title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2024-08 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Error in jump height estimation using the flight time method: simulation of the effect of ankle position between takeoff and landing link: https://peerj.com/articles/17704 last-modified: 2024-08-30 description: During vertical jump evaluations in which jump height is estimated from flight time (FT), the jumper must maintain the same body posture between vertical takeoff and landing. As maintaining identical posture is rare during takeoff and landing between different jump attempts and in different individuals, we simulated the effect of changes in ankle position from takeoff to landing in vertical jumping to determine the range of errors that might occur in real-life scenarios. Our simulations account for changes in center of mass position during takeoff and landing, changes in ankle position, different subject statures (1.44–1.98 m), and poor to above-average jump heights. Our results show that using FT to estimate jump height without controlling for ankle position (allowing dorsiflexion) during the landing phase of the vertical jump can overestimate jump height by 18% in individuals of average stature and performing an average 30 cm jump or may overestimate by ≤60% for tall individuals performing a poor 10 cm jump, which is common for individuals jumping with added load. Nevertheless, as assessing jump heights based on FT is common practice, we offer a correction equation that can be used to reduce error, improving jump height measurement validity using the FT method allowing between-subject fair comparisons. creator: Carlos Gonçalves creator: Roberto Baptista creator: James Tufano creator: Anthony J. Blazevich creator: Amilton Vieira uri: https://doi.org/10.7717/peerj.17704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gonçalves et al. title: Development and evaluation of a rapid visual loop-mediated isothermal amplification assay for the tcdA gene in Clostridioides difficile detection link: https://peerj.com/articles/17776 last-modified: 2024-08-30 description: BackgroundThe tcdA gene codes for an important toxin produced by Clostridioides difficile (C. difficile), but there is currently no simple and cost-effective method of detecting it. This article establishes and validates a rapid and visual loop-mediated isothermal amplification (LAMP) assay for the detection of the tcdA gene.MethodsThree sets of primers were designed and optimized to amplify the tcdA gene in C. difficile using a LAMP assay. To evaluate the specificity of the LAMP assay, C. difficile VPI10463 was used as a positive control, while 26 pathogenic bacterial strains lacking the tcdA gene and distilled water were utilized as negative controls. For sensitivity analysis, the LAMP assay was compared to PCR using ten-fold serial dilutions of DNA from C. difficile VPI10463, ranging from 207 ng/µl to 0.000207 pg/µl. The tcdA gene of C.difficile was detected in 164 stool specimens using both LAMP and polymerase chain reaction (PCR). Positive and negative results were distinguished using real-time monitoring of turbidity and chromogenic reaction.ResultsAt a temperature of 66 °C, the target DNA was successfully amplified with a set of primers designated, and visualized within 60 min. Under the same conditions, the target DNA was not amplified with the tcdA12 primers for 26 pathogenic bacterial strains that do not carry the tcdA gene. The detection limit of LAMP was 20.700 pg/µl, which was 10 times more sensitive than that of conventional PCR. The detection rate of tcdA in 164 stool specimens using the LAMP method was 17% (28/164), significantly higher than the 10% (16/164) detection rate of the PCR method (X2 = 47, p < 0.01).ConclusionLAMP method is an effective technique for the rapid and visual detection of the tcdA gene of C. difficile, and shows potential advantages over PCR in terms of speed, simplicity, and sensitivity. The tcdA-LAMP assay is particularly suitable for medical diagnostic environments with limited resources and is a promising diagnostic strategy for the screening and detection of C. difficile infection in populations at high risk. creator: Minyi Lin creator: Pu Wang creator: Bingyun Lu creator: Ming Jin creator: Jiasheng Tan creator: Wei Liu creator: Jing Yuan creator: Xiaomou Peng creator: Ye Chen uri: https://doi.org/10.7717/peerj.17776 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: Screening and affinity optimization of single domain antibody targeting the SARS-CoV-2 nucleocapsid protein link: https://peerj.com/articles/17846 last-modified: 2024-08-30 description: The coronavirus disease 2019 (COVID-19) pandemic, which caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), lead to a crisis with devastating disasters to global public economy and health. Several studies suggest that the SARS-CoV-2 nucleocapsid protein (N protein) is one of uppermost structural constituents of SARS-CoV-2 and is relatively conserved which could become a specific diagnostic marker. In this study, eight single domain antibodies recognized the N protein specifically which were named pN01–pN08 were screened using human phage display library. According to multiple sequence alignment and molecular docking analyses, the interaction mechanism between antibody and N protein was predicted. ELISA results indicated pN01–pN08 with high affinity to protein N. To improve their efficacy, two fusion proteins were prepared and their affinity was tested. These finding showed that fusion proteins had higher affinity than single domain antibodies and will be used as diagnosis for the pandemic of SARS-CoV-2. creator: Qian Yang creator: Mengru Yan creator: Juan Lin creator: Yongkang Lu creator: Shuang Lin creator: Zhong Li creator: He Wang creator: Juhua Yang creator: Nanwen Zhang creator: Xiaole Chen uri: https://doi.org/10.7717/peerj.17846 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Yang et al. title: Research on remote sensing ecological livability index based on Google Earth Engine: a case study from Urumqi-Changji-Shihezi urban cluster link: https://peerj.com/articles/17872 last-modified: 2024-08-30 description: The U-Chang-Shi (Urumqi-Changji-Shihezi) urban cluster, located at the heart of Xinjiang, boasts abundant natural resources. Over the past two decades, rapid urbanization, industrialization, and climate change have significantly threatened the region’s ecological livability. To comprehensively, scientifically, and objectively assess the ecological livability of this area, this study leverages the Google Earth Engine (GEE) platform and multi-source remote sensing data to develop a comprehensive evaluation metric: the Remote Sensing Ecological Livability Index (RSELI). This aims to examine the changes in the ecological livability of the U-Chang-Shi urban cluster from 2000 to 2020. The findings show that despite some annual improvements, the overall trend in ecological livability is declining, indicating that the swift pace of urbanization and industrialization has placed considerable pressure on the region’s ecological environment. Land use changes, driven by urban expansion and the growth in agricultural and industrial lands, have progressively encroached upon existing green spaces and water bodies, further deteriorating the ecological environment. Additionally, the region’s topographical features have influenced its ecological livability; large terrain fluctuations have made soil erosion and geological disasters common. Despite the central plains’ vast rivers providing ample water resources, over exploitation and ill-conceived hydrological constructions have led to escalating water scarcity. The area near the Gurbantunggut Desert in the north, with its extremely fragile ecological environment, has long been unsuitable for habitation. This study provides a crucial scientific basis for the future development of the U-Chang-Shi urban cluster and hopes to offer theoretical support and practical guidance for the sustainable development and ecological improvement of the region. creator: Mianwei Chen creator: Tianxing Wang creator: Yunqing Liu creator: Shikai Zhang creator: Yue Zhang uri: https://doi.org/10.7717/peerj.17872 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: miR-605-3p may affect caerulein-induced ductal cell injury and pyroptosis in acute pancreatitis by targeting the DUOX2/NLRP3/NF-κB pathway link: https://peerj.com/articles/17874 last-modified: 2024-08-30 description: Acute pancreatitis (AP) is a sudden-onset disease of the digestive system caused by abnormal activation of pancreatic enzymes. Dual oxidase 2 (DUOX2) has been found to be elevated in the progression of a variety of inflammatory diseases. Therefore, we analyzed the specific roles of DUOX2 in AP development. Blood samples were collected from of AP patients and healthy people, and the caerulein- stimulated human pancreatic duct cells (H6C7) were utilized to establish an AP cell model. Cell growth and apoptosis were measured using an MTT assay and TUNEL staining. Additionally, RT-qPCR and western blot assays were conducted to assess the RNA and protein expressions of the cells. ELISA kits were used to determine TNF-α, IL-6, IL-8, and IL-1β levels. The interaction between DUOX2 and miR-605-3p was predicted using the Targetscan database and confirmed by dual-luciferase report assay. We found that DUOX2 increased while miR-605-3p decreased in the blood of AP patients and caerulein-stimulated H6C7 cells. DUOX2 was targeted by miR-605-3p. Furthermore, DUOX2 knockdown or miR-605-3p overexpression promoted cell viability, decreased the TNF-α, IL-6, IL-8, and IL-1β levels, and inhibited apoptosis rate in caerulein-stimulated H6C7 cells. DUOX2 knockdown or miR-605-3p overexpression also increased the Bcl-2 protein levels and down-regulated Bax, cleaved-caspase-1, NLRP3 and p-p65. Interestingly, DUOX2 overexpression reversed the miR-605-3p mimic function in the caerulein-treated H6C7 cells. In conclusion, our research demonstrated that DUOX2 knockdown relieved the injury and inflammation in caerulein-stimulated H6C7 cells. creator: Gai Zhang creator: Yuanyuan Zhang creator: Bing Wang creator: Hao Xu creator: Donghui Xie creator: Zhenli Guo uri: https://doi.org/10.7717/peerj.17874 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: A roadmap for empowering cardiovascular disease patients: a 5P-Medicine approach and technological integration link: https://peerj.com/articles/17895 last-modified: 2024-08-30 description: This article explores the multifaceted concept of cardiovascular disease (CVD) patients’ empowerment, emphasizing a shift from compliance-oriented models to active patient participation. In recognizing that cardiovascular disease is a paramount global health challenge, this study illuminates the pressing need for empowering patients, underscoring their role as active participants in their healthcare journey. Grounded in 5P-Medicine principles—Predictive, Preventive, Participatory, Personalized, and Precision Medicine—the importance of empowering CVD patients through analytics, prevention, participatory decision making, and personalized treatments is highlighted. Incorporating a comprehensive overview of patient empowerment strategies, including self-management, health literacy, patient involvement, and shared decision making, the article advocates for tailored approaches aligned with individual needs, cultural contexts, and healthcare systems. Technological integration is examined to enhance patient engagement and personalized healthcare experiences. The critical role of patient-centered design in integrating digital tools for CVD management is emphasized, ensuring successful adoption and meaningful impact on healthcare outcomes. The conclusion proposes vital research questions addressing challenges and opportunities in CVD patient empowerment. These questions stress the importance of medical community research, understanding user expectations, evaluating existing technologies, defining ideal empowerment scenarios, and conducting a literature review for informed advancements. This article lays the foundation for future research, contributing to ongoing patient-centered healthcare evolution, especially in empowering individuals with a 5P-Medicine approach to cardiovascular diseases. creator: Hanna V. Denysyuk creator: Ivan Miguel Pires creator: Nuno M. Garcia uri: https://doi.org/10.7717/peerj.17895 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Denysyuk et al. title: Stochastic process drives the dissimilarity in biodiversity patterns between Pinus kwangtungensis coniferous forest and evergreen deciduous broad-leaved mixed forest in karst area link: https://peerj.com/articles/17899 last-modified: 2024-08-30 description: Pinus kwangtungensis is an endangered evergreen conifer tree species, and its in situ conservation has been considered one of the most critical issues. However, relative protection is limited by the lack of understanding of its community structure and underlying assembly processes. To study how the species diversity and assembly processes of Pinus kwangtungensis coniferous forest (CF) differed with regional climax community, this study established a series forest dynamic plots both in CF and evergreen deciduous broadleaved mixed forest (EDBM). By performing comparison analysis and PER-SIMPER approaches, we quantified the differences in species diversity and community assembly rules. The results showed that the species α-diversity of CF differed greatly from the EDBM both in species richness and evenness. In addition, the stochastic process acted a more important role in determining species composition, indicating the uncertainty in presence of species. The soil phosphorus and changeable calcium content were the main factors driving the differences in biodiversity, which the importance of soil nutrient factors in driving species composition. Our study highlighted that we should consider the community structure and ecological process when conducting conservation of Pinus kwangtungensis. creator: Xingying Fan creator: Longchenxi Meng creator: Yeheng Wang creator: Lipeng Zang uri: https://doi.org/10.7717/peerj.17899 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fan et al. title: Temperature and land use change are associated with Rana temporaria reproductive success and phenology link: https://peerj.com/articles/17901 last-modified: 2024-08-30 description: Chemical pollution, land cover change, and climate change have all been established as important drivers of amphibian reproductive success and phenology. However, little is known about the relative impacts of these anthropogenic stressors, nor how they may interact to alter amphibian population dynamics. Addressing this gap in our knowledge is important, as it allows us to identify and prioritise the most needed conservation actions. Here, we use long-term datasets to investigate landscape-scale drivers of variation in the reproductive success and phenology of UK Common frog (Rana temporaria) populations. Consistent with predictions, we found that increasing mean temperatures resulted in earlier initialisation of spawning, and earlier hatching, but these relationships were not consistent across all sites. Lower temperatures were also linked to increased spawn mortality. However, temperature increases were also strongly correlated with increases in urban area, arable area, and nitrate levels in the vicinity of spawning grounds. As with spawning and hatching, there was marked spatial variation in spawn mortality trends, where some sites exhibited steady increases over time in the proportion of dead or diseased spawn. These findings support previous work linking warming temperatures to shifts in timing of amphibian breeding, but also highlight the importance of assessing the effect of land use change and pollution on wild amphibian populations. These results have implications for our understanding of the response of wild amphibian populations to climate change, and the management of human-dominated landscapes for declining wildlife populations. creator: Kat E. Oliver creator: Xavier A. Harrison uri: https://doi.org/10.7717/peerj.17901 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Oliver and Harrison title: Association between celiac disease and fibromyalgia and their severity: a cross-sectional study link: https://peerj.com/articles/17949 last-modified: 2024-08-30 description: BackgroundFibromyalgia (FMS) is a common musculoskeletal disorder with many causes. People with fibromyalgia often have the same symptoms as people with celiac disease (CD). Demonstration of the coordination and frequency of FMS and CD is important for effective treatment.MethodsThis is a single center cross-sectional clinical study. The study included 60 patients who were diagnosed with CD by the Gastroenterology Clinic based on American College of Gastroenterology (ACG) criteria. Patients were also asked to complete the Widespread Pain Index (WPI), Symptom Severity Scale (SSS), and Fibromyalgia Impact Questionnaire (FIQ) to diagnose fibromyalgia and assess its severity. The results were used to analyze the frequency of concomitance and relationship between the two diseases.ResultsThe relationship between the clinical types of CD and the presence of fibromyalgia was insignificant. Analysis of the relationship between the pathologic typing of biopsy and fibromyalgia frequency was insignificant. Those with antibodies more frequently met criteria for fibromyalgia (P = 0.04, P = 0.04, respectively).ConclusionsPresence of clinical extraintestinal manifestations in patients with CD should lead clinicians to consider FMS as a possible diagnosis. This points to the importance for clinicians in all subspecialties to be aware of the various symptoms and diseases associated with FMS. creator: Mehmet Serkan Kılıçoğlu creator: Safiye Sayılır creator: Ozan Volkan Yurdakul creator: Teoman Aydin creator: Koray Koçhan creator: Metin Basaranoglu creator: Okan Kucukakkas uri: https://doi.org/10.7717/peerj.17949 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kılıçoğlu et al. title: Seasonal dynamics of seed dormancy and germination in the weed Diplachne fusca link: https://peerj.com/articles/17987 last-modified: 2024-08-30 description: BackgroundUnderstanding the reproductive biology of weeds is crucial for managing them effectively. Diplachne fusca (Poaceae) is a widely distributed weed species that poses significant challenges to agricultural productivity. Nevertheless, it remains unclear how the soil seed bank of D. fusca responds to environmental shifts, and whether a dormancy cycle is present in this species.MethodsWe investigated how seed dormancy in D. fusca is broken and how it responds to natural environmental changes. The impact of incubation temperature, light exposure, cold stratification at 4 °C, and gibberellic acid (GA3) on seed germination/dormancy-break was investigated, along with assessing seasonal changes in germinability through monthly excavation and laboratory incubation of buried seeds over 2 years.ResultsResults indicated that newly ripened seeds of D. fusca were dormant, with germination facilitated by GA3, cold stratification, and after-ripening at ambient room conditions. Exposure to darkness inhibited germination. Seasonal patterns of germination were observed, with peak germination occurring in cooler months and a marked decline during the hot summer months. After 2 years of being buried, approximately 40% of the seeds remained viable.ConclusionIn summary, seeds of D. fusca exhibit non-deep physiological dormancy and maintain a persistent soil seed bank. Seeds buried in the soil undergo a yearly dormancy/non-dormancy cycle. This dormancy cycle prevents seed germination and seedling emergence in autumn, which boosts the survival of seedlings in less favorable seasons, yet it also makes it more challenging to eradicate this weed. creator: Guiquan Song creator: Shufang Liu creator: Xuelian Jiang creator: Shuai Gong creator: Wenya Hao creator: Ying Cui creator: Yueling Zhao uri: https://doi.org/10.7717/peerj.17987 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Song et al. title: Association between BMI and health-related physical fitness in adolescents with hearing impairment in China: a cross-sectional study link: https://peerj.com/articles/17995 last-modified: 2024-08-30 description: BackgroundThis cross-sectional study aimed to address a critical gap in the understanding of the association between body mass index (BMI) and physical fitness levels in adolescents with hearing impairment (HI) in China. This study investigated how different BMI levels impact the physical fitness index (PFI) of HI adolescents.MethodsThis study employed a physical fitness test for HI adolescents attending special education schools. The test included eight components: height, weight, 50-m sprint, standing long jump, sit and reach, endurance run, bent-knee sit-up (for girls), and pull-up (for boys). Test scores for each student were standardized by age and gender. Individual Z-scores were then calculated, and the sum of these Z-scores constituted the PFI. Logistic regression was used to analyze the relationship between BMI and PFI across different gender and age groups. Statistical significance was set at P < 0.05.ResultsThe linear regression model showed an inverted U-shaped relationship between BMI and PFI. At the same BMI level, boys exhibited superior physical fitness compared to girls with the same BMI (P < 0.05). Statistically significant differences in PFI levels were observed between normal-weight and obese males, as well as between underweight and obese boys (P < 0.05). In the 13–15 and 16–18 age groups, the increase in BMI has a greater impact on boys PFI than on girls.ConclusionsAdolescents with HI generally demonstrated good physical fitness. Compared to individuals with normal weight, those who were underweight, overweight, or obese exhibited lower levels of physical fitness. Future interventions should focus on adolescents with HI with abnormal BMI. creator: Xiaowan Cai creator: Hanyue Zhang creator: Tingting Sun creator: Jingjing Yu creator: Xiao Jia uri: https://doi.org/10.7717/peerj.17995 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Cai et al. title: Surprising diversity of new plasmids in bacteria isolated from hemorrhoid patients link: https://peerj.com/articles/18023 last-modified: 2024-08-30 description: BackgroundHemorrhoids are common conditions at or around the anus, to which numerous people suffer worldwide. Previous research has suggested that microbes may play a role in the development of hemorrhoids, and the origins of these microbes have been preliminarily investigated. However, no detailed research on the microbes related to hemorrhoid patients has been conducted. This work aims to provide an initial investigation into the microbes related to hemorrhoid patients with high quality whole genome sequencing.MethodsForty-nine bacterial strains were isolated from seven hemorrhoid patients. Third-generation nanopore sequencing was performed to obtain high quality whole genome sequences. The presence of plasmids, particularly new plasmids, along with antibiotic resistance genes, was investigated for these strains. Phylogenetic analysis and genome comparisons were performed.ResultsOut of the 31 plasmids found in the strains, 15 new plasmids that have not been observed previously were discovered. Further structural analysis revealed new multidrug-resistant conjugative plasmids, virulent plasmids, and small, high-copy mobile plasmids that may play significant functional roles. These plasmids were found to harbor numerous integrases, transposases, and recombinases, suggesting their ability to quickly obtain genes to change functions. Analysis of antibiotic resistance genes revealed the presence of antibiotic resistant-integrons. Together with the surprising number of new plasmids identified, as well as the finding of transmission and modification events for plasmids in this work, we came to the suggestion that plasmids play a major role in genetic plasticity.ConclusionThis study reveals that the diversity of plasmids in human-associated microbes has been underestimated. With the decreasing cost of whole-genome sequencing, monitoring plasmids deserves increased attention in future surveillance efforts. creator: Yihua Wang creator: Wenya Su creator: Xiang Zeng creator: Zhaopeng Liu creator: Jiaming Zhu creator: Mingyu Wang creator: Ling Li creator: Wenlong Shen uri: https://doi.org/10.7717/peerj.18023 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Beyond 2D cell cultures: how 3D models are changing the in vitro study of ovarian cancer and how to make the most of them link: https://peerj.com/articles/17603 last-modified: 2024-08-29 description: 3D cell cultures are a fundamental tool in ovarian cancer research that can enable more effective study of the main features of this lethal disease, including the high rates of recurrence and chemoresistance. A clearer, more comprehensive understanding of the biological underpinnings of these phenomena could aid the development of more effective treatments thus improving patient outcomes. Selecting the most appropriate model to investigate the different aspects of cell biology that are relevant to cancer is challenging, especially since the assays available for the study of 3D cultures are not fully established yet. To maximise the usefulness of 3D cell cultures of ovarian cancer, we undertook an in-depth review of the currently available models, taking into consideration the strengths and limitations of each approach and of the assay techniques used to evaluate the results. This integrated analysis provides insight into which model-assay pair is best suited to study different parameters of ovarian cancer biology such as cell proliferation, gene expression or treatment response. We also describe how the combined use of multiple models is likely to be the most effective strategy for the in vitro characterisation of complex behaviours. creator: Marilisa Cortesi creator: Kristina Warton creator: Caroline E. Ford uri: https://doi.org/10.7717/peerj.17603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cortesi et al. title: Benthic and fish community composition on mesophotic reefs in Grand Cayman link: https://peerj.com/articles/17763 last-modified: 2024-08-29 description: Mesophotic Coral Ecosystems (MCEs) represent unique ecological habitats that range from 30 to 150 m deep, harbouring phylogenetically distinct species and offering refuge for many taxa during times of environmental stress. Yet owing to inaccessibility of ecosystems at these depths, most MCEs remain unexplored, with quantifications of ecological communities in these habitats lacking across many regions. Here, using open- and closed-circuit technical diving, we quantified benthic and fish community composition at four mesophotic reef sites (45 m depth) in Grand Cayman. We show significant differences in benthic community composition over a small spatial scale driven by disparate coverage of sponges, crustose coralline algae, and sand/rubble, yet consistent patterns of macroalgal dominance representing >50% coverage at each site and low hard coral cover at an average of 2.4%. Reef fish species richness, biomass, and density was consistent across sites, however the relative contribution of individual species to community composition differed significantly. Macrocarnivores were found to be the dominant contributors to biomass, with invertivores the most speciose, and omnivores and planktivores at the highest densities, consistent with previous descriptions of mesophotic fish assemblages in other regions. Similarly, the low hard coral cover and high macroalgae and sponge cover of the benthic communities also appear ecologically similar to several described mesophotic reefs yet is not uniform across the Caribbean. The ecological organisation of Grand Cayman’s MCEs may result from a variety of factors such as isolation from other major land masses, geology, local geography, and anthropogenic activity at both the local and global scale and highlight the importance of continued exploration and documentation of MCE communities. creator: Lucas Le Gall creator: Jack V. Johnson creator: Alex Chequer creator: Matthew Louis Doherty creator: Gretchen Goodbody-Gringley uri: https://doi.org/10.7717/peerj.17763 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Le Gall et al. title: Consumer-priced wearable sensors combined with deep learning can be used to accurately predict ground reaction forces during various treadmill running conditions link: https://peerj.com/articles/17896 last-modified: 2024-08-29 description: Ground reaction force (GRF) data is often collected for the biomechanical analysis of running, due to the performance and injury risk insights that GRF analysis can provide. Traditional methods typically limit GRF collection to controlled lab environments, recent studies have looked to combine the ease of use of wearable sensors with the statistical power of machine learning to estimate continuous GRF data outside of these restrictions. Before such systems can be deployed with confidence outside of the lab they must be shown to be a valid and accurate tool for a wide range of users. The aim of this study was to evaluate how accurately a consumer-priced sensor system could estimate GRFs whilst a heterogeneous group of runners completed a treadmill protocol with three different personalised running speeds and three gradients. Fifty runners (25 female, 25 male) wearing pressure insoles made up of 16 resistive sensors and an inertial measurement unit ran at various speeds and gradients on an instrumented treadmill. A long short term memory (LSTM) neural network was trained to estimate both vertical $(GRF_v)$(GRFv) and anteroposterior $(GRF_{ap})$(GRFap) force traces using leave one subject out validation. The average relative root mean squared error (rRMSE) was 3.2% and 3.1%, respectively. The mean $(GRF_v)$(GRFv) rRMSE across the evaluated participants ranged from 0.8% to 8.8% and from 1.3% to 17.3% in the $(GRF_{ap})$(GRFap) estimation. The findings from this study suggest that current consumer-priced sensors could be used to accurately estimate two-dimensional GRFs for a wide range of runners at a variety of running intensities. The estimated kinetics could be used to provide runners with individualised feedback as well as form the basis of data collection for running injury risk factor studies on a much larger scale than is currently possible with lab based methods. creator: Josh Carter creator: Xi Chen creator: Dario Cazzola creator: Grant Trewartha creator: Ezio Preatoni uri: https://doi.org/10.7717/peerj.17896 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Carter et al. title: Assessment of inter-rater and intra-rater reliability of the Luna EMG robot as a tool for assessing upper limb proprioception in patients with stroke—a prospective observational study link: https://peerj.com/articles/17903 last-modified: 2024-08-29 description: BackgroundThe aim of the study was to assess the inter-rater and intra-rater agreement of measurements performed with the Luna EMG (electromyography) multifunctional robot, a tool for evaluation of upper limb proprioception in individuals with stroke.MethodsThe study was conducted in a group of patients with chronic stroke. A total of 126 patients participated in the study, including 78 women and 48 men, on average aged nearly 60 years (mean = 59.9). Proprioception measurements were performed using the Luna EMG diagnostic and rehabilitation robot to assess the left and right upper limbs. The examinations were conducted by two raters, twice, two weeks apart. The results were compared between the raters and the examinations.ResultsHigh consistency of the measurements performed for the right and the left hand was reflected by the interclass correlation coefficients (0.996–0.998 and 0.994–0.999, respectively) and by Pearson’s linear correlation which was very high (r = 1.00) in all the cases for the right and the left hand in both the inter-rater and intra-rater agreement analyses.ConclusionsMeasurements performed by the Luna EMG diagnostic and rehabilitation robot demonstrate high inter-rater and intra-rater agreement in the assessment of upper limb proprioception in patients with chronic stroke. The findings show that Luna EMG is a reliable tool enabling effective evaluation of upper limb proprioception post-stroke. creator: Justyna Leszczak creator: Bogumiła Pniak creator: Mariusz Drużbicki creator: Anna Poświata creator: Michał Mikulski creator: Anna Roksela creator: Agnieszka Guzik uri: https://doi.org/10.7717/peerj.17903 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Leszczak et al. title: The role of acute stress recovery in emotional resilience link: https://peerj.com/articles/17911 last-modified: 2024-08-29 description: BackgroundResilience refers to the process of demonstrating better outcomes than would be expected based on the adversity one experienced. Resilience is increasingly measured using a residual approach, which typically assesses adversity and mental health outcomes over a longitudinal timeframe. It remains unknown to what extent such a residual-based measurement of resilience is sensitive to variation in acute stress resilience, a candidate resilience factor.MethodsFifty-seven emerging adults enrolled in tertiary education completed measures of adversity and emotional experiences. To assess stress recovery, participants were exposed to a lab-based adverse event from which a Laboratory Stress Resilience Index was derived.ResultsWe derived a residual-based measure of emotional resilience from regressing emotional experience scores onto adversity scores. This residual-based measure of emotional resilience predicted variance in the Laboratory Stress Resilience Index over and above that predicted by both a traditional resilience measure and the emotional experiences measure. These findings suggest that acute stress resilience may be a factor underpinning variation in emotional resilience, and that the residual-based approach to measuring resilience is sensitive to such variation in stress resilience. creator: Lies Notebaert creator: Roger Harris creator: Colin MacLeod creator: Monique Crane creator: Romola S. Bucks uri: https://doi.org/10.7717/peerj.17911 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Notebaert et al. title: Metabolites profiling of Sapota fruit pulp via a multiplex approach of gas and ultra performance liquid chromatography/mass spectroscopy in relation to its lipase inhibition effect link: https://peerj.com/articles/17914 last-modified: 2024-08-29 description: BackgroundSapota, Manilkara zapota L., are tasty, juicy, and nutrient-rich fruits, and likewise used for several medicinal uses.MethodsThe current study represents an integrated metabolites profiling of sapota fruits pulp via GC/MS and UPLC/MS, alongside assessment of antioxidant capacity, pancreatic lipase (PL), and α-glucosidase enzymes inhibitory effects.ResultsGC/MS analysis of silylated primary polar metabolites led to the identification of 68 compounds belonging to sugars (74%), sugar acids (18.27%), and sugar alcohols (7%) mediating the fruit sweetness. Headspace SPME-GC/MS analysis led to the detection of 17 volatile compounds belonging to nitrogenous compounds (72%), ethers (7.8%), terpenes (7.6%), and aldehydes (5.8%). Non-polar metabolites profiling by HR-UPLC/MS/MS-based Global Natural Products Social (GNPS) molecular networking led to the assignment of 31 peaks, with several novel sphingolipids and fatty acyl amides reported for the first time. Total phenolic content was estimated at 6.79 ± 0.12 mg gallic acid equivalent/gram extract (GAE/g extract), but no flavonoids were detected. The antioxidant capacities of fruit were at 1.62 ± 0.2, 1.49 ± 0.11, and 3.58 ± 0.14 mg Trolox equivalent/gram extract (TE/g extract) via DPPH, ABTS, and FRAP assays, respectively. In vitro enzyme inhibition assays revealed a considerable pancreatic lipase inhibition effect (IC50 = 2.2 ± 0.25 mg/mL), whereas no inhibitory effect towards α-glucosidase enzyme was detected. This study provides better insight into sapota fruit’s flavor, nutritional, and secondary metabolites composition mediating for its sensory and health attributes. creator: Mohamed A. Farag creator: Nermin Ahmed Ragab creator: Maii Abdelnaby Ismail Maamoun uri: https://doi.org/10.7717/peerj.17914 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Farag et al. title: The sicariid spiders in the state of Bahia, Brazil (Arachnida: Araneae) link: https://peerj.com/articles/17942 last-modified: 2024-08-29 description: BackgroundSicariidae is a small family of cryptic and recluse spiders, with 178 species grouped into three genera: Hexophtalma, Loxosceles and Sicarius. Only the last two occur in Brazil, where 29 species are recorded, with a greater number of records in the Southeast and South regions. To date, there is no regionalized study of the distribution of these spiders in the Northeast of Brazil. We presented more than four decades of data on the distribution of sicariid spiders in the state of Bahia. Our research aimed to identify and evaluate the distribution of sicariid species in this region, characterizing them in their biomes and phytophysiognomies.MethodsData covers a period from 1983 to 2024, obtained from articles describing species recorded in Bahia and from three scientific collections from Brazilian institutions: Universidade Federal da Bahia (MHNBA); Instituto Butantan (IBSP); Universidade Federal de Minas Gerais (UFMG). Maps were produced using the QGIS 3.34.1 software, based on geographic coordinates obtained from the original literature, when provided. Species without information on geographic coordinates were georeferenced using the SpeciesLink (geoLoc tool) for the municipalities. Biomes were consulted on the georeference Brazilian institute website and the phytophysiognomies were ignored when not specified in the data of collections or original literature.ResultsWe confirmed 14 species of sicariid spiders in the state of Bahia, eight from the genus Loxosceles (i) and six from Sicarius. The species were recorded in 48 municipalities, located mainly in the Caatinga biome. We recorded a distribution expansion of seven species: Loxosceles amazonica, L. chapadensis, L. karstica, L. similis, Sicarius cariri, S. ornatus and S. tropicus. There is a difference in species composition in the two regions separated by the São Francisco River, an important geographic barrier especially for small invertebrates. More than 75% of the species were registered in the east side and about 20% exclusively in the west side: L. boqueirao, L. cardosoi, L. carinhanha. This suggests the need for future studies to evaluate additional variables that determine community structure, especially considering their low vagility and reclusive behavior. Although Sicarius are found almost exclusively in the Caatinga, there are isolated records from Restinga and dry forest enclaves in the Cerrado domain and Atlantic Forest areas. This reinforces the possibility of them being able to adapt to slightly wetter environments erase colonize and survive in seasonally dry rainforest areas. Unlike Sicarius (i), Loxosceles (i) occupy a wide variety of habitats in natural, urban and domiciliary situations. Many of the records here such as for Loxosceles boqueirao, L. cardosoi, L. carinhanha, L. chapadensis, L. karstica and L. troglobia were obtained at caves or nearby areas, which appear to be attractive habitats for these nocturnal spiders. creator: Júlia Andrade-de-Sá creator: Tania Kobler Brazil creator: Rejâne Maria Lira-da-Silva creator: Antonio Domingos Brescovit uri: https://doi.org/10.7717/peerj.17942 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Andrade-de-Sá et al. title: The role of NF-kappaB in the inflammatory processes related to dental caries, pulpitis, apical periodontitis, and periodontitis–a narrative review link: https://peerj.com/articles/17953 last-modified: 2024-08-29 description: Tooth-related inflammatory disorders, including caries, pulpitis, apical periodontitis (AP), and periodontitis (PD), are primarily caused by resident oral microorganisms. Although these dental inflammatory conditions are typically not life-threatening, neglecting them can result in significant complications and greatly reduce an individual’s quality of life. Nuclear factor κB (NF-κB), a family formed by various combinations of Rel proteins, is extensively involved in inflammatory diseases and even cancer. This study reviews recent data on NF-κB signaling and its role in dental pulp stem cells (DPSCs), dental pulp fibroblasts (DPFs), odontoblasts, human periodontal ligament cells (hPDLCs), and various experimental animal models. The findings indicate that NF-κB signaling is abnormally activated in caries, pulpitis, AP, and PD, leading to changes in related cellular differentiation. Under specific conditions, NF-κB signaling occasionally interacts with other signaling pathways, affecting inflammation, bone metabolism, and tissue regeneration processes. In summary, data collected over recent years confirm the central role of NF-κB in dental inflammatory diseases, potentially providing new insights for drug development targeting NF-κB signaling pathways in the treatment of these conditions. Keywords: NF-κB, dental caries, pulpitis, apical periodontitis, periodontitis. creator: Zhonglan Chen creator: Guangping Lang creator: Xi Xu creator: Xinghua Liang creator: Yalin Han creator: Yingying Han uri: https://doi.org/10.7717/peerj.17953 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Chen et al. title: Phenotyping 172 strawberry genotypes for water soaking reveals a close relationship with skin water permeance link: https://peerj.com/articles/17960 last-modified: 2024-08-29 description: Water soaking is a commercially important disorder of field-grown strawberries that is exacerbated by surface wetness and high humidity. The objective was to establish the effect of genotype on susceptibility to water soaking. Three greenhouse-grown model ‘collections’ were used comprising a total of 172 different genotypes: (1) a segregating F2 population, (2) a collection of strawberry cultivars and breeding clones, and (3) a collection of wild Fragaria species. A standardized immersion assay was used to induce water soaking. Potential relationships between water soaking and water uptake characteristics, depth of the achene depressions, fruit firmness, cuticle mass and strain relaxation and microcracking were investigated. Further, the effect of downregulating the polygalacturonase genes (FaPG1 and FaPG2) on the susceptibility to water soaking was investigated. The collection of wild species was most susceptible to water soaking. This was followed by the collection of cultivars and breeding clones, and by the F2 population. Susceptibility to water soaking was strongly correlated with water uptake rate (mass of water, per fruit, per time). For the pooled dataset of 172 genotypes, 46% of the variability in water soaking was accounted for by the permeance of the skin to osmotic water uptake. Susceptibility to water soaking was not, or was only poorly correlated with measurements of fruit surface area or of the osmotic potential of the expressed fruit juice. The only exceptions were the wild Fragaria species which were highly variable in fruit size and also in fruit osmotic potential. For genotypes from the F2 and the wild species collections, firmer fruit were less susceptible to water soaking than softer fruit. There were no relationships between fruit firmness and susceptibility to water soaking in transgenic plants in which FaPG1 and FaPG2 were down-regulated. Susceptibility to water soaking was not related to cuticle mass per unit fruit surface area, nor to strain relaxation of the cuticle upon isolation, nor to achene position. In summary, strawberry’s susceptibility to water soaking has a significant genetic component and is closely and consistently related to the skin’s permeance to osmotic water uptake. creator: Grecia Hurtado creator: Klaus Olbricht creator: Jose A. Mercado creator: Sara Pose creator: Moritz Knoche uri: https://doi.org/10.7717/peerj.17960 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hurtado et al. title: Comparisons of genome assembly tools for characterization of Mycobacterium tuberculosis genomes using hybrid sequencing technologies link: https://peerj.com/articles/17964 last-modified: 2024-08-29 description: BackgroundNext-generation sequencing of Mycobacterium tuberculosis, the infectious agent causing tuberculosis, is improving the understanding of genomic diversity of circulating lineages and strain-types, and informing knowledge of drug resistance mutations. An increasingly popular approach to characterizing M. tuberculosis genomes (size: 4.4 Mbp) and variants (e.g., single nucleotide polymorphisms (SNPs)) involves the de novo assembly of sequence data.MethodsWe compared the performance of genome assembly tools (Unicycler, RagOut, and RagTag) on sequence data from nine drug resistant M. tuberculosis isolates (multi-drug (MDR) n = 1; pre-extensively-drug (pre-XDR) n = 8) generated using Illumina HiSeq, Oxford Nanopore Technology (ONT) PromethION, and PacBio platforms.ResultsOur investigation found that Unicycler-based assemblies had significantly higher genome completeness (~98.7%; p values = 0.01) compared to other assembler tools (RagOut = 98.6%, and RagTag = 98.6%). The genome assembly sizes (bp) across isolates and sequencers based on RagOut was significantly longer (p values < 0.001) (4,418,574 ± 8,824 bp) than Unicycler and RagTag assemblies (Unicycler = 4,377,642 ± 55,257 bp, and RagTag = 4,380,711 ± 51,164 bp). RagOut-based assemblies had the fewest contigs (~32) and the longest genome size (4,418,574 bp; vs. H37Rv reference size 4,411,532 bp) and therefore were chosen for downstream analysis. Pan-genome analysis of Illumina and PacBio hybrid assemblies revealed the greatest number of detected genes (4,639 genes; H37Rv reference contains 3,976 genes), while Illumina and ONT hybrid assemblies produced the highest number of SNPs. The number of genes from hybrid assemblies with ONT and PacBio long-reads (mean: 4,620 genes) was greater than short-read assembly alone (4,478 genes). All nine RagOut hybrid genome assemblies detected known mutations in genes associated with MDR-TB and pre-XDR-TB.ConclusionsUnicycler software performed the best in terms of achieving contiguous genomes, whereas RagOut improved the quality of Unicycler’s genome assemblies by providing a longer genome size. Overall, our approach has demonstrated that short-read and long-read hybrid assembly can provide a more complete genome assembly than short-read assembly alone by detecting pan-genomes and more genes, including IS6110, and SNPs. creator: Kanwara Trisakul creator: Yothin Hinwan creator: Jukgarin Eisiri creator: Kanin Salao creator: Angkana Chaiprasert creator: Phalin Kamolwat creator: Sissades Tongsima creator: Susana Campino creator: Jody Phelan creator: Taane G. Clark creator: Kiatichai Faksri uri: https://doi.org/10.7717/peerj.17964 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Trisakul et al. title: A short stature allele enhances tolerance to zinc deficiency and translocation of zinc in barley link: https://peerj.com/articles/17994 last-modified: 2024-08-29 description: BackgroundZinc (Zn) content is of great importance in healthy human diet, crop productivity and stress tolerance in soils with zinc deficiency. The genes used to increase yield per unit area such as semi-dwarf 1 (sdw1) is commonly considered to reduce mineral content of grain.MethodsIn the present study, influence of sdw1.d, a widely used allele for short plant height in barley breeding, on zinc accumulation and tolerance to zinc deficiency were investigated. A near isogenic line of sdw1.d allele, its recurrent parent Tokak 157/37 and donor parent Triumph were grown in zinc-deficient and-sufficient hydroponic cultures. Two experiments were conducted until heading stage and physiological maturity.ResultsIn zinc-deficient conditions, sdw1.d allele increased shoot dry weight by 112.4 mg plant−1, shoot Zn concentration by 0.9 ppm, but decreased root Zn concentration by 6.6 ppm. It did not affect grain characteristics, but increased grain Zn content. In zinc-sufficient conditions, sdw1.d allele increased shoot Zn content, and decreased root Zn content. sdw1.d did not affect grain weight but increased grain Zn concentration by about 30% under zinc-sufficient conditions. The results showed that sdw1.d allele has no negative effect on tolerance to zinc deficiency, and even promotes tolerance to zinc deficiency by more Zn translocation. It was revealed that sdw1.d allele improves Zn accumulation under both zinc-deficient and zinc-sufficient condition. The sdw1.d allele could contribute to solving the problems in plant growth and development caused by zinc-deficiency via improving tolerance to zinc-deficiency. It could also provide a better Zn biofortification. creator: Ibrahim Saygili uri: https://doi.org/10.7717/peerj.17994 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Saygili title: Genome-wide identification and characterization of the sucrose invertase gene family in Hemerocallis citrina link: https://peerj.com/articles/17999 last-modified: 2024-08-29 description: BackgroundSucrose invertase is an important catalytic enzyme that is widely distributed in plants and can irreversibly hydrolyze sucrose into fructose and glucose. Daylily is an important perennial flower worldwide and a traditional vegetable in East Asia. Previous studies have suggested that sucrose invertase is involved in the aging of daylily flowers. However, knowledge about the number, physicochemical properties, and expression patterns of daylily sucrose invertases is still lacking. Identifying the daylily sucrose invertase family genes in the genome is highly important for understanding phylogenetic evolution and determining the genetic function of sucrose invertase.MethodsTo obtain basic knowledge about the number, classification, sequence composition, and physicochemical properties of sucrose invertases in daylily, bioinformatics software was used to analyze the genome of Hemerocallis citrina (H. citrina), and the basic properties of sucrose invertase genes and proteins were obtained. Then, combined with transcriptome data from flower organs at different developmental stages, the expression patterns of each gene were clarified. Finally, the reliability of the transcriptome data was verified by quantitative real-time polymerase chain reaction (PCR).ResultsThrough software analysis, 35 sucrose invertases were identified from the H. citrina genome and named HcINV1-HcINV35; these enzymes belong to three subfamilies: cell wall invertases, vacuolar invertases, and chloroplast invertases. The amino acid composition, motif types, promoter composition, gene structure, protein physicochemical properties, gene chromosomal localization, and evolutionary adaptability of daylily invertases were determined; these results provided a comprehensive understanding of daylily invertases. The transcriptome expression profile combined with fluorescence quantitative reverse transcription-polymerase chain reaction (RT‒PCR) analysis suggested that almost all daylily invertase genes were expressed in flower organs, but even genes belonging to the same subfamily did not exhibit the same expression pattern at different developmental stages, suggesting that there may be redundancy or dissimilation in the function of daylily sucrose invertases. creator: Guangying Ma creator: Ziwei Zuo creator: Lupeng Xie creator: Jiao Han uri: https://doi.org/10.7717/peerj.17999 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ma et al. title: Marine catfishes (Ariidae—Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group? link: https://peerj.com/articles/17581 last-modified: 2024-08-28 description: BackgroundAriidae species play a significant role as fishing resources in the Amazon region. However, the family’s systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition.MethodsFollowing morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon.ResultsOur sampling efforts yielded 12 species, representing 92% of the coastal Amazon region’s diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification. creator: Ítalo Lutz creator: Thais Martins creator: Paula Santana creator: Charles Ferreira creator: Josy Miranda creator: Suane Matos creator: Valdemiro Muhala creator: Iracilda Sampaio creator: Marcelo Vallinoto creator: Grazielle Evangelista-Gomes uri: https://doi.org/10.7717/peerj.17581 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lutz et al. title: Levels of biomarkers associated with subconcussive head hits in mixed martial arts fighters link: https://peerj.com/articles/17752 last-modified: 2024-08-28 description: BackgroundConcussion and the damage resulting from this event related to brain function have been widely studied; however, little is known about subconcussive impacts, especially in Mixed Martial Arts (MMA) fighters, which is a combat and full contact sport in which most blows are aimed at the head.ObjectiveThis study aims to evaluate the biomarker levels associated with subconcussive hits to the head in MMA fighters.MethodsThis is an exploratory study in which 30 male subjects (10 MMA fighters, 10 healthy individuals who practice muscle training, and 10 healthy sedentary individuals) aged between 18 and 32 years (25.4 ± 3.8) were evaluated. These individuals underwent blood collection to assess their Ubiquitin C-terminal hydrolase (UCH-L1), Glial Fibrillary Acidic Protein (GFAP) and Brain Derived Neurotrophic Factor (BDNF) levels before, immediately after and 72 hours after the sparring session (for the fighters) and were compared between groups.ResultsSignificant differences were found at baseline between active and healthy fighters in BDNF levels (p = 0.03). A significant reduction of BDNF levels were also observed between the post-immediate and 72h after the sparring session (p = 0.03). No differences were observed in the number or severity of symptoms reported by the fighters.ConclusionDespite the exploratory approach, the findings of this study may help to understand the influence of repeated subconcussive hits to the head in MMA fighters, as well as to propose preventive interventions which can minimize the effects of the impact of hits, preserving fighters’ neuronal integrity and function. creator: Nelson Marinho de Lima Filho creator: Sabrina Gabrielle Gomes Fernandes creator: Valeria Costa creator: Daline Araujo creator: Clecio Godeiro Jr creator: Gerlane Guerra creator: Ricardo Oliveira Guerra creator: Karyna Figueiredo Ribeiro uri: https://doi.org/10.7717/peerj.17752 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 de Lima Filho et al. title: Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines link: https://peerj.com/articles/17797 last-modified: 2024-08-28 description: Numerous aspects of cellular signaling are regulated by the kinome—the network of over 500 protein kinases that guides and modulates information transfer throughout the cell. The key role played by both individual kinases and assemblies of kinases organized into functional subnetworks leads to kinome dysregulation driving many diseases, particularly cancer. In the case of pancreatic ductal adenocarcinoma (PDAC), a variety of kinases and associated signaling pathways have been identified for their key role in the establishment of disease as well as its progression. However, the identification of additional relevant therapeutic targets has been slow and is further confounded by interactions between the tumor and the surrounding tumor microenvironment. In this work, we attempt to link the state of the human kinome, or kinotype, with cell viability in treated, patient-derived PDAC tumor and cancer-associated fibroblast cell lines. We applied classification models to independent kinome perturbation and kinase inhibitor cell screen data, and found that the inferred kinotype of a cell has a significant and predictive relationship with cell viability. We further find that models are able to identify a set of kinases whose behavior in response to perturbation drive the majority of viability responses in these cell lines, including the understudied kinases CSNK2A1/3, CAMKK2, and PIP4K2C. We next utilized these models to predict the response of new, clinical kinase inhibitors that were not present in the initial dataset for model devlopment and conducted a validation screen that confirmed the accuracy of the models. These results suggest that characterizing the perturbed state of the human protein kinome provides significant opportunity for better understanding of signaling behavior and downstream cell phenotypes, as well as providing insight into the broader design of potential therapeutic strategies for PDAC. creator: Matthew E. Berginski creator: Madison R. Jenner creator: Chinmaya U. Joisa creator: Gabriela Herrera Loeza creator: Brian T. Golitz creator: Matthew B. Lipner creator: Jack R. Leary creator: Naim Rashid creator: Gary L. Johnson creator: Jen Jen Yeh creator: Shawn M. Gomez uri: https://doi.org/10.7717/peerj.17797 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Berginski et al. title: Investigating the influence of eco-friendly approaches on saline soil traits and growth of common bean plants (Phaseolus vulgaris L.) link: https://peerj.com/articles/17828 last-modified: 2024-08-28 description: Soil salinization significantly impacts agricultural lands and crop productivity in the study area. Moreover, freshwater scarcity poses a significant obstacle to soil reclamation and agricultural production. Therefore, eco-friendly strategies must be adopted for agro-ecosystem sustainability under these conditions. A study conducted in 2022 and 2023 examined the interaction effects of various soil mulching materials (unmulched, white plastic, rice straw, and sawdust) and chitosan foliar spray application (control, 250 mg L−1 of normal chitosan, 125 mg L−1 of nano chitosan, and 62.5 mg L−1 of nano chitosan) on the biochemical soil characteristics and productivity of common beans in clay-saline soil. Higher organic matter, available nutrient content, and total bacteria count in soils were found under organic mulching treatments (rice straw and sawdust). In contrast, the white plastic mulching treatment resulted in the lowest values of soil electrical conductivity (EC) and the highest soil water content. Conversely, chitosan foliar spray treatments had the least impact on the chemical properties of the soil. Plants sprayed with 62.5 mg L−1 of nano chitosan exhibited higher chlorophyll content, plant height, fresh weight of shoots and roots, seed yield, and nutrient content compared to other chitosan foliar spray applications. All treatments studied led to a significant reduction in fungal communities and Na% in plants. The combined effect of organic mulch materials and foliar spray application of 62.5 mg L−1 nano chitosan appeared to enhance biochemical saline soil properties and common bean productivity. creator: Tamer Khalifa creator: Nasser Ibrahim Abdel-Kader creator: Mohssen Elbagory creator: Mohamed ElSayed Ahmed creator: Esraa Ahmed Saber creator: Alaa El-Dein Omara creator: Rehab Mohamed Mahdy uri: https://doi.org/10.7717/peerj.17828 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Khalifa et al. title: Comparative analysis of biomechanical characteristics between the new Tai Chi elastic band exercise for opening and closing movement and elastic band resistance training for the reverse fly movement link: https://peerj.com/articles/17839 last-modified: 2024-08-28 description: BackgroundThe objective of this study was to compare and analyze the representative opening and closing movement of Tai Chi elastic band exercise with the reverse fly movement of elastic band resistance training. The aim was to explore the biomechanical differences between the two exercises and provide theoretical support for the application of Tai Chi elastic band exercise in health intervention.MethodsA total of 26 male participants were recruited and randomly divided into two groups in a 1:1 ratio. There were 13 participants in each Tai Chi elastic band exercise group and elastic band resistance training group. Both groups of participants used an elastic band to perform movement in the experiment. Experimental data were collected using the Vicon infrared motion capture system and Delsys surface EMG system. The AnyBody software was utilized to simulate the creation of a musculoskeletal model for both exercises.ResultThe study found that the Tai Chi elastic band exercise group exhibited smaller horizontal abduction angle and flexion angle of the shoulder joint, as well as normalized RMS of the anterior deltoid and triceps brachii, compared to the elastic band resistance training group (P < 0.01); the Tai Chi elastic band exercise group exhibited greater elbow flexion angle, elbow flexion torque, and muscle strength of the infraspinatus, coracobrachialis, biceps brachii, brachialis and brachioradialis, compared to the elastic band resistance training group (P < 0.01); the Tai Chi elastic band exercise group exhibited smaller horizontal abduction angular velocity of the shoulder joint and a lower normalized RMS of the posterior deltoid, compared to the elastic band resistance training group (P < 0.05).Conclusion(1) The opening and closing movement of Tai Chi elastic band exercise is characterized by a large elbow flexion angle, a small shoulder joint horizontal angle and flexion angle, and a slow and uniform speed of movement. The reverse fly movement of elastic band resistance training is characterized by a large horizontal abduction angle of the shoulder joint, a large flexion angle of the shoulder joint, a small flexion angle of the elbow joint, and a fast and uneven speed. (2) The opening and closing movement exerts a greater torque on the elbow flexion, while the reverse fly movement exerts a greater torque on the shoulder joint horizontal abduction and external rotation. (3) The opening and closing movement provide greater stimulation to the infraspinatus, coracobrachialis, and elbow flexor, while the reverse fly movement provides greater stimulation