in the 100 m buffer zone is more significant than the whole basin scale. While our study is consistent with the results of research conducted by relevant scholars in Aibi Lake in Xinjiang, and Erhai and Fuxian Lakes in Yunnan. Thus, it may be inferred that for the plateau lake basin, the 300 m riparian buffer is the strongest spatial scale for the LULC type to affect COD. creator: Shihua Li creator: Shuangyun Peng creator: Baoxuan Jin creator: Junsong Zhou creator: YingXin Li uri: https://doi.org/10.7717/peerj.7283 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Shoot and root traits of summer maize hybrid varieties with higher grain yields and higher nitrogen use efficiency at low nitrogen application rates link: https://peerj.com/articles/7294 last-modified: 2019-07-15 description: Breeding high-yielding and nitrogen-efficient maize (Zea mays L.) hybrid varieties is a strategy that could simultaneously solve the problems of resource shortages and environmental pollution. We conducted a 2-year field study using four nitrogen application rates (0, 150, 225, and 300 kg N hm−2) and two maize hybrid varieties (ZD958 and QS101) to understand the plant traits related to high grain yields and high nitrogen use efficiency (NUE). We found that ZD958 had a higher grain yield and nitrogen accumulation in the shoots at harvest as well as a higher NUE at lower nitrogen application rates (0 and 150 kg hm–2) than QS101. The grain yields and NUE were almost identical for the two hybrid varieties at nitrogen application rates of 225 and 300 kg N hm–2. Compared with QS101, ZD958 had higher above-ground and below-ground biomass amounts, a deeper root distribution, longer root length, root active absorption area, greater grain filling rate, and higher photosynthetic NUE than QS101 at lower nitrogen application rates. Our results showed that ZD958 can maintain a higher grain yield at lower nitrogen rates in a similar manner to N-efficient maize hybrid varieties. The selection of hybrids such as ZD958 with a deeper root distribution and higher photosynthetic NUE can increase the grain yield and NUE under low nitrogen conditions. creator: Wennan Su creator: Muhammad Kamran creator: Jun Xie creator: Xiangping Meng creator: Qingfang Han creator: Tiening Liu creator: Juan Han uri: https://doi.org/10.7717/peerj.7294 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Su et al. title: The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation link: https://peerj.com/articles/7297 last-modified: 2019-07-15 description: We examined genetic diversity of the wild Tsushima leopard cat—a regional population of the Amur leopard cat—using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation. creator: Hideyuki Ito creator: Miho Inoue-Murayama uri: https://doi.org/10.7717/peerj.7297 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ito and Inoue-Murayama title: Establishing an ecological security pattern for urban agglomeration, taking ecosystem services and human interference factors into consideration link: https://peerj.com/articles/7306 last-modified: 2019-07-15 description: The assessment of ecological security patterns is a topic of conversation in landscape ecology in recent years. However, ecosystem services and human activities are seldom considered comprehensively in the assessment of ecological security patterns. The present study employs the Beijing–Tianjin–Hebei urban agglomeration as a study area, and uses ecological services to determine the ecological sources. The importance of ecological sources is classified based on logical coding and functional types of ecological services. The research combines regional characteristics to select and quantitatively calculate three human disturbance factors: soil erosion sensitivity, geological hazard sensitivity, and night lighting. Then the basic surface resistance of land use to limit migration is modified and ecological corridors are identified by combining these three disturbance factors. The results indicate that the sources of water production, soil and water conservation, and carbon fixation are mainly provided in mountainous areas, recreation sources are mostly distributed in the plains, and these ecological sources improve the maintenance of ecological corridors. The modification of resistance surfaces significantly changes the length of ecological corridors in Tianjin, Tangshan, Cangzhou, and Beijing, and the modified resistance surface improves the recognition of ecological corridors. This study provides a new research framework for identifying the ecological security patterns of urban agglomerations and provides scientific guidance related to ecological protection and urban planning for the Beijing−Tianjin−Hebei urban agglomeration. creator: Dongchuan Wang creator: Junhe Chen creator: Lihui Zhang creator: Zhichao Sun creator: Xiao Wang creator: Xian Zhang creator: Wei Zhang uri: https://doi.org/10.7717/peerj.7306 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China link: https://peerj.com/articles/7307 last-modified: 2019-07-15 description: BackgroundDistinguishing among species in the genus Lepista is difficult because of their similar morphologies.MethodsTo identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations.ResultsThe results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades. creator: Siyu Wang creator: Hongbo Guo creator: JiaJia Li creator: Wei Li creator: Qin Wang creator: Xiaodan Yu uri: https://doi.org/10.7717/peerj.7307 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Predicting the potential distribution of the Asian citrus psyllid, Diaphorina citri (Kuwayama), in China using the MaxEnt model link: https://peerj.com/articles/7323 last-modified: 2019-07-15 description: BackgroundCitrus huanglongbing (HLB) is a destructive disease of citrus and a major threat to the citrus industry around the world. This disease accounts for substantial economic losses in China every year. Diaphorina citri Kuwayama is one of the major vectors by which citrus HLB is spread under natural conditions in China. Research is needed to identify the geographic distribution of D. citri and its major areas of occurrence and to formulate measures for early warning, monitoring, and control of this pest and citrus HLB.MethodsIn this study, the ecological niche modelling software MaxEnt (maximum entropy model) was combined with ArcGIS (a geographic information system) to predict the potential geographic distribution of D. citri in China. Key environmental factors and the appropriate ranges of their values were also investigated.ResultsOur results show that the training data provided a good forecast (AUCmean = 0.988). The highly suitable areas for D. citri in China are mainly concentrated to the south of the Yangtze River, and the total area is 139.83 × 104 km2. The area of the moderately suitable areas is 27.71 × 104 km2, with a narrower distribution than that of the highly suitable area. The important environmental factors affecting the distribution of D. citri were min temperature of coldest month, mean temperature of coldest quarter, precipitation of wettest quarter, mean temperature of warmest quarter, precipitation of warmest quarter, max temperature of warmest month, and temperature seasonality. These results provide a valuable theoretical basis for risk assessments and control of D. citri.DiscussionThe predicted results showed that there were highly suitable areas for D. citri in Chongqing, Hubei, Anhui, and Jiangsu. Therefore, the possibility exists for the further spread of D. citri in China in the future. Extreme temperature variables, especially the min temperature of the coldest month, play an important role in the distribution of D. citri and are most closely related to the distribution of D. citri. creator: Rulin Wang creator: Hua Yang creator: Wei Luo creator: Mingtian Wang creator: Xingli Lu creator: Tingting Huang creator: Jinpeng Zhao creator: Qing Li uri: https://doi.org/10.7717/peerj.7323 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Upregulation of SPOCK2 inhibits the invasion and migration of prostate cancer cells by regulating the MT1-MMP/MMP2 pathway link: https://peerj.com/articles/7163 last-modified: 2019-07-12 description: BackgroundIt is known that secreted protein acidic and cysteine rich (osteonectin), cwcv and kazal-like domains proteoglycan 2 (SPOCK2) plays a significant role in the development and progression of several human cancers; however, the role of SPOCK2 in prostate cancer (PCa) remains unclear. This study aimed to find the role and mechanism of SPOCK2 in the development and progression of PCa.MethodsThe messenger ribonucleic acid (mRNA) expression of SPOCK2 in PCa tissue was detected by real-time polymerase chain reaction (PCR). Upregulation of the SPOCK2 gene was achieved using the DU145 and LNCaP cells by transfecting the cells with SPOCK2 recombinant fragment. Cell invasion and migration ability were detected by transwell chamber and wound healing assay. The expression of membrane-type 1 matrix metalloproteinase (MT1-MMP) and matrix metalloproteinase 2 (MMP2) in the cells was detected by Western Blot and zymography gel assay.ResultsThe mRNA level of SPOCK2 was significantly lower in the PCa tissue compared to benign prostate hyperplasia. Upregulation of SPOCK2 inhibited cell invasion and migration in DU145 and LNCaP cells, inhibited the expression of MT1-MMP and MMP2 and, inhibited activation of MMP2 in DU145 and LNCaP cells.ConclusionSPOCK2 is associated with the progression of PCa. Upregulation of SPOCK2 can inhibit PCa cell invasion and metastasis by decreasing MT1-MMP and MMP2 gene expression and decreasing MMP2 protein activation. creator: Gang Liu creator: Fang Ren creator: Yongsheng Song uri: https://doi.org/10.7717/peerj.7163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: BioDinamica: a toolkit for analyses of biodiversity and biogeography on the Dinamica-EGO modelling platform link: https://peerj.com/articles/7213 last-modified: 2019-07-12 description: Biogeography and macroecology are at the heart of the debate on ecology and evolution. We have developed the BioDinamica package, a suite of user-friendly graphical programs for analysing spatial patterns of biogeography and macroecology. BioDinamica includes analyses of beta-diversity, species richness, endemicity, phylo-diversity, species distribution models, predictive models of biodiversity patterns, and several tools for spatial biodiversity analysis. BioDinamica consists of a sub-library of Dinamica-EGO operators developed by integrating EGO native functions with R scripts. The BioDinamica operators can be assembled to create complex analytical and simulation models through the EGO graphical programming interface. In addition, we make available “Wizard” tutorials for end users. BioDinamica can be downloaded free of charge from the Dinamica EGO submodel store. The tools made available in BioDinamica not only facilitate complex biodiversity analyses, they also help develop state-of-the-art spatial models for biogeography and macroecology studies. creator: Ubirajara Oliveira creator: Britaldo Soares-Filho creator: Rômulo Fernandes Machado Leitão creator: Hermann O. Rodrigues uri: https://doi.org/10.7717/peerj.7213 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Oliveira et al. title: Site specificity and attachment mode of Symcallio and Calliobothrium species (Cestoda: “Tetraphyllidea”) in smoothhound sharks of the genus Mustelus (Carcharhiniformes: Triakidae) link: https://peerj.com/articles/7264 last-modified: 2019-07-12 description: Previous studies suggest that cestodes (i.e., tapeworms) of the sister genera Symcallio and Calliobothrium attach in different specific regions of the spiral intestine of their triakid shark hosts, with species of Symcallio attaching in the anterior region of the spiral intestine and species of Calliobothrium attaching with a broader distribution centered around the middle of the spiral intestine. In the present study, we tested the generality of this pattern of site specificity in two additional species pairs: Symcallio peteri and Calliobothrium euzeti in Mustelus palumbes and S. leuckarti and C. wightmanorum in M. asterias. Finding that these cestodes also exhibit the aforementioned pattern, we investigated a series of functional explanations that might account for this phylogenetically conserved pattern of site specificity. The mucosal surface of the spiral intestine of both shark species was characterized, as were the attachment mechanisms of all four cestode species. Although anatomical differences in mucosal surface were seen along the length of the spiral intestine in both shark species, these differences do not appear to correspond to the attachment mode of these cestodes. We find that while species of Symcallio, like most cestodes, attach using their scolex, species of Calliobothrium attach with their scolex and, to a much greater extent, also with their strobila. Furthermore, attachment of Calliobothrium species appears to be enhanced by laciniations (flap-like extensions on the posterior margins of the proglottids) that interdigitate with elements of the mucosal surface of the spiral intestine. The role of proglottid laciniations in attachment in species of Calliobothrium helps reconcile a number of morphological features that differ between these two closely related cestode genera. creator: James P. Bernot creator: Janine N. Caira uri: https://doi.org/10.7717/peerj.7264 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bernot and Caira title: Association of single nucleotide polymorphism at long non-coding RNA 8138.1 with duration of fertility in egg-laying hens link: https://peerj.com/articles/7282 last-modified: 2019-07-12 description: A previous genome-wide transcriptional analysis identified long non-coding RNA 8138.1 (lncRNA8138.1) as a candidate gene related to hen duration of the fertility (DF) trait. LncRNA8138.1 gene response to growth factor and reproductive system development suggests it has a vital role in reproduction. In this study, we investigated the lncRNA8138.1 gene sequence in a population of egg-laying hens. The sequence analysis of the lncRNA8138.1 gene containing about 1.6 k nucleotides (nt) was observed with four single nucleotide polymorphisms (SNPs) and 7 nt indel including r.4937159A > G; r.4937219T > C; r.4937258G > C; r.4937318C > G and g.4937319_4937325delinsTGTGTGG. Next, the genomic DNAs from laying hen populations were subjected to polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) to detect a region of 457 bp carrying lncRNA8138.1 r.4937159A > G substitution. Further inspection of the region containing r.4937159A > G mutation revealed three genotypes viz., AA, AG, and GG were observed with respective frequencies of 0.106, 0.607, and 0.287 in laying hen population 1 (P1) (n = 1, 042) and respective frequencies of 0.176, 0.708, and 0.116 in laying hen population 2 (P2) (n = 826). Moreover, to further examining the frequencies of r.4937159A > G genotypes in P1 and P2, and their additive and dominance effects; r.4937159A > G locus was significantly associated with DF-trait in both P1 and P2 (EN: the number of eggs, FN: the number of fertile eggs after a single AI), and DN (the number of days post-insemination until last fertile egg). In testing for additive and dominance effects, additive effect was significant (P < 0.05) in both P1 and P2 for DF-trait, and the dominance effect was significant (P < 0.05) for EN and FN traits, suggesting that r.4937159A > G polymorphism is a potential biomarker for DF-trait. However, the identified novel r.4937159A > G mutation and others require further investigation to confirm phenotypic causality and potential genetic relationships with reproductive traits. Overall, our findings suggest the significance of genetic variation in long non-coding RNAs may assist in future breeding programs to improve selection for prolonged DF-trait. creator: Adeyinka Abiola Adetula creator: Syed Ali Azmal creator: Chenghao Sun creator: Abdelmotaleb Elokil creator: Shijun Li uri: https://doi.org/10.7717/peerj.7282 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Adetula et al. title: Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China link: https://peerj.com/articles/7318 last-modified: 2019-07-12 description: In river-lake systems, sediment and water column are two distinct habitats harboring different bacterial communities which play a crucial role in biogeochemical processes. In this study, we employed Phylogenetic Investigation of Communities by Reconstruction of Unobserved States to assess the potential functions and functional redundancy of the bacterial communities in sediment and water in a eutrophic river-lake ecosystem, Poyang Lake in China. Bacterial communities in sediment and water had distinct potential functions of carbon, nitrogen, and sulfur metabolisms as well as phosphorus cycle, while the differences between rivers and the lake were inconspicuous. Bacterial communities in sediment had a higher relative abundance of genes associated with carbohydrate metabolism, carbon fixation pathways in prokaryotes, methane metabolism, anammox, nitrogen fixation, and dissimilatory sulfate reduction than that of water column. Bacterial communities in water column were higher in lipid metabolism, assimilatory nitrate reduction, dissimilatory nitrate reduction, phosphonate degradation, and assimilatory sulfate reduction than that of sediment bacterial communities. Furthermore, the variations in functional composition were closely associated to the variations in taxonomic composition in both habitats. In general, the bacterial communities in water column had a lower functional redundancy than in sediment. Moreover, comparing to the overall functions, bacterial communities had a lower functional redundancy of nitrogen metabolism and phosphorus cycle in water column and lower functional redundancy of nitrogen metabolism in sediment. Distance-based redundancy analysis and mantel test revealed close correlations between nutrient factors and functional compositions. The results suggested that bacterial communities in this eutrophic river-lake system of Poyang Lake were vulnerable to nutrient perturbations, especially the bacterial communities in water column. The results enriched our understanding of the bacterial communities and major biogeochemical processes in the eutrophic river-lake ecosystems. creator: Ze Ren creator: Xiaodong Qu creator: Wenqi Peng creator: Yang Yu creator: Min Zhang uri: https://doi.org/10.7717/peerj.7318 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ren et al. title: In silico analyses of CD14 molecule reveal significant evolutionary diversity, potentially associated with speciation and variable immune response in mammals link: https://peerj.com/articles/7325 last-modified: 2019-07-12 description: The cluster differentiation gene (CD14) is a family of monocyte differentiating genes that works in conjunction with lipopolysaccharide binding protein, forming a complex with TLR4 or LY96 to mediate innate immune response to pathogens. In this paper, we used different computational methods to elucidate the evolution of CD14 gene coding region in 14 mammalian species. Our analyses identified leucine-rich repeats as the only significant domain across the CD14 protein of the 14 species, presenting with frequencies ranging from one to four. Importantly, we found signal peptides located at mutational hotspots demonstrating that this gene is conserved across these species. Out of the 10 selected variants analyzed in this study, only six were predicted to possess significant deleterious effect. Our predicted protein interactome showed a significant varying protein–protein interaction with CD14 protein across the species. This may be important for drug target and therapeutic manipulation for the treatment of many diseases. We conclude that these results contribute to our understanding of the CD14 molecular evolution, which underlays varying species response to complex disease traits. creator: Olanrewaju B. Morenikeji creator: Bolaji N. Thomas uri: https://doi.org/10.7717/peerj.7325 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Morenikeji and Thomas title: Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean link: https://peerj.com/articles/7263 last-modified: 2019-07-11 description: Respiratory burst oxidase homologs (RBOHs), which catalyze the production of superoxide from oxygen and NADPH, play key roles in plant growth and development, hormone signaling, and stress responses. Compared with extensive studies in model plants arabidopsis and rice, little is known about RBOHs in other species. This study presents a genome-wide analysis of Rboh family genes in jatropha (Jatropha curcas) as well as the comparison with castor bean (Ricinus communis), another economically important non-food oilseed crop of the Euphorbiaceae family. The family number of seven members identified from the jatropha genome is equal to that present in castor bean, and further phylogenetic analysis assigned these genes into seven groups named RBOHD, -C, -B, -E, -F, -N, and -H. In contrast to a high number of paralogs present in arabidopsis and rice that experienced several rounds of recent whole-genome duplications, no duplicate was identified in both jatropha and castor bean. Conserved synteny and one-to-one orthologous relationship were observed between jatropha and castor bean Rboh genes. Although exon-intron structures are usually highly conserved between orthologs, loss of certain introns was observed for JcRbohB, JcRbohD, and RcRbohN, supporting their divergence. Global gene expression profiling revealed diverse patterns of JcRbohs over various tissues. Moreover, expression patterns of JcRbohs during flower development as well as various stresses were also investigated. These findings will not only improve our knowledge on species-specific evolution of the Rboh gene family, but also provide valuable information for further functional analysis of Rboh genes in jatropha. creator: Yongguo Zhao creator: Zhi Zou uri: https://doi.org/10.7717/peerj.7263 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao and Zou title: Effects of guanylurea, the transformation product of the antidiabetic drug metformin, on the health of brown trout (Salmo trutta f. fario) link: https://peerj.com/articles/7289 last-modified: 2019-07-11 description: BackgroundGuanylurea is the main transformation product of the antidiabetic drug metformin, which is one of the most prescribed pharmaceuticals worldwide. Due to the high rate of microbial degradation of metformin in sewage treatment plants, guanylurea occurs in higher concentrations in surface waters than its parent compound and could therefore affect aquatic wildlife. In this context, data for fish are scarce up to now which made us investigate the health of brown trout (Salmo trutta f. fario) in response to guanylurea.MethodsIn two experiments, eggs plus developing larvae and juvenile brown trout were exposed to three different concentrations of guanylurea (10, 100 and 1,000 µg/L) and, as a negative control, filtered tap water without this compound. Low internal concentrations were determined. The investigated parameters were mortality, length, weight, condition factor, tissue integrity of the liver and kidney, levels of stress proteins and lipid peroxides, as well as behavioural and developmental endpoints. It was found that guanylurea did not significantly change any of these parameters in the tested concentration range.ResultsIn conclusion, these results do not give rise to concern that guanylurea could negatively affect the health or the development of brown trout under field conditions. Nevertheless, more studies focusing on further parameters and other species are highly needed for a more profound environmental risk assessment of guanylurea. creator: Stefanie Jacob creator: Sarah Knoll creator: Carolin Huhn creator: Heinz-R. Köhler creator: Selina Tisler creator: Christian Zwiener creator: Rita Triebskorn uri: https://doi.org/10.7717/peerj.7289 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jacob et al. title: A prognostic nomogram for neuroblastoma in children link: https://peerj.com/articles/7316 last-modified: 2019-07-11 description: IntroductionNeuroblastoma is one of the most common extracranial solid tumors in children, which accounts for about 7–10% in children’s tumors. The prognosis group of patients with neuroblastoma could not only improve the efficacy of high-risk patients, but also reduce the effects of drug complications for surviving patients.Material and MethodsPatients diagnosed with neuroblastoma between 1986 and 2012 were selected form the TARGET database. The nomogram was built with potential risk factors based on COX regression analysis. The precision of the 3-year and 5-year survival of the nomograms was evaluated by the area under receiver operating characteristic (ROC) curve (AUC).ResultsA total of 757 child neuroblastoma patients were selected from the TARGET database. Univariate analysis showed that age of diagnosis (>520 day), race of American Indian or Alaska Native, stage 4 in International Neuroblastoma Staging System (INSS), MYCN status, DNA ploidy, and high mitosis-karyorrhexis index were associated with overall survival (OS). Multivariate analysis showed age of diagnosis (>520 day), stage 4 in INSS and DNA ploidy were independent risk factors of OS. The concordance index (C-index) of the nomogram was 0.704 (95% CI [0.686–0.722]) in the training cohort while the C-index in the validation cohort was 0.672 (95% CI [0.644–0.700]). AUC values of ROC curves for 3-year OS and 5-year OS in the training cohort were 0.732 and 0.772, respectively. The nomogram performed better compared with INSS staging system, tumor histology and children’s oncology group (COG) risk group with C-indexes of 0.662 (95% CI [0.648–0.676]), 0.637 (95% CI [0.622–0.652]) and 0.651 (95% CI [0.637–0.665]), respectively.ConclusionsThe nomogram showed stronger predictive power than the INSS staging system, tumor histology and COG risk group. Precise estimates of the prognosis of childhood neuroblastoma might help doctors make better treatment decisions. creator: Xiaozhi Li creator: Yutong Meng uri: https://doi.org/10.7717/peerj.7316 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li and Meng title: The impact of irrigation on yield of alfalfa and soil chemical properties of saline-sodic soils link: https://peerj.com/articles/7148 last-modified: 2019-07-10 description: BackgroundForage production in the saline-sodic soil of the western Songnen Plain Northeast China depends on irrigation. Therefore, the water use efficiency (WUE) and soil chemical properties are key factors in the overall forage productivity in this water scarce region. Improving forage yield, WUE, and soil properties under irrigation are very important for food and ecological security in this water-deficient region. Additionally, a suitable irrigation schedule for this region is necessary.MethodsA field experiment was conducted between 2015 and 2018 to evaluate the effects of irrigation on artificial grassland productivity and the changes in soil chemical properties as well as to plan a reliable irrigation schedule for the western Songnen Plain. Eight irrigation treatments were designed, which depended on the three growth stages of alfalfa. The shoot height (SH), the chlorophyll content (SPAD), the dry yield (DM), the ratio of stem to leaves (SLR), the WUE, the changes in the chemical properties of the soil, and precipitation and evaporation were investigated.ResultsThe SH, DM, WUE, and SLR were significantly increased by irrigation (P < 0.01). However, the SPAD resulting from irrigation was not significantly higher than the SPAD of CK (no irrigation) (P < 0.05). In addition, the soil chemical properties at the depth of 0–100 cm were significantly decreased by irrigation P (0.05). For example, the soil electrical conductivity, sodium absorption ratio, and total alkalization were reduced 182–345 μS cm−1, 8.95–9.00 (mmolc/L)1/2, and 3.29–4.65 mmolc L−1 by different irrigation treatments, respectively. Finally, considering the highest WUE of I5 (irrigation at branch stage) (2.50 kg m−3), relative high DM of I5 (787.00 g m−2), the precipitation, the evaporation, the water resources, and the changes of the soil’s chemical properties, 236.50 mm of irrigation water was recommended at the branching stage of alfalfa for the western Songnen Plain, Northeast China. creator: Hongtao Yang creator: Fenghua An creator: Fan Yang creator: Zhichun Wang uri: https://doi.org/10.7717/peerj.7148 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: An avian femur from the Late Cretaceous of Vega Island, Antarctic Peninsula: removing the record of cursorial landbirds from the Mesozoic of Antarctica link: https://peerj.com/articles/7231 last-modified: 2019-07-10 description: In 2006, a partial avian femur (South Dakota School of Mines and Technology (SDSM) 78247) from the Upper Cretaceous (Maastrichtian) Sandwich Bluff Member of the López de Bertodano Formation of Sandwich Bluff on Vega Island of the northern Antarctic Peninsula was briefly reported as that of a cariamiform—a clade that includes extant and volant South American species and many extinct flightless and cursorial species. Although other authors have since rejected this taxonomic assignment, SDSM 78247 had never been the subject of a detailed description, hindering a definitive assessment of its affinities. Here we provide the first comprehensive description, illustration, and comparative study of this specimen. Comparison of characters that may be assessed in this femur with those of avian taxa scored in published character matrices refutes the inclusion of SDSM 78247 within Cariamiformes, instead supporting its assignment to a new, as-yet unnamed large-bodied species within the genus Vegavis, and therefore its referral to a clade of semiaquatic anseriforms. Important character states diagnostic of Vegavis + Polarornis include strong craniocaudal bowing of the femoral shaft, the presence of a distinct fossa just proximal to the fibular trochlea, and the broad and flat shape of the patellar sulcus. Referral to Vegavis is based on the presence of a distinctive proximocaudal fossa and distolateral scar. This genus was previously known only from Vegavis iaai, a smaller-bodied taxon from the same locality and stratigraphic unit. Our reassignment of SDSM 78247 to Vegavis sp. removes the record of cariamiform landbirds from the Antarctic Cretaceous. creator: Abagael R. West creator: Christopher R. Torres creator: Judd A. Case creator: Julia A. Clarke creator: Patrick M. O'Connor creator: Matthew C. Lamanna uri: https://doi.org/10.7717/peerj.7231 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 West et al. title: Testing relationship between plant productivity and diversity in a desertified steppe in Northwest China link: https://peerj.com/articles/7239 last-modified: 2019-07-10 description: The rapid global plant diversity and productivity loss has resulted in ecosystem functional degeneration in recent decades, and the relationship between plant diversity and productivity is a pressing issue around the world. Here, we sampled six plant communities that have not been grazed for 20 years, i.e., Agropyron mongolicum, Stipa bungeana, Cynanchum komarovii, Glycyrrhiza uralensis, Sophora alopecuroides, Artemisia ordosica, located in a desertified steppe, northwestern China, and tested the relationship between plant diversity and productivity in this region. We found a positive linear relationship between AGB (above-ground biomass) and BGB (below-ground biomass), and the curves between plant diversity and AGB were unimodal (R2 = 0.4572, p < 0.05), indicating that plant productivity increased at a low level of diversity but decreased at a high level of diversity. However, there was no significant relationship between BGB and plant diversity (p > 0.05). Further, RDA (redundancy analysis) indicated that soil factors had a strong effect on plant diversity and productivity. Totally, GAMs (generalized additive models) showed that soil factors (especially total nitrogen TN, total carbon TC, soil microbial biomass nitrogen SMB-N, soil microbial biomass carbon SMB-C) explained more variation in plant diversity and productivity (78.24%), which can be regarded as the key factors driving plant diversity and productivity. Therefore, strategies aiming to increase plant productivity and protect plant diversity may concentrate on promoting soil factors (e.g., increasing TC, TN, SMB-N and SMB-C) and plant species, which can be regarded as an effective and simple strategy to stabilize ecosystems to mitigate aridity in desertified steppes in northwestern China. creator: Yang Yang creator: Bingru Liu uri: https://doi.org/10.7717/peerj.7239 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang and Liu title: A new paravian dinosaur from the Late Jurassic of North America supports a late acquisition of avian flight link: https://peerj.com/articles/7247 last-modified: 2019-07-10 description: The last two decades have seen a remarkable increase in the known diversity of basal avialans and their paravian relatives. The lack of resolution in the relationships of these groups combined with attributing the behavior of specialized taxa to the base of Paraves has clouded interpretations of the origin of avialan flight. Here, we describe Hesperornithoides miessleri gen. et sp. nov., a new paravian theropod from the Morrison Formation (Late Jurassic) of Wyoming, USA, represented by a single adult or subadult specimen comprising a partial, well-preserved skull and postcranial skeleton. Limb proportions firmly establish Hesperornithoides as occupying a terrestrial, non-volant lifestyle. Our phylogenetic analysis emphasizes extensive taxonomic sampling and robust character construction, recovering the new taxon most parsimoniously as a troodontid close to Daliansaurus, Xixiasaurus, and Sinusonasus. Multiple alternative paravian topologies have similar degrees of support, but proposals of basal paravian archaeopterygids, avialan microraptorians, and Rahonavis being closer to Pygostylia than archaeopterygids or unenlagiines are strongly rejected. All parsimonious results support the hypothesis that each early paravian clade was plesiomorphically flightless, raising the possibility that avian flight originated as late as the Late Jurassic or Early Cretaceous. creator: Scott Hartman creator: Mickey Mortimer creator: William R. Wahl creator: Dean R. Lomax creator: Jessica Lippincott creator: David M. Lovelace uri: https://doi.org/10.7717/peerj.7247 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hartman et al. title: Recently-adopted foraging strategies constrain early chick development in a coastal breeding gull link: https://peerj.com/articles/7250 last-modified: 2019-07-10 description: Human-mediated food sources offer possibilities for novel foraging strategies by opportunistic species. Yet, relative costs and benefits of alternative foraging strategies vary with the abundance, accessibility, predictability and nutritional value of anthropogenic food sources. The extent to which such strategies may ultimately alter fitness, can have important consequences for long-term population dynamics. Here, we studied the relationships between parental diet and early development in free-ranging, cross-fostered chicks and in captive-held, hand-raised chicks of Lesser Black-backed Gulls (Larus fuscus) breeding along the Belgian coast. This traditionally marine and intertidal foraging species is now increasingly taking advantage of human activities by foraging on terrestrial food sources in agricultural and urban environments. In accordance with such behavior, the proportion of terrestrial food in the diet of free-ranging chicks ranged between 4% and 80%, and consistent stable isotope signatures between age classes indicated that this variation was mainly due to between-parent variation in feeding strategies. A stronger terrestrial food signature in free-ranging chicks corresponded with slower chick development. However, no consistent differences in chick development were found when contrasting terrestrial and marine diets were provided ad libitum to hand-raised chicks. Results of this study hence suggest that terrestrial diets may lower reproductive success due to limitations in food quantity, rather than quality. Recent foraging niche expansion toward terrestrial resources may thus constitute a suboptimal alternative strategy to marine foraging for breeding Lesser Black-backed Gulls during the chick-rearing period. creator: Alejandro Sotillo creator: Jan M. Baert creator: Wendt Müller creator: Eric W.M. Stienen creator: Amadeu M.V.M. Soares creator: Luc Lens uri: https://doi.org/10.7717/peerj.7250 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sotillo et al. title: Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus link: https://peerj.com/articles/7261 last-modified: 2019-07-10 description: BackgroundAnanas comosus var. bracteatus has high ornamental value due to its chimeric leaves. However, the chimeric trait is very unstable in red pineapple plants, and transcriptional variation between the two types of cells (white/green cells) and the molecular mechanism responsible for their albino phenotype remain poorly understood.MethodsComparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of chimeric leaves were performed.ResultsIn total, 1,685 differentially expressed genes (DEGs) (712 upregulated and 973 downregulated) and 1,813 differentially abundant proteins (DAPs) (1,018 with low abundance and 795 with high abundance) were identified. Based on Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the DEGs were mostly involved in carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolism and oxidative phosphorylation, while proteomic analysis revealed that DAPs were mostly related to ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed increased mRNA levels but low abundance of nine proteins level in Whs /Grs related to photosynthetic pigment and photosynthesis. Transcriptional changes, posttranscriptional regulation and translational alterations of key enzymes involved in chlorophyll biosynthesis and photosynthesis may play important roles in the albino parts of chimeric leaves. creator: Yanbin Xue creator: Jun Ma creator: Yehua He creator: Sanmiao Yu creator: Zhen Lin creator: Yingyuan Xiong creator: Fatima Rafique creator: Fuxing Jiang creator: Lingxia Sun creator: Mingdong Ma creator: Yujue Zhou creator: Xi Li creator: Zhuo Huang uri: https://doi.org/10.7717/peerj.7261 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xue et al. title: Towards sex identification of Asian Palmyra palm (Borassus flabellifer L.) by DNA fingerprinting, suppression subtractive hybridization and de novo transcriptome sequencing link: https://peerj.com/articles/7268 last-modified: 2019-07-10 description: BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries and de novo transcriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Although de novo transcriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species. creator: Kwanjai Pipatchartlearnwong creator: Piyada Juntawong creator: Passorn Wonnapinij creator: Somsak Apisitwanich creator: Supachai Vuttipongchaikij uri: https://doi.org/10.7717/peerj.7268 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pipatchartlearnwong et al. title: Structure and ion physiology of Brasenia schreberi glandular trichomes in vivo link: https://peerj.com/articles/7288 last-modified: 2019-07-10 description: Brasenia schreberi is a critically endangered aquatic basal angiosperm. In this work, we characterized the structure of the glandular trichomes of B. schreberi morphologically and histochemically. We used a variety of structural, histochemical and permeability stains for the characterization, and we tested the effects of stress in vivo using NaCl and ethanol. We observed that the glandular trichome of B. schreberi are composed of two disk-like stalk cells, and a glandular cell which surround a cuticular storage space. The cuticle is discontinuous at the surface of the shoots. Nearly half of young trichomes senesced in 0.9% NaCl, and mature trichomes senesced at 1.8% NaCl. About half of young trichomes senesced under 3% ethanol and mature trichomes senesced in 2% ethanol after 20 min of treatment. The physiology of glandular trichomes affects the way they secrete mucilage via storage space at a young stage. The trichomes become permeable and absorb ions when mature. This transition depends on the osmiophilic material and the dynamic protoplast. It can accelerate senescence and disassembly by ion accumulation. Permeability tests and ion treatments of glandular trichomes provide new insights for fertilizer research. Our study highlights the structure and physiology of B. schreberi glandular trichomes. creator: Chaodong Yang creator: Xia Zhang creator: Fan Zhang creator: Xiaoe Wang creator: Qingfeng Wang uri: https://doi.org/10.7717/peerj.7288 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: An attention bias test to assess anxiety states in laying hens link: https://peerj.com/articles/7303 last-modified: 2019-07-10 description: Fear is a response to a known threat, anxiety is a response to a perceived threat. Both of these affective states can be detrimental to animal welfare in modern housing environments. In