title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=288 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury link: https://peerj.com/articles/17333 last-modified: 2024-06-25 description: Acute heart attack is the primary cause of cardiovascular-related death worldwide. A common treatment is reperfusion of ischemic tissue, which can cause irreversible damage to the myocardium. The number of mitochondria in cardiomyocytes is large, which generate adenosine triphosphate (ATP) to sustain proper cardiac contractile function, and mitochondrial dysfunction plays a crucial role in cell death during myocardial ischemia-reperfusion, leading to an increasing number of studies investigating the impact of mitochondria on ischemia-reperfusion injury. The disarray of mitochondrial dynamics, excessive Ca2+ accumulation, activation of mitochondrial permeable transition pores, swelling of mitochondria, ultimately the death of cardiomyocyte are the consequences of ischemia-reperfusion injury. κ-opioid receptors can alleviate mitochondrial dysfunction, regulate mitochondrial dynamics, mitigate myocardial ischemia-reperfusion injury, exert protective effects on myocardium. The mechanism of κ-OR activation during myocardial ischemia-reperfusion to regulate mitochondrial dynamics and reduce myocardial ischemia-reperfusion injury will be discussed, so as to provide theoretical basis for the protection of ischemic myocardium. creator: Wen Zhang creator: Qi Zhang creator: Yali Liu creator: Jianming Pei creator: Na Feng uri: https://doi.org/10.7717/peerj.17333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow link: https://peerj.com/articles/17367 last-modified: 2024-06-25 description: Turbidity flows can transport massive amounts of sediment across large distances with dramatic, long-lasting impacts on deep-sea benthic communities. The 2016 Mw 7.8 Kaikōura Earthquake triggered a canyon-flushing event in Kaikōura Canyon, New Zealand, which included significant submarine mass wasting, debris, and turbidity flows. This event provided an excellent opportunity to investigate the effects of large-scale natural disturbance on benthic ecosystems. Benthic meiofauna community structure before and after the event was analysed from a time series of sediment cores collected 10 years and 6 years before, and 10 weeks, 10 months, and 4 years after the disturbance. Immediately after the 2016 event abundances of all meiofauna dramatically decreased. Four years later the meiofauna community had recovered and was no longer distinguishable from the pre-event community. However, the nematode component of the community was similar, but not fully comparable to the pre-event community by 4 years after the disturbance. Community recovery was systematically correlated to changes in the physical characteristics of the habitat caused by the disturbance, using physical and biochemical variables derived from sediment cores, namely: sediment texture, organic matter, and pigment content. While these environmental variables explained relatively little of the overall variability in meiofauna community structure, particle size, food availability and quality were significant components. The minimum threshold time for the meiofauna community to fully recover was estimated to be between 3.9 and 4.7 years, although the predicted recovery time for the nematode community was longer, between 4.6 and 5 years. We consider the management implications of this study in comparison to the few studies of large-scale disturbances in the deep sea, in terms of their relevance to the efficacy of the marine reserve that encompasses Kaikōura Canyon, along with potential implications for our understanding of the impacts of anthropogenic seafloor disturbances, such as seabed mining. creator: Katharine T. Bigham creator: Daniel Leduc creator: Ashley A. Rowden creator: David A. Bowden creator: Scott D. Nodder creator: Alan R. Orpin uri: https://doi.org/10.7717/peerj.17367 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bigham et al. title: TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets link: https://peerj.com/articles/17470 last-modified: 2024-06-25 description: TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X’s predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user’s web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researchers can use to better illuminate understudied proteins. creator: Vincent T. Metzger creator: Daniel C. Cannon creator: Jeremy J. Yang creator: Stephen L. Mathias creator: Cristian G. Bologa creator: Anna Waller creator: Stephan C. Schürer creator: Dušica Vidović creator: Keith J. Kelleher creator: Timothy K. Sheils creator: Lars Juhl Jensen creator: Christophe G. Lambert creator: Tudor I. Oprea creator: Jeremy S. Edwards uri: https://doi.org/10.7717/peerj.17470 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Metzger et al. title: Structured peer review: pilot results from 23 Elsevier journals link: https://peerj.com/articles/17514 last-modified: 2024-06-25 description: BackgroundReviewers rarely comment on the same aspects of a manuscript, making it difficult to properly assess manuscripts’ quality and the quality of the peer review process. The goal of this pilot study was to evaluate structured peer review implementation by: 1) exploring whether and how reviewers answered structured peer review questions, 2) analysing reviewer agreement, 3) comparing that agreement to agreement before implementation of structured peer review, and 4) further enhancing the piloted set of structured peer review questions.MethodsStructured peer review consisting of nine questions was piloted in August 2022 in 220 Elsevier journals. We randomly selected 10% of these journals across all fields and IF quartiles and included manuscripts that received two review reports in the first 2 months of the pilot, leaving us with 107 manuscripts belonging to 23 journals. Eight questions had open-ended fields, while the ninth question (on language editing) had only a yes/no option. The reviews could also leave Comments-to-Author and Comments-to-Editor. Answers were independently analysed by two raters, using qualitative methods.ResultsAlmost all the reviewers (n = 196, 92%) provided answers to all questions even though these questions were not mandatory in the system. The longest answer (Md 27 words, IQR 11 to 68) was for reporting methods with sufficient details for replicability or reproducibility. The reviewers had the highest (partial) agreement (of 72%) for assessing the flow and structure of the manuscript, and the lowest (of 53%) for assessing whether interpretation of the results was supported by data, and for assessing whether the statistical analyses were appropriate and reported in sufficient detail (52%). Two thirds of the reviewers (n = 145, 68%) filled out the Comments-to-Author section, of which 105 (49%) resembled traditional peer review reports. These reports contained a Md of 4 (IQR 3 to 5) topics covered by the structured questions. Absolute agreement regarding final recommendations (exact match of recommendation choice) was 41%, which was higher than what those journals had in the period from 2019 to 2021 (31% agreement, P = 0.0275).ConclusionsOur preliminary results indicate that reviewers successfully adapted to the new review format, and that they covered more topics than in their traditional reports. Individual question analysis indicated the greatest disagreement regarding the interpretation of the results and the conducting and the reporting of statistical analyses. While structured peer review did lead to improvement in reviewer final recommendation agreements, this was not a randomized trial, and further studies should be performed to corroborate this. Further research is also needed to determine whether structured peer review leads to greater knowledge transfer or better improvement of manuscripts. creator: Mario Malički creator: Bahar Mehmani uri: https://doi.org/10.7717/peerj.17514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Malički and Mehmani title: Development and validation of a multi-parameter nomogram for venous thromboembolism in gastric cancer patients: a retrospective analysis link: https://peerj.com/articles/17527 last-modified: 2024-06-25 description: ObjectiveGastric cancer (GC), one of the highest venous thromboembolism (VTE) incidence rates in cancer, contributes to considerable morbidity, mortality, and, prominently, extra cost. However, up to now, there is not a high-quality VTE model to steadily predict the risk for VTE in China. Consequently, setting up a prediction model to predict the VTE risk is imperative.MethodsData from 3,092 patients from December 15, 2017, to December 31, 2022, were retrospectively analyzed. Multiple logistic regression analysis was performed to assess risk factors for GC, and a nomogram was constructed based on screened risk factors. A receiver operating curve (ROC) and calibration plot was created to evaluate the accuracy of the nomogram.ResultsThe risk factors of suffering from VTE were older age (OR = 1.02, 95% CI [1.00–1.04]), Karnofsky Performance Status (KPS) ≥ 70 (OR = 0.45, 95% CI [0.25–0.83]), Blood transfusion (OR = 2.37, 95% CI [1.47–3.84]), advanced clinical stage (OR = 3.98, 95% CI [1.59–9.99]), central venous catheterization (CVC) (OR = 4.27, 95% CI [2.03–8.99]), operation (OR = 2.72, 95% CI [1.55–4.77]), fibrinogen degradation product (FDP) >5 µg/mL (OR = 1.92, 95% CI [1.13–3.25]), and D-dimer > 0.5 mg/L (OR = 2.50, 95% CI [1.19–5.28]). The area under the ROC curve (AUC) was 0.82 in the training set and 0.85 in the validation set.ConclusionOur prediction model can accurately predict the risk of the appearance of VTE in gastric cancer patients and can be used as a robust and efficient tool for evaluating the possibility of