to the posterior deltoid, anterior deltoid, subscapularis, and elbow extensor. In summary, the variation in joint angle, joint angular velocity, and hand position could be the factor contributing to the differences in joint torque and muscle activity between the opening and closing movement of Tai Chi elastic band exercise and the reverse fly movement of elastic band resistance training. creator: Mingyu Liu creator: Cuihan Li creator: Xiongfeng Li creator: Jianwei Zhang creator: Haojie Li creator: Yameng Li creator: Qiuyang Wei creator: Zaihao Chen creator: Jiahao Fu creator: Yanying Li creator: Meize Cui creator: Lujia Li creator: Peng Zhang creator: Yuerong Huang creator: Yuxin Ma creator: Jianan Xu creator: Shaojun Lyu creator: Yunchao Ma uri: https://doi.org/10.7717/peerj.17839 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: The role of DNA topoisomerase 1α (AtTOP1α) in regulating arabidopsis meiotic recombination and chromosome segregation link: https://peerj.com/articles/17864 last-modified: 2024-08-28 description: Meiosis is a critical process in sexual reproduction, and errors during this cell division can significantly impact fertility. Successful meiosis relies on the coordinated action of numerous genes involved in DNA replication, strand breaks, and subsequent rejoining. DNA topoisomerase enzymes play a vital role by regulating DNA topology, alleviating tension during replication and transcription. To elucidate the specific function of DNA topoisomerase 1α ($AtTOP1 \alpha$AtTOP1α) in male reproductive development of Arabidopsis thaliana, we investigated meiotic cell division in Arabidopsis flower buds. Combining cytological and biochemical techniques, we aimed to reveal the novel contribution of $AtTOP1 \alpha$AtTOP1α to meiosis. Our results demonstrate that the absence of $AtTOP1 \alpha$AtTOP1α leads to aberrant chromatin behavior during meiotic division. Specifically, the top1α1 mutant displayed altered heterochromatin distribution and clustered centromere signals at early meiotic stages. Additionally, this mutant exhibited disruptions in the distribution of 45s rDNA signals and a reduced frequency of chiasma formation during metaphase I, a crucial stage for genetic exchange. Furthermore, the atm-2×top1α1 double mutant displayed even more severe meiotic defects, including incomplete synapsis, DNA fragmentation, and the presence of polyads. These observations collectively suggest that $AtTOP1 \alpha$AtTOP1α plays a critical role in ensuring accurate meiotic progression, promoting homologous chromosome crossover formation, and potentially functioning in a shared DNA repair pathway with ATAXIA TELANGIECTASIA MUTATED (ATM) in Arabidopsis microspore mother cells. creator: Ibrahim Eid Elesawi creator: Ahmed M. Hashem creator: Li Yao creator: Mohamed Maher creator: Abdallah A. Hassanin creator: Diaa Abd El-Moneim creator: Fatmah A. Safhi creator: Nora M. Al Aboud creator: Salha Mesfer Alshamrani creator: Wael F. Shehata creator: Chen Chunli uri: https://doi.org/10.7717/peerj.17864 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Elesawi et al. title: Evolution of gene regulatory networks by means of selection and random genetic drift link: https://peerj.com/articles/17918 last-modified: 2024-08-28 description: The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. In this study, we implemented a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. The fitness effect of mutations is not constant, rather fitness of each individual is evaluated on the phenotypic level, by measuring its distance from an optimal phenotype. Each individual goes through a maturation period, where its GRN may reach an equilibrium, thus deciding its phenotype. Afterwards, individuals compete to produce the next generation. We examine properties of the GRN evolution, such as robustness against the deleterious effect of mutations and the role of genetic drift. We are able to confirm previous hypotheses regarding the effect of mutations and we provide new insights on the interplay between random genetic drift and natural selection. creator: Stefanos Papadadonakis creator: Antonios Kioukis creator: Charikleia Karageorgiou creator: Pavlos Pavlidis uri: https://doi.org/10.7717/peerj.17918 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Papadadonakis et al. title: Phylogenetic synthesis of morphological and molecular data reveals insights on the classification of diogenid hermit crabs (Crustacea: Decapoda: Anomura) link: https://peerj.com/articles/17922 last-modified: 2024-08-28 description: The family Diogenidae Ortmann, 1892 is a diverse and abundance group of hermit crabs, but their systematics and phylogenetic relationships are highly complex and unresolved. Herein, we gathered nucleotide sequence data from two mitochondrial (16S rRNA and COI) and two nuclear (NaK and PEPCK) genes for a total of 2,308 bp in length across 38 species from six extant diogenid genera. Molecular data were combined with 41 morphological characters to estimate the largest phylogeny of diogenid hermit crabs to date with the aim of testing the proposed taxonomic scheme of Diogenidae and addressing intergeneric relationships within this family. Despite conflicts between mitochondrial and nuclear DNA trees, the combined-data tree reflects the contributions of each dataset, and improves tree resolution and support for internal nodes. Contrary to traditional classification, our total evidence revealed a paraphyletic Diogenidae based on internally nested representatives of Coenobitidae Dana, 1851. Within Diogenidae, the studied diogenid hermit crabs were split between two clades with high support, which contradicts recent morphological classification scheme for Diogenidae sensu lato based on fossil records. The genus Diogenes Dana, 1851 was found nested inside Paguristes Dana, 1851, which formed a clade being separated from the remainder, pointing towards paraphyly in Paguristes. In another clade, Dardanus Paulson, 1875 occupied a basal position relative to the other diogenids, while Calcinus Dana, 1851 and Clibanarius Dana, 1852 showed sister relationships and formed a cluster with Ciliopagurus Forest, 1995. Among the morphological characters examined, carapace shield and telson were identified as phylogenetically significant for grouping diogenid genera, while phylogenetic insignificance of gill number was evidenced by its mosaic pattern in diogenid phylogeny. The present study sheds light on the controversial generic phylogeny of Diogenidae and highlights the necessity for thorough taxonomic revisions of this family as well as some genera (e.g., Paguristes) to reconcile current classifications with phylogenetic relationships. creator: Jiao Cheng creator: Wenjie Li creator: Yanrong Wang creator: Zhongli Sha uri: https://doi.org/10.7717/peerj.17922 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cheng et al. title: Lost, hidden, broken, cut-estimating and interpreting the shapes and masses of damaged assemblages of plesiosaur gastroliths link: https://peerj.com/articles/17925 last-modified: 2024-08-28 description: BackgroundGastroliths are stones of uncertain purpose that are commonly found inside the rib cages of plesiosaur fossils worldwide. Gastroliths from four Alberta (Canada) plesiosaurs were studied to determine both their shapes and masses, and their mass fractions relative to body mass. One animal’s set of gastroliths was 100% complete and fully visible, but the others showed varying degrees of loss, damage or obscuration, so estimations of their original states were needed.MethodsThe studied animals were: Albertonectes vanderveldei, Fluvionectes sloanae, Nichollssaura borealis and Wapuskanectes betsynichollsae. The animals come from three different palaeoenvironments: open marine, near shore marine, and fluvial. Gastrolith shapes were classified as either xiphoid, cylindrical, discoidal or spherical based on observed and/or estimated dimensions. Although not all methods could be applied in all cases, gastrolith shapes and masses were estimated four different ways: (1) direct measurement and weighing of a subset and predicting the properties of the remaining obscured and hidden stones; (2) measuring triaxial ellipsoid dimensions of free stones to calculate volumes and multiplying by the mass density of chert; (3) measuring two visible triaxial dimensions of embedded stones, estimating the hidden third dimension three different ways, and then determining volumes and masses by calculation; and (4) predicting the density and mass of a densely packed cluster of small gastroliths using geometrical arguments.ResultsTotal gastrolith mass never exceeded 0.2% of body mass in any plesiosaur, and is consistent with the idea that the amounts of gastroliths recovered with plesiosaurs would be ineffective as ballast. The largest plesiosaur in the sample had the largest single gastrolith and total gastrolith mass increases with body size. The shape characteristics of the gastroliths were different for different environments, but compositionally they are dominated by black cherts. A possible common source for the gastroliths was identified for the two geographically close and near-contemporanous Nichollssaura and Wapuskanectes. creator: Donald M. Henderson uri: https://doi.org/10.7717/peerj.17925 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Henderson title: The median effective concentration of ropivacaine for ultrasound-guided anterior iliopsoas muscle space block in the elderly undergoing hip surgery: a dose-finding study link: https://peerj.com/articles/17970 last-modified: 2024-08-28 description: BackgroundIn order to improve perioperative pain and reduce the adverse outcome of severe pain in elderly hip fractures, anterior iliopsoas muscle space block (AIMSB) can be used clinically to reduce pain. The aim of the study is to investigate the 50% effective concentration (EC50) of ropivacaine for ultrasound-guided anterior iliopsoas space block in elderly with hip fracture.MethodsA total of 27 patients were enrolled with aged ≥65 years, American society of Anesthesiologists (ASA) physical status classification II–III and undergoing Total Hip Arthroplasty (THA). We measured the EC50 using Dixon’s up-and-down method. Ultrasound-guided AIMSB was performed preoperatively with an initial concentration of 0.2% in the first patient. After a successful or unsuccessful postoperative analgesia, the concentration of local anesthetic was decreased or increased 0.05%, respectively in the next patient. The successful block effect was defined as no sensation to pinprick in the area with femoral nerve, obturator nerve, and lateral femoral cutaneous nerve in 30 min. Meanwhile, the EC50 of ropivacaine was determined by using linear model, linear-logarithmic model, probit regression model, and centered isotonic regression.ResultsA total of 12 patients (48%) had a successful block. All patients with a successful block had a postoperative visual analog scale score of <4 in the 12 h. The estimated EC50 values in linear model, linear-logarithmic model, probit regression model, and centered isotonic regression (a nonparametric method) were 0.268%, 0.259%, 0.277%, and 0.289%. The residual standard error of linear model was the smallest (0.1245).ConclusionThe EC50 of ropivacaine in anterior iliopsoas space block under ultrasound guidance is 0.259–0.289%. creator: Peng Ma creator: Rui Zeng creator: Jiang Peng creator: Juan Zhu creator: Zhaojun Jing creator: Yu Han uri: https://doi.org/10.7717/peerj.17970 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ma et al. title: Assessing the opportunity for selection to impact morphological traits in crosses between two Solanum species link: https://peerj.com/articles/17985 last-modified: 2024-08-28 description: Within biology, there have been long-standing goals to understand how traits impact fitness, determine the degree of adaptation, and predict responses to selection. One key step in answering these questions is to study the mode of gene action or genetic architecture of traits. The genetic architecture underlying a trait will ultimately determine whether selection can lead to a change in the phenotype. Theoretical and empirical research have shown that additive architectures are most responsive to selection. The genus Solanum offers a unique system to quantify the genetic architecture of traits. Crosses between Solanum pennellii and S. lycopersicum, which have evolved unique adaptive traits for very different environments, offer an opportunity to investigate the genetic architecture of a variety of morphological traits that often are not variable within species. We generated cohorts between strains of these two Solanum species and collected phenotypic data for eight morphological traits. The genetic architectures underlying these traits were estimated using an information-theoretic approach to line cross analysis. By estimating the genetic architectures of these traits, we were able to show a key role for maternal and epistatic effects and infer the accessibility of these traits to selection. creator: Jorja Burch creator: Crystal Nava creator: Heath Blackmon uri: https://doi.org/10.7717/peerj.17985 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Burch et al. title: Intervention effect of exercise on working memory in patients with depression: a systematic review link: https://peerj.com/articles/17986 last-modified: 2024-08-28 description: BackgroundThis article aims to systematically evaluate the intervention effect of exercise on working memory in patients with depression.MethodsSix Chinese and English databases were searched for randomized controlled trials (RCTs) about exercise on working memory in patients with depression. PEDro scale was adopted to evaluate the methodological quality of the included articles, GRADEpro scale was employed to evaluate the level of evidence for outcomes, and the Metafor Package in R 4.4.1 was used to analyze the combined effect size, subgroup analyses and publication bias.ResultsA total of 15 studies were included. The meta-analysis indicated that exercise had a statistically significant effect on working memory in patients with depression, with an effect size of 0.16 (95% CI [0.03–0.28], p = 0.02). Exercise type (F(3,34) = 1.99, p = 0.13), intervention content (F(1,36) = 1.60, p = 0.22), and exercise duration (F(1,36) = 0.05, p = 0.83) did not moderate the effect, whereas exercise intensity showed a moderating effect (F(2,35) = 8.83, p < 0.01). There was evidence of publication bias in the study results (t = 2.52, p = 0.02).ConclusionExercise can improve the working memory of patients with depression, and its moderating effect is the best when having low-intensity and moderate-intensity. Research plan was registered in international system evaluation platform PROSPERO (https://www.crd.york.ac.uk/PROSPERO/) (CRD42023475325). creator: Cong Liu creator: Rao Chen creator: So Mang Yun creator: Xing Wang uri: https://doi.org/10.7717/peerj.17986 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Quantifying and analysing the angular momentum in volleyball jump serve during the aerial phase: relationship to arm swing speed link: https://peerj.com/articles/18000 last-modified: 2024-08-28 description: BackgroundIn volleyball, the jump serve is a crucial and commonly used serving technique. Nonetheless, the angular momentum developed during the jump serve remains unexplored. The objectives of the current study were to determine the angular momentum manifesting during the airborne phase of the jump serve and to analyse the correlations between the angular momentum variables and arm swing speed.MethodsThree-dimensional coordinate data were obtained during the jump serves of 17 professional male volleyball players. Correlation and linear regression analyses were used to identify the angular momentum variables linked to the arm swing speed at ball impact (BI).ResultsThe arm swing speed at BI exhibited significant correlations with the peak angular momentum of the attack arm (r = 0.551, p = 0.024), non-attack arm (r = 0.608, p = 0.011), non-attack leg (r = −0.516, p = 0.034), forearm (r = 0.527, p = 0.032), and hand (r = 0.824, p < 0.001). A stepwise regression model (R2 = 0.35, p = 0.043) predicted arm swing speed based on the peak angular momentum of the non-attack leg, forearm, and hand.ConclusionsThe study results suggest that during the arm-acceleration phase, (1) increasing angular momentum with the non-attack leg helps maintain aerial body balance, thereby enhancing arm swing execution, and (2) controlling the magnitude and timing of the force exerted by the elbow and wrist is crucial for effectively transmitting angular momentum, contributing to an increase in arm swing speed. creator: Lingjun Liu creator: Zhenxiang Chen creator: Defeng Zhao creator: Zhizong Tan creator: Yaqian Qi uri: https://doi.org/10.7717/peerj.18000 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Mitochondria dysfunction is one of the causes of diclofenac toxicity in the green alga Chlamydomonas reinhardtii link: https://peerj.com/articles/18005 last-modified: 2024-08-28 description: BackgroundNon-steroidal anti-inflammatory drugs (NSAIDs), such as diclofenac (DCF), form a significant group of environmental contaminants. When the toxic effects of DCF on plants are analyzed, authors often focus on photosynthesis, while mitochondrial respiration is usually overlooked. Therefore, an in vivo investigation of plant mitochondria functioning under DCF treatment is needed. In the present work, we decided to use the green alga Chlamydomonas reinhardtii as a model organism.MethodsSynchronous cultures of Chlamydomonas reinhardtii strain CC-1690 were treated with DCF at a concentration of 135.5 mg × L−1, corresponding to the toxicological value EC50/24. To assess the effects of short-term exposure to DCF on mitochondrial activity, oxygen consumption rate, mitochondrial membrane potential (MMP) and mitochondrial reactive oxygen species (mtROS) production were analyzed. To inhibit cytochrome c oxidase or alternative oxidase activity, potassium cyanide (KCN) or salicylhydroxamic acid (SHAM) were used, respectively. Moreover, the cell’s structure organization was analyzed using confocal microscopy and transmission electron microscopy.ResultsThe results indicate that short-term exposure to DCF leads to an increase in oxygen consumption rate, accompanied by low MMP and reduced mtROS production by the cells in the treated populations as compared to control ones. These observations suggest an uncoupling of oxidative phosphorylation due to the disruption of mitochondrial membranes, which is consistent with the malformations in mitochondrial structures observed in electron micrographs, such as elongation, irregular forms, and degraded cristae, potentially indicating mitochondrial swelling or hyper-fission. The assumption about non-specific DCF action is further supported by comparing mitochondrial parameters in DCF-treated cells to the same parameters in cells treated with selective respiratory inhibitors: no similarities were found between the experimental variants.ConclusionsThe results obtained in this work suggest that DCF strongly affects cells that experience mild metabolic or developmental disorders, not revealed under control conditions, while more vital cells are affected only slightly, as it was already indicated in literature. In the cells suffering from DCF treatment, the drug influence on mitochondria functioning in a non-specific way, destroying the structure of mitochondrial membranes. This primary effect probably led to the mitochondrial inner membrane permeability transition and the uncoupling of oxidative phosphorylation. It can be assumed that mitochondrial dysfunction is an important factor in DCF phytotoxicity. Because studies of the effects of NSAIDs on the functioning of plant mitochondria are relatively scarce, the present work is an important contribution to the elucidation of the mechanism of NSAID toxicity toward non-target plant organisms. creator: Darya Harshkova creator: Elżbieta Zielińska creator: Magdalena Narajczyk creator: Małgorzata Kapusta creator: Anna Aksmann uri: https://doi.org/10.7717/peerj.18005 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Harshkova et al. title: Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability link: https://peerj.com/articles/17889 last-modified: 2024-08-27 description: Higher efficiency in large-scale and long-term biodiversity monitoring can be obtained through the use of Essential Biodiversity Variables, among which species population sizes provide key data for conservation programs. Relevant estimations and assessment of actual population sizes are critical for species conservation, especially in the current context of global biodiversity erosion. However, knowledge on population size varies greatly, depending on species conservation status and ranges. While the most threatened or restricted-range species generally benefit from exhaustive counts and surveys, monitoring common and widespread species population size tends to be neglected or is simply more challenging to achieve. In such a context, citizen science (CS) is a powerful tool for the long-term monitoring of common species through the engagement of various volunteers, permitting data acquisition on the long term and over large spatial scales. Despite this substantially increased sampling effort, detectability issues imply that even common species may remain unnoticed at suitable sites. The use of structured CS schemes, including repeated visits, enables to model the detection process, permitting reliable inferences of population size estimates. Here, we relied on a large French structured CS scheme (EPOC-ODF) comprising 27,156 complete checklists over 3,873 sites collected during the 2021–2023 breeding seasons to estimate the population size of 63 common bird species using hierarchical distance sampling (HDS). These population size estimates were compared to the previous expert-based French breeding bird atlas estimations, which did not account for detectability issues. We found that population size estimates from the former French breeding bird atlas were lower than those estimated using HDS for 65% of species. Such a prevalence of lower estimations is likely due to more conservative estimates inferred from semi-quantitative expert-based assessments used for the previous atlas. We also found that species with long-range songs such as the Common Cuckoo (Cuculus canorus), Eurasian Hoopoe (Upupa epops) or the Eurasian Blackbird (Turdus merula) had, in contrast, higher estimated population sizes in the previous atlas than in our HDS models. Our study highlights the need to rely on sound statistical methodology to ensure reliable ecological inferences with adequate uncertainty estimation and advocates for a higher reliance on structured CS in support of long-term biodiversity monitoring. creator: Jean Nabias creator: Luc Barbaro creator: Benoît Fontaine creator: Jérémy Dupuy creator: Laurent Couzi creator: Clément Vallé creator: Romain Lorrilliere uri: https://doi.org/10.7717/peerj.17889 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Nabias et al. title: Fecal shedding of SARS-CoV-2 in infants born to SARS-CoV-2 positive mothers: a pilot study link: https://peerj.com/articles/17956 last-modified: 2024-08-27 description: BackgroundFecal shedding of SARS-CoV-2 occurs during infection, particularly in pediatric populations. The gut microbiota are associated with resistance to enteric pathogens. COVID-19 is associated with alterations to the gut microbiome. We hypothesized that the gut microbiome of infants born to SARS-CoV-2+ mothers differs between infants with and without fecal shedding of the virus.MethodsWe enrolled 10 infants born to SARS-CoV-2+ mothers. We used qPCR on fecal RNA to test for SARS-CoV-2 and 16S rRNA gene sequencing of the V4 region to assess the gut microbiome. Infant SARS-CoV-2 status from nasal swabs was abstracted from medical records.ResultsOf the 10 included infants, nine were tested for SARS-CoV-2 by nasal swab with 1 testing positive. Four infants, including the nasal swab positive infant, had at least one sample with detectable levels of SARS-CoV-2 fecal shedding. Detection of both SARS-CoV-2 genes in feces was associated with increased gut alpha diversity compared to no detection by a linear mixed effects model (p < 0.001). Detection of both SARS-CoV-2 genes was associated with increased levels Erysipelotrichaceae, Lactobacillaceae, and Ruminococceae by MaAsLin2.ConclusionFecal shedding of SARS-CoV-2 occurs in infants who test negative on nasal swabs and is associated with differences in the gut microbiome. creator: Dylan K.P. Blaufus creator: Karen M. Kalanetra creator: Rosa Pesavento creator: Pranav Garlapati creator: Brittany C. Baikie creator: Kara M. Kuhn-Riordon creator: Mark A. Underwood creator: Diana H. Taft uri: https://doi.org/10.7717/peerj.17956 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Blaufus et al. title: Variation in floral morphology, histochemistry, and floral visitors of three sympatric morning glory species link: https://peerj.com/articles/17866 last-modified: 2024-08-26 description: Three morning glory species in the genus Argyreia Lour., A. lycioides (Choisy) Traiperm & Rattanakrajang, A. mekongensis Gagnep & Courchet, and A. versicolor (Kerr) Staples & Traiperm, were found co-occurring and co-flowering. Argyreia mekongensis and A. versicolor are rare, while A. lycioides is near threatened and distributed throughout Myanmar and Thailand. We investigated key floral characters (floral morphology and phenology, as well as the micromorphology of the floral nectary disc and staminal trichomes) and screened for important chemical compounds hypothesized to contribute to pollinator attraction. Our findings demonstrate that some aspects of floral morphology (e.g., corolla size, limb presence, and floral color) of the three studied congeners exhibit significant differences. Moreover, pollinator composition appears to be influenced by floral shape and size; morning glory species with wider corolla tubes were pollinated by larger bees. The morphology of the floral nectary disc was similar in all species, while variation in staminal trichomes was observed across species. Glandular trichomes were found in all three species, while non-glandular trichomes were found only in A. versicolor. Histochemical results revealed different compounds in the floral nectary and staminal trichomes of each species, which may contribute to both floral attraction and defense. These findings demonstrate some segregation of floral visitors among sympatric co-flowering morning glory species, which appears to be influenced by the macro- and micromorphology of flowers and their chemical compounds. Moreover, understanding the floral morphology and chemical attractants of these sympatric co-flowering Argyreia species may help to maintain their common pollinators in order to conserve these rare and endangered species, especially A. versicolor. creator: Awapa Jirabanjongjit creator: Alyssa B. Stewart creator: Natthaphong Chitchak creator: Chakkrapong Rattamanee creator: Paweena Traiperm uri: https://doi.org/10.7717/peerj.17866 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jirabanjongjit et al. title: The use of silver diamine fluoride to prevent/treat enamel carious lesions: a narrative review link: https://peerj.com/articles/17897 last-modified: 2024-08-26 description: This comprehensive literature review examines the use of silver diamine fluoride (SDF) for the prevention and treatment of enamel carious lesions. SDF has been approved by different international drug associations as a caries-preventing agent to be used on deep carious lesions (dentin). However, SDF can cause staining of exposed tooth structures. Furthermore, the effect of SDF on the bond of adhesives to the tooth structure is still being determined. This review explores various studies on the use of SDF to treat enamel carious lesions, highlighting its effectiveness and preventive action. The literature suggests that SDF inhibits bacterial growth, promotes remineralization, and does not negatively affect adhesive retentions. Potassium iodide (KI) or glutathione (GSH) can reduce staining and discoloration. However, the reviewed studies have limitations. Further research, including well-designed clinical trials, is necessary to validate the findings and evaluate the long-term implications of SDF treatment. Conclusion: Despite the above-mentioned limitations, SDF shows potential as a therapy for enamel caries prevention, remineralization, and use as an adjuvant to other dental treatments, warranting further investigation and the refinement of application methods. creator: Rasha N. AlSheikh uri: https://doi.org/10.7717/peerj.17897 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 AlSheikh title: Prochloraz induced alterations in the expression of mRNA in the reproductive system of male offspring mice link: https://peerj.com/articles/17917 last-modified: 2024-08-26 description: Prochloraz is a widely used fungicide worldwide. It is classified as an endocrine disrupting pesticide that affects the reproductive system. This study aimed to examine the impact of exposure to prochloraz of male mice on the reproductive system of their offspring male mice. Male father mice were intragastrically administered different dosages of prochloraz (group MA: 0 mg/kg/day; MB: 53.33 mg/kg/day; MD:160 mg/kg/day). Then, the testicular average weight of male offspring in the dose groups was found to be significantly lower than those in the control group (MB:0.312g, MD:0.294g, and MA:0.355 g; P < 0.05). Additionally, the testicular coefficient index in the MB and MD groups was also lower than that of the control group. Secondly,we observed that there were significantly different expressed genes clustered in groups B and D, in contrast to the control. Finally, the findings demonstrated a significant alteration in the response of male mice reproductive relative genes to prochloraz invasion. Two genes (Mt-nd6 and Slc12a4) were found to be involved in the regulation of sperm mitochondria function and six genes (Greb1, Esrrb, Catsperb, Mospd2, Sohlh1 and Specc1) were closely linked to sperm functions and estrogen response. The study revealed a significant impact of prochloraz on the reproductive system of male mice, thereby supporting further investigation into the reproductive toxicological effects of the drug. creator: Junhe Hu creator: Chang Liu creator: Xianghui Zeng creator: Tao Tang creator: Zhi Zeng creator: Juan Wu creator: Xiansheng Tan creator: Qingxiang Dai creator: Chenzhong Jin uri: https://doi.org/10.7717/peerj.17917 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hu et al. title: Evaluation of the forces applied by rubber dam clamps on mandibular first molar teeth with different endodontic access cavities: a 3D FEA study link: https://peerj.com/articles/17921 last-modified: 2024-08-26 description: BackgroundThis study aimed to examine the effect of the force applied by rubber dam clamps made from different materials on mandibular first molar teeth with various designs of endodontic access cavities using finite element analysis.MethodsA