title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2019-05 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Spray-dried immobilized lipase from Geobacillus sp. strain ARM in sago link: https://peerj.com/articles/6880 last-modified: 2019-05-31 description: Sago starch is traditionally used as food especially in Southeast Asia. Generally, sago is safe for consumption, biodegradable, easily available and inexpensive. Therefore, this research was done to expand the potential of sago by using it as a support for enzyme immobilization. In this study, ARM lipase, which was isolated from Geobacillus sp. strain ARM, was overexpressed in Escherichia coli system and then purified using affinity chromatography. The specific activity of the pure enzyme was 650 U/mg, increased 7 folds from the cell lysate. The purified enzyme was immobilized in gelatinized sago and spray-dried by entrapment technique in order to enhance the enzyme operational stability for handling at high temperature and also for storage. The morphology of the gelatinized sago and immobilized enzyme was studied by scanning electron microscopy. The results showed that the spray-dried gelatinized sago was shrunken and became irregular in structure as compared to untreated sago powder. The surface areas and porosities of spray-dried gelatinized sago with and without the enzyme were analyzed using BET and BJH method and have shown an increase in surface area and decrease in pore size. The immobilized ARM lipase showed good performance at 60–80  °C, with a half-life of 4 h and in a pH range 6–9. The immobilized enzyme could be stored at 10 °C with the half-life for 9 months. Collectively, the spray-dried immobilized lipase shows promising capability for industrial uses, especially in food processing. creator: Nur Syazwani Mohtar creator: Mohd Basyaruddin Abdul Rahman creator: Shuhaimi Mustafa creator: Mohd Shukuri Mohamad Ali creator: Raja Noor Zaliha Raja Abd. Rahman uri: https://doi.org/10.7717/peerj.6880 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mohtar et al. title: A simple model of a growing tumour link: https://peerj.com/articles/6983 last-modified: 2019-05-31 description: This paper presents the CellCycler, a model of a growing tumour which aims to simulate and predict the effect of treatment on xenograft studies or in the clinic. The model, which is freely available as a web application, uses ordinary differential equations (ODEs) to simulate cells as they pass through the phases of the cell cycle. However the guiding philosophy of the model is that it should only use parameters that can be observed or reasonably well approximated. There is no representation of the complex internal dynamics of each cell; instead the level of analysis is limited to cell state observables such as cell phase, apoptosis, and damage. We show that this approach, while limited in many respects, still naturally accounts for a heteregenous cell population with varying doubling time, and closely captures the dynamics of a growing tumour as it is exposed to treatment. The program is demonstrated using three case studies. creator: David Orrell creator: Hitesh B. Mistry uri: https://doi.org/10.7717/peerj.6983 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Orrell and Mistry title: ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data link: https://peerj.com/articles/6995 last-modified: 2019-05-31 description: Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readily identify contamination from closely-related organisms. To address this gap, we have developed a computational pipeline, ConFindr, for detection of intraspecies contamination. ConFindr determines the presence of contaminating sequences based on the identification of multiple alleles of core, single-copy, ribosomal-protein genes in raw sequencing reads. The performance of this tool was assessed using simulated and lab-generated Illumina short-read WGS data with varying levels of contamination (0–20% of reads) and varying genetic distance between the designated target and contaminant strains. Intraspecies and cross-species contamination was reliably detected in datasets containing 5% or more reads from a second, unrelated strain. ConFindr detected intraspecies contamination with higher sensitivity than existing tools, while also being able to automatically detect cross-species contamination with similar sensitivity. The implementation of ConFindr in quality-control pipelines will help to improve the reliability of WGS databases as well as the accuracy of downstream analyses. ConFindr is written in Python, and is freely available under the MIT License at github.com/OLC-Bioinformatics/ConFindr. creator: Andrew J. Low creator: Adam G. Koziol creator: Paul A. Manninger creator: Burton Blais creator: Catherine D. Carrillo uri: https://doi.org/10.7717/peerj.6995 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Low et al. title: Recommendations for dietary level of micro-minerals and vitamin D3 to Atlantic salmon (Salmo salar) parr and post-smolt when fed low fish meal diets link: https://peerj.com/articles/6996 last-modified: 2019-05-31 description: Atlantic salmon (Salmo salar) feeds have changed drastically in their composition from being predominantly marine-based to plant-based. This has altered the dietary supply and availability of micro-nutrients to Atlantic salmon. The impact of graded inclusion levels of a nutrient package (NP) comprising of 25 different micro-nutrients were studied in Atlantic salmon parr in freshwater (Trial 1) and post-smolts in seawater (Trial 2). In brief, the NP was included from 0 to 400%, where 100% corresponded to the recommendation by the National Research Council, 2011. Micro-nutrients, namely Zn, Mn, Se, Cu, Fe, Co, I and vitamin D3 were included in the NP with the objective of (re)evaluating the dietary need to meet the requirement of Atlantic salmon parr and post-smolt, when fed low fish meal, plant ingredient-based diets. Responses in apparent availability coefficient (AAC), whole body and vertebrae mineral concentrations, and retention were analysed. AAC of Cu, Mn, Se and Zn responded in a quadratic fashion with an increase in NP from 0 to 400% in freshwater parr; AAC could not be measured in post-smolt salmon. The whole-body concentration of Zn, Se, Co and I in Atlantic salmon parr were significantly affected by increasing NP inclusion; the same was observed for Zn, Se and Co in post-smolt Atlantic salmon. Vertebrae mineral concentration as the response criterion was non-responsive in parr; whereas, in post-smolt, Co had a linear increase, while Zn and Se showed a non-linear increase upon 0 to 400 NP inclusion. Zinc concentration and activities of alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRAP) in vertebrae indicated increased bone resorption in post-smolt Atlantic salmon; TRAP activity increased linearly with NP inclusion in post-smolt, but not in parr. Significant correlations between Zn and Se were observed in AAC and vertebral concentrations, indicating an interaction in intestinal uptake and vertebral deposition. Overall, Atlantic salmon parr held in freshwater were able to satisfy the requirement for the trace minerals Zn, Mn, Se, Cu, and Fe through supply from 100–150 NP, corresponding to 101–132, 47–63, 0.6–0.8, 12–16 and 150–166 mg kg −1, respectively; for iodine, dietary supply from 150–200 NP, corresponding to 0.7–1.6 mg kg−1, was required. In the seawater, Atlantic salmon post-smolt, in general, required micro-minerals and vitamin D3 levels as supplied through 150–200 NP, corresponding to 140–177, Zn; 61–67, Mn; 0.9–1, Se; 14–16, Cu; and vitamin D3, 0.06–0.09 mg kg −1 to fulfil the requirement, except for Cu which was satisfied at 100–150 NP, equivalent to 13–14 mg kg −1 diet. creator: P. Antony Jesu Prabhu creator: Erik-Jan Lock creator: Gro-Ingunn Hemre creator: Kristin Hamre creator: Marit Espe creator: Pål A. Olsvik creator: Joana Silva creator: Ann-Cecilie Hansen creator: Johan Johansen creator: Nini H. Sissener creator: Rune Waagbø uri: https://doi.org/10.7717/peerj.6996 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Antony Jesu Prabhu et al. title: Prevalence and contributing factors of dental caries of 6-year-old children in four regions of China link: https://peerj.com/articles/6997 last-modified: 2019-05-31 description: BackgroundFrom 2005 to 2015, the prevalence of dental caries in both primary and permanent dentitions was significantly increased in China. Previous studies have shown that the prevalence of permanent dental caries in school-aged children had already reached 19.7%–54.0%, 97.5% affecting first permanent molars. This study aimed to investigate the prevalence and contributing factors of dental caries in 6-year-old children in four regions of China to provide information for oral health promotion programs.MethodsA randomized cluster sampling method was employed in the study. All 6-year-old first grade children from the selected schools were invited to receive a clinical oral examination. Dental caries were diagnosed according to the World Health Organization criteria. The erupting first permanent molars were recorded using the modified International Caries Detection Assessment System. Questionnaires assessing children’s oral health-related behaviors and their caretakers’ oral health awareness and attitudes were completed by the children’s parents or guardians.ResultsOverall, 4,936 6-year-old school children participated in the survey. The prevalence of caries among these children was 87.7%, with a mean number of decayed, missing and filled teeth of 6.04 (SD, 4.24). In primary dentition, the caries prevalence was 87.7%, and the mean dmft score was 6.01 (SD, 4.22). In permanent dentition, the caries prevalence was 2.0%, the mean DFS score was 0.04 (SD, 0.31). All permanent dental caries occurred on the first permanent molars. Carious tooth surfaces were identified as modified ICDAS code “A” to indicate initial caries and distinct visual change in enamel. The mean DAS score of non-cavitated caries in the first permanent molars was 0.18 (SD, 0.67). Logistic regression analysis showed that regional and gender factors were significantly related to the caries experience of these children.ConclusionsThe 6-year-old children from four regions of China had sever primary dental caries and the first permanent molars were at high risk for dental caries. It is critical to protect permanent teeth from caries as early as the eruption of the first permanent molars. creator: Zhaoyou Wang creator: Wensheng Rong creator: Ying Zhang creator: Xiaojuan Zeng creator: Zhiqiang Li creator: Zhiwen Liu uri: https://doi.org/10.7717/peerj.6997 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Funmap2: an R package for QTL mapping using longitudinal phenotypes link: https://peerj.com/articles/7008 last-modified: 2019-05-31 description: Quantitative trait locus (QTL) mapping has been used as a powerful tool for inferring the complexity of the genetic architecture that underlies phenotypic traits. This approach has shown its unique power to map the developmental genetic architecture of complex traits by implementing longitudinal data analysis. Here, we introduce the R package Funmap2 based on the functional mapping framework, which integrates prior biological knowledge into the statistical model. Specifically, the functional mapping framework is engineered to include longitudinal curves that describe the genetic effects and the covariance matrix of the trait of interest. Funmap2 chooses the type of longitudinal curve and covariance matrix automatically using information criteria. Funmap2 is available for download at https://github.com/wzhy2000/Funmap2. creator: Nating Wang creator: Tinyi Chu creator: Jiangtao Luo creator: Rongling Wu creator: Zhong Wang uri: https://doi.org/10.7717/peerj.7008 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Integrating species and interactions into similarity metrics: a graph theory-based approach to understanding community similarity link: https://peerj.com/articles/7013 last-modified: 2019-05-31 description: Community similarity is often assessed through similarities in species occurrences and abundances (i.e., compositional similarity) or through the distribution of species interactions (i.e., interaction similarity). Unfortunately, the joint empirical evaluation of both is still a challenge. Here, we analyze community similarity in ecological systems in order to evaluate the extent to which indices based exclusively on species composition differ from those that incorporate species interactions. Borrowing tools from graph theory, we compared the classic Jaccard index with the graph edit distance (GED), a metric that allowed us to combine species composition and interactions. We found that similarity measures computed using only taxonomic composition could differ strongly from those that include composition and interactions. We conclude that new indices that incorporate community features beyond composition will be more robust for assessing similitude between natural systems than those purely based on species occurrences. Our results have therefore important conceptual and practical consequences for the analysis of ecological communities. creator: Daniela N. López creator: Patricio A. Camus creator: Nelson Valdivia creator: Sergio A. Estay uri: https://doi.org/10.7717/peerj.7013 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 López et al. title: Land cover drives large scale productivity-diversity relationships in Irish vascular plants link: https://peerj.com/articles/7035 last-modified: 2019-05-31 description: The impact of productivity on species diversity is often studied at small spatial scales and without taking additional environmental factors into account. Focusing on small spatial scales removes important regional scale effects, such as the role of land cover heterogeneity. Here, we use a regional spatial scale (10 km square) to establish the relationship between productivity and vascular plant species richness across the island of Ireland that takes into account variation in land cover. We used generalized additive mixed effects models to relate species richness, estimated from biological records, to plant productivity. Productivity was quantified by the satellite-derived enhanced vegetation index. The productivity-diversity relationship was fitted for three land cover types: pasture-dominated, heterogeneous, and non-pasture-dominated landscapes. We find that species richness decreases with increasing productivity, especially at higher productivity levels. This decreasing relationship appears to be driven by pasture-dominated areas. The relationship between species richness and heterogeneity in productivity (both spatial and temporal) varies with land cover. Our results suggest that the impact of pasture on species richness extends beyond field level. The effect of human modified landscapes, therefore, is important to consider when investigating classical ecological relationships, particularly at the wider landscape scale. creator: Hannah J. White creator: Willson Gaul creator: Dinara Sadykova creator: Lupe León-Sánchez creator: Paul Caplat creator: Mark C. Emmerson creator: Jon M. Yearsley uri: https://doi.org/10.7717/peerj.7035 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 White et al. title: Accelerated construction of an in vitro model of human periodontal ligament tissue: vacuum plasma combined with fibronectin coating and a polydimethylsiloxane matrix link: https://peerj.com/articles/7036 last-modified: 2019-05-31 description: Tying shape memory wires to crowded teeth causes the wires to deform according to the dental arch. This deformation results in a resilient force that is delivered to the tooth. The appropriate amount of force can activate the osteogenetic and osteoclastic ability of the periodontal ligament (PDL) and the tooth can be moved. This is the biological basis of orthodontic treatment. To achieve further insight into the mechanisms underlying orthodontic treatment, we examined whether accelerated construction of an in vitro human PDL fibroblast (HPdLF) stretching model can be achieved by combining fibronectin coating and vacuum plasma treatment with polydimethylsiloxane (PDMS) cell-culture chambers. Each chamber was randomly assigned to a no-surface modification (NN), fibronectin coating (FN), vacuum plasma treatment (PN), or vacuum plasma treatment followed by a fibronectin coating (PF) treatment protocol. The physical and chemical features and ability to promote cellular proliferation of the PDMS chamber surfaces were evaluated. Cellular adhesion of four materials were evaluated and two best-proliferated groups were considered as better model-constructing surfaces and used in subsequent experiments and used in subsequent experiments. HPdLFs were cultured on these two kinds of chambers without stretching for 3 days, then with stretching for 7 days. Time-course gene expression cellular morphology were evaluated. Chambers in the PN group had high wettability and surface component changes. The FN and PF chambers had high cellular proliferation ability. They were selected into subsequent experiments. After 3 days of culturing HPdLFs on the PF and PN chambers, the cells in the PF chambers had significantly higher levels of runt-related transcription factor 2 (Runx-2) and osteocalcin (OCN) gene expression compared with the cells in the PN chambers. After cyclic stretch application to the cells in the PN and PF chambers, expression of the type-3 collagen (COL-3) gene in PF group continued to increase for 7 days and was significantly higher than that in the PN group from day 5 onwards. The HPdLFs in the PF group showed parallel alignment from days 3 to 7 after imposition of cyclic stretch, while those in the PN group aligned in parallel from day 5 on. Our results suggested that applying a fibronectin coating to a PDMS chamber after plasma treatment can accelerate establishment of an in vitro PDL stretching model. creator: Wen Liao creator: Yoshiya Hashimoto creator: Yoshitomo Honda creator: Peiqi Li creator: Yang Yao creator: Zhihe Zhao creator: Naoyuki Matsumoto uri: https://doi.org/10.7717/peerj.7036 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liao et al. title: Climatic niche comparison across a cryptic species complex link: https://peerj.com/articles/7042 last-modified: 2019-05-31 description: According to current molecular evidence, the Chionaspis pinifoliae heterophyllae species complex has been recognized as 10 cryptic species. In this study, we construct potential distribution maps for seven cryptic species based on climatic variables. This was done to assess the main environmental factors that have contributed to the distribution map and test the degree of niche overlap across the seven cryptic species. We used MaxEnt to build the climatic niche models under climatic variables. For these models, the similarities and differences of the niches across the cryptic species were estimated. By comparing the potential distribution model of each cryptic species, our results suggested parapatric, sympatric and allopatry populations for this cryptic species complex. Our results showed high variability in niche overlap, and more often niche conservatism than niche divergence. The current species delimitation of the Chionaspis pinifoliae heterophyllae complex by molecular information and the hypothesis that the niche overlap in the sympatric population is higher than that of the allopatry population were supported based on the findings. This study will provide baseline data and a distribution range to facilitate the further control of these insects and formulate quarantine measures. creator: Qing Zhao creator: Hufang Zhang creator: Jiufeng Wei uri: https://doi.org/10.7717/peerj.7042 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Resilience of BST-2/Tetherin structure to single amino acid substitutions link: https://peerj.com/articles/7043 last-modified: 2019-05-31 description: Human tetherin, also known as BST-2 or CD317, is a dimeric, extracellular membrane-bound protein that consists of N and C terminal membrane anchors connected by an extracellular domain. BST-2 is involved in binding enveloped viruses, such as HIV, and inhibiting viral release in addition to a role in NF-kB signaling. Viral tethering by tetherin can be disrupted by the interaction with Vpu in HIV-1 in addition to other viral proteins. The structural mechanism of tetherin function is not clear and the effects of human tetherin mutations identified by sequencing consortiums are not known. To address this gap in the knowledge, we used data from the Ensembl database to construct and model known human missense mutations within the ectodomain to investigate how the structure of the ectodomain influences function. From the data, we identified an island of sequence stability within the ectodomain, which corresponds to a functionally and structurally important region identified in previous biochemical and biophysical studies. Most of the modeled mutations had little effect on the structure of the dimer and the coiled-coil, suggesting that the coiled-coil compensates for changes in primary structure. Thus, many of the functional defects observed in previous studies may not be due to changes in tetherin structure, but rather, due to in changes in protein-protein interactions or in aspects of tetherin not currently understood. The lack of structural effects by mutations known to decrease function further illustrates the need for more study of the structure-function connection for this system. Finally, apparent flexibility in tetherin sequence may allow for greater anti-viral activities with a larger number of viruses by reducing specific interactions with anti-tetherin proteins, while maintaining virus restriction. creator: Ian R. Roy creator: Camden K. Sutton creator: Christopher E. Berndsen uri: https://doi.org/10.7717/peerj.7043 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Roy et al. title: Influence of foetal inflammation on the development of meconium aspiration syndrome in term neonates with meconium-stained amniotic fluid link: https://peerj.com/articles/7049 last-modified: 2019-05-31 description: BackgroundMeconium-stained amniotic fluid is observed in approximately 10–15% of all deliveries; however, only 5% of neonates with meconium-stained amniotic fluid develop meconium aspiration syndrome (MAS). Although foetal distress and subsequent sympathetic stimulation have been considered as the primary upstream events of MAS, this clinical complication sometimes occurs due to other pathologies, such as intraamniotic inflammation. The aim of this study was to investigate whether the incidence of MAS is associated with the presence of funisitis and chorioamnionitis in term neonates with meconium-stained amniotic fluid.MethodsBetween April 2013 and March 2015, a total of 95 term neonates with meconium-stained amniotic fluid, who were hospitalized at a neonatal intensive care unit, were enrolled in the study. The placenta and umbilical cord were histopathologically examined. Clinical variables and histopathological findings associated with the incidence of MAS were studied.ResultsA total of 36 neonates developed MAS. Univariate logistic regression analysis revealed that a heavier birth weight, male sex, 1-min Apgar score ≤ 7, funisitis (but not chorioamnionitis), and elevated acute-phase inflammatory reaction score were associated with increased incidence of MAS (all p < 0.05). The multivariate model comprised funisitis (OR = 5.03, 95% CI [1.63–15.5], 1-min Apgar score ≤ 7 (OR = 2.74, 95% CI [1.06–7.09], and male sex (OR = 3.4, 95% CI [1.24–9.34].ConclusionIn neonates with meconium-stained amniotic fluid, funisitis, as well as low 1-min Apgar score and male sex, was identified as an independent variable for MAS development. Intraamniotic inflammation might be involved in the pathological mechanisms of MAS. creator: Kyoko Yokoi creator: Osuke Iwata creator: Satoru Kobayashi creator: Kanji Muramatsu creator: Haruo Goto uri: https://doi.org/10.7717/peerj.7049 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yokoi et al. title: Comparison of heparinized saline and 0.9% sodium chloride for maintaining central venous catheter patency in healthy dogs link: https://peerj.com/articles/7072 last-modified: 2019-05-31 description: BackgroundThe purpose of this study was to determine whether heparinized saline (HS) would be more effective in maintaining the patency of central venous catheters (CVCs) in dogs compared to 0.9% sodium chloride. This was a prospective randomized blinded study conducted at a University Veterinary Teaching Hospital.MethodsA total of 24 healthy purpose-bred dogs were randomized into two groups: a treatment and a control group. A CVC was placed in the jugular vein of each dog. Each dog in the treatment group had their CVC flushed with 10 IU/mL HS, while dogs in the control group had their CVC flushed with 0.9% sodium chloride every 6 h for 72 h. Immediately prior to flushing, each catheter was evaluated for patency by aspiration of blood. The catheter site was also evaluated for phlebitis, and a rectal temperature was obtained in each dog every 6 h. Prothrombin (PT) and activated partial thromboplastin (aPTT) times were evaluated prior to the administration of any flush solution. Results were then compared to values obtained 72 h later.ResultsAll CVCs in both groups were patent after 72 h, which was demonstrated by aspiration of blood and ease of flushing the catheter. Two CVCs in the 0.9% sodium chloride group had a negative aspiration at hour 12 and 36, respectively. One CVC in the HS group had a negative aspiration at hour 18. Signs of phlebitis occurred in three dog: two in the 0.9% sodium chloride group and one in the HS group. No dog was hyperthermic (>103 °F). Two catheters were inadvertently removed by dogs in the HS group during the study. There were no significant differences in catheter patency, incidence of phlebitis, or incidence of negative aspirations between both groups. aPTT and PT values remained within the normal reference range for all dogs in both groups. Ultimately, 0.9% sodium chloride was as effective as 10 IU/mL HS in maintaining the patency of CVCs for up to 72 h in healthy dogs. Further evaluation in clinical patients is warranted. creator: Julieann Vose creator: Adesola Odunayo creator: Joshua M. Price creator: Maggie Daves creator: Julie C. Schildt creator: M. Katherine Tolbert uri: https://doi.org/10.7717/peerj.7072 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Vose et al. title: Development and evaluation of the Parenting to Reduce Child Anxiety and Depression Scale (PaRCADS): assessment of parental concordance with guidelines for the prevention of child anxiety and depression link: https://peerj.com/articles/6865 last-modified: 2019-05-30 description: BackgroundInvolving parents in the prevention of mental health problems in children is prudent given their fundamental role in supporting their child’s development. However, few measures encapsulate the range of risk and protective factors for child anxiety and depression that parents can potentially modify. The Parenting to Reduce Child Anxiety and Depression Scale (PaRCADS) was developed as a criterion-referenced measure to assess parenting against a set of evidence-based parenting guidelines for the prevention of child anxiety and depressive disorders.MethodsIn Study 1, 355 parents of children 8–11 years old across Australia completed the PaRCADS and measures of parenting, general family functioning, child anxiety and depressive symptoms, and parent and child health-related quality of life. Their children completed measures of parenting, anxiety and depressive symptoms, and health-related quality of life. In Study 2, six subject-experts independently evaluated the PaRCADS items for item-objective congruence and item-relevance. Item analysis was conducted by examining item-total point-biserial correlation, difficulty index, B-index, and expert-rated content validity indices. Reliability (or dependability) was assessed by agreement coefficients for single administration. Construct validity was examined by correlational analyses with other measures.ResultsFour items were removed to yield a 79-item, 10-subscale PaRCADS. Reliability estimates for the subscale and total score range from .74 to .94. Convergent validity was indicated by moderate to strong correlations with other parenting and family functioning measures, and discriminant validity was supported by small to moderate correlations with a measure of parents’ health-related quality of life. Higher scores on the PaRCADS were associated with fewer anxiety and depressive symptoms and better health-related quality of life in the child. PaRCADS total score was associated with parental age, parent reported child’s history of mental health diagnosis and child’s current mental health problem.DiscussionResults showed that the PaRCADS demonstrates adequate psychometric properties that provide initial support for its use as a measure of parenting risk and protective factors for child anxiety and depression. The scale may be used for intervention and evaluative purposes in preventive programs and research. creator: Wan Hua Sim creator: Anthony F. Jorm creator: Katherine A. Lawrence creator: Marie B.H. Yap uri: https://doi.org/10.7717/peerj.6865 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sim et al. title: Identification of microRNA signatures in umbilical cord blood associated with maternal characteristics link: https://peerj.com/articles/6981 last-modified: 2019-05-30 description: BackgroundUmbilical cord blood could serve as useful source of blood markers enabling more efficient and reliable prenatal and neonatal diagnostics. MicroRNAs (miRNAs) are ubiquitous in body fluids where they were used for detecting and monitoring various physiological and pathological conditions. In this descriptive study, we aimed to identify changes in miRNA expression profiles associated with basic maternal somatic and epidemiological characteristics.MethodsStudy is based on 24 mothers from the Pilot phase of CELSPAC: TNG (Central European Longitudinal Studies of Parents and Children: The Next Generation) study. Cord blood was collected at time of delivery and global miRNA profiling was performed using microRNA Ready-to-use PCR Human Panel I+II TaqMan microarrays. Expression profiles were statistically evaluated in relation to maternal age, BMI, pregnancy weight gain, blood type, Rh factor status, allergies during pregnancy, addictive substance abuse and smoking status.ResultsWe analyzed expression of 752 human mature miRNAs in 24 samples of umbilical cord blood. For all maternal characteristics tested we described a specific signature of significantly deregulated miRNAs (P < 0.05). Analysis revealed seven miRNA associated with maternal age (three increased and four decreased in women younger than 35 years), 14 miRNAs associated with BMI status (five miRNAs increased and nine miRNAs decreased in women with BMI > 25) and nine miRNAs associated with maternal weight gain during pregnancy (eight miRNAs increased, and one miRNA decreased in women with weight gain < 12 kg). Additionally, 17 miRNAs correlated to blood type (two miRNAs decreased in blood type A, 11 increased in blood type B, two miRNAs increased in blood type AB and two miRNAs increased in blood type 0) and 17 miRNAs to Rh status of mother. We also detected seven miRNAs deregulated in umbilical cord blood of women with allergy (four increased and three decreased in women with allergy), four miRNAs associated to addictive substance abuse status (two up- and two downregulated in women with addictive substance abuse) and eight miRNAs associated with maternal cigarette smoking during pregnancy.ConclusionsWe successfully described differences in miRNA profiles in umbilical cord blood associated with basic characteristics connected with mother. Our data suggest that miRNAs in umbilical cord blood are detectable and associated with a wide range of maternal characteristics. These results indicate that miRNAs could potentially serve, and should be studied, as biomarkers for screening and diagnosis of pregnancy-associated complications and pathologies. creator: Jaroslav Juracek creator: Pavel Piler creator: Petr Janku creator: Lenka Radova creator: Ondrej Slaby uri: https://doi.org/10.7717/peerj.6981 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Juracek et al. title: One-year effect of wearing orthokeratology lenses on the visual quality of juvenile myopia: a retrospective study link: https://peerj.com/articles/6998 last-modified: 2019-05-30 description: ObjectiveTo study the one-year effect of wearing orthokeratology (OK) lenses on the visual quality of juvenile myopia.MethodsThe right eyes of 36 juvenile myopias were retrospectively studied in this work. Q-value, e-value, corneal curvature, strehl ratio (SR), modulation transfer function (MTF) and wavefront aberration (WA) were compared before and at 1, 3 and 12 months after wearing OK lenses. The SR, MTF and WA of cornea, internal optic and ocular were analyzed separately. The spherical and cylinder diopter, vision acuity, compensating factor (CF) and compensative rate (CF%) were compared before and at 12 months after wearing OK lenses.Results(1) The vision of LogMAR increased and the corneal curvature decreased significantly after wearing OK lenses. There was no significant difference for the e-value before and after wearing OK lenses. The Q-value increased at 1 month but decreased at 3 and 12 months remarkably. (2) The ocular and internal optic SR and MTF increased significantly at 1 month and then remained stable. The MTF in different spacial frequencies increased after wearing OK lenses. There was no significant difference for the corneal SR before and after wearing OK lenses, and the corneal MTF decreased significantly after wearing OK lenses. (3) For the ocular, the total higher order aberration (HOA), spherical, coma and trefoil aberrations increased, and the total aberration, total lower order aberration (LOA) and defocus aberration decreased obviously except astigmatism. The corneal aberrations increased significantly after wearing OK lenses except astigmatism. For the internal optic, the total aberration, total LOA and defocus aberration decreased, and the total HOA, coma and trefoil aberration increased significantly except the astigmatism and spherical aberrations. (4) The CF and CF% of total aberration, total LOA, total HOA and coma aberrations increased, and those of astigmatism and spherical decreased at 12 months.ConclusionsOrthokeratology is effective in correcting the refractive error and improving the vision quality of juvenile myopia over the one-year follow-up period. creator: Yewei Yin creator: Yang Zhao creator: Xiaoying Wu creator: Mengyang Jiang creator: Xiaobo Xia creator: Yao Chen creator: Weitao Song creator: Shengfa Hu creator: Xia Zhou creator: Kelly Young creator: Dan Wen uri: https://doi.org/10.7717/peerj.6998 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yin et al. title: Measuring urban vulnerability to climate change using an integrated approach, assessing climate risks in Beijing link: https://peerj.com/articles/7018 last-modified: 2019-05-30 description: This study is responding to the recommendation made by IPCC’s fifth Assessment Report on establishing a standard for measuring and reporting climate risk and vulnerability. It exemplifies the assessment of urban vulnerability to climate change by an integrated approach. The results indicate that Beijing is highly exposed to multiple climate threats in the context of global climate change, specifically urban heat waves, urban drainage floods and drought. Vulnerabilities to the climatic threats of heat waves, drainage floods and droughts have increased by 5%–15% during the period of 2008–2016 in Beijing. High vulnerabilities to both heat waves and drainage floods have been observed in the urban downtown area and high vulnerability to droughts have been observed in the outskirts. This vulnerability assessment, which addressed climatic threats, provides a holistic understanding of the susceptibility to climate change that could facilitate adaptation to climate change in the future. The developments of threats like flooding, heat waves and droughts are analyzed separately for 16 districts and an integrated vulnerability index for all of Beijing is provided as well. creator: Mingshun Zhang creator: Zelu Liu creator: Meine Pieter van Dijk uri: https://doi.org/10.7717/peerj.7018 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Ramification has little impact on shoot hydraulic efficiency in the sexually dimorphic genus Leucadendron (Proteaceae) link: https://peerj.com/articles/6835 last-modified: 2019-05-29 description: Despite the diversity of branching architectures in plants, the impact of this morphological variation on hydraulic efficiency has been poorly studied. Branch junctions are commonly thought to be points of high hydraulic resistance, but adjustments in leaf area or xylem conduit abundance or dimensions could compensate for the additional hydraulic resistance of nodal junctions at the level of the entire shoot. Here we used the sexually dimorphic genus Leucadendron (Proteaceae) to test whether variation in branch ramification impacts shoot hydraulic efficiency. We found that branch ramification was related to leaf traits via Corner’s rules such that more highly ramified shoots had smaller leaves, but that branch ramification had little consistent impact on shoot hydraulic efficiency, whether measured on a leaf area or stem cross-sectional area basis. These results suggest that the presumed increase in resistance associated with branching nodes can be compensated by other adjustments at the shoot level (e.g. leaf area adjustments, increased ramification to add additional branches in parallel rather than in series) that maintain hydraulic efficiency at the level of the entire shoot. Despite large morphological differences between males and females in the genus Leucadendron, which are due to differences in pollination and reproduction between the sexes, the physiological differences between males and females are minimal. creator: Adam B. Roddy creator: Justin J. van Blerk creator: Jeremy J. Midgley creator: Adam G. West uri: https://doi.org/10.7717/peerj.6835 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Roddy et al. title: Genetic diversity and phylogenetic analyses of 11 cohorts of captive rhesus macaques from Chinese zoos link: https://peerj.com/articles/6957 last-modified: 2019-05-29 description: Rhesus macaques are raised in almost every Chinese zoo due to their likeability and ease in feeding; however, little is yet known about the genetic diversity of rhesus macaques in captivity. In this study, a 475-base pair nucleotide sequence of the mitochondrial DNA control region was obtained from the fecal DNA of 210 rhesus macaque individuals in captivity. A total of 69 haplotypes were defined, 51 of which (73.9%) were newly identified. Of all haplotypes, seven were shared between two zoos, and 62 haplotypes (89.8%) appeared only in a specific zoo, indicating a low rate of animal exchange between Chinese zoos. Moreover, there was a relatively high level of genetic diversity among the rhesus macaques (Hd = 0.0623 ± 0.0009, Pi = 0.979 ± 0.003, K = 28.974). Phylogenetic analysis demonstrated that all haplotypes were clearly clustered into two major haplogroups—Clade A (southeastern China) and Clade B (southwestern China)—and each major clade contained several small sub-haplogroups. The haplotypes of rhesus macaques from the same zoo were not clustered together for the most part, but scattered among several subclades on the phylogenetic tree. This indicates that the rhesus macaques in most Chinese zoos may originat from a diverse collection of geographical areas. Our results demonstrate that zoos play an important role in the conservation of the genetic diversity of rhesus macaques, as well as provide useful information on the genetic management of captive rhesus macaques. creator: Qian Su creator: Yongfang Yao creator: Qin Zhao creator: Diyan Li creator: Meng Xie creator: Jiayun Wu creator: Anxiang Wen creator: Qin Wang creator: Guangxiang Zhu creator: Qingyong Ni creator: Mingwang Zhang creator: Huailiang Xu uri: https://doi.org/10.7717/peerj.6957 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Su et al. title: Active and passive procrastination in terms of temperament and character link: https://peerj.com/articles/6988 last-modified: 2019-05-29 description: BackgroundWhile passive procrastination is usually associated with distress and dysfunction active procrastination may be an effective coping style. To test this possibility, we examined passive and active procrastination in terms of temperament, character, and emotional intelligence (EI), as well as by a short-term longitudinal study.MethodsAdult community volunteers (N = 126) self-reported twice in an online short-term longitudinal study. At baseline on active and passive procrastination, as well as on the temperament and character inventory of personality (TCI-140) and EI. At first testing, they were asked to freely describe three personal goals and to make action plans to achieve each within the next two weeks. Two weeks later they reported on progress on their personal goals (PPG).ResultsPPG correlated positively with active procrastination and negatively with passive procrastination. Dividing the participants into median splits on active and passive procrastination resulted in four groups: Active, Passive, Active-Passive, and Non-Procrastinators. Analysis of variance showed that active procrastinators had an advantage in temperament and character traits as well as EI. Active procrastinators were also higher than the other groups on personality profiles i.e. combinations of traits; dependable temperament and well-developed character.ConclusionsActive procrastination can be an adaptive and productive coping style. It is associated with dependable temperament, well-developed character, and high emotional intelligence and predicts meeting personal goals. creator: Ada H. Zohar creator: Lior Pesah Shimone creator: Meirav Hen uri: https://doi.org/10.7717/peerj.6988 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zohar et al. title: Virus-induced gene silencing in the perennial woody Paeonia ostii link: https://peerj.com/articles/7001 last-modified: 2019-05-29 description: Tree peony is a perennial deciduous shrub with great ornamental and medicinal value. A limitation of its current functional genomic research is the lack of effective molecular genetic tools. Here, the first application of a Tobacco rattle virus (TRV)-based virus-induced gene silencing (VIGS) in the tree peony species Paeonia ostii is presented. Two different approaches, leaf syringe-infiltration and seedling vacuum-infiltration, were utilized for Agrobacterium-mediated inoculation. The vacuum-infiltration was shown to result in a more complete Agrobacterium penetration than syringe-infiltration, and thereby determined as an appropriate inoculation method. The silencing of reporter gene PoPDS encoding phytoene desaturase was achieved in TRV-PoPDS-infected triennial tree peony plantlets, with a typical photobleaching phenotype shown in uppermost newly-sprouted leaves. The endogenous PoPDS transcripts were remarkably down-regulated in VIGS photobleached leaves. Moreover, the green fluorescent protein (GFP) fluorescence was detected in leaves and roots of plants inoculated with TRV-GFP, suggesting the capability of TRV to silence genes in various tissues. Taken together, the data demonstrated that the TRV-based VIGS technique could be adapted for high-throughput functional characterization of genes in tree peony. creator: Lihang Xie creator: Qingyu Zhang creator: Daoyang Sun creator: Weizong Yang creator: Jiayuan Hu creator: Lixin Niu creator: Yanlong Zhang uri: https://doi.org/10.7717/peerj.7001 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xie et al. title: Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations link: https://peerj.com/articles/7007 last-modified: 2019-05-29 description: BackgroundMany tilapia species or varieties have been widely introduced and have become an economically important food fish in China. Information on the genetic backgrounds of these populations is deficient and requires more research, especially for red tilapia strains.MethodsIn the present study, displacement loop (D-loop) sequences were used to evaluate the genetic relationship and diversity of seven tilapia populations that are widely cultured in China; this was done specifically to speculate on the maternal ancestry of red tilapia strains. Three red tilapia varieties of Oreochromis ssp., Taiwan (TW), Israel (IL), and Malaysia (MY) strains and other populations, including O. aureus (AR), O. niloticus (NL), O. mossambicus (MS), and the GIFT strain of O. niloticus, were collected and analyzed in this study.ResultsA total of 146 polymorphic sites and 32 haplotypes of D-loop sequences were detected among 332 fish and four major haplotypes were shared among the populations. The TW and NL populations had a greater number of haplotypes (20 and 8, respectively). The haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.234 to 0.826, and 0 to 0.060, respectively. The significant positive Tajima’s D value of neutral test were detected in the NL, IL, and MY populations (P < 0.05), which indicated these populations might have not experienced historical expansion. According to the pairwise F-statistics, highly significant genetic differentiations were detected among populations (P < 0.01), with the exception of the IL and MY populations (P > 0.05). The nearest K2P genetic distance (D = 0.014) was detected between the MS and TW populations, whereas, the farthest (D = 0.101) was found between the GIFT and AR populations. The results from the molecular variance analysis (AMOVA) showed that there was an extremely significant genetic variation observed among the populations (P < 0.01), which contained 63.57% of the total variation. In view of the genetic relationship of red tilapia strains with other populations, TW and IL were detected with more similar genetic structures related to MS, and MY was more genetically similar to GIFT (or NL), which could provide more genetic evidence for the red tilapia strains maternal ancestry. creator: Bingjie Jiang creator: Jianjun Fu creator: Zaijie Dong creator: Min Fang creator: Wenbin Zhu creator: Lanmei Wang uri: https://doi.org/10.7717/peerj.7007 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jiang et al. title: Rutin ameliorates carbon tetrachloride (CCl4)-induced hepatorenal toxicity and hypogonadism in male rats link: https://peerj.com/articles/7011 last-modified: 2019-05-29 description: Rutin, a food derived-polyphenolic bioflavonoid, has been acknowledged for several health benefits. This study aims to explore the ameliorative effects of rutin against carbon tetrachloride (CCl4) toxicity in male rats. Adult male rats were given either CCl4 (30% in olive oil, 3 ml/kg b.w. intraperitoneally) alone or in combination with rutin (70 mg/kg intragastrically) twice a week for 4 weeks. Our data showed that rutin mitigated CCl4 hepatorenal damage, as indicated by diagnostic markers (i.e., transaminases, alkaline phosphatase, total bilirubin, total protein, albumin, urea, uric acid and creatinine), and histopathological findings. In addition, CCl4 induced profound elevation of free radical generation and oxidative stress, as evidenced by increasing lipid peroxidation and reducing catalase, superoxide dismutase and glutathione peroxidase activities in liver, kidney and testicular tissues; these effects were suppressed by coexposure with rutin. Moreover, the increase in the levels of serum triglycerides, cholesterol, low-density lipoprotein cholesterol, and very-low-density lipoprotein cholesterol induced by CCl4 was effectively counteracted by rutin. The decrease in the level of high-density lipoprotein cholesterol in the CCl4 group was also counteracted by rutin treatment. Interestingly, the decreased levels of hormonal mediators associated with sperm production, including serum testosterone, luteinizing hormone and follicle-stimulating hormone, and the impaired sperm quality induced by CCl4 were reversed by rutin. Data from the current study clearly demonstrated that rutin supplementation could at least partly overcome CCl4-induced hepatotoxicity, nephrotoxicity and reproductive toxicity by antioxidant and antidyslipidemic effects. creator: Hany Elsawy creator: Gehan M. Badr creator: Azza Sedky creator: Basem M. Abdallah creator: Abdullah M. Alzahrani creator: Ashraf M. Abdel-Moneim uri: https://doi.org/10.7717/peerj.7011 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Elsawy et al. title: Soil bacterial and fungal communities of six bahiagrass cultivars link: https://peerj.com/articles/7014 last-modified: 2019-05-29 description: BackgroundCultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance.ObjectivesThis study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities.MethodsSix bahiagrass cultivars (‘Argentine’, ‘Pensacola’, ‘Sand Mountain’, ‘Tifton 9’, ‘TifQuik’, and ‘UF-Riata’) were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano.ResultsThe soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under ‘Sand Mountain’ than ‘UF-Riata’. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists.ConclusionsOur results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynamics. The cultivars associated with presumptive plant pathogens or antagonists indicates that the ability of bahiagrass to control plant pathogens may be cultivar-dependent, however, physiological studies on plant-microbe interactions are required to confirm this presumption. We therefore suggest that future studies should explore the potential of different bahiagrass cultivars on plant pathogen control, particularly in sod-based crop rotation. creator: Lukas Beule creator: Ko-Hsuan Chen creator: Chih-Ming Hsu creator: Cheryl Mackowiak creator: Jose C.B. Dubeux Jr. creator: Ann Blount creator: Hui-Ling Liao uri: https://doi.org/10.7717/peerj.7014 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Beule et al. title: Unilateral hamstring foam rolling does not impair strength but the rate of force development of the contralateral muscle link: https://peerj.com/articles/7028 last-modified: 2019-05-29 description: BackgroundSelf-administered foam rolling (SAFR) is an effective massage technique often used in sport and rehabilitation settings to improve range of motion (ROM) without impairing the strength performance. However, the effects of unilateral SAFR on contralateral non-intervened muscle’s rate of force development (RFD) are unknown. Therefore, the purpose of this investigation was to examine the acute effects of unilateral hamstrings SAFR on the contralateral limb flexibility, the isometric strength, and the RFD parameters.MethodsThirty-four subjects (21 women) completed two separate randomly sequenced experimental visits, during which the control (rested for 10 min) or ten, 30-second SAFR were performed with the dominant hamstring muscle group. Before (Pre) and after (Post) the interventions, the contralateral hip flexion passive ROM, the maximal explosive isometric strength of the contralateral knee flexors with the corresponding prime mover muscles’ surface electromyographic (EMG) amplitude were measured. Separate two-way (time ×intervention) repeated measures analyses of variance (ANOVAs) were used to examine the potential changes of the dependent variables.ResultsThe SAFR significantly improved the contralateral limb ROM (Pre vs. Post: 68.3 ± 21.0 vs. 73.2 ± 23.2 degrees, p < 0.001; d = 0.22). No change was found for the contralateral isometric strength or the maximal EMG amplitude. For the RFD parameters, the percent changes of the RFDs for the first 50, 100, and 200 ms of the maximal explosive isometric contraction were −31.2%, −16.8%, and −10.1%, respectively, following the unilateral SAFR, relative to the control condition. In addition, the decrement of the first 50-ms RFD reached statistical significance (p = 0.007; Cohen’s d = 0.44).ConclusionTen sets of 30-second unilateral hamstring SAFR improved the ROM of the non-intervened contralateral limb, but decreased its ability to generate force, especially during the early phase (e.g., 50 ms) of the maximal explosive contraction. creator: Xin Ye creator: Benjamin S. Killen creator: Krista L. Zelizney creator: William M. Miller creator: Sunggun Jeon uri: https://doi.org/10.7717/peerj.7028 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ye et al. title: The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species link: https://peerj.com/articles/6944 last-modified: 2019-05-28 description: BackgroundThe rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy.MethodsWe reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato.ResultsThe molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confident lineage identification. Here, following the criteria of genetic and evolutionary species concepts, we describe the lineage from eastern Anatolia and parts of the Lesser and Great Caucasus as a new species E. urartica sp. nov.DiscussionElaphe urartica sp. nov. represents a cryptic species whose ancestors presumably diverged from their common ancestor with E. sauromates around the Miocene-Pliocene boundary. The intraspecific genetic structure indicates that the recent diversity of both species has been predominantly shaped by Pleistocene climatic oscillations, with glacial refugia mainly located in the Balkans, Crimea, and/or Anatolia in E. sauromates and Anatolia and/or the Caucasus in E. urartica sp. nov. creator: Daniel Jablonski creator: Oleg V. Kukushkin creator: Aziz Avcı creator: Sabina Bunyatova creator: Yusuf Kumlutaş creator: Çetin Ilgaz creator: Ekaterina Polyakova creator: Konstantin Shiryaev creator: Boris Tuniyev creator: David Jandzik uri: https://doi.org/10.7717/peerj.6944 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jablonski et al. title: Genetic assessment of three Fagaceae species in forest restoration trials link: https://peerj.com/articles/6958 last-modified: 2019-05-28 description: Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage. creator: Patcharawadee Thongkumkoon creator: Siriwadee Chomdej creator: Jatupol Kampuansai creator: Waranee Pradit creator: Pimubon Waikham creator: Stephen Elliott creator: Sutthathorn Chairuangsri creator: Dia Panitnard Shannon creator: Prasit Wangpakapattanawong creator: Aizhong Liu uri: https://doi.org/10.7717/peerj.6958 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Thongkumkoon et al. title: Secondary Succession under invasive species (Pteridium aquilinum) conditions in a seasonal dry tropical forest in southeastern Mexico link: https://peerj.com/articles/6974 last-modified: 2019-05-28 description: The role of invasive species in ecosystem functioning represents one of the main challenges in ecology. Pteridium aquilinum is a successful cosmopolitan invasive species with negative effects on the ecological mechanisms that allow secondary succession. In this study, we evaluated the influence of P. aquilinumon secondary succession under different disturbances in a seasonal dry forest of the Yucatán Peninsula. We determined species richness, composition and the relative importance value in four sampling units. Fabaceae followed by Asteraceae, Meliaceae, Rubiaceae, Sapindaceae and Verbenaceae were the most species rich families. A dissimilarity analysis determined significant differences in beta diversity between sampling units. With a generalized linear model we found that species richness was best explained by site conditions, followed by calcium and soil organic matter. Also, the generalized linear model showed that abundance resulted in a strong correlation with site conditions and soil characteristics. Specific soil conditions related to phosphoro and calcium were also detected as beneficiary to the successional processes. Our results suggest that applying fire restriction and periodic cutting of the bracken fern, this can increase a higher diversity of species. creator: Alberto Jean Baptiste creator: Pedro A. Macario creator: Gerald A. Islebe creator: Benedicto Vargas-Larreta creator: Luciano Pool creator: Mirna Valdez-Hernández creator: Jorge O. López-Martínez uri: https://doi.org/10.7717/peerj.6974 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jean Baptiste et al. title: Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images link: https://peerj.com/articles/6977 last-modified: 2019-05-28 description: BackgroundMalaria is a life-threatening disease caused by Plasmodium parasites that infect the red blood cells (RBCs). Manual identification and counting of parasitized cells in microscopic thick/thin-film blood examination remains the common, but burdensome method for disease diagnosis. Its diagnostic accuracy is adversely impacted by inter/intra-observer variability, particularly in large-scale screening under resource-constrained settings.IntroductionState-of-the-art computer-aided diagnostic tools based on data-driven deep learning algorithms like convolutional neural network (CNN) has become the architecture of choice for image recognition tasks. However, CNNs suffer from high variance and may overfit due to their sensitivity to training data fluctuations.ObjectiveThe primary aim of this study is to reduce model variance, improve robustness and generalization through constructing model ensembles toward detecting parasitized cells in thin-blood smear images.MethodsWe evaluate the performance of custom and pretrained CNNs and construct an optimal model ensemble toward the challenge of classifying parasitized and normal cells in thin-blood smear images. Cross-validation studies are performed at the patient level to ensure preventing data leakage into the validation and reduce generalization errors. The models are evaluated in terms of the following performance metrics: (a) Accuracy; (b) Area under the receiver operating characteristic (ROC) curve (AUC); (c) Mean squared error (MSE); (d) Precision; (e) F-score; and (f) Matthews Correlation Coefficient (MCC).ResultsIt is observed that the ensemble model constructed with VGG-19 and SqueezeNet outperformed the state-of-the-art in several performance metrics toward classifying the parasitized and uninfected cells to aid in improved disease screening.ConclusionsEnsemble learning reduces the model variance by optimally combining the predictions of multiple models and decreases the sensitivity to the specifics of training data and selection of training algorithms. The performance of the model ensemble simulates real-world conditions with reduced variance, overfitting and leads to improved generalization. creator: Sivaramakrishnan Rajaraman creator: Stefan Jaeger creator: Sameer K. Antani uri: https://doi.org/10.7717/peerj.6977 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma link: https://peerj.com/articles/6991 last-modified: 2019-05-28 description: BackroundTongue squamous cell carcinoma (TSCC) is the most common malignant tumor in the oral cavity. An increasing number of studies have suggested that long noncoding RNA (lncRNA) plays an important role in the biological process of disease and is closely related to the occurrence and development of disease, including TSCC. Although many lncRNAs have been discovered, there remains a lack of research on the function and mechanism of lncRNAs. To better understand the clinical role and biological function of lncRNAs in TSCC, we conducted this study.MethodsIn this study, 162 tongue samples, including 147 TSCC samples and 15 normal control samples, were investigated and downloaded from The Cancer Genome Atlas (TCGA). We constructed a competitive endogenous RNA (ceRNA) regulatory network. Then, we investigated two lncRNAs as key lncRNAs using Kaplan–Meier curve analysis and constructed a key lncRNA-miRNA-mRNA subnetwork. Furthermore, gene set enrichment analysis (GSEA) was carried out on mRNAs in the subnetwork after multivariate survival analysis of the Cox proportional hazards regression model.ResultsThe ceRNA regulatory network consists of six differentially expressed miRNAs (DEmiRNAs), 29 differentially expressed lncRNAs (DElncRNAs) and six differentially expressed mRNAs (DEmRNAs). Kaplan-Meier curve analysis of lncRNAs in the TSCC ceRNA regulatory network showed that only two lncRNAs, including LINC00261 and PART1, are correlated with the total survival time of TSCC patients. After we constructed the key lncRNA-miRNA -RNA sub network, the GSEA results showed that key lncRNA are mainly related to cytokines and the immune system. High expression levels of LINC00261 indicate a poor prognosis, while a high expression level of PART1 indicates a better prognosis. creator: Yidan Song creator: Yihua Pan creator: Jun Liu uri: https://doi.org/10.7717/peerj.6991 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Song et al. title: Fisher linear discriminant analysis for classification and prediction of genomic susceptibility to stomach and colorectal cancers based on six STR loci in a northern Chinese Han population link: https://peerj.com/articles/7004 last-modified: 2019-05-28 description: ObjectiveGastrointestinal cancer is the leading cause of cancer-related death worldwide. The aim of this study was to verify whether the genotype of six short tandem repeat (STR) loci including AR, Bat-25, D5S346, ER1, ER2, and FGA is associated with the risk of gastric cancer (GC) and colorectal cancer (CRC) and to develop a model that allows early diagnosis and prediction of inherited genomic susceptibility to GC and CRC.MethodsAlleles of six STR loci were determined using the peripheral blood of six colon cancer patients, five rectal cancer patients, eight GC patients, and 30 healthy controls. Fisher linear discriminant analysis (FDA) was used to establish the discriminant formula to distinguish GC and CRC patients from healthy controls. Leave-one-out cross validation and receiver operating characteristic (ROC) curves were used to validate the accuracy of the formula. The relationship between the STR status and immunohistochemical (IHC) and tumor markers was analyzed using multiple correspondence analysis.ResultsD5S346 was confirmed as a GC- and CRC-related STR locus. For the first time, we established a discriminant formula on the basis of the six STR loci, which was used to estimate the risk coefficient of suffering from GC and CRC. The model was statistically significant (Wilks’ lambda = 0.471, χ2 = 30.488, df = 13, and p = 0.004). The results of leave-one-out cross validation showed that the sensitivity of the formula was 73.7% and the specificity was 76.7%. The area under the ROC curve (AUC) was 0.926, with a sensitivity of 73.7% and a specificity of 93.3%. The STR status was shown to have a certain relationship with the expression of some IHC markers and the level of some tumor markers.ConclusionsThe results of this study complement clinical diagnostic criteria and present markers for early prediction of GC and CRC. This approach will aid in improving risk awareness of susceptible individuals and contribute to reducing the incidence of GC and CRC by prevention and early detection. creator: Shuhong Hao creator: Ming Ren creator: Dong Li creator: Yujie Sui creator: Qingyu Wang creator: Gaoyang Chen creator: Zhaoyan Li creator: Qiwei Yang uri: https://doi.org/10.7717/peerj.7004 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hao et al. title: Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis link: https://peerj.com/articles/7024 last-modified: 2019-05-28 description: BackgroundOsteoarthritis (OA) is one of the most important age-related degenerative diseases, and the leading cause of disability and chronic pain in the aging population. Recent studies have identified several lncRNA-associated functions involved in the development of OA. Because age is a key risk factor for OA, we investigated the differential expression of age-related lncRNAs in each stage of OA.MethodsTwo gene expression profiles were downloaded from the GEO database and differentially expressed genes (DEGs) were identified across each of the different developmental stages of OA. Next, gene ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the function of the DEGs. Finally, a lncRNA-targeted DEG network was used to identify hub-lncRNAs.ResultsA total of 174 age-related DEGs were identified. GO analyses confirmed that age-related degradation was strongly associated with cell adhesion, endodermal cell differentiation and collagen fibril organization. Significantly enriched KEGG pathways associated with these DEGs included the PI3K–Akt signaling pathway, focal adhesion, and ECM–receptor interaction. Further analyses via a protein–protein interaction (PPI) network identified two hub lncRNAs, CRNDE and LINC00152, involved in the process of age-related degeneration of articular cartilage. Our findings suggest that lncRNAs may play active roles in the development of OA. Investigation of the gene expression profiles in different development stages may supply a new target for OA treatment. creator: Pengfei Hu creator: Fangfang Sun creator: Jisheng Ran creator: Lidong Wu uri: https://doi.org/10.7717/peerj.7024 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hu et al. title: Returning a lost process by reintroducing a locally extinct digging marsupial link: https://peerj.com/articles/6622 last-modified: 2019-05-27 description: The eastern bettong (Bettongia gaimardi), a medium-sized digging marsupial, was reintroduced to a predator-free reserve after 100 years of absence from the Australian mainland. The bettong may have the potential to restore temperate woodlands degraded by a history of livestock grazing, by creating numerous small disturbances by digging. We investigated the digging capacity of the bettong and compared this to extant fauna, to answer the first key question of whether this species could be considered an ecosystem engineer, and ultimately if it has the capacity to restore lost ecological processes. We found that eastern bettongs were frequent diggers and, at a density of 0.3–0.4 animals ha−1, accounted for over half the total foraging pits observed (55%), with echidnas (Tachyglossus aculeatus), birds and feral rabbits (Oryctolagus cuniculus) accounting for the rest. We estimated that the population of bettongs present dug 985 kg of soil per ha per year in our study area. Bettongs dug more where available phosphorus was higher, where there was greater basal area of Acacia spp. and where kangaroo grazing was less. There was no effect on digging of eucalypt stem density or volume of logs on the ground. While bettong digging activity was more frequent under trees, digging also occurred in open grassland, and bettongs were the only species observed to dig in scalds (areas where topsoil has eroded to the B Horizon). These results highlight the potential for bettongs to enhance soil processes in a way not demonstrated by the existing fauna (native birds and echidna), and introduced rabbit. creator: Nicola T. Munro creator: Sue McIntyre creator: Ben Macdonald creator: Saul A. Cunningham creator: Iain J. Gordon creator: Ross B. Cunningham creator: Adrian D. Manning uri: https://doi.org/10.7717/peerj.6622 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Munro et al. title: Hierarchical generalized additive models in ecology: an introduction with mgcv link: https://peerj.com/articles/6876 last-modified: 2019-05-27 description: In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels. We describe the theoretical connection between HGAMs, HGLMs, and GAMs, explain how to model different assumptions about the degree of intergroup variability in functional response, and show how HGAMs can be readily fitted using existing GAM software, the mgcv package in R. We also discuss computational and statistical issues with fitting these models, and demonstrate how to fit HGAMs on example data. All code and data used to generate this paper are available at: github.com/eric-pedersen/mixed-effect-gams. creator: Eric J. Pedersen creator: David L. Miller creator: Gavin L. Simpson creator: Noam Ross uri: https://doi.org/10.7717/peerj.6876 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Pedersen et al. title: Detection of condition-specific marker genes from RNA-seq data with MGFR link: https://peerj.com/articles/6970 last-modified: 2019-05-27 description: The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups samples with similar gene expression levels and flags potential markers of a sample type if their highest expression values represent all replicates of this type. We have benchmarked MGFR against other methods and found that its proposed markers accurately characterize the functional identity of different tissues and cell types in standard and single cell RNA-seq datasets. Then, we performed a more detailed analysis for three of these datasets, which profile the transcriptomes of different human tissues, immune and human blastocyst cell types, respectively. MGFR’s predicted markers were compared to gold-standard lists for these datasets and outperformed the other marker detectors. Finally, we suggest novel candidate marker genes for the examined tissues and cell types. MGFR is implemented as a freely available Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.MGFR), which facilitates its use and integration with bioinformatics pipelines. creator: Khadija El Amrani creator: Gregorio Alanis-Lobato creator: Nancy Mah creator: Andreas Kurtz creator: Miguel A. Andrade-Navarro uri: https://doi.org/10.7717/peerj.6970 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 El Amrani et al. title: Enhanced mechanical, thermal and biocompatible nature of dual component electrospun nanocomposite for bone tissue engineering link: https://peerj.com/articles/6986 last-modified: 2019-05-27 description: Traditionally, in the Asian continent, oils are a widely accepted choice for alleviating bone-related disorders. The design of scaffolds resembling the extracellular matrix (ECM) is of great significance in bone tissue engineering. In this study, a multicomponent polyurethane (PU), canola oil (CO) and neem oil (NO) scaffold was developed using the electrospinning technique. The fabricated nanofibers were subjected to various physicochemical and biological testing to validate its suitability for bone tissue engineering. Morphological analysis of the multicomponent scaffold showed a reduction in fiber diameter (PU/CO—853 ± 141.27 nm and PU/CO/NO—633 ± 137.54 nm) compared to PU (890 ± 116.911 nm). The existence of CO and NO in PU matrix was confirmed by an infrared spectrum (IR) with the formation of hydrogen bond. PU/CO displayed a mean contact angle of 108.7° ± 0.58 while the PU/CO/NO exhibited hydrophilic nature with an angle of 62.33° ± 2.52. The developed multicomponent also exhibited higher thermal stability and increased mechanical strength compared to the pristine PU. Atomic force microscopy (AFM) analysis depicted lower surface roughness for the nanocomposites (PU/CO—389 nm and PU/CO/NO—323 nm) than the pristine PU (576 nm). Blood compatibility investigation displayed the anticoagulant nature of the composites. Cytocompatibility studies revealed the non-toxic nature of the developed composites with human fibroblast cells (HDF) cells. The newly developed porous PU nanocomposite scaffold comprising CO and NO may serve as a potential candidate for bone tissue engineering. creator: Guanbao Li creator: Pinquan Li creator: Qiuan Chen creator: Mohan Prasath Mani creator: Saravana Kumar Jaganathan uri: https://doi.org/10.7717/peerj.6986 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Effectiveness of nasal irrigation devices: a Thai multicentre survey link: https://peerj.com/articles/7000 last-modified: 2019-05-27 description: BackgroundNasal irrigation is widely used as an adjunctive treatment for nasal diseases. There is little evidence regarding the efficacy of the devices used in this procedure. The objective of this survey was to evaluate the effectiveness of nasal irrigation devices based on the experiences of patients and physicians.MethodsWe conducted a multicentre survey study between November 2017 and October 2018. Physician and patient questionnaires were developed based on the available literature and expert opinion. The physician questionnaire was submitted to the Otolaryngology residents and staff of each centre and their network. The physicians were also asked to distribute the patient questionnaire to their patients.ResultsInformation regarding 331 devices used by the patients was collected. The mean age of the patients was 45.46 ± 17.19 years (from 5 to 81). Roughly half were male, and half were female (48.6%: 51.4%). Among the high-pressure devices, we found that the high-pressure large-volume nasal irrigation devices yielded significantly higher symptom scores in seven of 12 domains (p < 0.05). Among the large-volume devices, we found that the large-volume high-pressure nasal irrigation devices received significantly higher symptom scores in 4 of 12 domains (p < 0.05). However, a higher proportion of patients using the large-volume high-pressure devices had retained fluid in the sinuses compared to those using large-volume low-pressure devices (p < 0.001).ConclusionsThis survey supports the regular use of nasal irrigation, particularly with large-volume high-pressure devices, as an effective treatment for nasal disease. It may be effective at clearing nasal secretion, improve nasal congestion, decrease post-nasal drip, improve sinus pain or headache, improve taste and smell, and improve sleep quality. It could be used by patients with good compliance and minimal side effects. creator: Patorn Piromchai creator: Charoiboon Puvatanond creator: Virat Kirtsreesakul creator: Saisawat Chaiyasate creator: Sanguansak Thanaviratananich uri: https://doi.org/10.7717/peerj.7000 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Piromchai et al. title: On the presence of Dipturus nidarosiensis (Storm, 1881) in the Central Mediterranean area link: https://peerj.com/articles/7009 last-modified: 2019-05-27 description: The Norwegian skate Dipturus nidarosiensis (Storm, 1881) has only recently been recorded in the western Mediterranean Sea along the coast of southern Sardinia, off Algeria and the Alboran Sea. The present study confirmed the presence of the species in the Central Mediterranean Sea by identifying morphometric, morphological features and molecular markers. Biological sampling was conducted from 2010 to 2016 on eight specimens collected through commercial landings, offshore observer programmes and scientific surveys in Adriatic and Ionian waters at depths between 320 and 720 m. The total lengths of the specimens (juveniles and adults) ranged from 268 to 1,422 mm, and their body weights ranged from 44.5 to 12,540.0 g. They showed morphometric features that corresponded to those of Norwegian skates in the Northeast Atlantic and the Western Mediterranean. In previous analyses, molecular data were obtained by mitochondrial COI sequences. The haplotype network showed the occurrence of a common haplotype (Hap_1) shared by the individuals from areas in the North Atlantic, Sardinian, Algerian and Spanish Mediterranean Sea areas but not South Africa. The occurrence of individuals in different stages of life (i.e., juveniles, sub-adults and adults) and sexual development (immature and mature) suggested the presence of a species with a permanent reproductive allocation in the deep waters of the Mediterranean, which was exposed to a low level of fishing exploitation. Indeed, the deep depth distribution of the species could be the reason for the absence of information about this species in onshore or offshore fishery data collection programmes and scientific surveys. creator: Pierluigi Carbonara creator: Rita Cannas creator: Marilena Donnaloia creator: Riccardo Melis creator: Cristina Porcu creator: Maria Teresa Spedicato creator: Walter Zupa creator: Maria Cristina Follesa uri: https://doi.org/10.7717/peerj.7009 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Carbonara et al. title: One-class land-cover classification using MaxEnt: the effect of modelling parameterization on classification accuracy link: https://peerj.com/articles/7016 last-modified: 2019-05-27 description: Multiple-class land-cover classification approaches can be inefficient when the main goal is to classify only one or a few classes. Under this scenario one-class classification algorithms could be a more efficient alternative. Currently there are several algorithms that can fulfil this task, with MaxEnt being one of the most promising. However, there is scarce information regarding parametrization for performing land-cover classification using MaxEnt. In this study we aimed to understand how MaxEnt parameterization affects the classification accuracy of four different land-covers (i.e., built-up, irrigated grass, evergreen trees and deciduous trees) in the city of Santiago de Chile. We also evaluated if MaxEnt manual parameterization outperforms classification results obtained when using MaxEnt default parameters setting. To accomplish our objectives, we generated a set of 25,344 classification maps (i.e., 6,336 for each assessed land-cover), which are based on all the potential combination of 12 different classes of features restrictions, four regularization multipliers, four different sample sizes, three training/testing proportions, and 11 thresholds for generating the binary maps. Our results showed that with a good parameterization, MaxEnt can effectively classify different land covers with kappa values ranging from 0.68 for deciduous trees to 0.89 for irrigated grass. However, the accuracy of classification results is highly influenced by the type of land-cover being classified. Simpler models produced good classification outcomes for homogenous land-covers, but not for heterogeneous covers, where complex models provided better outcomes. In general, manual parameterization improves the accuracy of classification results, but this improvement will depend on the threshold used to generate the binary map. In fact, threshold selection showed to be the most relevant factor impacting the accuracy of the four land-cover classification. The number of sampling points for training the model also has a positive effect on classification results. However, this effect followed a logarithmic distribution, showing an improvement of kappa values when increasing the sampling from 40 to 60 points, but showing only a marginal effect if more than 60 sampling points are used. In light of these results, we suggest testing different parametrization and thresholds until satisfactory kappa or other accuracy metrics values are achieved. Our results highlight the huge potential that MaxEnt has a as a tool for one-class classification, but a good understanding of the software settings and model parameterization is needed to obtain reliable results. creator: Ignacio C. Fernández creator: Narkis S. Morales uri: https://doi.org/10.7717/peerj.7016 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fernández and Morales title: Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic Ocean link: https://peerj.com/articles/6794 last-modified: 2019-05-24 description: BackgroundIn the ocean, the variability of environmental conditions found along depth gradients exposes populations to contrasting levels of perturbation, which can be reflected in the overall patterns of species genetic diversity. At shallow sites, resource availability may structure large, persistent and well-connected populations with higher levels of diversity. In contrast, the more extreme conditions, such as thermal stress during heat waves, can lead to population bottlenecks and genetic erosion, inverting the natural expectation. Here we examine how genetic diversity varies along depth for a long-lived, important ecosystem-structuring species, the red gorgonian, Paramuricea clavata.MethodsWe used five polymorphic microsatellite markers to infer differences in genetic diversity and differentiation, and to detect bottleneck signs between shallow and deeper populations across the Atlantic Ocean and the Mediterranean Sea. We further explored the potential relationship between depth and environmental gradients (temperature, ocean currents, productivity and slope) on the observed patterns of diversity by means of generalized linear mixed models.ResultsAn overall pattern of higher genetic diversity was found in the deeper sites of the Atlantic Ocean and the Mediterranean Sea. This pattern was largely explained by bottom temperatures, with a linear pattern of decreasing genetic diversity with increasing thermal stress. Genetic differentiation patterns showed higher gene flow within sites (i.e., shallow vs. deeper populations) than between sites. Recent genetic bottlenecks were found in two populations of shallow depths.DiscussionOur results highlight the role of deep refugial populations safeguarding higher and unique genetic diversity for marine structuring species. Theoretical regression modelling demonstrated how thermal stress alone may reduce population sizes and diversity levels of shallow water populations. In fact, the examination of time series on a daily basis showed the upper water masses repeatedly reaching lethal temperatures for P. clavata. Differentiation patterns showed that the deep richer populations are isolated. Gene flow was also inferred across different depths; however, not in sufficient levels to offset the detrimental effects of surface environmental conditions on genetic diversity. The identification of deep isolated areas with high conservation value for the red gorgonian represents an important step in the face of ongoing and future climate changes. creator: Joanna Pilczynska creator: Silvia Cocito creator: Joana Boavida creator: Ester A. Serrão creator: Jorge Assis creator: Eliza Fragkopoulou creator: Henrique Queiroga uri: https://doi.org/10.7717/peerj.6794 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pilczynska et al. title: Fragility Index, power, strength and robustness of findings in sports medicine and arthroscopic surgery: a secondary analysis of data from a study on use of the Fragility Index in sports surgery link: https://peerj.com/articles/6813 last-modified: 2019-05-24 description: BackgroundA recent study concluded that most findings reported as significant in sports medicine and arthroscopic surgery are not “robust” when evaluated with the Fragility Index (FI). A secondary analysis of data from a previous study was performed to investigate (1) the correctness of the findings, (2) the association between FI, p-value and post hoc power, (3) median power to detect a medium effect size, and (4) the implementation of sample size analysis in these randomized controlled trials (RCTs).MethodsIn addition to the 48 studies listed in the appendix accompanying the original study by Khan et al. (2017) we did a follow-up literature search and 18 additional studies were found. In total 66 studies were included in the analysis. We calculated post hoc power, p-values and confidence intervals associated with the main outcome variable. Use of a priori power analysis was recorded. The median power to detect small (h > 0.2), medium (h > 0.5), or large effect (h > 0.8) with a baseline proportion of events of 10% and 30% in each study included was calculated. Three simulation data sets were used to validate our findings.ResultsInconsistencies were found in eight studies. A priori power analysis was missing in one-fourth of studies (16/66). The median power to detect a medium effect size with a baseline proportion of events of 10% and 30% was 42% and 43%, respectively. The FI was inherently associated with the achieved p-value and post hoc power.DiscussionA relatively high proportion of studies had inconsistencies. The FI is a surrogate measure for p-value and post hoc power. Based on these studies, the median power in this field of research is suboptimal. There is an urgent need to investigate how well research claims in orthopedics hold in a replicated setting and the validity of research findings. creator: Aleksi Reito creator: Lauri Raittio creator: Olli Helminen uri: https://doi.org/10.7717/peerj.6813 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Reito et al. title: Application of the urban exposome framework using drinking water and quality of life indicators: a proof-of-concept study in Limassol, Cyprus link: https://peerj.com/articles/6851 last-modified: 2019-05-24 description: BackgroundCities face rapid changes leading to increasing inequalities and emerging public health issues that require cost-effective interventions. The urban exposome concept refers to the continuous monitoring of urban environmental and health indicators using the city and smaller intra-city areas as measurement units in an interdisciplinary approach that combines qualitative and quantitative methods from social sciences, to epidemiology and exposure assessment.MethodsIn this proof of concept study, drinking water and quality of life indicators were described as part of the development of the urban exposome of Limassol (Cyprus) and were combined with agnostic environment-wide association analysis. This study was conducted as a two-part project with a qualitative part assessing the perceptions of city stakeholders, and quantitative part using a cross-sectional study design (an urban population study). We mapped the water quality parameters and participants’ opinions on city life (i.e., neighborhood life, health care, and green space access) using quarters (small administrative areas) as the reference unit of the city. In an exploratory, agnostic, environment-wide association study analysis, we used all variables (questionnaire responses and water quality metrics) to describe correlations between them.ResultsOverall, urban drinking-water quality using conventional indicators of chemical (disinfection byproducts-trihalomethanes (THM)) and microbial (coliforms, E. coli, and Enterococci) quality did not raise particular concerns. The general health and chronic health status of the urban participants were significantly (false discovery rate corrected p-value < 0.1) associated with different health conditions such as hypertension and asthma, as well as having financial issues in access to dental care. Additionally, correlations between THM exposures and participant behavioral characteristics (e.g., household cleaning, drinking water habits) were documented.ConclusionThis proof-of-concept study showed the potential of using integrative approaches to develop urban exposomic profiles and identifying within-city differences in environmental and health indicators. The characterization of the urban exposome of Limassol will be expanded via the inclusion of biomonitoring tools and untargeted metabolomics. creator: Xanthi D. Andrianou creator: Chava van der Lek creator: Pantelis Charisiadis creator: Solomon Ioannou creator: Kalliopi N. Fotopoulou creator: Zoe Papapanagiotou creator: George Botsaris creator: Carijn Beumer creator: Konstantinos C. Makris uri: https://doi.org/10.7717/peerj.6851 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Andrianou et al. title: We need to talk about reliability: making better use of test-retest studies for study design and interpretation link: https://peerj.com/articles/6918 last-modified: 2019-05-24 description: Neuroimaging, in addition to many other fields of clinical research, is both time-consuming and expensive, and recruitable patients can be scarce. These constraints limit the possibility of large-sample experimental designs, and often lead to statistically underpowered studies. This problem is exacerbated by the use of outcome measures whose accuracy is sometimes insufficient to answer the scientific questions posed. Reliability is usually assessed in validation studies using healthy participants, however these results are often not easily applicable to clinical studies examining different populations. I present a new method and tools for using summary statistics from previously published test-retest studies to approximate the reliability of outcomes in new samples. In this way, the feasibility of a new study can be assessed during planning stages, and before collecting any new data. An R package called relfeas also accompanies this article for performing these calculations. In summary, these methods and tools will allow researchers to avoid performing costly studies which are, by virtue of their design, unlikely to yield informative conclusions. creator: Granville J. Matheson uri: https://doi.org/10.7717/peerj.6918 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Matheson title: Double decoupling effectiveness of water consumption and wastewater discharge in China’s textile industry based on water footprint theory link: https://peerj.com/articles/6937 last-modified: 2019-05-24 description: As a traditional pillar industry in China, the textile industry has been intensifying the pressure of the water resource load and its reduction of water environment emissions over the years. Decoupling water resource consumption and wastewater discharge require decoupling from economic growth to realise the sustainable development of the textile industry. On the basis of water footprint and decoupling theories, this paper analysed the water consumption decoupling, wastewater discharge decoupling, as well as the double decoupling of water consumption and wastewater discharge of China’s textile industry and its three sub-industries (Manufacture of Textile, Manufacture of Textile Wearing and Apparel, Manufacture of Chemistry) from 2001 to 2015. In those years, the sum of the decoupling index in the double-decoupling years is 249, lower than that in high-decoupling years of water consumption (250) and wastewater discharge (325). Compared with the decoupling of water consumption and of wastewater discharge, the double decoupling is lower, which proves that the conditions for realizing double decoupling are stricter. The double decoupling analysis of water consumption and wastewater discharge, namely, the overall consideration of water resource consumption and water environment pollution, could be used to more effectively promote the realisation of water decoupling in the textile industry. creator: Yi Li creator: Yi Wang uri: https://doi.org/10.7717/peerj.6937 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li and Wang title: Conservation and sustainable use of the medicinal Leguminosae plants from Angola link: https://peerj.com/articles/6736 last-modified: 2019-05-23 description: Leguminosae is an economically important family that contains a large number of medicinal plants, many of which are widely used in African traditional medicine. Angola holds a great socio-cultural diversity and is one of the richest floristic regions of the world, with over 900 native Leguminosae species. This study is the first to assess the medicinal uses of the legumes in Angola and provides new data to promote the conservation and the sustainable use of these unique resources. We document the ethnobotanical knowledge on Angola by reviewing the most important herbarium collections and literature, complemented by recent field surveys. Our results revealed that 127 native legume species have medicinal uses and 65% of them have other important uses by local populations. The species with most medicinal applications are Erythrina abyssinica, Bauhinia thonningii and Pterocarpus angolensis. The rich flora found in Angola suggests an enormous potential for discovery of new drugs with therapeutic value. However, the overexploitation and the indiscriminate collection of legumes for multiple uses such as forage, food, timber and medical uses, increases the threats upon the native vegetation. Efforts to assess the conservation status of these species are urgently needed, and future actions should promote the sustainable use of medicinal plants in Angola together with the implementation of conservation strategies. creator: Silvia Catarino creator: Maria Cristina Duarte creator: Esperança Costa creator: Paula Garcia Carrero creator: Maria M. Romeiras uri: https://doi.org/10.7717/peerj.6736 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Catarino et al. title: Molecular serotyping of clinical strains of Haemophilus (Glaesserella) parasuis brings new insights regarding Glässer’s disease outbreaks in Brazil link: https://peerj.com/articles/6817 last-modified: 2019-05-23 description: Glässer’s disease (GD) is an important infectious disease of swine caused by Haemophilus (Glaesserella) parasuis. Vaccination with inactivated whole cell vaccines is the major approach for prevention of H. parasuis infection worldwide, but the immunity induced is predominantly against the specific polysaccharide capsule. As a consequence, the available vaccines may not induce adequate protection against the field strains, when the capsules present in the vaccine strains are different from those in strains isolated from the farms. Therefore, it is crucial to map H. parasuis serovars associated with regional outbreaks so that appropriate bacterin vaccines can be developed and distributed for prevention of infection. In this study, 459 H. parasuis field strains isolated from different Glässer’s disease outbreaks that occurred in 10 different Brazilian States were analyzed for serotype using PCR-based approaches. Surprisingly, non-typeable (NT) strains were the second most prevalent group of field strains and along with serovars 4, 5 and 1 comprised more than 70% of the isolates. A PCR-based approach designed to amplify the entire polysaccharide capsule locus revealed 9 different band patterns in the NT strains, and 75% of the NT strains belonged to three clusters, suggesting that a number of new serovars are responsible for a substantial proportion of disease. These results indicate that commercially available vaccines in Brazil do not cover the most prevalent H. parasuis serovars associated with GD. creator: Julia Pires Espíndola creator: Natalia Balbinott creator: Letícia Trevisan Gressler creator: Gustavo Machado creator: Catia Silene Klein creator: Raquel Rebelatto creator: César Bernardo Gutiérrez Martín creator: Luiz Carlos Kreutz creator: Anthony Bernard Schryvers creator: Rafael Frandoloso uri: https://doi.org/10.7717/peerj.6817 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pires Espíndola et al. title: Serum heparan sulfate and chondroitin sulfate concentrations in patients with newly diagnosed exfoliative glaucoma link: https://peerj.com/articles/6920 last-modified: 2019-05-23 description: BackgroundExfoliative glaucoma (XFG) is typically classified as a high-pressure type of secondary open-angle glaucoma that develops as a consequence of exfoliation syndrome (XFS). Exfoliation syndrome is an age-related, generalized disorder of the extracellular matrix characterized by production and progressive accumulation of a fibrillar exfoliation material (XFM) in intra- and extraocular tissues. Exfoliation material represents complex glycoprotein/proteoglycan structure composed of a protein core surrounded by glycosaminoglycans such as heparan sulfate (HS) and chondroitin sulfate (CS). The purpose of the present study was to investigate HS and CS concentrations in serum samples of patients with newly diagnosed XFG and compare the obtained values with those pertaining to newly diagnosed primary open-angle glaucoma (POAG), normal controls (NC) and subjects with XFS.MethodsThis case–control study involved 165 subjects, including patients with newly diagnosed XFG, patients with newly diagnosed POAG, subjects with XFS and age- and sex-matched NC. The study was conducted at the Glaucoma Department of Clinic for Eye Diseases, Clinical Centre of Serbia, as the referral center for glaucoma in Serbia.ResultsThe mean age in the XFG, POAG, XFS and NC groups was 73.3 ± 9.0, 66.3 ± 7.8, 75.5 ± 7.0 and 73.5 ± 9.5 years, respectively, XFG vs. POAG, p < 0.001. Mean serum HS concentrations in the XFG, POAG, NC and XFS groups were 3,189.0 ± 1,473.8 ng/mL, 2,091.5 ± 940.9 ng/mL, 2,543.1 ± 1,397.3 ng/mL and 2,658.2 ± 1,426.8 ng/mL respectively, XFG vs. POAG, p = 0.001 and XFG vs. NC, p = 0.032. Mean serum CS concentrations in the XFG, POAG, NC and XFS group were 43.9 ± 20.7 ng/mL, 38.5 ± 22.0 ng/mL, 35.8 ± 16.4 ng/mL and 43.3 ± 21.8 ng/mL, respectively, XFG vs. NC, p = 0.041.ConclusionsOur findings revealed greater HS and CS concentrations in XFG patients and XFS subjects compared to those without XFM. Implications of HS and CS in the pathophysiology of XFS and glaucoma should be studied further. Serum is easily accessible and should thus be explored as rich sources of potential biomarkers. Further research should aim to identify XFG biomarkers that could be utilized in routine blood analysis tests, aiding in timely disease diagnosis. creator: Vesna D. Maric creator: Marija M. Bozic creator: Andja M. Cirkovic creator: Sanja Dj Stankovic creator: Ivan S. Marjanovic creator: Anita D. Grgurevic uri: https://doi.org/10.7717/peerj.6920 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Maric et al. title: Identification and characterization of mRNAs and lncRNAs in the uterus of polytocous and monotocous Small Tail Han sheep (Ovis aries) link: https://peerj.com/articles/6938 last-modified: 2019-05-23 description: BackgroundLong non-coding RNAs (lncRNAs) regulate endometrial secretion and uterine volume. However, there is little research on the role of lncRNAs in the uterus of Small Tail Han sheep (FecB++). Herein, RNA-seq was used to comparatively analyze gene expression profiles of uterine tissue between polytocous and monotocous sheep (FecB++) in follicular and luteal phases.MethodsTo identify lncRNA and mRNA expressed in the uterus, the expression of lncRNA and mRNA in the uterus of Small Tail Han sheep (FecB++) from the polytocous group (n = 6) and the monotocous group (n = 6) using RNA-sequencing and real-time polymerase chain reaction (RT-PCR). Identification of differentially expressed lncRNAs and mRNAs were performed between the two groups and two phases . Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA co-expression network was constructed to further analyses the function of related genes.ResultsIn the follicular phase, 473 lncRNAs and 166 mRNAs were differentially expressed in polytocous and monotocous sheep; in the luteal phase, 967 lncRNAs and 505 mRNAs were differentially expressed in polytocous and monotocous sheep. GO and KEGG enrichment analysis showed that the differentially expressed lncRNAs and their target genes are mainly involved in ovarian steroidogenesis, retinol metabolism, the oxytocin signaling pathway, steroid hormone biosynthesis, and the Foxo signaling pathway. Key lncRNAs may regulate reproduction by regulating genes involved in these signaling pathways and biological processes. Specifically, UGT1A1, LHB, TGFB1, TAB1, and RHOA, which are targeted by MSTRG.134747, MSTRG.82376, MSTRG.134749, MSTRG.134751, and MSTRG.134746, may play key regulatory roles. These results offer insight into molecular mechanisms underlying sheep prolificacy. creator: Yongfu La creator: Jishun Tang creator: Xiaoyun He creator: Ran Di creator: Xiangyu Wang creator: Qiuyue Liu creator: Liping Zhang creator: Xiaosheng Zhang creator: Jinlong Zhang creator: Wenping Hu creator: Mingxing Chu uri: https://doi.org/10.7717/peerj.6938 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 La et al. title: Gene expression in Tribolium castaneum life stages: Identifying a species-specific target for pest control applications link: https://peerj.com/articles/6946 last-modified: 2019-05-23 description: The red flour beetle, Tribolium castaneum, is a major agricultural pest of post-harvest products and stored grain. Control of T. castaneum in stored products and grain is primarily by fumigants and sprays, but insecticide resistance is a major problem, and new control strategies are needed. T. castaneum is a genetic model for coleopterans, and the reference genome can be used for discovery of candidate gene targets for molecular-based control, such as RNA interference. Gene targets need to be pest specific, and ideally, they are expressed at low levels for successful control. Therefore, we sequenced the transcriptome of four major life stages of T. castaneum, sorted data into groups based on high or low expression levels, and compared relative gene expression among all life stages. We narrowed our candidate gene list to a cuticle protein gene (CPG) for further analysis. We found that the CPG sequence was unique to T. castaneum and expressed only in the larval stage. RNA interference targeting CPG in newly-emerged larvae caused a significant (p < 0.05) decrease in CPG expression (1,491-fold) compared to control larvae and 64% mortality over 18 d. RNA-Seq of survivors after 18 d identified changes in the expression of other genes as well, including 52 long noncoding RNAs. Expression of three additional cuticle protein genes were increased and two chitinase genes were decreased in response to injection of CPG dsRNA. The data demonstrate that RNA-Seq can identify genes important for insect survival and thus may be used to develop novel biologically-based insect control products. creator: Lindsey C. Perkin creator: Brenda Oppert uri: https://doi.org/10.7717/peerj.6946 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Perkin and Oppert title: Transcriptomic study of the mechanism of anoikis resistance in head and neck squamous carcinoma link: https://peerj.com/articles/6978 last-modified: 2019-05-23 description: BackgroundNormal epithelial cells rapidly undergo apoptosis as soon as they lose contact with the extracellular matrix (ECM), which is termed as anoikis. However, cancer cells tend to develop a resistance mechanism to anoikis. This acquired ability is termed as anoikis resistance. Cancer cells, with anoikis resistance, can spread to distant tissues or organs via the peripheral circulatory system and cause cancer metastasis. Thus, inhibition of anoikis resistance blocks the metastatic ability of cancer cells.MethodsAnoikis-resistant CAL27 (CAL27AR) cells were induced from CAL27 cells using the suspension culture approach. Transcriptome analysis was performed using RNA-Seq to study the differentially expressed genes (DEGs) between the CAL27ARcells and the parental CAL27 cells. Gene function annotation and Gene Ontology (GO) enrichment analysis were performed using DAVID database. Signaling pathways involved in DEGs were analyzed using Gene Set Enrichment Analysis (GSEA) software. Analysis results were confirmed by reverse transcription PCR (RT-PCR), western blotting, and gene correlation analysis based on the TCGA database.ResultsGO enrichment analysis indicated that the biological process (BP) of the DEGs was associated with epidermal development, DNA replication, and G1/S transition of the mitotic cell cycle. The analysis of cellular component (CC) showed that the most significant up-regulated genes were related to extracellular exosome. KEGG Pathway analysis revealed that 23 signaling pathways were activated (p-value ≤ 0.05, FDR q-value ≤ 0.05) and 22 signaling pathways were suppressed (p-value ≤ 0.05, FDR q-value ≤ 0.05). The results from the GSEA indicated that in contrast to the inhibition of EGFR signaling pathway, the VEGF signaling pathway was activated. The VEGF signaling pathway possibly activates STAT3 though induction of STAT3 phosphorylation. Gene correlation analysis revealed that the VEGFA- STAT3-KLF4-CDKN1A signal axis was not only present in head and neck squamous carcinoma (HNSCC) but also two other epithelial-derived carcinomas that highly express VEGFA, including kidney renal clear cell carcinoma (KIRC) and ovarian serous cystadenocarcinoma (OV). creator: Chen Guo creator: Ling-feng Xu creator: Hui-min Li creator: Wei Wang creator: Ji-hua Guo creator: Meng-qi Jia creator: Rong Jia creator: Jun Jia uri: https://doi.org/10.7717/peerj.6978 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guo et al. title: Simphony: simulating large-scale, rhythmic data link: https://peerj.com/articles/6985 last-modified: 2019-05-23 description: Simulated data are invaluable for assessing a computational method’s ability to distinguish signal from noise. Although many biological systems show rhythmicity, there is no general-purpose tool to simulate large-scale, rhythmic data. Here we present Simphony, an R package for simulating data from experiments in which the abundances of rhythmic and non-rhythmic features (e.g., genes) are measured at multiple time points in multiple conditions. Simphony has parameters for specifying experimental design and each feature’s rhythmic properties (e.g., amplitude and phase). In addition, Simphony can sample measurements from Gaussian and negative binomial distributions, the latter of which approximates read counts from RNA-seq data. We show an example of using Simphony to evaluate the accuracy of rhythm detection. Our results suggest that Simphony will aid experimental design and computational method development. Simphony is thoroughly documented and freely available at https://github.com/hugheylab/simphony. creator: Jordan M. Singer creator: Darwin Y. Fu creator: Jacob J. Hughey uri: https://doi.org/10.7717/peerj.6985 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Singer et al. title: A mathematical landmark-based method for measuring worn molars in hominoid systematics link: https://peerj.com/articles/6990 last-modified: 2019-05-23 description: Worn teeth pose a major limitation to researchers in the fields of extinct and extant hominoid systematics because they lack clearly identifiable anatomical landmarks needed to take measurements on the crown enamel surface and are typically discarded from a study. This is particularly detrimental when sample sizes for some groups are already characteristically low, if there is an imbalance between samples representing populations, sexes or dietary strategies, or if the worn teeth in question are type specimens of fossil species or other key specimens. This study proposes a methodology based predominantly on mathematically-derived landmarks for measuring size and shape features of molars, irrespective of wear. With 110 specimens of lower second molars from five species of extant hominoids (Pan troglodytes, P. paniscus, Gorilla gorilla, G. beringei, Homo sapiens), n ≥ 20 per species, n ≥ 10 per subspecies, good species separation in morphospace is achieved in a principal components analysis. Classification accuracy in a discriminant function analysis is 96.4% at the species level and 88.2% at the subspecies level (92.7% and 79.1%, respectively, on cross-validation). The classification accuracy compares favorably to that achieved by anatomically-derived measurements based on published research (94% and 84% at the species and subspecies level respectively; 91% and 76% on cross-validation). The mathematical landmarking methodology is rapid and uncomplicated. The results support the use of mathematical landmarks to enable the inclusion of worn molar teeth in dental studies so as to maximize sample sizes and restore balance between populations and/or sexes in hominoid systematic studies. creator: Susan J. Dykes creator: Varsha C. Pilbrow uri: https://doi.org/10.7717/peerj.6990 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dykes and Pilbrow title: Effect of GARP on osteogenic differentiation of bone marrow mesenchymal stem cells via the regulation of TGFβ1 in vitro link: https://peerj.com/articles/6993 last-modified: 2019-05-23 description: Mesenchymal stem cells (MSCs), which have multipotential differentiation and self-renewal potential, are possible cells for tissue engineering. Transforming growth factor β1 (TGFβ1) can be produced by MSCs in an inactive form, and the activation of TGFβ1 functions as an important regulator of osteogenic differentiation in MSCs. Recently, studies showed that Glycoprotein A repetitions predominant (GARP) participated in the activation of latent TGFβ1, but the interaction between GARP and TGFβ1 is still undefined. In our study, we successfully isolated the MSCs from bone marrow of rats, and showed that GARP was detected in bone mesenchymal stem cells (BMSCs). During the osteogenic differentiation of BMSCs, GARP expression was increased over time. To elucidate the interaction between GARP and TGFβ1, we downregulated GARP expression in BMSCs to examine the level of active TGFβ1. We then verified that the downregulation of GARP decreased the secretion of active TGFβ1. Furthermore, osteogenic differentiation experiments, alkaline phosphatase (ALP) activity analyses and Alizarin Red S staining experiments were performed to evaluate the osteogenic capacity. After the downregulation of GARP, ALP activity and Alizarin Red S staining significantly declined and the osteogenic indicators, ALP, Runx2, and OPN, also decreased, both at the mRNA and protein levels. These results demonstrated that downregulated GARP expression resulted in the reduction of TGFβ1 and the attenuation of osteoblast differentiation of BMSCs in vitro. creator: Ruixue Li creator: Jian Sun creator: Fei Yang creator: Yang Sun creator: Xingwen Wu creator: Qianrong Zhou creator: Youcheng Yu creator: Wei Bi uri: https://doi.org/10.7717/peerj.6993 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Boat anchoring contributes substantially to coral reef degradation in the British Virgin Islands link: https://peerj.com/articles/7010 last-modified: 2019-05-23 description: Community decline is often linked to anthropogenic activities. Coral reef declines, for example, have been linked to overfishing and climate change, but impacts of coastal development, pollution, and tourism have received increasing attention. Here, we isolated the impact of one little-studied aspect of recreational activity on coral reefs—damage from boat anchoring—by performing a survey of 24 sites in the British Virgin Islands (BVI) subject to varying levels of anchoring activity. The percent cover of hard corals and sea fans was reduced by a factor of ∼1.7 and ∼2.6 respectively at highly anchored sites. Hard coral colonies were  40% smaller in surface area and ∼60% less dense at sites experiencing high anchoring frequency. In addition, highly anchored sites supported only ∼60% of the species richness of little anchored sites. Frequently anchored sites were ∼60% as structurally complex and supported less than half as many fish as those rarely anchored, with 5 of 7 fish functional groups affected. Roughly 24% of BVI coral reef by area appears suitable for anchoring, suggesting that impacts associated with boat anchoring may be both locally severe and more pervasive than previously appreciated. creator: Rebecca L. Flynn creator: Graham E. Forrester uri: https://doi.org/10.7717/peerj.7010 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Flynn and Forrester title: The braincase of Mesosuchus browni (Reptilia, Archosauromorpha) with information on the inner ear and description of a pneumatic sinus link: https://peerj.com/articles/6798 last-modified: 2019-05-22 description: Rhynchosauria is a group of archosauromorph reptiles abundant in terrestrial ecosystems of the Middle Triassic. Mesosuchus is one of the earliest and basalmost rhynchosaurs, playing an important role not only for the understanding of the evolution of the group as a whole, but also of archosauromorphs in general. The braincase of Mesosuchus has been previously described, albeit not in detail, and the middle and inner ears were missing. Here, we provide new information based on micro-computed tomography scanning of the best-preserved specimen of Mesosuchus, SAM-PK-6536. Contrary to what has been stated previously, the braincase of Mesosuchus is dorso-ventrally tall. The trigeminal foramen lies in a deep recess on the prootic whose flat ventral rim could indicate the articulation surface to the laterosphenoid, although no such element was found. The middle ear of Mesosuchus shows a small and deeply recessed fenestra ovalis, with the right stapes preserved in situ. It has a rather stout, imperforated and posteriorly directed shaft with a small footplate. These features suggest that the ear of Mesosuchus was well-suited for the detection of low-frequency sounds. The semicircular canals are slender and elongate and the floccular fossa is well-developed. This is indicative of a refined mechanism for gaze stabilization, which is usually related to non-sprawling postures. The most striking feature of the Mesosuchus braincase is, however, the presence of a pneumatic sinus in the basal tubera. The sinus is identified as originating from the pharyngotympanic system, implying ossified Eustachian tubes. Braincase pneumatization has not yet been a recognized feature of stem-archosaurs, but the potential presence of pneumatic foramina in an array of taxa, recognized here as such for the first time, suggests braincase sinuses could be present in many other archosauromorphs. creator: Gabriela Sobral creator: Johannes Müller uri: https://doi.org/10.7717/peerj.6798 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sobral and Müller title: FunPred 3.0: improved protein function prediction using protein interaction network link: https://peerj.com/articles/6830 last-modified: 2019-05-22 description: Proteins are the most versatile macromolecules in living systems and perform crucial biological functions. In the advent of the post-genomic era, the next generation sequencing is done routinely at the population scale for a variety of species. The challenging problem is to massively determine the functions of proteins that are yet not characterized by detailed experimental studies. Identification of protein functions experimentally is a laborious and time-consuming task involving many resources. We therefore propose the automated protein function prediction methodology using in silico algorithms trained on carefully curated experimental datasets. We present the improved protein function prediction tool FunPred 3.0, an extended version of our previous methodology FunPred 2, which exploits neighborhood properties in protein–protein interaction network (PPIN) and physicochemical properties of amino acids. Our method is validated using the available functional annotations in the PPIN network of Saccharomyces cerevisiae in the latest Munich information center for protein (MIPS) dataset. The PPIN data of S. cerevisiae in MIPS dataset includes 4,554 unique proteins in 13,528 protein–protein interactions after the elimination of the self-replicating and the self-interacting protein pairs. Using the developed FunPred 3.0 tool, we are able to achieve the mean precision, the recall and the F-score values of 0.55, 0.82 and 0.66, respectively. FunPred 3.0 is then used to predict the functions of unpredicted protein pairs (incomplete and missing functional annotations) in MIPS dataset of S. cerevisiae. The method is also capable of predicting the subcellular localization of proteins along with its corresponding functions. The code and the complete prediction results are available freely at: https://github.com/SovanSaha/FunPred-3.0.git. creator: Sovan Saha creator: Piyali Chatterjee creator: Subhadip Basu creator: Mita Nasipuri creator: Dariusz Plewczynski uri: https://doi.org/10.7717/peerj.6830 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Saha et al. title: Chemodiversity of Calophyllum inophyllum L. oil bioactive components related to their specific geographical distribution in the South Pacific region link: https://peerj.com/articles/6896 last-modified: 2019-05-22 description: BackgroundDifferent parts of the tree Calophyllum inophyllum L. (nuts, leaves, roots, bark, fruits, nut oil and resin) are used as traditional medicines and cosmetics in most of the Pacific Islands. The oil efficiency as a natural cure and in traditional cosmetics has been largely described throughout the South Pacific, which led us to investigate C. inophyllum’s chemical and genetic diversity. A correlative study of the nut resin and leaf DNA from three distinct archipelagos in the South Pacific was carried out in order to identify diversity patterns in C. inophyllum across the South Pacific.MethodsCalophyllum inophyllum plants were sampled from French Polynesia, New Caledonia and Fiji. We extracted tamanu oil (nut oil) resin for chemo-diversity studies and sampled leaf tissues for genetic studies. We applied an analysis method designed for small quantities (at a microscale level), and used High Performance Liquid Chromatography (HPLC) to establish the chemo-diversity of tamanu oil resin. In-house standards were co-eluted for qualitative determination. Genetic diversity was assessed using chloroplast barcoding markers (the Acetyl-CoA carboxylase (accD) gene and the psaA-ycf3 intergenic spacer region).ResultsOur HPLC analysis revealed 11 previously known tamanu oil constituents, with variability among plant samples. We also isolated and characterized two new neoflavonoids from tamanu oil resin namely, tamanolide E1 and E2 which are diastereoisomers. Although genetic analysis revealed low genetic variation, our multivariate analysis (PCA) of the tamanu oil resin chemical profiles revealed differentiation among geographic regions.ConclusionWe showed here that chromatographic analysis using formalized in-house standards of oil resin compounds for co-elution studies against oil resin samples could identify patterns of variation among samples of C. inophyllum, and discriminate samples from different geographical origins. creator: Joape Ginigini creator: Gaël J. Lecellier creator: Mael Nicolas creator: Mohammed Nour creator: Edouard Hnawia creator: Nicolas Lebouvier creator: Gaëtan Herbette creator: Peter Lockhart creator: Phila Raharivelomanana uri: https://doi.org/10.7717/peerj.6896 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ginigini et al. title: Evaluation of in-vitro methods to select effective streptomycetes against toxigenic fusaria link: https://peerj.com/articles/6905 last-modified: 2019-05-22 description: Biocontrol microorganisms are emerging as an effective alternative to pesticides. Ideally, biocontrol agents (BCAs) for the control of fungal plant pathogens should be selected by an in vitro method that is high-throughput and is predictive of in planta efficacy, possibly considering environmental factors, and the natural diversity of the pathogen. The purpose of our study was (1) to assess the effects of Fusarium strain diversity (N = 5) and culture media (N = 6) on the identification of biological control activity of Streptomyces strains (N = 20) against Fusarium pathogens of wheat in vitro and (2) to verify the ability of our in vitro screening methods to simulate the activity in planta. Our results indicate that culture media, Fusarium strain diversity, and their interactions affect the results of an in vitro selection by dual culture assay. The results obtained on the wheat-based culture media resulted in the highest correlation score (r = 0.5) with the in planta root rot (RR) inhibition, suggesting that this in vitro method was the best predictor of in planta performance of streptomycetes against Fusarium RR of wheat assessed as extension of the necrosis on the root. Contrarily, none of the in vitro plate assays using the media tested could appropriately predict the activity of the streptomycetes against Fusarium foot rot symptoms estimated as the necrosis at the crown level. Considering overall data of correlation, the activity in planta cannot be effectively predicted by dual culture plate studies, therefore improved in vitro methods are needed to better mimic the activity of biocontrol strains in natural conditions. This work contributes to setting up laboratory standards for preliminary screening assays of Streptomyces BCAs against fungal pathogens. creator: Elena Maria Colombo creator: Cristina Pizzatti creator: Andrea Kunova creator: Claudio Gardana creator: Marco Saracchi creator: Paolo Cortesi creator: Matias Pasquali uri: https://doi.org/10.7717/peerj.6905 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Colombo et al. title: Imagery ability of elite level athletes from individual vs. team and contact vs. no-contact sports link: https://peerj.com/articles/6940 last-modified: 2019-05-22 description: BackgroundIn the sport context, imagery has been described as the condition in which persons imagine themselves while executing skills to deal with the upcoming task or enhance performance. Systematic reviews have shown that mental imagery improves performance in motor tasksMethodsThe aim of the present study was to explore whether imagery vividness (i.e., the clarity or realism of the imagery experience) and controllability (i.e., the ease and accuracy with which an image can be manipulated mentally) differ by sport types (team vs. individual and contact vs. non-contact). Participants were athletes from team contact and non-contact sports (rugby and volleyball, respectively), and individual contact and non-contact sports (karate and tennis, respectively) between the ages of 20 and 33 years (M = 24.37, SD = 2.85). The participants completed the Vividness of Visual Imagery Questionnaire, the Vividness of Movement Imagery Questionnaire-2, and the Mental Image Transformation Tasks.ResultsA 2 ×2 × 2 (gender × 2 contact-no-contact × 2 sport type) between groups MANOVA showed differences in imagery ability by sport type. Practical indications deriving from the findings of this study can help coaches and athletes to develop mental preparation programs using sport-specific imagery. creator: Donatella Di Corrado creator: Maria Guarnera creator: Francesca Vitali creator: Alessandro Quartiroli creator: Marinella Coco uri: https://doi.org/10.7717/peerj.6940 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Di Corrado et al. title: Aromatisation of steroids in the bivalve Mytilus trossulus link: https://peerj.com/articles/6953 last-modified: 2019-05-22 description: In this study, we demonstrated the presence of the enzymatic complex able to perform aromatization (estrogen synthesis) in both, the microsomal and mitochondrial fractions of gills and gonads from Mytilus trossulus. Based on in vitro experiments, we highlighted the importance of temperature as the limiting factor of aromatisation efficiency (AE) in mussels. After testing range of temperatures (4–23 °C), the highest AE was found during incubation at 8 °C and pH 7.6 (41.66 pmol/h/mg protein in gills and 58.37 pmol/h/mg protein in gonads). The results were confirmed during field studies where the most efficient aromatisation occurred in bivalves collected in spring while the least effective in those collected in winter. During in vitro studies, AE turned out to be more intensive in female gonads than in male gonads. The process was also more intensive in mitochondrial fraction than in microsomal one (62.97 pmol/h/mg protein in male gills and 73.94 pmol/h/mg protein in female gonads). Enzymatic complex (aromatase-like enzyme) catalysing aromatisation in mussels was found to be insensitive to inhibitory effect of selective inhibitors of mammalian aromatase such as letrozole and anastrazole, suggesting its different structure from vertebrate aromatase. Further in vivo studies using 13C-labeled steroids at 8 °C temperature window confirmed that bivalves are able to uptake testosterone and androstenedione from the ambient environment and metabolise them to estrone and 17β-estradiol thus confirming endogenous estrogen’ synthesis. creator: Anna Hallmann creator: Lucyna Konieczna creator: Justyna Swiezak creator: Ryszard Milczarek creator: Katarzyna Smolarz uri: https://doi.org/10.7717/peerj.6953 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hallmann et al. title: The use of bat houses as day roosts in macadamia orchards, South Africa link: https://peerj.com/articles/6954 last-modified: 2019-05-22 description: The loss of roost sites is one of the major drivers of the worldwide decline in bat populations and roost site preferences, either natural or artificially provided, are not well known for African bat species specifically. In this study we focus on the preference for different artificial roost sites by insectivorous bats in macadamia orchards in northern South Africa. From June 2016 to July 2017 we monitored 31 bat houses, mounted on poles in six macadamia orchards, for presence of bats or other occupants. Twenty-one multi-chambered bat houses of three different designs were erected in sets of three. Additionally, five Rocket boxes, four bat houses in sets of two (painted black and white) and one colony bat house were erected. Bats were counted and visually identified to family or species level. From December 2016 to the end of March 2017 iButtons were installed to record and analyze temperature variation within one set of three bat houses. We related the occupancy of bat houses to the different types of houses and the environmental variables: distance to water, altitude and height of the bat houses above the ground. Overall bat house occupancy was significantly higher in the central bat house, in the set of three, and the black bat house, in the set of two. Mean temperatures differed between houses in the set of three with the central bat house having a significantly higher mean temperature than the houses flanking it. Our study might confirm previous assumptions that the microclimate of bat houses appears to be an important factor influencing occupancy. In conclusion, from the different bat houses tested in this study the designs we assume the warmest and best insulated attracted the most bats. Further research is needed on the preferred microclimate of different bat species, co-habitation within bat houses and the potential importance of altitude and distance to water. Our study provided little variation in both altitude and the distance to water. creator: Sina M. Weier creator: Valerie M.G. Linden creator: Ingo Grass creator: Teja Tscharntke creator: Peter J. Taylor uri: https://doi.org/10.7717/peerj.6954 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Weier et al. title: Crossmodal congruency effect scores decrease with repeat test exposure link: https://peerj.com/articles/6976 last-modified: 2019-05-22 description: The incorporation of feedback into a person’s body schema is well established. The crossmodal congruency task (CCT) is used to objectively quantify incorporation without being susceptible to experimenter biases. This visual-tactile interference task is used to calculate the crossmodal congruency effect (CCE) score as a difference in response time between incongruent and congruent trials. Here we show that this metric is susceptible to a learning effect that causes attenuation of the CCE score due to repeated task exposure sessions. We demonstrate that this learning effect is persistent, even after a 6 month hiatus in testing. Two mitigation strategies are proposed: 1. Only use CCE scores that are taken after learning has stabilized, or 2. Use a modified CCT protocol that decreases the task exposure time. We show that the modified and shortened CCT protocol, which may be required to meet time or logistical constraints in laboratory or clinical settings, reduced the impact of the learning effect on CCT results. Importantly, the CCE scores from the modified protocol were not significantly more variable than results obtained with the original protocol. This study highlights the importance of considering exposure time to the CCT when designing experiments and suggests two mitigation strategies to improve the utility of this psychophysical assessment. creator: Daniel Blustein creator: Satinder Gill creator: Adam Wilson creator: Jon Sensinger uri: https://doi.org/10.7717/peerj.6976 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Blustein et al. title: Purification of plant-derived anti-virus mAb through optimized pH conditions for coupling between protein A and epoxy-activated beads link: https://peerj.com/articles/6828 last-modified: 2019-05-21 description: The main goal of this research was to determine optimum pH conditions for coupling between protein A and epoxy-activated Sepharose beads for purification of monoclonal antibodies (mAbs) expressed in plants. To confirm the effect of pH conditions on purification efficacy, epoxy-activated agarose beads were coupled to protein A under the pH conditions of 8.5, 9.5, 10.5, and 11.5 (8.5R, 9.5R, 10.5R, and 11.5R, respectively). A total of 300 g of fresh leaf tissue of transgenic Arabidopsis expressing human anti-rabies mAb (mAbP) SO57 were harvested to isolate the total soluble protein (TSP). An equal amount of TSP solution was applied to five resin groups including commercial protein A resin (GR) as a positive control. The modified 8.5R, 9.5R, 10.5R, and 11.5R showed delayed elution timing compared to the GR control resin. Nano-drop analysis showed that the total amount of purified mAbPSO57 mAbs from 60 g of fresh leaf mass were not significantly different among 8.5R (400 μg), 9.5R (360 μg), 10.5R (380 μg), and GR (350 μg). The 11.5R (25 μg) had the least mAbPSO57. SDS–PAGE analysis showed that the purity of mAbPSO57 was not significantly different among the five groups. Rapid fluorescent focus inhibition tests revealed that virus-neutralizing efficacies of purified mAbPSO57 from all the five different resins including the positive control resin were similar. Taken together, both pH 8.5 and 10.5 coupling conditions with high recovery rate should be optimized for purification of mAbPSO57 from transgenic Arabidopsis plant, which will eventually reduce down-stream cost required for mAb production using the plant system. creator: Ilchan Song creator: Yang Joo Kang creator: Su-Lim Choi creator: Dalmuri Han creator: Deuk-Su Kim creator: Hae Kyung Lee creator: Joon-Chul Lee creator: Jeanho Park creator: Do-Sun Kim creator: Kisung Ko uri: https://doi.org/10.7717/peerj.6828 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Song et al. title: Dietary supplementation of black soldier fly (Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron (Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets link: https://peerj.com/articles/6891 last-modified: 2019-05-21 description: The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture. creator: Md Javed Foysal creator: Ravi Fotedar creator: Chin-Yen Tay creator: Sanjay Kumar Gupta uri: https://doi.org/10.7717/peerj.6891 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Foysal et al. title: Enzyme characterization and biological activities of a resuscitation promoting factor from an oil degrading bacterium Rhodococcus erythropolis KB1 link: https://peerj.com/articles/6951 last-modified: 2019-05-21 description: Resuscitation-promoting factors (Rpf) are a class of muralytic enzymes, which participate in recovery of dormant cells and promoting bacteria growth in poor media. In the present study the expression vector of the rpf-1 gene from an oil-degrading bacterium Rhodococcus erythropolis KB1 was constructed and expressed in Escherichia coli. The expressed protein was purified by Ni2+-affinity chromatography, and showed muralytic activity when measured with 4-methylumbelliferyl-β-D-N,N′,N″-triacetyl chitotrioside as substrate. Addition of purified Rpf-1 to R. erythropolis culture efficiently improved bacterial cell growth. The purified protein also increased resuscitation of viable but nonculturable cells of R. erythropolis to culturable state. The conserved amino acid residues including Asp45, Glu51, Cys50, Thr60, Gln69, Thr74, Trp75 and Cys114 of the Rpf-1 were replaced with different amino acids. The mutant proteins were also expressed and purified with Ni2+-affinity chromatography. The muralytic activities of the mutant proteins decreased to different extents when compared with that of the wild type Rpf-1. Gln69 was found to play the most important role in the enzyme activity, substitution of Gln69 with lysine (Q69K) resulted in the greatest decrease of muralytic activity. The other amino acid residues such as Asp45, Glu51, Cys50 and Cys114 were also found to be very important in maintaining muralytic activity and biological function of the Rpf-1. Our results indicated that Rpf-1 from R. erythropolis showed muralytic activities and weak protease activity, but the muralytic activity was responsible for its growth promotion and resuscitation activity. creator: Dan Luo creator: Jixiang Chen creator: Gang Xie creator: Liang Yue creator: Yonggang Wang uri: https://doi.org/10.7717/peerj.6951 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Luo et al. title: Genetic variability and structure of the Olive Field Mouse: a sigmodontine rodent in a biodiversity hotspot of southern Chile link: https://peerj.com/articles/6955 last-modified: 2019-05-21 description: The temperate rainforests of southern Chile, a recognized biodiversity hotspot, were significantly affected by Pleistocene glacial cycles in their southern portion and have been severely disrupted mainly due to recent human activities. Additionally, the landscape is characterized by a series of potential barriers to gene flow, such as the Chacao Channel, Cordillera de Piuche in Chiloé and both the Ancud and the Corcovado gulfs. We used mitochondrial DNA sequences and microsatellite data across several populations to evaluate the genetic variability and structure of the sigmodontine rodent Abrothrix olivacea brachiotis, one of the most common species of small mammals and an inhabitant of these biodiverse forests. Sequencing data showed that along with the recovery of high haplotype variation for this species, there was a low nucleotide diversity between haplotypes, showing no genetic differences between the Chiloé Island and continental populations in southern Chile or through any other geographic barrier in the study area. However, microsatellite data exhibited some level of population structuring. The most evident clusterings were those of the Chiloé Island and that of North Patagonia. These findings are corroborated by a barrier analysis that showed a genetic barrier in the latter areas, whereas the Chacao Channel was not a significant barrier for this rodent. Overall, the genetic variability and structure of A. o. brachiotis was concordant with historical factors, such as the Last Glacial Maximum and the presence of geographic elements that isolate populations. creator: Paulo S. Zepeda creator: Enrique Rodríguez-Serrano creator: Fernando Torres-Pérez creator: Juan L. Celis-Diez creator: R Eduardo Palma uri: https://doi.org/10.7717/peerj.6955 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zepeda et al. title: Actuopaleoichnology of a modern Bay of Fundy macro-tidal flat: analogy with a Mississippian tidal flat deposit (Hartselle Sandstone) from Alabama link: https://peerj.com/articles/6975 last-modified: 2019-05-21 description: Trace fossil zonation in the Hartselle Sandstone of Mississippian age (Chesterian: Visean-Serpukhovian) exposed on Fielder Ridge, Alabama is compared with modern macro-tidal flat ichnocoenoses on the Bay of Fundy at Lubec, Maine, and demonstrated to be analogous by sedimentologic and ichnotaxonomic criteria. The modern flat has minimal influence from either waves or freshwater influx, and can be divided into five distinct ichnocoenoses, characterized by surface traces (epichnia) and four sedimentologic facies defined by gross grain texture or hydrodynamic characteristics, but lacking significant surface traces. Several characteristics of tidal flat deposits in a fetch-limited, marine (i.e., non-estuarine), meso- to macro-tidal regime can be used to recognize similar environments as old as the late Paleozoic. These criteria include (1) limited influence of wind and waves on the depositional environment, (2) lack of significant freshwater influence and therefore any persistent brackish environments, (3) a distinct spatial distribution of microenvironments defined by substrate and exposure period, (4) high diversity of epichnial traces directly associated with microenvironments across the tidal flat, (5) generally low degree of reworking of traces by bioturbation but high degree of reworking by tidal currents, and (6) preservation of traces of predation and scavenging behavior on an exposed surface. These features, together with the regional depositional pattern of the Hartselle Sandstone interpreted as tide-influenced bars and shoals, support a meso- to macro-tidal interpretation of the depositional environment. creator: Louis G. Zachos creator: Brian F. Platt uri: https://doi.org/10.7717/peerj.6975 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zachos and Platt title: Evidence for low prevalence of ranaviruses in Ontario, Canada’s freshwater turtle population link: https://peerj.com/articles/6987 last-modified: 2019-05-20 description: BackgroundOntario, Canada is home to eight native species of turtles; all eight are federally listed as Species At Risk, due to anthropogenic threats. However, until recently, reports of infectious disease have been lacking. Ranavirus is seen as an emerging threat for ectotherms globally, with mass die-offs most often reported in amphibians. Ranavirus has been detected in Ontario’s amphibian populations, can be transmitted via water, and can be transmitted from amphibians to turtles. However, no studies on the prevalence of this virus in Ontario’s turtles have previously been carried out. With recent reports of two confirmed positive case of ranavirus in turtles in Ontario, a knowledge of the ecology of ranavirus in Ontario’s turtles has become even more important. This study estimates the prevalence of ranavirus in Ontario’s turtles, and investigates the hypothesis that this is a newly emergent disease.MethodsSixty-three samples were tested for ranavirus via PCR. These included a variety of turtle species, across their home range in Southern Ontario. Fifty-two of the samples originated from the liver and kidney of turtles who had succumbed to traumatic injuries after being admitted to the Ontario Turtle Conservation Centre; ten of the samples were taken from cloacal swabs, lesion swabs, or tail clips collected from live turtles showing signs of clinical disease. One of the live turtles was later euthanized for humane reasons and PCR was also carried out on the liver/kidney.ResultsNone of the 63 samples were found to be positive for ranavirus via PCR. The zero prevalence found in this study translates into a population prevalence estimate of less than 5%, with no change in prevalence from 2014–2018.DiscussionThis is the first report on the prevalence of ranavirus in Ontario’s turtles, and will help build an understanding of the ecology of this virus in Ontario. Ranavirus has historically been underreported in reptiles, but there has been an increase in global reports recently, most likely due to increased awareness. A carrier state is thought to exist in reptiles which makes surveillance in the population via random sampling a viable method of detection of prevalence. The first report of ranavirus in Ontario turtles occurred in 2018. This study suggests a continued low population prevalence for the years 2014–2018, however. Ongoing surveillance is necessary, as well as investigation of the eDNA presence in waterways as compared to the PCR of resident turtles, to further understand the sensitivity of these species to ranavirus infection. The utilization of qPCR would be helpful, to better quantify any positives encountered. creator: Sue J. Carstairs uri: https://doi.org/10.7717/peerj.6987 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Carstairs title: Candiduria in hospitalized patients: an investigation with the Sysmex UF-1000i urine analyzer link: https://peerj.com/articles/6935 last-modified: 2019-05-20 description: BackgroundCandiduria is common in hospitalized patients. Its management is limited because of inadequate understanding. Previous epidemiological studies based on culture assay have been limited to small study populations. Therefore, data collected by automated systems from a large target population are necessary for more comprehensive understanding of candiduria in hospitalized patients.MethodsTo determine the performance of the Sysmex UF-1000i in detecting candiduria, a cross-sectional study was designed and conducted. A total of 203 yeast-like cell (YLC)-positive and 127 negative samples were randomly chosen and subjected to microbiologic analysis. The receiver operating characteristic curve (ROC) was used to evaluate the ability of YLC counts as measured by the Sysmex UF1000i to predict candiduria. Urinalysis data from 31,648 hospitalized patients were retrospectively investigated, and statistical analysis was applied to the data collected.ResultsUsing a cutoff value of 84.6 YLCs/µL, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the yeast like cell (YLC) counts to predict candiduria were 61.7%, 84.1%, 88.6% and 66.3%, respectively. C. glabrata (33.6%) and C. tropicalis (31.4%) were more prevalent