title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1288 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Prevalence of near-death experiences in people with and without REM sleep intrusion link: https://peerj.com/articles/7585 last-modified: 2019-08-27 description: BackgroundThe origin and prevalence of near-death experiences are unknown. A recent study suggested a link with REM sleep intrusion but was criticized for its selection of control participants. We therefore assessed the association of REM intrusion and near-death experiences with different methods.MethodsUsing a crowd-sourcing platform, we recruited 1,034 lay people from 35 countries to investigate the prevalence of near-death experiences and self-reported REM sleep intrusion. Reports were validated using the Greyson Near-Death Experiences Scale (GNDES) with ≥7 points as cut-off for near-death experiences.ResultsNear-death experiences were reported by 106 of 1,034 participants (10%; 95% CI [8.5–12%]). Evidence of REM intrusion was more common in people with near-death experiences (n = 50∕106; 47%) than in people with experiences with 6 points or less on the GNDES (n = 47∕183; 26%) or in those without such experiences (n = 107∕744; 14%; p =  < 0.0001). Following multivariate regression analysis to adjust for age, gender, place of residence, employment and perceived danger, this association remained highly significant; people with REM intrusion were more likely to exhibit near-death experiences than those without (OR 2.85; 95% CI [1.68–4.88]; p = 0.0001).DiscussionUsing a crowd-sourcing approach, we found a prevalence of near-death experiences of 10%. While age, gender, place of residence, employment status and perceived threat do not seem to influence the prevalence of near-death experiences, we confirmed a possible association with REM sleep intrusion. creator: Daniel Kondziella creator: Jens P. Dreier creator: Markus Harboe Olsen uri: https://doi.org/10.7717/peerj.7585 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kondziella et al. title: Insights from the proteome profile of Phytophthora capsici in response to the novel fungicide SYP-14288 link: https://peerj.com/articles/7626 last-modified: 2019-08-27 description: Phytophthora capsica is a destructive oomycete plant pathogen that causes huge losses to crop production worldwide. However, the novel fungicide SYP-14288 has shown excellent activity against various stages of the oomycete life cycle as well against fungal plant pathogens. The current study utilized isobaric tags for relative and absolute quantitation technology to generate proteome profiles of P. capsici in the presence or absence of SYP-14288 in order to gain a greater understanding of the SYP-14288 mode of action. A total of 1,443 individual proteins were identified during the investigation, of which 599 were considered to have significantly altered expression. Further investigation using Cluster of Orthologous Groups of proteins analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated most of the proteins with altered expression were associated with carbohydrate metabolism, energy metabolism and their downstream biological functions, especially with regard to oxidoreductase activity and subsequent adenosine triphosphate (ATP) production associated pathways. Quantitative expression analysis using qRT-PCR validated the proteomic data. These results seem to indicate that SYP-14288 treatment caused a shift in energy metabolism that resulted in the activation of compensatory mechanisms affecting carbohydrate and lipid metabolism. The study also found evidence that the up-regulation of transmembrane transporters and proteins associated with stress response might also be coopted to compensate for the disrupted proton gradient and other downstream effects. Taken together these results provide strong evidence that SYP-14288 has a similar mode of action to the oxidative phosphorylation uncoupler Fluazinam but further investigation, including molecular studies, is required to completely characterize the SYP-14288 mode of action in P. capsici. However, the proteomic data collected in the current study does provide important insight into the overall effect of SYP-14288 in P. capsici, which could be useful for the registration and application of this novel fungicide. creator: Meng Cai creator: Zhiwen Wang creator: Xiaoxia Ni creator: Yanhua Hou creator: Qin Peng creator: Xiang Gao creator: Xili Liu uri: https://doi.org/10.7717/peerj.7626 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cai et al. title: Filter feeding in Late Jurassic pterosaurs supported by coprolite contents link: https://peerj.com/articles/7375 