intact tooth (IT) and seven different endodontic access cavities namely, a traditional endodontic cavity (TRADAC), a guided endodontic cavity (GEC), a conservative endodontic cavity (CAC), an ultra-conservative access cavity (UAC), a truss access endodontic cavity (TRSAC), a mesial caries access cavity (MCAC), and a distal caries access cavity (DCAC), along with two different clamp finite element models, were created. The clamp models were made of polyether ether ketone (PEEK) and stainless steel (SS). The forces applied by the clamps were calculated based on the axial section distance of the tooth, and these forces were applied to the contact areas on the tooth. Stress distribution models were calculated using maximum von Mises (vM) stress.ResultsThe lowest vM stress under the forces applied by the SS and PEEK clamps was found in the IT model (80.914 MPa) with the PEEK clamp. The highest vM stress was found in the DCAC model (759.49 MPa) applied with the SS clamp. The forces applied by SS clamps resulted in higher vM stress values in every cavity design than those applied by PEEK clamps.ConclusionPEEK clamps generated less force than SS clamps. However, clinicians should follow various isolation strategies (clamp made of different materials, split dam, etc.) according to different cavity types of the tooth. creator: Mehmet Eskibağlar creator: Serkan Erdem creator: Büşra Karaağaç Eskibağlar creator: Mete Onur Kaman uri: https://doi.org/10.7717/peerj.17921 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Eskibağlar et al. title: Effect of exogenous melatonin on growth and antioxidant system of pumpkin seedlings under waterlogging stress link: https://peerj.com/articles/17927 last-modified: 2024-08-26 description: Melatonin regulates defense responses in plants under environmental stress. This study aimed to explore the impact of exogenous melatonin on the phenotype and physiology of ‘BM1’ pumpkin seedlings subjected to waterlogging stress. Waterlogging stress was induced following foliar spraying of melatonin at various concentrations (CK, 0, 10, 100, 200, and 300 μmol·L−1). The growth parameters, malondialdehyde (MDA) content, antioxidant enzyme activity, osmoregulatory substance levels, and other physiological indicators were assessed to elucidate the physiological mechanisms underlying the role of exogenous melatonin in mitigating waterlogging stress in pumpkin seedlings. The results indicate that pumpkin seedlings exhibit waterlogging symptoms, such as leaf wilting, water loss, edge chlorosis, and fading, under waterlogging stress conditions. Various growth indicators of the seedlings, including plant height, stem diameter, root length, fresh and dry weight, and leaf chlorophyll content, were significantly reduced. Moreover, the MDA content in leaves and roots increased significantly, along with elevated activities of superoxide dismutase, catalase, peroxidase, and soluble protein contents. When different concentrations of melatonin were sprayed on the leaves post waterlogging stress treatment, pumpkin seedlings showed varying degrees of recovery, with the 100 μmol·L−1 treatment displaying the best growth status and plant morphological phenotypes. There were no significant differences compared to the control group. Seedling growth indicators, chlorophyll content, root activity, antioxidant enzyme activities, soluble protein content, and osmotic adjustment substance content all increased to varying degrees with increasing melatonin concentration, peaking at 100 μmol·L−1. Melatonin also reduced membrane damage caused by oxidative stress and alleviated osmotic imbalance. Exogenous melatonin enhanced the activities of antioxidant enzymes and systems involved in scavenging reactive oxygen species, with 100 μmol·L−1 as the optimal concentration. These findings underscore the crucial role of exogenous melatonin in alleviating waterlogging stress in pumpkins. The findings of this study offer a theoretical framework and technical assistance for cultivating waterlogging-resistant pumpkins in practical settings. Additionally, it establishes a theoretical groundwork for the molecular breeding of pumpkins with increased tolerance to waterlogging. creator: Zhenyu Liu creator: Li Sun creator: Zhenwei Liu creator: Xinzheng Li uri: https://doi.org/10.7717/peerj.17927 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Comparison of the recovery quality between remimazolam and propofol after general anesthesia: systematic review and a meta-analysis of randomized controlled trials link: https://peerj.com/articles/17930 last-modified: 2024-08-26 description: IntroductionTo evaluate the recovery quality between remimazolam and propofol after general anesthesia surgery.MethodsWe included eligible randomized controlled trials (RCTs) in EMBASE, PubMed, Cochrane Central, Scopus, and Web of Science up to June 26, 2024 for comparison the recovery quality of remimazolam and propofol after general anaesthesia. The primary outcomes were the total Quality of Recovery-15 (QoR-15) and five dimensions of QoR-15 on postoperative day 1 (POD1). Secondary outcomes were adverse events, the Quality of Recovery-40 (QoR-40) on POD1, and the intraoperative and postoperative time characteristics.ResultsThirteen RCTs with a total of 1,305 patients were included in this meta-analysis. Our statistical analysis showed that remimazolam group had higher QoR-15 score on POD1, with no significant difference (Mean Difference (MD) = 1.24; 95% confidence interval (CI), [−1.67–4.15]; I2 = 75%; P = 0.41). In the five dimensions of QoR-15, remimazolam group was superior to propofol group in terms of physical independence (MD = 0.79; 95% CI [0.31–1.27]; I2 = 0%; P = 0.001). Remimazolam group was lower than propofol group in incidence of hypotension (Risk Ratio (RR) = 0.48; 95% CI [0.40–0.59]; I2 = 14%; P < 0.00001), bradycardia (RR = 0.18; 95% CI [0.08–0.38]; I2 = 0%; P < 0.0001) and injection pain (RR = 0.03; 95% CI [0.01–0.12]; I2 = 48%; P < 0.00001), respectively. The intraoperative and postoperative time characteristics and the QoR-40 were similar in the two groups.ConclusionsOur analysis showed that the recovery quality of the remimazolam group after general anaesthesia was similar to propofol group, while the incidence of adverse events was low in remimazolam group. As a potential anesthetic, remimazolam can be used in place of propofol for surgical general anesthesia. creator: Caiyun Zhu creator: Ran Xie creator: Fang Qin creator: Naiguo Wang creator: Hui Tang uri: https://doi.org/10.7717/peerj.17930 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhu et al. title: Advances in understanding the role of lncRNA in ferroptosis link: https://peerj.com/articles/17933 last-modified: 2024-08-26 description: LncRNA is a type of transcript with a length exceeding 200 nucleotides, which was once considered junk transcript with no biological function during the transcription process. In recent years, lncRNA has been shown to act as an important regulatory factor at multiple levels of gene expression, affecting various programmed cell death modes including ferroptosis. Ferroptosis, as a new form of programmed cell death, is characterized by a deficiency of cysteine or inactivation of glutathione peroxidase, leading to depletion of glutathione, aggregation of iron ions, and lipid peroxidation. These processes are influenced by many physiological processes, such as the Nrf2 pathway, autophagy, p53 pathway and so on. An increasing number of studies have shown that lncRNA can block the expression of specific molecules through decoy effect, guide specific proteins to function, or promote interactions between molecules as scaffolds. These modes of action regulate the expression of key factors in iron metabolism, lipid metabolism, and antioxidant metabolism through epigenetic or genetic regulation, thereby regulating the process of ferroptosis. In this review, we snapshotted the regulatory mechanism of ferroptosis as an example, emphasizing the regulation of lncRNA on these pathways, thereby helping to fully understand the evolution of ferroptosis in cell fate. creator: Yating Wen creator: Wenbo Lei creator: Jie Zhang creator: Qiong Liu creator: Zhongyu Li uri: https://doi.org/10.7717/peerj.17933 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wen et al. title: Favour the best in case of emergency cricothyroidotomy–a randomized cross-over trial on manikin focused training and simulation of common devices link: https://peerj.com/articles/17788 last-modified: 2024-08-23 description: BackgroundPerforming an emergency cricothyroidotomy (EC) is extremely challenging, the devices used should be easy to handle and the selected technique reliable. However, there is still an ongoing debate concerning the most superior technique.MethodsThree different techniques were compared using a standardized, simulated scenario regarding handling, performing, training and decision making: The scalpel-bougie technique (SBT), the surgical anatomical preparation technique (SAPT) and the Seldinger technique (ST). First, anaesthesia residents and trainees, paramedics and medical students (each group n = 50) performed a cricothyroidotomy randomly assigned with each of the three devices on a simulator manikin. The time needed for successful cricothyroidotomy was the primary endpoint. Secondary endpoints included first-attempt success rate, number of attempts and user-satisfaction. The second part of the study investigated the impact of prior hands-on training on both material selection for EC and on time to decision-making in a simulated “cannot intubate cannot ventilate” situation.ResultsThe simulated scenario revealed that SBT and SAPT were significantly faster than percutaneous EC with ST (p < 0.0001). Success rate was 100% for the first attempt with SBT and SAPT. Significant differences were found with regard to user-satisfaction between individual techniques (p < 0.0001). In terms of user-friendliness, SBT was predominantly assessed as easy (87%). Prior training had a large impact regarding choice of devises (p < 0.05), and time to decision making (p = 0.05; 180 s vs. 233 s).ConclusionThis study supports the use of a surgical technique for EC and also a regular training to create familiarity with the materials and the process itself.The trial was registered before study start on 11.11.2018 at ClinicalTrials.gov (NCT: 2018-13819) with Nicole Didion as the principal investigator. creator: Nicole Didion creator: Fabian Pohlmann creator: Nina Pirlich creator: Eva Wittenmeier creator: Christoph Jänig creator: Daniel Wollschläger creator: Eva-Verena Griemert uri: https://doi.org/10.7717/peerj.17788 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Didion et al. title: Prevalence of physical, psychological and sexual intimate partner violence among women of reproductive age during COVID-19 in Ethiopia: a systematic review and meta-analysis link: https://peerj.com/articles/17812 last-modified: 2024-08-23 description: IntroductionCOVID-19 preventive measures such as stay at home and isolation leads to violence against women. Intimate partner violence (IPV) is one of the common violence during this pandemic. This study aimed to assess the prevalence of physical, psychological and sexual intimate partner violence among reproductive age women during COVID-19 in Ethiopia.Materials and MethodsElectronic databases such as PubMed, Google Scholar and African journals online and studies available from the occurrence of the pandemic to April 2023 were searched. Two researchers collected the data and independently performed the methodological quality assessment. To pool the collected data for each outcome with 95% confidence interval (CI), DerSimonian-Laird random effects meta-analysis was used. Publication bias was measured by Doi plot LFK index and Egger’s test. Stata version 14.0 (StataCorp, College Station, Texas, USA) software was used for statistical analysis.ResultsA total of seven studies reported the prevalence of intimate partner violence among women in reproductive age during COVID-19, and the pooled prevalence of physical intimate partner violence was 22% (95% CI [0.12–0.32], I2 = 98.9%, tau2 = 0.0184, p < 0.001). The pooled prevalence of psychological intimate partner violence was 28% (95% CI [0.18–0.37], I2 = 98.1%, tau2 = 0.0142, p < 0.001). The pooled prevalence of sexual intimate partner violence was 23% (95% CI [0.13–0.34], I2 = 99.1%, tau2 = 0.0208, p < 0.001).ConclusionsDuring COVID-19 reproductive age women in Ethiopia were affected by intimate partner violence. Physical, psychological and sexual intimate partner violence were reported, and their prevalence was high due to the pandemic. Future studies on impact of COVID-19 on IPV among reproductive age women should be conducted in nationwide to make more comprehensive conclusion.PROSPERO registration number:CRD42023417628. creator: Aragaw Asfaw Hasen creator: Abubeker Alebachew Seid creator: Ahmed Adem Mohammed creator: Kassaye Getaneh Arge uri: https://doi.org/10.7717/peerj.17812 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hasen et al. title: Study of LY9 as a potential biomarker for prognosis and prediction of immunotherapy efficacy in lung adenocarcinoma link: https://peerj.com/articles/17816 last-modified: 2024-08-23 description: BackgroundLymphocyte antigen 9 (LY9) participates in the development of several tumors and diseases but has not been reported yet in lung adenocarcinoma (LUAD).MethodsFirst, we analyzed the expression and prognostic value of LY9 in pan-cancer, including LUAD. Additionally, we conducted a correlation analysis of LY9 expression in LUAD with immune cell infiltration using the TIMER database and the CIBERSORT algorithm, and with immune checkpoints using the GEPIA database. Also, we constructed a potential ceRNA network for LY9. Furthermore, we explored LY9-related pathways by Gene Set Enrichment Analysis (GSEA). Finally, validation of differential expression at the mRNA level was obtained from the GEO database. We collected LUAD tissues for Quantitative Real-time PCR (qRT-PCR) to verify the expression of LY9, CD8, and CD4 and calculated the correlation between them. We also conducted immunohistochemistry (IHC) to verify the protein expression of LY9.ResultsResults showed that LY9 was highly expressed in various tumors, including LUAD. Besides, patients with high LY9 expression presented longer overall survival (OS) and more multiple lymphocyte infiltrations. The expression of LY9 in LUAD strongly and positively correlates with multiple immune cell infiltration and immune checkpoints. The functional enrichment analysis indicated that LY9 was involved in multiple immune-related pathways and non-small cell lung cancer. Moreover, a ceRNA regulatory network of LINC00943-hsa-miR-141-3p-LY9 might be involved. Finally, GSE68465 dataset confirmed differential expression of LY9 mRNA levels in LUAD and the qRT-PCR results verified LY9 had a strong and positive correlation with CD4 and CD8 T cells. Unfortunately, IHC did not detect the expression of LY9 protein level in tumor tissues and WB experiments validated the protein expression of LY9 in the OCI-AML-2 cell line.ConclusionsTherefore, we hypothesized that LY9 could serve as a potential, novel prognostic biomarker for LUAD and could predict immunotherapy efficacy at the mRNA level. creator: Kun Deng creator: Liqiang Yuan creator: Zhanyu Xu creator: Fanglu Qin creator: Zhiwen Zheng creator: Liuliu Huang creator: Wei Jiang creator: Junqi Qin creator: Yu Sun creator: Tiaozhan Zheng creator: Xinhuai Ou creator: Liping Zheng creator: Shikang Li uri: https://doi.org/10.7717/peerj.17816 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Deng et al. title: The contribution of energy systems during 15-second sprint exercise in athletes of different sports specializations link: https://peerj.com/articles/17863 last-modified: 2024-08-23 description: BackgroundLong-term adaptations and ongoing training seem to modify the energy system contribution in highly trained individuals. We aimed to compare the energy metabolism profile during sprint exercise in athletes of different specialties.MethodsEndurance (n = 17, 20.3 ± 6.0 yrs), speed-power (n = 14, 20.3 ± 2.5 yrs), and mixed (n = 19, 23.4 ± 4.8 yrs) athletes performed adapted 15-second all-out test before and after a general preparation training period. The contribution of phosphagen, glycolytic, and aerobic systems was calculated using the three-component PCr-LA-O2 method.ResultsBetween-group differences were observed in the contribution of energy systems in the first and second examinations. The proportions were 47:41:12 in endurance, 35:57:8 in team sports, and 45:48:7 in speed-power athletes. Endurance athletes differed in the phosphagen (p < 0.001) and glycolytic systems (p = 0.006) from team sports and in the aerobic system from speed-power athletes (p = 0.003). No substantial shifts were observed after the general preparatory phase, except a decrease in aerobic energy contribution in team sports athletes (p = 0.048).ConclusionSports specialization and metabolic profile influence energy system contribution during sprint exercise. Highly trained athletes show a stable energy profile during the general preparation phase, indicative of long-term adaptation, rather than immediate training effects. creator: Damian Archacki creator: Jacek Zieliński creator: Barbara Pospieszna creator: Michał Włodarczyk creator: Krzysztof Kusy uri: https://doi.org/10.7717/peerj.17863 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Archacki et al. title: Long-term passage impacts human dental pulp stem cell activities and cell response to drug addition in vitro link: https://peerj.com/articles/17913 last-modified: 2024-08-23 description: BackgroundDental pulp stem cells (DPSCs) possess mesenchymal stem cell characteristics and have potential for cell-based therapy. Cell expansion is essential to achieve sufficient cell numbers. However, continuous cell replication causes cell aging in vitro, which usually accompanies and potentially affect DPSC characteristics and activities. Continuous passaging could alter susceptibility to external factors such as drug treatment. Therefore, this study sought to investigate potential outcome of in vitro passaging on DPSC morphology and activities in the absence or presence of external factor.MethodsHuman DPSCs were subcultured until reaching early passages (P5), extended passages (P10), and late passages (P15). Cells were evaluated and compared for cell and nuclear morphologies, cell adhesion, proliferative capacity, alkaline phosphatase (ALP) activity, and gene expressions in the absence or presence of external factor. Alendronate (ALN) drug treatment was used as an external factor.ResultsContinuous passaging of DPSCs gradually lost their normal spindle shape and increased in cell and nuclear sizes. DPSCs were vulnerable to ALN. The size and shape were altered, leading to morphological abnormality and inhomogeneity. Long-term culture and ALN interfered with cell adhesion. DPSCs were able to proliferate irrespective of cell passages but the rate of cell proliferation in late passages was slower. ALN at moderate dose inhibited cell growth. ALN caused reduction of ALP activity in early passage. In contrast, extended passage responded differently to ALN by increasing ALP activity. Late passage showed higher collagen but lower osteocalcin gene expressions compared with early passage in the presence of ALN.ConclusionAn increase in passage number played critical role in cell morphology and activities as well as responses to the addition of an external factor. The effects of cell passage should be considered when used in basic science research and clinical applications. creator: Somying Patntirapong creator: Juthaluck Khankhow creator: Sikarin Julamorn uri: https://doi.org/10.7717/peerj.17913 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Patntirapong et al. title: DNA methylation and gene expression profiling reveal potential association of retinol metabolism related genes with hepatocellular carcinoma development link: https://peerj.com/articles/17916 last-modified: 2024-08-23 description: BackgroundAberrant DNA methylation patterns play a critical role in the development of hepatocellular carcinoma (HCC). However, the molecular mechanisms associated with these aberrantly methylated genes remain unclear. This study aimed to comprehensively investigate the methylation-driven gene expression alterations in HCC using a multi-omics dataset.MethodsWhole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) techniques were used to assess the methylation and gene expression profiles of HCC tissues (HCCs) and normal adjacent tissues (NATs). The candidate genes’ potential function was further investigated using single-cell RNA sequencing (scRNA seq) data.ResultsWe observed widespread hypomethylation in HCCs compared to NATs. Methylation levels in distinct genomic regions exhibited significant differences between HCCs and NATs. We identified 247,632 differentially methylated regions (DMRs) and 4,926 differentially expressed genes (DEGs) between HCCs and NATs. Integrated analysis of DNA methylation and RNA-seq data identified 987 methylation-driven candidate genes, with 970 showing upregulation and 17 showing downregulation. Four genes involved in the retinol metabolic pathway, namely ADH1A, CYP2A6, CYP2C8, and CYP2C19, were identified as hyper-downregulated genes. Their expression levels could stratify HCCs into three subgroups with distinct survival outcomes, immune cell infiltration, and tumor microenvironments. Validation of these findings in an independent dataset yielded similar outcomes, confirming the high concordance and potential prognostic value of these genes. ScRNA seq data revealed the low expression of these genes in immune cells, emphasizing their role in promoting malignant cell proliferation and migration. In conclusion, this study provides insights into the molecular characteristics of HCC, revealing the involvement of retinol metabolism-related genes in the development and progression of HCC. These findings have implications for HCC diagnosis, prognosis prediction, and the development of therapeutic targets. creator: Yanteng Zhao creator: Kangkang Wan creator: Jing Wang creator: Shuya Wang creator: Yanli Chang creator: Zhuanyun Du creator: Lianglu Zhang creator: Lanlan Dong creator: Dihan Zhou creator: Wei Zhang creator: Shaochi Wang creator: Qiankun Yang uri: https://doi.org/10.7717/peerj.17916 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al. title: Changes of Tamarix austromongolica forests with embankment dams along the Laizhou bay link: https://peerj.com/articles/17934 last-modified: 2024-08-23 description: BackgroundEmbankment dams were built south of the Laizhou bay in China for controlling storm surge disasters, but they are not enough to replace coastal forests in protecting the land. This study was designed to evaluate the effects of embankment dams on natural forests dominated by Tamarix austromongolica and test whether the dam-shrub system is a preferable updated defense.MethodsCoastal forests on two typical flats, one before and one behind embankment dams, were investigated using quadrats and lines. Land bareness, vegetation composition and species co-occurrence were assessed; structures of T. austromongolica populations were evaluated; and spatial patterns of the populations were analyzed using Ripley’s K and K1,2 functions.ResultsIn the area before embankment dams, 84.8% of T. austromongolica were juveniles (basal diameter ≤ 3 cm), and 15.2% were adults (basal diameter > 3 cm); behind the dams, 52.9% were juveniles, and 47.1 were adults. In the area before the dams, the land bareness was 13.7%, four species occurred, and they all were ready to co-occur with T. austromongolica; behind the dams, the land bareness was 0%, and 16 species occurred whereas they somewhat resisted co-occurrence with T. austromongolica. In the area before the dams, the T. austromongolica population was aggregated in heterogeneous patches, and the juveniles tended to co-occur with the adults; behind the dams, they were over-dispersed as nearly uniform distributions, while the juveniles could recruit and were primarily independent of the adults. These results indicate that the T. austromongolica species did not suffer from the unnatural dams, but benefited somehow in population expansion and development. Overall, the T. austromongolica species can adapt to artificial embankment dams to create a synthetic defense against storm surges. creator: Hongxiao Yang creator: Fangfang Liu creator: Xinwei Liu creator: Zhenfeng Zhou creator: Yanxia Pan creator: Jianmin Chu uri: https://doi.org/10.7717/peerj.17934 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Yang et al. title: Broad-scale ecological niches of pathogens vectored by the ticks Ixodes scapularis and Amblyomma americanum in North America link: https://peerj.com/articles/17944 last-modified: 2024-08-23 description: Environmental dimensions, such as temperature, precipitation, humidity, and vegetation type, influence the activity, survival, and geographic distribution of tick species. Ticks are vectors of various pathogens that cause disease in humans, and Ixodes scapularis and Amblyomma americanum are among the tick species that transmit pathogens to humans across the central and eastern United States. Although their potential geographic distributions have been assessed broadly via ecological niche modeling, no comprehensive study has compared ecological niche signals between ticks and tick-borne pathogens. We took advantage of National Ecological Observatory Network (NEON) data for these two tick species and associated bacteria pathogens across North America. We used two novel statistical tests that consider sampling and absence data explicitly to perform these explorations: a univariate analysis based on randomization and resampling, and a permutational multivariate analysis of variance. Based on univariate analyses, in Amblyomma americanum, three pathogens (Borrelia lonestari, Ehrlichia chaffeensis, and E. ewingii) were tested; pathogens showed nonrandom distribution in at least one environmental dimension. Based on the PERMANOVA test, the null hypothesis that the environmental position and variation of pathogen-positive samples are equivalent to those of A. americanum could not be rejected for any of the pathogens, except for the pathogen E. ewingii in maximum and minimum vapor pressure and minimum temperature. For Ixodes scapularis, six pathogens (A. phagocytophilum, Babesia microti, Borrelia burgdorferi sensu lato, B. mayonii, B. miyamotoi, and Ehrlichia muris-like) were tested; only B. miyamotoi was not distinct from null expectations in all environmental dimensions, based on univariate tests. In the PERMANOVA analyses, the pathogens departed from null expectations for B. microti and B. burgdorferi sensu lato, with smaller niches in B. microti, and larger niches in B. burgdorferi sensu lato, than the vector. More generally, this study shows the value of large-scale data resources with consistent sampling methods, and known absences of key pathogens in particular samples, for answering public health questions, such as the relationship of presence and absence of pathogens in their hosts respect to environmental conditions. creator: Abdelghafar Alkishe creator: Marlon E. Cobos creator: A. Townsend Peterson uri: https://doi.org/10.7717/peerj.17944 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Alkishe et al. title: Efficacy and safety of etrolizumab in the treatment of inflammatory bowel disease: a meta-analysis link: https://peerj.com/articles/17945 last-modified: 2024-08-23 description: BackgroundTo explore the efficacy and safety of etrolizumab in treating inflammatory bowel disease (IBD) through meta-analysis.MethodA comprehensive exploration encompassed randomized controlled trials examining the efficacy of etrolizumab in treating IBD across PubMed, Embase, Cochrane library, and Web of Science, with a search deadline of 1 December 2023. Quality assessment leaned on the Cochrane manual’s risk-of-bias evaluation, while Stata 15 undertook the data analysis.ResultFive randomized controlled studies involving 1682 individuals were finally included, Meta-analysis results suggested that compared with placebo, etrolizumab could improve clinical response (RR = 1.26, 95% CI [1.04–1.51]), clinical remission (RR = 1.26, 95% CI [1.04–1.51]) in IBD patients. Endoscopic alleviate (RR = 2.10, 95% CI [1.56–2.82]), endoscopic improvement (RR = 2.10, 95% CI [1.56–2.82]), endoscopic remission (RR = 2.10, 95% CI [1.56–2.82]), Endoscopic improvement (RR = 1.56, 95% CI [1.30–1.89]), histological remission (RR = 1.62, 95% CI [1.26–2.08]), and did not increase any adverse events (RR = 0.95, 95% CI [0.90–1.01]) and serious adverse events (RR = 0.94, 95% CI [0.68–1.31]).ConclusionAccording to our current study, etrolizumab is a promising drug in IBD. creator: Yong gang Dai creator: Dajuan Sun creator: Jiahui Liu creator: Xiunan Wei creator: Lili Chi creator: Hongya Wang uri: https://doi.org/10.7717/peerj.17945 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dai et al. title: Test-retest reliability of a single isometric mid-thigh pull protocol to assess peak force and strength-endurance link: https://peerj.com/articles/17951 last-modified: 2024-08-23 description: The purpose of this study was to examine the test-retest reliability of strength-endurance protocols using isometric mid-thigh pull (IMTP). Twenty-eight participants (23.2 ± 4.9 years) completed two protocols across four testing sessions. Protocol one consisted of 10 maximal IMTP tests lasting 5 seconds each with 10 seconds rest between. Protocol two consisted of a prolonged 60 second maximal IMTP. Data from protocol 1 was analysed in two ways; (a) use of the highest peak value from the first three IMTP efforts, and the lowest peak value from the final three IMTP efforts, and (b) use of the mean peak force from the first three IMTP efforts and mean peak force from the final three IMTP efforts. Data from protocol two used the highest and lowest peak values in the first- and final-15 seconds. Analyses revealed excellent reliability for peak force across all four testing sessions (ICC = 0.94), as well as good test-retest reliability for strength-endurance for protocol 1 (a; ICC = 0.81, b; ICC = 0.79). Test-retest reliability for protocol 2 was poor (ICC = 0.305). Bland-Altman bias values were smaller for protocol 1(a = −8.8 Nm, b = 21.7 Nm) compared to protocol 2 = (119.3 Nm). Our data suggest that 10 maximal IMTP tests performed as described herein is a reliable method for exercise professionals to assess both peak force and strength-endurance in a single, time-efficient protocol. creator: Zak Grover creator: James McCormack creator: Jonathan Cooper creator: James P. Fisher uri: https://doi.org/10.7717/peerj.17951 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Grover et al. title: Unveiling the urban colonization of the Asian water monitor (Varanus salvator) across its distribution range using citizen science link: https://peerj.com/articles/17357 last-modified: 2024-08-22 description: BackgroundThis study aims to investigate the urban colonization of the Asian water monitor (Varanus salvator) across its entire range of distribution, addressing the paucity of research on this species in urban ecosystems. The research spans the geographic range of the Asian water monitor, focusing on urbanized areas where the species accumulates more observations (Bangkok, Colombo, Jakarta, Kuala Lumpur and Singapore).MethodsWe conducted a systematic review to comprehensively assess the current knowledge of the species’ presence in cities. Additionally, citizen science data from repositories like GBIF (Global Biodiversity Information facility ) were utilized to analyze the distribution patterns of V. salvator in urban environments. To elucidate urban distribution and correct collection biases, observations were weighted by sampling effort, using as a proxy all squamate occurrences available from 2010–2023, including V. salvator.ResultsDespite the widespread presence of the Asian water monitor in numerous cities within its distribution range, the available studies on the topic appear to be scarce. Existing research primarily consists of descriptive reports on diet and behavior. Our findings indicate that V. salvator predominantly colonizes green patches in urban areas, such as parks and small gardens. Larger cities exhibit higher records, potentially due to both permanent populations and increased citizen science reporting.ConclusionsThe Asian water monitor, as the largest lizard with established populations in cities, remains scarcely studied on a broader scale. However, the urban design of each city seems relevant to understand the distribution patterns within each context. Our study highlights the need for further research to explore the ecological and human dimensions associated with the species’ presence in urban environments. creator: Álvaro Luna creator: Armand Rausell-Moreno uri: https://doi.org/10.7717/peerj.17357 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Luna and Rausell-Moreno title: Clinical and dosimetric correlation in terms of treatment response, bladder and rectal toxicities in cervical cancer patients treated with cobalt 60 high dose rate brachytherapy link: https://peerj.com/articles/17759 last-modified: 2024-08-22 description: BackgroundHigh dose rate (HDR) image-guided brachytherapy with Cobalt-60 isotope is a relatively recent approach. The aim of the study is to evaluate the clinical and dosimetric parameters in terms of tumour response, bladder, and rectal toxicity in patients undergoing Co-60 HDR brachytherapy.Materials and MethodAll patients were initially treated with chemoradiation (CT-RT) at our center or other referral centers with external beam radiation therapy (EBRT) for a dose of 45 Gy–60 Gy at 1.8-2Gy/fraction (including nodal boost) with concomitant chemotherapy with either cisplatin or carboplatin. Patients were then scheduled for brachytherapy within 1 week after completion of CT-RT and are assessed by local examination. Depending on local examination parameters at the time of brachytherapy they were eligible either for intracavitary brachytherapy (ICBT) or interstitial brachytherapy (ISBT).ResultsThe complete response (CR) observed in stage I, II, III, IVA were 60%, 79.4%, 86% and 76.2% respectively. Complete response was seen in patients with mean EQD2 of 78.67 Gy10, 83.33 Gy10, 84.23 Gy10, 85.63 Gy10 in stages I, II, III, IVA respectively. 