than C. albicans (24.3%) in the present study. Of the investigated hospitalized patients, 509 (1.61%) were considered candiduria-positive. Age, gender and basic condition were associated with candiduria in hospitalized patients. In the ICU setting, urinary catheterization appeared to be the only independent risk factor contributing to candiduria according to our investigation. Although antibiotic therapy has been reported to be a very important risk factor, we could not confirm its significance in ICU candiduria patients because of excessive antibiotic usage in our hospital.ConclusionsThe YLC measured by Sysmex UF-1000i is a practical and convenient tool for clinical candiduria screening prior to microbiologic culture. Candiduria is common in hospitalized patients, and its incidence varies according to age, gender and the wards where it is isolated. Candiduria had no direct connection with mortality but might be considered a marker of seriously ill patients who need particular attention in the clinic. creator: Zhengxin He creator: Yanli Liu creator: Tingting Wang creator: Yan Cheng creator: Jing Chen creator: Fukun Wang uri: https://doi.org/10.7717/peerj.6935 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 He et al. title: Clinicopathological characteristics and prognosis of pulmonary large cell neuroendocrine carcinoma aged ≥65 years link: https://peerj.com/articles/6824 last-modified: 2019-05-20 description: ObjectiveThe present study was designed to better characterize the clinicopathological features and prognosis in patients aged ≥65 years with pulmonary large cell neuroendocrine carcinoma (LCNEC).MethodsEligible patients with pulmonary LCNEC were retrieved from the Surveillance, Epidemiology, and End Results database between January 2004 and December 2013. The primary endpoints included cancer-specific survival (CSS) and overall survival (OS).ResultsData of 1,619 eligible patients with pulmonary LCNEC were collected. These patients were subsequently categorized into two groups: 890 patients in the older group (age ≥65 years), and 729 in the younger group (age <65 years). More patients were of white ethnicity, stage I, married, and with tumor size <5 cm in the older group in comparison to the younger group. However, there were a significantly lower proportion of patients undergoing surgery, chemotherapy, and radiotherapy in the older group. The 5-year CSS rates of the younger group and older group were 23.94% and 17.94% (P = 0.00031), respectively, and the 5-year OS rates were 20.51% and 13.47% (P < 0.0001), respectively. Multivariate analyses indicated that older age (CSS: HR 1.20, 95% CI [1.07–1.36], P = 0.0024; OS: HR 1.26, 95% CI [1.12–1.41], P < 0.0001) was an independent risk factor for poor prognosis. The mortality risk of the elderly increased in almost every subgroup, especially in OS. Finally, significant predictors for better OS and CSS in patients over age 65 included tumor size <5 cm, lower stage, and receiving surgery, chemotherapy, or radiotherapy.ConclusionThe prognosis of patients aged ≥65 years with pulmonary LCNEC was worse than that of younger patients. However, active and effective therapy could significantly improve the survival of older patients with pulmonary LCNEC. creator: Ling Cao creator: Ling Zhao creator: Min Wang creator: Xu he Zhang creator: Zhu-chun Yang creator: Yun-peng Liu uri: https://doi.org/10.7717/peerj.6824 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cao et al. title: Retrospective study on the impact of ulnar nerve dislocation on the pathophysiology of ulnar neuropathy at the elbow link: https://peerj.com/articles/6972 last-modified: 2019-05-20 description: IntroductionHigh resolution ultrasonography (US) has been used for diagnosis and evaluation of entrapment peripheral neuropathy. Ulnar neuropathy at the elbow (UNE) is the second most common focal entrapment neuropathy. The ulnar nerve tends to move to the anteromedial side and sometimes subluxates or dislocates over the medial epicondyle as the elbow is flexed. Dislocation of the ulnar nerve during elbow flexion may contribute to friction injury. We aimed to investigate the effects which the dislocation of ulnar nerve at the elbow could have on the electrophysiologic pathology of UNE.MaterialsWe retrospectively reviewed 71 arms of UNE. The demographic data, electrodiagnosis findings and US findings of ulnar nerve were analyzed. We classified the electrodiagnosis findings of UNE into three pathologic types; demyelinating, sensory axonal loss, and mixed sensorimotor axonal loss. The arms were grouped into non-dislocation, partial dislocation, and complete dislocation groups according to the findings of nerve dislocation in US examination. We compared the electrodiagnosis findings, ulnar nerve cross sectional areas in US and electrodiagnosis pathology types among the groups.ResultsA total of 18 (25.3%) arms showed partial dislocation, and 15 (21.1%) arms showed complete dislocation of ulnar nerve in US. In the comparison of electrodiagnosis findings, the partial and complete dislocation groups showed significantly slower conduction velocities and lower amplitudes than non-dislocation group in motor conduction study. In the sensory conduction study, the conduction velocity was significantly slower in partial dislocation group and the amplitude was significantly lower in complete dislocation group than non-dislocation group. In the comparison of US findings, patients in partial and complete dislocation groups showed significantly larger cross sectional areas of the ulnar nerve. The comparison of electrodiagnosis pathologic types among the groups revealed that there were significantly larger proportions of the axonal loss (sensory axonal loss or mixed sensorimotor axonal loss) in partial and complete dislocation groups than non-dislocation group.ConclusionThe ulnar nerve dislocation could influence on the more severe damage of the ulnar nerve in patients with UNE. It might be important to evaluate the dislocation of the ulnar nerve using US in diagnosing ulnar neuropathy for predicting the prognosis and determining the treatment direction of UNE. creator: Seok Kang creator: Joon Shik Yoon creator: Seung Nam Yang creator: Hyuk Sung Choi uri: https://doi.org/10.7717/peerj.6972 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kang et al. title: Lateralization (handedness) in Magellanic penguins link: https://peerj.com/articles/6936 last-modified: 2019-05-20 description: Lateralization, or asymmetry in form and/or function, is found in many animal species. Brain lateralization is considered adaptive for an individual, and often results in “handedness,” “footedness,” or a side preference, manifest in behavior and morphology. We tested for lateralization in several behaviors in a wild population of Magellanic penguins Spheniscus magellanicus breeding at Punta Tombo, Argentina. We found no preferred foot in the population (each penguin observed once) in stepping up onto an obstacle: 53% stepped up with the right foot, 47% with the left foot (n = 300, binomial test p = 0.27). We found mixed evidence for a dominant foot when a penguin extended a foot for thermoregulation, possibly depending on the ambient temperature (each penguin observed once). Penguins extended the right foot twice as often as the left foot (n = 121, p < 0.0005) in 2 years when we concentrated our effort during the heat of the day. In a third year when we observed penguins early and late in the day, there was no preference (n = 232, p = 0.59). Penguins use their flippers for swimming, including searching for and chasing prey. We found morphological evidence of a dominant flipper in individual adults: 60.5% of sternum keels curved one direction or the other (n = 76 sterna from carcasses), and 11% of penguins had more feather wear on one flipper than the other (n = 1217). Right-flippered and left-flippered penguins were equally likely in both samples (keels: p = 0.88, feather wear: p = 0.26), indicating individual but not population lateralization. In fights, aggressive penguins used their left eyes preferentially, consistent with the right side of the brain controlling aggression. Penguins that recently fought (each penguin observed once) were twice as likely to have blood only on the right side of the face (69%) as only on the left side (31%, n = 175, p < 0.001). The proportion of penguins with blood only on the right side increased with the amount of blood. In most fights, the more aggressive penguin used its left eye and attacked the other penguin’s right side. Lateralization depended on the behavior tested and, in thermoregulation, likely on the temperature. We found no lateralization or mixed results in the population of Magellanic penguins in three individual behaviors, stepping up, swimming, and thermoregulation. We found lateralization in the population in the social behavior fighting. creator: Thaís Stor creator: Ginger A. Rebstock creator: Pablo García Borboroglu creator: P. Dee Boersma uri: https://doi.org/10.7717/peerj.6936 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Stor et al. title: Comprehensive transcriptional profiling of aging porcine liver link: https://peerj.com/articles/6949 last-modified: 2019-05-17 description: BackgroundAging is a major risk factor for the development of many diseases, and the liver, as the most important metabolic organ, is significantly affected by aging. It has been shown that the liver weight tends to increase in rodents and decrease in humans with age. Pigs have a genomic structure, with physiological as well as biochemical features that are similar to those of humans, and have therefore been used as a valuable model for studying human diseases. The molecular mechanisms of the liver aging of large mammals on a comprehensive transcriptional level remain poorly understood. The pig is an ideal model animal to clearly and fully understand the molecular mechanism underlying human liver aging.MethodsIn this study, four healthy female Yana pigs (an indigenous Chinese breed) were investigated: two young sows (180-days-old) and two old sows (8-years-old). High throughput RNA sequencing was performed to evaluate the expression profiles of messenger RNA, long non-coding RNAs, micro RNAs, and circular RNAs during the porcine liver aging process. Gene Ontology (GO) analysis was performed to investigate the biological functions of age-related genes.ResultsA number of age-related genes were identified in the porcine liver. GO annotation showed that up-regulated genes were mainly related to immune response, while the down-regulated genes were mainly related to metabolism. Moreover, several lncRNAs and their target genes were also found to be differentially expressed during liver aging. In addition, the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks were assessed during liver aging.ConclusionsNumerous age-related genes were identified and circRNA-miRNA co-expression networks that are active during porcine liver aging were constructed. These findings contribute to the understanding of the transcriptional foundations of liver aging and also provide further references that clarify human liver aging at the molecular level. creator: Jianning Chen creator: Qin Zou creator: Daojun Lv creator: Muhammad Ali Raza creator: Xue Wang creator: Yan Chen creator: Xiaoyu Xi creator: Peilin Li creator: Anxiang Wen creator: Li Zhu creator: Guoqing Tang creator: Mingzhou Li creator: Xuewei Li creator: Yanzhi Jiang uri: https://doi.org/10.7717/peerj.6949 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Application of dynamic expansion tree for finding large network motifs in biological networks link: https://peerj.com/articles/6917 last-modified: 2019-05-17 description: Network motifs play an important role in the structural analysis of biological networks. Identification of such network motifs leads to many important applications such as understanding the modularity and the large-scale structure of biological networks, classification of networks into super-families, and protein function annotation. However, identification of large network motifs is a challenging task as it involves the graph isomorphism problem. Although this problem has been studied extensively in the literature using different computational approaches, still there is a lot of scope for improvement. Motivated by the challenges involved in this field, an efficient and scalable network motif finding algorithm using a dynamic expansion tree is proposed. The novelty of the proposed algorithm is that it avoids computationally expensive graph isomorphism tests and overcomes the space limitation of the static expansion tree (SET) which makes it enable to find large motifs. In this algorithm, the embeddings corresponding to a child node of the expansion tree are obtained from the embeddings of a parent node, either by adding a vertex or by adding an edge. This process does not involve any graph isomorphism check. The time complexity of vertex addition and edge addition are O(n) and O(1), respectively. The growth of a dynamic expansion tree (DET) depends on the availability of patterns in the target network. Pruning of branches in the DET significantly reduces the space requirement of the SET. The proposed algorithm has been tested on a protein–protein interaction network obtained from the MINT database. The proposed algorithm is able to identify large network motifs faster than most of the existing motif finding algorithms. creator: Sabyasachi Patra creator: Anjali Mohapatra uri: https://doi.org/10.7717/peerj.6917 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Patra and Mohapatra title: Moderating factors influence the relative age effect in Australian cricket link: https://peerj.com/articles/6867 last-modified: 2019-05-17 description: BackgroundThe relative age effect is a commonly occurring phenomenon whereby there is a tendency for relatively older players to be over-represented during high level competitions. This effect is often seen to diminish as player’s age, however, there has been far less investigation on other potential moderating factors.MethodThis study investigated the impact of the relative age effect, and potential moderating factors, within the talent selection process of Australian cricket. Relative age distribution of 2,415 male and female junior and senior state level cricket players, who played in the Junior National Championships or State competition (senior level) between 2011 and 2015, were analysed.ResultsPlayers born in the first quartile of the cricket season were significantly over-represented in both male Under-15, Under-17, Under-19 and female Under-15 and Under-18 levels. However, there was no significant difference at the senior state level for either male or female cricketers. Further investigation of the relative age effect in the junior talent pathway revealed that male all-rounders, batters and pace bowlers, and female all-rounders and batters, born in first quartile were over-represented. Right-handed batters and bowlers were also influenced by the relative age effect at all Junior National levels, while left-handed batters and bowlers were only influenced at the Under-15 and Under-17 levels. These results highlight the impact relative age has on junior cricket talent pathways, including sex, age, handedness and primary skills. Only state level, and left-handedness at the Under-19 level, were unaffected by relative age.DiscussionThe findings of this study highlight the influence of relative age effects for both male and female junior cricket players. Interestingly, there may be an advantage to being left-handed that is more prevalent at the older (male Under-19; female Under-18) age levels. creator: Jonathan D. Connor creator: Ian Renshaw creator: Kenji Doma uri: https://doi.org/10.7717/peerj.6867 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Connor et al. title: Cmah deficiency may lead to age-related hearing loss by influencing miRNA-PPAR mediated signaling pathway link: https://peerj.com/articles/6856 last-modified: 2019-05-17 description: BackgroundPrevious evidence has indicated CMP-Neu5Ac hydroxylase (Cmah) disruption inducesaging-related hearing loss (AHL). However, its function mechanisms remain unclear. This study was to explore the mechanisms of AHL by using microarray analysis in the Cmah deficiency animal model.MethodsMicroarray dataset GSE70659 was available from the Gene Expression Omnibus database, including cochlear tissues from wild-type and Cmah-null C57BL/6J mice with old age (12 months, n = 3). Differentially expressed genes (DEGs) were identified using the Linear Models for Microarray data method and a protein–protein interaction (PPI) network was constructed using data from the Search Tool for the Retrieval of Interacting Genes database followed by module analysis. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery. The upstream miRNAs and potential small-molecule drugs were predicted by miRwalk2.0 and Connectivity Map, respectively.ResultsA total of 799 DEGs (449 upregulated and 350 downregulated) were identified. Upregulated DEGs were involved in Cell adhesion molecules (ICAM1, intercellular adhesion molecule 1) and tumor necrosis factor (TNF) signaling pathway (FOS, FBJ osteosarcoma oncogene; ICAM1), while downregulated DEGs participated in PPAR signaling pathway (PPARG, peroxisome proliferator-activated receptor gamma). A PPI network was constructed, in which FOS, ICAM1 and PPARG were ranked as hub genes and PPARG was a transcription factor to regulate other target genes (ICAM1, FOS). Function analysis of two significant modules further demonstrated PPAR signaling pathway was especially important. Furthermore, mmu-miR-130b-3p, mmu-miR-27a-3p, mmu-miR-27b-3p and mmu-miR-721 were predicted to regulate PPARG. Topiramate were speculated to be a potential small-molecule drug to reverse DEGs in AHL.ConclusionsPPAR mediated signaling pathway may be an important mechanism for AHL. Downregulation of the above miRNAs and use of topiramate may be potential treatment strategies for ALH by upregulating PPARG. creator: Juhong Zhang creator: Na Wang creator: Anting Xu uri: https://doi.org/10.7717/peerj.6856 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: A new balaenopterid whale from the late Miocene of the Southern North Sea Basin and the evolution of balaenopterid diversity (Cetacea, Mysticeti) link: https://peerj.com/articles/6915 last-modified: 2019-05-17 description: BackgroundBalaenopterid mysticetes represent the most successful family-rank group of this clade. Their evolutionary history is characterized by a rich fossil record but the origin of the living genera is still largely not understood. Recent discoveries in the southern border of the North Sea revealed a number of well preserved fossil balaenopterid whales that may help resolving this problem. In particular, skull NMR 14035 shares morphological characters with the living humpback whale, Megaptera novaeangliae and, for this reason, its characteristics are investigated here.MethodsThe comparative anatomical analysis of the new specimen formed the basis of a new phylogenetic analysis of the Mysticeti based on a matrix including 350 morphological character states scored for 82 Operational Taxonomic Units. The stratigraphic age of the specimen was determined based on the analysis of the dinocyst assemblage recovered in the associated sediment. We assessed clade diversity in Balaenopteridae by counting the numbers of clades in given time intervals and then plotted the results.ResultsNehalaennia devossi n. gen. et sp. is described for the first time from the late Tortonian (8.7–8.1 Ma) of the Westerschelde (The Netherlands). This new taxon belongs to Balaenopteridae and shows a surprisingly high number of advanced characters in the skull morphology. Nehalaennia devossi is compared to a large sample of balaenopterid mysticetes and a phylogenetic analysis placed it as the sister group of a clade including the genus Archaebalaenoptera. The inclusion of this fossil allowed to propose a phylogenetic hypothesis for Balaenopteridae in which (1) Eschrichtiidae (gray whales) represents a family of its own, (2) Balaenopteridae + Eschrichtiidae form a monophyletic group (superfamily Balaenopteroidea), (3) Cetotheriidae is the sister group of Balaenopteroidea, (4) living Balaenoptera species form a monophyletic group and (5) living M. novaeangliae is the sister group of Balaenoptera. Our work reveals a complex phylogenetic history of Balaenopteridae and N. devossi informs us about the early morphological transformations in this family. Over time, this family experienced a number of diversity pulses suggesting that true evolutionary radiations had taken place. The paleoecological drivers of these pulses are then investigated. creator: Michelangelo Bisconti creator: Dirk K. Munsterman creator: Klaas Post uri: https://doi.org/10.7717/peerj.6915 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bisconti et al. title: Genotypic analyses and virulence characterization of Glaesserella parasuis isolates from Taiwan link: https://peerj.com/articles/6960 last-modified: 2019-05-17 description: BackgroundGlaesserella (Haemophilus) parasuis (G. parasuis) causes severe economic losses in the swine industry. Multiple G. parasuis strains can exist in single animals. Typing techniques are required for identifying G. parasuis isolates. Different strains within a serovar display varying virulence. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) can assess the heterogeneity. The group 1 virulence-associated trimeric autotransporters (vtaA) gene is an indicator of virulence. The aim of this study was to characterize Taiwanese G. parasuis isolates via molecular serotyping, vtaA PCR and ERIC-PCR.MethodsOne hundred and forty-five strains were collected between November 2013 and March 2017 in Taiwan and further examined by molecular serotyping, vtaA PCR and ERIC-PCR.ResultsThe dendrogram revealed heterogeneous genetic diversity within many clusters. Partial correlation between the ERIC-PCR clusters of different strains, serovars and lesion patterns was observed. Twelve herds (8.3%) infected with more than one strain. Group 1 vtaA positive rate reached 98.6%.DiscussionThis study showed the high genetic diversity of G. parasuis in Taiwan by a high discriminatory capability of ERIC-PCR. Group 1 vtaA commonly exists in G. parasuis isolates and may play important roles in the pathogenesis of Taiwanese G. parasuis isolates. creator: Wei-Hao Lin creator: Hsing-Chun Shih creator: Chuen-Fu Lin creator: Cheng-Yao Yang creator: Chao-Nan Lin creator: Ming-Tang Chiou uri: https://doi.org/10.7717/peerj.6960 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lin et al. title: Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep link: https://peerj.com/articles/6961 last-modified: 2019-05-17 description: Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes and candidate phyla Patescibacteria and Marinimicrobia. Distinct dominant groups in the microbial communities were observed in trench-axis sediment (water depth >8,600 m), compared to the slopes of the Challenger Deep. A sampling site at the northern slope was enriched with archaea from mesophilic Euryarchaeota Marine Group II (MGII) as a biomarker of specific geochemical setting. Among archaeal community, Thaumarchaeota represented by Nitrosopumilus were dominant in the upper layers and diminished drastically in the deeper layers. “Ca. Woesearchaeota”, however, became the dominant group in the deeper layers. Overall, our study provides a better understanding on the pattern of the microbial communities in the deepest hadal sediments on Earth, and highlights the extraordinary diversity still waiting to be discovered. creator: Guojie Cui creator: Jun Li creator: Zhaoming Gao creator: Yong Wang uri: https://doi.org/10.7717/peerj.6961 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cui et al. title: Adsorption of thallium(I) on rutile nano-titanium dioxide and environmental implications link: https://peerj.com/articles/6820 last-modified: 2019-05-16 description: Rutile nano-titanium dioxide (RNTD) characterized by loose particles with diameter in 20–50 nm has a very large surface area for adsorption of Tl, a typical trace metal that has severe toxicity. The increasing application of RNTD and widespread discharge of Tl-bearing effluents from various industrial activities would increase the risk of their co-exposure in aquatic environments. The adsorption behavior of Tl(I) (a prevalent form of Tl in nature) on RNTD was studied as a function of solution pH, temperature, and ion strength. Adsorption isotherms, kinetics, and thermodynamics for Tl(I) were also investigated. The adsorption of Tl(I) on RNTD started at very low pH values and increased abruptly, then maintained at high level with increasing pH >9. Uptake of Tl(I) was very fast on RNTD in the first 15 min then slowed down. The adsorption of Tl(I) on RNTD was an exothermic process; and the adsorption isotherm of Tl(I) followed the Langmuir model, with the maximum adsorption amount of 51.2 mg/g at room temperature. The kinetics of Tl adsorption can be described by a pseudo-second-order equation. FT-IR spectroscopy revealed that -OH and -TiOO-H play an important role in the adsorption. All these results indicate that RNTD has a fast adsorption rate and excellent adsorption amount for Tl(I), which can thus alter the transport, bioavailability and fate of Tl(I) in aqueous environment. creator: Weilong Zhang creator: Yang Wu creator: Jin Wang creator: Juan Liu creator: Haifeng Lu creator: Shuijing Zhai creator: Qiaohui Zhong creator: Siyu Liu creator: Wanying Zhong creator: Chunling Huang creator: Xiaoxiang Yu creator: Wenhui Zhang creator: Yongheng Chen uri: https://doi.org/10.7717/peerj.6820 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Incorporating acoustic objectives into Forest Management Planning when sensitive bird species are relevant link: https://peerj.com/articles/6922 last-modified: 2019-05-16 description: BackgroundThe potentially negative effects of timber harvesting on biodiversity and habitat conservation leads to the consideration of a wide range of restrictions to forest logging in natural areas. In particular, high noise levels produced by forest machinery present a challenge to developing sustainable forest management plans. The Cinereous vulture (Aegypius monachus), the largest bird of prey whose nests are located in mature trees, is considered to be appropriate as an indicator species for environment-friendly forest planning. In this work, we evaluated spatially differences in sound propagation between stands. We hypothesized that differences due to the influence of orography in mountainous forests would allow the relaxation of spatial and temporary restrictions to timber logging, without causing any great disturbance at nesting sites of sensitive species.MethodsOur study was conducted in a Scots pine (Pinus sylvestris) forest of Spain, where an important colony of the Western European population of Cinereous vulture is located. We built 62 noise maps to characterize noise pollution due to tree logging at planning level. We modeled two different scenarios, in order to characterize; (i) the effect of a chainsaw operator during a complete cycle for felling a tree (Scenario 1), and (ii) the effect of the peak level produced by the breaking noise emitted by the trunk of the tree and its impact on the ground (Scenario 2). A strategy of three logical steps was designed; (i) landscape-scale analysis of noise propagation in stands, (ii) hierarchical cluster analysis of stands, (iii) assessment of the potentially significant influence of noise management in timber harvesting.ResultsThe minimum distance (DIST) from chainsaw operator sites to the 40 dB(A) contour lines was the only variable that had a significant influence on the clustering results. On the other hand, mean values of a newly proposed metric called average radius or radial distance (ARD) oscillated between 174 m in cluster #1 (Scenario 1) and 407 m in cluster #2 (Scenario 2).DiscussionOur results highlight the convenience of considering noise modeling tools at a forest planning level in order to address the compatibility of forest logging and the necessity of protecting nature. We found that spatial propagation of noise made by chainsaws at felling sites does not differ between stands even in a mountainous terrain, contrary to what we initially hypothesized. However, temporary logging restrictions could be excluded in about 36% of the current conditioned management areas according to ARD results in Scenario 2 (400 m). This proposal could be based on a sound pressure level (in decibels) criteria instead of conventional buffer protection distance criteria. In addition, it is suggested that the current size of restricted management areas could be generally extended from a 100 m radius to a 200 m one around the Cinereous vulture nest sites. creator: Carlos Iglesias-Merchan creator: Esther Ortiz-Urbina creator: Marta Ezquerro creator: Luis Diaz-Balteiro uri: https://doi.org/10.7717/peerj.6922 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Iglesias-Merchan et al. title: Towards a distributed connectionist account of cognates and interlingual homographs: evidence from semantic relatedness tasks link: https://peerj.com/articles/6725 last-modified: 2019-05-16 description: BackgroundCurrent models of how bilinguals process cognates (e.g., “wolf”, which has the same meaning in Dutch and English) and interlingual homographs (e.g., “angel”, meaning “insect’s sting” in Dutch) are based primarily on data from lexical decision tasks. A major drawback of such tasks is that it is difficult—if not impossible—to separate processes that occur during decision making (e.g., response competition) from processes that take place in the lexicon (e.g., lateral inhibition). Instead, we conducted two English semantic relatedness judgement experiments.MethodsIn Experiment 1, highly proficient Dutch–English bilinguals (N = 29) and English monolinguals (N = 30) judged the semantic relatedness of word pairs that included a cognate (e.g., “wolf”–“howl”; n = 50), an interlingual homograph (e.g., “angel”–“heaven”; n = 50) or an English control word (e.g., “carrot”–“vegetable”; n = 50). In Experiment 2, another group of highly proficient Dutch–English bilinguals (N = 101) read sentences in Dutch that contained one of those cognates, interlingual homographs or the Dutch translation of one of the English control words (e.g., “wortel” for “carrot”) approximately 15 minutes prior to completing the English semantic relatedness task.ResultsIn Experiment 1, there was an interlingual homograph inhibition effect of 39 ms only for the bilinguals, but no evidence for a cognate facilitation effect. Experiment 2 replicated these findings and also revealed that cross-lingual long-term priming had an opposite effect on the cognates and interlingual homographs: recent experience with a cognate in Dutch speeded processing of those items 15 minutes later in English but slowed processing of interlingual homographs. However, these priming effects were smaller than previously observed using a lexical decision task.ConclusionAfter comparing our results to studies in both the bilingual and monolingual domain, we argue that bilinguals appear to process cognates and interlingual homographs as monolinguals process polysemes and homonyms, respectively. In the monolingual domain, processing of such words is best modelled using distributed connectionist frameworks. We conclude that it is necessary to explore the viability of such a model for the bilingual case.Data, scripts, materials and pre-registrations.Experiment 1: http://www.osf.io/ndb7p; Experiment 2: http://www.osf.io/2at49. creator: Eva D. Poort creator: Jennifer M. Rodd uri: https://doi.org/10.7717/peerj.6725 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Poort and Rodd title: Facial flatness indices: application in orthodontics link: https://peerj.com/articles/6889 last-modified: 2019-05-16 description: Facial flatness indices have been used in anthropology to discern differences among populations. They were evaluated on skulls from around the world.Aims(1) to evaluate the use of facial flatness indices in orthodontics and (2) to assess their variation among malocclusions, age and sex.Materials and MethodsA total of 322 cone beam computed tomography radiographs were digitized and three facial indices (frontal, simotic and zygomaxillary) along with three transverse distances (fmo1–fmo2, zma1–zma2 and n1–n2) were assessed and compared between different groups.ResultsThe zygomaxillary index was increased in Class II (32.6 ± 0.42; p < 0.001) and decreased in Class III malocclusions (29.4 ± 0.66; p < 0.001) compared to Class I (31.18 ± 0.3; p < 0.001). The frontal and nasal flatness are not characteristic features of any of the sagittal malocclusions. Facial flatness indices did not differ between males and females and between growing and non-growing patients.ConclusionThe position of subspinale point (A point) forward or backward relative to the zygomaxillary width is a factor of assessment of facial flatness. The zygomaxillary index could be helpful in weighting proportionally the width of the maxilla (expansion) relative to its sagittal position in Class II and Class III malocclusions. creator: Chimène Chalala creator: Maria Saadeh creator: Fouad Ayoub uri: https://doi.org/10.7717/peerj.6889 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chalala et al. title: Expression of ICOSL is associated with decreased survival in invasive breast cancer link: https://peerj.com/articles/6903 last-modified: 2019-05-16 description: BackgroundInducible co-stimulator (ICOS) is a CD28-related molecule exclusively expressed on activated T cells and plays a critical role in modulating the immune response in breast cancer. The blockage of ICOS pathway has been shown to inhibit the activity of Type 2 T helper cells, thus potentially protecting against cancer growth. The current study aims to investigate the correlation between inducible co-stimulator ligand (ICOSL) expression in tumor tissues and the prognoses of patients with invasive breast cancer.MethodsTumor samples from 562 Chinese patients with invasive breast carcinomas were collected between 2003 and 2010. The expression of ICOSL on breast tumor and adjacent non-cancerous tissue was determined via immunohistochemistry. The overall survival (OS) of patients with positive and negative ICOSL expression were described using Kaplan–Meier curves, respectively. Parametric correlation method was used to analyze the correlation between ICOSL expression and other clinicopathological parameters. ICOSL was selected as a dependent variable for multivariate analysis.ResultsPositive ICOSL expression was identified on the plasma membrane in both cytoplasm and the nucleus of breast cancer cells. Membrane-expressed ICOSL is determined as an independent prognostic factor for OS in breast cancer but without significantly correlating with other clinicopathologic parameters such as age, menopausal status, depth of invasion, lymph node metastasis status, histologic classification, etc.ConclusionOur study suggests that the up-regulated expression of ICOSL protein in breast tumor cells can be associated with poor prognoses in invasive breast carcinomas. creator: Bin Wang creator: Huayong Jiang creator: Tingyang Zhou creator: Ning Ma creator: Wei Liu creator: Yajie Wang creator: Li Zuo uri: https://doi.org/10.7717/peerj.6903 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Phylogeography of Dictyota fasciola and Dictyota mediterranea (Dictyotales, Phaeophyceae): unexpected patterns on the Atlantic-Mediterranean marine transition and taxonomic implications link: https://peerj.com/articles/6916 last-modified: 2019-05-16 description: The Atlantic-Mediterranean marine transition is a fascinating biogeographic region, but still very poorly studied from the point of view of seaweed phylogeography. Dictyota fasciola and D. mediterranea (Dictyotales, Phaeophyceae) are two currently recognized sister species that share a large part of their distribution along the Mediterranean Sea and the Atlantic Ocean, representing a unique study model to understand the diversification processes experienced by macroalgae during and after Messinian at this marine region. In this study, we sampled 102 individuals of D. fasciola and D. mediterranea from 32 localities along their distribution range and sequenced the mitochondrial cox1 and the chloroplast rbcL-rbcS DNA regions for all the samples. Our data do not support the occurrence of two sister species but a morphologically variable and highly genetic diverse species or a complex of species. Most of the observed genetic diversity corresponds to the Mediterranean populations, whereas the Atlantic ones are much more homogeneous. The early-diverged lineages inferred from both mtDNA and cpDNA phylogenetic reconstructions were constituted by samples from the Mediterranean Sea. Together, these results suggest that the Mediterranean Sea acted as a refugium for the D. fasciola–D. mediterranea lineage during the geologic and climatic changes occurred on the region since the Miocene, subsequently dispersing to the Atlantic Ocean. creator: Daniel Vitales creator: Joana Aragay creator: Teresa Garnatje creator: Amelia Gómez Garreta creator: Jordi Rull Lluch uri: https://doi.org/10.7717/peerj.6916 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Vitales et al. title: Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain link: https://peerj.com/articles/6931 last-modified: 2019-05-16 description: Forests and woodlands worldwide are being severely impacted by invasive Phytophthora species, with initial outbreaks in some cases occurring on host trees located in public parks and gardens. These highly disturbed sites with diverse planting practices may indeed act as harbours for invasive Phytophthora pathogens which are particularly well adapted to surviving in soil. High throughput Illumina sequencing was used to analyse Phytophthora species diversity in soil samples collected from 14 public garden/amenity woodland sites in northern Britain. Bioinformatic analyses revealed some limitations to using internal transcribed spacer as the barcode region; namely reporting of false positives and ambiguous species matches. Taking this into account, 35 distinct sequences were amplified across the sites, corresponding to 23 known Phytophthora species as well as twelve oomycete sequences with no match to any known Phytophthora species. Phytophthora pseudosyringae and P. austrocedri, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain, were the two most abundant Phytophthora species detected. There was no evidence that any of the detected Phytophthora species were more associated with any one type of host, healthy or otherwise. This study has demonstrated the ubiquity and diversity of Phytophthora species endemic in highly managed, extensively planted soil environments in Britain. Suggested improvements to the methodology and the practical implications of the findings in terms of mitigating Phytophthora spread and impact are discussed. creator: Carolyn E. Riddell creator: Debbie Frederickson-Matika creator: April C. Armstrong creator: Matt Elliot creator: Jack Forster creator: Pete E. Hedley creator: Jenny Morris creator: Peter Thorpe creator: David EL Cooke creator: Leighton Pritchard creator: Paul M. Sharp creator: Sarah Green uri: https://doi.org/10.7717/peerj.6931 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Riddell et al. title: Vehicle emission and atmospheric pollution in China: problems, progress, and prospects link: https://peerj.com/articles/6932 last-modified: 2019-05-16 description: China has been the largest vehicle market in the world since 2009. The stalemate between the rapid development of the vehicle industry and delayed vehicle emission control has become increasingly prominent. Vehicle emission has become a significant source of air pollution in China’s cities. Understanding the current barriers in the vehicle industry is necessary for the development of effective and sustainable measures and policy to manage vehicle-induced air pollution. This review provides insight into the circumstances and causes of vehicle-induced air pollution and outlines recent progress in policy-makers’ long-term strategies and regulations. The development of an integrated mechanism of social participation, technical revolution, and regulatory innovation in vehicles, fuel, and roads is suggested to break the stalemate between air pollution and the automobile boom in China; the implications of this review extend to other countries facing the similar atmospheric pollution problems. creator: Jin Wang creator: Qiuxia Wu creator: Juan Liu creator: Hong Yang creator: Meiling Yin creator: Shili Chen creator: Peiyu Guo creator: Jiamin Ren creator: Xuwen Luo creator: Wensheng Linghu creator: Qiong Huang uri: https://doi.org/10.7717/peerj.6932 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Identification of RyR2-PBmice and the effects of transposon insertional mutagenesis of the RyR2 gene on cardiac function in mice link: https://peerj.com/articles/6942 last-modified: 2019-05-16 description: Ryanodine receptor 2 (RyR2) plays an important role in maintaining the normal heart function, and mutantions can lead to arrhythmia, heart failure and other heart diseases. In this study, we successfully identified a piggyBac translocated RyR2 gene heterozygous mouse model (RyR2-PBmice) by tracking red fluorescent protein (RFP) and genotyping PCR. Cardiac function tests showed that there was no significant difference between the RyR2-PBmice and corresponding wild-type mice (WTmice), regardless of whether they were in the basal state or injected with epinephrine and caffeine. However, the sarcoplasmic reticulum Ca2+ content was significantly reduced in the cardiomyocytes of RyR2-PBmice as assessed by measuring caffeine-induced [Ca2+]i transients; the cardiac muscle tissue of RyR2-PBmice displayed significant mitochondrial swelling and focal dissolution of mitochondrial cristae, and the tissue ATP content in the RyR2-PBmice heart was significantly reduced. To further analyze the molecular mechanism behind these changes, we tested the expression levels of related proteins using RT-PCR and Western blot analyses. The mRNA level of RyR2 in RyR2-PBmice cardiac tissue decreased significantly compared with the WTmice, and the protein expression associated with the respiratory chain was also downregulated. These results suggested that the piggyBac transposon inserted into the RyR2 gene substantively affected the structure and function of mitochondria in the mouse cardiomyocytes, leading to disorders of energy metabolism. creator: Qianqian Wang creator: Chao Wang creator: Bo Wang creator: Qirui Shen creator: Leilei Qiu creator: Shuaijun Zou creator: Tao Wang creator: Guoyan Liu creator: Beilei Wang creator: Liming Zhang uri: https://doi.org/10.7717/peerj.6942 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Comparison of the National Early Warning Score (NEWS) and the Modified Early Warning Score (MEWS) for predicting admission and in-hospital mortality in elderly patients in the pre-hospital setting and in the emergency department link: https://peerj.com/articles/6947 last-modified: 2019-05-16 description: The aim of this study is to evaluate the usefulness of the pre-hospital National Early Warning Score (pNEWS) and the pre-hospital Modified Early Warning Score (pMEWS) for predicting admission and in-hospital mortality in elderly patients presenting to the emergency department (ED). We also compare the value of the pNEWS with that of the ED NEWS (eNEWS) and ED MEWS (eMEWS) for predicting admission and in-hospital mortality. This retrospective, single-centre observational study was carried out in the ED of Jikei University Kashiwa Hospital, in Chiba, Japan, from 1st April 2017 to 31st March 2018. All patients aged 65 years or older were included in this study. The pNEWS/eNEWS were derived from seven common physiological vital signs: respiratory rate, peripheral oxygen saturation, the presence of inhaled oxygen parameters, body temperature, systolic blood pressure, pulse rate and Alert, responds to Voice, responds to Pain, Unresponsive (AVPU) score, whereas the pMEWS/eMEWS were derived from six common physiological vital signs: respiratory rate, peripheral oxygen saturation, body temperature, systolic blood pressure, pulse rate and AVPU score. Discrimination was assessed by plotting the receiver operating characteristic (ROC) curve and calculating the area under the ROC curve (AUC). The median pNEWS, pMEWS, eNEWS and eMEWS were significantly higher at admission than at discharge (p < 0.001). The median pNEWS, pMEWS, eNEWS and eMEWS of non-survivors were significantly higher than those of the survivors (p < 0.001). The AUC for predicting admission was 0.559 for the pNEWS and 0.547 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting admission (p = 0.102). The AUCs for predicting in-hospital mortality were 0.678 for the pNEWS and 0.652 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting in-hospital mortality (p = 0.081). The AUC for predicting admission was 0.628 for the eNEWS and 0.591 for the eMEWS. The AUC of the eNEWS was significantly greater than that of the eMEWS for predicting admission (p < 0.001). The AUC for predicting in-hospital mortality was 0.789 for the eNEWS and 0.720 for the eMEWS. The AUC of the eNEWS was significantly greater than that of the eMEWS for predicting in-hospital mortality (p < 0.001). For admission and in-hospital mortality, the AUC of the eNEWS was significantly greater than that of the pNEWS (p < 0.001, p < 0.001), and the AUC of the eMEWS was significantly greater than that of the pMEWS (p < 0.01, p < 0.05). Our single-centre study has demonstrated the low utility of the pNEWS and the pMEWS as predictors of admission and in-hospital mortality in elderly patients, whereas the eNEWS and the eMEWS predicted admission and in-hospital mortality more accurately. Evidence from multicentre studies is needed before introducing pre-hospital versions of risk-scoring systems. creator: Toshiya Mitsunaga creator: Izumu Hasegawa creator: Masahiko Uzura creator: Kenji Okuno creator: Kei Otani creator: Yuhei Ohtaki creator: Akihiro Sekine creator: Satoshi Takeda uri: https://doi.org/10.7717/peerj.6947 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mitsunaga et al. title: Biochemical changes throughout early- and middle-stages of embryogenesis in lobsters (Homarus americanus) under different thermal regimes link: https://peerj.com/articles/6952 last-modified: 2019-05-16 description: Most marine crustacean eggs contain the full complement of nutritional resources required to fuel their growth and development. Given the propensity of many ovigerous (egg-bearing) American lobsters (Homarus americanus) to undergo seasonal inshore-to-offshore migrations, thereby potentially exposing their eggs to varying thermal