comparison to the well-validated tests for assessing fear in laying hens, tests for measuring anxiety are less developed. Perception of a threat can result in an attention bias that may indicate anxious affective states in individual hens following playback of an alarm call. In Experiment 1, an attention bias test was applied to hens that differed in their range access to show that hens that never ranged were more vigilant (stretching of the neck and looking around: P < 0.001) and slower to feed following the second alarm call playback (P = 0.01) compared with hens that ranged daily. All hens showed a reduction in comb temperature following the first alarm call (P < 0.001). In Experiment 2, an open field test was used to determine an effective dose of 2 mg/kg for the anxiogenic drug meta-Chlorophenylpiperazine (m-CPP) in adult laying hens. Hens dosed with 2 mg/kg showed reduced locomotion compared with a saline solution (P < 0.05). In Experiment 3, 2 mg/kg m-CPP or saline was administered to adult hens previously habituated to the open field arena to pharmacologically validate an attention bias test as a measure of anxiety. Hens dosed with m-CPP were slower to feed (P = 0.02) and faster to vocalize following a second alarm call playback (P = 0.03) but these hens did not exhibit the same vigilance behavior as documented in Experiment 1. The m-CPP hens also spent more time stepping and vocalizing (both P < 0.001) than the saline hens. An attention bias test could be used to assess anxiety. However, behavioral responses of hens may vary depending on their age or test environment familiarity, thus further refinement of the test is required. In these tests, 2 mg/kg of m-CPP resulted in motionless behavior when the environment was novel, but more movement and vocalizing when the environment was familiar. The extreme behavioral phenotypes exhibited by individually-tested birds may both be indicators of negative states. creator: Dana L.M. Campbell creator: Peta S. Taylor creator: Carlos E. Hernandez creator: Mairi Stewart creator: Sue Belson creator: Caroline Lee uri: https://doi.org/10.7717/peerj.7303 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Campbell et al. title: Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma link: https://peerj.com/articles/7313 last-modified: 2019-07-10 description: BackgroundLung adenocarcinoma (LUAD) is the major subtype of lung cancer and the most lethal malignant disease worldwide. However, the molecular mechanisms underlying LUAD are not fully understood.MethodsFour datasets (GSE118370, GSE85841, GSE43458 and GSE32863) were obtained from the gene expression omnibus (GEO). Identification of differentially expressed genes (DEGs) and functional enrichment analysis were performed using the limma and clusterProfiler packages, respectively. A protein–protein interaction (PPI) network was constructed via Search Tool for the Retrieval of Interacting Genes (STRING) database, and the module analysis was performed by Cytoscape. Then, overall survival analysis was performed using the Kaplan–Meier curve, and prognostic candidate biomarkers were further analyzed using the Oncomine database.ResultsTotally, 349 DEGs were identified, including 275 downregulated and 74 upregulated genes which were significantly enriched in the biological process of extracellular structure organization, leukocyte migration and response to peptide. The mainly enriched pathways were complement and coagulation cascades, malaria and prion diseases. By extracting key modules from the PPI network, 11 hub genes were screened out. Survival analysis showed that except VSIG4, other hub genes may be involved in the development of LUAD, in which MYH10, METTL7A, FCER1G and TMOD1 have not been reported previously to correlated with LUAD. Briefly, novel hub genes identified in this study will help to deepen our understanding of the molecular mechanisms of LUAD carcinogenesis and progression, and to discover candidate targets for early detection and treatment of LUAD. creator: Tingting Guo creator: Hongtao Ma creator: Yubai Zhou uri: https://doi.org/10.7717/peerj.7313 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al. title: Exploring regulatory networks in plants: transcription factors of starch metabolism link: https://peerj.com/articles/6841 last-modified: 2019-07-09 description: Biological networks are complex (non-linear), redundant (cyclic) and compartmentalized at the subcellular level. Rational manipulation of plant metabolism may have failed due to inherent difficulties of a comprehensive understanding of regulatory loops. We first need to identify key factors controlling the regulatory loops of primary metabolism. The paradigms of plant networks are revised in order to highlight the differences between metabolic and transcriptional networks. Comparison between animal and plant transcription factors (TFs) reveal some important differences. Plant transcriptional networks function at a lower hierarchy compared to animal regulatory networks. Plant genomes contain more TFs than animal genomes, but plant proteins are smaller and have less domains as animal proteins which are often multifunctional. We briefly summarize mutant analysis and co-expression results pinpointing some TFs regulating starch enzymes in plants. Detailed information is provided about biochemical reactions, TFs and cis regulatory motifs involved in sucrose-starch metabolism, in both source and sink tissues. Examples about coordinated responses to hormones and environmental cues in different tissues and species are listed. Further advancements require combined data from single-cell transcriptomic and metabolomic approaches. Cell fractionation and subcellular inspection may provide valuable insights. We propose that shuffling of promoter elements might be a promising strategy to improve in the near future starch content, crop yield or food quality. creator: Cristal López-González creator: Sheila Juárez-Colunga creator: Norma Cecilia Morales-Elías creator: Axel Tiessen uri: https://doi.org/10.7717/peerj.6841 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 López-González et al. title: Polyp expansion of passive suspension feeders: a red coral case study link: https://peerj.com/articles/7076 last-modified: 2019-07-09 description: Polyp activity in passive suspension feeders has been considered to be affected by several environmental factors such as hydrodynamics, water temperature and food concentration. To better elucidate the driving forces controlling polyp expansion in these organisms and the potential role of particle concentration, the octocoral Corallium rubrum was investigated in accordance with two approaches: (1) high-frequency in-situ observations examining various environmental and biological variables affecting the water column, and (2) video-recorded flume-controlled laboratory experiments performed under a range of environmental and biological conditions, in terms of water temperature, flow speed, chemical signals and zooplankton. In the field, C. rubrum polyp expansion correlated positively with particle (seston and zooplankton) concentration and current speed. This observation was confirmed by the flume video records of the laboratory experiments, which showed differences in polyp activity due to changes in temperature and current speed, but especially in response to increasing nutritional stimuli. The maximum activity was observed at the highest level of nutritional stimulus consisting of zooplankton. Zooplankton and water movement appeared to be the main factors controlling polyp expansion. These results suggest that the energy budget of passive suspension feeders (and probably the benthic community as a whole) may rely on their ability to maximise prey capture during food pulses. The latter, which may be described as discontinuous organic matter (dead or alive) input, may be the key to a better understanding of benthic-pelagic coupling processes and trophic impacts on animal forests composed of sessile suspension feeders. creator: Sergio Rossi creator: Lucia Rizzo creator: Jean-Claude Duchêne uri: https://doi.org/10.7717/peerj.7076 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rossi et al. title: A new comprehensive eye-tracking test battery concurrently evaluating the Pupil Labs glasses and the EyeLink 1000 link: https://peerj.com/articles/7086 last-modified: 2019-07-09 description: Eye-tracking experiments rely heavily on good data quality of eye-trackers. Unfortunately, it is often the case that only the spatial accuracy and precision values are available from the manufacturers. These two values alone are not sufficient to serve as a benchmark for an eye-tracker: Eye-tracking quality deteriorates during an experimental session due to head movements, changing illumination or calibration decay. Additionally, different experimental paradigms require the analysis of different types of eye movements; for instance, smooth pursuit movements, blinks or microsaccades, which themselves cannot readily be evaluated by using spatial accuracy or precision alone. To obtain a more comprehensive description of properties, we developed an extensive eye-tracking test battery. In 10 different tasks, we evaluated eye-tracking related measures such as: the decay of accuracy, fixation durations, pupil dilation, smooth pursuit movement, microsaccade classification, blink classification, or the influence of head motion. For some measures, true theoretical values exist. For others, a relative comparison to a reference eye-tracker is needed. Therefore, we collected our gaze data simultaneously from a remote EyeLink 1000 eye-tracker as the reference and compared it with the mobile Pupil Labs glasses. As expected, the average spatial accuracy of 0.57° for the EyeLink 1000 eye-tracker was better than the 0.82° for the Pupil Labs glasses (N = 15). Furthermore, we classified less fixations and shorter saccade durations for the Pupil Labs glasses. Similarly, we found fewer microsaccades using the Pupil Labs glasses. The accuracy over time decayed only slightly for the EyeLink 1000, but strongly for the Pupil Labs glasses. Finally, we observed that the measured pupil diameters differed between eye-trackers on the individual subject level but not on the group level. To conclude, our eye-tracking test battery offers 10 tasks that allow us to benchmark the many parameters of interest in stereotypical eye-tracking situations and addresses a common source of confounds in measurement errors (e.g., yaw and roll head movements). All recorded eye-tracking data (including Pupil Labs’ eye videos), the stimulus code for the test battery, and the modular analysis pipeline are freely available (https://github.com/behinger/etcomp). creator: Benedikt V. Ehinger creator: Katharina Groß creator: Inga Ibs creator: Peter König uri: https://doi.org/10.7717/peerj.7086 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ehinger et al. title: Comparison of olive leaf, olive oil, palm oil, and omega-3 oil in acute kidney injury induced by sepsis in rats link: https://peerj.com/articles/7219 last-modified: 2019-07-09 description: BackgroundHypotension, increased production of reactive oxygen species, and inflammation are all observed in experimental models of sepsis induced by lipopolysaccharide (LPS).PurposeThe aim of this study was to evaluate the effects of an ethanolic extract of Brazilian olive leaf (Ex), Brazilian olive oil (Olv), Ex + Olv (ExOlv), and palm oil (Pal) in comparison to the effects of omega-3 fish oil (Omg) in a rat model of sepsis-induced acute kidney injury.MaterialsWistar rats were divided into seven groups (seven per group), which were either untreated (control) or treated with LPS, LPS + Ex, LPS + ExOlv, LPS + Olv, LPS + Omg, or LPS + Pal.ResultsLower values of creatinine clearance and blood pressure were observed in the LPS-treated group, and these values were not affected by Ex, Olv, ExOlv, Pal, or Omg treatment. Mortality rates were significantly lower in rats exposed to LPS when they were also treated with Ex, ExOlv, Olv, Pal, or Omg. These treatments also decreased oxidative stress and inflammation (Tumor necrosis factor alpha, interleukin-1 beta) and increased interleukin-10 levels and cell proliferation, which were associated with decreased apoptosis in kidney tissue.ConclusionEx and Pal treatments were beneficial in septic rats, since they increased survival rate and did not aggravate inflammation. However, the most effective treatments for septic rats were Olv in comparison to Omg. These natural food substances could enable the development of effective therapeutic interventions to sepsis. creator: Maria Fátima de Paula Ramos creator: Olvania Basso Oliveira creator: Alceni do Carmo Morais Monteiro de Barros creator: Clara Versolato Razvickas creator: Edson de Andrade Pessoa creator: Rinaldo Florêncio da Silva creator: Ana Maria Soares Pereira creator: Marcia Bastos Convento creator: Fernanda Teixeira Borges creator: Nestor Schor uri: https://doi.org/10.7717/peerj.7219 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ramos et al. title: BioShake: a Haskell EDSL for bioinformatics workflows link: https://peerj.com/articles/7223 last-modified: 2019-07-09 description: Typical bioinformatics analyses comprise of long running computational workflows. An important part of reproducible research is the management and execution of these workflows to allow robust execution and to minimise errors. BioShake is an embedded domain specific language in Haskell for specifying and executing computational workflows for bioinformatics that significantly reduces the possibility of errors occurring. Unlike other workflow frameworks, BioShake raises many properties to the type level allowing the correctness of a workflow to be statically checked during compilation, catching errors before any lengthy execution process. BioShake builds on the Shake build tool to provide robust dependency tracking, parallel execution, reporting, and resumption capabilities. Finally, BioShake abstracts execution so that jobs can either be executed directly or submitted to a cluster. BioShake is available at http://github.com/PapenfussLab/bioshake. creator: Justin Bedő uri: https://doi.org/10.7717/peerj.7223 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bedő title: Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae link: https://peerj.com/articles/7260 last-modified: 2019-07-09 description: Teucrium is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of T. stocksianum subsp. stenophyllum R.A.King (TSS), T. stocksianum subsp. stocksianum Boiss. (TS) and T. mascatense Boiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae (Ajuga reptans L., Caryopteris mongholica Bunge, Lamium album L., Lamium galeobdolon (L.) Crantz, and Stachys byzantina K.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψrps19 was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, the pbsA gene was present in the LSC at varying distances from the JLA (IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genus Teucrium and its subspecies that may be applied to a more comprehensive study. creator: Arif Khan creator: Sajjad Asaf creator: Abdul Latif Khan creator: Adil Khan creator: Ahmed Al-Harrasi creator: Omar Al-Sudairy creator: Noor Mazin AbdulKareem creator: Nadiya Al-Saady creator: Ahmed Al-Rawahi uri: https://doi.org/10.7717/peerj.7260 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Khan et al. title: Identification of conserved genes involved in nitrogen metabolic activities in wheat link: https://peerj.com/articles/7281 last-modified: 2019-07-09 description: Nitrogen (N) plays a very important role in crop growth and development. Many N-metabolism-related genes responsive to N application have been identified in many plants such as Arabidopsis, rice and maize; however, few genes have been reported in wheat, which is one of the most widely grown crops in the world. In this study, a wheat wild type with N dependent lesion mimic (LM) and its mutants without LM were used to identify conserved N-metabolism-related genes. TaPAP, TaUPS and TaNMR were differentially expressed among N levels both in the wild type and two of its mutants, and the expression patterns of these genes were further studied under application of three chemotypes of N (NH4+, NO3- and NH4NO3). The results showed that these genes are conserved N-metabolism-related genes and TaNMR is a novel player in N-metabolism. creator: Lei Li creator: Hao Gong creator: Zhengxi Sun creator: Tao Li uri: https://doi.org/10.7717/peerj.7281 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Controls of plant diversity and composition on a desert archipelago link: https://peerj.com/articles/7286 last-modified: 2019-07-09 description: AimWith the most robust floristic data set for any arid archipelago, we use statistical modeling to determine the underlying controls of plant diversity and species composition.LocationThe study was undertaken in the Midriff Islands of the Gulf of California, Mexico.MethodsUsing the area–diversity relationship we estimate the power coefficient z with generalized linear models (GLM). We tested eight predictors (area, human presence, habitat diversity, topography, distance to mainland, island type, precipitation, and seabird dynamics) using a step-wise process on the same GLM procedure. Plant species composition was assessed by conducting a non-standardized principal component analysis on a presence-absence matrix of the 476 (plant species) × 14 (islands). Finally, families were tested for over or under representation with a X2 analysis subjected to a Bonferroni correction.ResultsThe classic species-area model explained 85% of the variance in island plant diversity and yielded a slope (z) of 0.303 (±0.01). When the effect of area is removed, four additional factors were shown to account for observed variation; habitat diversity (34%), seabird dynamics (23%), island type (21%), topography (14%). Human presence and distance to mainland were not predictors of species richness. Species composition varies significantly with island area; small islands have a particular flora where certain families are overrepresented, such as Cactaceae, while the flora of larger islands is strongly dependent on the continental source.Main conclusionsThe factors that control diversity levels are expressions of geology, landscape heterogeneity, and land-sea connections. Species assemblages in small islands are governed by copious marine nutrients in the form of guano that depress species diversity. Distance to mainland and human presence hold no predictive power on diversity. The results show these islands to be isolated arid ecosystems with functioning ecological networks. creator: Benjamin T. Wilder creator: Richard S. Felger creator: Exequiel Ezcurra uri: https://doi.org/10.7717/peerj.7286 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wilder et al. title: Association of transcription factor WRKY56 gene from Populus simonii × P. nigra with salt tolerance in Arabidopsis thaliana link: https://peerj.com/articles/7291 last-modified: 2019-07-09 description: The WRKY transcription factor family is one of the largest groups of transcription factor in plants, playing important roles in growth, development, and biotic and abiotic stress responses. Many WRKY genes have been cloned from a variety of plant species and their functions have been analyzed. However, the studies on WRKY transcription factors in tree species under abiotic stress are still not well characterized. To understand the effects of the WRKY gene in response to abiotic stress, mRNA abundances of 102 WRKY genes in Populus simonii × P. nigra were identified by RNA sequencing under normal and salt stress conditions. The expression of 23 WRKY genes varied remarkably, in a tissue-specific manner, under salt stress. Since the WRKY56 was one of the genes significantly induced by NaCl treatment, its cDNA fragment containing an open reading frame from P. simonii × P. nigra was then cloned and transferred into Arabidopsis using the floral dip method. Under salt stress, the transgenic Arabidopsis over-expressed the WRKY56 gene, showing an increase in fresh weight, germination rate, proline content, and peroxidase and superoxide dismutase activity, when compared with the wild type. In contrast, transgenic Arabidopsis displayed a decrease in malondialdehyde content under salt stress. Overall, these results indicated that the WRKY56 gene played an important role in regulating salt tolerance in transgenic Arabidopsis. creator: Lei Wang creator: Wenjing Yao creator: Yao Sun creator: Jiying Wang creator: Tingbo Jiang uri: https://doi.org/10.7717/peerj.7291 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: A highly diverse fungal