79.2% of cisplatin-treated patients and 87.5% of carboplatin-treated patients had a complete response indicating that patients treated with either chemotherapy had similar response rates.ConclusionsAccording to results obtained from the study we conclude by saying that higher rates of complete response to treatment in cervical cancer is seen in patients with shorter overall treatment time (OTT), shorter interval between end of definitive CT-RT and beginning of brachytherapy and squamous cell histology. The study also noted the trend of increasing mean EQD2 to tumor with increasing stage for achieving complete response. Higher acute bladder and rectal toxicity is seen in patients who received EQD2 of ¿70-90Gy3 and ¿70Gy3 respectively. The study findings suggest that the clinical outcomes and the toxicities are clinically comparable with other radioisotope based HDR brachytherapy treatment. creator: Bharat Sai Makkapati creator: Srinivas Challapalli creator: Athiyamaan MariappanSenthiappan creator: Johan Sunny Kilikunnel creator: Abhishek Krishna creator: Dilson Lobo creator: Vaishak Jawahar creator: Sourjya Banerjee uri: https://doi.org/10.7717/peerj.17759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Makkapati et al. title: Forage yields and nutritive values of oat and triticale pastures for grazing sheep in early spring link: https://peerj.com/articles/17840 last-modified: 2024-08-22 description: BackgroundSmall-grain winter cereals can be utilized as early spring pastures in temperate climates to relieve grazing pressure and potentially mitigate feed shortages. This study was conducted to determine the effects of triticale and oat cereal pastures grazed by sheep during early spring on forage yields, nutritive values, and nutritional requirements of sheep.MethodsThe research was carried out over three consecutive years, from 2015 to 2017, at the Sheep Research Institute in Bandırma-Balıkesir, located in the Marmara region of Türkiye. The treatments were arranged in a completely randomized block design, with the two forage species, triticale and oat, randomized within each of three blocks. The animal material for the study consisted of 24 Karacabey Merino sheep, each 2 years old, with an average live weight of 57.6 ± 0.5 kg, all in the late lactation stage. In each replication, four sheep were included, resulting in a total of 12 sheep grazing in each of the triticale and oat pastures. The sheep grazed exclusively on the cereal pastures without any additional feed, and had unrestricted access to water throughout the entire period of the experiment. The dry matter yields (DMY), dry matter intakes (DMI), nutritive values, and mineral contents of the cereal species were determined.ResultsThe DMY showed significant differences over the years (P < 0.05). No differences in DMY were observed between pastures, with oats yielding 11.99 t ha−1 and triticale yielding 11.08 t ha−1. During the grazing period, the change in DMY was significant in all years (P < 0.05). The average DMI of the sheep was 2,003.5 g d−1 for triticale and 2,156.6 g d−1 for oat, respectively, and DMI exhibited no significant differences across pastures. Although there was no difference in DMI between 2015 and 2016, the lowest consumption occurred in 2017 (P < 0.05). Additionally, while DMI showed different trends each year based on the periods, it generally decreased by the end of the grazing period. While both pastures provided similar nutritive values, significant differences were observed in the crude protein (CP), acid detergent fiber (ADF), in vitro true DM digestibility (DDM), and metabolisable energy (ME) values across the years. Over the years, as the grazing period progressed, CP levels decreased while neutral detergent fiber (NDF), ADF, and acid detergent lignin (ADL) increased, resulting in reduced DDM and ME values. The phosphorus (P) content in triticale was higher than in oats, but there were no differences in the content of other minerals between them. Between the years, significant differences were observed in the levels of phosphorus (P) and iron (Fe), while changes in other elements were insignificant. The variation in mineral content during the grazing process differed over the three years. Study results indicated that the nutritional values of triticale and oat pastures are similar, and both can effectively be used to provide sufficient feed to meet the early spring forage requirements for sheep. creator: Hülya Hanoğlu Oral uri: https://doi.org/10.7717/peerj.17840 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Hanoğlu Oral title: Achilles tendon thickness and serum asprosin level significantly increases in patients with polycystic ovary syndrome link: https://peerj.com/articles/17905 last-modified: 2024-08-22 description: AimIn our study, we aimed to investigate the Achilles tendon thickness (ATT) and asprosin levels in patients with polycystic ovary syndrome (PCOS) and to evaluate the relationship of these parameters, which may be related to cardio-metabolic diseases.MethodsIn our prospective cross-sectional study, 45 female patients with PCOS and 30 female healthy individuals similar in age were included. Serum dehydroepiandrosterone sulfate (DHEAS), total testosterone, anti-Müllerian hormone (AMH) and asprosin levels were measured using appropriate kits and homeostatic model assessment of insulin resistance (HOMA-IR), luteinizing hormone (LH) to follicle-stimulating hormone (FSH) ratio was calculated. ATT measurements were performed by two radiologists using a high-resolution ultrasound doppler system.ResultsSerum DHEAS, total testosterone, AMH and asprosin levels, HOMA-IR value, LF/FSH ratio, and ATT values were higher in patients with PCOS compared to healthy controls. Correlation analysis was performed between ATT and other parameters in patients with PCOS. In univariate analysis, parameters associated with ATT were detected as asprosin, DHEAS and AMH. In the linear regression analysis performed with significant parameters, asprosin and DHEAS levels were found to be associated with ATT.ConclusionATT values and serum asprosin levels were found to be significantly increased in patients with PCOS, and there is a very close positive relationship between ATT and serum asprosin levels. For this reason, it was thought that ATT measurement could be a cheap, simple and non-invasive monitoring parameter that can be used in the routine cardiometabolic follow-up of patients with PCOS. creator: Huseyin Ali Ozturk creator: Fatih Necip Arici uri: https://doi.org/10.7717/peerj.17905 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ozturk and Arici title: Polyandry contributes to Gonipterus platensis (Coleoptera: Curculionidae) rearing link: https://peerj.com/articles/17929 last-modified: 2024-08-22 description: BackgroundGonipterus platensis Marelli, 1926 (Coleoptera: Curculionidae) is one of the main defoliating beetles in Eucalyptus plantations. Biological control with egg parasitoids is one of the main control strategies for this pest and a constant supply of fresh host eggs is required to rear the parasitoids. Polyandry can influence Gonipterus oviposition by increasing female fecundity and fertility; however, the high density of individuals in laboratory colonies can lead to male harassment, resulting in lower reproduction rate. The aim of this study was to measure the effects of monoandry and polyandry on the reproduction of G. platensis and the effects of male harassment on laboratory rearing conditions.MethodsReproductive parameters were compared between three treatments: monoandry, where the female was allowed to mate daily with the same male; no choice polyandry, where the female was allowed to mate daily with a different male; and polyandry with choice, where the female was allowed to mate daily, but with a choice between five different males. Another experiment varying the density of males was conducted to evaluate the effect of male harassment.ResultsPolyandry with choice resulted in the longest period of oviposition, highest fecundity and highest number of eggs per egg capsules when compared to monoandrous females. No negative effect related to male harassment in the laboratory, such as decreased fertility, fecundity, or number of eggs per egg capsule, was detected.ConclusionPolyandry contributes to mass rearing as it increases fecundity and oviposition period on females and there is no evidence of male harassment on G. platensis. creator: Murilo Fonseca Ribeiro creator: Gabriela Cavallini creator: Gabriel Negri Solce creator: Ana Laura Favoreto creator: José Raimundo De Souza Passos creator: Brett Hurley creator: Carlos Frederico Wilcken uri: https://doi.org/10.7717/peerj.17929 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ribeiro et al. title: Inter-subspecies diversity of maize to drought stress with physio-biochemical, enzymatic and molecular responses link: https://peerj.com/articles/17931 last-modified: 2024-08-22 description: BackgroundDrought is the most significant factor limiting maize production, given that maize is a crop with a high water demand. Therefore, studies investigating the mechanisms underlying the drought tolerance of maize are of great importance. There are no studies comparing drought tolerance among economically important subspecies of maize. This study aimed to reveal the differences between the physio-biochemical, enzymatic, and molecular mechanisms of drought tolerance in dent (Zea mays indentata), popcorn (Zea mays everta), and sugar (Zea mays saccharata) maize under control (no-stress), moderate, and severe drought stress.MethodsThree distinct irrigation regimes were employed to assess the impact of varying levels of drought stress on maize plants at the V14 growth stage. These included normal irrigation (80% field capacity), moderate drought (50% field capacity), and severe drought (30% field capacity). All plants were grown under controlled conditions. The following parameters were analyzed: leaf relative water content (RWC), loss of turgidity (LOT), proline (PRO) and soluble protein (SPR) contents, membrane durability index (MDI), malondialdehyde (MDA), and hydrogen peroxide (H2O2) content, the antioxidant enzyme activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT). Additionally, the expression of heat shock proteins (HSPs) was examined at the transcriptional and translational levels.ResultsThe effects of severe drought were more pronounced in sugar maize, which had a relatively high loss of RWC and turgor, membrane damage, enzyme activities, and HSP90 gene expression. Dent maize, which is capable of maintaining its RWC and turgor in both moderate and severe droughts, and employs its defense mechanism effectively by maintaining antioxidant enzyme activities at a certain level despite less MDA and H2O2 accumulation, exhibited relatively high drought tolerance. Despite the high levels of MDA and H2O2 in popcorn maize, the up-regulation of antioxidant enzyme activities and HSP70 gene and protein expression indicated that the drought coping mechanism is activated. In particular, the positive correlation of HSP70 with PRO and HSP90 with enzyme activities is a significant result for studies examining the relationships between HSPs and other stress response systems. The discrepancies between the transcriptional and translational findings provide an opportunity for more comprehensive investigations into the role of HSPs in stress conditions. creator: Gokhan Eskikoy creator: Imren Kutlu uri: https://doi.org/10.7717/peerj.17931 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Eskikoy and Kutlu title: Kinesiophobia among health professionals’ interventions: a scoping review link: https://peerj.com/articles/17935 last-modified: 2024-08-22 description: Health professionals are regularly confronted with patients suffering from a fear of movement-related pain (unknown as kinesiophobia). The fear-avoidance attitudes and beliefs of healthcare professionals are likely to play a key role in their patients’ therapeutic approach. However, kinesiophobia among health professionals is a relatively young topic. This scoping review aims to explore and catalogue the extent of scientific research that identifies the causes and consequences of kinesiophobia among health professionals while they perform their interventions. The review was based on the Joanna Briggs Institute manual and the PRISMA method for a scoping review. The research was conducted in May 2024 using CINHAL, Medline and Sportdiscus databases with the search terms “fear-avoidance”, ”kinesiophobia“, “pain-related” and “physical therapist”. Out of 2,162 potential studies, thirteen articles were included. No study directly mentioned kinesiophobia among health professionals, but it was studied through fear-avoidance beliefs. Two-thirds of the articles indicate that professionals with fear-avoidance beliefs tend to refer their patients to other specialists less frequently and limit their patients’ activity, despite treatment guidelines. Most of the studies found were physiotherapists’ interventions for chronic back pain patients. The current review emphasizes the need for additional studies involving more healthcare professionals and diverse health conditions. creator: Lilian Doutre creator: Maryse Beaumier creator: Andrée-Anne Parent creator: Sébastien Talbot creator: Mathieu Tremblay uri: https://doi.org/10.7717/peerj.17935 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Doutre et al. title: Rapid estimation of soil water content based on hyperspectral reflectance combined with continuous wavelet transform, feature extraction, and extreme learning machine link: https://peerj.com/articles/17954 last-modified: 2024-08-22 description: BackgroundSoil water content is one of the critical indicators in agricultural systems. Visible/near-infrared hyperspectral remote sensing is an effective method for soil water estimation. However, noise removal from massive spectral datasets and effective feature extraction are challenges for achieving accurate soil water estimation using this technology.MethodsThis study proposes a method for hyperspectral remote sensing soil water content estimation based on a combination of continuous wavelet transform (CWT) and competitive adaptive reweighted sampling (CARS). Hyperspectral data were collected from soil samples with different water contents prepared in the laboratory. CWT, with two wavelet basis functions (mexh and gaus2), was used to pre-process the hyperspectral reflectance to eliminate noise interference. The correlation analysis was conducted between soil water content and wavelet coefficients at ten scales. The feature variables were extracted from these wavelet coefficients using the CARS method and used as input variables to build linear and non-linear models, specifically partial least squares (PLSR) and extreme learning machine (ELM), to estimate soil water content.ResultsThe results showed that the correlation between wavelet coefficients and soil water content decreased as the decomposition scale increased. The corresponding bands of the extracted wavelet coefficients were mainly distributed in the near-infrared region. The non-linear model (ELM) was superior to the linear method (PLSR). ELM demonstrated satisfactory accuracy based on the feature wavelet coefficients of CWT with the mexh wavelet basis function at a decomposition scale of 1 (CWT(mexh_1)), with R2, RMSE, and RPD values of 0.946, 1.408%, and 3.759 in the validation dataset, respectively. Overall, the CWT(mexh_1)-CARS-ELM systematic modeling method was feasible and reliable for estimating the water content of sandy clay loam. creator: Shaomin Chen creator: Jiachen Gao creator: Fangchuan Lou creator: Yunfei Tuo creator: Shuai Tan creator: Yuyang Shan creator: Lihua Luo creator: Zhilin Xu creator: Zhengfu Zhang creator: Xiangyu Huang uri: https://doi.org/10.7717/peerj.17954 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay link: https://peerj.com/articles/17707 last-modified: 2024-08-21 description: Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis. creator: Marianela Gastaldi creator: M. Sabrina Pankey creator: Guillermo Svendsen creator: Alonso Medina creator: Fausto Firstater creator: Maite Narvarte creator: Mariana Lozada creator: Michael Lesser uri: https://doi.org/10.7717/peerj.17707 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gastaldi et al. title: Validation of PozQoL scale in Turkish population living with HIV: a cross-cultural adaptation study link: https://peerj.com/articles/17873 last-modified: 2024-08-21 description: BackgroundThe increasing number of people living with HIV requires a simple and easy-to-use quality of life (QoL) scale for people living with HIV (PLWH). This study aims to adapt the PozQoL scale into Turkish and assess its reliability and validity for the PLWH population in Turkey.MethodsTranslation-back-translation methodology was employed, and face-to-face interviews were conducted with 130 patients using the PozQoL, socio-demographic, and clinical data questionnaire. Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) were utilized to identify the underlying factor structure and examine the validity of the measurement model, respectively. Cronbach’s alpha and intraclass correlation coefficients (ICCs) were used to assess internal consistency and test-retest reliability, respectively.ResultsEFA revealed four factors with an eigenvalue of 0.88, explaining 62.1% of the cumulative variance. CFA indicated that the four-factor solution achieved good levels of fit. The total Cronbach’s alpha was 0.81, indicating high internal consistency. The ICC for the total score was 0.92 (95% confidence interval (CI) [0.90–0.94]; p < 0.05), demonstrating high test-retest reliability.ConclusionThe Turkish version of the PozQoL was found to be a valid and reliable tool for assessing the health-related QoL of PLWH in Turkey. creator: Sabri Atalay creator: Zeynep Sedef Varol creator: Sarp Singil creator: Ufuk Sönmez uri: https://doi.org/10.7717/peerj.17873 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Atalay et al. title: Focused ultrasound-induced cell apoptosis for the treatment of tumours link: https://peerj.com/articles/17886 last-modified: 2024-08-21 description: Cancer is a serious public health problem worldwide. Traditional treatments, such as surgery, radiotherapy, chemotherapy, and immunotherapy, do not always yield satisfactory results; therefore, an efficient treatment for tumours is urgently needed. As a convenient and minimally invasive modality, focused ultrasound (FUS) has been used not only as a diagnostic tool but also as a therapeutic tool in an increasing number of studies. FUS can help treat malignant tumours by inducing apoptosis. This review describes the three apoptotic pathways, apoptotic cell clearance, and how FUS affects these three apoptotic pathways. This review also discusses the role of thermal and cavitation effects on apoptosis, including caspase activity, mitochondrial dysfunction, and Ca2+ elease. Finally, this article reviews various aspects of FUS combination therapy, including sensitization by radiotherapy and chemotherapy, gene expression upregulation, and the introduction of therapeutic gases, to provide new ideas for clinical tumour therapy. creator: Na Wang creator: Li Luo creator: Xinzhi Xu creator: Hang Zhou creator: Fang Li uri: https://doi.org/10.7717/peerj.17886 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Use of an age-simulation suit as an empathy-building method for dental students: a pre-post study link: https://peerj.com/articles/17908 last-modified: 2024-08-21 description: BackgroundThe aging of the population highlights the need to establish empathetic connections with older adults. To achieve this, age simulation suits have been designed, allowing users to experience the physical limitations associated with aging. This study aimed to evaluate the experience of dental students with these devices, using psychometric tools to measure the impact on their understanding and empathy.MethodsA pre/post-test study was conducted with the participation of 63 dental students from Rey Juan Carlos University who were fitted with an age simulation suit and asked to perform different tasks. Psychometric tools were used to assess specific parameters. Empathy was measured using the Jefferson Empathy Scale, emotional intelligence was assessed with the Trait Meta-Mood Scale-24 (TMMS-24), and the emotional attention dimension was analyzed using the Positive and Negative Affect Schedule (PANAS).ResultsThe scores on the Jefferson Empathy Scale significantly improved from 88.44 ± 6.8 to 91.06 ± 10.11 after using the simulation suit (P < 0.026). Pearson’s product moment correlation analysis showed no significant positive association or correlation between age and scores from the three questionnaires. In the rest, a positive and significant correlation was observed (P < 0.0001).ConclusionsAge simulation activities effectively enhance empathy among dental students. However, more studies are needed to foster positive attitudes toward aging and prevent negative stereotypes. creator: Jesus Rodriguez-Molinero creator: Esther Delgado-Somolinos creator: Blanca C. Miguelañez-Medrán creator: Rosario Ramirez-Puerta creator: Inmaculada Corral-Liria creator: Raquel Jiménez-Fernández creator: Marta Elena Losa-Iglesias creator: Antonio F. López-Sánchez uri: https://doi.org/10.7717/peerj.17908 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rodriguez-Molinero et al. title: Association between NKILA and some apoptotic gene expression in atherosclerosis link: https://peerj.com/articles/17915 last-modified: 2024-08-21 description: Oxidized light-density lipoprotein (ox-LDL) causes endothelial dysfunction, which is an important determinant of atherogenesis, and subsequently leads to apoptosis. Atherosclerosis is one of the most significant cardiovascular diseases (CVDs) threatening human health and causes death worldwide. Recently, long noncoding RNAs (lncRNAs) have been suggested to involved in vascular biology. Ox-LDL activates nuclear factor kappa-B (NF-κB), and NF-κB interacting lncRNA (NKILA) inhibits NF-κB signaling. In this study, the hypothesis is that NKILA may regulate endothelial cell (EC) apoptosis and, therefore, play a role in the pathogenesis of atherosclerosis. This hypothesis is based on the knowledge that EC apoptosis contributes to atherosclerosis development and that NKILA has become a prominent lncRNA in CVDs. The expression of Bcl-2-associated X protein (BAX), caspase 9 (CASP9), cytochrome c (Cyt c, CYCS), apoptotic protease activating factor 1 (APAF1), and B-cell lymphoma 2 (BCL-2) genes in human umbilical vein endothelial cells (HUVEC) treated with ox-LDL and transfected with NKILA siRNA was analyzed using quantitative reverse transcription polymerase chain reaction (RT-qPCR). BAX, CASP9, CYCS, APAF1, and BCL-2 gene expression was downregulated in ox-LDL and NKILA siRNA-treated HUVEC. In addition, when threshold/quantification cycle (Cq) values of NKILA gene expression increased, Cq values of BAX, CASP9, APAF1, and BCL-2 gene expression increased statistics significantly. The expression detection of all these genes, resulting from NKILA gene silencing, may provide guidance for epigenetic studies on EC apoptosis in atherosclerosis. creator: Burcu Bayyurt creator: Şeyda Akın creator: Nil Özbilüm Şahin creator: İzzet Yelkuvan uri: https://doi.org/10.7717/peerj.17915 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bayyurt et al. title: Comparison of visual quality after wavefront-guided LASIK in patients with different levels of preoperative total ocular higher-order aberrations: a retrospective study link: https://peerj.com/articles/17940 last-modified: 2024-08-21 description: PurposeTo compare the visual quality after wavefront-guided femtosecond LASIK (WFG FS-LASIK) in patients with different levels of preoperative total ocular higher-order aberrations to guide clinical decision-making regarding patient selection and treatment strategies.MethodsThis study included 112 right eyes of 112 patients who previously underwent WFG FS-LASIK for correcting myopia and myopic astigmatism. The patients were divided into two groups based on the mean values of preoperative total ocular HOAs (0.30 ± 0.09 µm): HOA ≤ 0.3 and > 0.3 groups. The visual acuity, manifest refraction, corneal Strehl ratio (SR), root mean square (RMS) of corneal and ocular aberrations, and area under the log contrast sensitivity function (AULCSF) of both groups were compared preoperatively and at 1, 3, 6, and 12 months postoperatively.ResultsThe induced ocular HOAs and coma (Δ = 1 mo − Preop) were significantly lower in the HOAs > 0.3 group than in the HOAs ≤ 0.3 group (ΔHOAs: 0.39 ± 0.19 vs. 0.29 ± 0.18 μm, t = 2.797, P = 0.006; Δ coma: 0.30 ± 0.19 vs. 0.20 ± 0.21 μm, t = 2.542, P = 0.012). In the HOAs > 0.3 group, ΔHOAs were negatively correlated with the preoperative ocular HOAs (r = −0.315, P = 0.019). In the HOAs ≤ 0.3 group, the regression equation for Δ HOAs = 0.098 + 0.053 |SE| (F = 21.756, P < 0.001). In the HOAs > 0.3 group, the regression equation for ΔHOAs = 0.534 − 1.081 HOAs + 0.038|Sphere| (F = 7.954, P = 0.001). The postoperative uncorrected distance visual acuity, spherical equivalent, corneal aberrations, SR and AULCSF of both groups were similar (all P > 0.05). Furthermore, the ocular aberrations were not significantly different between both groups at 3, 6, and 12 months postoperatively (all P > 0.05). In addition, compared with the preoperative period, the AULCSF of both groups were significantly increased in the postoperative period (all P < 0.05).ConclusionsThe induced ocular HOAs and coma in HOAs > 0.3 group were lower. However, both groups achieved equivalent and excellent visual quality after WFG FS-LASIK. WFG FS-LASIK may provide significant visual benefits for a wider range of patients. creator: Yu Zhang creator: Yangrui Du creator: Ming He creator: Youdan Zhang creator: Zhiyu Du uri: https://doi.org/10.7717/peerj.17940 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review link: https://peerj.com/articles/17882 last-modified: 2024-08-20 description: Plants and bacteria are co-evolving and interact with one another in a continuous process. This interaction enables the plant to assimilate the nutrients and acquire protection with the help of beneficial bacteria known as plant growth-promoting bacteria (PGPB). These beneficial bacteria naturally produce bioactive compounds that can assist plants’ stress tolerance. Moreover, they employ various direct and indirect processes to induce plant growth and protect plants against pathogens. The direct mechanisms involve phytohormone production, phosphate solubilization, zinc solubilization, potassium solubilization, ammonia production, and nitrogen fixation while, the production of siderophores, lytic enzymes, hydrogen cyanide, and antibiotics are included under indirect mechanisms. This property can be exploited to prepare bioformulants for biofertilizers, biopesticides, and biofungicides, which are convenient alternatives for chemical-based products to achieve sustainable agricultural practices. However, the application and importance of PGPB in sustainable agriculture are still debatable despite its immense diversity and plant growth-supporting activities. Moreover, the performance of PGPB varies greatly and is dictated by the environmental factors affecting plant growth and development. This review emphasizes the role of PGPB in plant growth-promoting activities (stress tolerance, production of bioactive compounds and phytohormones) and summarises new formulations and opportunities. creator: Awmpuizeli Fanai creator: Beirachhitha Bohia creator: Felicia Lalremruati creator: Nancy Lalhriatpuii creator: Lalrokimi creator: Rosie Lalmuanpuii creator: Prashant Kumar Singh