regimes, the goal of this study was to determine the impact of water temperature on egg quality over their course of development. This was accomplished by documenting changes in total lipids, proteins, and size (volume) of eggs subjected to one of three thermal regimes: inshore, offshore, and constant (16 °C) conditions. Total egg lipids showed a marked decrease over time, while protein levels increased over the same period. Although there were no significant differences in total lipids, proteins, or egg sizes between eggs exposed to inshore and offshore temperatures, they differed from values for eggs exposed to a constant temperature, which also hatched almost three months sooner. This is most likely due to the fact that eggs held at a constant temperature did not experience a period of slow development during the colder months from November to March that are important for synchronizing egg hatch and may be compromised by elevated seawater temperatures. creator: Jason S. Goldstein creator: Winsor H. Watson III uri: https://doi.org/10.7717/peerj.6952 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Goldstein and Watson III title: Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.) link: https://peerj.com/articles/6966 last-modified: 2019-05-16 description: BackgroundThousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100–RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location.MethodA total of 12 populations were used. The ZC9 population comprised 203 S1:2 families derived from a residual heterozygous (RH) plant in the F9 generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100–RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S1 plants derived from one RH plant in F7 of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100–RM228. The other ten populations were all derived from Ti52-1, including five S1 populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM.ResultThree QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704–RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions.ConclusionThree QTL for grain size that were tightly linked on the long arm of chromosome 10 of rice were separated using NIL populations with sequential segregating regions. One of them, qGS10.1, had a stable and relatively high effect on grain weight, GL, and GW, providing a good candidate for gene cloning. Another QTL, qGS10.2, had a significant effect on all the three traits but the effect was inconsistent across different experiments, providing an example of genotype-by-environmental interaction. creator: Yu-Jun Zhu creator: Zhi-Chao Sun creator: Xiao-Jun Niu creator: Jie-Zheng Ying creator: Ye-Yang Fan creator: Tong-Min Mou creator: Shao-Qing Tang creator: Jie-Yun Zhuang uri: https://doi.org/10.7717/peerj.6966 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhu et al. title: Retrospective correlation analysis of plasma Immunoglobulin G and clinical performance in CIDP link: https://peerj.com/articles/6969 last-modified: 2019-05-16 description: BackgroundChronic inflammatory demyelinating polyneuropathy (CIDP) can be successfully treated with immunoglobulin either intravenously (IVIG) or subcutaneously (SCIG). Measurement of plasma immunoglobulin G levels (P-IgG) and its correlation to clinical improvement has shown conflicting results. This study aims to clarify whether changes in P-IgG are related to clinical development in patients with CIDP treated with IVIG or SCIG.MethodsPatients from five previous studies treated with either IVIG or SCIG with evaluation at baseline and re-evaluation after two or 10/12 weeks, respectively were included. At evaluation and re-evaluation, the following tests were done: combined isokinetic muscle strength (cIKS), grip strength, 9-hole-peg test (9-HPT), 40-meter-walk test (40-MWT), clinical examination of muscle strength score by the Medical Research Council (MRC) and measurement of plasma immunoglobulin G (P-IgG).ResultsFifty-five patients were included in the IVIG group and 41 in the SCIG group. There was no correlation between the changes in P-IgG and cIKS in neither the IVIG group (r = 0.137, p = 0.32) nor the SCIG group (r =  − 0.048, p = 0.77). Similarly, no correlations could be demonstrated between P-IgG and grip strength, 9-HPT, 40-MWT or MRC.ConclusionsIn patients with CIDP receiving SCIG or IVIG, changes in P-IgG during treatment did not correlate with changes in muscle strength or other motor performance skills. creator: Lars Kjøbsted Markvardsen creator: Stine Bruun-Sørensen creator: Ingelise Christiansen creator: Henning Andersen uri: https://doi.org/10.7717/peerj.6969 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Markvardsen et al. title: Fish nursery value of algae habitats in temperate coastal reefs link: https://peerj.com/articles/6797 last-modified: 2019-05-15 description: The nursery function of coastal habitats is one of the most frequently mentioned and recognized ecosystem services in the valuation of coastal ecosystems. Despite its importance our understanding of the precise habitat parameters and mechanisms that make a habitat important as a nursery area is still limited for many species. The study aimed to establish the importance of different algae morphotypes in providing shelter and food for juvenile coastal fish during the main settlement peaks, in early spring and late summer, in littoral rocky reef systems in the Northwestern Mediterranean. The results of our study showed strong seasonal differences in algae cover, composition and height between the two sampling periods. Overall, during spring the algae were well developed, while in late summer, both density and height, of most algae decreased considerably. Equally, prey biomass, in form of suitable sized invertebrate fauna associated to the algae, decreased. Accordingly, the shelter and food for the fish settling in this habitat during late summer were less abundant, indicating a mismatch between the observed presence of juvenile fish and optimal habitat conditions. Differences in prey densities were detected between algae morphotypes, with structurally more complex algae, such as Cystoseira spp. and Halopteris spp. consistently containing more prey, independent of season, compared to simpler structured morphotypes such as Dictoytales. The study furthermore related juvenile fish density to habitats dominated by different algae morphotypes. Out of the three-study species (Diplodus vulgaris, Symphodus ocellatus, Coris julis) only S. ocellatus showed a significant association with an algae habitat. S. ocellatus related positively to habitats dominated by Dictoytales which provided the highest cover during late summer but had the lowest prey densities. A strong association of this species with Cystoseira, as reported by other studies, could not be confirmed. Cystoseira was abundant within the study area but in a state of dieback, showing loss and reduced height of foliage, typical for the time of year within the study area. It is therefore likely that algae-fish associations are context-dependent and that several algae species may fulfil similar functions. We also discovered that prey biomass did not appear to have an important effect on juvenile abundances. Nevertheless, the availability of prey may influence juvenile fish condition, growth performance and ultimately long-term survival. We therefore suggest that future studies on habitat quality should also include, besides abundance, indicators related to the condition and growth of juveniles. creator: Hilmar Hinz creator: Olga Reñones creator: Adam Gouraguine creator: Andrew F. Johnson creator: Joan Moranta uri: https://doi.org/10.7717/peerj.6797 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hinz et al. title: Cosmetic colouring by Bearded Vultures Gypaetus barbatus: still no evidence for an antibacterial function link: https://peerj.com/articles/6783 last-modified: 2019-05-15 description: Bearded Vultures regularly visit ferruginous springs for cosmetic purposes to obtain their reddish plumage colouration. Different hypotheses have been proposed to explain this deliberate application of adventitious colouration: (1) to signal individual dominance status; (2) to exploit an anti-bacterial effect of iron oxides or ochre to reduce feather degradation by bacteria and, in parallel (3) to enable incubating birds to transfer this protection to their developing embryos to increase hatching success. Here, we re-evaluate the antibacterial hypothesis using three experimental approaches: (a) by applying feather-degrading bacteria to stained and unstained bearded vulture feathers; (b) by assessing the antibacterial activity of ochre; and (c) by comparing the breeding success of orange individuals with pale ones. Our findings suggest that the in vitro addition of feather degrading Bacillus licheniformis to naturally stained Bearded Vulture feathers did not retard feather degradation compared to controls. Iron particles from red soil (ochre) or iron salts had no antibacterial effect on the growth of three species of bacteria (Escherichia coli, Kocuria rhizophila and Bacillus licheniformis), incubated either in the dark or under visible light. Finally, breeding success did not differ between territories occupied by pale individuals versus orange ones. These results run counter to the hypothesis that iron oxides have an antibacterial role in Bearded Vultures. The use of red soils by Bearded Vultures may function as a territorial status signal, but may also be involved in other processes, such as pair formation and the long-term maintenance of the pair bond, as suggested for the closely related Egyptian vulture Neophron percnopterus. creator: Antoni Margalida creator: Markus S. Braun creator: Juan José Negro creator: Karl Schulze-Hagen creator: Michael Wink uri: https://doi.org/10.7717/peerj.6783 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Margalida et al. title: Foot pressure distribution in White Rhinoceroses (Ceratotherium simum) during walking link: https://peerj.com/articles/6881 last-modified: 2019-05-15 description: White rhinoceroses (Ceratotherium simum) are odd-toed ungulates that belong to the group Perissodactyla. Being second only to elephants in terms of large body mass amongst extant tetrapods, rhinoceroses make fascinating subjects for the study of how large land animals support and move themselves. Rhinoceroses often are kept in captivity for protection from ivory poachers and for educational/touristic purposes, yet a detrimental side effect of captivity can be foot disease (i.e., enthesopathies and osteoarthritis around the phalanges). Foot diseases in large mammals are multifactorial, but locomotor biomechanics (e.g., pressures routinely experienced by the feet) surely can be a contributing factor. However, due to a lack of in vivo experimental data on rhinoceros foot pressures, our knowledge of locomotor performance and its links to foot disease is limited. The overall aim of this study was to characterize peak pressures and center of pressure trajectories in white rhinoceroses during walking. We asked two major questions. First, are peak locomotor pressures the lowest around the fat pad and its lobes (as in the case of elephants)? Second, are peak locomotor pressures concentrated around the areas with the highest reported incidence of pathologies? Our results show a reduction of pressures around the fat pad and its lobes, which is potentially due to the material properties of the fat pad or a tendency to avoid or limit “heel” contact at impact. We also found an even and gradual concentration of foot pressures across all digits, which may be a by-product of the more horizontal foot roll-off during the stance phase. While our exploratory, descriptive sample precluded hypothesis testing, our study provides important new data on rhinoceros locomotion for future studies to build on, and thus impetus for improved implementation in the care of captive/managed rhinoceroses. creator: Olga Panagiotopoulou creator: Todd C. Pataky creator: John R. Hutchinson uri: https://doi.org/10.7717/peerj.6881 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Panagiotopoulou et al. title: Cells released from S. epidermidis biofilms present increased antibiotic tolerance to multiple antibiotics link: https://peerj.com/articles/6884 last-modified: 2019-05-15 description: Biofilm released cells (Brc) are thought to present an intermediary phenotype between biofilm and planktonic cells and this has the potential of affecting their antimicrobial tolerance.AimCompare the antimicrobial tolerance profiles of Brc, planktonic or biofilm cultures of S. epidermidis.MethodologyPlanktonic, biofilm cultures or Brc from 11 isolates were exposed to peak serum concentrations (PSC) of antibiotics. The antimicrobial killing effect in the three populations was determined by CFU.ResultsIncreased Brc tolerance to vancomycin, teicoplanin, rifampicin, erythromycin, and tetracycline was confirmed in model strain 9142. Furthermore, significant differences in the susceptibility of Brc to vancomycin were further found in 10 other clinical isolates.ConclusionsBrc from distinct clinical isolates presented a decreased susceptibility to most antibiotics tested and maintained that enhanced tolerance despite growing planktonically for up to 6 h. Our data suggest that Brc maintain the typical enhanced antibiotic tolerance of biofilm populations, further suggesting that addressing antimicrobial susceptibility in planktonic cultures might not reflect the full potential of biofilm-associated bacteria to survive therapy. creator: Vânia Gaio creator: Nuno Cerca uri: https://doi.org/10.7717/peerj.6884 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gaio and Cerca title: Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions link: https://peerj.com/articles/6888 last-modified: 2019-05-15 description: BackgroundPoa annua L. is an example of a plant characterized by abundant, worldwide distribution from polar to equatorial regions. Due to its high plasticity and extraordinary expansiveness, P. annua is considered an invasive species capable of occupying and surviving in a wide range of habitats including pioneer zones, areas intensively transformed by human activities, remote subarctic meadows and even the Antarctic Peninsula region.MethodsIn the present study, we evaluated the utility of inter-primer binding site (iPBS) markers for assessing the genetic variation of P. annua populations representing contrasting environments from the worldwide range of this species. The electrophoretic patterns of polymerase chain reaction products obtained for each individual were used to estimate the genetic diversity and differentiation between populations.ResultsiPBS genotyping revealed a pattern of genetic variation differentiating the six studied P. annua populations characterized by their different climatic conditions. According to the analysis of molecular variance, the greatest genetic variation was recorded among populations, whereas 41.75% was observed between individuals within populations. The results of principal coordinates analysis (PCoA) and model-based clustering analysis showed a clear subdivision of analyzed populations. According to PCoA, populations from Siberia and the Kola Peninsula were the most different from each other and showed the lowest genetic variability. The application of STRUCTURE software confirmed the unique character of the population from the Kola Peninsula.DiscussionThe lowest variability of the Siberia population suggested that it was subjected to genetic drift. However, although demographic expansion was indicated by negative values of Fu’s FS statistic and analysis of mismatch distribution, it was not followed by significant traces of a bottleneck or a founder effect. For the Antarctic population, the observed level of genetic variation was surprisingly high, despite the observed significant traces of bottleneck/founder effect following demographic expansion, and was similar to that observed in populations from Poland and the Balkans. For the Antarctic population, the multiple introduction events from different sources are considered to be responsible for such an observation. Moreover, the results of STRUCTURE and PCoA showed that the P. annua from Antarctica has the highest genetic similarity to populations from Europe.ConclusionsThe observed polymorphism should be considered as a consequence of the joint influence of external abiotic stress and the selection process. Environmental changes, due to their ability to induce transposon activation, lead to the acceleration of evolutionary processes through the production of genetic variability. creator: Piotr Androsiuk creator: Justyna Koc creator: Katarzyna Joanna Chwedorzewska creator: Ryszard Górecki creator: Irena Giełwanowska uri: https://doi.org/10.7717/peerj.6888 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Androsiuk et al. title: Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae link: https://peerj.com/articles/6899 last-modified: 2019-05-15 description: BackgroundChlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa.MethodsWe sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae.ResultsConcatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome.DiscussionWhile the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypotheses are possible for Sphaeropleales s.l. Given this uncertainty as well as the higher-taxonomic disorder seen in other algal groups, dwelling on well-defined, strongly supported Linnaean orders is not currently practical in Chlorophyceae and a less formal clade system may be more useful in the foreseeable future. For example, we identify two strongly and unequivocally supported clades: Treubarinia and Scenedesminia, as well as other smaller groups that could serve a practical purpose as named clades. This system does not preclude future establishment of new orders, or emendment of the current ordinal classification if new data support such conclusions. creator: Karolina Fučíková creator: Paul O. Lewis creator: Suman Neupane creator: Kenneth G. Karol creator: Louise A. Lewis uri: https://doi.org/10.7717/peerj.6899 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fučíková et al. title: Development and feasibility study of an app (Ladle) for weight loss and behaviour change link: https://peerj.com/articles/6907 last-modified: 2019-05-15 description: BackgroundWeight management interventions involving behaviour change often utilise face to face interventions which include evidence based behaviour change strategies yet are costly and time intensive. In contrast, digital interventions cost less and have a wider reach yet tend to lack an evidence base and are less effective.AimsThe present study therefore aimed to develop an evidence based behaviour change low cost app for weight management and to provide a preliminary analysis of its effectiveness.MethodsThe Ladle app was developed through evidence review and feedback from health care professionals and patients and consists of a 12 week course focusing on six habits and weight loss facilitated through 36 audio psychological lessons and 12 lessons specifically on the six habits. Each lesson was between 2–5 min (approx. 168 min of lessons). It was evaluated in terms of completion rate, weight loss, adoption of the six habits and participant feedback.ResultsThe results showed a completion rate of 44%, that 52% of Completers showed weight loss of at least 5%, 79% showed weight loss of at least 3%, the median % weight lost was −5% and the median weight loss was −3.8 kg. Further, by the end of 12 weeks the majority (>80%) of participants had adopted four of the six habits for at least 5 days a week and nearly half (45%) had adopted the remaining two habits for at least 4 days out of 7. Feedback comments were mainly positive (n = 80) focusing mostly on the content of the lessons. Some comments were neutral (n = 56) and involved a statement of commitment or a description of a challenge and a minority were negative (n = 23) describing some technical issues which were addressed as the evaluation progressed.ConclusionThe new Ladle app offers an evidenced based alternative to more intensive face to face interventions. On preliminary analysis it would seem to have lower completion rates than some more intensive interventions but comparable effectiveness for weight loss. It can also improve habits and is less time-intensive and costly to deliver. Participant feedback was generally positive. creator: Jane Ogden creator: Hazel Maxwell creator: Adrian Wong uri: https://doi.org/10.7717/peerj.6907 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ogden et al. title: The Equidae from Cooper’s D, an early Pleistocene fossil locality in Gauteng, South Africa link: https://peerj.com/articles/6909 last-modified: 2019-05-15 description: Cooper’s D is a fossil locality in the Bloubank Valley close to other important sites such as Sterkfontein and Kromdraai in Gauteng, South Africa. The fossil deposits of Cooper’s D date to 1.38 ± 0.11 Ma. Hominins like Paranthropus robustus and early Homo have been recovered from Cooper’s Cave. We report here on the Equidae remains. Our sample contains specimens from the extinct Equus capensis, and a specimen which represents an extinct hipparion Eurygnathohippus cf. cornelianus. This particular specimen was previously identified as plains zebra (Equus quagga). The contribution of Equidae to the total fossil assemblage of Cooper’s D is relatively low, and these remains were likely accumulated by various predators such as spotted and brown hyenas and leopards. The Equidae, as well as the other fauna from Cooper’s D supports the existence of grassland, wooded and water components in the vicinity of the site. creator: Shaw Badenhorst creator: Christine M. Steininger uri: https://doi.org/10.7717/peerj.6909 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Badenhorst and Steininger title: The effect of differential spatiotopic information on the acquisition and generalization of fear of movement-related pain link: https://peerj.com/articles/6913 last-modified: 2019-05-15 description: Fear of movement-related pain significantly contributes to musculoskeletal chronic pain disability. Previous research has shown that fear of movement-related pain can be classically conditioned. That is, in a differential fear conditioning paradigm, after (repeatedly) pairing a neutral joystick movement (conditioned stimulus; CS+) with a painful stimulus (unconditioned stimulus; pain-US), that movement in itself starts to elicit self-reported fear and elevated psychophysiological arousal compared to a control joystick movement (CS−) that was never paired with pain. Further, it has been demonstrated that novel movements that are more similar to the original CS+ elicit more fear than novel movements that are more similar to the CS−, an adaptive process referred to as stimulus generalization. By default, movement/action takes place in reference to the three-dimensional space: a movement thus not only involves proprioceptive information, but it also contains spatiotopic information. Therefore, the aim of this study was to investigate to what extent spatiotopic information (i.e., endpoint location of movement) contributes to the acquisition and generalization of such fear of movement-related pain besides proprioception (i.e., movement direction). In a between-subjects design, the location group performed joystick movements from the middle position to left and right; the movement group moved the joystick from left and right to the middle. One movement (CS+) was paired with pain, another not (CS−). Feature overlap between CSs typically reduces differential learning. The endpoint of both CSs in the movement group is an overlapping feature whereas in the location group the endpoint of both CSs is distinct; therefore we hypothesized that there would be less differential fear learning in the movement group compared to the location group. We also tested generalization to movements with similar proprioceptive features but different endpoint location. Following the principle of stimulus generalization, we expected that novel movements in the same direction as the CS+ but with a different endpoint would elicit more fear than novel movement in the same direction of the CS− but with a different endpoint. Main outcome variables were self-reported fear and pain-US expectancy and eyeblink startle responses (electromyographic). Corroborating the feature overlap hypothesis, the location group showed greater differential fear acquisition. Fear generalization emerged for both groups in the verbal ratings, suggesting that fear indeed accrued to proprioceptive CS features; these effects, however, were not replicated in the startle measures. creator: Ann Meulders creator: Johan W. Vlaeyen uri: https://doi.org/10.7717/peerj.6913 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Meulders and Vlaeyen title: Effects of water level fluctuation on thermal stratification in a typical tributary bay of Three Gorges Reservoir, China link: https://peerj.com/articles/6925 last-modified: 2019-05-15 description: Xiangxi River is a typical tributary of Three Gorges Reservoir (TGR) in China. Based on field observations in 2010, thermal stratification was significant in most months of the year. Through field data analysis and numerical simulations, the seasonal and spatial variation of thermal stratification as related to the impact of the operation of TGR were investigated. Thermal stratification was most pronounced from April to September in the Xiangxi River tributary. Air temperature (AT) and water level (WL) were the two dominant variables impacting thermal stratification. AT affected the surface water temperature promoting the formation of thermal stratification, and high WLs in TGR deepened the thermocline depth and thermocline bottom depth. These results provide a preliminary description of the seasonal variation and spatial distribution of thermal stratification, which is important for better understanding how thermal stratification affects algae blooms in Xiangxi River. creator: Juxiang Jin creator: Scott A. Wells creator: Defu Liu creator: Guolu Yang creator: Senlin Zhu creator: Jun Ma creator: Zhengjian Yang uri: https://doi.org/10.7717/peerj.6925 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jin et al. title: Ellipse packing in two-dimensional cell tessellation: a theoretical explanation for Lewis’s law and Aboav-Weaire’s law link: https://peerj.com/articles/6933 last-modified: 2019-05-15 description: BackgroundLewis’s law and Aboav-Weaire’s law are two fundamental laws used to describe the topology of two-dimensional (2D) structures; however, their theoretical bases remain unclear.MethodsWe used R software with the Conicfit package to fit ellipses based on the geometric parameters of polygonal cells of ten different kinds of natural and artificial 2D structures.ResultsOur results indicated that the cells could be classified as an ellipse’s inscribed polygon (EIP) and that they tended to form the ellipse’s maximal inscribed polygon (EMIP). This phenomenon was named as ellipse packing. On the basis of the number of cell edges, cell area, and semi-axes of fitted ellipses, we derived and verified new relations of Lewis’s law and Aboav-Weaire’s law.ConclusionsEllipse packing is a short-range order that places restrictions on the cell topology and growth pattern. Lewis’s law and Aboav-Weaire’s law mainly reflect the effect of deformation from circle to ellipse on cell area and the edge number of neighboring cells, respectively. The results of this study could be used to simulate the dynamics of cell topology during growth. creator: Kai Xu uri: https://doi.org/10.7717/peerj.6933 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu title: Transcriptional regulation of Bcl-2 gene by the PR/SET domain family member PRDM10 link: https://peerj.com/articles/6941 last-modified: 2019-05-15 description: Bcl-2 (B-cell lymphoma 2) protein is localized in the outer membrane of mitochondria, where it plays an important role in promoting cellular survival and inhibiting the actions of pro-apoptotic proteins. PRDM10 is a member of the PR/SET family of epigenetic regulators and may play a role in development and cell differentiation. Here we show that human PRDM10 contributes to the transcriptional regulation of human Bcl-2 gene. We found that PRDM10-depletion in human cells reduced the expression of Bcl-2 protein and over-expression of PRDM10 promoted Bcl-2 protein expression. Furthermore, luciferase reporter activity of Bcl-2 gene P1 promoter was significantly increased in cells co-transfected with PRDM10, and PRDM10 was able to bind to the Bcl-2 P1 promoter in vivo. Using The Cancer Genome Atlas (TCGA) data set, we found weak positive correlation between PRDM10 and Bcl-2 in several cancer types including cancers of the breast, colon, and lung tissues. These data identify a novel function for PRDM10 protein and provide insights on the transcriptional control of Bcl-2 expression. creator: Na Chen creator: Taobo Hu creator: Yuanyuan Gui creator: Jieying Gao creator: Zhihong Li creator: Shi Huang uri: https://doi.org/10.7717/peerj.6941 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Effect of music interventions on anxiety during labor: a systematic review and meta-analysis of randomized controlled trials link: https://peerj.com/articles/6945 last-modified: 2019-05-15 description: BackgroundAnxiety is commonly experienced during the delivery process and has shown to have adverse effects on maternal and infant health outcomes. Music interventions tend to reduce the effects of anxiety in diverse populations, are low cost, are easily accessible, and have high acceptability. The aim of this review and meta-analysis was to assess the effectiveness of music interventions in reducing anxiety levels among women during labor.MethodsSeven databases from inception to the end of December, 2018, without any language or time restriction including Embase, PubMed, the Cochrane Library, the Cumulative Index to Nursing and Allied Health, PsycINFO, Airiti Library, and PerioPath: Index to Taiwan Periodical Literature were searched using key terms related to pregnancy, anxiety, and music. Randomized controlled trials that assessed the effect of music during labor and measured anxiety levels as an outcome were included. Meta-analyses were conducted to assess anxiety reduction following a music intervention compared to that after placebo treatment.ResultsA total of 14 studies that investigated a total of 1,310 participants were included in this review. The meta-analyses indicated that those in the intervention group had a significant decrease in anxiety scores (standardized mean difference = −2.40, 95% confidence interval (CI) [−3.29 to −1.52], p < 0.001; I2 = 97.66%), heart rate (HR) (difference in means = −3.04 beats/min, 95% CI [−4.79 to −1.29] beats/min, p = 0.001; I2 = 0.00%), systolic blood pressure (SBP) (difference in means = −3.71 mmHg, 95% CI [−7.07 to −0.35] mmHg, p = 0.031; I2 = 58.47%), and diastolic blood pressure (DBP) (difference in means = −3.54 mmHg, 95% CI [−5.27 to −1.81] mmHg, p < 0.001; I2 = 0.00%) as compared to the women in the control group.ConclusionsMusic interventions may decrease anxiety scores and physiological indexes related to anxiety (HR, SBP, and DBP). Music interventions may be a good non-pharmacological approach for decreasing anxiety levels during labor. creator: Hsin-Hui Lin creator: Yu-Chen Chang creator: Hsiao-Hui Chou creator: Chih-Po Chang creator: Ming-Yuan Huang creator: Shu-Jung Liu creator: Chin-Han Tsai creator: Wei-Te Lei creator: Tzu-Lin Yeh uri: https://doi.org/10.7717/peerj.6945 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lin et al. title: Clarifying a trophic black box: stable isotope analysis reveals unexpected dietary variation in the Peruvian anchovy Engraulis ringens link: https://peerj.com/articles/6968 last-modified: 2019-05-15 description: BackgroundSmall fishes play fundamental roles in pelagic ecosystems, channelling energy and nutrients from primary producers to higher trophic levels. They support globally important fisheries in eastern boundary current ecosystems like the Humboldt Current System (HCS) of the SE Pacific (Chile and Peru), where fish catches are the highest in the world (per unit area). This production is associated with coastal upwelling where fisheries target small pelagic fishes including the Peruvian anchovy (Engraulis ringens). The elevated biomass attained by small pelagics is thought to reflect their low trophic position in short/simple food chains. Despite their global importance, large gaps exist in our understanding of the basic ecology of these resources. For instance, there is an ongoing debate regarding the relative importance of phytoplankton versus animal prey in anchovy diet, and ecosystem models typically assign them a trophic position (TP) of ∼2, assuming they largely consume phytoplankton. Recent work based on both relative energetic content and stable isotope analysis (SIA) suggests that this value is too low, with δ15N values indicating that anchovy TP is ca. 3.5 in the Peruvian HCS.MethodsWe characterised the trophic ecology of adult anchovies (n = 30), their putative prey and carnivorous jack mackerel (n = 20) captured from N Chile. SIA (δ13C and δ15N) was used to estimate the relative contribution of different putative prey resources. δ15N was used to estimate population level trophic position.ResultsAnchovies showed little variability in δ13C (−18.7 to −16.1‰) but varied greatly in δ15N (13.8 to 22.8‰)—individuals formed two groups with low or high δ15N values. When considered as a single group, mixing models indicated that anchovy diet was largely composed of zooplankton (median contribution: 95% credibility limits), with major contributions of crustacean larvae (0.61: 0.37–0.77) and anchovy (preflexion) larvae (0.15: 0.02–0.34), and the assimilation of phytoplankton was negligible (0.05: 0–0.22). The modal (95% credibility limits) estimate of TP for the pooled anchovy sample was 3.23 (2.93–3.58), overlapping with recent SIA-based estimates from Peru. When the two δ15N groups were analysed separately, our results indicate that the lower δ15N group largely assimilated materials from crustacean larvae (0.73: 0.42–0.88), with a TP of 2.91 (2.62–3.23). Mixing models suggested high δ15N anchovies were cannibalistic, consuming anchovy preflexion larvae (0.55: 0.11–0.74). A carnivorous trophic niche was supported by high TP (3.79: 3.48–4.16), mirroring that of carnivorous juvenile jack mackerel (Trachurus murphyi; 3.80: 3.51–4.14). Our results support recent conclusions regarding high TP values of anchovy from Peru and reveal new insights into their trophic behaviour. These results also highlight the existence of cryptic trophic complexity and ecosystem function in pelagic food webs, classically considered as simple. creator: Jessica Pizarro creator: Felipe Docmac creator: Chris Harrod uri: https://doi.org/10.7717/peerj.6968 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pizarro et al. title: PEST sequences from a cactus dehydrin regulate its proteolytic degradation link: https://peerj.com/articles/6810 last-modified: 2019-05-14 description: Dehydrins (DHNs) are intrinsically disordered proteins expressed under cellular dehydration-related stresses. In this study, we identified potential proteolytic PEST sequences located at the central and C-terminal regions from the Opuntia streptacantha OpsDHN1 protein. In order to evaluate these PEST sequences as proteolytic tags, we generated a translational fusion with the GUS reporter protein and OpsDHN1 coding sequence. We found a GUS degradation effect in tobacco agro-infiltrated leaves and Arabidopsis transgenic lines that expressed the fusion GUS::OpsDHN1 full-length. Also, two additional translational fusions between OpsDHN1 protein fragments that include the central (GUS::PEST-1) or the C-terminal (GUS::PEST-2) PEST sequences were able to decrease the GUS activity, with PEST-2 showing the greatest reduction in GUS activity. GUS signal was abated when the OpsDHN1 fragment that includes both PEST sequences (GUS::PEST-1-2) were fused to GUS. Treatment with the MG132 proteasome inhibitor attenuated the PEST-mediated GUS degradation. Point mutations of phosphorylatable residues in PEST sequences reestablished GUS signal, hence these sequences are important during protein degradation. Finally, in silico analysis identified potential PEST sequences in other plant DHNs. This is the first study reporting presence of PEST motifs in dehydrins. creator: Adriana L. Salazar-Retana creator: Israel Maruri-López creator: Itzell E. Hernández-Sánchez creator: Alicia Becerra-Flora creator: María de la Luz Guerrero-González creator: Juan Francisco Jiménez-Bremont uri: https://doi.org/10.7717/peerj.6810 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Salazar-Retana et al. title: Exploring perceptions of meaningfulness in visual representations of bivariate relationships link: https://peerj.com/articles/6853 last-modified: 2019-05-14 description: Researchers often need to consider the practical significance of a relationship. For example, interpreting the magnitude of an effect size or establishing bounds in equivalence testing requires knowledge of the meaningfulness of a relationship. However, there has been little research exploring the degree of relationship among variables (e.g., correlation, mean difference) necessary for an association to be interpreted as meaningful or practically significant. In this study, we presented statistically trained and untrained participants with a collection of figures that displayed varying degrees of mean difference between groups or correlations among variables and participants indicated whether or not each relationship was meaningful. The results suggest that statistically trained and untrained participants differ in their qualification of a meaningful relationship, and that there is significant variability in how large a relationship must be before it is labeled meaningful. The results also shed some light on what degree of relationship is considered meaningful by individuals in a context-free setting. creator: Nataly Beribisky creator: Heather Davidson creator: Robert A. Cribbie uri: https://doi.org/10.7717/peerj.6853 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Beribisky et al. title: Functional analysis of the GbDWARF14 gene associated with branching development in cotton link: https://peerj.com/articles/6901 last-modified: 2019-05-14 description: Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in Gossypium barbadense and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements. creator: Ping Wang creator: Sai Zhang creator: Jing Qiao creator: Quan Sun creator: Qian Shi creator: Chaowei Cai creator: Jianchuan Mo creator: Zongyan Chu creator: Youlu Yuan creator: Xiongming Du creator: Yuchen Miao creator: Xiao Zhang creator: Yingfan Cai uri: https://doi.org/10.7717/peerj.6901 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: P5CR1 protein expression and the effect of gene-silencing on lung adenocarcinoma link: https://peerj.com/articles/6934 last-modified: 2019-05-14 description: The present study aimed to investigate the expression of pyrroline-5-carboxylate reductase 1 (P5CR1) protein in lung adenocarcinoma and paracancerous tissues and to explore the effect of silencing the encoding gene PYCR1 on the proliferation, migration, invasion, and cisplatin sensitivity in lung adenocarcinoma cells, thereby providing a novel therapeutic target for the treatment of the disease. Immunohistochemistry staining was used to detect the P5CR1 protein expression in lung adenocarcinoma and paracancerous tissues, and statistical analysis evaluated the correlation between P5CR1 protein expression and gender, age, tissue part, or pathological grade. The CCK8 assay was performed to detect the proliferation and cisplatin sensitivity, while the effect of PYCR1 on the migration and invasion of lung adenocarcinoma cells was detected by scratch test and transwell chamber assay. The findings demonstrated that the P5CR1 protein expression was significantly elevated in lung adenocarcinoma tissues and correlated with the pathological grade, whereas no significant correlation was established between the protein expression and gender, age, or tissue part. Furthermore, after PYCR1 gene silencing, the proliferation and invasion were significantly suppressed, while the sensitivity to cisplatin was significantly enhanced. Therefore, it can be speculated that the PYCR1 gene affects the biological behavior of lung adenocarcinoma and cisplatin resistance, serving as a potential therapeutic target for lung adenocarcinoma. creator: Yang She creator: Aiyou Mao creator: Feng Li creator: Xiaobin Wei uri: https://doi.org/10.7717/peerj.6934 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 She et al. title: Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis link: https://peerj.com/articles/6950 last-modified: 2019-05-14 description: Haemophilus parasuis is an economically important bacterial pathogen of swine. Extensive genetic and phenotypic heterogeneity among H. parasuis strains have been observed, which hinders the deciphering of the population structure and its association with clinical virulence. In this study, two highly divergent clades were defined according to iron–sulphur cluster regulator (iscR)-based phylogeny analysis of 148 isolates. Clear separation of serovars and potential virulence markers (PVMs) were observed between the two clades, which are indicative of independent evolution of the two lineages. Previously suggested virulence factors showed no correlation with clinical virulence, and were probably clade or serovar specific genes emerged during different stage of evolution. PVMs profiles varied widely among isolates in the same serovar. Higher strain diversity in respect of PVMs was found for isolates from multi-strain infected farms than those from single strain infected ones, which indicates that multi-strain infection in one farm may increase the frequency of gene transfer in H. parasuis. Systemic isolates were more frequently found in serovar 13 and serovar 12, while no correlation between clinical virulence and iscR-based phylogeny was observed. It shows that iscR is a reliable marker for studying population structure of H. parasuis, while other factors should be included to avoid the interference of gene exchange of iscR between isolates. The two lineages of H. parasuis may have undergone independent evolution, but show no difference in clinical virulence. Wide distribution of systemic isolates across the entire population poses new challenge for development of vaccine with better cross-protection. Our study provides new information for better deciphering the population structure of H. parasuis, which helps understanding the extreme diversity within this pathogenic bacterium. creator: Junxing Li creator: Lihua Xu creator: Fei Su creator: Bin Yu creator: Xiufang Yuan uri: https://doi.org/10.7717/peerj.6950 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Alternative bait trials in the Barents Sea snow crab fishery link: https://peerj.com/articles/6874 last-modified: 2019-05-13 description: Commercial harvesting of snow crab (Chionoecetes opilio) in the Barents Sea started in 2012 by Norwegian fishing vessels. This new fishery has significant bait requirements, representing an emerging conservation challenge. In this study, we evaluate the performance of five alternative (natural) baits manufactured from the waste stream of existing and sustainably managed harp seal (Pagophilus groenlandicus) and minke whale (Balaenoptera acutorostrata) capture. Five different types of new bait were evaluated, including seal fat (SF), seal fat with skin (SFS), seal meat with bone (SMB), whale fat with skin (WFS), and whale meat with fat (WMF). A comparative fishing experiment was conducted onboard a commercial snow crab fishing vessel in the Barents Sea (May–June, 2016) to evaluate the performance of traditional bait (squid, Illexs spp.) and alternative baits at catching snow crabs. Performance of the different baits were compared on the basis of the number of commercial crab caught per trap haul catch per unit effort (CPUE) and carapace width (CW). Our results showed that SF and SFS performed equally well to traditional bait, with no statistical difference in CPUE (p-value = 0.325 and 0.069, respectively). All of the other experimental baits significantly decreased CPUE, when compared to squid. No significant effect of bait treatment on CW was detected and the cumulative distribution of CW was the same between control traps and each of the bait treatments. Overall the results indicated that SF and SFS represent a viable alternative to replace traditional bait, addressing a key conservation challenge in this bait intensive snow crab fishery. creator: Tomas Araya-Schmidt creator: Leonore Olsen creator: Lasse Rindahl creator: Roger B. Larsen creator: Paul D. Winger uri: https://doi.org/10.7717/peerj.6874 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Araya-Schmidt et al. title: The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast link: https://peerj.com/articles/6883 last-modified: 2019-05-13 description: The clinging jellyfish Gonionemus sp. is a small hydromedusa species known historically from the Swedish west coast but not reported in recent times. This species is thought to be native to the northwest Pacific where it is notorious for causing severe stings in humans and is considered invasive or cryptogenic elsewhere. This year, unlike in the past, severe stings in swimmers making contact with Gonionemus sp. medusae occurred in Swedish waters from a sheltered eelgrass bed in the inner Skagerrak archipelago. To the best of our knowledge, this is only the second sting record of Gonionemus sp. from the Northeast Atlantic—with the first record occurring off the Belgian coast in the 1970s. Stinging Gonionemus sp. medusae have also been recently reported from the northwestern Atlantic coast, where, like on the Swedish coast, stings were not reported in the past. We analyzed sea surface temperature data from the past 30 years and show that 2018 had an exceptionally cold spring followed by an exceptionally hot summer. It is suggested that the 2018 temperature anomalies contributed to the Swedish outbreak. An analysis of mitochondrial COI sequences showed that Swedish medusae belong to the same clade as those from toxic populations in the Sea of Japan and northwest Atlantic. Gonionemus sp. is particularly prone to human-mediated dispersal and we suggest that it is possible that this year’s outbreak is the result of anthropogenic factors either through a climate-driven northward range shift or an introduction via shipping activity. We examined medusa growth rates and details of medusa morphology including nematocysts. Two types of penetrating nematocysts: euryteles and b-mastigophores were observed, suggesting that Gonionemus sp. medusae are able to feed on