title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1416 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Nursing knowledge of and attitude in cardiopulmonary arrest: cross-sectional survey analysis link: https://peerj.com/articles/6410 last-modified: 2019-02-07 description: BackgroundNurses are often the first to activate the chain of survival when a cardiorespiratory arrest happens. That is why it is crucial that they keep their knowledge and skills up-to-date and their attitudes to resuscitation are very important. The main aim of this study was to analyse whether the level of theoretical and practical understanding affected the attitudes of nursing staff.MethodsA questionnaire was designed using the Delphi technique (three rounds). The questionnaire was adjusted and it was piloted on a test-retest basis with a convenience sample of 30 registered nurses. The psychometric characteristics were evaluated using a sample of 347 nurses using Cronbach’s alpha. Descriptive analysis was performed to describe the sociodemographic variables and Spearman’s correlation coefficient to assess the relationship between two scale variables. Pearson’s chi-squared test has been used to study the relationship between two categorical variables. Wilcoxon Mann Whitney test and the Kruskal–Wallis test were performed to establish relationships between the demographic/work related characteristics and the level of understanding.ResultsThe Knowledge and Attitude of Nurses in the Event of a Cardiorespiratory Arrest (CAEPCR) questionnaire comprised three sections: sociodemographic information, theoretical and practical understanding, and attitudes of ethical issues. Cronbach’s alpha for the internal consistency of the attitudes questionnaire was 0.621. The knowledge that nurses self-reported with regard to cardiopulmonary arrest directly affected their attitudes. Their responses raised a number of bioethical issues.ConclusionsCAEPCR questionnaire is the first one which successfully linked knowledge of cardiopulmonary resuscitation to the attitudes towards ethical issues Health policies should ensure that CPR training is mandatory for nurses and all healthcare workers, and this training should include the ethical aspects. creator: Verónica Tíscar-González creator: Joan Blanco-Blanco creator: Montserrat Gea-Sánchez creator: Ascensión Rodriguez Molinuevo creator: Teresa Moreno-Casbas uri: https://doi.org/10.7717/peerj.6410 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tíscar-González et al. title: Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure link: https://peerj.com/articles/6154 last-modified: 2019-02-06 description: NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis. creator: Ivan Koludarov creator: Steven D. Aird uri: https://doi.org/10.7717/peerj.6154 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Koludarov and Aird title: A survey on zoo mortality over a 12-year period in Italy link: https://peerj.com/articles/6198 last-modified: 2019-02-06 description: BackgroundThe zoo is a unique environment in which to study animals. Zoos have a long history of research into aspects of animal biology, even if this was not the primary purpose for which they were established. The data collected from zoo animals can have a great biological relevance and it can tell us more about what these animals are like outside the captive environment. In order to ensure the health of all captive animals, it is important to perform a post-mortem examination on all the animals that die in captivity.MethodsThe causes of mortality of two hundred and eighty two mammals which died between 2004 and 2015 in three different Italian zoos (a Biopark, a Safari Park and a private conservation center) have been investigated.ResultsPost mortem findings have been evaluated reporting the cause of death, zoo type, year and animal category. The animals frequently died from infectious diseases, in particular the causes of death in ruminants were mostly related to gastro-intestinal pathologies. pulmonary diseases were also very common in each of the zoos in the study. Moreover, death was sometimes attributable to traumas, as a result of fighting between conspecifics or during mating. Cases of genetic diseases and malformations have also been registered.DiscussionThis research was a confirmation of how conservation, histology and pathology are all connected through individual animals. These areas of expertise are extremely important to ensure the survival of rare and endangered species and to learn more about their morphological and physiological conditions. They are also useful to control pathologies, parasites and illnesses that can have a great impact on the species in captivity. Finally, this study underlines the importance of a close collaboration between veterinarians, zoo biologists and pathologists. Necropsy findings can help conservationists to determine how to support wild animal populations. creator: Frine Eleonora Scaglione creator: Cristina Biolatti creator: Paola Pregel creator: Enrica Berio creator: Francesca Tiziana Cannizzo creator: Bartolomeo Biolatti creator: Enrico Bollo uri: https://doi.org/10.7717/peerj.6198 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Scaglione et al. title: Turtles of the genera Geoemyda and Pangshura (Testudines: Geoemydidae) lack differentiated sex chromosomes: the end of a 40-year error cascade for Pangshura link: https://peerj.com/articles/6241 last-modified: 