title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1040 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Spatial benthic community analysis of shallow coral reefs to support coastal management in Culebra Island, Puerto Rico link: https://peerj.com/articles/10080 last-modified: 2020-10-14 description: Caribbean coral reefs provide essential ecosystem services to society, including fisheries, tourism and shoreline protection from coastal erosion. However, these reefs are also exhibiting major declining trends, leading to the evolution of novel ecosystems dominated by non-reef building taxa, with potentially altered ecological functions. In the search for effective management strategies, this study characterized coral reefs in front of a touristic beach which provides economic benefits to the surrounding coastal communities yet faces increasing anthropogenic pressures and conservation challenges. Haphazard photo-transects were used to address spatial variation patterns in the reef’s benthic community structure in eight locations. Statistically significant differences were found with increasing distance from the shoreline, reef rugosity, Diadema antillarum density, among reef locations, and as a function of recreational use. Nearshore reefs reflected higher percent macroalgal cover, likely due to increased exposure from both recreational activities and nearby unsustainable land-use practices. However, nearshore reefs still support a high abundance of the endangered reef-building coral Orbicella annularis, highlighting the need to conserve these natural shoreline protectors. There is an opportunity for local stakeholders and regulatory institutions to collaboratively implement sea-urchin propagation, restoration of endangered Acroporid coral populations, and zoning of recreational densities across reefs. Our results illustrate vulnerable reef hotspots where these management interventions are needed and recommend guidelines to address them. creator: Nicolás X. Gómez-Andújar creator: Edwin A. Hernandez-Delgado uri: https://doi.org/10.7717/peerj.10080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gómez-Andújar and Hernandez-Delgado title: Ecological stoichiometry of plant leaves, litter and soils in a secondary forest on China’s Loess Plateau link: https://peerj.com/articles/10084 last-modified: 2020-10-14 description: Ecological stoichiometry can reveal nutrient cycles in soil and plant ecosystems and their interactions. However, the ecological stoichiometry characteristics of leaf-litter-soil system of dominant grasses, shrubs and trees are still unclear as are their intrinsic relationship during vegetation restoration. This study selected three dominant plant types of grasses (Imperata cylindrica (I. cylindrica) and Artemisiasacrorum (A.sacrorum)), shrubs (Sophora viciifolia (S. viciifolia) and Hippophae rhamnoides (H. rhamnoides)) and trees (Quercus liaotungensis (Q. liaotungensis) and Betula platyphylla (B. platyphylla)) in secondary forest areas of the Chinese Loess Plateau to investigate ecological stoichiometric characteristics and their intrinsic relationships in leaf-litter-soil systems. The results indicated that N concentration and N:P ratios in leaf and litter were highest in shrubland; leaf P concentration in grassland was highest and litter in forestland had the highest P concentration. Soil C, N and P concentrations were highest in forestland (P < 0.05) and declined with soil depth. Based on the theory that leaf N:P ratio indicates nutritional limitation of plant growth, this study concluded that grass and shrub growth was limited by N and P element, respectively, and forest growth was limited by both of N and P elements. The relationships between the N concentration in soil, leaf and litter was not significant (P >0.5), but the soil P concentration was significantly correlated with litter P concentration (P < 0.05). These finding enhance understanding of nutrient limitations in different plant communities during vegetation restoration and provide insights for better management of vegetation restoration. creator: Zongfei Wang creator: Fenli Zheng uri: https://doi.org/10.7717/peerj.10084 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang and Zheng title: Quantile-dependent expressivity of plasma adiponectin concentrations may explain its sex-specific heritability, gene-environment interactions, and genotype-specific response to postprandial lipemia link: https://peerj.com/articles/10099 last-modified: 2020-10-14 description: Background“Quantile-dependent expressivity” occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g. adiponectin) is high or low relative to its distribution. We have previously shown that the heritability (h2) of adiposity, lipoproteins, postprandial lipemia, pulmonary function, and coffee and alcohol consumption are quantile-specific. Whether adiponectin heritability is quantile specific remains to be determined.MethodsPlasma adiponectin concentrations from 4,182 offspring-parent pairs and 1,662 sibships from the Framingham Heart Study were analyzed. Quantile-specific