hard-bodied organisms like copepods and cladocerans. Given the now-regular occurrence and regional spread of Gonionemus sp. in the northwest Atlantic, it seems likely that outbreaks in Sweden will continue. More information on its life cycle, dispersal mechanisms, and ecology are thus desirable. creator: Annette F. Govindarajan creator: Björn Källström creator: Erik Selander creator: Carina Östman creator: Thomas G. Dahlgren uri: https://doi.org/10.7717/peerj.6883 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Govindarajan et al. title: Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons link: https://peerj.com/articles/6898 last-modified: 2019-05-13 description: High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage. creator: Xavier Pochon creator: Patricia Wecker creator: Michael Stat creator: Véronique Berteaux-Lecellier creator: Gaël Lecellier uri: https://doi.org/10.7717/peerj.6898 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Pochon et al. title: The interactive effect of herbivory, nutrient enrichment and mucilage on shallow rocky macroalgal communities link: https://peerj.com/articles/6908 last-modified: 2019-05-13 description: This paper focuses on the interactive short and long-term effect of three different stressors on a macroalgal assemblage. Three stressors are considered: herbivory, nutrients and mucilage. The experiment was conducted in Tavolara Punta Coda Cavallo Marine Protected Area (Mediterranean Sea) during a bloom of the benthic mucilage-producing microalga Chrysophaeum taylorii (Pelagophyceae); this microalga is recently spreading in the Mediterranean Sea. On a rocky substratum, 36 plots 20 × 20 cm in size were prepared. Factorial combinations of three experimental treatments were applied in triplicate, including three grazing levels crossed with two nutrient enrichment and two mucilage removal treatments. Significant differences were observed among treatments 8 weeks later, at the end of summer. In particular, dark filamentous algae were more abundant in all enriched plots, especially where mucilage and macroalgae had been removed; a higher percent cover of crustose coralline algae was instead observed where nutrients had been increased and no grazing pressure acted. Furthermore, the abundance of Dictyota spp. and Laurencia spp. was significantly higher in enriched mucilage-free plots where the grazing pressure was null or low. However, the effects of the treatments on the overall assemblage of the macroalgal community were not long persistent (36 weeks later). These results illustrate the capacity of a shallow-water macroalgal community to quickly recover from the simultaneous impacts of herbivory, nutrient enrichment, and mucilage. creator: Sarah Caronni creator: Chiara Calabretti creator: Sandra Citterio creator: Maria Anna Delaria creator: Rodolfo Gentili creator: Giovanni Macri creator: Chiara Montagnani creator: Augusto Navone creator: Pieraugusto Panzalis creator: Giulia Piazza creator: Giulia Ceccherelli uri: https://doi.org/10.7717/peerj.6908 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Caronni et al. title: Using GIS to examine biogeographic and macroevolutionary patterns in some late Paleozoic cephalopods from the North American Midcontinent Sea link: https://peerj.com/articles/6910 last-modified: 2019-05-13 description: Geographic range is an important macroevolutionary parameter frequently considered in paleontological studies as species’ distributions and range sizes are determined by a variety of biotic and abiotic factors well known to affect the differential birth and death of species. Thus, considering how distributions and range sizes fluctuate over time can provide important insight into evolutionary dynamics. This study uses Geographic Information Systems (GIS) and analyses of evolutionary rates to examine how in some species within the Cephalopoda, an important pelagic clade, geographic range size and rates of speciation and extinction changed throughout the Pennsylvanian and early Permian in the North American Midcontinent Sea. This period is particularly interesting for biogeographic and evolutionary studies because it is characterized by repetitive interglacial-glacial cycles, a global transition from an icehouse to a greenhouse climate during the Late Paleozoic Ice Age, and decelerated macroevolutionary dynamics, i.e. low speciation and extinction rates. The analyses presented herein indicate that cephalopod species diversity was not completely static and actually fluctuated throughout the Pennsylvanian and early Permian, matching findings from other studies. However, contrary to some other studies, the mean geographic ranges of cephalopod species did not change significantly through time, despite numerous climate oscillations; further, geographic range size did not correlate with rates of speciation and extinction. These results suggest that pelagic organisms may have responded differently to late Paleozoic climate changes than benthic organisms, although additional consideration of this issue is needed. Finally, these results indicate that, at least in the case of cephalopods, macroevolution during the late Paleozoic was more dynamic than previously characterized, and patterns may have varied across different clades during this interval. creator: Kayla M. Kolis creator: Bruce S. Lieberman uri: https://doi.org/10.7717/peerj.6910 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kolis and Lieberman title: Conspecific coprophagy stimulates normal development in a germ-free model invertebrate link: https://peerj.com/articles/6914 last-modified: 2019-05-13 description: Microbial assemblages residing within and on animal gastric tissues contribute to various host beneficial processes that include diet accessibility and nutrient provisioning, and we sought to examine the degree to which intergenerational and community-acquired gut bacteria impact development in a tractable germ-free (GF) invertebrate model system. Coprophagy is a common behavior in cockroaches and termites that provides access to both nutrients and the primary means by which juveniles are inoculated with beneficial gut bacteria. This hypothesis was tested in the American cockroach (Periplaneta americana) by interfering with this means of acquiring gut bacteria, which resulted in GF insects that exhibited prolonged growth rates and gut tissue dysmorphias relative to wild-type (WT) P. americana. Conventionalization of GF P. americana via consumption of frass (feces) from conspecifics and siblings reared under non-sterile conditions resulted in colonization of P. americana gut tissues by a diverse microbial community and a significant (p < 0.05) recovery of WT level growth and hindgut tissue development phenotypes. These data suggest that coprophagy is essential for normal gut tissue and organismal development by introducing beneficial gut bacteria to P. americana, and that the GF P. americana model system is a useful system for examining how gut bacteria impact host outcomes. creator: Benjamin C. Jahnes creator: Madeline Herrmann creator: Zakee L. Sabree uri: https://doi.org/10.7717/peerj.6914 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jahnes et al. title: Plant diversity is closely related to the density of zokor mounds in three alpine rangelands on the Tibetan Plateau link: https://peerj.com/articles/6921 last-modified: 2019-05-13 description: BackgroundPlateau zokor (Myospalax baileyi) is a subterranean rodent endemic to the Tibetan Plateau. This species has been generally viewed as a pest in China due to the competition for food with livestock and also causing soil erosion. As a result, plateau zokor has been the target of widespread poisoning or trapping campaigns designed to control or eliminate it since 1970s. But there is little research on the effect of plateau zokor on plant diversity in alpine rangelands. Therefore, objectively evaluating the positive effects of the plateau zokors disturbance on their living environment and plant communities is of great significance to understand the function of plateau zokor in alpine ecosystem.MethodsHere, we selected three rangelands (alpine meadow, alpine steppe and alpine shrub meadow) in which plateau zokors are typically distributed on the Tibetan Plateau, and five zokor mound density gradients were selected in each rangeland type to study the effects of the mounds on soil moisture and temperature related to plant species diversity.ResultsThe results showed that, with the mound density increasing, the soil temperature decreased significantly in all three rangeland types, and the soil moisture significantly increased in all three rangeland types. In the alpine meadow, both the plant diversity and cumulative species richness increased significantly with increasing mound density. The increase in broad-leaved forbs is the main reason for the increase of plant diversity in the alpine meadow disturbed by zokor mounds. In the alpine steppe, the plant diversity decreased significantly with increasing mound density, while the cumulative species richness initially decreased and then increased. In the alpine shrub meadow, the plant diversity first increased and then decreased with increasing mound density as did the cumulative species richness. In conclusion, plateau zokor mounds dominated the distribution of soil moisture and temperature and significantly affected plant diversity in these three rangelands on Tibetan Plateau; the results further deepen our understanding toward a co-evolved process. creator: Yujie Niu creator: Jianwei Zhou creator: Siwei Yang creator: Bin Chu creator: Huimin Zhu creator: Bo Zhang creator: Qiangen Fang creator: Zhuangsheng Tang creator: Limin Hua uri: https://doi.org/10.7717/peerj.6921 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Niu et al. title: Automated pupillometry to detect command following in neurological patients: a proof-of-concept study link: https://peerj.com/articles/6929 last-modified: 2019-05-13 description: BackgroundLevels of consciousness in patients with acute and chronic brain injury are notoriously underestimated. Paradigms based on electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) may detect covert consciousness in clinically unresponsive patients but are subject to logistical challenges and the need for advanced statistical analysis.MethodsTo assess the feasibility of automated pupillometry for the detection of command following, we enrolled 20 healthy volunteers and 48 patients with a wide range of neurological disorders, including seven patients in the intensive care unit (ICU), who were asked to engage in mental arithmetic.ResultsFourteen of 20 (70%) healthy volunteers and 17 of 43 (39.5%) neurological patients, including 1 in the ICU, fulfilled prespecified criteria for command following by showing pupillary dilations during ≥4 of five arithmetic tasks. None of the five sedated and unconscious ICU patients passed this threshold.ConclusionsAutomated pupillometry combined with mental arithmetic appears to be a promising paradigm for the detection of covert consciousness in people with brain injury. We plan to build on this study by focusing on non-communicating ICU patients in whom the level of consciousness is unknown. If some of these patients show reproducible pupillary dilation during mental arithmetic, this would suggest that the present paradigm can reveal covert consciousness in unresponsive patients in whom standard investigations have failed to detect signs of consciousness. creator: Alexandra Vassilieva creator: Markus Harboe Olsen creator: Costanza Peinkhofer creator: Gitte Moos Knudsen creator: Daniel Kondziella uri: https://doi.org/10.7717/peerj.6929 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Vassilieva et al. title: Large-scale insect outbreak homogenizes the spatial structure of ectomycorrhizal fungal communities link: https://peerj.com/articles/6895 last-modified: 2019-05-10 description: Ectomycorrhizal fungi (plant symbionts) are diverse and exist within spatially variable communities that play fundamental roles in the functioning of terrestrial ecosystems. However, the underlying ecological mechanisms that maintain and regulate the spatial structuring of ectomycorrhizal fungal communities are both complex and remain poorly understood. Here, we use a gradient of mountain pine beetle (Dendroctonus ponderosae) induced tree mortality across eleven stands in lodgepole pine (Pinus contorta) forests of western Canada to investigate: (i) the degree to which spatial structure varies within this fungal group, and (ii) how these patterns may be driven by the relative importance of tree mortality from changes in understory plant diversity, productivity and fine root biomass following tree death. We found that the homogeneity of the ectomycorrhizal fungal community increased with increasing tree death, aboveground understory productivity and diversity. Whereas, the independent effect of fine root biomass, which declined along the same gradient of tree mortality, increased the heterogeneity of the ectomycorrhizal fungal community. Together, our results demonstrate that large-scale biotic disturbance homogenizes the spatial patterns of ectomycorrhizal fungal communities. creator: Gregory J. Pec creator: James F. Cahill, Jr. uri: https://doi.org/10.7717/peerj.6895 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pec and Cahill title: Species delimitation of the Dermacentor ticks based on phylogenetic clustering and niche modeling link: https://peerj.com/articles/6911 last-modified: 2019-05-10 description: Three species belonging to the genus Dermacentor (Acari: Ixodidae), D. marginatus, D. nuttalli and D. silvarum are well known as vectors for a great variety of infection pathogens. All three of them are host ticks, which are very similar in morphology characteristics, life cycle, seasonal variation and ecological conditions, making it difficult to distinguish the three species. In the present study, these three species were delimitated based on molecular data and ecological niche. The molecular analysis showed that the three species can be distinguished by COI and ITS2 sequences. We created future potential distribution maps for the three species under climate changes with MaxEnt, which highlighted the different levels of the suitable habitats for each tick species. In addition, niche comparisons among the three species in Dermacentor were conducted, and the analysis suggested that niche overlap was relatively high with D. nuttalli and D. silvarum compared to the other species pairs, which was consistent with the molecular data. Niche equivalency and similarity test confirmed that these Dermacentor species were closely related but distinct species. In conclusion, delimitation of these three species within Dermacentor was supported by molecular phylogeny and quantitative ecological space. This study will provide deep insights into the biology, ecology, and diversification processes within Dermacentor species, and for the development of effective control for ticks. creator: Fang Wang creator: Duo Wang creator: Ge Guo creator: Yonghong Hu creator: Jiufeng Wei creator: Jingze Liu uri: https://doi.org/10.7717/peerj.6911 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Use of aerial thermography to reduce mortality of roe deer fawns before harvest link: https://peerj.com/articles/6923 last-modified: 2019-05-10 description: In agricultural landscape, there are thousands of young wild animals killed every year. Their deaths are caused mostly by agricultural fieldworks during spring harvest. Among the affected animals there are also fawns of roe deer (Capreolus capreolus), which react to danger by pressing themselves against the ground in order to be protected from predators. There were various methods tested in the past aimed at decreasing roe deer mortality caused by agriculture machinery with varied levels of success. This contribution presents technology that documents the possibility of searching for fawns with a thermal imaging device carried by an unmanned aerial vehicles (UAV). The results are based on field research that estimated the ideal height of flight being ±40 meters above ground. If the climatic conditions are favourable, it is possible to monitor and mark fawn locations using GPS coordinates in an area of about 14 ha in 25 minutes, which is the average flight time of UAV on one battery charge. The thermo-camera is very reliable in finding fawns in early morning hours (4 to 6 a.m.) when there is the highest temperature contrast between the searched object and its surroundings. The main limiting factors are climatic conditions and the short time span in which the thermo-camera can be used. If the basic requirements are met, the rate of successful fawn detection can be even up to 100%. An undisputed advantage of this method is the possibility of involvement of local gamekeepers. Thus the agricultural fieldworks are not interrupted. creator: Jan Cukor creator: Jan Bartoška creator: Jan Rohla creator: Jan Sova creator: Antonín Machálek uri: https://doi.org/10.7717/peerj.6923 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cukor et al. title: A multi-generational risk assessment of Cry1F on the non-target soil organism Folsomia candida (Collembola) based on whole transcriptome profiling link: https://peerj.com/articles/6924 last-modified: 2019-05-10 description: The Bacillus thuringiensis toxin Cry1F has been used to develop insect-resistant genetically engineered crops. There has been great interest in evaluating its potential risk to non-target organisms (NTOs). However, the majority of previous risk assessments only examined one generation of NTOs using several physiological indicators, which cannot comprehensively detect some potential sub-lethal effects at the molecular level. In this study, we conducted a laboratory-based, multi-generational risk assessment of Cry1F for the collembolan Folsomia candida, an important representative of soil arthropods in terms of survival, reproduction, and differentially expressed genes (DEGs) identified from whole transcriptome profiles. Our results demonstrated that Cry1F was continuously ingested by collembolans over three consecutive generations, but it did not affect the survival or reproduction of F. candida. There were no significant differences in the global gene expression between F. candida—fed diets with and without Cry1F, and no consistent co-expressed DEGs over three generations. In addition, Cry1F did not obviously alter the expression profiles of seven sensitive biological markers. Our composite data indicates that Cry1F had no long-term harmful effects on collembolan F. candida. creator: Cheng-Wang Huang creator: Wan-Jun Chen creator: Xin Ke creator: Yunhe Li creator: Yun-Xia Luan uri: https://doi.org/10.7717/peerj.6924 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Huang et al. title: Hybrid identification in Nothofagus subgenus using high resolution melting with ITS and trnL approach link: https://peerj.com/articles/6779 last-modified: 2019-05-09 description: The genus Nothofagus is the main component of southern South American temperate forests. The 40 Nothofagus species, evergreen and deciduous, and some natural hybrids are spread among Central and Southern Chile, Argentina, New Zealand, Australia, New Guinea and New Caledonia. Nothofagus nervosa, Nothofagus obliqua and Nothofagus dombeyi are potentially very important timber producers due to their high wood quality and relative fast growth; however, indiscriminate logging has degraded vast areas the Chilean forest causing a serious state of deterioration of their genetic resource. The South of Chile has a large area covered by secondary forests of Nothofagus dombeyi. These forests have a high diversity of species, large amount of biomass and high silvicultural potential. This work shows a case of hybrid identification in Nothofagus subgenus in different secondary forests of Chile, using high resolution melting. Unknown samples of Nothofagus subgenus are genetically distinguishable with the ITS region of Nothofagus antarctica, Nothofagus nitida and N. obliqua species. It was not possible to distinguish between unknown samples of Andean versus coastal origin. Melting curves with ITS approach of unknown material are genetically similar, positioned between N. dombeyi and N. antarctica and distant from N. nitida. The unknown samples are genetically very close to Nothofagus dombeyi. This suggests the presence of hybrid individuality between species (N. dombeyi × N. antarctica) with the possibility of introgression towards the gene pool of N. antarctica, producing the deciduous foliage that is both present. The trnL locus has no distinction between the N. dombeyi and N. antarctica species, since a similar melting curve is present and equal Tm (80.00 °C). The trnL locus cannot be genetically distinguished from one unknown sample of Nothofagus to another, as highlighted in this study. creator: Jaime Solano creator: Leonardo Anabalón creator: Francisco Encina creator: Carlos Esse creator: Diego Penneckamp uri: https://doi.org/10.7717/peerj.6779 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Solano et al. title: Dominance in dogs as rated by owners corresponds to ethologically valid markers of dominance link: https://peerj.com/articles/6838 last-modified: 2019-05-09 description: Dominance is well defined in ethology, debated in psychology, and is often unclear among the dog owning public and in the press. However, to date, no study has examined how owners perceive dominance in dogs, and what different behaviours and personality types are used to describe dominant and subordinate individuals. A questionnaire study was launched to investigate the external validity of owner-derived estimates of dominance in dog dyads sharing the same household (N = 1,151). According to the owners, dogs rated as dominant (87%) have priority access to resources (resting place, food, and rewards), undertake certain tasks (defend and lead the group, bark more), display dominance (win fights, lick the other’s mouth less, and mark over the other’s urine), share certain personality traits (smarter, more aggressive and impulsive), and are older than their partner dog (all p < 0.0001). An age-related hypothesis has been suggested to explain dominance in dogs; but we found that dog age did not explain the occurrence of dominance related behaviours over the owners’ estimate of dominance status. Results suggest that owner-derived reports of dominance ranks of dogs living in multi-dog households correspond to ethologically valid behavioural markers of dominance. Size and physical condition were unrelated to the perceived dominance. Surprisingly, in mixed-sex dyads, females were more frequently rated as dominant than males, which might correspond to a higher proportion of neutered females in this subgroup. For future studies that wish to allocate dominance status using owner report, we offer a novel survey. creator: Enikő Kubinyi creator: Lisa J. Wallis uri: https://doi.org/10.7717/peerj.6838 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kubinyi and Wallis title: Optimizing de novo genome assembly from PCR-amplified metagenomes link: https://peerj.com/articles/6902 last-modified: 2019-05-09 description: BackgroundMetagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes.MethodsHere we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes.ResultsRead mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes.ConclusionsPCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes. creator: Simon Roux creator: Gareth Trubl creator: Danielle Goudeau creator: Nandita Nath creator: Estelle Couradeau creator: Nathan A. Ahlgren creator: Yuanchao Zhan creator: David Marsan creator: Feng Chen creator: Jed A. Fuhrman creator: Trent R. Northen creator: Matthew B. Sullivan creator: Virginia I. Rich creator: Rex R. Malmstrom creator: Emiley A. Eloe-Fadrosh uri: https://doi.org/10.7717/peerj.6902 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Roux et al. title: The vaccinaTion & Hpv Knowledge (THinK) questionnaire: a reliability and validity study on a sample of women living in Sicily (southern-Italy) link: https://peerj.com/articles/6254 last-modified: 2019-05-09 description: ObjectiveThe aim of this study was to introduce the VaccinaTion & Hpv Knowledge (THinK) questionnaire to assess knowledge about human papillomavirus (HPV) and attitude to HPV-vaccination. Its reliability and validity was demonstrated in a sample of women living in Sicily (southern Italy).MethodsA cross-sectional survey was conducted on a sample of 220 women at the “Paolo Giaccone” University Hospital in Palermo (Sicily), aged 18–61. Data were analyzed through Cronbach’s alpha and exploratory factor analysis, followed by a structural equation model with measurement component. The two-level data structure was explicitly considered.ResultsThree dimensions were found: “knowledge of HPV infection (kHPV), “Attitude to be vaccinated against HPV (aHPV)” and “Knowledge about vaccines (KV)” (97% overall explained variance). Internal consistency was good for the whole questionnaire (0.82) and the first dimension (0.88) and acceptable for the second (0.78) and the third dimension (0.73). 23% of women showed no or little knowledge of HPV and 44.3% of women had no or little knowledge about HPV induced lesions.DiscussionThe use of a validated questionnaire may serve as a useful measure to assess general knowledge about HPV and attitude towards vaccination against HPV in the primary prevention setting. creator: Domenica Matranga creator: Cristina Lumia creator: Rossella Guarneri creator: Vincenza Maria Arculeo creator: Marcello Noto creator: Alessia Pivetti creator: Gregorio Serra creator: Maria Francesca Guarneri creator: Antonio Spera uri: https://doi.org/10.7717/peerj.6254 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Matranga et al. title: Water permeability/impermeability in seeds of 15 species of Caragana (Fabaceae) link: https://peerj.com/articles/6870 last-modified: 2019-05-09 description: Majority legumes in the temperate and arctic zones have water-impermeable seeds (physical dormancy, PY). However, various authors have reported that seeds of some Caragana species are water-permeable and thus non-dormant. We (1) tested seeds of 15 species of Caragana matured in the same site in 2014, 2016 and/or 2017 for presence of PY, (2) determined if dry storage decreased or increased the percentage of seeds with PY and (3) located the site on the seed coat of 11 species where water enters the seed. Sixty-three percent and 45% of the seeds of C. roborovskyi had PY in 2016 and 2017, respectively, but only 0–14% of the seeds of the other 14 species had PY. The palisade layer in the seed coat of water impermeable seeds had no cracks in it, whereas cracks were present in the palisade layer of water-permeable seeds. Year of collection and dry storage had significant effects on imbibition of two species (C. acanthophylla and C. roborovskyi). In two (C. acanthophylla and C. roborovskyi) of the 11 species tested, the hilum was the site of water entry into seeds (control seeds, not any dormant broken treatments), but for the other nine species tested water entered through all parts of the seed coat. creator: Dali Chen creator: Rui Zhang creator: Carol C. Baskin creator: Xiaowen Hu uri: https://doi.org/10.7717/peerj.6870 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Heracleum sosnowskyi seed development under the effect of exogenous application of GA3 link: https://peerj.com/articles/6906 last-modified: 2019-05-09 description: Numerous studies have demonstrated the impact of exogenous gibberellin on fleshy fruit formation, but the effect on dry fruits is not yet well known. To test the role of gibberellin (GA3) in dry fruit formation, we analysed the impact of exogenous GA3 on the invasive plant Sosnowsky’s hogweed (H. sosnowskyi Manden.) seed development and germination. Treatment of GA3 concentrations of 0.07 mM, 0.14 mM, 0.28 mM, 0.43 mM was applied to flowers at the early stage of development. Seeds were collected from treated satellite umbels. It was observed that GA3treatment did not have a significant effect on the size of H. sosnowskyi seeds, but caused various changes in their shape. The data on semi-thin longitudinal sections of H. sosnowskyi mericarps and SEM micrographs of embryos showed that the embryos in GA3 (0.43 mM) treated variants were at torpedo stage, while in control variants—mature embryos. The germination of seeds of each variant was estimated by burying them in the soil. Our studies indicated that GA3 application reduced the germination of H. sosnowskyi seed from 98.0% (control) to 16.5% (GA3 concentration 0.43 mM). It was assumed that exogenous application of GA3 had influence on the development of dry Sosnowsky’s hogweed seeds and could be used to inhibit the spread of this invasive plant. creator: Dalia Koryznienė creator: Sigita Jurkonienė creator: Tautvydas Žalnierius creator: Virgilija Gavelienė creator: Elžbieta Jankovska-Bortkevič creator: Nijolė Bareikienė creator: Vincas Būda uri: https://doi.org/10.7717/peerj.6906 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Koryznienė et al. title: Intermittent reproduction, mortality patterns and lifetime breeding frequency of females in a population of the adder (Vipera berus) link: https://peerj.com/articles/6912 last-modified: 2019-05-09 description: Female adders (Vipera berus) are “capital breeders” that exhibit delayed maturity and intermittent reproductive frequency. We studied the attainment of sexual maturity, the initiation of annual breeding in mature females, the energy and mortality costs associated with breeding, the length of the reproductive cycle and female lifetime reproductive frequency. We use longitudinal data obtained during an 18-year (2000–2017) mark–recapture study in a large population of adders in northern Belgium. A minority (15%) of the females gave birth to their first litter when they attained the actual age of 3 years, upon surpassing a minimum snout-vent-length of 38 cm. However, most females reproduced for the first time when they were 4 years or older. In mature females, breeding in a given year depends to a large extent on their body condition at the onset of the active season, indicating that a threshold level of energy reserves is necessary to start a reproductive cycle. During breeding years females stop growing, lose about one-third of their initial body mass and are very emaciated after parturition. The decrease in relative body mass was most notable initially in the largest and fattiest females. During the non-breeding years, females forage intensely to rebuild their fat reserves; their abilities to do so will strongly affect whether and when they engage in subsequent reproductive bouts. We used a multistate mark–recapture analytical method to simultaneously estimate the capture and survival rates of breeding and non-breeding females, a necessary procedure to obtain accurate estimates of survival probabilities. The analysis indicated much higher capture rates during the breeding years, but did not reveal a substantial effect of reproductive state on annual survival rates. Although some females were observed to breed in successive years, the reproductive cycle was most often biennial or triennial. However, most females (ca. 70%) that attained sexual maturity reproduced only once during their lifetime, while a minority of the females (ca. 5%) were observed to breed on 3–5 annual occasions. On average, females produced only ca. 1.3 litters during their reproductive lifetime. The short reproductive lifetime is a consequence not only of mortality directly related to the reproductive activities, but also of mortality associated with recovering from the weakened post-parturient body condition during the long intervals (1–2 years) between reproductive bouts. creator: Dirk Bauwens creator: Katja Claus uri: https://doi.org/10.7717/peerj.6912 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bauwens and Claus title: Changes in precipitation may alter food preference in an ecosystem engineer, the black land crab, Gecarcinus ruricola link: https://peerj.com/articles/6818 last-modified: 2019-05-08 description: Gecarcinid land crabs are ecosystem engineers playing an important role in nutrient recycling and seedling propagation in coastal forests. Given a predicted future decline in precipitation for the Caribbean, the effects of dehydration on feeding preferences of the black land crab Gecarcinus ruricola were investigated. G. ruricola were offered novel food items of lettuce, apple, or herring to test for food choice based on water and nutritional (energetic) content in single and multiple choice experimental designs. The effect of dehydration was incorporated by depriving crabs of water for 0, 4, or 8 days, leading to an average body water loss of 0%, 9%, and 17%, respectively, (crabs survived a body water loss of 23% + 2% and 14–16 days without access to water). The results were consistent between the single and multiple choice experiments: crabs consumed relatively more apple and fish and only small amounts of lettuce. Overall, no selective preferences were observed as a function of dehydration, but crabs did consume less dry food when deprived of water and an overall lower food intake with increasing dehydration levels occurred. The decrease in feeding was likely due to loss of water from the gut resulting in the inability to produce ample digestive juices. Future climatic predictions suggest a 25–50% decline in rainfall in the Caribbean, which may lead to a lower food intake by the crabs, resulting in compromised growth. The subsequent reduction in nutrient recycling highlights possible long-term effects on coastal ecosystems and highlights the importance of future work on climate relative behavioral interactions that influence ecosystem function. creator: Iain J. McGaw creator: Travis E. Van Leeuwen creator: Rebekah H. Trehern creator: Amanda E. Bates uri: https://doi.org/10.7717/peerj.6818 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 McGaw et al. title: Circular RNAs as potential biomarkers and therapeutics for cardiovascular disease link: https://peerj.com/articles/6831 last-modified: 2019-05-08 description: Circular RNAs (circRNAs) are genetic regulators that were earlier considered as “junk”. In contrast to linear RNAs, they have covalently linked ends with no polyadenylated tails. CircRNAs can act as RNA-binding proteins, sequestering agents, transcriptional regulators, as well as microRNA sponges. In addition, it is reported that some selected circRNAs are transformed into functional proteins. These RNA molecules always circularize through covalent bonds, and their presence has been demonstrated across species. They are usually abundant and stable as well as evolutionarily conserved in tissues (liver, lung, stomach), saliva, exosomes, and blood. Therefore, they have been proposed as the “next big thing” in molecular biomarkers for several diseases, particularly in cancer. Recently, circRNAs have been investigated in cardiovascular diseases (CVD) and reported to play important roles in heart failure, coronary artery disease, and myocardial infarction. Here, we review the recent literature and discuss the impact and the diagnostic and prognostic values of circRNAs in CVD. creator: Weitie Wang creator: Yong Wang creator: Hulin Piao creator: Bo Li creator: Maoxun Huang creator: Zhicheng Zhu creator: Dan Li creator: Tiance Wang creator: Rihao Xu creator: Kexiang Liu uri: https://doi.org/10.7717/peerj.6831 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Modulation of stress response and productive performance of Litopenaeus vannamei through diet link: https://peerj.com/articles/6850 last-modified: 2019-05-08 description: The high tolerance of Litopenaeus vannamei to a wide range of salinity (1–50 psu) makes this species an excellent candidate for culture under low salinity, decreasing shrimp epidemics and water pollution in some coastal areas. However, salinity levels outside the optimal range could impose several physiological constraints that would in turn affect growth and survival, particularly in the presence of additional stressors (e.g. high densities, handling practices, and hypoxia). Despite shrimp susceptibility to individual stressors has been widely addressed, information regarding response to chronic and acute stressors combined and its relation to diet is scarce. Thus, the aim of our study was to determine the effect of diet on the susceptibility to chronic (low salinity) and acute (hypoxia and escape response) stressors in terms of culture performance and physiological indicators. We evaluated overall performance during culture of L. vannamei at low salinity (6 psu), fed with an experimental diet with low protein and high carbohydrate content (26% protein and 6% fish meal plus probiotic mixture) and compared to a commercial formula with high protein and low carbohydrate content (40% crude protein and 20% fish meal without probiotic mixture). At the end of the rearing experiment, shrimp were exposed to two types of acute stress, hypoxia and escape. Biochemical (hemocyanin, total proteins, glucose, and lactate) and bioenergetic (adenylic energy charge and arginine phosphate levels) variables were measured to assess chronic stress response (salinity) and acute stress response (hypoxia or escape). The experimental diet resulted in higher muscle energy status that was not affected by low salinity, although lipid levels were lower under this condition. This diet partially counteracted the low performance at low salinity and promoted greater protein efficiency. Hypoxia induced strong hyperglycemic and lactate increase as response, whereas escape response was characterized by a depletion of arginine phosphate levels, with a stronger decrease in shrimp fed experimental diet, due to the high initial level of this reserve. Some data (glucose levels in hemolymph and lipids in hepatopancreas) suggest that shrimp under chronic stress conditions (low salinity and high densities) present a low ability to respond to subsequent acute stressors such as hypoxia or escape. This work indicates that diet can increase the energy status of shrimp, enabling them to overcome potential multifactorial stressors, which are common in farming systems. creator: Eliza M. Martínez-Antonio creator: Ilie S. Racotta creator: Juan C. Ruvalcaba-Márquez creator: Francisco Magallón-Barajas uri: https://doi.org/10.7717/peerj.6850 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Martínez-Antonio et al. title: Comparison of microbial community structures in soils with woody organic amendments and soils with traditional local organic amendments in Ningxia of Northern China link: https://peerj.com/articles/6854 last-modified: 2019-05-08 description: BackgroundAddition of organic amendments has been commonly adopted as a means to restore degraded soils globally. More recently, the use of woody organic amendments has been recognized as a viable method of capturing and retaining water and restoring degraded and desertified soil, especially in semi-arid regions. However, the impacts of woody amendments on soil microbial community structure, versus other traditional organic supplements is less understood.MethodsThree locally available natural organic materials of different qualities, i.e., cow manure (CM), corn straw (CS), and chipped poplar branches (PB) were selected as treatments in Ningxia, Northern China and compared with control soils. Four microcosms served as replicates for each treatment. All treatments contained desertified soil; treatments with amendments were mixed with 3% (w/w) of one of the above organic materials. After 7 and 15 months from the start of the experiment, soil samples were analyzed for chemical and physical properties, along with biological properties, which included microbial α-diversity, community structure, and relative abundance of microbial phyla.ResultsBoth bacterial and fungal α-diversity indices were weakly affected by amendments throughout the experimental period. All amendments yielded different microbial community compositions than the Control soils. The microbial community composition in the CS and PB treatments also were different from the CM treatment. After 15 months of the experiment, CS and PB exhibited similar microbial community composition, which was consistent with their similar soil physical and chemical properties. Moreover, CS and PB also appeared to exert similar effects on the abundance of some microbial taxa, and both of these treatments yield different abundances of microbial taxa than the CM treatment.ConclusionNew local organic amendment with PB tended to affect the microbial community in a similar way to the traditional local organic amendment with CS, but different from the most traditional local organic amendment with CM in Ningxia, Northern China. Moreover, the high C/N-sensitive, and lignin and cellulose decompose-related microbial phyla increased in CS and PB have benefits in decomposing those incorporated organic materials and improving soil properties. Therefore, we recommend that PB should also be considered as a viable soil organic amendment for future not in Ningxia, but also in other places. creator: Zhigang Li creator: Kaiyang Qiu creator: Rebecca L. Schneider creator: Stephen J. Morreale creator: Yingzhong Xie uri: https://doi.org/10.7717/peerj.6854 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Leaf functional trait variation in a humid temperate forest, and relationships with juvenile tree light requirements link: https://peerj.com/articles/6855 last-modified: 2019-05-08 description: The species-rich arborescent assemblages of humid tropical forests encompass much of the known range of the leaf economics spectrum, often including >20-fold variation in leaf lifespan. This suite of traits underpins a life-history continuum from fast-growing pioneers to slow-growing shade-tolerant species. Less is known about the range of leaf traits in humid temperate forests, and there are conflicting reports about relationships of these traits with the light requirements of temperate evergreen angiosperms. Here I quantify the range of leaf functional traits in a New Zealand temperate evergreen forest, and relationships of these traits with light requirements of juvenile trees and shrubs. Foliage turnover of saplings of 19 evergreen angiosperms growing beneath gaps (12–29% canopy openness) and in understories (1.2–2.9%) was measured over 12 months. Dry mass per area (LMA), dry matter content, thickness, density and nitrogen content (N) of leaves were also measured. Species minimum light requirements were indexed as the 10th percentile of the distribution of saplings in relation to canopy openness. Interspecific variation of leaf lifespan was ∼6-fold in gaps (0.6 to 3.8 yrs), and ∼11-fold in the understorey (0.7 to 7.7 yrs). Six small tree and shrub species are effectively leaf-exchangers, with leaf lifespans of c.1 year in gaps—albeit usually longer in the shade. Interspecific variation in other leaf traits was 2.5 to 4-fold. Lifespans and LMA of both sun and shade leaves were negatively correlated with species light requirements i.e., positively correlated with shade tolerance. However, light environment (gap vs shade) explained about the same amount of variation in LMA as species’ identity did. Species light requirements were not significantly correlated with leaf N, dry matter content, density or thickness—except for a marginally significant correlation with dry matter content of shade leaves. Species light requirements were thus less consistently related to leaf structural traits than appears to be the case in humid tropical forests. Whereas the wide interspecific variation in leaf economic traits of tropical rainforest species outweighs plastic response to light availability, temperate evergreen woody angiosperms appear to occupy a narrower range of the leaf economic spectrum. Standardization of the light environments in which LMA is measured is vital in comparative studies of humid temperate forest evergreens, because of countergradient responses of this trait to light, and because of the relative magnitudes of plastic and interspecific variation in LMA in these forests. creator: Christopher H. Lusk uri: https://doi.org/10.7717/peerj.6855 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lusk title: Ecosystem effects of fishing & El Niño at the Galápagos Marine Reserve link: https://peerj.com/articles/6878 last-modified: 2019-05-08 description: The Galápagos Archipelago is home to a diverse range of marine bioregions due to the confluence of several cold and warm water currents, resulting in some of the most productive tropical marine ecosystems in the world. These ecosystems are strongly influenced by El Niño events which can reduce primary production by an order of magnitude, dramatically reducing energy available throughout the food web. Fisheries are an important component of the local economy, although artisanal and illegal overfishing have dramatically reduced the productivity of invertebrate and finfish resources in recent decades, resulting in reductions in catches for local fishers. The regionally-endemic sailfin grouper (Myctereoperca olfax), locally known as bacalao, was once the most important fished species in the Galápagos, but is now listed as vulnerable by the IUCN due to its limited range and dramatic declines in catch over time. It is unknown how reduction of this predatory species has affected ecosystem structure and function. In the absence of stock assessments, we used an estimate of unfished bacalao biomass from fishers’ ecological knowledge along with unfished biomass estimates of other heavily exploited stocks—lobster (Panulirus penicillatus and P. gracilis) and sea cucumber (Isostichopus fuscus)—to create historical, unfished versions of existing modern day ecosystem models. We used the unfished and modern versions of the ecosystem models to test the ecosystem effects of bacalao exploitation at the Bolivar Channel, located in the cold, west upwelling bioregion of the archipelago during both El Niño and non El Niño years, and at Floreana Island, in the warmer, central bioregion. Fishers’ ecological knowledge indicates that at present, the biomass of bacalao is at least seven times lower than when unfished. This reduced bacalao biomass is linked with a greatly reduced ecosystem role compared to when unfished, and ecosystem role is further reduced in El Niño years. Allowing bacalao populations to rebuild to at least half of unfished biomass would partially restore their role within these ecosystems, while also resulting in greater fisheries catches. Comparing ecosystem impacts caused by fishing and El Niño, fishing has had a greater negative impact on bacalao ecosystem role than regular El Niño events. creator: Tyler D. Eddy creator: Alan M. Friedlander creator: Pelayo Salinas de León uri: https://doi.org/10.7717/peerj.6878 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Eddy et