last-modified: 2019-08-26 description: Diets of pterosaurs have mainly been inferred from indirect evidence such as comparative anatomy, associations of co-occurring fossils, and functional morphology. Gut contents are rare, and until now there is only a single coprolite (fossil dropping), with unidentified inclusions, known. Here we describe three coprolites collected from a palaeosurface with numerous pterosaur tracks found in early Kimmeridgian (Hypselocyclum Zone) intertidal deposits of the Wierzbica Quarry, Poland. The specimens’ morphology and association to the tracks suggest a pterosaur producer. Synchrotron scans reveal numerous small inclusions, with foraminifera making up the majority of the identifiable ones. Other small remains include shells/carapaces (of bivalves, ostracods, and other crustaceans/arthropods) and bristles (some possibly of polychaete worms). The high density of the small shelly inclusions suggest that they were not accidently ingested, but constituted an important food source for the pterosaur(s), perhaps together with unpreserved soft-bodied animals. The combined evidence from the tracks and coprolites suggest a filter-feeding ctenochasmatid as the most likely tracemaker. If true, this significantly expands the bromalite record for this pterosaur group, which was previously only known from gastroliths. Moreover, this study also provides the first direct evidence of filter feeding in Jurassic pterosaurs and shows that they had a similar diet to the recent Chilean flamingo (Phoenicopterus chilensis). creator: Martin Qvarnström creator: Erik Elgh creator: Krzysztof Owocki creator: Per E. Ahlberg creator: Grzegorz Niedźwiedzki uri: https://doi.org/10.7717/peerj.7375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qvarnström et al. title: The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations link: https://peerj.com/articles/7447 last-modified: 2019-08-26 description: BackgroundThe RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes.ResultsWe demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses.ConclusionThis software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses. creator: Stephanie van Wyk creator: Christopher H. Harrison creator: Brenda D. Wingfield creator: Lieschen De Vos creator: Nicolaas A. van der Merwe creator: Emma T. Steenkamp uri: https://doi.org/10.7717/peerj.7447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 van Wyk et al. title: Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer link: https://peerj.com/articles/7451 last-modified: 2019-08-26 description: BackgroundBecause of the increasing dysplasia rate in the lifelong course of inflammatory bowel disease (IBD) patients, it is imperative to characterize the crosstalk between IBD and colorectal cancer (CRC). However, there have been no reports revealing the occurrence of the ceRNA network in IBD-related CRC.MethodsIn this study, we conducted gene expression profile studies of databases and performed an integrated analysis to detect the potential of lncRNA-miRNA-mRNA ceRNA in regulating disease transformation. R packages were used to screen differentially expressed mRNA, lncRNA and miRNA among CRC, IBD and normal tissue. The lncRNA-miRNA-mRNA network was constructed based on predicted miRNA-targeted lncRNAs and miRNA-targeted mRNAs. Functional analyses were then conducted to identify genes involved in the ceRNA network, and key lncRNAs were evaluated based on several clinical outcomes.ResultsA total of three lncRNAs, 15 miRNAs, and 138 mRNAs were identified as potential mediators in the pathophysiological processes of IBD-related CRC. Gene Ontology annotation enrichment analysis confirmed that the dysplasia process was strongly associated with immune response, response to lipopolysaccharide, and inflammatory response. Survival analysis showed that LINC01106 (HR = 1.7; p < 0.05) were strongly associated with overall survival of colorectal cancer patients. The current study identified a series of IBD-related mRNAs, miRNA, and lncRNAs, and highlighted the important role of ceRNAs in the pathogenesis of IBD-related CRC. Among them, the LINC01106-miRNA-mRNA axis was identified as vital targets for further research. creator: Fangfang Sun creator: Weiwei Liang creator: Kejun Tang creator: Mengying Hong creator: Jing Qian uri: https://doi.org/10.7717/peerj.7451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sun et al. title: Effectiveness of small road tunnels and fences in reducing amphibian roadkill and barrier effects at retrofitted roads in Sweden link: https://peerj.com/articles/7518 last-modified: 2019-08-26 description: Schemes to reduce road impacts on amphibians have been implemented