2019-02-06 description: For a long time, turtles of the family Geoemydidae have been considered exceptional because representatives of this family were thought to possess a wide variety of sex determination systems. In the present study, we cytogenetically studied Geoemyda spengleri and G. japonica and re-examined the putative presence of sex chromosomes in Pangshura smithii. Karyotypes were examined by assessing the occurrence of constitutive heterochromatin, by comparative genome hybridization and in situ hybridization with repetitive motifs, which are often accumulated on differentiated sex chromosomes in reptiles. We found similar karyotypes, similar distributions of constitutive heterochromatin and a similar topology of tested repetitive motifs for all three species. We did not detect differentiated sex chromosomes in any of the species. For P. smithii, a ZZ/ZW sex determination system, with differentiated sex chromosomes, was described more than 40 years ago, but this finding has never been re-examined and was cited in all reviews of sex determination in reptiles. Here, we show that the identification of sex chromosomes in the original report was based on the erroneous pairing of chromosomes in the karyogram, causing over decades an error cascade regarding the inferences derived from the putative existence of female heterogamety in geoemydid turtles. creator: Sofia Mazzoleni creator: Barbora Augstenová creator: Lorenzo Clemente creator: Markus Auer creator: Uwe Fritz creator: Peter Praschag creator: Tomáš Protiva creator: Petr Velenský creator: Lukáš Kratochvíl creator: Michail Rovatsos uri: https://doi.org/10.7717/peerj.6241 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mazzoleni et al. title: kuenm: an R package for detailed development of ecological niche models using Maxent link: https://peerj.com/articles/6281 last-modified: 2019-02-06 description: BackgroundEcological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way.ResultsThis package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric.DiscussionUse of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes. creator: Marlon E. Cobos creator: A. Townsend Peterson creator: Narayani Barve creator: Luis Osorio-Olvera uri: https://doi.org/10.7717/peerj.6281 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cobos et al. title: The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes link: https://peerj.com/articles/6343 last-modified: 2019-02-06 description: In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or high-degree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D. creator: Keren Jia creator: Yingcheng Wu creator: Jingyi Ju creator: Liyang Wang creator: Lili Shi creator: Huiqun Wu creator: Kui Jiang creator: Jiancheng Dong uri: https://doi.org/10.7717/peerj.6343 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jia et al. title: Species turnover reveals hidden effects of decreasing nitrogen deposition in mountain hay meadows link: https://peerj.com/articles/6347 last-modified: 2019-02-06 description: Nitrogen (N) deposition is a major threat to biodiversity in many habitats. The recent introduction of cleaner technologies in Switzerland has led to a reduction in the emissions of nitrogen oxides, with a consequent decrease in N deposition. We examined different drivers of plant community change, that is, N deposition, climate warming, and land-use change, in Swiss mountain hay meadows, using data from the Swiss biodiversity monitoring program. We compared indicator values of species that disappeared from or colonized a site (species turnover) with the indicator values of randomly chosen species from the same site. While oligotrophic plant species were more likely to colonize, compared to random expectation, we found only weak shifts in plant community composition. In particular, the average nutrient value of plant communities remained stable over time (2003–2017). We found the largest deviations from random expectation in the nutrient values of colonizing species, suggesting that N deposition or other factors that change the nutrient content of soils were important drivers of the species composition change over the last 15 years in Swiss mountain hay meadows. In addition, we observed an overall replacement of species with lower indicator values for temperature with species with higher values. Apparently, the community effects of the replacement of eutrophic species with oligotrophic species was outweighed by climate warming. Our results add to the increasing evidence that plant communities in changing environments may be relatively stable regarding average species richness or average indicator values, but that this apparent stability is often accompanied by a marked turnover of species. creator: Tobias Roth creator: Lukas Kohli creator: Christoph Bühler creator: Beat Rihm creator: Reto Giulio Meuli creator: Reto Meier creator: Valentin Amrhein uri: https://doi.org/10.7717/peerj.6347 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Roth et al. title: Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis link: https://peerj.com/articles/6375 last-modified: 2019-02-06 description: BackgroundAlcohol-related hepatocellular carcinoma (HCC) was reported to be diagnosed at a later stage, but the mechanism was unknown. This study aimed to identify special key genes (SKGs) during alcohol-related HCC development and progression.MethodsThe mRNA data of 369 HCC patients and the clinical