community associated with leaves of the mangrove plant Acanthus ilicifolius var. xiamenensis revealed by isolation and metabarcoding analyses link: https://peerj.com/articles/7293 last-modified: 2019-07-09 description: A high diversity of culturable foliar endophytic fungi is known from various mangrove plants, and the core taxa include species from Colletotrichum, Pestalotiopsis, Phoma, Phomopsis, Sporomiella, among others. Since a small fraction of fungi is able to grow in culture, this study investigated the diversity of fungi associated with leaves of Acanthus ilicifolius var. xiamenensis using both isolation and metabarcoding approaches. A total of 203 isolates were cultured from surface-sterilized leaves, representing 47 different fungal species: 30 species from the winter samples (104 isolates), and 26 species from the summer samples (99 isolates). Ascomycota was dominant in both types of leaf samples, while Basidiomycota was isolated only from the summer samples. Drechslera dematioidea (10.58%, percentage of occurrence), Colletotrichum sp. 3 (7.69%) and Alternaria sp. (7.69%) were dominant in the winter samples; Fusarium oxysporum (13.13%), Diaporthe endophytica (10.10%) and Colletotrichum sp. 1 (9.09%) in the summer samples. Overall, Corynespora cassiicola (6.90%), F. oxysporum (6.40%) and Guignardia sp. (6.40%) had the highest overall percentage of occurrence. In the metabarcoding analysis, a total of 111 operational taxonomic units (OTUs) were identified from 17 leaf samples: 96 OTUs from the winter and 70 OTUs from the summer samples. Sequences belonging to Ascomycota and Basidiomycota were detected in both samples but the former phylum was dominant over the latter. Based on read abundance, taxa having the highest percentage of occurrence included Alternaria sp. (3.46%), Cladosporium delicatulum (2.56%) and Pyrenochaetopsis leptospora (1.41%) in the winter leaves, and Aureobasidium sp. (10.72%), Cladosporium sp. (7.90%), C. delicatulum (3.45%) and Hortaea werneckii (3.21%) in the summer leaves. These latter four species also had the highest overall percentage of occurrence. Combining the results from both methods, a high diversity of fungi (at least 110 species) was found associated with leaves of A. ilicifolius var. xiamenensis. Many of the fungi identified were plant pathogens and may eventually cause diseases in the host. creator: Wei-Chiung Chi creator: Weiling Chen creator: Chih-Chiao He creator: Sheng-Yu Guo creator: Hyo-Jung Cha creator: Ling Ming Tsang creator: Tsz Wai Ho creator: Ka-Lai Pang uri: https://doi.org/10.7717/peerj.7293 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chi et al. title: Soil carbon mineralization in response to nitrogen enrichment in surface and subsurface layers in two land use types link: https://peerj.com/articles/7130 last-modified: 2019-07-08 description: Atmospheric nitrogen (N) deposition increases N availability in soils, with consequences affecting the decomposition of soil carbon (C). The impacts of increasing N availability on surface soil C dynamics are well studied. However, subsurface soils have been paid less attention although more than 50% soil C stock is present below this depth (below 20 cm). This study was designed to investigate the response of surface (0–20 cm) and subsurface (20–40 cm and 40–60 cm) C dynamics to 0 (0 kg N ha−1), low (70 kg N ha−1) and high (120 kg N ha−1) levels of N enrichment. The soils were sampled from a cropland and a grass lawn and incubated at 25 °C and 60% water holding capacity for 45 days. Results showed that N enrichment significantly decreased soil C mineralization (Rs) in all the three soil layers in the two studied sites (p < 0.05). The mineralization per unit soil organic carbon (SOC) increased with profile depth in both soils, indicating the higher decomposability of soil C down the soil profile. Moreover, high N level exhibited stronger suppression effect on Rs than low N level. Rs was significantly and positively correlated with microbial biomass carbon explaining 80% of variation in Rs. Overall; these results suggest that N enrichment may increase C sequestration both in surface and subsurface layers, by reducing C loss through mineralization. creator: Nazia Perveen creator: Mariam Ayub creator: Tanvir Shahzad creator: Muhammad Rashid Siddiq creator: Muhammad Sohail Memon creator: Sébastien Barot creator: Hamid Saeed creator: Ming Xu uri: https://doi.org/10.7717/peerj.7130 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Perveen et al. title: Transcription factors involved in abiotic stress responses in Maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era link: https://peerj.com/articles/7211 last-modified: 2019-07-08 description: BackgroundMaize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in various regions around the world, and recently, this has become a constant threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activities of transcription factors (TFs), which are families of genes coding for specific TF proteins. TF target genes form a regulon that is involved in the repression/activation of genes associated with abiotic stress responses. Therefore, it is of utmost importance to have a systematic study on each TF family, the downstream target genes they regulate, and the specific TF genes involved in multiple abiotic stress responses in maize and other staple crops.MethodIn this review, the main TF families, the specific TF genes and their regulons that are involved in abiotic stress regulation will be briefly discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from different plants like rice, Arabidopsis, wheat, and barley will be used.ResultsWe have described in detail the main TF families in maize that take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning, and RNA-Seq.ConclusionIn conclusion, it is expected that all the information provided in this review will in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars. creator: Roy Njoroge Kimotho creator: Elamin Hafiz Baillo creator: Zhengbin Zhang uri: https://doi.org/10.7717/peerj.7211 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kimotho et al. title: Behavioral adjustments to prior predation experience and food deprivation of a common cyprinid fish species vary between singletons and a group link: https://peerj.com/articles/7236 last-modified: 2019-07-08 description: Fish often undergo predation stress and food shortages in nature, and living in groups may provide the ecological benefits of decreased predator risk but the costs of increased food competition. The main aim of the present study was to test whether the behavioral response of qingbo (Spinibarbus sinensis) to predators and/or starvation differed between a singleton and a group. We measured the locomotor activity and distance to a predator and/or food item of prior predator-experienced, starved, double-treated and control qingbo; the qingbo were tested both as singletons and in a group (five individuals). Fish from all groups showed increased activity when tested collectively compared to individually. The predator-experienced fish showed decreased locomotor activity to predators as an antipredator strategy when tested as singletons; however, increased locomotor activity occurred when tested in a group, which might be partially due to the decreased predator risk when living in a group and thus higher levels of boldness. As expected, starvation elicited increased activity indicating increased foraging willingness when tested in a group; however, the difference between starved and normal-fed fish was no longer significant when they were tested as singletons, possibly due to the increased predation risk and decreased food competition when living individually and higher behavioral variation among individual fish than among those in a shoal. Compared with the control fish, the double-treated fish showed no difference in activity when tested both individually and collectively (except a slower speed when tested in a group). The reason for the results from the singletons might be an offset of the effect of predator exposure and starvation. The reason for this difference in the group might be due to the impaired body condition indicated by a slower swimming speed as a consequence of severe stress. The present study demonstrated that behavioral adjustment was closely related to the size of the group, which might be due to differences in the predation risk and food competition. creator: Ya Wang creator: Shi-Jian Fu creator: Cheng Fu uri: https://doi.org/10.7717/peerj.7236 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Prognostic value of mean platelet volume/platelet count ratio in patients with resectable esophageal squamous cell carcinoma: a retrospective study link: https://peerj.com/articles/7246 last-modified: 2019-07-08 description: BackgroundMean platelet volume (MPV) to platelet count (PC) ratio (MPV/PC) is a useful indicator in several cancers. However, the role for MPV/PC ratio in esophageal squamous cell carcinoma (ESCC) is still controversial.MethodsA retrospective study was conducted including 277 resectable ESCC patients. The optimal cut-off values were calculated by the X-tile program. The receiver operator characteristic (ROC) curves were also created to show the candidate cut-off points. The comparisons between the X-tile plot and ROC curve were performed. The Kaplan-Meier method was utilized to analyze the cancer-specific survival (CSS). Prognostic factors for CSS were calculated with Cox regression univariate and multivariate analyses.ResultsAccording to the X-tile program, the cut-off values for MPV, PC and MPV/PC ratio were 8.5 (fl), 200 (giga/l) and 0.04, respectively. However, the cut-off values for MPV, PC and MPV/PC ratio by the ROC curves were 8.25 (fl), 243.5 (giga/l) and 0.0410, respectively. The cut-off values were similar between the X-tile and ROC curve. A low MPV/PC ratio level (≤0.04) was associated with poor CSS (22.4% vs. 43.1%, P < 0.001). In multivariate analyses, we found that MPV/PC ratio was an independent predictor for CSS (P < 0.001). When we set the cut-off point using ROC curve, the MPV/PC ratio was still an independent predictor for CSS (P < 0.001).ConclusionThe MPV/PC ratio is a useful predictive indicator in patients with ESCC. creator: Ji-Feng Feng creator: Chen Sheng creator: Qiang Zhao creator: Pengcheng Chen uri: https://doi.org/10.7717/peerj.7246 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Feng et al. title: A proposed update for the classification and description of bacterial lipolytic enzymes link: https://peerj.com/articles/7249 last-modified: 2019-07-08 description: Bacterial lipolytic enzymes represent an important class of proteins: they provide their host species with access to additional resources and have multiple applications within the biotechnology sector. Since the formalisation of lipolytic enzymes into families and subfamilies, advances in molecular biology have led to the discovery of lipolytic enzymes unable to be classified via the existing system. Utilising sequence-based comparison methods, we have integrated these novel families within the classification system so that it now consists of 35 families and 11 true lipase subfamilies. Representative sequences for each family and subfamily have been defined as well as methodology for accurate comparison of novel sequences against the reference proteins, facilitating the future assignment of novel proteins. Both the code and protein sequences required for integration of additional families are available at: https://github.com/thh32/Lipase_reclassification. creator: Thomas C.A. Hitch creator: Thomas Clavel uri: https://doi.org/10.7717/peerj.7249 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hitch et al. title: An integrative approach to the anatomy of Syllis gracilis Grube, 1840 (Annelida) using micro-computed X-ray tomography link: https://peerj.com/articles/7251 last-modified: 2019-07-08 description: BackgroundThe overall anatomy of the genus Syllis (Annelida: Syllidae) has been largely studied; however, an integrative approach considering different anatomical techniques has never been considered. Here, we use micro-computed X-ray tomography (micro-CT) to examine the internal anatomy of Syllis gracilis Grube, 1840, along with other widely available techniques.MethodsWe studied the anatomy of the marine annelid S. gracilis through an integrative approach, including micro-CT along with stereo and light compound microscopy (STM, LCM), scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) and histological sectioning (HIS). In this manner, we evaluated the applicability of micro-CT for the examination of annelid anatomy by testing whether the images obtained make it possible to visualize the main body structures, in comparison with other current techniques, of the various elements of its internal anatomy.ResultsOverall external and internal body elements are clearly shown by the integrative use of all techniques, thus overcoming the limitations of each when studied separately.Any given method shows disparate results, depending on the body part considered. For instance, micro-CT provided good images of the external anatomy, including relevant characters such as the shape, length and number of articles of dorsal parapodial cirri. However, it is especially useful for the examination of internal anatomy, thus allowing for 3D visualization of the natural spatial arrangement of the different organs. The features best visualized are those of higher tissue density (i.e., body musculature, anterior parts of the digestive tract), particularly in 3D images of unstained specimens, whereas less electrodense tissues (i.e., the peritoneal lining of septa and nervous system) are less clearly visualized. The use of iodine stain with micro-CT has shown advantages against non-staining for the adequate observation of delicate elements of low density, such as the segmental organs, the connective between the ganglia, the ventral nerve cord and segmental nerves.DiscussionMain external anatomical elements of S. gracilis are well shown with micro-CT, but images show lesser optical resolution and contrast when compared to micrographs provided by SEM and CLSM, especially for fine structural features of chaetae. Comparison of micro-CT and HIS images revealed the utility and reliability of the former to show the presence, shape and spatial disposition of most internal body organs; the resolution of micro-CT images at a cellular level is, however, much lower than that of HIS, which makes both techniques complementary. creator: Julio Parapar creator: Carlos Caramelo creator: María Candás creator: Xela Cunha-Veira creator: Juan Moreira uri: https://doi.org/10.7717/peerj.7251 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Parapar et al. title: Different neurocognitive patterns of conflict control in Tibetans living above and below 4,000 m link: https://peerj.com/articles/7269 last-modified: 2019-07-08 description: BackgroundThe existence of a particular threshold of hypoxia severity, beyond which neuropsychological functioning is compromised, is unclear. We investigated the neurocognitive profile related to conflict control in healthy young Tibetans born and living at three different altitudes (2,700 m, 3,700 m, and 4,500 m) in Tibet to investigate the existence of this threshold.MethodsUsing event-related potentials (ERPs), the conflict control functions of individuals in the three altitude groups were investigated by means of a flanker task, using congruent and incongruent stimuli. The data were analyzed using mixed-model analyses of variance.ResultsAlthough effect of altitude was not significant at a behavioral level (p > 0.05), the ERPs showed cognitive conflict modulation. The N2 difference wave (for incongruent minus congruent conditions) was smaller in the 4,500-m group than in the groups living below 4,000 m (p < 0.05). The study’s findings suggest that the influence of high altitude in the conflict monitoring stage becomes significant above 4,000 m. Thus, the altitude threshold for impairment of cognition may be 4,000 m. creator: Hailin Ma creator: Buxin Han creator: Yan Wang uri: https://doi.org/10.7717/peerj.7269 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Three-dimensional printing with biomaterials in craniofacial and dental tissue engineering link: https://peerj.com/articles/7271 last-modified: 2019-07-08 description: With the development of technology, tissue engineering (TE) has been widely applied in the medical field. In recent years, due to its accuracy and the demands of solid freeform fabrication in TE, three-dimensional printing, also known as additive manufacturing (AM), has been applied for biological scaffold fabrication in craniofacial and dental regeneration. In this review, we have compared several types of AM techniques and summarized their advantages and limitations. The range of printable materials used in craniofacial and dental tissue includes all the biomaterials. Thus, basic and clinical studies were discussed in this review to present the application of AM techniques in craniofacial and dental tissue and their advances during these years, which might provide information for further AM studies in craniofacial and dental TE. creator: Wen Liao creator: Lin Xu creator: Kaijuan Wangrao creator: Yu Du creator: Qiuchan Xiong creator: Yang Yao uri: https://doi.org/10.7717/peerj.7271 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liao et al. title: Factors encouraging mobile instant messaging service use in medical education link: https://peerj.com/articles/7275 last-modified: 2019-07-08 description: BackgroundMobile instant messaging services are being increasingly used for educational purposes, but their effectiveness in medical education is not well known. We assessed whether students’ use of Kakao Talk (a mobile instant messaging service) during the early period of a week of clinical education influenced its use for academic purposes during a later period of the same week.MethodsThe online communication records of 151 third-year medical students (in 39 clinical education groups) who used Kakao Talk during clinical education were reviewed. The 39 groups were categorized as low, middle, or high according to the number of total chats (on all subjects, not just academic) per student over five days. The relationship between the number of total chats during the first two days and the number of academic chats during the last three days (of five-day chatroom weeks) was analyzed.ResultsThe number of total and academic chats over all five days, the first two days, and the last three days was highest in groups with the highest number of total chats per student. Similarly, the highest number of students posting total and academic chats was found in these groups. In addition, the number of academic chats per student and the frequency of questions raised by students were also highest in these groups. During the last three days, the number of students posting total chats was lower than that during the first two days, and the number of academic chats per student posting academic chats was higher. The number of total chats on the first or second day positively correlated with the maximum value of academic chats on the third to fifth days.ConclusionHigh frequency mobile instant messaging use early on in clinical education might encourage its use for academic purposes during later periods. creator: Kidong Kim creator: Banghyun Lee creator: Youngmi Park creator: Eun Young Jung creator: Seul Ki Kim creator: Dong Hoon Suh creator: Bo Ram Choi uri: https://doi.org/10.7717/peerj.7275 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kim et al. title: Factors affecting relative abundance of low-mobility fishing resources: spiny lobster in the Galapagos Marine Reserve link: https://peerj.com/articles/7278 last-modified: 2019-07-08 description: Management of low-mobility or benthic fisheries is a difficult task because variation in the spatial distribution and population dynamics of the resources make the monitoring and assessment of these fisheries challenging. We assumed that environmental, spatial, and temporal factors can contribute to the variability of the relative abundance of such species; we used Generalized Additive Models for Location Scale and Shape (GAMLSS) to test this hypothesis using as a case study the lobster fishery (targeting two species) in the Galapagos Marine Reserve, Ecuador. We gathered data on each of the two species of lobster on a monthly basis over seven years, including: (a) onboard observers’ records of catch data, fishing effort, and ground location by trip, and (b) data from interviews undertaken with fishers at their arrival to port, recording