heritability from offspring-parent (βOP,h2 = 2βOP/(1 + rspouse)) and full-sib regression slopes (βFS, h2 = {(1 + 8rspouseβFS)0.05-1}/(2rspouse)) were robustly estimated by quantile regression with nonparametric significance assigned from 1,000 bootstrap samples.ResultsQuantile-specific h2 (± SE) increased with increasing percentiles of the offspring’s age- and sex-adjusted adiponectin distribution when estimated from βOP (Ptrend = 2.2 × 10−6): 0.30 ± 0.03 at the 10th, 0.33 ± 0.04 at the 25th, 0.43 ± 0.04 at the 50th, 0.55 ± 0.05 at the 75th, and 0.57 ± 0.08 at the 90th percentile, and when estimated from βFS (Ptrend = 7.6 × 10−7): 0.42 ± 0.03 at the 10th, 0.44 ± 0.04 at the 25th, 0.56 ± 0.05 at the 50th, 0.73 ± 0.08 at the 75th, and 0.79 ± 0.11 at the 90th percentile. Consistent with quantile-dependent expressivity, adiponectin’s: (1) heritability was greater in women in accordance with their higher adiponection concentrations; (2) relationships to ADIPOQ polymorphisms were modified by adiposity in accordance with its adiponectin-lowering effect; (3) response to rosiglitazone was predicted by the 45T> G ADIPOQ polymorphism; (4) difference by ADIPOQ haplotypes increased linearly with increasing postprandial adiponectin concentrations.ConclusionAdiponectin heritability is quantile dependent, which may explain sex-specific heritability, gene-environment and gene-drug interactions, and postprandial response by haplotypes. creator: Paul T. Williams uri: https://doi.org/10.7717/peerj.10099 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Williams title: Heparin-binding protein as a novel biomarker for sepsis-related acute kidney injury link: https://peerj.com/articles/10122 last-modified: 2020-10-14 description: BackgroundSepsis-related acute kidney injury (AKI) is associated with high morbidity and mortality among patients. Underlying pathomechanisms include capillary leakage and fluid loss into the interstitial tissue and constant exposure to pathogens results in activation of inflammatory cascades, organ dysfunction and subsequently organ damage.MethodsTo identify novel factors that trigger sepsis-related acute kidney injury, plasma levels of Granzyme A, as representative of a lymphocyte-derived protease, and heparin-binding protein as indicator for neutrophil-derived mediators, were investigated retrospectively in 60 sepsis patients.ResultsWhile no association was found between plasma levels of lymphocyte-derived Granzyme A and the incidence of sepsis-related AKI, sepsis patients with AKI had significantly higher plasma levels of heparin-binding protein compared to those without AKI. This applies both to heparin-binding protein peak values (43.30 ±  23.34 vs. 30.25 ±  15.63 pg/mL; p = 0.005) as well as mean values (27.93 ±  14.39 vs. 22.02 ±  7.65 pg/mL; p = 0.021). Furthermore, a heparin-binding protein cut-off value of 23.89 pg/mL was established for AKI diagnosis.ConclusionThis study identifies the neutrophil-derived heparin-binding protein as a valuable new biomarker for AKI in sepsis. Beyond the diagnostic perspective, this offers prospect for further research on pathogenesis of AKI and novel therapeutic approaches. creator: Sahra Pajenda creator: Andreja Figurek creator: Ludwig Wagner creator: Daniela Gerges creator: Alice Schmidt creator: Harald Herkner creator: Wolfgang Winnicki uri: https://doi.org/10.7717/peerj.10122 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pajenda et al. title: Association of pre-pregnancy body mass index with adverse pregnancy outcome among first-time mothers link: https://peerj.com/articles/10123 last-modified: 2020-10-14 description: BackgroundStudies have reported an increased risk of adverse pregnancy outcome associated with pre-pregnancy body mass index (BMI). However, the data on such associations in urban areas of southern Chinese women is limited, which drive us to clarify the associations of pre-pregnancy BMI and the risks of adverse pregnancy outcomes (preterm birth (PTB) and low birth weight (LBW)) and maternal health outcomes (gestational hypertension and cesarean delivery).MethodsWe performed a hospital-based case-control study including 3,864 Southern Chinese women who gave first birth to a live singleton infant from January 2015 to December 2015. PTB was stratified into three subgroups according to gestational age (extremely PTB, very PTB and moderate PTB). Besides, we combined birth weight and gestational age to dichotomise as being small for gestational age (SGA, less than the tenth percentile of weight for gestation) and non-small for gestational age (NSGA, large than the tenth percentile of weight for gestation), gestational week was also classified into categories of term, 34-36 week and below 34 week.. We then divided newborns into six groups: (1) term and NSGA; (2) 34–36 week gestation and NSGA; (3) below 34 week gestation and NSGA; (4) term and SAG; (5) 34–36 week gestation and SAG; (6) below 34 week gestation and SAG. Adjusted logistic regression models was used to estimate the odds ratios of adverse outcomes.ResultsUnderweight women were