al. title: Effect of isolation on coat colour polymorphism of Polynesian rats in Island Southeast Asia and the Pacific link: https://peerj.com/articles/6894 last-modified: 2019-05-08 description: Populations of vertebrate species introduced onto islands regularly develop similar phenotypic changes, e.g., larger or smaller body size, shortened limbs, duller coats, as well as behavioural changes such as increased tameness and reduced flight-initiation distance. These changes overlap in part with those associated with the ‘domestication syndrome’, especially tameness and changes in coat patterns, and might indicate a similar neural crest involvement in the concurrent development of multiple phenotypic traits. Here I examine long-term data on free-living populations of wild Polynesian rats from seven mainland countries and 117 islands (n = 3,034), covering the species’ native and introduced range. Mainland populations showed no aberrant coat patterns, with the exception of one albino, whereas aberrant coat patterns were found in 12 island populations. Observed coat colour polymorphisms consisted of leucistic (including singular white patches), melanistic (darkly pigmented) and piebald (mixed) coat patterns. After isolation for at least seven centuries, wild Polynesian rat populations on islands seem to exhibit a trend towards a higher incidence of aberrant coat patterns. These phenotypic changes are here explained as a neutral, non-adaptive process, likely part of the ‘domestication syndrome’ (via the commensal pathway of domestication), in combination with genetic drift, little or no gene flow between the islands and/or the mainland and a relaxed selection (as a result of the weakening or removal of competitor/predator pressure) under commensality. creator: Alexandra A.E. van der Geer uri: https://doi.org/10.7717/peerj.6894 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 van der Geer title: Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau link: https://peerj.com/articles/6746 last-modified: 2019-05-07 description: Microbial community assembly is influenced by a continuum (actually the trade-off) between deterministic and stochastic processes. An understanding of this ecological continuum is of great significance for drawing inferences about the effects of community assembly processes on microbial community structure and function. Here, we investigated the driving forces of soil microbial community assembly in three different environmental contexts located on subalpine coniferous forests of the Loess Plateau in Shanxi, China. The variation in null deviations and phylogenetic analysis showed that a continuum existed between deterministic and stochastic processes in shaping the microbial community structure, but deterministic processes prevailed. By integrating the results of redundancy analysis (RDA), multiple regression tree (MRT) analysis and correlation analysis, we found that soil organic carbon (SOC) was the main driver of the community structure and diversity patterns. In addition, we also found that SOC had a great influence on the community assembly processes. In conclusion, our results show that deterministic processes always dominated assembly processes in shaping bacterial community structure along the three habitat contexts. creator: Pengyu Zhao creator: Jiabing Bao creator: Xue Wang creator: Yi Liu creator: Cui Li creator: Baofeng Chai uri: https://doi.org/10.7717/peerj.6746 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Pronounced social inequality in health-related factors and quality of life in women and men from Austria who are overweight or obese link: https://peerj.com/articles/6773 last-modified: 2019-05-07 description: BackgroundThe burden of social inequalities in health as well as the association between obesity with morbidity and mortality is a worldwide problem. Therefore, the aim of our study was to investigate health-related factors, health, and quality of life in Austrian women and men with normal weight, overweight, and obesity with a different socioeconomic status (SES) based on actual data from 2015.MethodsThis representative population-based study was based on self-reported data of 15,338 Austrian adults (8,425 women and 6,933 men) in 2014/2015. Data of the Austrian Health Interview Survey was analyzed stratified by sex and adjusted for age concerning health-related behavior, health, and quality of life.ResultsThe results have shown that people with a low SES differ significantly from those of high SES concerning health-related factors (e.g., eating behavior, physical activity), health and impairment due to chronic conditions, as well as quality of life. Obesity in women and men was associated with poorer health-related factors and more chronic conditions as well as unfavorable psychological aspects. In women, the results showed a significant body mass index*SES interaction for impairment due to disorders, the number of chronic conditions and quality of life in the domain of physical health. In men, the interaction was significant regarding alcohol consumption, as well as health impairment. The SES has a strong negative impact on health which implies that people of low SES have more health problems which especially concerns individuals who are obese. Therefore, a continuous target group-oriented, non-discriminatory, interdisciplinary public health program is required, prioritizing women, and men with obesity with a low SES. creator: Nathalie Tatjana Burkert creator: Wolfgang Freidl uri: https://doi.org/10.7717/peerj.6773 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Burkert and Freidl title: The microbiome profiling of fungivorous black tinder fungus beetle Bolitophagus reticulatus reveals the insight into bacterial communities associated with larvae and adults link: https://peerj.com/articles/6852 last-modified: 2019-05-07 description: Saproxylic beetles play a crucial role in key processes occurring in forest ecosystems, and together with fungi contribute to the decomposition and mineralization of wood. Among this group are mycetophilic beetles which associate with wood-decaying fungi and use the fruiting body for nourishment and development. Therefore, their feeding strategy (especially in the case of fungivorous species) requires special digestive capabilities to take advantage of the nutritional value of fungal tissue. Although polypore-beetle associations have been investigated in numerous studies, detailed studies focusing on the microbiome associated with species feeding on fruiting bodies of polypores remain limited. Here we investigated the bacterial communities associated with larvae and adults of Bolitophagus reticulatus collected from Fomes fomentarius growing on two different host tree: beech (Fagus sp.) and birch (Betula sp.), respectively. Among 24 identified bacterial phyla, three were the most relatively abundant (Proteobacteria, Actinobacteria and Bacteroidetes). Moreover, we tried to find unique patterns of bacteria abundances which could be correlated with the long-term field observation showing that the fruiting bodies of F. fomentarius, growing on birch are more inhabited by beetles than fruiting bodies of the same fungus species growing on beech. Biochemical analyses showed that the level of protease inhibitors and secondary metabolites in F. fomentarius is higher in healthy fruiting bodies than in the inhabited ones. However, tested microbiome samples primarily clustered by developmental stage of B. reticulatus and host tree did not appear to impact the taxonomic distribution of the communities. This observation was supported by statistical analyses. creator: Agnieszka Kaczmarczyk-Ziemba creator: Grzegorz K. Wagner creator: Krzysztof Grzywnowicz creator: Marek Kucharczyk creator: Sylwia Zielińska uri: https://doi.org/10.7717/peerj.6852 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kaczmarczyk-Ziemba et al. title: Promotion of growth and metal accumulation of alfalfa by coinoculation with Sinorhizobium and Agrobacterium under copper and zinc stress link: https://peerj.com/articles/6875 last-modified: 2019-05-07 description: The Legume-Rhizobium symbiosis has been proposed as a promising technique for the phytoremediation of contaminated soils due to its beneficial activity in symbiotic nitrogen fixation. However, numerous studies have shown that excessive heavy metals reduce the efficiency of symbiotic nodulation with Rhizobium and inhibit plant growth. In this study, we aimed to evaluate the synergistic effects of IAA-producing bacteria and Rhizobium on Medicago lupulina growth under Cu and Zn stress. Pot experiments showed that 400 mg kg−1 Cu2 + and Zn2 + greatly inhibited plant growth, but dual inoculation of Medicago lupulina with Sinorhizobium meliloti CCNWSX0020 and Agrobacterium tumefaciens CCNWGS0286 significantly increased the number of nodules and plant biomass by enhancing antioxidant activities. Under double stress of 400 mg kg−1 Cu2 + and Zn2 +, the nodule number and nitrogenase activities of dual-inoculated plants were 48.5% and 154.4% higher, respectively, than those of plants inoculated with Sinorhizobium meliloti. The root and above-ground portion lengths of the dual-inoculated plants were 32.6% and 14.1% greater, respectively, than those of the control, while the root and above-ground portion dry weights were 34.3% and 32.2% greater, respectively, than those of the control. Compared with S. meliloti and A. tumefaciens single inoculation, coinoculation increased total Cu uptake by 39.1% and 47.5% and increased total Zn uptake by 35.4% and 44.2%, respectively, under double metal stress conditions. Therefore, coinoculation with Sinorhizobium meliloti and Agrobacterium tumefaciens enhances metal phytoextraction by increasing plant growth and antioxidant activities under Cu/Zn stress, which provides a new approach for bioremediation in heavy metal-contaminated soil. creator: Liru Jian creator: Xiaoli Bai creator: Hui Zhang creator: Xiuyong Song creator: Zhefei Li uri: https://doi.org/10.7717/peerj.6875 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jian et al. title: Cortical modulation of pupillary function: systematic review link: https://peerj.com/articles/6882 last-modified: 2019-05-07 description: BackgroundThe pupillary light reflex is the main mechanism that regulates the pupillary diameter; it is controlled by the autonomic system and mediated by subcortical pathways. In addition, cognitive and emotional processes influence pupillary function due to input from cortical innervation, but the exact circuits remain poorly understood. We performed a systematic review to evaluate the mechanisms behind pupillary changes associated with cognitive efforts and processing of emotions and to investigate the cerebral areas involved in cortical modulation of the pupillary light reflex.MethodologyWe searched multiple databases until November 2018 for studies on cortical modulation of pupillary function in humans and non-human primates. Of 8,809 papers screened, 258 studies were included.ResultsMost investigators focused on pupillary dilatation and/or constriction as an index of cognitive and emotional processing, evaluating how changes in pupillary diameter reflect levels of attention and arousal. Only few tried to correlate specific cerebral areas to pupillary changes, using either cortical activation models (employing micro-stimulation of cortical structures in non-human primates) or cortical lesion models (e.g., investigating patients with stroke and damage to salient cortical and/or subcortical areas). Results suggest the involvement of several cortical regions, including the insular cortex (Brodmann areas 13 and 16), the frontal eye field (Brodmann area 8) and the prefrontal cortex (Brodmann areas 11 and 25), and of subcortical structures such as the locus coeruleus and the superior colliculus.ConclusionsPupillary dilatation occurs with many kinds of mental or emotional processes, following sympathetic activation or parasympathetic inhibition. Conversely, pupillary constriction may occur with anticipation of a bright stimulus (even in its absence) and relies on a parasympathetic activation. All these reactions are controlled by subcortical and cortical structures that are directly or indirectly connected to the brainstem pupillary innervation system. creator: Costanza Peinkhofer creator: Gitte M. Knudsen creator: Rita Moretti creator: Daniel Kondziella uri: https://doi.org/10.7717/peerj.6882 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Peinkhofer et al. title: Chemovariation and antibacterial activity of extracts and isolated compounds from species of Ixora and Greenea (Ixoroideae, Rubiaceae) link: https://peerj.com/articles/6893 last-modified: 2019-05-07 description: BackgroundA large number of secondary metabolites can be obtained from plants used for traditional medicine in two related genera (Ixora and Greenea) in the subfamily Ixoroideae (Rubiaceae), but there are only a few detailed studies on their bioactivities. Therefore, the main goals of this study were to determine the antibacterial activities of lipophilic extracts from plants of some Ixora and Greenea species native to Thailand, and to isolate some pure compounds from those extracts. Moreover, we compared the occurrence of compounds in different plant parts of samples from different habitats to better understand their variation.MethodsA total of 56 lipophilic extracts were obtained from the leaves, stem bark, and root bark of eight Ixora and two Greenea species collected at various locations in Thailand. Isolated compounds were identified using nuclear magnetic resonance. Antimicrobial activities were evaluated against four Gram-positive and nine Gram-negative human pathogenic bacterial strains.ResultsExtracts from I. javanica, I. nigricans, I. brunonis, and G. montana, along with isolated scopoletin, exhibited antibacterial activities against Gram-positive methicillin-resistant Staphylococcus aureus ATCC 43300, with minimum inhibitory concentration values ranging from 64 to 256 µg/mL. The occurrence of scopoletin, isofraxidin, and geniposidic acid in lipophilic extracts showed some variation among different plant parts and species.ConclusionsLipophilic extracts of Ixora and Greenea species have the potential to be developed as anti-Gram-positive agents, in particular to counter infections of methicillin-resistant S. aureus strains. The chemical profiles showed differences between floristic regions but similarity within the same plant parts. creator: Raveevatoo Buathong creator: Voradol Chamchumroon creator: Johann Schinnerl creator: Markus Bacher creator: Wichai Santimaleeworagun creator: Ekaphan Kraichak creator: Srunya Vajrodaya uri: https://doi.org/10.7717/peerj.6893 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Buathong et al. title: Accuracy of a deep convolutional neural network in detection of retinitis pigmentosa on ultrawide-field images link: https://peerj.com/articles/6900 last-modified: 2019-05-07 description: Evaluating the discrimination ability of a deep convolution neural network for ultrawide-field pseudocolor imaging and ultrawide-field autofluorescence of retinitis pigmentosa. In total, the 373 ultrawide-field pseudocolor and ultrawide-field autofluorescence images (150, retinitis pigmentosa; 223, normal) obtained from the patients who visited the Department of Ophthalmology, Tsukazaki Hospital were used. Training with a convolutional neural network on these learning data objects was conducted. We examined the K-fold cross validation (K = 5). The mean area under the curve of the ultrawide-field pseudocolor group was 0.998 (95% confidence interval (CI) [0.9953–1.0]) and that of the ultrawide-field autofluorescence group was 1.0 (95% CI [0.9994–1.0]). The sensitivity and specificity of the ultrawide-field pseudocolor group were 99.3% (95% CI [96.3%–100.0%]) and 99.1% (95% CI [96.1%–99.7%]), and those of the ultrawide-field autofluorescence group were 100% (95% CI [97.6%–100%]) and 99.5% (95% CI [96.8%–99.9%]), respectively. Heatmaps were in accordance with the clinician’s observations. Using the proposed deep neural network model, retinitis pigmentosa can be distinguished from healthy eyes with high sensitivity and specificity on ultrawide-field pseudocolor and ultrawide-field autofluorescence images. creator: Hiroki Masumoto creator: Hitoshi Tabuchi creator: Shunsuke Nakakura creator: Hideharu Ohsugi creator: Hiroki Enno creator: Naofumi Ishitobi creator: Eiko Ohsugi creator: Yoshinori Mitamura uri: https://doi.org/10.7717/peerj.6900 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Masumoto et al. title: Metacommunity patterns of Amazonian Odonata: the role of environmental gradients and major rivers link: https://peerj.com/articles/6472 last-modified: 2019-05-06 description: BackgroundWe identified and classified damselfly (Zygoptera) and dragonfly (Anisoptera) metacommunities in Brazilian Amazonia, relating species distribution patterns to known biological gradients and biogeographical history. We expected a random distribution of both Zygoptera and Anisoptera within interfluves. At the Amazonian scale, we expected Anisoptera metacommunities to be randomly distributed due to their higher dispersal ability and large environmental tolerance. In contrast, we expected Zygoptera communities to exhibit a Clementsian pattern, limited by the large Amazonia rivers due to their low dispersal ability.MethodsWe used a dataset of 58 first-to-third order well-sampled streamlets in four Amazonian interfluves and applied an extension of the Elements of Metacommunity Structure (EMS) framework, in which we order Zygoptera and Anisoptera metacommunities by known spatial and biogeographic predictors.ResultsAt the Amazonian scale, both Zygoptera and Anisoptera presented a Clementsian pattern, driven by the same environmental and biogeographical predictors, namely biogeographic region (interfluve), annual mean temperature, habitat integrity and annual precipitation. At the interfluve scale, results were less consistent and only partially support our hypothesis. Zygoptera metacommunities at Guiana and Anisoptera metacommunities at Tapajós were classified as random, suggesting that neutral processes gain importance at smaller spatial scales.DiscussionOur findings were consistent with previous studies showing that environmental gradients and major rivers limit the distribution of Odonata communities, supporting that larger Amazonian rivers act as barriers for the dispersal of this group. In addition, the importance of habitat integrity indicates that intactness of riparian vegetation is an important filter shaping metacommunity structure of Amazonian stream Odonata. creator: Fernanda Alves-Martins creator: Leandro Schlemmer Brasil creator: Leandro Juen creator: Paulo De Marco Jr creator: Juliana Stropp creator: Joaquín Hortal uri: https://doi.org/10.7717/peerj.6472 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Alves-Martins et al. title: Molecular evolution of the VacA p55 binding domain of Helicobacter pylori in mestizos from a high gastric cancer region of Colombia link: https://peerj.com/articles/6634 last-modified: 2019-05-06 description: The stomach bacterium Helicobacter pylori is one of the most prevalent pathogens in humans, closely linked with serious diseases such as gastric cancer. The microbe has been associated with its host for more than 100,000 years and escorted modern humans out of Africa. H. pylori is predominantly transmitted within families and dispersed globally, resulting in distinct phylogeographic patterns, which can be utilized to investigate migrations and bioturbation events in human history. Latin America was affected by several human migratory waves due to the Spanish colonisation that drastically changed the genetic load and composition of the bacteria and its host. Genetic evidence indicates that independent evolutionary lines of H. pylori have evolved in mestizos from Colombia and other countries in the region during more than 500 years since colonisation. The vacuolating cytotoxin VacA represents a major virulence factor of the pathogen comprising two domains, p33 and p55, the latter of which is essential for binding to the host epithelial cell. The evolution of the VacA toxin in Colombia has been strongly biased due to the effects of Spanish colonization. However, the variation patterns and microevolution of the p55 domain have not yet been described for this population. In the present study, we determined the genetic polymorphisms and deviations in the neutral model of molecular evolution in the p55 domain of 101 clinical H. pylori isolates collected in Bogotá, a city located in Andean mountains characterized by its high gastric cancer risk and its dominant mestizo population. The microevolutionary patterns of the p55 domain were shaped by recombination, purifying and episodic diversifying positive selection. Furthermore, amino acid positions 261 and 321 in the p55 domain of VacA show a high variability among mestizos clinical subsets, suggesting that natural selection in H. pylori may operate differentially in patients with different gastric diseases. creator: Andrés J. Gutiérrez-Escobar creator: María M. Bravo creator: Orlando Acevedo creator: Steffen Backert uri: https://doi.org/10.7717/peerj.6634 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gutiérrez-Escobar et al. title: Optimization of extraction conditions and determination of purine content in marine fish during boiling link: https://peerj.com/articles/6690 last-modified: 2019-05-06 description: BackgroundGout is the second most common metabolic disease affecting human health. The disease of gout is closely related to the level of uric acid, which is the end-product of human purine metabolism. Moreover, food is the main way of external ingestion of purine.MethodA simple and time-saving method was developed to extract purines like adenine, hypoxanthine, guanine, and xanthine from marine fish by single factor design combined with Box–Behnken. The contents of these purines in the edible parts and internal organs of marine fish, as well as Scophthalmus maximus, were determined by high-performance liquid chromatography to investigate the relationship between the boiling process and purine content.ResultThe mixed-acid method was chosen for the extraction of purine bases and the extraction conditions were as follows: mixture acid 90.00% TFA/80.00% FA (v/v, 1:1); hydrolysis temperature 90.00 °C; time 10.00 min; liquid-to-solid ratio 30:1. The total purine content of the edible parts (eyes, dorsal muscles, abdominal muscles, and skin) was the highest in Scophthalmus maximus, followed by sphyraena, Sardinella, Trichiurus lepturus, Scomberomorus niphonius, Pleuronectiformes, Sea catfish, Anguillidae, and Rajiformes. Moreover, boiling significantly reduced the purine content in the marine fish because of the transfer of the purines to the cooking liquid during boiling. Scophthalmus maximus, Sphyraena, and Sardinella were regard as high-purine marine fish, which we should eat less. We also confirmed that boiling significantly transferred purine bases from fish to cooking liquid. Thus, boiling could reduce the purine content of fish, thereby reducing the risk of hyperuricemia and gout. creator: Tingting Li creator: Likun Ren creator: Dangfeng Wang creator: Minjie Song creator: Qiuying Li creator: Jianrong Li uri: https://doi.org/10.7717/peerj.6690 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States link: https://peerj.com/articles/6749 last-modified: 2019-05-06 description: BackgroundCoagulase negative Staphylococcus (CNS) species are currently the most prevalent intra-mammary pathogens causing subclinical mastitis and occasional clinical mastitis or persistent infection in lactating dairy cattle. More than 10 CNS species have been identified, but they are generally managed as one group on most dairies in the United States. However, improved management decisions and treatment outcomes may be achieved with better understanding of the prevalent species, pathogenicity and strain diversity within and across dairies.MethodologyA total of 604 CNS isolates were cultured from milk samples collected during a dry-cow treatment clinical trial conducted on 6 dairy herds in 4 states in the US. All the study cows were randomized to receive 1 of the 3 different intra-mammary antimicrobial infusions (Quatermaster, Spectramast DC or ToMorrow Dry Cow) at dry-off. Milk samples were collected at dry-off, calving (0–6 days in milk, DIM), post-calving (7–13 DIM) and at mastitis events within the first 100 DIM. The CNS isolates were identified to species level by partial sequencing of the rpoβ gene, and genetic relatedness within species was investigated by phylogenetic analysis of the pulse-field gel electrophoresis profiles of the isolates.ResultsThe major CNS species identified were S. chromogenes (48.3%), S. haemolyticus (17.9%), S. simulans and S. epidermidis (each at 6.5%). Other CNS species identified at lower frequencies included S. hominis, S. auricularis, S. sciuri, S. spp KS-SP, S. capitis, S. cohnii, S. warneri, S. pasteuri, S. xylosus, S. hyicus, S. equorum, S. microti, S. rostri, S. gallinarum, S. saprophyticus and S. succinus. Phylogenetic analyses of the major species types demonstrated an association between genetic relatedness and epidemiological distributions of S. chromogenes, S. simulans, S. haemolyticus and S. auricularis. Additionally, identical strains of S. chromogenes and S. simulans were isolated from the same udder quarter of several cows at consecutive sample stages. The rest of the minor species had no deducible genetic-epidemiological link.DiscussionThe observed association between genetic and epidemiological distributions indicated animal-adapted nature of four CNS species, suggesting possible host-adapted and environmental transmission of these species. Multi-stage isolation of the same udder quarter strain was evidence for chronic intra-mammary infection.ConclusionThe different CNS species and strains circulating on US dairy herds were genetically diverse. Four species identified were likely udder-adapted pathogens, 2 of which caused persistent infection. Our findings are important in guiding the design of effective mastitis control strategies. creator: Stephen N. Jenkins creator: Emmanuel Okello creator: Paul V. Rossitto creator: Terry W. Lehenbauer creator: John Champagne creator: Maria C.T. Penedo creator: Andréia G. Arruda creator: Sandra Godden creator: Paul Rapnicki creator: Patrick J. Gorden creator: Leo L. Timms creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.6749 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jenkins et al. title: Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis link: https://peerj.com/articles/6836 last-modified: 2019-05-06 description: IntroductionA hatchery-reared silver carp (Hypophthalmichthys molitrix) program has been intensively carried out since 2010 to enhance the rapidly declining fisheries production in the middle Yangtze River. However, only a little information regarding the effectiveness of the enhancement program has been reported. In this context, this study investigates on an enhancement program through monitoring the efficacy based on parentage analysis.MethodsA total of 1,529 hatchery-reared fish and 869 larvae were sampled from the middle Yangtze River in 2016 and 2017 and were genotyped by thirteen microsatellite loci. Based on the results of parentage analysis the larvae were divided into three populations: (1) larvae population with both parents being hatchery-reared fish (=R), (2) larvae population with only a male or a female parent being hatchery-reared fish (=H), and (3) larvae population with no hatchery-reared fish parent (=W). The following analyses were also carried out: (1) assessing the contribution of hatchery-reared offspring to larval resources, and (2) evaluating the genetic effect of stock enhancement on the wild population.ResultsIn total, 10.37% and 11.56% of larvae were identified as the offspring produced by hatchery-reared fish released in 2016 and 2017, respectively. In 2017, some of the larvae were assigned unambiguously to hatchery-reared fish released in 2016. In terms of the number of offspring produced, the hatchery-reared fish have shown significant variations. No significant differences were found among all the larvae populations concerning genetic parameters for diversity. High levels of genetic diversity of all larvae populations were obtained. Low FSTvalues obtained from pairwise FST analysis, as well as the analysis of molecular variance (AMOVA), revealed high genetic structural similarity among all the larvae populations. The genetic composition of the W larvae population in 2017 was different from that of all other larvae populations (all larvae populations in 2016, and R and H larvae populations in 2017), as demonstrated from the results of STRUCTURE and PCA analyses.ConclusionIt was demonstrated that hatchery-reared fish are successful in producing the offspring in the natural environment during multiple years, which might assist in increasing the abundance of larvae. The hatchery-reared fish had variations in terms of the success rates on reproduction. Also, the hatchery-reared enhancement program had no significant effect on the genetic diversity or the genetic structure of wild populations. However, the genetic component of the W larvae population in 2017 was changed as compared to 2016, which was not due to the hatchery-reared enhancement program for silver carp. This could be due to flooding, but the specific causes need further studies. Our results clearly show the necessity to continuously inspect the genetic impact of the enhancement program so that historical information can be utilized for further research. creator: Huijuan Chen creator: Dengqiang Wang creator: Xinbin Duan creator: Shaoping Liu creator: Daqing Chen creator: Yun Li uri: https://doi.org/10.7717/peerj.6836 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis link: https://peerj.com/articles/6859 last-modified: 2019-05-06 description: ObjectivesThis study aims to evaluate the changes of development trends and research hotspots of biomaterials research from 2013 to 2017, which can identify the general information of papers and explore the changes of research content, thus providing perspectives for the development of biomaterials in China and other countries.MethodsData of the paper were retrieved from the Web of Science Core Collection, and then analyzed by the bibliometric and CiteSpace visualization analysis.ResultsIt was found that a total of 3,839 related papers had been published from the year 2013 to 2017. The analysis of the articles showed that the annual quantity and quality of the articles in the biomaterials research have been increasing since 2013, and the Wang L / Chinese Academy of Sciences were the most productive author/institution. Meanwhile, the keywords “in vitro”, “scaffold”, “nanoparticle” , “mechanical property”, and “biocompatibility” have the relatively higher frequency, and the keywords “apatite”, “deposition”, and “surface modification” have the strongest burst citation.ConclusionsAfter statistics and analysis, we found that biomaterials is a promising research field. The study may be helpful in understanding research trends in this field. creator: Dandan Hou creator: Xuewei Bi creator: Zhinan Mao creator: Yubo Fan creator: Xiangming Hu creator: Xiaoming Li uri: https://doi.org/10.7717/peerj.6859 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hou et al. title: Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway link: https://peerj.com/articles/6885 last-modified: 2019-05-06 description: The limb-bud and heart development (LBH) gene is a highly conserved, tissue-specific transcription cofactor in vertebrates that regulates multiple key genes in embryonic development. The role of LBH in various cancer types is still controversial, and its specific role and molecular mechanism in the oncogenesis of gastric cancer (GC) remains largely unexplored. In the present study, the prognostic significance and clinicopathological characteristics of LBH in GC was determined. The LBH mRNA expression was first investigated in four independent public datasets (TCGA-STAD, GSE15459, GSE29272, and GSE62254) and then validated with our samples at the protein level. LBH was overexpressed at both the mRNA and protein levels in cancer compared with normal tissues. High LBH expression was correlated with advanced T, N, and M stages. Kaplan–Meier analysis and log-rank test indicated that higher LBH expression was statistically correlated with shorter overall survival (OS) in the public datasets and our study samples. Univariate and multivariate Cox regression analysis showed that LBH was an independent prognostic biomarker for survival in TCGA-STAD, GSE15459, GSE62254 cohorts, and our GC patients. In vitro experiments showed that knockdown of LBH can significantly inhibit the proliferation and invasion of HGC-27 cells, while overexpression of LBH can significantly enhance the proliferation and invasion of BGC-823 cells. Gene Set Enrichment Analysis (GSEA), Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) indicated that high LBH expression is associated with the PI3K-Akt pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction. Western blot analysis showed that knockdown of LBH significantly inhibited the expression of integrin α5, integrin β1, p-FAK, and p-Akt. Therefore, results from the present study indicate that LBH is a potential independent prognostic biomarker and promotes proliferation and invasion of GC cells by activating the integrin/FAK/Akt pathway. creator: Ruoxi Yu creator: Zhi Li creator: Chuang Zhang creator: Huicong Song creator: Mingming Deng creator: Liping Sun creator: Ling Xu creator: Xiaofang Che creator: Xuejun Hu creator: Xiujuan Qu creator: Yunpeng Liu creator: Ye Zhang uri: https://doi.org/10.7717/peerj.6885 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yu et al. title: Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem link: https://peerj.com/articles/6738 last-modified: 2019-05-03 description: BackgroundPatch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitats using a patchy application of fire and grazing. We tested two assumptions of the patch-burn approach, namely that: (1) fire and grazing drive spatial patch differentiation in community structure and (2) species composition of patches change through time in response to disturbance.MethodsWe analyzed species cover data on 100 m2 square quadrats from 128 sites located on a 1 × 1 km UTM grid in the grassland habitats of the Tallgrass Prairie Preserve. A total of 20 of these sites were annually sampled for 12 years. We examined how strongly changes in species richness and species composition correlated with changes in management variables relative to independent spatial and temporal drivers using multiple regression and direct ordination, respectively.ResultsSite effects, probably due to edaphic differences, explained the majority of variation in richness and composition. Interannual variation in fire and grazing management was relatively unimportant relative to inherent site and year drivers with respect to both richness and composition; however, the effects of fire and grazing variables were statistically significant and interpretable, and bison management was positively correlated with plant richness.ConclusionsThere was some support for the two assumptions of patch-burn management we examined; however, in situ spatial and temporal environmental heterogeneity played a much larger role than management in shaping both plant richness and composition. Our results suggest that fine-tuning the application of fire and grazing may not be critical for maintaining landscape scale plant diversity in disturbance-prone ecosystems. creator: Daniel J. McGlinn creator: Michael W. Palmer uri: https://doi.org/10.7717/peerj.6738 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 McGlinn and Palmer title: Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation link: https://peerj.com/articles/6790 last-modified: 2019-05-03 description: Ultraviolet radiation can cause many serious problems for all living organisms. With a growing population, the UV sensitivity of crop plants presents a particular problem. To evaluate the suitability of growing in areas under UV irradiance, the influence of different doses of UV-B (3.042, 6.084 and 9.126 kJm−2d−1) on the sugar beet (Beta vulgaris L) plants was studied. UV-B induced a significant decrease in growth displayed as reduced height and fresh and dry weight. This reduction is not dose dependent and was associated with diminishing photosynthetic O2 evolution, relative chlorophyll content, photosynthetic pigments and chlorophyll fluorescence. On the other hand, antioxidant enzyme activities, total protein content, compatible solutes, total free amino acids and total betalain content were increased under 9.126 kJm−2d−1 UV-B treatments, representing mechanisms by which the plants coped with the stress. The oxidative stress upon UV-B treatment was evident by increased malondialdehyde (MDA) content, however, hydrogen peroxide (H2O2) was not affected in UV-B exposed plants. Thus, the studied sugar beet variety BR1seems to be suitable particularly for areas with high doses of UV-B irradiation. creator: Parisa Rahimzadeh Karvansara creator: Seyed Mehdi Razavi uri: https://doi.org/10.7717/peerj.6790 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rahimzadeh Karvansara and Razavi title: Gene drives as a new quality in GMO releases—a comparative technology characterization link: https://peerj.com/articles/6793 last-modified: 2019-05-03 description: Compared to previous releases of genetically modified organisms (GMOs) which were primarily plants, gene drives represent a paradigm shift in the handling of GMOs: Current regulation of the release of GMOs assumes that for specific periods of time a certain amount of GMOs will be released in a particular region. However, now a type of genetic technology arises whose innermost principle lies in exceeding these limits—the transformation or even eradication of wild populations. The invasive character of gene drives demands a thorough analysis of their functionalities, reliability and potential impact. But such investigations are hindered by the fact that an experimental field test would hardly be reversible. Therefore, an appropriate prospective assessment is of utmost importance for an estimation of the risk potential associated with the application of gene drives. This work is meant to support the inevitable characterization of gene drives by a comparative approach of prospective technology assessment with a focus on potential sources of risk. Therein, the hazard and exposure potential as well as uncertainties with regard to the performance of synthetic gene drives are addressed. Moreover, a quantitative analysis of their invasiveness should enable a differentiated evaluation of their power to transform wild populations. creator: Johannes L. Frieß creator: Arnim von Gleich creator: Bernd Giese uri: https://doi.org/10.7717/peerj.6793 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Frieß et al. title: Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids link: https://peerj.com/articles/6808 last-modified: 2019-05-03 description: BackgroundFeeding habits are central to animal ecology, but it is often difficult to characterize the diet of organisms that are arboreal, nocturnal, rare, or highly mobile. Genetic analysis of gut contents is a promising approach for expanding our understanding of animal feeding habits. Here, we adapt a laboratory protocol for extracting and sequencing plant material from gut contents and apply it to Neotropical forest katydids (Orthoptera: Tettigoniidae) on Barro Colorado Island (BCI) in Panama.MethodsOur approach uses three chloroplast primer sets that were previously developed to identify vegetation on BCI. We describe the utility and success rate of each primer set. We then test whether there is a significant difference in the amplification and sequencing success of gut contents based on the size or sex of the katydid, the time of day that it was caught, and the color of the extracted gut contents.ResultsWe find that there is a significant difference in sequencing success as a function of gut color. When extracts were yellow, green, or colorless the likelihood of successfully amplifying DNA ranged from ~30–60%. When gut extracts were red, orange, or brown, amplification success was exceptionally low (0–8%). Amplification success was also higher for smaller katydids and tended to be more successful in katydids that were captured earlier in the night. Strength of the amplified product was indicative of the likelihood of sequencing success, with strong bands having a high likelihood of success. By anticipating which samples are most likely to succeed, we provide information useful for estimating the number of katydids that need to be collected and minimizing the costs of purifying, amplifying, and sequencing samples that are unlikely to succeed. This approach makes it possible to understand the herbivory patterns of these trophically important katydids and can be applied more broadly to understand the diet of other tropical herbivores. creator: Laurel B. Symes creator: Nicole L. Wershoven creator: Lars-Olaf Hoeger creator: Jessica S. Ralston creator: Sharon J. Martinson creator: Hannah M. ter Hofstede creator: Christine M. Palmer uri: https://doi.org/10.7717/peerj.6808 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Symes et al. title: Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize link: https://peerj.com/articles/6815 last-modified: 2019-05-03 description: BackgroundThe spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation.MethodsWe used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals.ResultsIntrogression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize.DiscussionAlthough there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized. creator: Eric Gonzalez-Segovia creator: Sergio Pérez-Limon creator: G. Carolina Cíntora-Martínez creator: Alejandro Guerrero-Zavala creator: Garrett M. Janzen creator: Matthew B. Hufford creator: Jeffrey Ross-Ibarra creator: Ruairidh J. H. Sawers uri: https://doi.org/10.7717/peerj.6815 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gonzalez-Segovia et al. title: Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.) link: https://peerj.com/articles/6832 last-modified: 2019-05-03 description: In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley. creator: Jie Li creator: Xinhao Liu uri: https://doi.org/10.7717/peerj.6832 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li and Liu title: Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task link: https://peerj.com/articles/6833 last-modified: 2019-05-03 description: BackgroundCognitive processes are required during walking to appropriately respond to environmental and task demands. There are now many studies that have used functional Near-Infrared Spectroscopy (fNIRS) to record brain activation to investigate neural bases of cognitive contributions in gait. The aim of this systematic review was to summarize the published research regarding Prefrontal cortical (PFC) activation patterns during simple and complex walking tasks in young adults, older adults and clinical groups with balance disorders using fNIRS. Our secondary aim was to evaluate each included study based on methodological reporting criteria important for good data quality.MethodsWe conducted searches in June 2018 using four databases: Embase, PubMed, Scopus and PsycINFO. The strategy search used was: (((((near infrared spectroscopy) OR functional near infrared spectroscopy) OR nirs) OR fnirs) AND (((gait) OR walking) OR locomotion) AND (((((young) OR adult) OR older) OR elderly) NOT children)) AND (((Brain) OR cortex) OR cortical) for our search. The papers included met the specific review criteria: (i) used fNIRS to measure PFC activation patterns; (ii) included walking tasks (simple and complex) and; (iii) assessed young people, older people and/or clinical groups with balance disorders.ResultsThirty five (describing 75 brain activation comparisons) of the 308 studies retrieved through our search met the inclusion criteria. Based on 6 methodological reporting considerations, 20 were of high quality, 10 were of medium quality and 5 were of low quality. Eleven/20 comparisons in young people, 23/37 comparisons in older people and 15/18 comparisons in clinical groups reported increased PFC activation with increased walking task complexity. The majority of comparisons that used verbal fluency, counting backwards or secondary motor tasks reported increases in PFC activation (83%, 64% and 58% of these studies, respectively). In contrast, no studies found secondary visual tasks increased PFC activation.ConclusionIncreased PFC activation was most common in studies that involved walks comprising secondary verbal fluency and arithmetic tasks. Clinical groups generally showed increased PFC activation irrespective of type of secondary task performed during walking which suggests these groups require more attentional resources for safe walking. Systematic review registration number: PROSPERO 2017 - CRD42017059501. creator: Paulo H.S. Pelicioni creator: Mylou Tijsma creator: Stephen R. Lord creator: Jasmine Menant uri: https://doi.org/10.7717/peerj.6833 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pelicioni et al. title: Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio) link: https://peerj.com/articles/6848 last-modified: 2019-05-03 description: We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide “knockdown”, recombinant Leptin-a “rescue”, and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca2+/calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling. creator: Matthew Tuttle creator: Mark R. Dalman creator: Qin Liu creator: Richard L. Londraville uri: https://doi.org/10.7717/peerj.6848 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tuttle et al. title: Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations link: https://peerj.com/articles/6861 last-modified: 2019-05-03 description: AimIn this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application.ResultNo deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region.ConclusionThis study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations. creator: Weian Du creator: Chunlei Feng creator: Ting Yao creator: Cheng Xiao creator: Hongyan Huang creator: Weibin Wu creator: Linnan Zhu creator: Honghua Qiao creator: Chao Liu creator: Ling Chen uri: https://doi.org/10.7717/peerj.6861 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Du et al. title: Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci link: https://peerj.com/articles/6864 last-modified: 2019-05-03 description: The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web. creator: Marshal Hedin creator: Shahan Derkarabetian creator: Adan Alfaro creator: Martín J. Ramírez