title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=297 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah link: https://peerj.com/articles/17591 last-modified: 2024-06-26 description: Eight fossil tetrapod footprints from lake-shore deposits in the Lower Jurassic Moenave Formation at the St. George Dinosaur Discovery Site (SGDS) in southwestern Utah cannot be assigned to the prevalent dinosaurian (Anomoepus, Eubrontes, Gigandipus, Grallator, Kayentapus) or crocodyliform (Batrachopus) ichnotaxa at the site. The tridactyl and tetradactyl footprints are incomplete, consisting of digit- and digit-tip-only imprints. Seven of the eight are likely pes prints; the remaining specimen is a possible manus print. The pes prints have digit imprint morphologies and similar anterior projections and divarication angles to those of Brasilichnium, an ichnotaxon found primarily in eolian paleoenvironments attributed to eucynodont synapsids. Although their incompleteness prevents clear referral to Brasilichnium, the SGDS tracks nevertheless suggest a eucynodont track maker and thus represent a rare, Early Mesozoic occurrence of such tracks outside of an eolian paleoenvironment. creator: Holly Hurtado creator: Jerald D. Harris creator: Andrew R.C. Milner uri: https://doi.org/10.7717/peerj.17591 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hurtado et al. title: The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study link: https://peerj.com/articles/17594 last-modified: 2024-06-26 description: The disruption in daily activity performance during COVID-19 lockdowns is widely understood to have impacted health, but a better understanding of how restricted performance of specific activities are associated with health is needed. This cross-sectional study answers the following question: How were changes in the performance of 16 daily activities associated with health during COVID-19 lockdowns? A total of 116 participants completed an online survey rating their health before and during COVID-19 lockdowns and comparing their recollection of the performance of 16 activities before COVID-19 with their performance during lockdowns. Multiple stepwise linear regression analysis was used to estimate the relationship between self-reported changes in activities during lockdowns and concurrent (during-lockdown) health status, while controlling for pre-COVID-19 health status. Only changes in activities that were uniquely and significantly associated with lockdown health status were retained in the final model. Health before COVID-19 accounted for 3.7% (P = 0.039) of the variance in health during COVID-19 lockdowns. After controlling for health before COVID-19, five types of activity were significantly and uniquely predictive of health during lockdowns, together accounting for 48.3% of the variance. These activities and the variances they accounted for were rest and sleep (29.5%, P < 0.001), play and recreational activities (8%, P < 0.001), work (4.8%, P = 0.002), personal hygiene (3.2%, P = 0.01), and healthy eating (2.8%, P = 0.013). The study suggests that these five types of activity should be prioritized in policy or interventions when participation in activity is constrained by lockdowns or comparable factors. creator: Bernard Austin Kigunda Muriithi creator: R. Curtis Bay uri: https://doi.org/10.7717/peerj.17594 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Muriithi and Bay title: Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis link: https://peerj.com/articles/17604 last-modified: 2024-06-26 description: BackgroundThe methods previously proposed in the literature to assess patients with rotator cuff related shoulder pain, based on special orthopedic tests to precisely identify the structure causing the shoulder symptoms have been recently challenged. This opens the possibility of a different way of physical examination.ObjectiveTo analyze the differences in shoulder range of motion, strength and thoracic kyphosis between rotator cuff related shoulder pain patients and an asymptomatic group.MethodThe protocol of the present research was registered in the International Prospective Register of Systematic Review (PROSPERO) (registration number CRD42021258924). Database search of observational studies was conducted in MEDLINE, EMBASE, WOS and CINHAL until July 2023, which assessed shoulder or neck neuro-musculoskeletal non-invasive physical examination compared to an asymptomatic group. Two investigators assessed eligibility and study quality. The Newcastle Ottawa Scale was used to evaluate the methodology quality.ResultsEight studies (N = 604) were selected for the quantitative analysis. Meta-analysis showed statistical differences with large effect for shoulder flexion (I2 = 91.7%, p < 0.01, HG = −1.30), external rotation (I2 = 83.2%, p < 0.01, HG = −1.16) and internal rotation range of motion (I2 = 0%, p < 0.01, HG = −1.32). Regarding to shoulder strength; only internal rotation strength showed statistical differences with small effect (I2 = 42.8%, p < 0.05, HG = −0.3).ConclusionsThere is moderate to strong evidence that patients with rotator cuff related shoulder pain present less shoulder flexion, internal and external rotation range of motion and less internal rotation strength than asymptomatic individuals. creator: Daniel Manoso-Hernando creator: Javier Bailón-Cerezo creator: Santiago Angulo-Díaz-Parreño creator: Álvaro Reina-Varona creator: Ignacio Elizagaray-García creator: Alfonso Gil-Martínez uri: https://doi.org/10.7717/peerj.17604 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Manoso-Hernando et al. title: The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study link: https://peerj.com/articles/17617 last-modified: 2024-06-26 description: Antiphospholipid syndrome (APS) is a systemic autoimmune syndrome characterized by arterial or venous thrombosis, pregnancy complications and thrombocytopenia. The aim of this study is to investigate the association between APS and atrial fibrillation (AF) among patients in Peking University People’s Hospital. A single center retrospective study was conducted. Cases were hospitalized patients diagnosed with AF by a cardiologist while the control group patients did not exhibit cardiac diseases. The results of the study revealed that in multivariable logistic regression, APS, anticardiolipin antibody (aCL) positivity and anti-beta-2-glycoprotein antibody (anti-β2GPI) positivity are independent risk factors of AF. APS, aCL positivity and anti-β2GPI positivity are statistically different between AF patients and non-AF patients. Forthcoming studies are needed to clarify the potential link between APS and AF. creator: Zechuan Zhou creator: Yuansheng Liu uri: https://doi.org/10.7717/peerj.17617 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhou and Liu title: Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length link: https://peerj.com/articles/17625 last-modified: 2024-06-26 description: Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the Gossypium. hirsutum genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of GhPDCB9 peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43–4.77 mm. The results indicated that GhPDCB9 played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield. creator: Haibo Zhang creator: Xianghui Xiao creator: Ziyin Li creator: Yu Chen creator: Pengtao Li creator: Renhai Peng creator: Quanwei Lu creator: Youwu Wang uri: https://doi.org/10.7717/peerj.17625 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. 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.