more likely to give LBW (AOR = 1.44, 95% CI [1.11–1.89]), the similar result was seen in term and SAG as compared with term and NSAG (AOR = 1.78, 95% CI [1.45–2.17]), whereas underweight was significantly associated with a lower risk of gestational hypertension (AOR = 0.45, 95% CI [0.25–0.82) and caesarean delivery (AOR = 0.74, 95% CI [0.62–0.90]). The risk of extremely PTB is relatively higher among overweight and obese mothers in a subgroup analysis of PTB (AOR = 8.12, 95% CI [1.11–59.44]; AOR = 15.06, 95% CI [1.32–172.13], respectively). Both maternal overweight and obesity were associated with a greater risk of gestational hypertension (AOR = 1.71, 95% CI [1.06–2.77]; AOR = 5.54, 95% CI [3.02–10.17], respectively) and caesarean delivery (AOR = 1.91, 95% CI [1.53–2.38]; AOR = 1.85, 95% CI [1.21–2.82], respectively).ConclusionsOur study suggested that maternal overweight and obesity were associated with a significantly higher risk of gestational hypertension, caesarean delivery and extremely PTB. Underweight was correlated with an increased risk of LBW and conferred a protective effect regarding the risk for gestational hypertension and caesarean delivery for the first-time mothers among Southern Chinese. creator: Li Li creator: Yanhong Chen creator: Zhifeng Lin creator: Weiyan Lin creator: Yangqi Liu creator: Weilin Ou creator: Chengli Zeng creator: Li Ke uri: https://doi.org/10.7717/peerj.10123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Long non-coding RNA LINC01234 regulates proliferation, migration and invasion via HIF-2α pathways in clear cell renal cell carcinoma cells link: https://peerj.com/articles/10149 last-modified: 2020-10-14 description: Long non-coding RNAs (lncRNAs) have been proved to have an important role in different malignancies including clear cell renal cell carcinoma (ccRCC). However, their role in disease progression is still not clear. The objective of the study was to identify lncRNA-based prognostic biomarkers and further to investigate the role of one lncRNA LINC01234 in progression of ccRCC cells. We found that six adverse prognostic lncRNA biomarkers including LINC01234 were identified in ccRCC patients by bioinformatic analysis using The Cancer Genome Atlas database. LINC01234 knockdown impaired cell proliferation, migration and invasion in vitro as compared to negative control. Furthermore, the epithelial-mesenchymal transition was inhibited after LINC01234 knockdown. Additionally, LINC01234 knockdown impaired hypoxia-inducible factor-2a (HIF-2α) pathways, including a suppression of the expression of HIF-2α, vascular endothelial growth factor A, epidermal growth factor receptor, c-Myc, Cyclin D1 and MET. Together, these datas showed that LINC01234 was likely to regulate the progression of ccRCC by HIF-2α pathways, and LINC01234 was both a promising prognostic biomarker and a potential therapeutic target for ccRCC. creator: Feilong Yang creator: Cheng Liu creator: Guojiang Zhao creator: Liyuan Ge creator: Yimeng Song creator: Zhigang Chen creator: Zhuo Liu creator: Kai Hong creator: Lulin Ma uri: https://doi.org/10.7717/peerj.10149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems link: https://peerj.com/articles/9732 last-modified: 2020-10-13 description: Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive effect on fungal communities in winter wheat crops. creator: Sigisfredo Garnica creator: Ronja Rosenstein creator: Max Emil Schön uri: https://doi.org/10.7717/peerj.9732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Garnica et al. title: Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat link: https://peerj.com/articles/9849 last-modified: 2020-10-13 description: The pathology of cerebrovascular disorders, such as hypertension, is associated with genetic changes and dysfunction of basilar artery smooth muscle cells (BASMCs). Long-term high-salt diets have been associated with the development of hypertension. However, the molecular mechanisms underlying salt-sensitive hypertension-induced BASMC modifications have not been well defined, especially at the level of variations in gene transcription. Here, we utilized high-throughput sequencing and subsequent signaling pathway analyses to find a two–fold change or greater upregulated expression of 203 transcripts and downregulated expression of 165 transcripts in BASMCs derived from rats fed a high-salt diet compared with those from control rats. These differentially expressed transcripts were enriched in pathways involved in cellular, morphological, and structural plasticity, autophagy, and endocrine regulation. These transcripts changes in the BASMCs derived from high-salt intake–induced hypertensive rats may provide critical information about multiple cellular processes and biological functions that occur during the development of cerebrovascular disorders and provide potential new targets to help control or block the development of hypertension. creator: Junhao Huang creator: Lesha Zhang creator: Yang Fang creator: Wan Jiang creator: Juan Du creator: Jinhang Zhu creator: Min Hu creator: Bing Shen uri: https://doi.org/10.7717/peerj.9849 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports link: https://peerj.com/articles/9924 last-modified: 2020-10-13 description: BackgroundMany scholarly journals have established their own data-related policies, which specify their enforcement of data sharing, the types of data to be submitted, and their procedures for making data available. However, except for the journal impact factor and the subject area, the factors associated with the overall strength of the data sharing policies of scholarly journals remain unknown. This study examines how factors, including impact factor, subject area, type of journal publisher, and geographical location of the publisher are related to the strength of the data sharing policy.MethodsFrom each of the 178 categories of the Web of Science’s 2017 edition of Journal Citation Reports, the top journals in each quartile (Q1, Q2, Q3, and Q4) were selected in December 2018. Of the resulting 709 journals (5%), 700 in the fields of life, health, and physical sciences were selected for analysis. Four of the authors independently reviewed the results of the journal website searches, categorized the journals’ data sharing policies, and extracted the characteristics of individual journals. Univariable multinomial logistic regression analyses were initially conducted to determine whether there was a relationship between each factor and the strength of the data sharing policy. Based on the univariable analyses, a multivariable model was performed to further investigate the factors related to the presence and/or strength of the policy.ResultsOf the 700 journals, 308 (44.0%) had no data sharing policy, 125 (17.9%) had a weak policy, and 267 (38.1%) had a strong policy (expecting or mandating data sharing). The impact factor quartile was positively associated with the strength of the data sharing policies. Physical science journals were less likely to have a strong policy relative to a weak policy than Life science journals (relative risk ratio [RRR], 0.36; 95% CI [0.17–0.78]). Life science journals had a greater probability of having a weak policy relative to no policy than health science journals (RRR, 2.73; 95% CI [1.05–7.14]). Commercial publishers were more likely to have a weak policy relative to no policy than non-commercial publishers (RRR, 7.87; 95% CI, [3.98–15.57]). Journals by publishers in Europe, including the majority of those located in the United Kingdom and the Netherlands, were more likely to have a strong data sharing policy than a weak policy (RRR, 2.99; 95% CI [1.85–4.81]).ConclusionsThese findings may account for the increase in commercial publishers’ engagement in data sharing and indicate that European national initiatives that encourage and mandate data sharing may influence the presence of a strong policy in the associated journals. Future research needs to explore the factors associated with varied degrees in the strength of a data sharing policy as well as more diverse characteristics of journals related to the policy strength. creator: Jihyun Kim creator: Soon Kim creator: Hye-Min Cho creator: Jae Hwa Chang creator: Soo Young Kim uri: https://doi.org/10.7717/peerj.9924 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kim et al. title: Plasma miRNA profiles associated with stable warfarin dosage in Chinese patients link: https://peerj.com/articles/9995 last-modified: 2020-10-13 description: BackgroundWe used bioinformatic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays to investigate the association between plasma microRNAs (miRNAs) and stable warfarin dosage in a Chinese Han population.MethodsBioinformatics analysis was used to screen out potential warfarin dose-associated miRNAs. Three plasma miRNAs were validated in 99 samples by RT-qPCR. Kruskal–Wallis test and multivariate logistic regression were used to compare differences in plasma miRNAs expression levels between three warfarin dosage groups.ResultsThere were significant between-group differences among the three dose groups for hsa-miR-133b expression (p = 0.005), but we observed an “n-shaped” dose-dependent curve rather than a linear relationship. Expression levels of hsa-miR-24-3p (p = 0.475) and hsa-miR-1276 (p = 0.558) were not significantly different in the multivariate logistic regression.ConclusionmiRNAs have received extensive attention as ideal biomarkers and possible therapeutic targets for various diseases. However, they are not yet widely used in precision medicine. Our results indicate that hsa-miR-133b may be a possible reference factor for the warfarin dosage algorithm. These findings emphasize the importance of a comprehensive evaluation of complex relationships in warfarin dose prediction models and provide new avenues for future pharmacogenomics studies. creator: Li Zhao creator: Jin Wang creator: Shaoxin Shi creator: Yuan Wu creator: Jumei Liu creator: Shiwei He creator: Yue Zou creator: Huabin Xie creator: Shengxiang Ge creator: Huiming Ye uri: https://doi.org/10.7717/peerj.9995 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al.