the same type of information as obtained from onboard observers. We use this information to analyze the effect of the measured variables and to standardize the Catch per Unit Effort (CPUE) in each case, using the GAMLSS. For both species, the temperature, region, fishing schedule, month, distance, and the monitoring system were significant variables of the selected models associated with the variability of the catch rate. For Panulirus penicillatus, CPUE was higher at night than during the day, and for Panulirus gracilis it was higher during the day. Increased temperature resulted in a decrease of CPUE values. It was evident that temporal, spatial scales and monitoring system can influence the variability of this indicator. We contend that the identification of drivers of change of relative abundance in low-mobility species can help to support the development of monitoring and assessment programs for this type of fisheries. creator: Juan Carlos Murillo-Posada creator: Silvia Salas creator: Iván Velázquez-Abunader uri: https://doi.org/10.7717/peerj.7278 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Murillo-Posada et al. title: Evolutionary couplings detect side-chain interactions link: https://peerj.com/articles/7280 last-modified: 2019-07-08 description: Patterns of amino acid covariation in large protein sequence alignments can inform the prediction of de novo protein structures, binding interfaces, and mutational effects. While algorithms that detect these so-called evolutionary couplings between residues have proven useful for practical applications, less is known about how and why these methods perform so well, and what insights into biological processes can be gained from their application. Evolutionary coupling algorithms are commonly benchmarked by comparison to true structural contacts derived from solved protein structures. However, the methods used to determine true structural contacts are not standardized and different definitions of structural contacts may have important consequences for interpreting the results from evolutionary coupling analyses and understanding their overall utility. Here, we show that evolutionary coupling analyses are significantly more likely to identify structural contacts between side-chain atoms than between backbone atoms. We use both simulations and empirical analyses to highlight that purely backbone-based definitions of true residue–residue contacts (i.e., based on the distance between Cα atoms) may underestimate the accuracy of evolutionary coupling algorithms by as much as 40% and that a commonly used reference point (Cβ atoms) underestimates the accuracy by 10–15%. These findings show that co-evolutionary outcomes differ according to which atoms participate in residue–residue interactions and suggest that accounting for different interaction types may lead to further improvements to contact-prediction methods. creator: Adam J. Hockenberry creator: Claus O. Wilke uri: https://doi.org/10.7717/peerj.7280 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hockenberry and Wilke title: Temperature change in pulp chamber of primary teeth during curing of coloured compomers: an in vitro study using pulpal blood microcirculation model link: https://peerj.com/articles/7284 last-modified: 2019-07-08 description: IntroductionAn increase in the temperature of the pulp chamber occurs during polymerisation of all types of light-curing resin-containing restorative materials, due to both the exothermic reaction of the material and the energy absorbed during the curing process. Increase in temperature of the pulp chamber of primary teeth during the curing process or the thermal conductivity properties of coloured compomers (CCs) have not yet been investigated in detail. The aim of the present study was to investigate the increase in pulpal temperature in primary teeth during curing of CCs.Materials and MethodsA Class-II cavity was prepared on the extracted primary mandibular second molar. Pulpal microcirculation of the tooth was performed using an experimental mechanism. The study included 15 groups and 10 experiments in each. Seven different CCs: pink, blue, gold, silver, orange, lemon, green, respectively from two different manufacturers (Groups 1–7: Twinky Star; VOCO, Cuxhaven, Germany. Groups 8–14: Nova Rainbow; IMICRYL, Konya, Turkey.) and a tooth-CC (Group 15: Dyract XP; DENTSPLY, Weybridge, UK.) were applied in prepared cavity. In all groups the compomers were light cured for 40 s. Intrapulpal temperature changes (Δt) in 20th and 40th second were recorded. In Group-15 the Δt values in 10th second were also recorded as per the manufacturer’s instructions. The Kruskal–Wallis test and the Mann–Whitney-U test were used for statistical analyses.ResultsAt the end of 40-s irradiation time, the orange, lemon and green colours of Nova Rainbow resulted in significantly lower Δt values than the same colours of Twinky Star (p = 0.0001), and silver, blue, lemon, green, orange, and pink CCs of Nova Rainbow and the blue and silver shades of Twinky Star demonstrated lower Δt values than the reported critical temperature increase (5.5 °C).ConclusionAn increase in the irradiation time consequently led to an increase in the intrapulpal temperature. Therefore, manufacturers should focus on production of new CCs with shorter polimerization time. creator: Ceylan Çağıl Ertuğrul creator: Ihsan Furkan Ertuğrul uri: https://doi.org/10.7717/peerj.7284 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ertuğrul and Ertuğrul title: Structural and evolutionary characteristics of dynamin-related GTPase OPA1 link: https://peerj.com/articles/7285 last-modified: 2019-07-08 description: OPA1 is a dynamin-related GTPase that controls mitochondrial fusion, cristae remodeling, energetics and mtDNA maintenance. However, the molecular architecture of OPA1 is poorly understood. Here we modeled the structure of human OPA1 by the threading approach. We found that the C-terminal region of the OPA1 protein had multiple functional domains, while the N-terminal region was rich in alpha helices and did not include specific domains. For the short soluble forms of OPA1, we observed that there were obvious hydrophobic regions near the two cleavage sites and the N-terminal was positively charged after cleavage. The blue native analysis revealed that the protein could form stable homodimers. In addition, the evolutionary conservation of the C-terminal region, where most of the known mutated disease-related sites were located, was significantly higher than that of the N-terminal region. These findings provided new insights into the structure and biochemical function of OPA1. creator: Dandan Li creator: Jinlan Wang creator: Zichen Jin creator: Zheng Zhang uri: https://doi.org/10.7717/peerj.7285 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: The effects of gluteal squeezes compared to bilateral bridges on gluteal strength, power, endurance, and girth link: https://peerj.com/articles/7287 last-modified: 2019-07-08 description: BackgroundHip extension weakness is correlated with low back, hip, and knee pathology. Isometric gluteal squeezes have been shown to elicit high electromyographic gluteal activity. However, there is little research regarding the specific effects of isometric gluteal squeezes on hip strength and functional outcomes. The purpose of this study was to identify the effects of gluteal squeezes on hip extension strength, vertical jump, broad jump, single-leg bridge endurance, and gluteal girth compared to bilateral gluteal bridging.MethodsA total of 32 healthy university students (mean age 23.28 ± 2.15 years) were randomly assigned to perform either gluteal squeezes or bilateral bridges daily. Subjects were tested at baseline and after 8 weeks of training. Subjects’ hip extension strength, vertical jump, broad jump, single-leg bridge endurance, and gluteal girth were tested.ResultsNo statistically significant differences were found between the bridge and squeeze groups after 8 weeks of training. Both groups significantly improved hip extension strength bilaterally (p = 0.000–0.011). The squeeze group significantly increased gluteal girth at the level of the greater trochanter (p = 0.007), but no significant girth increase was seen in the bridge group (p = 0.742). Although increases were seen in both groups for the endurance and jump tasks, no statistically significant changes occurred for those outcomes. All outcome measurements demonstrated high reliability (ICC = 0.93–0.99).ConclusionGluteal squeezes were as effective as bilateral bridges for increasing hip extension strength. Gluteal squeezes also significantly increased girth at the level of the greater trochanter. These results provide clinical and aesthetic reasons to perform gluteal squeezes. creator: Bryan J. Lehecka creator: Jessica Turley creator: Aaron Stapleton creator: Kyle Waits creator: John Zirkle uri: https://doi.org/10.7717/peerj.7287 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lehecka et al. title: Patterns of richness of freshwater mollusks from Chile: predictions of its distribution based on null models link: https://peerj.com/articles/7097 last-modified: 2019-07-05 description: The freshwater mussels from Chile are characterized by a high percentage of endemism and a fragmented latitudinal diversity, which has been attributed to the features and geomorphological history sculpted by the hydrographic basins. In this work, a set of hypothesis under a macroecological approach is addressed, with the aim to explore environmental, topographic and hydrological factors that define the latitudinal distribution of this mussel group. In order to achieve this goal, Rapoport’s rule, geometrics limits and co-ocurrence were evaluated. In addition, we analyze the source and sink hypotheses through the nested analysis. We observed a noticeable mid-domain effect (MDE), where a major richness than expected was randomly observed between 40 and 41°S. The results revealed that the distribution pattern was not concordant with Rapoport’s rule (r = 0.123; p = 0.128). Regarding to historical dynamic of the distribution, the results show a significant nestedness pattern, suggesting a source-sink dynamic, that is, poorer communities are a subset of richer communities in species. According to the co-occurrence analysis, an aggregate pattern existed, suggesting potential regulatory mechanisms. The specific richness pattern is explained by the variable seasonality of the temperature with a variance percentage explained of 35%. The full model indicated that variables which characterize the heterogeneity of habitat (i.e. range, Shannon), water availability (i.e., precipitation, density of water bodies) and topography (i.e., altitude area available) jointly explain 40% of the variability of the observed richness. This study shows that the geographical distribution of mollusc richness is mainly explained by mainly climatic and topographical environmental components, as well as by the source-sink dynamics. creator: Carmen Gloria Fuentealba Jara creator: Reinaldo Rivera creator: Cristian Franco creator: Ricardo Figueroa creator: Victor Faúndez uri: https://doi.org/10.7717/peerj.7097 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fuentealba Jara et al. title: Bats from different foraging guilds prey upon the pine processionary moth link: https://peerj.com/articles/7169 last-modified: 2019-07-05 description: Outbreaks of the processionary moth Thaumetopoea pityocampa (Denis & Schiffermüller, 1775), a forest pest from the Palearctic, are thought to induce a behavioral response of bats, but up to now the moth has been seldom identified as bats’ prey. Studies on bat diets suggest moths with cyclical outbreaks attract a wide array of bat species from different foraging guilds. We test whether bats feed upon T. pityocampa in the Iberian Peninsula irrespective of the predator’s ecological and morphological features. We found that seven out of ten bat species belonging to different foraging guilds contained T. pityocampa DNA in their faeces and no difference was found in the foraging frequency among foraging guilds. A different size of the typical prey or the lack of fondness for moths can explain the absence of the pest in some bat species. Moreover, the intraspecific foraging frequency of T. pityocampa also changed with the sampling site likely representing differential availability of the moth. Lack of information on flight and dispersal behavior or the tympanate nature of the adult moth complicates understanding how different foraging guilds of bats prey upon the same prey. Our data suggests that T. pityocampa is a remarkable food source for many thousands of individual bats in the study area and we anticipate that more bats besides the species studied here are consuming this moth. creator: Inazio Garin creator: Joxerra Aihartza creator: Urtzi Goiti creator: Aitor Arrizabalaga-Escudero creator: Jesús Nogueras creator: Carlos Ibáñez uri: https://doi.org/10.7717/peerj.7169 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Garin et al. title: Curcumin ameliorates atrophy of seminal vesicle via reduction of oxidative stress in castrated mice link: https://peerj.com/articles/7192 last-modified: 2019-07-05 description: BackgroundThe growth and function of seminal vesicle are dependent on androgen. This study was conducted to investigate the role of oxidative stress in castration-induced seminal vesicle atrophy and to explore the effects of curcumin, an antioxidant extracted from rhizome of turmeric, on seminal vesicle of castrated mice.MethodsC57BL/6J mice were randomly divided into three groups: control, castration, and castration with curcumin (n = 10 for each group). After surgical castration, mice in the curcumin treatment group received intragastric administration of curcumin at 100 mg/kg body weight for 4 weeks, whereas mice in the other two groups were treated with olive oil. After that, the body weight, seminal vesicle weight and serum testosterone of mice were measured. Apoptosis and oxidative stress levels in seminal vesicle were also determined.ResultsAfter castration, both the weight and size of seminal vesicle decreased dramatically. The expression of three NADPH oxidase (NOX) subtypes: NOX1, NOX2 and NOX4, increased in seminal vesicle of castrated mice, resulting in high level oxidative stress. The ratio of Bax to Bcl-2 was also elevated after castration, accompanied by enhanced caspase3 activity. Additionally, castration increased the number of apoptotic cells in seminal vesicle. Curcumin treatment could inhibit the expression of NOX1, NOX2 and NOX4, decreasing oxidative stress and apoptosis. The atrophy of seminal vesicle caused by castration was ameliorated by curcumin.ConclusionCastration could cause atrophy of seminal vesicle probably via inducing oxidative stress. Curcumin treatment could reduce the oxidative stress in seminal vesicle by decreasing the expression of NOX1, NOX2 and NOX4, thereby ameliorating apoptosis and atrophy of seminal vesicle. Oxidative stress might play a role in castration-induced seminal vesicle atrophy. creator: Rui Li creator: Hao Li creator: Ke Rao creator: Kang Liu creator: Yan Zhang creator: Xiaming Liu creator: Tao Wang creator: Shaogang Wang creator: Zhuo Liu creator: Jihong Liu uri: https://doi.org/10.7717/peerj.7192 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori link: https://peerj.com/articles/7222 last-modified: 2019-07-05 description: Cys2-His2 zinc finger (C2H2-ZF) proteins comprise the largest class of putative eukaryotic transcription factors. The zinc finger motif array is highly divergent, indicating that most proteins will have distinctive binding sites and perform different functions. However, the binding sites and functions of the majority of C2H2-ZF proteins remain unknown. In this study, we identified 327 C2H2-ZF protein genes in the silkworm, 290 in the monarch butterfly, 243 in the fruit fly, 107 in elegans, 673 in mouse, and 1,082 in human. The C2H2-ZF protein genes of the silkworm were classified into three main grouping clades according to a phylogenetic classification, and 312 of these genes could be mapped onto 27 chromosomes. Most silkworm C2H2-ZF protein genes exhibited specific expression in larval tissues. Furthermore, several C2H2-ZF protein genes had sex-specific expression during metamorphosis. In addition, we found that some C2H2-ZF protein genes are involved in metamorphosis and female reproduction by using expression clustering and gene annotation analysis. Among them, five genes were selected, BGIBMGA002091 (CTCF), BGIBMGA006492 (fru), BGIBMGA006230 (wor), BGIBMGA004640 (lola), and BIGBMGA004569, for quantitative real-time PCR analysis from larvae to adult ovaries. The results showed that the five genes had different expression patterns in ovaries, among which BGIBMGA002091 (CTCF) gene expression level was the highest, and its expression level increased rapidly in late pupae and adult stages. These findings provide a basis for further investigation of the functions of C2H2-ZF protein genes in the silkworm, and the results offer clues for further research into the development of metamorphosis and female reproduction in the silkworm. creator: SongYuan Wu creator: Xiaoling Tong creator: ChunLin Li creator: KunPeng Lu creator: Duan Tan creator: Hai Hu creator: Huai Liu creator: FangYin Dai uri: https://doi.org/10.7717/peerj.7222 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wu et al. title: An artificial-vision- and statistical-learning-based method for studying the biodegradation of type I collagen scaffolds in bone regeneration systems link: https://peerj.com/articles/7233 last-modified: 2019-07-05 description: This work proposes a method based on image analysis and machine and statistical learning to model and estimate osteocyte growth (in type I collagen scaffolds for bone regeneration systems) and the collagen degradation degree due to cellular growth. To achieve these aims, the mass of collagen -subjected to the action of osteocyte growth and differentiation from stem cells- was measured on 3 days during each of 2 months, under conditions simulating a tissue in the human body. In addition, optical microscopy was applied to obtain information about cellular growth, cellular differentiation, and collagen degradation. Our first contribution consists of the application of a supervised classification random forest algorithm to image texture features (the structure tensor and entropy) for estimating the different regions of interest in an image obtained by optical microscopy: the extracellular matrix, collagen, and image background, and nuclei. Then, extracellular-matrix and collagen regions of interest were determined by the extraction of features related to the progression of the cellular growth and collagen degradation (e.g., mean area of objects and the mode of an intensity histogram). Finally, these critical features were statistically modeled depending on time via nonparametric and parametric linear and nonlinear models such as those based on logistic functions. Namely, the parametric logistic mixture models provided a way to identify and model the degradation due to biological activity by estimating the corresponding proportion of mass loss. The relation between osteocyte growth and differentiation from stem cells, on the one hand, and collagen degradation, on the other hand, was determined too and modeled through analysis of image objects’ circularity and area, in addition to collagen mass loss. This set of imaging techniques, machine learning procedures, and statistical tools allowed us to characterize and parameterize type I collagen biodegradation when collagen acts as a scaffold in bone regeneration tasks. Namely, the parametric logistic mixture models provided a way to identify and model the degradation due to biological activity and thus to estimate the corresponding proportion of mass loss. Moreover, the proposed methodology can help to estimate the degradation degree of scaffolds from the information obtained by optical microscopy. creator: Yaroslava Robles-Bykbaev creator: Salvador Naya creator: Silvia Díaz-Prado creator: Daniel Calle-López creator: Vladimir Robles-Bykbaev creator: Luis Garzón creator: Clara Sanjurjo-Rodríguez creator: Javier Tarrío-Saavedra uri: https://doi.org/10.7717/peerj.7233 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Robles-Bykbaev et al. title: Modeling the impacts of agricultural best management practices on runoff, sediment, and crop yield in an agriculture-pasture intensive watershed link: https://peerj.com/articles/7093 last-modified: 2019-07-04 description: Best management practices (BMPs) are commonly used to reduce sediment loadings. In this study, we modeled the