creator: Zothanpuia uri: https://doi.org/10.7717/peerj.17882 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fanai et al. title: Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species link: https://peerj.com/articles/17712 last-modified: 2024-08-20 description: Centrolenidae is a Neotropical family widely distributed in Central and South America, with its species richness concentrated in the tropical Andes. Several taxonomic problems have been identified within this family, mostly related to species with broad geographic distributions. In this study, we assessed and redefined the species boundaries of the Centrolene buckleyi species complex, and formally described two new species from the Andes of Ecuador. These new taxa are recognized by a combination of morphometric, osteological, acoustic, and genetic data. Following IUCN criteria, we propose that the two new species should to be considered as Endangered (EN), mainly because of their small distributions and habitat loss. The C. buckleyi complex provides insights into the biogeography of closely related Andean species. As in other glassfrogs, speciation in Centrolene seems to be mediated by the linearity of the Andes, where gene flow can be restricted by topography and, also, local extinctions. creator: Daniela Franco-Mena creator: Ignacio De la Riva creator: Mateo A. Vega-Yánez creator: Paul Székely creator: Luis Amador creator: Diego Batallas creator: Juan P. Reyes-Puig creator: Diego F. Cisneros-Heredia creator: Khristian Venegas-Valencia creator: Sandra P. Galeano creator: Jaime Culebras creator: Juan M. Guayasamin uri: https://doi.org/10.7717/peerj.17712 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Franco-Mena et al. title: Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years link: https://peerj.com/articles/17888 last-modified: 2024-08-20 description: The Pedregal de San Ángel Ecological Reserve (REPSA) is located within the central campus of the National Autonomous University of Mexico (UNAM), in southwestern Mexico City. This area is known for its bird richness, which has been documented over time. However, this historical information has not been compiled, nor has it been assessed whether species composition has changed over time. In this study, we generated the historical checklist of avifauna in the REPSA by integrating data from systematic monitoring, bibliographic review and citizen science. Additionally, we calculated Jaccard’s dissimilarity Index (nestedness and species turnover) among bird checklists from each year and evaluated whether this index and its components changed over time. In addition, we estimate whether the proportion of species arriving and becoming extinct in the REPSA is influenced by time (census interval) and by the migratory status of the species. Finally, we identified the core species of the REPSA. Our results indicate that from 1967 to 2023, 258 bird species have been recorded in the REPSA. The Jaccard’s dissimilarity and turnover increased and reached an asymptotic trend over time while nestedness showed similar values throughout time. The time and species residency status did not have significant effect on the proportion of species that arrival and become extinct in the reserve. We identified 58 core species based on their persistence; 35 of these are residents, 22 have some migratory movement and one exotic species. Our results highlight the importance of the REPSA as a fundamental habitat for the avifauna of Mexico City, including a wide variety of migratory bird species. creator: Ubaldo Márquez-Luna creator: Pablo Arenas creator: M. Isabel Herrera-Juárez creator: Hilda Marcela Pérez-Escobedo creator: Gustavo Hernández-Orta creator: Guillermo Gil-Alarcón uri: https://doi.org/10.7717/peerj.17888 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Márquez-Luna et al. title: Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa ‘ja ‘ag hydrothermal vent fields in the Pescadero Basin, Gulf of California link: https://peerj.com/articles/17724 last-modified: 2024-08-19 description: Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa ‘ja ‘ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem. creator: Manet E. Peña-Salinas creator: Daan R. Speth creator: Daniel R. Utter creator: Ronald M. Spelz creator: Sujung Lim creator: Robert Zierenberg creator: David W. Caress creator: Patricia G. Núñez creator: Roberto Vázquez creator: Victoria J. Orphan uri: https://doi.org/10.7717/peerj.17724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Peña-Salinas et al. title: Trichoderma based formulations control the wilt disease of chickpea (Cicer arietinum L.) caused by Fusarium oxysporum f. sp. ciceris, better when inoculated as consortia: findings from pot experiments under field conditions link: https://peerj.com/articles/17835 last-modified: 2024-08-19 description: BackgroundCommercial/chemical pesticides are available to control Fusarium wilt of chickpea, but these antifungals have numerous environmental and human health hazards. Amongst various organic alternatives, use of antagonistic fungi like Trichoderma, is the most promising option. Although, Trichoderma spp. are known to control Fusarium wilt in chickpea but there are no reports that indicate the biocontrol efficacy of indigenous Trichoderma spp. against the local pathogen, in relation to environmental conditions.MethodsIn the present study, biological control activity of Trichoderma species formulations viz., Trichoderma asperellum, Trichoderma harzianum (strain 1), and Trichoderma harzianum (strain 2), either singly or in the form of consortia, was investigated against Fusarium oxysporum f. sp. ciceris, the cause of Fusarium wilt in chickpea, in multiyear pot trials under open field conditions. The antagonistic effect of Trichoderma spp. was first evaluated in in vitro dual culture experiments. Then the effects of Trichoderma as well as F. oxysporum, were investigated on the morphological parameters, disease incidence (DI), and disease severity (DS) of chickpea plants grown in pots.ResultsIn dual culture experiments, all the Trichoderma species effectively reduced the mycelial growth of F. oxysporum. T. asperellum, T. harzianum (strain 1), and T. harzianum(strain 2) declined the mycelial growth of F. oxysporumby 37.6%, 40%, and 42%. In open field pot trials, the infestation of F. oxysporum in chickpea plants significantly reduced the morphological growth of chickpea. However, the application of T. asperellum, T. harzianum (strain 1), and T. harzianum (strain 2), either singly or in the form of consortia, significantly overcome the deleterious effects of the pathogen, thereby resulted in lower DI (22.2% and 11.1%) and DS (86% and 92%), and ultimately improved the shoot length, shoot fresh weight and shoot dry weight by 69% and 72%, 67% and 73%, 68% and 75%, during the years 1 and 2, respectively, in comparison with infested control. The present study concludes the usefulness and efficacy of Trichoderma species in controlling wilt disease of chickpea plants under variable weather conditions. creator: Safeer A. Chohan creator: Muhammad Akbar creator: Umer Iqbal uri: https://doi.org/10.7717/peerj.17835 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chohan et al. title: Biological factors associated with long COVID and comparative analysis of SARS-CoV-2 spike protein variants: a retrospective study in Thailand link: https://peerj.com/articles/17898 last-modified: 2024-08-19 description: BackgroundPost-acute COVID-19 syndrome (long COVID) refers to the persistence of COVID-19 symptoms or exceptional symptoms following recovery. Even without conferring fatality, it represents a significant global public health burden. Despite many reports on long COVID, the prevalence and data on associated biological factors remain unclear and limited. This research aimed to determine the prevalence of long COVID during the two distinct epidemic periods in Thailand, due to the Delta and Omicron variants of SARS-CoV-2, and to investigate the biological factors associated with long COVID. In addition, the spike protein amino acid sequences of the Delta and Omicron variants were compared to determine the frequency of mutations and their potential biological implications.MethodsA retrospective cross-sectional study was established to recruit confirmed COVID-19 participants at Maharat Nakhon Ratchasima Hospital who had recovered for at least three months and were infected between June 2021 and August 2022. The demographic data and long COVID experience were collected via telephone interview. The biological factors were analyzed through binary logistic regression. The datasets of the SARS-CoV-2 spike protein amino acid sequence of the Delta and Omicron variants in Thailand were retrieved from GIDSAID to determine mutation frequencies and to identify possible roles of the mutations based on published data.ResultsData was collected from a total of 247 participants comprising 106 and 141 participants of the Delta and Omicron epidemic periods, respectively. Apart from the COVID-19 severity and health status, the baseline participant data of the two time periods were remarkably similar. The prevalence of long COVID observed in the Omicron period was higher than in the Delta period (74.5% vs. 66.0%). The biological factors associated with long COVID were epidemic variant, age, treatment with symptomatic medicines, and vaccination status. When the spike protein sequence data of the two variants were compared, it was observed that the Omicron variant exhibited a greater quantity of amino acid changes in its receptor-binding domain (RBD) and receptor-binding motif (RBM). The critical changes of the Omicron variant within these regions had a significant function in enhancing virus transmissibility and host immune response resistance.ConclusionThis study revealed informative data associated with long COVID in Thailand. More attention should be given to long COVID caused by unique virus variants and other biological factors to prepare a healthcare management strategy for COVID-19 patients after recovery. creator: Supanchita Kiatratdasakul creator: Pirom Noisumdaeng creator: Nattamon Niyomdecha uri: https://doi.org/10.7717/peerj.17898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kiatratdasakul et al. title: Bioinformatics analysis of oxidative stress genes in the pathogenesis of ulcerative colitis based on a competing endogenous RNA regulatory network link: https://peerj.com/articles/17213 last-modified: 2024-08-16 description: BackgroundUlcerative colitis (UC) is a common chronic disease associated with inflammation and oxidative stress. This study aimed to construct a long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network based on bioinformatics analysis and to explore oxidative stress-related genes underlying the pathogenesis of UC.MethodsThe GSE75214, GSE48959, and GSE114603 datasets were downloaded from the Gene Expression Omnibus database. Following differentially expressed (DE) analysis, the regulatory relationships among these DERNAs were identified through miRDB, miRTarBase, and TargetScan; then, the lncRNA-miRNA-mRNA network was established. The Molecular Signatures Database (MSigDB) was used to search oxidative stress-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotation and enrichment analyses. Based on the drug gene interaction database DGIdb, drugs that interact with oxidative stress-associated genes were explored. A dextran sulfate sodium (DSS)-induced UC mouse model was used for experimental validation.ResultsA total of 30 DE-lncRNAs, 3 DE-miRNAs, and 19 DE-mRNAs were used to construct a lncRNA-miRNA-mRNA network. By comparing these 19 DE-mRNAs with oxidative stress-related genes in MSigDB, three oxidative stress-related genes (CAV1, SLC7A11, and SLC7A5) were found in the 19 DEM sets, which were all negatively associated with miR-194. GO and KEGG analyses showed that CAV1, SLC7A11, and SLC7A5 were associated with immune inflammation and steroid hormone synthesis. In animal experiments, the results showed that dexamethasone, a well-known glucocorticoid drug, could significantly decrease the expression of CAV1, SLC7A11, and SLC7A5 as well as improve UC histology, restore antioxidant activities, inhibit inflammation, and decrease myeloperoxidase activity.ConclusionSLC7A5 was identified as a representative gene associated with glucocorticoid therapy resistance and thus may be a new therapeutic target for the treatment of UC in the clinic. creator: Qifang Li creator: Yuan Liu creator: Bingbing Li creator: Canlei Zheng creator: Bin Yu creator: Kai Niu creator: Yi Qiao uri: https://doi.org/10.7717/peerj.17213 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: A retrospective evaluation of individual thigh muscle volume disparities based on hip fracture types in followed-up patients: an AI-based segmentation approach using UNETR link: https://peerj.com/articles/17509 last-modified: 2024-08-16 description: BackgroundHip fractures are a common and debilitating condition, particularly among older adults. Loss of muscle mass and strength is a common consequence of hip fractures, which further contribute to functional decline and increased disability. Assessing changes in individual thigh muscles volume in follow-up patients can provide valuable insights into the quantitative recovery process and guide rehabilitation interventions. However, accurately measuring anatomical individual thigh muscle volume can be challenging due to various, labor intensive and time-consuming.Materials and MethodsThis study aimed to evaluate differences in thigh muscle volume in followed-up hip fracture patients computed tomography (CT) scans using an AI based automatic muscle segmentation model. The study included a total of 18 patients at Gyeongsang National University, who had undergone surgical treatment for a hip fracture. We utilized the automatic segmentation algorithm which we have already developed using UNETR (U-net Transformer) architecture, performance dice score = 0.84, relative absolute volume difference 0.019 ± 0.017%.ResultsThe results revealed intertrochanteric fractures result in more significant muscle volume loss (females: −97.4 cm3, males: –178.2 cm3) compared to femoral neck fractures (females: −83 cm3, males: −147.2 cm3). Additionally, the study uncovered substantial disparities in the susceptibility to volume loss among specific thigh muscles, including the Vastus lateralis, Adductor longus and brevis, and Gluteus maximus, particularly in cases of intertrochanteric fractures.ConclusionsThe use of an automatic muscle segmentation model based on deep learning algorithms enables efficient and accurate analysis of thigh muscle volume differences in followed up hip fracture patients. Our findings emphasize the significant muscle loss tied to sarcopenia, a critical condition among the elderly. Intertrochanteric fractures resulted in greater muscle volume deformities, especially in key muscle groups, across both genders. Notably, while most muscles exhibited volume reduction following hip fractures, the sartorius, vastus and gluteus groups demonstrated more significant disparities in individuals who sustained intertrochanteric fractures. This non-invasive approach provides valuable insights into the extent of muscle atrophy following hip fracture and can inform targeted rehabilitation interventions. creator: Hyeon Su Kim creator: Shinjune Kim creator: Hyunbin Kim creator: Sang-Youn Song creator: Yonghan Cha creator: Jung-Taek Kim creator: Jin-Woo Kim creator: Yong-Chan Ha creator: Jun-Il Yoo uri: https://doi.org/10.7717/peerj.17509 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Kim et al. title: A systematic review on the morphology structure, propagation characteristics, resistance physiology and exploitation and utilization of Nitraria tangutorum Bobrov. link: https://peerj.com/articles/17830 last-modified: 2024-08-16 description: Nitraria tangutorum Bobrov., belonging to the family Nitrariaceae, is a drought-tolerant and salt-loving plant and has drawn attention for its good economic and ecological value. As one of the main group species and dominant species in China’s desert and semi-desert regions, N. tangutorum possesses superior tolerance to drought, high temperature, cold, barren, high salinity and alkalinity and wind and sand. Its root system is well developed, with many branches and a strong germination capacity. Once buried in sandy soil, N. tangutorum can quickly produce a large number of adventitious roots, forming new plants and continuously expanding the shrubs, forming fixed and semi-fixed shrub sand dunes. Sand dune shrubs can trap and fix a large amounts of quicksand, prevent desert expansion and erosion, and play an important role in maintaining regional ecosystem balance and improving ecological environmental quality. In addition, the phytochemical screening studies report that N. tangutorum contains an abundance of various compounds including flavonoids, alkaloids, phenolic acids and polysaccharides. These compounds confer a range of beneficial bioactivities such as antioxidant, anti-inflammatory, anti-tumor, anti-fatigue, liver protection, neuroprotection, cardiovascular protection, lowering blood lipid, regulating blood sugar level and immunoregulation. The fruits of N. tangutorum also contain vitamin C, amino acids, minerals and microelements. It has been traditionally used as a nutritional food source and in folk medicine to treat diseases of the spleen and stomach, abnormal menstruation, indigestion, and hyperlipidemia. N. tangutorum, as a wild plant with medicinal and edible homology, possesses remarkable economic and medicinal values. This detailed, comprehensive review gathers and presents all the information related to the morphological structure, propagation characteristics, resistance physiology and exploitation and utilization of N. tangutorum, providing a theoretical basis for the researchers to conduct future in-depth research on N. tangutorum. creator: Xiaolan Li creator: Hanghang Liu creator: Chaoqun Li creator: Yi Li uri: https://doi.org/10.7717/peerj.17830 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Comparative study of the antibacterial effects of wound secretions of different cultivars of Chinese fir link: https://peerj.com/articles/17850 last-modified: 2024-08-16 description: BackgroundThe bark of Chinese fir (Cunninghamia lanceolata), the largest afforestation tree species in the forest areas of southern China, is susceptible to injuries and bites from small animals. The population of small animals has recently increased owing to improvements in the ecological environment across various forested areas, thus increasing the incidence of injuries in the bark of Chinese fir. Following such injuries, the bark secretes light yellow or milky white secretions, the function of which remains unclear. The present study aimed to reveal the antibacterial effect of exudates of different Chinese fir cultivars on five bacterial species.MethodsThe research involved three-year-old plantations of Taxus chinensis var. koraiensis and Yangkou3 and three-year-old container plantations of Taxus chinensis var. pendula, Yang 061, and Yang 020. The antibacterial effects of exudates were analyzed using the filter paper diffusion method. The minimum inhibitory concentration for each secretion and the bacterial inhibition zone were determined.ResultsThe exudates of the different Chinese fir bark exhibited notable antibacterial effects on Bacillus subtilis, Salmonella paratyphi B, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. However, the extent of these antibacterial effects varied among the different Chinese fir cultivars, as the minimum inhibitory concentrations (MICs) of the exudates against the five bacterial species varied. The mean MIC of Pseudomonas aeruginosa was lower potency, whereas that of Escherichia coli was the lowest. Notably, the antibacterial efficacy of the exudates was mainly influenced by the composition of the secretions rather than the number of secretions, with organic acid compounds and terpenoids potentially contributing to the antibacterial effects against E. coli and Bacillus subtilis, respectively.ConclusionThis study demonstrates the antibacterial effect of wound secretion of different Chinese fir cultivars, highlighting their varying efficacy on different bacterial species. Moreover, the antibacterial ability of the exudates of the strains was mainly determined by the composition of the wound secretions, and there was no noticeable relationship with the number of wound secretions. The results of this study offers a theoretical basis for screen Chinese fir cultivars with high-disease-resistant. creator: Yu Jiang creator: Yalin Zeng creator: Jianing Zhu creator: Linjun Sun creator: Pengfei Wu creator: Ming Li creator: Xiangqing Ma uri: https://doi.org/10.7717/peerj.17850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jiang et al. title: Efficacy of tanshinone IIA in rat models with myocardial ischemia–reperfusion injury: a systematic mini-review and meta-analysis link: https://peerj.com/articles/17885 last-modified: 2024-08-16 description: BackgroundMyocardial ischemia–reperfusion injury (MIRI) refers to severe damage to the ischemic myocardium following the restoration of blood flow, and it is a major complication of reperfusion therapy for myocardial infarction. Notably, drugs such as metoprolol have been utilized to reduce ischemia–reperfusion injury. Tanshinone IIA is a major constituent extracted from Salvia miltiorrhiza Bunge. Recently, tanshinone IIA has been studied extensively in animal models for controlling MIRI. Therefore, we conducted a meta-analysis on the application of tanshinone IIA in rat models with MIRI to evaluate the therapeutic effects of tanshinone IIA.MethodsA comprehensive search was conducted across PubMed, Web of Science, Embase, the Cochrane Library, the China National Knowledge Infrastructure database, the Wanfang database, and the Chinese Scientific Journal Database to gather studies on tanshinone IIA intervention in rat models with MIRI.We employed SYRCLE’s risk of bias tool to assess study quality. The primary outcome indicators were superoxide dismutase (SOD) and malondialdehyde (MDA). Myocardial infarction area was a secondary outcome indicator. This study was registered at PROSPERO (registration number CRD 42022344447).ResultsAccording to the inclusion and exclusion criteria, 15 eligible studies were selected from 295 initially identified studies. In rat models with MIRI, tanshinone IIA significantly increased SOD levels while reducing MDA levels and myocardial infarction area. Moreover, the duration of myocardial ischemia influenced the effectiveness of tanshinone IIA. However, additional high-quality research studies are needed to establish the efficacy and definitive guidelines for the use of tanshinone IIA. Animal studies demonstrated that tanshinone IIA exerted a significant therapeutic effect when the ischemia duration was less than 40 minutes. Tanshinone IIA was found to be more effective when administered via intravenous, intraperitoneal, and intragastric routes at doses above 5 mg/kg. Additionally, treatment with tanshinone IIA at all stages—prior to myocardial ischemia, after ischemia but before reperfusion, prior to ischemia and after reperfusion, and after reperfusion—showed satisfactory results.ConclusionsTanshinone IIA enhanced SOD activity and reduced MDA levels, thereby ameliorating oxidative stress damage during MIRI. Additionally, it reduced the myocardial infarction area, indicating its effectiveness in mitigating MIRI-induced damage in rats and demonstrating a myocardial protective effect. These findings contribute valuable insights for developing MIRI treatment strategies. creator: Xiaobin Zhang creator: Hehe Jiang creator: Linlin Zhang creator: Chen Chen creator: Mengzhen Xing creator: Dongqing Du creator: Yujie Li creator: Yuning Ma creator: Yuxia Ma creator: Chunjing Li uri: https://doi.org/10.7717/peerj.17885 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Zhang et al. title: Seasonality and alternative floral resources affect reproductive success of the alfalfa leafcutting bee, Megachile rotundata link: https://peerj.com/articles/17902 last-modified: 2024-08-16 description: BackgroundManaged populations of the alfalfa leafcutting bee (ALCB), Megachile rotundata (F.), are often not sustainable. In addition to numerous mortality factors that contribute to this, the dense bee populations used to maximize alfalfa pollination quickly deplete floral resources available to bees later in the summer. Providing alternative floral resources as alfalfa declines may help to improve ALCB reproduction.MethodsWe examined the relationship between floral resource availability and ALCB reproduction and offspring condition via (1) a field study using alfalfa plots with and without late-blooming wildflower strips to supply food beyond alfalfa bloom, and (2) a field-cage study in which we provided bees with alfalfa, wildflowers, or both as food resources.ResultsIn the field study, bee cell production closely followed alfalfa floral density with an initial peak followed by large declines prior to wildflower bloom. Few bees visited wildflower strips, whose presence or absence was not associated with any measure of bee reproduction. However, we found that female offspring from cells provisioned earlier in the season, when alfalfa predominated as a source of provisions, eclosed with greater body sizes and proportion body lipids relative to total body mass. For bees restricted to cages, the proportion of offspring that survived to adults was highest on pure alfalfa diets. Adding wildflowers to cages with alfalfa did not affect adult offspring production or female offspring body size and lipid content. Furthermore, although similar numbers of adults were produced on wildflowers alone as with alfalfa alone, females eclosed with smaller body sizes and lower proportion body lipids on wildflowers despite the higher protein content we estimated for wildflower pollen. We found no evidence that adding the late-season wildflower species that we chose to plant enhanced ALCB offspring numbers. Our results highlight the importance of considering multiple measures of reproductive success, including offspring body size and lipid stores, when designing and evaluating floral resource management strategies for agroecosystems. creator: Casey M. Delphia creator: Laura A. Burkle creator: Joshua M. Botti-Anderson creator: Kevin M. O’Neill uri: https://doi.org/10.7717/peerj.17902 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Delphia et al. title: Does how individuals handle social situations exacerbate the relationship between physique anxiety and food addiction? The role of emotional expressive suppression and social avoidance and distress link: https://peerj.com/articles/17910 last-modified: 2024-08-16 description: BackgroundResearch on food addiction has increased significantly in recent years. It has been demonstrated that food addiction can lead to impairments in physiological, psychological, and social functioning in individuals. However, there is a lack of studies investigating the influence of how individuals handle social situations on food addiction and the specific mechanisms involved.MethodA cross-sectional survey was conducted with 1,151 university students, with a mean age of 21.44 (SD = 4.77) years. The sample comprised 74.46% female and 25.54% male students. Participants completed the Chinese version of the modified Yale Food Addiction Scale 2.0, the Social Physique Anxiety Scale, the Expressive Suppression Scale, and the Social Avoidance and Distress Scale. Statistical analyses were performed using SPSS 26.0 and the Process (Version 3.4) plug-in.ResultThe results of the study supported our hypothesis that the association between social physique anxiety and food addiction symptoms could be partially explained by expressive suppression and social avoidance and distress. This association remained significant even after adjusting for covariates such as gender, number of cigarettes smoked per day, bedtime, education, and BMI. Specifically, more severe social physique anxiety was found to be associated with frequent use of expressive suppression and social avoidance and distress, which in turn was associated with more severe food addiction symptoms.ConclusionThis study explored the role of expression suppression and social avoidance and distress in the relationship between social physique anxiety and food addiction symptoms. The findings provide a theoretical basis for developing interventions for food addiction in college students. These interventions could include helping students develop a healthy perception of body image, encouraging emotional expression, and promoting active social participation to reduce food addiction symptoms. creator: Yan Li creator: Yuxia Fan creator: Jing Lin creator: Shaobo Shi uri: https://doi.org/10.7717/peerj.17910 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Preoperative bedside test indicators as predictors of difficult video laryngoscopy in obese patients: a prospective observational study link: https://peerj.com/articles/17838 last-modified: 2024-08-15 description: PurposeThe aim of this study was to identify factors associated with difficult video laryngoscopy in obese patients.MethodsA total of 579 obese patients undergoing elective laparoscopic weight loss surgery were intubated with a single-lumen endotracheal tube using a video laryngoscopy under general anesthesia, and the patients were divided into two groups based on the Cormack-Lehane classification (difficult video laryngoscopy defined as ≥ 3): the easy video laryngoscopy group and the difficult video laryngoscopy group. Record the general condition of the patient, bedside testing indicators related to the airway, Cormack-Lehane classification during intubation, and intubation failure rate.ResultsThe findings of this study show that the incidence of difficult video laryngoscopy in obese patients is 4.8%. Multivariate logistic regression analysis indicated that body mass index was significantly associated with difficult video laryngoscopy (OR = 1.082, 95% CI [1.033–1.132], P < 0.001).ConclusionFor Chinese obese patients without known difficult airways, the incidence of difficult video laryngoscopy is 4.8%. Body mass index is associated factors for the occurrence of difficult video laryngoscopy, with an increased risk observed as body mass index rise. creator: Liumei Li creator: Guanyu Yang creator: ShiYing Li creator: Xue Liu creator: Ya Fei Zhu creator: Qinjun Chu uri: https://doi.org/10.7717/peerj.17838 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: PCSK9 inhibitor effectively alleviated cognitive dysfunction in a type 2 diabetes mellitus rat model link: https://peerj.com/articles/17676 last-modified: 2024-08-14 description: BackgroundThe incidence of diabetes-associated cognitive dysfunction (DACD) is increasing; however, few clinical intervention measures are available for the prevention and treatment of this disease. Research has shown that proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors, particularly SBC-115076, have a protective effect against various