for decades in Europe, yet, several aspects on the effectiveness of such schemes remain poorly understood. Particularly in northern Europe, including Sweden, there is a lack of available information on road mitigation for amphibians, which is hampering implementation progress and cost-effectiveness analyses of mitigation options. Here, we present data derived from systematic counts of amphibians during spring migration at three previous hot-spots for amphibian roadkill in Sweden, where amphibian tunnels with guiding fences have been installed. We used the data in combination with a risk model to estimate the number of roadkills and successful crossings before vs. after mitigation and mitigated vs. adjacent non-mitigated road sections. In mitigated road sections, the estimated number of amphibians killed or at risk of being killed by car traffic decreased by 85–100% and the estimated number successfully crossing the road increased by 25–340%. Data, however, suggested fence-end effects that may moderate the reduction in roadkill. We discuss possible explanations for the observed differences between sites and construction types, and implications for amphibian conservation. We show how effectiveness estimates can be used for prioritizing amphibian passages along the existing road network. Finally, we emphasize the importance of careful monitoring of amphibian roadkill and successful crossings before and after amphibian passages are constructed. creator: Jan Olof Helldin creator: Silviu O. Petrovan uri: https://doi.org/10.7717/peerj.7518 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Helldin and Petrovan title: Detecting the impact of land cover change on observed rainfall link: https://peerj.com/articles/7523 last-modified: 2019-08-26 description: Analysis of observational data to pinpoint impact of land cover change on local rainfall is difficult due to multiple environmental factors that cannot be strictly controlled. In this study we use a statistical approach to identify the relationship between removal of tree cover and rainfall with data from best available sources for two large areas in Australia. Gridded rainfall data between 1979 and 2015 was used for the areas, while large scale (exogenous) effects were represented by mean rainfall across a much larger area and climatic indicators, such as Southern Oscillation Index and Indian Ocean Dipole. Both generalised additive modelling and step trend tests were used for the analysis. For a region in south central Queensland, the reported change in tree clearing between 2002–2005 did not result in strong statistically significant precipitation changes. On the other hand, results from a bushfire affected region on the border of New South Wales and Victoria suggest significant changes in the rainfall due to changes in tree cover. This indicates the method works better when an abrupt change in the data can be clearly identified. The results from the step trend test also mainly identified a positive relationship between the tree cover and the rainfall at p < 0.1 at the NSW/Victoria region. High rainfall variability and possible regrowth could have impacted the results in the Queensland region. creator: Chun Xia Liang creator: Floris F. van Ogtrop creator: R. Willem Vervoort uri: https://doi.org/10.7717/peerj.7523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liang et al. title: Three new species, one new genus and subfamily of Dorylaimida (de Man, 1876) Pearse, 1942, and revisions on the families Tylencholaimellidae Jairajpuri, 1964 and Mydonomidae Thorne, 1964 (Nematoda: Dorylaimida) link: https://peerj.com/articles/7541 last-modified: 2019-08-26 description: Three new species of the order Dorylaimida (de Man, 1876) Pearse, 1942 were identified and described. Paratylencholaimus sanshaensis gen. nov. sp. nov. from Hainan is proposed as a new member of the family Tylencholaimellidae Jairajpuri, 1964. Paratylencholaimus gen. nov. is close to Phellonema Thorne, 1964 and Goferus Jairajpuri & Ahmad, 1992 but can be differentiated mainly by having basal part of odontophore rod-like and without knobs, and basal part of pharynx expanded gradually. Tylencholaimus zhongshanensis sp. nov. from Guangdong and Dorylaimoides shapotouensis sp. nov. from the Ningxia Hui Autonomous Region are also described herein. Phylogenetic analyses based on the 18S rDNA and the D2–D3 region of the 28S rDNA support that the three new species are valid. The classifications of the families Tylencholaimellidae and Mydonomidae Thorne, 1964 are revised mainly based on the analysis of the morphology of odontostyle and odontophore. After these revisions, Paratylencholaiminae subfam. nov. including