Fort Cobb Reservoir watershed located in southwestern Oklahoma, USA using the Soil and Water Assessment Tool (SWAT) and evaluated the impacts of five agricultural BMP scenarios on surface runoff, sediment yield, and crop yield. The hydrological model, with 43 sub-basins and 15,217 hydrological response units, was calibrated (1991–2000) and validated (2001–2010) against the monthly observations of streamflow, sediment grab samples, and crop-yields. The coefficient of determination (R2), Nash-Sutcliffe efficiency (NS) and percentage bias (PB) were used to determine model performance with satisfactory values of R2 (0.64 and 0.79) and NS (0.61 and 0.62) in the calibration and validation period respectively for streamflow. We found that contouring practice reduced surface runoff by more than 18% in both conservation tillage and no-till practices for all crops used in this modeling study. In addition, contour farming with either conservation tillage or no-till practice reduced sediment yield by almost half. Compared to the conservation tillage practice, no-till practice decreased sediment yield by 25.3% and 9.0% for cotton and grain sorghum, respectively. Using wheat as cover crop for grain sorghum generated the lowest runoff followed by its rotation with canola and cotton regardless of contouring. Converting all the crops in the watershed into Bermuda grass resulted in significant reduction in sediment yield (72.5–96.3%) and surface runoff (6.8–38.5%). The model can be used to provide useful information for stakeholders to prioritize ecologically sound and feasible BMPs at fields that are capable of reducing sediment yield while increasing crop yield. creator: Solmaz Rasoulzadeh Gharibdousti creator: Gehendra Kharel creator: Arthur Stoecker uri: https://doi.org/10.7717/peerj.7093 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rasoulzadeh Gharibdousti et al. title: Spread of the non-native anemone Anemonia alicemartinae Häussermann & Försterra, 2001 along the Humboldt-current large marine ecosystem: an ecological niche model approach link: https://peerj.com/articles/7156 last-modified: 2019-07-04 description: The geographical expansion of invasive species depends mainly on its dispersal potential, and the abiotic and biotic factors affecting it. Knowing the invasive dynamic of non-native species, as well as its behavior at different natural or anthropogenic scenarios, is fundamental for planning conservation management policies and control plans. The invasive sea anemone Anemonia alicemartinae in habits from the north (18°S) to the south-central (36°S) coast of Chile and its distribution range has expanded by approximately 1,928 km in the last 50 years. Previous works have proposed that human-mediated southward transport associated with regional-scale maritime activities could explain its rapid spread. To evaluate this hypothesis, we used ecological niche models (ENM) to evaluate the potential colonization of the southernmost area of South America. Additionally, we conducted a post hoc analysis to evaluate the relationship between the prediction of the ENM and human activity measured as the number of landings of ships in ports. The models were built based on presence records of A. alicemartinae, and oceanographic variables. Results showed that sea surface salinity and annual sea surface temperature (variance) are the best predictor variables to explain the distribution of A. alicemartinae. There was a positive and significant relationship between the geographical distribution of the sea anemone predicted by the ENM and the number of landings, as a proxy of anthropogenic activity. The most susceptible areas to invasion were those that showed the highest variability in both oceanographic predictors. These areas included the Biobío region, Chiloé´s inland sea, Aysén, and Chacabuco regions, which together comprise two biogeographical provinces. These results sustain the proposed hypothesis and, overall, the results suggest that along with the characteristics of the life history of A. alicemartinae, oceanographic conditions and maritime transport as vector contribute to the southern range expansion of this invasive cryptogenic species in the Humboldt-current large marine ecosystem. creator: Javier Pinochet creator: Reinaldo Rivera creator: Paula E. Neill creator: Antonio Brante creator: Cristián E. Hernández uri: https://doi.org/10.7717/peerj.7156 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Pinochet et al. title: A new species of the Asian music frog genus Nidirana (Amphibia, Anura, Ranidae) from Southwestern China link: https://peerj.com/articles/7157 last-modified: 2019-07-04 description: The Asian music frog genus Nidirana is widely distributed in East and Southeastern Asia. Systematic profiles of the group remain on debate, and cryptic species are expected especially in the species with wide distributional range. Here, we describe a new species of the genus from Southwestern China. Phylogenetic analyses based on mitochondrial DNA and nuclear DNA supported the new species as an independent clade nested into the Nidirana clade and sister to N. hainanensis. Morphologically, the new species could be distinguished from its congeners by a combination of the following characters: a large body size in males (SVL > 49 mm); the presence of lateroventral grooves both on fingers and toes; relative finger lengths: II < IV < I < III; tibiotarsal articulation reaching the level between eye and nostril when leg stretched forward; a pair of subgular internal vocal sacs at corners of throat in males; nuptial pad present on the inner side of base of fingers I and II in males in breading season; webbing formula: I 2 –21/3 II 2 –22/3 III 31/2 –32/3 IV 32/3 –3V. The findings provided a better knowledge on phylogenetic assignments of the genus Nidirana, and indicated future deeper investigations necessarily for exploring systematic settings of the group. creator: Shize Li creator: Gang Wei creator: Ning Xu creator: Jianguo Cui creator: Liang Fei creator: Jianping Jiang creator: Jing Liu creator: Bin Wang uri: https://doi.org/10.7717/peerj.7157 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Seasonal denning behavior and population dynamics of the late Pleistocene peccary Platygonus compressus (Artiodactyla: Tayassuidae) from Bat Cave, Missouri link: https://peerj.com/articles/7161 last-modified: 2019-07-04 description: The late Pleistocene faunal assemblage from Bat Cave, central Ozarks, Missouri provides an opportunity to assess specific aspects of behavior, ecology, and ontogeny of the Rancholabrean species Platygonus compressus. All identifiable elements referable to this taxon were catalogued and examined, and a minimum number of individuals of 73 was determined for the sample. Evidence of seasonal behavioral patterns are reported for the first time in a fossil peccary. Maturation of individuals was assessed using the tooth eruption sequence and occlusal wear patterns for all tooth-bearing mandibular elements and isolated lower dentition. Approximate ages were established through comparison with the extant collared peccary. The presence of distinct, developmentally non-overlapping age groups suggests that P. compressus was seasonally present at the Bat Cave locality, with the cave functioning as seasonal shelter in which individuals would occasionally die. The study also suggests the peccaries engaged in synchronous, seasonal breeding behaviors. Demographic assessment of the Bat Cave peccary population suggests that younger individuals formed the bulk of the population at a given time with progressively older individuals becoming scarcer until the age of about 10 years, which matches the typical demographic patterns and life expectancy of extant peccaries. creator: Aaron L. Woodruff creator: Blaine W. Schubert uri: https://doi.org/10.7717/peerj.7161 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Woodruff and Schubert title: Morphology and development of a novel murine skeletal dysplasia link: https://peerj.com/articles/7180 last-modified: 2019-07-04 description: BackgroundLimb bones develop and grow by endochondral ossification, which is regulated by specific cell and molecular pathways. Changes in one or more of these pathways can have severe effects on normal skeletal development, leading to skeletal dysplasias. Many skeletal dysplasias are known to result from mis-expression of major genes involved in skeletal development, but the etiology of many skeletal dysplasias remains unknown. We investigated the morphology and development of a mouse line with an uncharacterized mutation exhibiting a skeletal dysplasia-like phenotype (Nabo).MethodsWe used µCT scanning and histology to comprehensively characterize the phenotype and its development, and to determine the developmental stage when this phenotype first appears.ResultsNabo mice have shorter limb elements compared to wildtype mice, while clavicles and dermal bones of the skull are not affected. Nabo embryos at embryonic stage E14 show shorter limb cartilage condensations. The tibial growth plate in Nabo mice is wider than in wildtype, particularly in the proliferative zone, however proliferative chondrocytes show less activity than wildtype mice. Cell proliferation assays and immunohistochemistry against the chondrogenic marker Sox9 suggest relatively lower, spatially-restricted, chondrocyte proliferation activity in Nabo. Bone volume and trabecular thickness in Nabo tibiae are also decreased compared to wildtype.DiscussionOur data suggest that the Nabo mutation affects endochondral ossification only, with the strongest effects manifesting in more proximal limb structures. The phenotype appears before embryonic stage E14, suggesting that outgrowth and patterning processes may be affected. Nabo mice present a combination of skeletal dysplasia-like characteristics not present in any known skeletal dysplasia. Further genomic and molecular analysis will help to identify the genetic basis and precise developmental pathways involved in this unique skeletal dysplasia. creator: Marta Marchini creator: Elizabeth Silva Hernandez creator: Campbell Rolian uri: https://doi.org/10.7717/peerj.7180 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Marchini et al. title: Molecular characterization of nearshore baitfish populations in Bermuda to inform management link: https://peerj.com/articles/7244 last-modified: 2019-07-04 description: Small-bodied marine fishes play an important role in the food web, feeding both larger fishes and seabirds. Often referred to as baitfishes, they concentrate seasonally in coastal areas in large, often heterospecific assemblages that are targeted by both commercial and recreational fishers. Given apparent declines in at least some of Bermuda’s baitfish species over the past 40 years, it is useful to determine the species composition of baitfish assemblages, and how it varies among sites, in order to inform management. Using genetic barcoding of the Cytochrome c oxidase 1 gene (COI), we confirm species identity, assess intraspecific genetic diversity locally, and determine rates of broader genetic connectivity for baitfish assemblages in Bermuda. Species analyzed included Hypoatherina harringtonensis, Anchoa choerostoma, Jenkinsia lamprotaenia, Harengula humeralis, Opisthonema oglinum and Sardinella aurita. Species identification based on molecular barcoding revealed some misidentification of individuals based solely on gross morphological characteristics, with an error rate of 11%, validating the usefulness of this approach. Interestingly, sequence results for the endemic Bermuda anchovy, A. choerostoma, were within 1% similarity to the more broadly distributed big-eye anchovy, A. lamprotaenia, and thus additional analyses are warranted to evaluate the genetic basis for endemism. Estimates of genetic diversity within and among baitfish assemblages in Bermuda were high, indicating high rates of local connectivity among sites for all species. As such, management should consider Bermuda’s baitfish species as single, highly mixed populations. However, with the exception of H. humeralis and the endemic A. choerostoma, significant genetic differentiation and population structure were found when comparing Bermuda’s baitfish populations with those from other regions, suggesting limited gene flow between other regions and Bermuda for these species. Limited regional connectivity has implications for management, as strong genetic divergence suggests that populations in Bermuda are predominantly self-seeding and thus not likely to be replenished from distant populations. These results therefore support precautionary management of baitfish species in Bermuda. creator: Gretchen Goodbody-Gringley creator: Emma Strand creator: Joanna M. Pitt uri: https://doi.org/10.7717/peerj.7244 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Goodbody-Gringley et al. title: The prognostic impact of age in different molecular subtypes of breast cancer: a population-based study link: https://peerj.com/articles/7252 last-modified: 2019-07-04 description: BackgroundThe aim of current study was to use competing risk model to calculate the potential differences that age played in the prognosis of different breast cancer subtypes.MethodsThe cohort was selected from Surveillance, Epidemiology, and End Results (SEER) program. The cumulative incidences of death (CID) was assessed for breast cancer caused deaths and other causes of mortality. The multivariate Cox proportional hazards regression model and the multivariate subdistribution hazard (SH) model were used to evaluate the prognostic value of age in different breast cancer subtypes.ResultsWe involved 33,968 breast cancer patients into our cohort. We found older patients had worse overall survival (OS) than young patients in hormone receptor positive and human epidermal growth factor receptor 2 positive breast cancer (HR+/HER2+) (≥40 vs. <40, HR = 2.07, 95% CI [1.28–3.35], p < 0.05). However, when we used competing risk model, we found young age was an independent risk factor only for triple negative breast cancer (TNBC) (≥40 vs. <40, HR = 0.71, 95% CI [0.56–0.89], p < 0.05). No association was found in other groups.ConclusionOur research was currently the largest sample size study and the first competing risk model-based study on the prognostic association between age and different breast cancer subtypes. We found <40 years patients had worse breast cancer specific survival (BCSS) than older patients in the TNBC subtype. creator: Dongjun Dai creator: Yiming Zhong creator: Zhuo Wang creator: Neelum Aziz Yousafzai creator: Hongchuan Jin creator: Xian Wang uri: https://doi.org/10.7717/peerj.7252 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dai et al. title: colocr: an R package for conducting co-localization analysis on fluorescence microscopy images link: https://peerj.com/articles/7255 last-modified: 2019-07-04 description: BackgroundThe co-localization analysis of fluorescence microscopy images is a widely used technique in biological research. It is often used to determine the co-distribution of two proteins inside the cell, suggesting that these two proteins could be functionally or physically associated. The limiting step in conducting microscopy image analysis in a graphical interface tool is the selection of the regions of interest for the co-localization of two proteins.ImplementationThis package provides a simple straightforward workflow for loading fluorescence images, choosing regions of interest and calculating co-localization measurements. Included in the package is a shiny app that can be invoked locally to interactively select the regions of interest where two proteins are co-localized.Availabilitycolocr is available on the comprehensive R archive network, and the source code is available on GitHub under the GPL-3 license as part of the ROpenSci collection, https://github.com/ropensci/colocr. creator: Mahmoud Ahmed creator: Trang Huyen Lai creator: Deok Ryong Kim uri: https://doi.org/10.7717/peerj.7255 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ahmed et al. title: A survey of the sperm whale (Physeter catodon) commensal microbiome link: https://peerj.com/articles/7257 last-modified: 2019-07-04 description: BackgroundMammalian commensal microbiota play important roles in the health of its host. In comparison to terrestrial mammals, commensal microbiota of marine mammals is mainly focused on the composition and function of skin and gut microbiota, with less attention paid to the health impact of bacteria and viruses. Previous studies on sperm whales (Physeter catodon) have affirmed their important phylogenetic position; however, studies on their commensal microbiota have not been published, due to difficulty in sample collection.MethodsHere, we sequenced the metagenomes of blood, muscle and fecal samples from a stranded sperm whale using the BGISEQ-500 platform. We compared the diversity and abundance of microbiomes from three different tissues and tried to search pathogenic bacterial and virulence genes probably related to the health of the sperm whale. We also performed 16S rDNA sequencing of the fecal sample to compare to published gut metagenome data from other marine mammals.ResultsOur results demonstrated notable differences in species richness and abundance in the three samples. Extensive bacteria, including Enterococcus faecium, Fusobacterium nucleatum, Pseudomonas aeruginosa, Streptococcus anginosus, Streptococcus pneumoniae, and Streptococcus suis, and five toxigenic Clostridium species usually associated with infection, were found in the three samples. We also found the taxa composition of sperm whale gut microbiota was similar to that of other whales, suggesting co-evolution with its host. This study is the first report of the sperm whale gut microbiome, and provides a foundation for the pathogen detection and health assessment of the sperm whale. creator: Chang Li creator: Xiaoxuan Tan creator: Jie Bai creator: Qiwu Xu creator: Shanshan Liu creator: Wenjie Guo creator: Cong Yu creator: Guangyi Fan creator: Yishan Lu creator: He Zhang creator: Huanming Yang creator: Jianwei Chen creator: Xin Liu uri: https://doi.org/10.7717/peerj.7257 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils link: https://peerj.com/articles/7265 last-modified: 2019-07-04 description: Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for ∼4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available at protocols.io, where community feedback creates ‘living’ protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils. creator: Gareth Trubl creator: Simon Roux creator: Natalie Solonenko creator: Yueh-Fen Li creator: Benjamin Bolduc creator: Josué Rodríguez-Ramos creator: Emiley A. Eloe-Fadrosh creator: Virginia I. Rich creator: Matthew B. Sullivan uri: https://doi.org/10.7717/peerj.7265 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Trubl et al. title: Monitoring the critically endangered Clanwilliam cedar with freely available Google Earth imagery link: https://peerj.com/articles/7005 last-modified: 2019-07-03 description: Monitoring of species and populations is essential for biodiversity observation and reporting at local, national and global scales, but can be an exceedingly difficult task for many, if not most, species. We tested the viability of using Google Earth™ imagery to manually map and monitor all individuals of the critically endangered Clanwilliam cedar, Widdringtonia wallichii Endl. ex Carrière, across its global native distribution; the remote and rugged Cederberg mountains. Comparison with sampling from field surveys reveals this to be a highly efficient and effective method for mapping healthy adult tree localities, but it fails to detect small or unhealthy individuals with green canopies <4 m2, or discern the number of individuals in clumps. This approach is clearly viable as a monitoring tool for this species and, with the rapid progress being made in machine learning approaches and satellite technology, will only become easier and more feasible for a greater number of species in the near future. Sadly, our field surveys revealed that the number of trees that have recently died (dead leaves still present) outnumbered live trees by a ratio of 2:1. creator: Jasper A. Slingsby creator: Peter W. O. Slingsby uri: https://doi.org/10.7717/peerj.7005 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Slingsby and Slingsby title: A possible new spawning area for Atlantic bluefin tuna (Thunnus thynnus): the first histologic evidence of reproductive activity in the southern Gulf of Mexico link: https://peerj.com/articles/7187 last-modified: 2019-07-03 description: The number of studies of reproductive biology for Atlantic bluefin tuna