neurodegenerative diseases. However, their role in DACD remains unknown. In this study, we aimed to explore the impact of PCSK9 inhibitors on DACD.MethodsMale Sprague-Dawley (SD) rats were used to establish an animal model of type 2 diabetes mellitus (T2DM). The rats were randomly divided into three groups: the Control group (Control, healthy rats, n = 8), the Model group (Model, rats with T2DM, n = 8), and the PCSK9 inhibitor-treated group (Treat, T2DM rats treated with PCSK9 inhibitors, n = 8). To assess the spatial learning and memory of the rats in each group, the Morris water maze (MWM) test was conducted. Hematoxylin-eosin staining and Nissl staining procedures were performed to assess the structural characteristics and functional status of the neurons of rats from each group. Transmission electron microscopy was used to examine the morphology and structure of the hippocampal neurons. Determine serum PCSK9 and lipid metabolism indicators in each group of rats. Use qRT-PCR to detect the expression levels of interleukin (IL)-1β, IL-6, and tumor necrosis factor-alpha (TNF-α) in the hippocampal tissues of each group of rats. Western blot was used to detect the expression of PCSK9 and low-density lipoprotein receptor (LDLR) in the hippocampal tissues of rats. In addition, a 4D label-free quantitative proteomics approach was used to analyse protein expression in rat hippocampal tissues. The expression of selected proteins in hippocampal tissues was verified by parallel reaction monitoring (PRM) and immunohistochemistry (IHC).ResultsThe results showed that the PCSK9 inhibitor alleviated cognitive dysfunction in T2DM rats. PCSK9 inhibitors can reduce PCSK9, total cholesterol (TC), and low-density lipoprotein (LDL) levels in the serum of T2DM rats. Meanwhile, it was found that PCSK9 inhibitors can reduce the expression of PCSK9, IL-1β, IL-6, and TNF-α in the hippocampal tissues of T2DM rats, while increasing the expression of LDLR. Thirteen potential target proteins for the action of PCSK9 inhibitors on DACD rats were identified. PRM and IHC revealed that PCSK9 inhibitors effectively counteracted the downregulation of transthyretin in DACD rats.ConclusionThis study uncovered the target proteins and specific mechanisms of PCSK9 inhibitors in DACD, providing an experimental basis for the clinical application of PCSK9 inhibitors for the potential treatment of DACD. creator: Yang Yang creator: Yeying Wang creator: Yuwen Wang creator: Tingyu Ke creator: Ling Zhao uri: https://doi.org/10.7717/peerj.17676 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Starvation and re-feeding of Gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax) co-cultured with glasswort (Salicornia europaea) in a polyculture aquaponic system link: https://peerj.com/articles/17814 last-modified: 2024-08-14 description: The aim of this study was to evaluate the effect of starvation and refeeding on the growth and food intake of gilthead seabream (Sparus aurata) and seabass (Dicentrarchus labrax) and on the growth and nitrogen uptake of glasswort (Salicornia europaea) in a polyculture aquaponic system under 12 ppt salinity for 75 days. Nine small-scale autonomous aquaponic systems were used, each containing 10 gilthead seabreams (average weight of 6.33 ± 0.73 g and average length of 5.73 ± 0.72 cm) and 10 seabasses (5.82 ± 0.77 g and 6.35 ± 0.45 cm), as well as five glasswort plants. Three fish feeding treatments were performed, a control (A), in which fish were fed daily until satiation, and two fasting treatments for 4 (B) and 7 days (C). Fish growth performance was significantly lower (p < 0.05) in the C treatment for both species compared to treatments A and B. Food consumption (FC) and feed conversion ratio (FCR) were significantly higher (p < 0.05) in treatment C. Glasswort growth performance was significantly higher in treatment C (p < 0.05). The results showed that the 4-day food-deprived fish were similar to the control fish by achieving partial compensatory growth. The more extended fasting period (7 days) resulted in significantly lower growth performance. The lipid and nitrogen retention levels in both species were significantly lower in food-deprived fish than in the control fish both before and during compensatory growth. The results suggest that a feeding schedule involving starvation–refeeding cycles is a promising feed management option for these species in polyculture aquaponic systems. The effect of food deprivation was also significantly beneficial (p < 0.05) for the growth performance of glasswort compared to the control treatment. creator: Ioannis Mitsopoulos creator: Iliana Gesthimani Kontou creator: Konstantinos Babouklis creator: Nikolaos Vlahos creator: Panagiotis Berillis creator: Efi Levizou creator: Eleni Mente uri: https://doi.org/10.7717/peerj.17814 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mitsopoulos et al. title: Lumpfish, Cyclopterus lumpus, distribution in the Gulf of Maine, USA: observations from fisheries independent and dependent catch data link: https://peerj.com/articles/17832 last-modified: 2024-08-14 description: The Gulf of Maine (GoM) is one of the fastest-warming parts of the world’s oceans. Some species’ distributional shifts have already been documented, especially for commercially-important species. Less is known about species that are not currently exploited but may become so in the future. As a case study into these issues, we focus on lumpfish (Cyclopterus lumpus) because of the recognized and timely need to understand wild lumpfish population dynamics to support sustainable fisheries and aquaculture developments. Using occurrence data from five different fisheries-dependent and independent surveys, we examined lumpfish distribution over time in the GoM. We found that lumpfish presence was more likely in Fall and correlated with deeper waters and colder bottom temperatures. Since 1980, lumpfish presence has increased over time and shifted north. Given a limited set of data, these findings should be interpreted with caution as additional work is needed to assess if the actual distribution of lumpfish is changing. Nevertheless, our work provides preliminary information for resource managers to ensure that lumpfish are harvested sustainably for use in emergent lumpfish aquaculture facilities. creator: Elizabeth A. Fairchild creator: Sophie Wulfing creator: Easton R. White uri: https://doi.org/10.7717/peerj.17832 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fairchild et al. title: Processing causal structure sentences in Mandarin Chinese: an eye movements study link: https://peerj.com/articles/17878 last-modified: 2024-08-14 description: It remains uncertain whether causal structure prediction can improve comprehension in Chinese sentences and whether the position of the headword mediates the prediction effect. We conducted an experiment to explore the effect of causal prediction and headword position in Chinese sentence reading. Participants were asked to read sentences containing causal connectives with their eye movements recorded. In the experiment, we manipulated the causal structure of the sentence and the position of the headword. We found a promoting effect of causal structure on first-pass reading time and a hindering impact on total reading time. However, the effect was not mediated by the headword position. The results show that causal syntactic prediction facilitated early-stage processing and increased the integration cost in the late stage of Chinese sentence processing. These findings also support the constraint-based approach, which suggests an isolation between semantic and syntactic processing. creator: Lei Gao creator: Lin Li creator: Xiaolei Gao creator: Xue Sui uri: https://doi.org/10.7717/peerj.17878 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gao et al. title: New species of Ontocetus (Pinnipedia: Odobenidae) from the Lower Pleistocene of the North Atlantic shows similar feeding adaptation independent to the extant walrus (Odobenus rosmarus) link: https://peerj.com/articles/17666 last-modified: 2024-08-13 description: Ontocetus is one of the most notable extinct odobenines owing to its global distribution in the Northern Hemisphere. Originating in the Late Miocene of the western North Pacific, this lineage quickly spread to the Atlantic Ocean during the Pliocene, with notable occurrences in England, Belgium, The Netherlands, Morocco and the eastern seaboard of the United States. Reassessment of a pair of mandibles from the Lower Pleistocene of Norwich (United Kingdom) and a mandible from the Upper Pliocene of Antwerp (Belgium) that were referred to as Ontocetus emmonsi reveals existences of features of both Ontocetus and Odobenus. The presence of four post-canine teeth, a lower canine larger than the cheek-teeth and a lower incisor confirms the assignment to Ontocetus; simultaneously, characteristics such as a fused and short mandibular symphysis, a well-curved mandibular arch and thin septa between teeth align with traits usually found in Odobenus. Based on a combination of these characters, we describe Ontocetus posti, sp. nov. Its mandibular anatomy suggests, a better adaptation to suction-feeding than what was previously described in the genus suggesting that Ontocetus posti sp. nov. likely occupied a similar ecological niche to the extant walrus Odobenus rosmarus. Originating from the North Pacific Ocean, Ontocetus most likely dispersed via the Central American Seaway. Although initially discovered in the Lower Pliocene deposits of the western North Atlantic, Ontocetus also left its imprint in the North Sea basin and Moroccan Plio-Pleistocene deposits. The closure of the Isthmus of Panama during the Mio-Pliocene boundary significantly impacted the contemporary climate, inducing global cooling. This event constrained Ontocetus posti in the North Sea basin leaving the taxon unable to endure the abrupt climate changes of the Early Pleistocene, ultimately going extinct before the arrival of the extant counterpart, Odobenus rosmarus. creator: Mathieu Boisville creator: Narimane Chatar creator: Naoki Kohno uri: https://doi.org/10.7717/peerj.17666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Boisville et al. title: Effects of adding dual-task or sport-specific task constrains to jump-landing tests on biomechanical parameters related to injury risk factors in team sports: a systematic review link: https://peerj.com/articles/17720 last-modified: 2024-08-13 description: BackgroundJumping and landing tests are frequently used as a tool to assess muscle function. However, they are performed in a controlled and predictable environment. The physical tests commonly used as part of the criteria for return to sport after injury are often performed with little or no cognitive load and low coordinative demand compared to game-specific actions. The aim of this systematic review was to examine the influence of performing a dual task (DT) or sport-specific task constrains during jump-landing tests on biomechanical variables related to lower limb injury risk in team sports.MethodsThis systematic review followed the specific methodological guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The search was conducted in the databases Medline (PubMed), Web of Science, Cochrane Plus, and SportDiscus for studies published from 2013 until June 30, 2023. To be eligible, studies had to include: (1) kinematic and/or kinetic assessment of injury risk factors in the lower extremity; (2) a comparison between a simple jump or landing test and a DT jump or landing test which included cognitive information. The risk of bias in the selected articles was analyzed using the recommendations of the Cochrane Collaboration.ResultsOf the 656 records identified, 13 met the established criteria. Additionally, two more articles were manually included after screening references from the included articles and previous related systematic reviews. Regarding the Risk of bias assessment, 12 studies did not surpass a score of 3 points (out of a total of 7). Only three studies exceeded a score of 3 points, with one article achieving a total score of 6. From the included studies, comparative conditions included actions influenced by the inclusion of a sports ball (n = 6), performing tasks in virtual environments or with virtual feedback (n = 2), participation in cognitive tasks (n = 6), and tasks involving dual processes (n = 7). The execution of decision-making (DM) during the jump-landing action resulted in biomechanical changes such as lower peak angles of hip flexion and knee flexion, along with increased vertical ground reaction force, knee abduction, and tibial internal rotation. Regarding limitations, discrepancies arise in defining what constitutes DT. As a result, it is possible that not all studies included in this review fit all conceptual definitions of DT. The inclusion of DT or constraints in jump-landing tests significantly alters biomechanical variables related to lower extremity injury risk in team sports. In future research, it would be beneficial to incorporate tasks into jumping tests that simulate the specific cognitive demands of team sports. This systematic review was registered in PROSPERO (registration number: CRD42023462102) and this research received no external funding. creator: Sara González-Millán creator: Víctor Illera-Domínguez creator: Víctor Toro-Román creator: Bruno Fernández-Valdés creator: Mónica Morral-Yepes creator: Lluís Albesa-Albiol creator: Carla Pérez-Chirinos Buxadé creator: Toni Caparrós uri: https://doi.org/10.7717/peerj.17720 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 González-Millán et al. title: The dentition of the Late Jurassic dwarf sauropod Europasaurus holgeri from northern Germany: ontogeny, function, and implications for a rhamphotheca-like structure in Sauropoda link: https://peerj.com/articles/17764 last-modified: 2024-08-13 description: The basal macronarian sauropod Europasaurus holgeri is known only from the Late Jurassic of the Langenberg Quarry near Goslar, Lower Saxony, Germany. Europasaurus has been identified as an insular dwarf and shows a clear resemblance to Camarasaurus and Giraffatitan. This study provides a detailed description of the dentition of Europasaurus based on an array of fossils outstanding in their abundance, variety of preservation, and ontogenetic range. Dental morphology for the replacement and functional dentitions, the tooth replacement pattern, and implications for food intake are described for the Europasaurus dentition, which is characterized by broad-crowned teeth. Characteristic features for Europasaurus are the presence of denticles on replacement teeth, the wrinkled enamel, and large wear facets both on the apex and on the carinae of the tooth crowns. The partially articulated skull SNHM-2207-R and isolated tooth rows DfmMh/FV 580.1 and DfmMh/FV 896.7 suggest the presence of strong connective tissue partially covering the teeth. This connective tissue would have provided stability and protection for the teeth. Evidence for this connective tissue include exposed tooth necks, in-situ teeth with strongly resorbed roots which no longer would have been connected to the jaw bone, and wrinkled enamel and its surface pattern. The same features can be observed in other sauropod taxa as well. We therefore suggest that eusauropods in general possessed this connective tissue structure, which may be an autapomorphy of the group. Possibly, this hypothetical structure is homologous to the rhamphotheca in birds and some non-avian theropods, which, however rarely, show such a close integration of keratinous tissue and teeth that we hypothesize here. creator: Verena Régent creator: Kayleigh Wiersma-Weyand creator: Oliver Wings creator: Nils Knötschke creator: P. Martin Sander uri: https://doi.org/10.7717/peerj.17764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Régent et al. title: Policies and opportunities for physical activity engagement in Austrian schools: a census survey link: https://peerj.com/articles/17794 last-modified: 2024-08-13 description: BackgroundCompelling evidence suggests that schools’ infrastructure and policy represent potential predictors of health and physical activity (PA) in children and adolescents. However, the translation of these findings into practice has not been examined. This study investigated the activity friendliness of Austrian schools.MethodsUsing a census sampling method, principals of Austrian schools (n = 342) were invited to participate in an online survey assessing 1) the availability of PA facilities (e.g. playgrounds, sports courts, swimming halls) and 2) applied PA policies (e.g. cooperation with sports clubs and involvement in PA projects).ResultsA total of 130 principals answered the survey which corresponds to a minimal response rate of 38%. While most schools (87.4%, n = 111) had a gymnastic hall, only one third (37%, n = 47) had access to a swimming hall. On average, the schools had 4.2 ± 2 PA facilities with significant variation between school types (i.e., high schools: 5 ± 2 vs. primary schools: 3.5 ± 2, p < 0.05). The most common facilities were meadow areas (89%, n = 113), sports fields (71.7%, n = 91), and playgrounds (64.6%, n = 82). Almost half of the schools were part of a PA project (e.g. “active break”, 45%, n = 56) and offered extracurricular PA programs and courses (54%, n = 67), but only one in five (22%, n = 27) regularly conducted fitness tests. PA policies varied between school types (p < 0.05) but almost all principals (94%, n = 117) would welcome a stronger promotion of activity friendliness at their school.ConclusionSchools are mostly activity-friendly regarding infrastructure although the limited possibilities for swimming lessons seem worrisome. PA promotion through projects, extracurricular PA offerings and fitness tests may be expanded. creator: Alexandra Unger creator: Andrea Schwarzenlander creator: Jan Wilke uri: https://doi.org/10.7717/peerj.17794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Unger et al. title: A frog in hot water: the effect of temperature elevation on the adrenal stress response of an African amphibian link: https://peerj.com/articles/17847 last-modified: 2024-08-13 description: Amphibians, with their unique physiology and habitat requirements, are especially vulnerable to changes in environmental temperatures. While the activation of the physiological stress response can help to mitigate the impact of such habitat alteration, chronic production of elevated glucocorticoid levels can be deleterious in nature. There is no empirical evidence indicating the physiological response of African amphibians to temperature changes, where individuals are unable to emigrate away from potential stressors. To rectify this, we used the edible bullfrog (Pyxicephalus edulis) as a model species to determine the effect of elevated temperature on the adrenocortical response of the species using a recently established matrix. While a control group was kept at a constant temperature (25 °C) throughout the study period, an experimental group was exposed to control (25 °C) and elevated temperatures (30 °C). Mucous swabs were collected throughout the study period to determine dermal glucocorticoid (dGC) concentrations, as a proxy for physiological stress. In addition to this, individual body mass measurements were collected. The results showed that individuals within the experimental group who experienced increased temperatures had significantly elevated dGC levels compared to the control animals. Furthermore, there was a significant difference in the percentage mass change between experimental and control animals . These findings indicate the physiological sensitivity of the edible bullfrog to a thermal stressor in captivity. While this study shows the importance of proper amphibian management within the captive environment, it also highlights the coming danger of global climate change to this and similar amphibian species. creator: Juan Scheun creator: Leanne Venter creator: Andre Ganswindt uri: https://doi.org/10.7717/peerj.17847 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Scheun et al. title: Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest link: https://peerj.com/articles/17900 last-modified: 2024-08-13 description: The activities of microbiomes in river sediments play an important role in sustaining ecosystem functions by driving many biogeochemical cycles. However, river ecosystems are frequently affected by anthropogenic activities, which may lead to microbial biodiversity loss and/or changes in ecosystem functions and related services. While parts of the Atlantic Forest biome stretching along much of the eastern coast of South America are protected by governmental conservation efforts, an estimated 89% of these areas in Brazil are under threat. This adds urgency to the characterization of prokaryotic communities in this vast and highly diverse biome. Here, we present prokaryotic sediment communities in the tropical Juliana River system at three sites, an upstream site near the river source in the mountains (Source) to a site in the middle reaches (Valley) and an estuarine site near the urban center of Ituberá (Mangrove). The diversity and composition of the communities were compared at these sites, along with environmental conditions, the former by using qualitative and quantitative analyses of 16S rRNA gene amplicons. While the communities included distinct populations at each site, a suite of core taxa accounted for the majority of the populations at all sites. Prokaryote diversity was highest in the sediments of the Mangrove site and lowest at the Valley site. The highest number of genera exclusive to a given site was found at the Source site, followed by the Mangrove site, which contained some archaeal genera not present at the freshwater sites. Copper (Cu) concentrations were related to differences in communities among sites, but none of the other environmental factors we determined was found to have a significant influence. This may be partly due to an urban imprint on the Mangrove site by providing organic carbon and nutrients via domestic effluents. creator: Carolina O. de Santana creator: Pieter Spealman creator: Eddy Oliveira creator: David Gresham creator: Taise de Jesus creator: Fabio Chinalia uri: https://doi.org/10.7717/peerj.17900 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 de Santana et al. title: The postcranial anatomy of Moschorhinus kitchingi (Therapsida: Therocephalia) from the Karoo Basin of South Africa link: https://peerj.com/articles/17765 last-modified: 2024-08-12 description: Therocephalia are an important clade of non-mammalian therapsids that evolved a diverse array of morphotypes and body sizes throughout their evolutionary history. The postcranial anatomy of therocephalians has largely been overlooked, but remains important towards understanding aspects of their palaeobiology and phylogenetic relationships. Here, we provide the first postcranial description of the large akidnognathid eutherocephalian Moschorhinus kitchingi by examining multiple specimens from fossil collections in South Africa. We also compare the postcranial anatomy with previously described therocephalian postcranial material and provide an updated literature review to ensure a reliable foundation of comparison for future descriptive work. Moschorhinus shares all the postcranial features of eutherocephalians that differentiate them from early-diverging therocephalians, but is differentiated from other eutherocephalian taxa by aspects concerning the scapula, interclavicle, sternum, manus, and femur. The novel anatomical data from this contribution shows that Moschorhinus possessed a stocky bauplan with a particularly robust scapula, humerus, and femur. These attributes, coupled with the short and robust skull bearing enlarged conical canines imply that Moschorhinus was well equipped to grapple with and subdue prey items. Additionally, the combination of these attributes differ from those of similarly sized coeval gorgonopsians, which would have occupied a similar niche in late Permian ecosystems. Moreover, Moschorhinus was the only large carnivore known to have survived the Permo-Triassic mass extinction. Thus, the subtle but important postcranial differences may suggest a type of niche partitioning in the predator guild during the Permo-Triassic mass extinction interval. creator: Brandon P. Stuart creator: Adam K. Huttenlocker creator: Jennifer Botha uri: https://doi.org/10.7717/peerj.17765 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Stuart et al. title: The role of protein post-translational modifications in prostate cancer link: https://peerj.com/articles/17768 last-modified: 2024-08-12 description: Involving addition of chemical groups or protein units to specific residues of the target protein, post-translational modifications (PTMs) alter the charge, hydrophobicity, and conformation of a protein, which in turn influences protein function, protein–protein interaction, and protein aggregation. These alterations, which include phosphorylation, glycosylation, ubiquitination, methylation, acetylation, lipidation, and lactylation, are significant biological events in the development of cancer, and play vital roles in numerous biological processes. The processes behind essential functions, the screening of clinical illness signs, and the identification of therapeutic targets all depend heavily on further research into the PTMs. This review outlines the influence of several PTM types on prostate cancer (PCa) diagnosis, therapy, and prognosis in an effort to shed fresh light on the molecular causes and progression of the disease. creator: Yinghui Hao creator: Chenqiong Gu creator: Wenfeng Luo creator: Jian Shen creator: Fangmei Xie creator: Ying Zhao creator: Xiaoyu Song creator: Zeping Han creator: Jinhua He uri: https://doi.org/10.7717/peerj.17768 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Hao et al. title: New taxonomic insights for Brazilian Syrbatus Reitter (Coleoptera: Staphylinidae: Pselaphinae), including three new species and their mitochondrial genomes link: https://peerj.com/articles/17783 last-modified: 2024-08-12 description: Here we present a taxonomic treatment for the Brazilian species of Syrbatus (Reitter, 1882), including the description of three new species (Syrbatus moustache Asenjo & Valois sp. nov., Syrbatus obsidian Asenjo & Valois sp. nov. and Syrbatus superciliata Asenjo & Valois sp. nov.) from the Quadrilátero Ferrífero (Minas Gerais, Brazil). In addition, we designated lectotypes for the Brazilian species of species-group 2, Syrbatus centralis (Raffray, 1898), Syrbatus hetschkoi (Reitter, 1888), Syrbatus hiatusus (Reitter, 1888), Syrbatus transversalis (Raffray, 1898), and Syrbatus trinodulus (Schaufuss, 1887), besides recognizing the holotype for Syrbatus brevispinus (Reitter, 1882), Syrbatus bubalus (Raffray, 1898), and Syrbatus grouvellei (Raffray, 1898). The mitochondrial genomes (mitogenomes) of the three new species are presented, for which we present the phylogenetic placement among Staphylinidae with previously published data. creator: Angélico Asenjo creator: Marcely Valois creator: Robson de Almeida Zampaulo creator: Michele Molina creator: Renato R.M. Oliveira creator: Guilherme Oliveira creator: Santelmo Vasconcelos uri: https://doi.org/10.7717/peerj.17783 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Asenjo et al. title: Evolution of tooth morphological complexity and its association with the position of tooth eruption in the jaw in non-mammalian synapsids link: https://peerj.com/articles/17784 last-modified: 2024-08-12 description: Heterodonty and complex molar morphology are important characteristics of mammals acquired during the evolution of early mammals from non-mammalian synapsids. Some non-mammalian synapsids had only simple, unicuspid teeth, whereas others had complex, multicuspid teeth. In this study, we reconstructed the ancestral states of tooth morphological complexity across non-mammalian synapsids to show that morphologically complex teeth evolved independently multiple times within Therapsida and that secondary simplification of tooth morphology occurred in some non-mammalian Cynodontia. In some mammals, secondary evolution of simpler teeth from complex molars has been previously reported to correlate with an anterior shift of tooth eruption position in the jaw, as evaluated by the dentition position relative to the ends of component bones used as reference points in the upper jaw. Our phylogenetic comparative analyses showed a significant correlation between an increase in tooth complexity and a posterior shift in the dentition position relative to only one of the three specific ends of component bones that we used as reference points in the upper jaw of non-mammalian synapsids. The ends of component bones depend on the shape and relative area of each bone, which appear to vary considerably among the synapsid taxa. Quantification of the dentition position along the anteroposterior axis in the overall cranium showed suggestive evidence of a correlation between an increase in tooth complexity and a posterior shift in the dentition position among non-mammalian synapsids. This correlation supports the hypothesis that a posterior shift of tooth eruption position relative to the morphogenetic fields that determine tooth form have contributed to the evolution of morphologically complex teeth in non-mammalian synapsids, if the position in the cranium represents a certain point in the morphogenetic fields. creator: Tomohiro Harano creator: Masakazu Asahara uri: https://doi.org/10.7717/peerj.17784 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Harano and Asahara title: Effect of chronic alcohol consumption on oral microbiota in rats with periodontitis link: https://peerj.com/articles/17795 last-modified: 2024-08-12 description: BackgroundThe imbalance of oral microbiota can contribute to various oral disorders and potentially impact general health. Chronic alcohol consumption beyond a certain threshold has been implicated in influencing both the onset and progression of periodontitis. However, the mechanism by which chronic alcohol consumption affects periodontitis and its association with changes in the oral microbial community remains unclear.ObjectiveThis study used 16S rRNA gene amplicon sequencing to examine the dynamic changes in the oral microbial community of rats with periodontitis influenced by chronic alcohol consumption.MethodsTwenty-four male Wistar rats were randomly allocated to either a periodontitis (P) or periodontitis + alcohol (PA) group. The PA group had unrestricted access to alcohol for 10 weeks, while the P group had access to water only. Four weeks later, both groups developed periodontitis. After 10 weeks, serum levels of alanine aminotransferase and aspartate aminotransferase in the rats’ serum were measured. The oral swabs were obtained from rats, and 16S rRNA gene sequencing was conducted. Alveolar bone status was assessed using hematoxylin and eosin staining and micro-computed tomography.ResultsRats in the PA group exhibited more severe periodontal tissue damage compared to those in the periodontitis group. Although