VTE. creator: Hang Zhou creator: Haike Lei creator: Huai Zhao creator: Kaifeng Huang creator: Yundong Wang creator: Ruixia Hong creator: Jishun Huo creator: Li Luo creator: Fang Li uri: https://doi.org/10.7717/peerj.17527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Land-cover change in Cuba and implications for the area of distribution of a specialist’s host-plant link: https://peerj.com/articles/17563 last-modified: 2024-06-25 description: Changes in land cover directly affect biodiversity. Here, we assessed land-cover change in Cuba in the past 35 years and analyzed how this change may affect the distribution of Omphalea plants and Urania boisduvalii moths. We analyzed the vegetation cover of the Cuban archipelago for 1985 and 2020. We used Google Earth Engine to classify two satellite image compositions into seven cover types: forest and shrubs, mangrove, soil without vegetation cover, wetlands, pine forest, agriculture, and water bodies. We considered four different areas for quantifications of land-cover change: (1) Cuban archipelago, (2) protected areas, (3) areas of potential distribution of Omphalea, and (4) areas of potential distribution of the plant within the protected areas. We found that “forest and shrubs”, which is cover type in which Omphalea populations have been reported, has increased significantly in Cuba in the past 35 years, and that most of the gained forest and shrub areas were agricultural land in the past. This same pattern was observed in the areas of potential distribution of Omphalea; whereas almost all cover types were mostly stable inside the protected areas. The transformation of agricultural areas into forest and shrubs could represent an interesting opportunity for biodiversity conservation in Cuba. Other detailed studies about biodiversity composition in areas of forest and shrubs gain would greatly benefit our understanding of the value of such areas for conservation. creator: Claudia Nuñez-Penichet creator: Juan Maita creator: Jorge Soberon uri: https://doi.org/10.7717/peerj.17563 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Nuñez-Penichet et al. title: Mechanism of Brevibacillus brevis strain TR-4 against leaf disease of Photinia×fraseri Dress link: https://peerj.com/articles/17568 last-modified: 2024-06-25 description: BackgroundColletotrichum species are among the most common pathogens in agriculture and forestry, and their control is urgently needed.MethodsIn this study, a total of 68 strains of biocontrol bacteria were isolated and identified from Photinia × fraseri rhizosphere soil.ResultsThe isolates were identified as Brevibacillus brevis by 16S rRNA. The inhibitory effect of TR-4 on Colletotrichum was confirmed by an in vitro antagonistic experiment. The inhibitory effect of TR-4 was 98% at a concentration of 10 µl/ml bacterial solution, protection of the plant and inhibition of C. siamense was evident. Moreover, the secretion of cellulase and chitosan enzymes in the TR-4 fermentation liquid cultured for three days was 9.07 mol/L and 2.15 µl/mol, respectively. Scanning electron microscopy and transmission electron microscopy confirmed that TR-4 destroyed the cell wall of C. siamense, resulting in leakage of the cell contents, thus weakening the pathogenicity of the bacteria. creator: Chenxinyu Ji creator: Yun-Fei Li creator: Yao Yao creator: Zengrui Zhu creator: Shengfeng Mao uri: https://doi.org/10.7717/peerj.17568 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Not so cryptic–differences between mating calls of Hyla arborea and Hyla orientalis from Bulgaria link: https://peerj.com/articles/17574 last-modified: 2024-06-25 description: Anurans are among the most vocally active vertebrate animals and emit calls with different functions. In order to attract a mate, during the breeding season male frogs produce mating calls which have species-specific structure and parameters, and have been successfully used to resolve issues in taxonomy and phylogenetic relations. This is particularly useful when closely related taxa are concerned, as many species are morphologically almost identical, but still their status is well-supported by molecular and genetic data, suggesting the existence of mechanisms for reproductive isolation. Such is the case for treefrogs from the Hyla arborea group, which are now recognized as several distinct species. The present study aims to establish differences in call parameters between the European tree frog, Hyla arborea, and the Eastern tree frog, Hyla orientalis, which both occur on the territory of Bulgaria. Using autonomous audio loggers, calls from six sites (three in the range of H. arborea and three in the range of H. orientalis) were recorded between 7 p.m. and 12 a.m. during the breeding season in 2020–2023. The following parameters in a total of 390 mating calls were analyzed: call count, pulse count, call series duration, call period, peak (dominant) frequency, entropy. Results indicated that sites formed two distinct groups, which corresponded to the known distribution ranges of H. arborea and H. orientalis. The first two components of the PCA explained 71% of the total variance, with variables call count, call series duration, peak frequency and entropy being most important for differentiation between the sites. This study presents the first attempt to differentiate between the calls of these two sister taxa, which both fall within the “short-call treefrogs” group, and results are discussed in terms of known data for mating calls in Hyla sp., as well as limitations and future perspectives. creator: Simeon Lukanov uri: https://doi.org/10.7717/peerj.17574 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lukanov title: Applying different levels of practice variability for motor learning: More is not better link: https://peerj.com/articles/17575 last-modified: 2024-06-25 description: BackgroundVariable practice is a broadly used tool to improve motor learning processes. However, controversial results can be found in literature about the success of this type of practice compared to constant practice. This study explored one potential reason for this controversy: the manipulation of variable practice load applied during practice and its effects according to the initial performance level and the initial intrinsic variability of the learner.MethodSixty-five participants were grouped into four practice schedules to learn a serial throwing task, in which the training load of variable practice was manipulated: one constant practice group and three groups with different variable practice loads applied. After a pre-test, participants trained for 2 weeks. A post-test and three retests (96 h, 2 weeks and 1 month) were carried out after training. The participants’ throwing accuracy was assessed through error parameters and their initial intrinsic motor variability was assessed by the autocorrelation coefficient of the error.ResultsThe four groups improved their throwing performance. Pairwise comparisons and effect sizes showed larger error reduction in the low variability group. Different loads of variable practice seem to induce different performance improvements in a throwing task. The modulation of the variable practice load seems to be a step forward to clarify the controversy about its benefits, but it has to be guided by the individuals’ features, mainly by the initial intrinsic variability of the learner. creator: Carla Caballero creator: David Barbado creator: Manuel Peláez creator: Francisco J. Moreno uri: https://doi.org/10.7717/peerj.17575 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Caballero et al. title: Isolation and characterization of native antagonistic rhizobacteria against Fusarium wilt of chilli to promote plant growth link: https://peerj.com/articles/17578 last-modified: 2024-06-25 description: In the eastern coastal regions of Odisha, wilt caused by Fusarium oxysporum f. sp.capsici is an extremely damaging disease in chilli. This disease is very difficult to manage with chemical fungicides since it is soil-borne in nature. The natural rhizosphere soil of the chilli plant was used to isolate and test bacterial antagonists for their effectiveness and ability to promote plant growth. Out of the fifty-five isolates isolated from the rhizosphere of healthy chilli plants, five isolates, namely Iso 01, Iso 17, Iso 23, Iso 24, and Iso 32, showed their highly antagonistic activity against F. oxysporum f. sp. capsici under in vitro. In a dual culture, Iso 32 (73.3%) and Iso 24 (71.5%) caused the highest level of pathogen inhibition. In greenhouse trials, artificially inoculated chilli plants treated with Iso 32 (8.8%) and Iso 24 (10.2%) had decreased percent disease incidence (PDI), with percent disease reduction over control of 85.6% and 83.3%, respectively. Iso 32 and Iso 24 treated chilli seeds have shown higher seed vigor index of 973.7 and 948.8, respectively, as compared to untreated control 636.5. Furthermore, both the isolates significantly increased plant height as well as the fresh and dry weight of chilli plants under the rolled paper towel method. Morphological, biochemical, and molecular characterization identified Bacillus amyloliquefaciens (MH491049) as the key antagonist. This study demonstrates that rhizobacteria, specifically Iso 32 and Iso 24, can effectively protect chilli plants against Fusarium wilt while promoting overall plant development. These findings hold promise for sustainable and eco-friendly management of Fusarium wilt in chilli cultivation. creator: Bhanothu Shiva creator: Petikam Srinivas creator: Deepa Khulbe creator: Lellapalli Rithesh creator: Penumatsa Kishore Varma creator: Rahul Kumar Tiwari creator: Milan Kumar Lal creator: Ravinder Kumar uri: https://doi.org/10.7717/peerj.17578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shiva et al.