carried out in the Gulf of Mexico is significantly lower than those undertaken in the Mediterranean Sea. Four spawning areas have been found for the eastern Atlantic bluefin tuna stock in the Mediterranean Sea, so it is not implausible that there is more than one spawning area in the Gulf of Mexico for the western Atlantic bluefin tuna stock. The individuals used in this study were caught as bycatch by the Mexican surface longline fleet between January and April 2015. A total of 63 individuals ranging between 192 and 293 cm LF (mean = 238 ± 22.52 cm) were measured. Gonads from 46 fish (31 females and 15 males) were collected for histological examination. All the individuals were classified as mature; 25 were reproductively active (in spawning capable and spawning stages). The histological analysis indicates spawning activity in Mexican waters (the southern Gulf of Mexico). Spawning occurred in March and April, when the sea surface temperature was 25.57 °C ± 0.69 in March and 27.03 °C ± 0.69 in April. Information on the location of the spawning areas is necessary for a correct management of species. The present study provides the first histological evidence of reproductive activity in Mexican waters, and indicates a wider spawning area, beyond just the northern zone, potentially encompassing the entire Gulf of Mexico. creator: Roberto Cruz-Castán creator: Sámar Saber creator: David Macías creator: María José Gómez Vives creator: Gabriela Galindo-Cortes creator: Sergio Curiel-Ramirez creator: César Meiners-Mandujano uri: https://doi.org/10.7717/peerj.7187 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cruz-Castán et al. title: CRISPR/Cas9-mediated VDR knockout plays an essential role in the growth of dermal papilla cells through enhanced relative genes link: https://peerj.com/articles/7230 last-modified: 2019-07-03 description: BackgroundHair follicles in cashmere goats are divided into primary and secondary hair follicles (HFs). HF development, which determines the morphological structure, is regulated by a large number of vital genes; however, the key functional genes and their interaction networks are still unclear. Although the vitamin D receptor (VDR) is related to cashmere goat HF formation, its precise effects are largely unknown. In the present study, we verified the functions of key genes identified in previous studies using hair dermal papilla (DP) cells as an experimental model. Furthermore, we used CRISPR/Cas9 technology to modify the VDR in DP cells to dissect the molecular mechanism underlying HF formation in cashmere goats.ResultsThe VDR expression levels in nine tissues of Shaanbei white cashmere goats differed significantly between embryonic day 60 (E60) and embryonic day 120 (E120). At E120, VDR expression was highest in the skin. At the newborn and E120 stages, the VDR protein was highly expressed in the root sheath and hair ball region of Shaanbei cashmere goats. We cloned the complete CDS of VDR in the Shaanbei white cashmere goat and constructed a VDR-deficient DP cell model by CRISPR/Cas9. Heterozygous and homozygous mutant DP cells were produced. The growth rate of mutant DP cells was significantly lower than that of wild-type DP cells (P < 0.05) and VDR mRNA levels in DP cells decreased significantly after VDR knockdown (P < 0.05). Further, the expression levels of VGF, Noggin, Lef1, and β-catenin were significantly downregulated (P < 0.05).ConclusionsOur results indicated that VDR has a vital role in DP cells, and that its effects are mediated by Wnt and BMP4 signaling. creator: Ye Gao creator: Miaohan Jin creator: Yiyuan Niu creator: Hailong Yan creator: Guangxian Zhou creator: Yulin Chen uri: https://doi.org/10.7717/peerj.7230 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gao et al. title: RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean link: https://peerj.com/articles/7242 last-modified: 2019-07-03 description: Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise FST: 0.00036–0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies. creator: Bai-Dong Zhang creator: Dong-Xiu Xue creator: Yu-Long Li creator: Jin-Xian Liu uri: https://doi.org/10.7717/peerj.7242 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: 2HybridTools, a handy software to facilitate clone identification and mutation mapping from yeast two-hybrid screening link: https://peerj.com/articles/7245 last-modified: 2019-07-03 description: Yeast Two-Hybrid (Y2H) and reverse Two-Hybrid (RY2H) are powerful protein–protein interaction screening methods that rely on the interaction of bait and prey proteins fused to DNA binding (DB) and activation domains (AD), respectively. Y2H allows identification of protein interaction partners using screening libraries, while RY2H is used to determine residues critical to a given protein–protein interaction by exploiting site-directed mutagenesis. Currently, both these techniques still rely on sequencing of positive clones using conventional Sanger sequencing. For Y2H, a screen can yield several positives; the identification of such clones is further complicated by the fact that sequencing products usually contain vector sequence. For RY2H, obtaining a complete sequence is required to identify the full range of residues involved in protein–protein interactions. However, with Sanger sequencing limited to 500–800 nucleotides, sequencing is usually carried from both ends for clones greater than this length. Analysis of such RY2H data thus requires assembly of sequencing products combined with trimming of vector sequences and of low-quality bases at the beginning and ends of sequencing products. Further, RY2H analysis requires collation of mutations that abrogate a DB/AD interaction. Here, we present 2HybridTools, a Java program with a user-friendly interface that allows addressing all these issues inherent to both Y2H and RY2H. Specifically, for Y2H, 2HybridTools enables automated identification of positive clones, while for RY2H, 2HybridTools provides detailed mutation reports as a basis for further investigation of given protein–protein interactions. creator: Pierre Cauchy creator: Brigitte Kahn-Perlès creator: Pierre Ferrier creator: Jean Imbert creator: Patrick Lécine uri: https://doi.org/10.7717/peerj.7245 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cauchy et al. title: An automatic fascicle tracking algorithm quantifying gastrocnemius architecture during maximal effort contractions link: https://peerj.com/articles/7120 last-modified: 2019-07-02 description: BackgroundUltrasound has become a commonly used imaging modality for making dynamic measurements of muscle structure during functional movements in biomechanical studies. Manual measurements of fascicle length and pennation angle are time intensive which limits the clinical utility of this approach while also limiting sample sizes in research. The purpose of this study was to develop an automatic fascicle tracking program to quantify the length and pennation angle of a muscle fascicle during maximal effort voluntary contractions and to evaluate its repeatability between days and reproducibility between different examiners.MethodsFive healthy adults performed maximal effort isometric and isokinetic contractions at 30, 120, 210, and 500 degrees per second about their ankle on an isokinetic dynamometer while their medial gastrocnemius muscle was observed using ultrasound. Individual muscle fascicles and the two aponeuroses were identified by the user in the first frame and automatically tracked by the algorithm by three observers on three separate days. Users also made manual measurements of the candidate fascicle for validation. Repeatability within examiners across days and reproducibility across examiners and days were evaluated using intra-class correlation coefficients (ICC). Agreement between manual and automatic tracking was evaluated using the coefficient of multiple correlations (CMC) and root-mean-square error. Supervised automatic tracking, where the program could be reinitialized if poor tracking was observed, was performed on all videos by one examiner to evaluate the performance of automatic tracking in a typical use case. We also compared the performance our program to a preexisting automatic tracking program.ResultsWe found both manual and automatic measurements of fascicle length and pennation angle to be strongly repeatable within examiners and strongly reproducible across examiners and days (ICCs > 0.74). There was greater agreement between manual and automatic measurements of fascicle length than pennation angle, however the mean CMC value was found to be strong in both cases (CMC > 0.8). Supervision of automatic tracking showed very strong agreement between manual and automatic measurements of fascicle length and pennation angle (CMC > 0.94). It also had considerably less error relative to the preexisting automatic tracking program.ConclusionsWe have developed a novel automatic fascicle tracking algorithm that quantifies fascicle length and pennation angle of individual muscle fascicles during dynamic contractions during isometric and across a range of isokinetic velocities. We demonstrated that this fascicle tracking algorithm is strongly repeatable and reproducible across different examiners and different days and showed strong agreement with manual measurements, especially when tracking is supervised by the user so that tracking can be reinitialized if poor tracking quality is observed. creator: John F. Drazan creator: Todd J. Hullfish creator: Josh R. Baxter uri: https://doi.org/10.7717/peerj.7120 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Drazan et al. title: The impact of one-decade ecological disturbance on genetic changes: a study on the brine shrimp Artemia urmiana from Urmia Lake, Iran link: https://peerj.com/articles/7190 last-modified: 2019-07-02 description: Urmia Lake, the largest natural habitat of the brine shrimp Artemia urmiana, has progressively desiccated over the last two decades, resulting in a loss of 80% of its surface area and producing thousands of hectares of arid salty land. This ecological crisis has seriously affected the lake’s native biodiversity. Artemia urmiana has lost more than 90% of its population during the decade from 1994 (rainy period) to 2004 (drought period) due to salinity increasing to saturation levels (∼300 g/l). We studied the influence of this ecological crisis on the genetic diversity of A. urmiana in Urmia Lake, based on one cyst collections in 1994 and 2004. AMOVA analysis on ISSR data demonstrated a 21% genetic variation and there was a 5.5% reduction of polymorphic loci between samples. PCoA showed that 77.42% and 68.75% of specimens clustered separately in 1994 and 2004, respectively. Our analyses of four marker genes revealed different genetic diversity patterns with a decrease of diversity at ITS1 and an increase for Na+/K+ ATPase. There was no notable difference in genetic variation detected for COI and 16S genes between the two periods. However, they represented distinctly different haplotypes. ITS1 and COI followed a population expansion model, whereas Na+/K+ ATPase and 16S were under demographic equilibrium without selective pressure in the 1994 samples. Neutrality tests confirmed the excess of rare historical and recent mutations present in COI and ITS1 in both samples. It is evident that a short-term ecological disturbance has impacted the genetic diversity and structure of A. urmiana. creator: Alireza Asem creator: Amin Eimanifar creator: Gilbert van Stappen creator: Shi-Chun Sun uri: https://doi.org/10.7717/peerj.7190 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Asem et al. title: Population demography of Oldham’s leaf turtle (Cyclemys oldhamii) in protected and disturbed habitats in Thailand link: https://peerj.com/articles/7196 last-modified: 2019-07-02 description: BackgroundFreshwater turtle populations are vulnerable to a range of human activities because of particular life history attributes, and anthropogenic impacts can cause shifts in demographic traits, including survival, density and population structure. Asian freshwater turtles have undergone dramatic population declines in recent decades principally because of collection for food, pet, and traditional medicine markets. Despite this, few studies have been conducted on the population demography of these turtles, thereby limiting our understanding of population trends and the development of conservation actions. Oldham’s leaf turtle (Cyclemys oldhamii) is one of the most commonly traded turtles in Asian markets, but previous published studies have focused solely on systematics.MethodsWe conducted a mark-recapture study of C. oldhamii at three sites in northeastern Thailand—a protected stream, a degraded stream, and human-constructed ponds—and evaluated differences in survival, density, population structure, and sexual dimorphism among sites.ResultsWe captured 77 turtles at the protected stream, 67 at the constructed ponds, and two in the degraded stream. Survival was 12% lower and density was 35% lower in the constructed ponds than in the protected stream. Size class structure was skewed toward smaller individuals at the constructed ponds, and both sites exhibited subadult-skewed age class structure. Sex ratios were not statistically different than 1:1 at either site and did not differ between sites. We did not document sexual dimorphism in either population.DiscussionExplanations for lower survival, lower densities, and skewed size class structure at the constructed ponds include collection for consumption or Buddhist prayer release locally, collection for illegal export from Thailand, predation by domestic dogs associated with humans living nearby, or lower habitat quality. Evidence from our study suggests that collection, either for local use or export, is the most likely explanation for differences in demographic characteristics between the two sites. The information gained from this study may contribute to a status assessment for C. oldhamii and development of conservation actions should they become necessary to protect populations in Thailand. creator: Sengvilay Seateun creator: Nancy E. Karraker creator: Bryan L. Stuart creator: Anchalee Aowphol uri: https://doi.org/10.7717/peerj.7196 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Seateun et al. title: Improving clinical refractive results of cataract surgery by machine learning link: https://peerj.com/articles/7202 last-modified: 2019-07-02 description: AimTo evaluate the potential of the Support Vector Machine Regression model (SVM-RM) and Multilayer Neural Network Ensemble model (MLNN-EM) to improve the intraocular lens (IOL) power calculation for clinical workflow.BackgroundCurrent IOL power calculation methods are limited in their accuracy with the possibility of decreased accuracy especially in eyes with an unusual ocular dimension. In case of an improperly calculated power of the IOL in cataract or refractive lens replacement surgery there is a risk of re-operation or further refractive correction. This may create potential complications and discomfort for the patient.MethodsA dataset containing information about 2,194 eyes was obtained using data mining process from the Electronic Health Record (EHR) system database of the Gemini Eye Clinic. The dataset was optimized and split into the selection set (used in the design for models and training), and the verification set (used in the evaluation). The set of mean prediction errors (PEs) and the distribution of predicted refractive errors were evaluated for both models and clinical results (CR).ResultsBoth models performed significantly better for the majority of the evaluated parameters compared with the CR. There was no significant difference between both evaluated models. In the ±0.50 D PE category both SVM-RM and MLNN-EM were slightly better than the Barrett Universal II formula, which is often presented as the most accurate calculation formula.ConclusionIn comparison to the current clinical method, both SVM-RM and MLNN-EM have achieved significantly better results in IOL calculations and therefore have a strong potential to improve clinical cataract refractive outcomes. creator: Martin Sramka creator: Martin Slovak creator: Jana Tuckova creator: Pavel Stodulka uri: https://doi.org/10.7717/peerj.7202 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sramka et al. title: Production and purification of mannan oligosaccharide with epithelial tight junction enhancing activity link: https://peerj.com/articles/7206 last-modified: 2019-07-02 description: BackgroundMannanan oligosaccharide (MOS) is well-known as effective supplement food for livestock to increase their nutrients absorption and health status, but the structure and identification of bioactive MOS remain unclear. In this study, MOS production was accomplished, using enzymatic hydrolysis of pretreated coconut meal substrate with recombinant mannanase.MethodsThe mannanase gene was cloned from Bacillus subtilis cAE24, then expressed in BL21. Purified Mannanase exhibit stability over a wide range of pH and temperature from pH 6–8 and 4 °C to 70 °C, respectively. SEM analysis revealed that sonication could change the surface characteristic of copra meal, which gave better MOS yield, compared to untreated substrates. The separation and purification of each MOS were achieved using Biogel-P2 column chromatography. Determination of biological active MOS species was also investigated. T84 cells were cultured and treated with each of the purified MOS species to determine their tight junction enhancing activity.ResultsScanning electron microscope imaging showed that pretreatment using sonication could disrupt the surface of copra meal better than grinding alone, which can improve the production of MOS. Pentamer of MOS (M5) significantly increased tight junction integration of T84 cells measured with TEER (p < 0.0001). creator: Chatchai Nopvichai creator: Thanapon Charoenwongpaiboon creator: Navaporn Luengluepunya creator: Kazuo Ito creator: Chatchai Muanprasat creator: Rath Pichyangkura uri: https://doi.org/10.7717/peerj.7206 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nopvichai et al. title: Mitochondrial unfolded protein response gene CLPP changes mitochondrial dynamics and affects mitochondrial function link: https://peerj.com/articles/7209 last-modified: 2019-07-02 description: Mitochondrial dynamics is associated with mitochondrial function, which is associated with diabetes. Although an important indicator of the mitochondrial unfolded protein response, to the best of our knowledge, CLPP and its effects on mitochondrial dynamics in islet cells have not been studied to date. We analyzed the effects of CLPP on mitochondrial dynamics and mitochondrial function in the mice islet β-cell line Min6 under high glucose and high fat conditions. Min6 cells were assigned to: Normal, HG, HG+NC, HG+siCLPP, HF, HF+NC and HF+ siCLPP groups. High glucose and high fat can promote the mRNA and protein expression of CLPP in mitochondria. The increase of mitochondrial fission, the decrese of mitochondrial fusion, and the damage of mintocondrial ultrastructure were significant in the siCLPP cell groups as compared to no-siCLPP treated groups. Meanwhile, mitochondrial functions of MIN6 cells treated with siCLPP were impaired, such as ATP decreased, ROS increased, mitochondrial membrane potential decreased. In addition, cell insulin secretion decreased and cell apoptosis rate increased in siCLPP groups. These results revealed that mitochondrial unfolded protein response geneCLPP alleviated high glucose and high fat-induced mitochondrial dynamics imbalance and mitochondrial dysfunction. creator: GuiJun Wu creator: Qing Xiong creator: XiaoJun Wei creator: Ye Wang creator: XueMei Hu creator: GuangZhen He creator: LinJie Liu creator: QianHui Lai creator: Zhe Dai creator: Dhakal Anushesh creator: Yancheng Xu uri: https://doi.org/10.7717/peerj.7209 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wu et al. title: Conflict of interest explains the size of student evaluation of teaching and learning correlations in multisection studies: a meta-analysis link: https://peerj.com/articles/7225 last-modified: 2019-07-02 description: We examined the associations between the size of student evaluation of teaching and learning (SET/learning) correlations and presence of several conflicts of interest (COIs) including corporate, administrative, evaluation unit, SET author, and funder interests. Our meta-analyses of SET/learning correlations reported by multisection studies show that researchers with a vested interest in finding large positive SET/learning correlations found, on average, large positive SET/learning correlations. In contrast, researchers