creator: Jason E. Bond uri: https://doi.org/10.7717/peerj.6864 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hedin et al. title: Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center link: https://peerj.com/articles/6868 last-modified: 2019-05-03 description: BackgroundThe objective of this study is to investigate small cell neuroendocrine carcinoma of the cervix (SCCC), using a retrospective clinicopathological characteristic and treatment approach.MethodWe retrospectively analyzed cases of early-stage SCCC, identified between 2006 and 2016, in women who received radical surgery and adjuvant chemotherapy with or without radiotherapy. Kaplan–Meier and one-way ANOVA analyses were performed.ResultA total of 37 cases of SCCC are presented in this study, of which 21 had stage IB1 SCCC, 12 had stage IB2, 3 had stage IIA1, and 1 had stage IIA2. All patients were treated with radical surgery and adjuvant chemotherapy, specifically, 26 with radical surgery followed by adjuvant chemotherapy plus radiation and 11 with neoadjuvant chemotherapy (NACT) followed by radical surgery. After a median follow-up time of 27 months (range, 8–115 months), the 2-year and 5-year disease-free survival rate for all patients was 51.9% and 34.1%, respectively, and the overall survival rate was 60.3% and 38.6%, respectively. Univariate analysis showed that International Federation of Gynecology and Obstetrics (FIGO) stage and tumor size may be a predictor of a poor prognosis. NACT and adjuvant radiation did not improve survival over adjuvant chemotherapy alone but should not be a significant independent prognostic factor for survival.ConclusionEven in patients with early-stage SCCC, the prognosis is poor, although FIGO stage and tumor size may act as surrogate factors prognostic of survival. creator: Dandan Zhang creator: Xiaoxin Ma uri: https://doi.org/10.7717/peerj.6868 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang and Ma title: Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis link: https://peerj.com/articles/6871 last-modified: 2019-05-03 description: BackgroundElaiosomes are specialized fleshy and edible seed appendages dispersed by ants. Lipids are the primary components of elaiosomes. Chelidonium majus is a well-known plant, the seeds of which are dispersed by ants. Previous studies have identified the presence of primary fatty acids in its elaiosomes and seeds. However, the molecular mechanisms underlying fatty acid biosynthesis in elaiosomes remain unknown.MethodsIn order to gain a comprehensive transcriptional profile of the elaiosomes and seeds of C. majus, and understand the expression patterns of genes associated with fatty acid biosynthesis, four different developmental stages, including the flower-bud (Ch01), flowering (Ch02), young seed (Ch03), and mature seed (Ch04) stages, were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing).ResultsA total of 63,064 unigenes were generated from 12 libraries. Of these, 7,323, 258, and 11,540 unigenes were annotated with 25 Cluster of Orthologous Groups, 43 Gene Ontology terms, and 373 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. In addition, 322 genes were involved in lipid transport and metabolism, and 508 genes were involved in the lipid metabolism pathways. A total of 41 significantly differentially expressed genes (DEGs) involved in the lipid metabolism pathways were identified, most of which were upregulated in Ch03 compared to Ch02, indicating that fatty acid biosynthesis primarily occurs during the flowering to the young seed stages. Of the DEGs, acyl-ACP thioesterases, acyl carrier protein desaturase (DESA1), and malonyl CoA-ACP transacylase were involved in palmitic acid synthesis; stearoyl-CoA desaturase and DESA1 were involved in oleic acid synthesis, and acyl-lipid omega-6 desaturase was involved in linoleic acid synthesis. creator: Jiayue Wu creator: Linlin Peng creator: Shubin Dong creator: Xiaofei Xia creator: Liangcheng Zhao uri: https://doi.org/10.7717/peerj.6871 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wu et al. title: Effects of species-dominated patches on soil organic carbon and total nitrogen storage in a degraded grassland in China link: https://peerj.com/articles/6897 last-modified: 2019-05-03 description: BackgroundPatchy vegetation is a very common phenomenon due to long-term overgrazing in degraded steppe grasslands, which results in substantial uncertainty associated with soil carbon (C) and nitrogen (N) dynamics because of changes in the amount of litter accumulation and nutrition input into soil.MethodsWe investigated soil C and N stocks beneath three types of monodominant species patches according to community dominance. Stipa krylovii patches, Artemisia frigida patches, and Potentilla acaulis patches represent better to worse vegetation conditions in a grassland in northern China.ResultsThe results revealed that the soil C stock (0–40 cm) changed significantly, from 84.7 to 95.7 Mg ha−1, and that the soil organic carbon content (0–10 cm) and microbial biomass carbon (0–10 and 10–20 cm) varied remarkably among the different monodominant species communities (P < 0.05). However, soil total nitrogen and microbial biomass nitrogen showed no significant differences among different plant patches in the top 0–20 cm of topsoil. The soil C stocks under the P. acaulis and S. krylovii patches were greater than that under the A. frigida patch. Our study implies that accurate estimates of soil C and N storage in degenerated grassland require integrated analyses of the concurrent effects of differences in plant community composition. creator: Yujuan Zhang creator: Shiming Tang creator: Shu Xie creator: Kesi Liu creator: Jinsheng Li creator: Qian Chen creator: Ding Huang creator: Kun Wang uri: https://doi.org/10.7717/peerj.6897 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China link: https://peerj.com/articles/6919 last-modified: 2019-05-03 description: BackgroundThis study aims to describe the epidemiological patterns of influenza-like illness (ILI) in Huludao, China and seek scientific evidence on the link of ILI activity with weather factors.MethodsSurveillance data of ILI cases between January 2012 and December 2015 was collected in Huludao Central Hospital, meteorological data was obtained from the China Meteorological Data Service Center. Generalized additive model (GAM) was used to seek the relationship between the number of ILI cases and the meteorological factors. Multiple Smoothing parameter estimation was made on the basis of Poisson distribution, where the number of weekly ILI cases was treated as response, and the smoothness of weather was treated as covariates. Lag time was determined by the smallest Akaike information criterion (AIC). Smoothing coefficients were estimated for the prediction of the number of ILI cases.ResultsA total of 29, 622 ILI cases were observed during the study period, with children ILI cases constituted 86.77%. The association between ILI activity and meteorological factors varied across different lag periods. The lag time for average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity were 2, 2, 1, 1 and 0 weeks, respectively. Average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity could explain 16.5%, 9.5%, 18.0%, 15.9% and 7.7% of the deviance, respectively. Among the temperature indexes, the minimum temperature played the most important role. The number of ILI cases peaked when minimum temperature was around −13 °C in winter and 18 °C in summer. The number of cases peaked when the relative humidity was equal to 43% and then began to decrease with the increase of relative humidity. When the humidity exceeded 76%, the number of ILI cases began to rise.ConclusionsThe present study first analyzed the relationship between meteorological factors and ILI cases with special consideration of the length of lag period in Huludao, China. Low air temperature and low relative humidity (cold and dry weather condition) played a considerable role in the epidemic pattern of ILI cases. The trend of ILI activity could be possibly predicted by the variation of meteorological factors. creator: Ying-Long Bai creator: De-Sheng Huang creator: Jing Liu creator: De-Qiang Li creator: Peng Guan uri: https://doi.org/10.7717/peerj.6919 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bai et al. title: Combining UAV-based hyperspectral imagery and machine learning algorithms for soil moisture content monitoring link: https://peerj.com/articles/6926 last-modified: 2019-05-03 description: Soil moisture content (SMC) is an important factor that affects agricultural development in arid regions. Compared with the space-borne remote sensing system, the unmanned aerial vehicle (UAV) has been widely used because of its stronger controllability and higher resolution. It also provides a more convenient method for monitoring SMC than normal measurement methods that includes field sampling and oven-drying techniques. However, research based on UAV hyperspectral data has not yet formed a standard procedure in arid regions. Therefore, a universal processing scheme is required. We hypothesized that combining pretreatments of UAV hyperspectral imagery under optimal indices and a set of field observations within a machine learning framework will yield a highly accurate estimate of SMC. Optimal 2D spectral indices act as indispensable variables and allow us to characterize a model’s SMC performance and spatial distribution. For this purpose, we used hyperspectral imagery and a total of 70 topsoil samples (0–10 cm) from the farmland (2.5 × 104 m2) of Fukang City, Xinjiang Uygur AutonomousRegion, China. The random forest (RF) method and extreme learning machine (ELM) were used to estimate the SMC using six methods of pretreatments combined with four optimal spectral indices. The validation accuracy of the estimated method clearly increased compared with that of linear models. The combination of pretreatments and indices by our assessment effectively eliminated the interference and the noises. Comparing two machine learning algorithms showed that the RF models were superior to the ELM models, and the best model was PIR (R2val = 0.907, RMSEP = 1.477, and RPD = 3.396). The SMC map predicted via the best scheme was highly similar to the SMC map measured. We conclude that combining preprocessed spectral indices and machine learning algorithms allows estimation of SMC with high accuracy (R2val = 0.907) via UAV hyperspectral imagery on a regional scale. Ultimately, our program might improve management and conservation strategies for agroecosystem systems in arid regions. creator: Xiangyu Ge creator: Jingzhe Wang creator: Jianli Ding creator: Xiaoyi Cao creator: Zipeng Zhang creator: Jie Liu creator: Xiaohang Li uri: https://doi.org/10.7717/peerj.6926 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ge et al. title: Cytotoxic and apoptosis-inducing effects of wildtype and mutated Hydra actinoporin-like toxin 1 (HALT-1) on various cancer cell lines link: https://peerj.com/articles/6639 last-modified: 2019-05-02 description: BackgroundHydra actinoporin like toxin -1 (HALT-1), is a small 18.5 kDa pore forming toxin derived from Hydra magnipapillata which has been shown to elicit strong haemolytic and cytolytic activity when in contact with cell membranes. Due to its cytotoxic potency, HALT-1 was further investigated for its potential as a toxin moiety candidate in immunotoxin developmental efforts, ideally as a form of targeted therapy against cancer.MethodsIn this study, wtHALT-1 (wild type) and its Y110A mutated binding domain counterpart (mHALT-1) were produced and evaluated for their cytotoxic and apoptotic effects on various cancer cell lines. A total of seven different tumour and non-tumour cell lines including HeLa, HepG2, SW-620, MCF-7, CCD841CoN, NHDF and HCT116 were used. Immunofluorescence assays were used to observe membrane binding and localization changes between both HALT-1 recombinant proteins based on 6xHis-tag detection.ResultBased on MTT data, mHALT-1 demonstrated a significant reduction of 82% ±  12.21% in cytotoxic activity across all cell lines after the membrane recognition domain had been mutated in comparison to the wtHALT-1. Annexin V FITC/PI assay data also indicated that HeLa, HepG2 and MCF-7 demonstrated an apoptosis-mediated cell death after being treated with wtHALT-1. Additionally, a notable difference between wtHALT-1 and mHALT-1 binding affinity was clearly observed where emission of green fluorescence along the cell membrane was observed only in wtHALT-1 treated cells.DiscussionThese results suggest that mHALT-1 (Y110A) can be potentially developed as a toxin-moiety candidate for the development of future immunotoxins against various human cell-based diseases. creator: Teng Jia Ng creator: Michelle Yee Mun Teo creator: Dek Shen Liew creator: Paul Etim Effiong creator: Jung Shan Hwang creator: Crystale Siew Ying Lim creator: Lionel L.A. In uri: https://doi.org/10.7717/peerj.6639 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ng et al. title: Century-scale changes in phytoplankton phenology in the Gulf of Maine link: https://peerj.com/articles/6735 last-modified: 2019-05-02 description: The phenology of major seasonal events is an important indicator of climate. We analyzed multiple datasets of in situ chlorophyll measurements from the Gulf of Maine dating back to the early 20th century in order to detect climate-scale changes in phenology. The seasonal cycle was consistently characterized by a two-bloom pattern, with spring and autumn blooms. The timing of both spring and autumn blooms has shifted later in the year at rates ranging from ∼1 to 9 days per decade since 1960, depending on the phenology metric, and trends only emerged at time scales of >40 years. Bloom phenology had only weak correlations with major climate indices. There were stronger associations between bloom timing and physical and chemical variables. Autumn bloom initiation correlated strongly with surface temperature and salinity, and spring bloom with nutrients. A later spring bloom also correlated with an increased cohort of Calanus finmarchicus, suggesting broader ecosystem implications of phytoplankton phenology. creator: Nicholas R. Record creator: William M. Balch creator: Karen Stamieszkin uri: https://doi.org/10.7717/peerj.6735 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Record et al. title: Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters link: https://peerj.com/articles/6858 last-modified: 2019-05-02 description: A 2016 collaborative survey of commercial fish parasites in Moreton Bay, Queensland, Australia led to the discovery of two new species of parasitic copepods belonging to the family Bomolochidae. Females of Nothobomolochus johndaveorum n. sp. were found attached to the gill filaments of Gerres subfasciatus and Gerres oyena. The new species most closely resembles N. leiognathicola and N. quadriceros. All 3 species possess 3 modified setae on the first antennulary segment that are approximately the same length and have a robust seta on the second antennulary segment adjacent to the 3 modified setae giving a superficial appearance of 4 modified setae on the antennule. The new species can be distinguished from these two species in its possession of longer inner setae on the first two endopodal segments of leg 4: the seta on endopodal segment 1 extends past the midline of the distal segment in the new species vs to the proximal margin of the distal segment in the other two species, and the seta on segment 2 extends well beyond the distal margin of the endopod in the new species vs just to the margin in the other two species. Females and males of Unicolax longicrus n. sp. were found in the nasal sinuses of Sillago maculata and Sillago ciliata. The new species differs from 6 of its 7 congeners in having a leg 4 exopod formula of II, I, 4 rather than II, I, 3 or II, I, 5. The new species resembles U. anonymous in this feature, but differs in its possession of a leg 5 that is relatively longer and less wide, and, whereas U. anonymous possesses inner and outer distal spines on leg 5 that are approximately the same length, those of the new species are relatively longer and asymmetrical. Unicolax longicrus n. sp. is unique among its congeners in its possession of a leg 4 with highly elongated endopodal segments 2 and 3, from which its name is derived. In addition to describing the two new species, host and locality reports for all species of Nothobomolochus and Unicolax are reviewed. creator: James P. Bernot creator: Geoffrey A. Boxshall uri: https://doi.org/10.7717/peerj.6858 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bernot and Boxshall title: Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae) link: https://peerj.com/articles/6866 last-modified: 2019-05-02 description: A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov.Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae. creator: Gengyun Niu creator: Yaoyao Zhang creator: Zhenyi Li creator: Meicai Wei uri: https://doi.org/10.7717/peerj.6866 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Niu et al. title: Coupling and metabolic analysis of urbanization and environment between two resource-based cities in North China link: https://peerj.com/articles/6869 last-modified: 2019-05-02 description: BackgroundThe complex relationship between urbanization and environment in resource-based cities is of increasing concern.MethodsAs typical examples of rapid economic growth, obvious urbanization, and successful transformed production models, the cities of Dongying and Binzhou in Yellow River Delta High-tech Economic Zone were chosen for research. First, this study examines the coupling relationship between urbanization and the environment over the last seventeen years using the coupling degree model. Second, the emergy analysis method is used to further study the energy metabolism and environmental load in the two cities to reveal these couplings.ResultsDongying and Binzhou were well-coupled and the coupling coordination degree was in the stage of mild coordination coupling showing an upward trend. The total metabolic energy of the two cities increased yearly from 2000 to 2016, and the emergy extroversion ratio data showed the cities’ dependence on external elements such as continuously increased imported resources. The total emergy used in the two cities showed an upward trend during 2000 and 2016, while the emergy per capita consumption increased significantly, suggesting that the society’s energy efficiency improved. During the same period, the environmental loading ratio increased gradually, and the elements causing the environmental load shifted from internal to external.DiscussionThe study shows that the factors of environmental load in developing cities are gradually shifting from internal to external, which is vital to understanding the impact of urban transformation and upgrading of resource-based cities on the environment. creator: Hao Chen creator: Linyu Xu creator: Qingqing Cao creator: Miansong Huang creator: Minghua Song creator: Quan Quan creator: Jian Liu uri: https://doi.org/10.7717/peerj.6869 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species link: https://peerj.com/articles/6873 last-modified: 2019-05-02 description: Restoration of depleted populations is an important method in biological conservation. Reintroduction strategies frequently aim to restore stable, increasing, self-sustaining populations. Knowledge of asymptotic system dynamics may provide advantage in selecting reintroduction strategies. We introduce interactive software that is designed to identify strategies for release of females that are immediately aligned with stable population dynamics from species represented by 2-, 3-, 4-, and 5-stage life history strategies. The software allows managers to input a matrix of interest, the desired number of breeding females, and the desired management timeline, and calls upon stable population theory to give release strategies that are in concert with both stable population status and the management goals. We demonstrate how the software can aid in assessing various strategies ahead of a hypothetical restoration. For the purpose of demonstration of the tool only, we use published vital rates of an ungulate species, but remark that the selection of species for demonstration is not central to the use of this tool. Adaption of this tool to real-life restorations of any 2-, 3-, 4-, or 5-stage iteroparous species may aid in understanding how to minimize undesirable recovery complications that may naturally arise from transient population dynamics. The software is freely available at: https//cwhl.vet.cornell.edu/tools/stapopd. creator: Brenda J. Hanley creator: Elizabeth M. Bunting creator: Krysten L. Schuler uri: https://doi.org/10.7717/peerj.6873 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hanley et al. title: Galantamine plasma concentration and cognitive response in Alzheimer’s disease link: https://peerj.com/articles/6887 last-modified: 2019-05-02 description: BackgroundGalantamine has been approved for the treatment of Alzheimer’s disease (AD). However, there are few studies which have reported the association between cognitive responses and galantamine plasma concentration. The aim of this study was to determine the correlation between galantamine plasma concentration and the subsequent cognitive response following treatment in AD patients.MethodsAD sufferers who continuously took 8 mg/d galantamine for at least 6 months without previous exposure to other kinds of AChEI such as donepezil, rivastigmine, or memantine were included in this cohort study. The assessments included the Mini Mental Status Examination (MMSE), Clinical Dementia Rating Scale (CDR) and the Cognitive Assessment Screening Instrument (CASI). Each subdomain of the CASI assessment was conducted at baseline and after 6 months of galantamine. The plasma concentrations of galantamine were measured by capillary electrophoresis after 6 months of the treatment. Logistic regression was performed to adjust for age, gender, apolipoprotein E ε4 genotype status, and baseline score to investigate the association between galantamine plasma concentrations and the cognitive response.ResultsThe total sample consisted of 33 clinically diagnosed AD patients taking galantamine 8 mg/d for 6 months. There was no linear correlation between galantamine concentration and cognitive response in patients. However, 22 patients were responsive to the treatment in the long-term memory domain. In CASI subset domain, concentration improved during the 6 months follow up.ConclusionsIn the limited samples study, galantamine mostly benefitted the cognitive domain of long-term memory. The benefits were not related to the galantamine plasma concentration. Objective intra-individual evaluation of therapeutic response should be encouraged. creator: Yi-Ting Lin creator: Mei-Chuan Chou creator: Shyh-Jong Wu creator: Yuan-Han Yang uri: https://doi.org/10.7717/peerj.6887 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lin et al. title: A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast link: https://peerj.com/articles/6892 last-modified: 2019-05-02 description: Benthic–pelagic coupling refers to the ecological relationships between benthic and pelagic environments. Studying such links is particularly useful to understand biological variation in intertidal organisms along marine coasts. Filter-feeding invertebrates are ecologically important on marine rocky shores, so they have often been used to investigate benthic–pelagic coupling. Most studies, however, have been conducted on eastern ocean boundaries. To evaluate benthic–pelagic coupling on a western ocean boundary, we conducted a 5-year study spanning 415 km of the Atlantic coast of Nova Scotia (Canada). We hypothesized that the summer size of intertidal barnacles (Semibalanus balanoides) recruited in the preceding spring would be positively related to the nearshore abundance (biomass) of phytoplankton, as phytoplankton constitutes food for the nauplius larvae and benthic stages of barnacles. Every year between 2014 and 2018, we measured summer barnacle size in clearings created before spring recruitment on the rocky substrate at eight wave-exposed locations along this coast. We then examined the annual relationships between barnacle size and chlorophyll-a concentration (Chl-a), a proxy for phytoplankton biomass. For every year and location, we used satellite data to calculate Chl-a averages for a period ranging from the early spring (when most barnacle larvae were in the water) to the summer (when barnacle size was measured after weeks of growth following spring benthic recruitment). The relationships were always positive, Chl-a explaining nearly half, or more, of the variation in barnacle size in four of the five studied years. These are remarkable results because they were based on a relatively limited number of locations (which often curtails statistical power) and point to the relevance of pelagic food supply to explain variation in intertidal barnacle size along this western ocean boundary coast. creator: Ricardo A. Scrosati creator: Julius A. Ellrich uri: https://doi.org/10.7717/peerj.6892 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Scrosati and Ellrich title: The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment link: https://peerj.com/articles/6743 last-modified: 2019-05-01 description: BackgroundThe increasing production of sewage sludge (SS) engenders the problem of its responsible utilization and disposal. Likewise, urban sediments (SED) are deposited at the bottom of urban reservoirs and sedimentation ponds, and these require periodical dredging and utilization. However, while the SS and SED deposits often contain nutrients such as nitrogen and phosphorus; however, they also contain a variety of hazardous compounds including heavy metals, Persistent Organic Pollutants (POPs) and microbial pollutants. Fortunately, some species of Cucurbitaceae can accumulate high levels of POPs, such as polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF) and polychlorinated biphenyls (PCB), in their tissues.MethodsSS was collected from the Lodz Municipal Wastewater Treatment Plant and SED from the Sokołówka Sequential Biofiltration System. The SS and SED samples were added to soil in flower pots at three concentrations (1.8 g, 5.4 g and 10.8 g per flower pot), and one pot was left as an unamended control (C). Soil PCB concentrations were determined before cucumber planting, and after five weeks of growth. Also, total soluble protein, total chlorophyll content, chlorophyll a/b ratio and degree of lipid peroxidation (TBARS) were examined in the leaves of the cucumber plants (Cucumis sativus L.) cv. Cezar after five weeks. Antioxidative response was assessed by ascorbate peroxidase (APx) and catalase (CAT) assay.ResultsThe initial PCB concentration in soil after application of SS or SED was dependent on the applied dose. After five weeks, PCB concentration fell significantly for all samples and confirmed that the dose of SS/SED had a strong effect. Soil remediation was found to be more effective after SS application. Total soluble protein content in the cucumber leaf tissues was dependent on both the type and the dose of the applied amendments, and increased with greater SS doses in the soil. The total chlorophyll content remained unchanged, and the chlorophyll a/b ratio was slightly elevated only after the application of the highest SS and SED dose. The use of SS and SED did not significantly affect TBARS content. APx activity fell after SS or SED application; however, CAT activity tended to increase, but only in the leaves of plants grown in SS-amended soil.DiscussionThe cultivation of cucumber plants reduces PCB concentration in soil amended with SS or SED; however, this effect is more evident in the case of SS. SS application also induced more intensive changes in the activity of enzymes engaged in antioxidative response and oxidative stress markers in plant tissues than SED. The levels of PCB in the SS may have triggered a more severe imbalance between pro- and antioxidative reactions in plants. Cucumber plants appear to be resistant to the presence of toxic substances in SS and SED, and the addition of SS and SED not only acts as a fertilizer, but also protects against accelerated aging. creator: Anna Wyrwicka creator: Magdalena Urbaniak creator: Mirosław Przybylski uri: https://doi.org/10.7717/peerj.6743 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wyrwicka et al. title: Predicting gene expression using DNA methylation in three human populations link: https://peerj.com/articles/6757 last-modified: 2019-05-01 description: BackgroundDNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative correlation in the promoter region. However, its correlation with gene expression across genome at human population level has not been well studied. In particular, it is unclear if genome-wide DNA methylation profile of an individual can predict her/his gene expression profile. Previous studies were mostly limited to association analyses between single CpG site methylation and gene expression. It is not known whether DNA methylation of a gene has enough prediction power to serve as a surrogate for gene expression in existing human study cohorts with DNA samples other than RNA samples.ResultsWe examined DNA methylation in the gene region for predicting gene expression across individuals in non-cancer tissues of three human population datasets, adipose tissue of the Multiple Tissue Human Expression Resource Projects (MuTHER), peripheral blood mononuclear cell (PBMC) from Asthma and normal control study participates, and lymphoblastoid cell lines (LCL) from healthy individuals. Three prediction models were investigated, single linear regression, multiple linear regression, and least absolute shrinkage and selection operator (LASSO) penalized regression. Our results showed that LASSO regression has superior performance among these methods. However, the prediction power is generally low and varies across datasets. Only 30 and 42 genes were found to have cross-validation R2 greater than 0.3 in the PBMC and Adipose datasets, respectively. A substantially larger number of genes (258) were identified in the LCL dataset, which was generated from a more homogeneous cell line sample source. We also demonstrated that it gives better prediction power not to exclude any CpG probe due to cross hybridization or SNP effect.ConclusionIn our three population analyses DNA methylation of CpG sites at gene region have limited prediction power for gene expression across individuals with linear regression models. The prediction power potentially varies depending on tissue, cell type, and data sources. In our analyses, the combination of LASSO regression and all probes not excluding any probe on the methylation array provides the best prediction for gene expression. creator: Huan Zhong creator: Soyeon Kim creator: Degui Zhi creator: Xiangqin Cui uri: https://doi.org/10.7717/peerj.6757 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhong et al. title: Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids link: https://peerj.com/articles/6811 last-modified: 2019-05-01 description: Knowledge of the early evolution of sea turtles (Chelonioidea) has been limited by conflicting phylogenetic hypotheses resulting from sparse taxon sampling and a superficial understanding of the morphology of key taxa. This limits our understanding of evolutionary adaptation to marine life in turtles, and in amniotes more broadly. One problematic group are the protostegids, Early–Late Cretaceous marine turtles that have been hypothesised to be either stem-cryptodires, stem-chelonioids, or crown-chelonioids. Different phylogenetic hypotheses for protostegids suggest different answers to key questions, including (1) the number of transitions to marine life in turtles, (2) the age of the chelonioid crown-group, and (3) patterns of skeletal evolution during marine adaptation. We present a detailed anatomical study of one of the earliest protostegids, Rhinochelys pulchriceps from the early Late Cretaceous of Europe, using high-resolution μCT. We synonymise all previously named European species and document the variation seen among them. A phylogeny of turtles with increased chelonioid taxon sampling and revised postcranial characters is provided, recovering protostegids as stem-chelonioids. Our results imply a mid Early Cretaceous origin of total-group chelonioids and an early Late Cretaceous age for crown-chelonioids, which may inform molecular clock analyses in future. Specialisations of the chelonioid flipper evolved in a stepwise-fashion, with innovations clustered into pulses at the origin of total-group chelonioids, and subsequently among dermochelyids, crown-cheloniids, and gigantic protostegids from the Late Cretaceous. creator: Serjoscha W. Evers creator: Paul M. Barrett creator: Roger B. J. Benson uri: https://doi.org/10.7717/peerj.6811 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Evers et al. title: Impacts of the invasive shot hole borer (Euwallacea kuroshio) are linked to sewage pollution in southern California: the Enriched Tree Hypothesis link: https://peerj.com/articles/6812 last-modified: 2019-05-01 description: The Kuroshio Shot Hole Borer (KSHB, Euwallacea kuroshio) and the Polyphagous Shot Hole Borer (E. whitfordiodendrus; Coleoptera: Curculionidae: Scolytinae) have recently invaded southern California and are attacking live trees in commercial agriculture groves, urban parks and native riparian forests. Among native forests the worst impacts observed to date have been in the Tijuana River Valley in south San Diego County, where approximately 30% of the native willows (Salix spp.), or 120,000 trees, have died as a result of a KSHB infestation. This paper examines wood densities, wood moisture contents, KSHB infestation rates, and KSHB-induced mortality rates in two willow species (Salixlasiolepis and S. gooddingii) at sites near and far from sewage input. Comparisons were made on two spatial scales: broadly among sites within San Diego County; and locally among sites within the Tijuana River Valley. The results showed that, on average, willow trees growing closest to sewage pollution had significantly lower wood density, higher wood moisture content, higher KSHB infestation rates, and higher KSHB-induced willow mortality rates than those growing farther away. We present the Enriched Tree Hypothesis to explain the link between sewage pollution and KSHB impacts; it is as follows: (A) Riparian trees subject to nutrient enrichment from frequent sewage pollution grow quickly, and their fast growth results in wood of low density and high moisture content. If attacked by the KSHB, the trunks and branches of these nutrient-enriched trees provide an environment conducive to the fast growth of the symbiotic fungi upon which the KSHB feeds. With an abundant food supply, the KSHB population increases rapidly and the trees are heavily damaged by thousands of KSHB galleries in their trunks and branches. (B) Riparian trees not subject to frequent sewage pollution grow more slowly and have denser, drier wood. Conditions in their trunks and branches are not conducive to the fast growth of the KSHB’s symbiotic fungi. The KSHB generally ignores, or has low abundances in, these slow-growing trees. This new hypothesis explains current patterns of KSHB impact in San Diego County and focuses attention on the important roles of the environment and preexisting conditions of trees in determining the extent of KSHB impact. It highlights the Tijuana River Valley as an unusual site due to high sewage inputs and predicts that the high KSHB-induced willow mortality seen there should not occur in other natural riparian habitats in southern California. Most importantly, by identifying sewage pollution (or nutrient enrichment) as a major risk factor for KSHB impacts, the hypothesis ratchets down the KSHB-threat level for most riparian sites in southern California and directs attention to other nutrient-enriched sites as those most at risk. creator: John M. Boland creator: Deborah L. Woodward uri: https://doi.org/10.7717/peerj.6812 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Boland and Woodward title: ERISNet: deep neural network for Sargassum detection along the coastline of the Mexican Caribbean link: https://peerj.com/articles/6842 last-modified: 2019-05-01 description: Recently, Caribbean coasts have experienced atypical massive arrivals of pelagic Sargassum with negative consequences both ecologically and economically. Based on deep learning techniques, this study proposes a novel algorithm for floating and accumulated pelagic Sargassum detection along the coastline of Quintana Roo, Mexico. Using convolutional and recurrent neural networks architectures, a deep neural network (named ERISNet) was designed specifically to detect these macroalgae along the coastline through remote sensing support. A new dataset which includes pixel values with and without Sargassum was built to train and test ERISNet. Aqua-MODIS imagery was used to build the dataset. After the learning process, the designed algorithm achieves a 90% of probability in its classification skills. ERISNet provides a novel insight to detect accurately algal blooms arrivals. creator: Javier Arellano-Verdejo creator: Hugo E. Lazcano-Hernandez creator: Nancy Cabanillas-Terán uri: https://doi.org/10.7717/peerj.6842 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Arellano-Verdejo et al. title: Manganese affects the growth and metabolism of Ganoderma lucidum based on LC-MS analysis link: https://peerj.com/articles/6846 last-modified: 2019-05-01 description: BackgroundAs a metal-enriched edible fungus, Ganoderma lucidum is capable of adsorbing manganese effectively. And the manganese ion is demonstrated to play an important role in the synthesis of manganese peroxidase (Mnp) and other physiological activities during G. lucidum growth. Recently, the influence of manganese on the metabolites of G. lucidum fruiting bodies can be revealed through metabonomics technique.MethodsIn this study, we uncovered the changes between the control and 200 mg/kg Mn-treated fruiting bodies with liquid chromatography coupled to mass spectrometry (LC-MS).ResultsThe mycelial growth rate, dry yield, Mnp activity , total polysaccharide content, triterpenoid content, and total manganese content in the mature fruiting bodies of G. lucidum changed between the control and different Mn-treated groups. Based on LC-MS method, a total of 16 significantly different metabolites were obtained and identified, among which, five presented significantly down-regulated and 11 up-regulated in Mn-treated samples. The metabolites chavicol and palmitoylethanolamide were particularly significantly up-regulated, and were found the strong promotion relationship. Dependent on the MetPA database, four KEGG pathways were detected and glycerophospholipid metabolism was most impacted, in which, choline was involved in.DiscussionThe added manganese ion in the substrate enhanced Mnp activities, and consequently promoted the mycelial growth, yield , metabolites in the fruiting bodies including triterpenoids, total manganese, chavicol, etc. Our finding can provide a theoretical reference to regulation of manganese on the physiological metabolism of G. lucidum. creator: Bo Zhang creator: Jie Zhou creator: Qiang Li creator: Bingcheng Gan creator: Weihong Peng creator: Xiaoping Zhang creator: Wei Tan creator: Lin Jiang creator: Xiaolin Li uri: https://doi.org/10.7717/peerj.6846 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: A large scale evaluation of TBProfiler and Mykrobe for antibiotic resistance prediction in Mycobacterium tuberculosis link: https://peerj.com/articles/6857 last-modified: 2019-05-01 description: Recent years saw a growing interest in predicting antibiotic resistance from whole-genome sequencing data, with promising results obtained for Staphylococcus aureus and Mycobacterium tuberculosis. In this work, we gathered 6,574 sequencing read datasets of M. tuberculosis public genomes with associated antibiotic resistance profiles for both first and second-line antibiotics. We performed a systematic evaluation of TBProfiler and Mykrobe, two widely recognized softwares allowing to predict resistance in M. tuberculosis. The size of the dataset allowed us to obtain confident estimations of their overall predictive performance, to assess precisely the individual predictive power of the markers they rely on, and to study in addition how these softwares behave across the major M. tuberculosis lineages. While this study confirmed the overall good performance of these tools, it revealed that an important fraction of the catalog of mutations they embed is of limited predictive power. It also revealed that these tools offer different sensitivity/specificity trade-offs, which is mainly due to the different sets of mutation they embed but also to their underlying genotyping pipelines. More importantly, it showed that their level of predictive performance varies greatly across lineages for some antibiotics, therefore suggesting that the predictions made by these softwares should be deemed more or less confident depending on the lineage inferred and the predictive performance of the marker(s) actually detected. Finally, we evaluated the relevance of machine learning approaches operating from the set of markers detected by these softwares and show that they present an attractive alternative strategy, allowing to reach better performance for several drugs while significantly reducing the number of candidate mutations to consider. creator: Pierre Mahé creator: Meriem El Azami creator: Philippine Barlas creator: Maud Tournoud uri: https://doi.org/10.7717/peerj.6857 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mahé et al. title: A novel conserved family of Macro-like domains—putative new players in ADP-ribosylation signaling link: https://peerj.com/articles/6863 last-modified: 2019-05-01 description: The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers a full understanding of the functioning of living cells. One such example is the human protein C12ORF4, which belongs to the DUF2362 family, present in many eukaryotic lineages and conserved in metazoans. The only functional information available on C12ORF4 (Chromosome 12 Open Reading Frame 4) is its involvement in mast cell degranulation and its being a genetic cause of autosomal intellectual disability.Bioinformatics analysis of the DUF2362 family provides strong evidence that it is a novel member of the Macro clan/superfamily. Sequence similarity analysis versus other representatives of the Macro superfamily of ADP-ribose-binding proteins and mapping sequence conservation on predicted three-dimensional structure provides hypotheses regarding the molecular function for members of the DUF2362 family. For example, the available functional data suggest a possible role for C12ORF4 in ADP-ribosylation signaling in asthma and related inflammatory diseases.This novel family appears to be a likely novel ADP-ribosylation “reader” and “eraser,” a previously unnoticed putative new player in cell signaling by this emerging post-translational modification. creator: Małgorzata Dudkiewicz creator: Krzysztof Pawłowski uri: https://doi.org/10.7717/peerj.6863 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dudkiewicz and Pawłowski title: Distribution and colocalization of melatonin 1a-receptor and NADPH-d in the trigeminal system of rat link: https://peerj.com/articles/6877 last-modified: 2019-05-01 description: Melatonin and nitric oxide (NO) are involved in orofacial signal processing in the trigeminal sensory system. The aim of the present study was to examine the distribution of melatonin 1a-receptor (MT1) and its colocalization with nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d) in the spinal trigeminal nucleus (STN), the trigeminal ganglion (TG), and the mesencephalic trigeminal nucleus (MTN) in the rat, using histochemistry and immunohistochemistry. Our results show that MT1-positive neurons are widely distributed in the TG and the subnucleus caudalis of the STN. Furthermore, we found that MT1 colocalizes with NADPH-d throughout the TG and MTN, most extensively in the TG. The distribution pattern of MT1 and its colocalization with NADPH-d indicate that melatonin might play an important role in the trigeminal sensory system, which could be responsible for the regulation of NO levels. creator: Yifan He creator: Wenguo Fan creator: Yue Xu creator: Yong liang Liu creator: Hongwen He creator: Fang Huang uri: https://doi.org/10.7717/peerj.6877 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 He et al. title: Development of an in vitro diagnostic method to determine the genotypic sex of Xenopus laevis link: https://peerj.com/articles/6886 last-modified: 2019-05-01 description: A genotypic sex determination assay provides accurate gender information of individuals with well-developed phenotypic characters as well as those with poorly developed or absent of phenotypic characters. Determination of genetic sex for Xenopus laevis can be used to validate the outcomes of Tier 2 amphibian assays, and is a requirement for conducting the larval amphibian growth and development assay (LAGDA), in the endocrine disruptor screening program (EDSP), test guidelines. The assay we developed uses a dual-labeled TaqMan probe-based real-time polymerase chain reaction (real-time PCR) method to determine the genotypic sex. The reliability of the assay was tested on 37 adult specimens of X. laevis collected from in-house cultures in Eurofins EAG Agroscience, Easton. The newly designed X. laevis-specific primer pair and probe targets the DM domain gene linked-chromosome W as a master female-determining gene. Accuracy of the molecular method was assessed by comparing with phenotypic sex, determined by necropsy and histological examination of gonads for all examined specimens. Genotypic sex assignments were strongly concordant with observed phenotypic sex, confirming that the 19 specimens were male and 18 were female. The results indicate that the TaqMan® assay could be practically used to determine the genetic sex of animals with poorly developed or no phenotypic sex characteristics with 100% precision. Therefore, the TaqMan® assay is confirmed as an efficient and feasible method, providing a diagnostic molecular sex determination approach to be used in the amphibian endocrine disrupting screening programs conducted by regulatory industries. The strength of an EDSP is dependent on a reliable method to determine genetic sex in order to identify reversals of phenotypic sex in animals exposed to endocrine active compounds. creator: Amin Eimanifar creator: John Aufderheide creator: Suzanne Z. Schneider creator: Henry Krueger creator: Sean Gallagher uri: https://doi.org/10.7717/peerj.6886 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Eimanifar et al.