title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1352 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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.