with no identifiable COIs found that SET/learning correlations were zero or nearly zero. The largest SET/learning correlations were reported by authors with ties to SET selling corporations. Smaller but still substantial SET/learning correlations were reported by researchers with administrative assignments and by researchers in evaluation units/departments responsible for the administration of SET. Moreover, authors with the most significant COIs were publishing their studies primarily prior to 1981 whereas authors with no or less significant COIs were publishing their studies in 1981 or afterwards. Studies published prior to 1981 reported small but significant (r = .31) SET/learning correlations whereas studies published in 1981 and after reported near zero, non-significant SET/learning correlations (r = .06). The presence of COIs was associated with earlier publication date but also with smaller samples. Finally, whereas corporate, administrative, and evaluation unit authors nearly ceased publishing multisection studies on SET/learning correlations, authors from business and economics departments are now responsible for the substantial portion of newer, larger, and higher quality studies published in 1981 and after. creator: Bob Uttl creator: Kelsey Cnudde creator: Carmela A. White uri: https://doi.org/10.7717/peerj.7225 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Uttl et al. title: The role of dispersal for shaping phylogeographical structure of flightless beetles from the Andes link: https://peerj.com/articles/7226 last-modified: 2019-07-02 description: BackgroundPáramo is a tropical alpine ecosystem present in the northern Andes. Its patchy distribution imposes limits and barriers to specialist inhabitants. We aim to assess the effects of this habitat distribution on divergence across two independently flightless ground beetle lineages, in the genera Dyscolus and Dercylus.MethodsOne nuclear and one mitochondrial gene from 110 individuals from 10 sites across the two lineages were sequenced and analyzed using a combination of phylogenetics, population genetic analyses, and niche modeling methods.ResultsThe two lineages show different degrees of population subdivision. Low levels of gene flow were found in Dyscolus alpinus, where one dominant haplotype is found in four out of the six populations analyzed for both molecular markers. However, complete population isolation was revealed in species of the genus Dercylus, where high levels of differentiation exist at species and population level for both genes. Maximum entropy models of species in the Dercylus lineage show overlapping distributions. Still, species distributions appear to be restricted to small areas across the Andes.ConclusionEven though both beetle lineages are flightless, the dispersal ability of each beetle lineage appears to influence the genetic diversity across fragmented páramo populations, where Dyscolus alpinus appears to be a better disperser than species in the genus Dercylus. creator: Sofia I. Muñoz-Tobar creator: Michael S. Caterino uri: https://doi.org/10.7717/peerj.7226 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Muñoz-Tobar and Caterino title: Mitochondrial genomics of human pathogenic parasite Leishmania (Viannia) panamensis link: https://peerj.com/articles/7235 last-modified: 2019-07-02 description: BackgroundThe human parasite Leishmania (V.) panamensis is one of the pathogenic species responsible for cutaneous leishmaniasis in Central and South America. Despite its importance in molecular parasitology, its mitochondrial genome, divided into minicircles and maxicircles, haven’t been described so far.MethodsUsing NGS-based sequencing (454 and ILLUMINA), and combining de novo genome assembly and mapping strategies, we report the maxicircle kDNA annotated genome of L. (V.) panamensis, the first reference of this molecule for the subgenus Viannia. A comparative genomics approach is performed against other Leishmania and Trypanosoma species.ResultsThe results show synteny of mitochondrial genes of L. (V.) panamensis with other kinetoplastids. It was also possible to identify nucleotide variants within the coding regions of the maxicircle, shared among some of them and others specific to each strain. Furthermore, we compared the minicircles kDNA sequences of two strains and the results show that the conserved and divergent regions of the minicircles exhibit strain-specific associations. creator: Daniel Alfonso Urrea creator: Omar Triana-Chavez creator: Juan F. Alzate uri: https://doi.org/10.7717/peerj.7235 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Urrea et al. title: Engineering Escherichia coli for the production of butyl octanoate from endogenous octanoyl-CoA link: https://peerj.com/articles/6971 last-modified: 2019-07-01 description: Medium chain esters produced from fruits and flowering plants have a number of commercial applications including use as flavour and fragrance ingredients, biofuels, and in pharmaceutical formulations. These esters are typically made via the activity of an alcohol acyl transferase (AAT) enzyme which catalyses the condensation of an alcohol and an acyl-CoA. Developing a microbial platform for medium chain ester production using AAT activity presents several obstacles, including the low product specificity of these enzymes for the desired ester and/or low endogenous substrate availability. In this study, we engineered Escherichia coli for the production of butyl octanoate from endogenously produced octanoyl-CoA. This was achieved through rational protein engineering of an AAT enzyme from Actinidia chinensis for improved octanoyl-CoA substrate specificity and metabolic engineering of E. coli fatty acid metabolism for increased endogenous octanoyl-CoA availability. This resulted in accumulation of 3.3 + 0.1 mg/L butyl octanoate as the sole product from E. coli after 48 h. This study represents a preliminary examination of the feasibility of developing E. coli platforms for the synthesis single medium chain esters from endogenous fatty acids. creator: Micaela G. Chacón creator: Emanuele G. Kendrick creator: David J. Leak uri: https://doi.org/10.7717/peerj.6971 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chacón et al. title: Nature representation in South American protected areas: country contrasts and conservation priorities link: https://peerj.com/articles/7155 last-modified: 2019-07-01 description: BackgroundSouth America faces strong environmental pressures as a result of agriculture and infrastructure expansion and also of demographic growth, demanding immediate action to preserve natural assets by establishing protected areas. Currently, 7.1% of the (sub)continent is under strict conservation categories (I to IV, IUCN), but the spatial distribution of these 1.3 × 106 km2 is poorly understood. We evaluated the representation of nature within the networks of protected areas, map conservation priorities and assess demographic, economic or geopolitical causes of existing protection patterns.MethodsWe characterized nature representation by looking at two components: the extent and the equality of protection. The first refers to the fraction of territory under protection, while the second refers to the homogeneity in the distribution along natural conditions of this protected fraction. We characterized natural conditions by either 113 biogeographical units (specifically, ecoregions) or a series of limited and significant climatic, topographic and edaphic traits. We analyzed representation every ten years since 1960 at national and continental levels. In the physical approach, histograms allowed us to map the degree of conservation priorities. Finally, we ranked the importance of different economic or geopolitical variables driving the observed distributions with a random forest technique.ResultsNature representation varied across countries in spite of its priority in conservation agendas. In Brazil, Peru and Argentina there are still natural conditions with no formal protection, while in Bolivia and Venezuela, protected areas incorporate the natural diversity in a more balanced manner. As protected networks have increased their extent, so did their equality across and within countries over time. Our maps revealed as top continental priorities the southern temperate, subhumid and fertile lowland environments, and other country-specific areas. Protection extent was generally driven by a low population density and isolation, while other variables like distance to frontiers, were relevant only locally (e.g., in Argentina).DiscussionOur description of the spatial distribution of protected areas can help societies and governments to improve the allocation of conservation efforts. We identified the main limitations that future conservation efforts will face, as protection was generally driven by the opportunities provided by low population density and isolation. From a methodological perspective, the physical approach reveals new properties of protection and provides tools to explore nature representation at different spatial, temporal and conceptual levels, complementing the traditional ones based on biodiversity or biogeographical attributes. creator: Germán Baldi creator: Santiago Schauman creator: Marcos Texeira creator: Sofía Marinaro creator: Osvaldo A. Martin creator: Patricia Gandini creator: Esteban G. Jobbágy uri: https://doi.org/10.7717/peerj.7155 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Baldi et al. title: Radiation dose-response (a Bayesian model) in the radiotherapy of the localized prostatic adenocarcinoma: the reliability of PSA slope changes as a response surrogate endpoint link: https://peerj.com/articles/7172 last-modified: 2019-07-01 description: PurposeOne of the characteristics of Prostate-Specific Antigen (PSA) is PSA slope. It is the rate of diminishing PSA marker over time after radiotherapy (RT) in prostate cancer (PC) patients. The purpose of this study was to evaluate the relationship between increasing RT doses and PSA slope as a potential surrogate for PC recurrence.Patients and MethodsThis retrospective study was conducted on PC patients who were treated by radiotherapy in the Cancer Institute of Iran during 2007–2012. By reviewing the records of these patients, the baseline PSA measurement before treatment (iPSA), Gleason score (GS), clinical T stage (T. stage), and periodic PSA measurements after RT and the total radiation dose received were extracted for each patient separately. We used a Bayesian dose-response model, analysis of variance, Kruskal–Wallis test, Kaplan–Meier product-limit method for analysis. Probability values less 0.05 were considered statistically significant.ResultsBased on the D’Amico risk assessment system, 13.34% of patients were classified as “Low Risk”, 51.79% were “Intermediate Risk”, and 34.87% were “High Risk”. In terms of radiation doses, 12.31% of the patients received fewer than 50 Gy, 15.38% received 50 to 69 Gy, 61.03% received 70 Gy, and 11.28% received more than 70 Gy. The PSA values decreased after RT for all dose levels. The slope of PSA changes was negative for 176 of 195 patients. By increasing the dosage of radiation, the PSA decreased but these changes were not statistically significant (p = 0.701) and PSA slope as a surrogate end point cannot met the Prentice’s criteria for PC recurrence.ConclusionSignificant changes in the dose-response relationship were not observed when the PSA slope was considered as the response criterion. Therefore, although the absolute value of the PSA decreased with increasing doses of RT, the relationship between PSA slope changes and increasing doses was not clear and cannot be used as a reliable response surrogate endpoint. creator: Reza Ali Mohammadpour creator: Jamshid Yazdani- Charati creator: SZahra Faghani creator: Ahad Alizadeh creator: Mohammadreza Barzegartahamtan uri: https://doi.org/10.7717/peerj.7172 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mohammadpour et al. title: An improved framework to predict river flow time series data link: https://peerj.com/articles/7183 last-modified: 2019-07-01 description: Due to non-stationary and noise characteristics of river flow time series data, some pre-processing methods are adopted to address the multi-scale and noise complexity. In this paper, we proposed an improved framework comprising Complete Ensemble Empirical Mode Decomposition with Adaptive Noise-Empirical Bayesian Threshold (CEEMDAN-EBT). The CEEMDAN-EBT is employed to decompose non-stationary river flow time series data into Intrinsic Mode Functions (IMFs). The derived IMFs are divided into two parts; noise-dominant IMFs and noise-free IMFs. Firstly, the noise-dominant IMFs are denoised using empirical Bayesian threshold to integrate the noises and sparsities of IMFs. Secondly, the denoised IMF’s and noise free IMF’s are further used as inputs in data-driven and simple stochastic models respectively to predict the river flow time series data. Finally, the predicted IMF’s are aggregated to get the final prediction. The proposed framework is illustrated by using four rivers of the Indus Basin System. The prediction performance is compared with Mean Square Error, Mean Absolute Error (MAE) and Mean Absolute Percentage Error (MAPE). Our proposed method, CEEMDAN-EBT-MM, produced the smallest MAPE for all four case studies as compared with other methods. This suggests that our proposed hybrid model can be used as an efficient tool for providing the reliable prediction of non-stationary and noisy time series data to policymakers such as for planning power generation and water resource management. creator: Hafiza Mamona Nazir creator: Ijaz Hussain creator: Ishfaq Ahmad creator: Muhammad Faisal creator: Ibrahim M. Almanjahie uri: https://doi.org/10.7717/peerj.7183 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nazir et al. title: Diversity and distribution of nearshore barnacle cyprids in southern California through the 2015–16 El Niño link: https://peerj.com/articles/7186 last-modified: 2019-07-01 description: Abundance, species diversity, and horizontal distributions of barnacle cyprids offshore of La Jolla, southern California were described from May 2014 to August 2016 to determine how the nearshore barnacle larval assemblage changed before, during, and after the 2015–16 El Niño. The entire water column was sampled at five stations located within one km of shore with water depths of 4, 6, 8, 10, and 12 m during 33 cruises that encompassed the time when El Niño conditions impacted the area. Nearshore temperature and thermal stratification was concurrently measured using a CTD. Six identified cyprid species, including Chthamalus fissus, Pollicipes polymerus, Megabalanus rosa, Tetraclita rubescens, Balanus glandula, and B. trigonus, along with four unknown species, were collected in our samples. DNA barcoding was used to confirm identifications in a subset of the larvae. C. fissus was more than eight times more abundant than any other species, and while abundance varied by species, cyprid density was highest for all species except for M. rosa before and after the El Niño event, and lower during the environmental disturbance. There were significant differences in cross-shore distributions among cyprid species, with some located farther offshore than others, along with variability in cross-shore distributions by season. C. fissus cyprids were closest to shore during spring-summer cruises when waters were the most thermally stratified, which supports previous findings that C. fissus cyprids are constrained nearshore when thermal stratification is high. Relative species proportions varied throughout the study, but there was no obvious change in species assemblage or richness associated with El Niño. We speculate that barnacle cyprid species diversity did not increase at our study site during the 2015–16 El Niño, as it has in other areas during previous El Niño Southern Oscillation events, due to the lack of anomalous northward flow throughout the 2015–16 event. creator: Malloree L. Hagerty creator: Nathalie Reyns creator: Jesús Pineda creator: Annette F. Govindarajan uri: https://doi.org/10.7717/peerj.7186 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hagerty et al. title: The effects of resveratrol feeding and exercise training on the skeletal muscle function and transcriptome of aged rats link: https://peerj.com/articles/7199 last-modified: 2019-07-01 description: This study investigated the effects of resveratrol feeding and exercise training on the skeletal muscle function and transcriptome of aged rats. Male SD rats (25 months old) were divided into the control group (Old), the daily exercise training group (Trained), and the resveratrol feeding group (Resveratrol). After 6 weeks of intervention, the body mass, grip strength, and gastrocnemius muscle mass were determined, and the muscle samples were analyzed by transcriptome sequencing. The differentially expressed genes were analyzed followed by GO enrichment analysis and KEGG analysis. The Old group showed positive increases in body mass, while both the Trained and Resveratrol groups showed negative growth. No significant differences in the gastrocnemius muscle index and absolute grip strength were found among the three groups. However, the relative grip strength was higher in the Trained group than in the Old group. Only 21 differentially expressed genes were identified in the Trained group vs. the Old group, and 12 differentially expressed genes were identified in the Resveratrol group vs. the Old group. The most enriched GO terms in the Trained group vs. the Old group were mainly associated with RNA metabolic processes and transmembrane transporters, and the significantly upregulated KEGG pathways included mucin-type O-glycan biosynthesis, drug metabolism, and pyrimidine metabolism. The most enriched GO terms in the Resveratrol group vs. the Old group were primarily associated with neurotransmitter transport and synaptic vesicle, and the upregulated KEGG pathways included synaptic vesicle cycle, nicotine addiction, retinol metabolism, insulin secretion, retrograde endocannabinoid signaling, and glutamatergic synapse. Neither exercise training nor resveratrol feeding has a notable effect on skeletal muscle function and related gene expression in aged rats. However, both exercise training and resveratrol feeding have strong effects on weight loss, which is beneficial for reducing the exercise loads of the elderly. creator: Jing Zhou creator: Zhiyin Liao creator: Jia Jia creator: Jin-Liang Chen creator: Qian Xiao uri: https://doi.org/10.7717/peerj.7199 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhou et al. title: Nomogram to predict the prognosis of parotid gland mucoepidermoid carcinoma: a population-based study of 1306 cases link: https://peerj.com/articles/7237 last-modified: 2019-07-01 description: BackgroundMucoepidermoid carcinoma (MEC) is a common cancer in the oral salivary gland malignancy, which mainly occurs in the parotid gland. The aim of this study is to identify independent prognostic factors and establish a nomogram model for parotid gland mucoepidermoid carcinoma (P-MEC) patients using the National Cancer Institute’s Surveillance, Epidemiology, and End Results (SEER) database.MethodPatients with P-MEC were selected from between 2004 and 2015. The overall survival (OS) and cancer-specific survival (CSS) rates were estimated using the Kaplan-Meier method with the log-rank test. Univariate and multivariate Cox proportional hazards regression analyses were performed to identify the independent prognostic factors.ResultsA total of 1,306 patients with P-MEC were enrolled. Age, grade, T stage, N stage, M stage, chemotherapy, and surgery type were independent prognostic factors for OS and CSS. A nomogram for OS was formulated based on these independent prognostic factors and validated using an internal bootstrap resampling approach, which showed that the nomogram exhibited a sufficient level of discrimination according to the C-index (0.877, 95% CI [0.855–0.898]).ConclusionSeveral prognostic factors for P-MEC were identified. The nomogram developed in this study accurately predicted the 5- and 10-year OS rates of American patients with P-MEC based on individual characteristics. Risk stratification using the survival nomogram can optimize individual therapies and follow-up. creator: Jian Sun creator: Yang Sun creator: Fei Yang creator: Qianrong Zhou creator: Wenjuan Liu creator: Yong Cheng creator: Xingwen Wu creator: Tinglan Chen creator: Ruixue Li creator: Borui Huang creator: Wael Att creator: Youcheng Yu creator: Wei Bi uri: https://doi.org/10.7717/peerj.7237 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sun et al.