information were downloaded from the Cancer Genome Atlas project (TCGA). The 310 patients with certain HCC-related risk factors were included for analysis and divided into seven groups according to the risk factors. Survival analyses were applied for the HCC patients of different groups. The patients with hepatitis B virus or hepatitis C virus infection only were combined into the HCC-V group for further analysis. The differentially expressed genes (DEGs) between the HCCs with alcohol consumption only (HCC-A) and HCC-V tumors were identified through limma package in R with cutoff criteria│log2 fold change (logFC)|>1.0 and p < 0.05. The DEGs between eight alcohol-related HCCs and their paired normal livers of GSE59259 from the Gene Expression Omnibus (GEO) were identified through GEO2R (a built-in tool in GEO database) with cutoff criteria |logFC|> 2.0 and adj.p < 0.05. The intersection of the two sets of DEGs was considered SKGs which were then investigated for their specificity through comparisons between HCC-A and other four HCC groups. The SKGs were analyzed for their correlations with HCC-A stage and grade and their prognostic power for HCC-A patients. The expressional differences of the SKGs in the HCCs in whole were also investigated through Gene Expression Profiling Interactive Analysis (GEPIA). The SKGs in HCC were validated through Oncomine database analysis.ResultsPathological stage is an independent prognostic factor for HCC patients. HCC-A patients were diagnosed later than HCC patients with other risk factors. Ten SKGs were identified and nine of them were confirmed for their differences in paired samples of HCC-A patients. Three (SLC22A10, CD5L, and UROC1) and four (SLC22A10, UROC1, CSAG3, and CSMD1) confirmed genes were correlated with HCC-A stage and grade, respectively. SPP2 had a lower trend in HCC-A tumors and was negatively correlated with HCC-A stage and grade. The SKGs each was differentially expressed between HCC-A and at least one of other HCC groups. CD5L was identified to be favorable prognostic factor for overall survival while CSMD1 unfavorable prognostic factor for disease-free survival for HCC-A patients and HCC patients in whole. Through Oncomine database, the dysregulations of the SKGs in HCC and their clinical significance were confirmed.ConclusionThe poor prognosis of HCC-A patients might be due to their later diagnosis. The SKGs, especially the four stage-correlated genes (CD5L, SLC22A10, UROC1, and SPP2) might play important roles in HCC development, especially alcohol-related HCC development and progression. CD5L might be useful for overall survival and CSMD1 for disease-free survival predication in HCC, especially alcohol-related HCC. creator: Xiuzhi Zhang creator: Chunyan Kang creator: Ningning Li creator: Xiaoli Liu creator: Jinzhong Zhang creator: Fenglan Gao creator: Liping Dai uri: https://doi.org/10.7717/peerj.6375 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient link: https://peerj.com/articles/6379 last-modified: 2019-02-06 description: BackgroundEffective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna.MethodsWe here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA.ResultsUsing 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases.DiscussionOverall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance. creator: Joseph D. DiBattista creator: James D. Reimer creator: Michael Stat creator: Giovanni D. Masucci creator: Piera Biondi creator: Maarten De Brauwer creator: Michael Bunce uri: https://doi.org/10.7717/peerj.6379 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 DiBattista et al. title: Genetic alteration of histone lysine methyltransferases and their significance in renal cell carcinoma link: https://peerj.com/articles/6396 last-modified: 2019-02-06 description: BackgroundHistone lysine methyltransferases (HMTs), a category of enzymes, play essential roles in regulating transcription, cellular differentiation, and chromatin construction. The genomic landscape and clinical significance of HMTs in renal cell carcinoma (RCC) remain uncovered.MethodsWe conducted an integrative analysis of 50 HMTs in RCC and discovered the internal relations among copy number alterations (CNAs), expressive abundance, mutations, and clinical outcome.ResultsWe confirmed 12 HMTs with the highest frequency of genetic alterations, including seven HMTs with high-level amplification, two HMTs with somatic mutation, and three HMTs with putative homozygous deletion. Patterns of copy number and expression varied among different subtypes of RCC, including clear cell renal cell carcinoma, papillary cell carcinoma, and chromophobe renal carcinoma. Kaplan–Meier survival analysis and multivariate analysis identified that CNA or mRNA expression in some HMTs were significantly associated with shorter overall patient survival. Systematic analysis identified six HMTs (ASH1L, PRDM6, NSD1, EZH2, WHSC1L1, SETD2) which were dysregulated by genetic alterations as candidate therapeutic targets.DiscussionIn summary, our findings strongly evidenced that genetic alteration of HMTs may play an important role in generation and development of RCC, which lays a solid foundation for the mechanism for further research in the future. creator: Libin Yan creator: Yangjun Zhang creator: Beichen Ding creator: Hui Zhou creator: Weimin Yao creator: Hua Xu uri: https://doi.org/10.7717/peerj.6396 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yan et al.