Paratylencholaimus gen. nov. and Goferus is proposed. Athernema and Agmodorus of Tylencholaimellidae are transferred into Mydonomidae, and the subfamily Athernematinae of Tylencholaimellidae is dismissed. The main characteristics of the family Mydonomidae and Tylencholaimellidae are revised. Keys to the genera of Mydomonidae and Tylencholaimellidae are included. creator: Wen-Jia Wu creator: Chun-Ling Xu creator: Hui Xie creator: Dong-Wei Wang uri: https://doi.org/10.7717/peerj.7541 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wu et al. title: Cell-free supernatants from cultures of lactic acid bacteria isolated from fermented grape as biocontrol against Salmonella Typhi and Salmonella Typhimurium virulence via autoinducer-2 and biofilm interference link: https://peerj.com/articles/7555 last-modified: 2019-08-26 description: BackgroundSalmonella Typhi and Salmonella Typhimurium are the causative pathogens of salmonellosis, and they are mostly found in animal source foods (ASF). The inappropriate use of antibiotics enhances the possibility for the emergence of antibiotic resistance in pathogens and antibiotic residue in ASF. One promising alternative to antibiotics in animal farming is the use of lactic acid bacteria (LAB).MethodsThe present study was carried out the cells and/or the cell-free culture supernatants (CFCS) from beneficial LAB against S. Typhi and S. Typhimurium. The antibacterial mechanisms of LAB-CFCS as biocontrol agents against both Salmonella serovars were investigated through the analysis of anti-salmonella growth activity, biofilm inhibition and quorum quenching activity.ResultsAmong 146 LAB strains isolated from 110 fermented food samples, the 2 strong inhibitory effect strains (WM33 and WM36) from fermented grapes against both Salmonella serovars were selected. Out of the selected strains, WM36 was the most effective inhibitor, which indicated S. Typhi by showing 95.68% biofilm inhibition at 20% biofilm inhibition concentration (BIC) and reduced 99.84% of AI-2 signaling interference. The WM33 was the best to control S. Typhimurium by producing 66.46% biofilm inhibition at only 15% BIC and 99.99% AI-2 signaling a reduction. The 16S rDNA was amplified by a polymerase chain reaction (PCR). The selected isolates were identified as Weissella viridescens WM33 and Weissella confusa WM36 based on nucleotide homology and phylogenetic analysis.ConclusionThe metabolic extracts from Weissella spp. inhibit Salmonella serovars with the potential to be used as biocontrol agents to improve microbiological safety in the production of ASF. creator: Wattana Pelyuntha creator: Chaiyavat Chaiyasut creator: Duangporn Kantachote creator: Sasithorn Sirilun uri: https://doi.org/10.7717/peerj.7555 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pelyuntha et al. title: Association between serum uric acid and nonalcoholic fatty liver disease in community patients with type 2 diabetes mellitus link: https://peerj.com/articles/7563 last-modified: 2019-08-26 description: BackgroundTo investigate whether SUA is associated with NAFLD in men and women with T2DM.MethodsThis cross-sectional study enrolled patients with T2DM at Shanxi High-Tech Development Zone Central Hospital (June 2011 to September 2017). Patients were stratified according to gender and presence/absence of NAFLD. Parameters associated with NAFLD were identified using multivariate stepwise linear regression and univariate/multivariate logistic regression.ResultsAmong 597 patients (325 males) enrolled, 352 had NAFLD. SUA was higher in the NAFLD group than in the non-NAFLD group for both men and women (P < 0.001). Multiple linear regression showed that body mass index (positively), triglycerides (positively) and estimated glomerular filtration rate (negatively) were independently related to SUA (P < 0.001). Univariate logistic regression revealed increased odds of NAFLD for SUA tertiles 2 (P = 0.022) and 3 (P = 0.001) in women and tertile 3 (P = 0.039) in men. After adjustment for multiple clinical parameters, SUA tertiles were significantly associated with NAFLD for tertile 3 in women (P = 0.014), although there were trends toward associations for tertile 2 in women (P = 0.074) and tertiles 2 and 3 in men (P = 0.085 and 0.054, respectively).ConclusionSUA is not independently associated with NAFLD in men or women with T2DM after rigorous adjustment for other metabolic parameters. creator: Linxin Xu creator: Ting Li creator: Jianhong Yin creator: Gang Lin creator: Yali Xu creator: Yi Ren creator: Yan Wang creator: Jing Yang creator: Liming Chen uri: https://doi.org/10.7717/peerj.7563 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu et al.