oral microbial diversity remained stable, the relative abundance of certain microbial communities differed significantly between the two groups. Actinobacteriota and Desulfobacterota were more prevalent at the phylum level in the PA group. At the genus level, Cutibacterium, Tissierella, Romboutsia, Actinomyces, Lawsonella, Anaerococcus, and Clostridium_sensu_stricto_1 were significantly more abundant in the PA group, while Haemophilus was significantly less abundant. Additionally, functional prediction using Tax4Fun revealed a significant enrichment of carbohydrate metabolism in the PA group.ConclusionChronic alcohol consumption exacerbated periodontitis in rats and influenced the composition and functional characteristics of their oral microbiota, as indicated by 16S rRNA gene sequencing results. These microbial alterations may contribute to the exacerbation of periodontitis in rats due to chronic alcohol consumption. creator: Zirui Zhao creator: Xiao Zhang creator: Wanqing Zhao creator: Jianing Wang creator: Yanhui Peng creator: Xuanning Liu creator: Na Liu creator: Qing Liu uri: https://doi.org/10.7717/peerj.17795 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhao et al. title: Decomposition and scenario analysis of agricultural carbon emissions in Heilongjiang, China link: https://peerj.com/articles/17856 last-modified: 2024-08-12 description: BackgroundAs a key agricultural region in China, Heilongjiang Province has experienced significant carbon emissions over the past few decades. To understand the underlying factors and future trends in these emissions, a comprehensive analysis was conducted from 1993 to 2030.MethodsThe agricultural carbon emissions from 1993 to 2020 were estimated using the emission factor method. To analyze the influencing factors and future trends of these emissions, the study employed the Logarithmic Mean Divisia Index (LMDI) and integrated it with the Stochastic Impacts by Regression on Population, Affluence, and Technology (STIRPAT) model.ResultsResults showed that (1) the agricultural carbon emissions in Heilongjiang were primarily driven by rice cultivation, followed by fertilizer production and irrigation electricity. (2) The economic and labor structure effects were the main driving factors of agricultural carbon emissions, while the population, demographic, and intensity effects were the main inhibitors. (3) Agricultural carbon emissions in Heilongjiang Province peaked in 2016 with 69.6 Mt CO2-eq and could subsequently decline by −3.92% to −4.52% between 2020 and 2030 in different scenario simulations. In the future, Heilongjiang Province should prioritize the reduction of agricultural carbon emissions from rice production. Adjusting the planting structure, managing the layout of rice paddies, and promoting the cultivation of dry rice varieties would significantly contribute to mitigating agricultural carbon emissions. creator: Luyang Zhang creator: Junyan Chu creator: Haiyang You creator: Zhihua Liu uri: https://doi.org/10.7717/peerj.17856 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Cuproptosis related ceRNA axis AC008083.2/miR-142-3p promotes the malignant progression of nasopharyngeal carcinoma through STRN3 link: https://peerj.com/articles/17859 last-modified: 2024-08-12 description: BackgroundCeRNA axis is an important way to regulate the occurrence and development of Nasopharyngeal carcinoma (NPC). Although the research on inducing cuproptosis of tumor cells is in the early stage of clinical practice, its mechanism of action is still of great significance for tumor treatment, including NPC. However, the regulation mechanism of cuproptosis in NPC by ceRNA network remains unclear.MethodsThe ceRNA network related to the survival of nasopharyngeal carcinoma related genes was constructed by bioinformatics. Dual-luciferase reporter assay and other experiments were used to prove the conclusion.ResultsOur findings indicate that the AC008083.2/miR-142-3p axis drives STRN3 to promote the malignant progression of NPC. By performing enrichment analysis and phenotypic assays, we demonstrated that the changes in the expressions of AC008083.2/miR-142-3p/NPC can affect the proliferation of NPC. Mechanistically, luciferase reporter gene assays suggested that AC008083.2 acts as a ceRNA of miR-142-3p to regulate the content of STRN3. Furthermore, the regulations of STRN3 and the malignant progression of NPC by AC008083.2 depends on miR-142-3p to some extent.ConclusionsOur study reveals an innovative ceRNA regulatory network in NPC, which can be considered a new potential target for diagnosing and treating NPC. creator: Dandan Feng creator: Xiaoping Wu creator: Genping Li creator: Junhui Yang creator: Jianguo Jiang creator: Shunan Liu creator: Jichuan Chen uri: https://doi.org/10.7717/peerj.17859 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Feng et al. title: Research and progress on the mechanism of lower urinary tract neuromodulation: a literature review link: https://peerj.com/articles/17870 last-modified: 2024-08-12 description: The storage and periodic voiding of urine in the lower urinary tract are regulated by a complex neural control system that includes the brain, spinal cord, and peripheral autonomic ganglia. Investigating the neuromodulation mechanisms of the lower urinary tract helps to deepen our understanding of urine storage and voiding processes, reveal the mechanisms underlying lower urinary tract dysfunction, and provide new strategies and insights for the treatment and management of related diseases. However, the current understanding of the neuromodulation mechanisms of the lower urinary tract is still limited, and further research methods are needed to elucidate its mechanisms and potential pathological mechanisms. This article provides an overview of the research progress in the functional study of the lower urinary tract system, as well as the key neural regulatory mechanisms during the micturition process. In addition, the commonly used research methods for studying the regulatory mechanisms of the lower urinary tract and the methods for evaluating lower urinary tract function in rodents are discussed. Finally, the latest advances and prospects of artificial intelligence in the research of neuromodulation mechanisms of the lower urinary tract are discussed. This includes the potential roles of machine learning in the diagnosis of lower urinary tract diseases and intelligent-assisted surgical systems, as well as the application of data mining and pattern recognition techniques in advancing lower urinary tract research. Our aim is to provide researchers with novel strategies and insights for the treatment and management of lower urinary tract dysfunction by conducting in-depth research and gaining a comprehensive understanding of the latest advancements in the neural regulation mechanisms of the lower urinary tract. creator: Shutong Pang creator: Junan Yan uri: https://doi.org/10.7717/peerj.17870 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pang and Yan title: Potential role of Manilkara Zapota L in treating bacterial infection link: https://peerj.com/articles/17890 last-modified: 2024-08-12 description: The increasing problem of antibiotic resistance in bacteria leads to an urgent need for new antimicrobial agents. Alternative treatments for bacterial infections need to be explored to tackle this issue. Plant-based substances are emerging as promising options. Manilkara zapota L. contains compounds with antibiotic activities, and anti-inflammatory, antitumor, antipyretic, and antioxidant properties. It has medicinal properties and contains bioactive compounds, like tannins, flavonoids, and triterpenoids. This review aimed to comprehensively evaluate the existing literature on the potential medicinal and therapeutic benefits of M. zapota in bacterial infections by utilizing data from in vivo and in vitro studies. M. zapota has the potential to be a nutritional source of antimicrobial food. Numerous preclinical studies have demonstrated the antibacterial activities of M. zapota and its components. The antibacterial mechanisms of this fruit could interact with bacterial cell structures such as cell walls or membranes. creator: Ami Febriza creator: Fityatun Usman creator: Andi Ulfah Magefirah Rasyid creator: Hasta Handayani Idrus creator: Mohd Helmy Mokhtar uri: https://doi.org/10.7717/peerj.17890 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Febriza et al. title: Effects of semaglutide on gut microbiota, cognitive function and inflammation in obese mice link: https://peerj.com/articles/17891 last-modified: 2024-08-12 description: ObjectiveThis study aims to investigate the effects of semaglutide on gut microbiota, cognitive function, and inflammation in obese mice.MethodTwenty-four C57BL/6J male mice were randomly assigned to three groups: a normal-chow diet group (NCD, n = 8), high-fat diet group (HFD, n = 8), and HFD+semaglutide group (Sema, n = 8). The mice were fed a HFD to establish an animal model of obesity and then administered with semaglutide or saline for 12 weeks. Cognitive function was assessed using the Morris water maze test. Serum pro-inflammatory cytokines were measured. 16S rRNA gene sequencing technology was used to explore gut microbiota characteristics in obese mice.ResultObese mice showed significant cognitive impairment and inflammation. Semaglutide improved cognitive function and attenuated inflammation induced by a HFD diet. The abundance of gut microbiota was significantly changed in the HFD group, including decreased Akkermansia, Muribaculaceae, Coriobacteriaceae_UCG_002, Clostridia_UCG_014 and increased Romboutsia, Dubosiella, Enterorhabdus. Whereas semaglutide could dramatically reverse the relative abundance of these gut microbiota. Correlation analysis suggested that cognitive function was positively correlated with Muribaculaceae and Clostridia_UCG_014, and negatively associated with Romboutsia and Dubosiella. Romboutsia was positively correlated with TNFα, IL-6 and IL-1β. While Clostridia_UCG_014 was negatively related to TNFα, IL-6 and IL-1β.ConclusionsFor the first time semaglutide displayed different regulatory effects on HFD-induced gut microbiota dysbiosis. Semaglutide could regulate the structure and composition of gut microbiota associated with cognitive function and inflammation. Thus, affecting gut microbiota might be a potential mechanism of semaglutide in attenuating cognitive function and inflammation. creator: Jing Feng creator: Zhenjie Teng creator: Yu Yang creator: Jingzhen Liu creator: Shuchun Chen uri: https://doi.org/10.7717/peerj.17891 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Feng et al. title: Characterization of indigenous Durio species from Sarawak, Borneo: relationships between chemical composition and sensory attributes link: https://peerj.com/articles/17688 last-modified: 2024-08-09 description: Sarawak, Borneo, harbours 16 unique Durio species, half of which are edible, with only Durio zibethinus widely cultivated. Despite their nutritional and economic significance to the rural communities in Sarawak, the lesser-known indigenous durians remain underrepresented in the scientific literature while facing the risk of extinction in the wild. Thus, the aim of this study was to conduct comprehensive chemical analyses of these wild edible durians, offering insights into their nutritional and sensory taste attributes. The edible part was separated at optimal ripeness, and the samples were subjected to further analysis. Wild edible durian genotypes exhibit varied characteristics, even within the same species. The majority of wild durians are characterized by a sugar composition consisting predominantly of sucrose, constituting 67.38–96.96%, except for the red-fleshed Durio graveolens renowned for its low total sugar content (0.49 ± 0.17 g per 100 g). Despite its bland taste, this species possessed significantly greater fat (14.50 ± 0.16%) and fibre (12.30 ± 0.14%) content. Durio dulcis exhibited a significantly greater carbohydrate content (29.37–30.60%), and its intense smell was attributed to its low protein content (2.03–2.04%). Indigenous durians offer substantial percentages of daily mineral intake, with 100 g servings providing approximately 15.71–26.80% of potassium, 71.72–86.52% of phosphorus, 9.33–27.31% of magnesium, and sufficient trace minerals. The vibrant flesh colours of yellow-, orange- and red-fleshed Durio graveolens and Durio kutejensis show high levels of ascorbic acid (31.41–61.56 mg 100 g−1), carotenoids (976.36–2627.18 µg 100 g−1) and antioxidant properties, while Durio dulcis and Durio oxleyanus, despite their dull flesh, contained high phenolic (67.95–74.77 mg GAE 100 g−1) and flavonoid (8.71–13.81 QE mg 100 g−1) levels. These endeavours provide a deeper understanding of the nutritional richness of wild edible durians, thereby supporting commercialization and conservation efforts. creator: Gerevieve Bangi Sujang creator: Shiamala Devi Ramaiya creator: Shiou Yih Lee creator: Muta Harah Zakaria uri: https://doi.org/10.7717/peerj.17688 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sujang et al. title: The role of lncRNAs related ceRNA regulatory network in multiple hippocampal pathological processes during the development of perioperative neurocognitive disorders link: https://peerj.com/articles/17775 last-modified: 2024-08-09 description: BackgroundPerioperative neurocognitive disorders (PND) refer to neurocognitive abnormalities during perioperative period, which are a great challenge for elderly patients and associated with increased morbidity and mortality. Our studies showed that long non-coding RNAs (lncRNAs) regulate mitochondrial function and aging-related pathologies in the aged hippocampus after anesthesia, and lncRNAs are associated with multiple neurodegenerations. However, the regulatory role of lncRNAs in PND-related pathological processes remains unclear.MethodsA total of 18-month mice were assigned to control and surgery (PND) groups, mice in PND group received sevoflurane anesthesia and laparotomy. Cognitive function was assessed with fear conditioning test. Hippocampal RNAs were isolated for sequencing, lncRNA and microRNA libraries were constructed, mRNAs were identified, Gene Ontology (GO) analysis were performed, and lncRNA-microRNA-mRNA networks were established. qPCR was performed for gene expression verification.ResultsA total of 312 differentially expressed (DE) lncRNAs, 340 DE-Transcripts of Uncertain Coding Potential (TUCPs), and 2,003 DEmRNAs were identified in the hippocampus between groups. The lncRNA-microRNA-mRNA competing endogenous RNA (ceRNA) network was constructed with 29 DElncRNAs, 90 microRNAs, 493 DEmRNAs, 148 lncRNA-microRNA interaction pairs, 794 microRNA-mRNA interaction pairs, and 110 lncRNA-mRNA co-expression pairs. 795 GO terms were obtained. Based on the frequencies of involved pathological processes, BP terms were divided into eight categories: neurological system alternation, neuronal development, metabolism alternation, immunity and neuroinflammation, apoptosis and autophagy, cellular communication, molecular modification, and behavior changes. LncRNA-microRNA-mRNA ceRNA networks in these pathological categories were constructed, and involved pathways and targeted genes were revealed. The top relevant lncRNAs in these ceRNA networks included RP23-65G6.4, RP24-396L14.1, RP23-251I16.2, XLOC_113622, RP24-496E14.1, etc., and the top relevant mRNAs in these ceRNA networks included Dlg4 (synaptic function), Avp (lipophagy), Islr2 (synaptic function), Hcrt (regulation of awake behavior), Tnc (neurotransmitter uptake).ConclusionIn summary, we have constructed the lncRNA-associated ceRNA network during PND development in mice, explored the role of lncRNAs in multiple pathological processes in the mouse hippocampus, and provided insights into the potential mechanisms and therapeutic gene targets for PND. creator: Bowen Zhou creator: Yuxiang Zheng creator: Zizheng Suo creator: Mingzhu Zhang creator: Wenjie Xu creator: Lijuan Wang creator: Dazhuang Ge creator: Yinyin Qu creator: Qiang Wang creator: Hui Zheng creator: Cheng Ni uri: https://doi.org/10.7717/peerj.17775 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Prognostic role of chemokine-related genes in acute myeloid leukemia link: https://peerj.com/articles/17862 last-modified: 2024-08-09 description: BackgroundChemotactic cytokines play a crucial role in the development of acute myeloid leukemia (AML). Thus, investigating the mechanisms of chemotactic cytokine-related genes (CCRGs) in AML is of paramount importance.MethodsUsing the TCGA-AML, GSE114868, and GSE12417 datasets, differential expression analysis identified differentially expressed CCRGs (DE-CCRGs). These genes were screened by overlapping differentially expressed genes (DEGs) between AML and control groups with CCRGs. Subsequently, functional enrichment analysis and the construction of a protein-protein interaction (PPI) network were conducted to explore the functions of the DE-CCRGs. Univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses identified relevant prognostic genes and developed a prognostic model. Survival analysis of the prognostic gene was performed, followed by functional similarity analysis, immune analysis, enrichment analysis, and drug prediction analysis.ResultsDifferential expression analysis revealed 6,743 DEGs, of which 29 DE-CCRGs were selected for this study. Functional enrichment analysis indicated that DE-CCRGs were primarily involved in chemotactic cytokine-related functions and pathways. Six prognostic genes (CXCR3, CXCR2, CXCR6, CCL20, CCL4, and CCR2) were identified and incorporated into the risk model. The model’s performance was validated using the GSE12417 dataset. Survival analysis showed significant differences in AML overall survival (OS) between prognostic gene high and low expression groups, indicating that prognostic gene might be significantly associated with patient survival. Additionally, nine different immune cells were identified between the two risk groups. Correlation analysis revealed that CCR2 had the most significant positive correlation with monocytes and the most significant negative correlation with resting mast cells. The tumor immune dysfunction and exclusion score was lower in the high-risk group.ConclusionCXCR3, CXCR2, CXCR6, CCL20, CCL4, and CCR2 were identified as prognostic genes correlated to AML and the tumor immune microenvironment. These findings offerred novel insights into the prevention and treatment of AML. creator: Yanfei Hou creator: Yu Chen creator: Yaofang Zhang creator: Mengyao Li creator: Jianfang Chen uri: https://doi.org/10.7717/peerj.17862 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Hou et al. title: Correlation between gross motor coordination and basic coordination capacities in normal-weight and overweight/obese children aged 9–10 years link: https://peerj.com/articles/17865 last-modified: 2024-08-09 description: BackgroundGross motor coordination (GMC) plays a crucial factor in children’s motor development and daily activities. It encompasses various sub-capacities, such as spatial orientation, rhythm, and motor reaction, collectively referred to as basic coordination capacities (BCC). However, children who are overweight and obese (OW/OB) often display poorer GMC. This study aims to examine the impact of gender and weight status (BMI categories) on children’s GMC and BCC. It also seeks to investigate the impact of BCC and BMI on GMC.MethodThe study involved 266 participants, 135 in the NW group (boys: n = 75; girls: n = 60) and 131 in the OW/OB group (boys: n = 68; girls: n = 63). An NW status is defined by a BMI z-score between ≥−2SD to ≤1SD, while an OW/OB status corresponds to a BMI z-score > 1SD. Physical activity was assessed using the Physical Activity Questionnaire for Children, developed by the University of Saskatchewan, Canada. We used six field tests to evaluate BCC, including single leg standing test (static balance), YBT (dynamic balance), rhythmic sprint test (rhythm), reaction time test (motor reaction), target standing broad test (kinesthetic differentiation), and numbered medicine ball running test (spatial orientation). GMC was evaluated with Kiphard-Schilling’s Body Coordination Test (KTK).ResultThe motor quotient (MQ) was primarily affected by weight status (F = 516.599, p < 0.001; gender: F = 6.694, p = 0.01), with no significant interaction effect (F = 0.062, p = 0.803). In BCC, gender had a significant main effect on rhythm capacity (F = 29.611, p < 0.001) and static balance (F = 11.257, p = 0.001) but did not significant influence other sub-capacities (p > 0.05). Weight status impacted dynamic balance (F = 11.164, p = 0.001). The interaction of gender and weight status significantly impacted motor reaction (F = 1.471, p = 0.024) and kinesthetic differentiation (F = 5.454, p = 0.02), but did not affect other sub-capacities (p > 0.05). The physical activity was not significant affected by gender (F = 0.099, p = 0.753), weight status (F = 0.171, p = 0.679) and the interactions of two variables (F = 0.06, p = 0.806). In the regression analysis, except motor reaction (p > 0.05), other BCC sub-capacities influenced GMC to varying extents (β = −0.103–0.189, p < 0.05). Nonetheless, only two types of balance significantly mediated the relationship between BMI and GMC (BMI→MQ: β = −0.543, p < 0.001; BMI→YBT: β = −0.315, p < 0.001; BMI→SLS: β = −0.282, p < 0.001; SLS→MQ: β = 0.189, p < 0.001; YBT→MQ: β = 0.182, p < 0.001).ConclusionCompared to gender, the main effect of weight status on most GMC and BCC’s sub-capacities was more pronounced. OW/OB children exhibited poorer GMC, which is related to their reduced static and dynamic balance due to excess weight. Kinesthetic differentiation, spatial orientation, and rhythm capacity are not significantly associated with BMI, but these sub-capacities positively influence gross motor coordination (GMC), except for hand-eye motor reaction. creator: Yuan Sui creator: Lin Cui creator: Binbin Jia creator: Xiangyang Ding creator: Min He creator: Yingen Da creator: Yue Shi creator: Fei Li creator: Pan Li uri: https://doi.org/10.7717/peerj.17865 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Sui et al. title: Tree regeneration and ontogenetic strategies of northern European hemiboreal forests: transitioning towards closer-to-nature forest management link: https://peerj.com/articles/17644 last-modified: 2024-08-08 description: BackgroundTree ontogeny is the genetic trajectories of regenerative processes in trees, repeating in time and space, including both development and reproduction. Understanding the principles of tree ontogeny is a key priority in emulating natural ecological patterns and processes that fall within the calls for closer-to-nature forest management. By recognizing and respecting the growth and development of individual trees and forest stands, forest managers can implement strategies that align with the inherent dynamics of forest ecosystem. Therefore, this study aims to determine the ontogenetic characteristics of tree regeneration and growth in northern European hemiboreal forests.MethodologyWe applied a three-step process to review i) the ontogenetic characteristics of forest trees, ii) ontogenetic strategies of trees for stand-forming species, and iii) summarise the review findings of points i and ii to propose a conceptual framework for transitioning towards closer-to-nature management of hemiboreal forest trees. To achieve this, we applied the super-organism approach to forest development as a holistic progression towards the establishment of natural stand forming ecosystems.ResultsThe review showed multiple aspects; first, there are unique growth and development characteristics of individual trees at the pre-generative and generative stages of ontogenesis under full and minimal light conditions. Second, there are four main modes of tree establishment, growth and development related to the light requirements of trees; they were described as ontogenetic strategies of stand-forming tree species: gap colonisers, gap successors, gap fillers and gap competitors. Third, the summary of our analysis of the ontogenetic characteristics of tree regeneration and growth in northern European hemiboreal forests shows that stand-forming species occupy multiple niche positions relative to forest dynamics modes.ConclusionsThis study demonstrates the importance of understanding tree ontogeny under the pretext of closer-to-nature forest management, and its potential towards formulating sustainable forest management that emulates the natural dynamics of forest structure. We suggest that scientists and foresters can adapt closer-to-nature management strategies, such as assisted natural regeneration of trees, to improve the vitality of tree communities and overall forest health. The presented approach prioritizes ecological integrity and forest resilience, promoting assisted natural regeneration, and fostering adaptability and connectivity among plant populations in hemiboreal tree communities. creator: Raimundas Petrokas creator: Michael Manton creator: Darius Kavaliauskas uri: https://doi.org/10.7717/peerj.17644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Petrokas et al. title: Towards unified reporting of genome sequencing results in clinical microbiology link: https://peerj.com/articles/17673 last-modified: 2024-08-08 description: Whole genome sequencing (WGS) has become a vital tool in clinical microbiology, playing an important role in outbreak investigations, molecular surveillance, and identification of bacterial species, resistance mechanisms and virulence factors. However, the complexity of WGS data presents challenges in interpretation and reporting, requiring tailored strategies to enhance efficiency and impact. This study explores the diverse needs of key stakeholders in healthcare, including clinical management, laboratory work, public surveillance and epidemiology, infection prevention and control, and academic research, regarding WGS-based reporting of clinically relevant bacterial species. In order to determine preferences regarding WGS reports, human-centered design approach was employed, involving an online survey and a subsequent workshop with stakeholders. The survey gathered responses from 64 participants representing the above mentioned healthcare sectors across geographical regions. Key findings include the identification of barriers related to data accessibility, integration with patient records, and the complexity of interpreting WGS results. As the participants designed their ideal report using nine pre-defined sections of a typical WGS report, differences in needs regarding report structure and content across stakeholders became evident. The workshop discussions further highlighted the need to feature critical findings and quality metrics prominently in reports, as well as the demand for flexible report designs. Commonalities were observed across stakeholder-specific reporting templates, such as the uniform ranking of certain report sections, but preferences regarding the depth of content within these sections varied. Using these findings, we suggest stakeholder-specific structures which should be considered when designing customized reporting templates. In conclusion, this study underscores the importance of tailoring WGS-based reports of clinically relevant bacteria to meet the distinct needs of diverse healthcare stakeholders. The evolving landscape of digital reporting increases the opportunities with respect to WGS reporting and its utility in managing infectious diseases and public health surveillance. creator: Eugenio Mutschler creator: Tim Roloff creator: Aitana Neves creator: Hege Vangstein Aamot creator: Belén Rodriguez-Sanchez creator: Mario Ramirez creator: John Rossen creator: Natacha Couto creator: Ângela Novais creator: Benjamin P. Howden creator: Sylvain Brisse creator: Sandra Reuter creator: Oliver Nolte creator: Adrian Egli creator: Helena M. B. Seth-Smith uri: https://doi.org/10.7717/peerj.17673 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Mutschler et al. title: Museomics allows comparative analyses of mitochondrial genomes in the family Gryllidae (Insecta, Orthoptera) and confirms its phylogenetic relationships link: https://peerj.com/articles/17734 last-modified: 2024-08-08 description: BackgroundNext-generation sequencing technology can now be used to sequence historical specimens from natural history collections, an approach referred to as museomics. The museomics allows obtaining molecular data from old museum-preserved specimens, a resource of biomolecules largely underexploited despite the fact that these specimens are often unique samples of nomenclatural types that can be crucial for resolving scientific questions. Despite recent technical progress, cricket mitogenomes are still scarce in the databases, with only a handful of new ones generated each year from freshly collected material.MethodsIn this study, we used the genome skimming method to sequence and assemble three new complete mitogenomes representing two tribes of the cricket subfamily Eneopterinae: two were obtained from old, historical type material of Xenogryllus lamottei (68 years old) and X. maniema (80 years old), the third one from a freshly collected specimen of Nisitrus vittatus. We compared their genome organization and base composition, and reconstructed the molecular phylogeny of the family Gryllidae.ResultsOur study not only confirmed that the genome skimming method used by next generation sequencing allows us to efficiently obtain the whole mitogenome from dry-pinned historical specimens, but we also confirmed how promising it is for large-scale comparative studies of mitogenomes using resources from natural history collections. Used in a phylogenetic context the new mitogenomes attest that the mitogenomic data contain valuable information and also strongly support phylogenetic relationships at multiple time scales. creator: Jiajia Dong creator: Yong Liu creator: Ming Kai Tan creator: Rodzay Abdul Wahab creator: Romain Nattier creator: Pascaline Chifflet-Belle creator: Tony Robillard uri: https://doi.org/10.7717/peerj.17734 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dong et al. title: Quantitating primer-template interactions using deconstructed PCR link: https://peerj.com/articles/17787 last-modified: 2024-08-08 description: When the polymerase chain reaction (PCR) is used to amplify complex templates such as metagenomic DNA using single or degenerate primers, preferential amplification of templates (PCR bias) leads to a distorted representation of the original templates in the final amplicon pool. This bias can be influenced by mismatches between primers and templates, the locations of mismatches, and the nucleotide pairing of mismatches. Many studies have examined primer-template interactions through interrogation of the final products of PCR amplification with controlled input templates. Direct measurement of primer-template interactions, however, has not been possible, leading to uncertainty when optimizing PCR reactions and degenerate primer pools. In this study, we employed a method developed to reduce PCR bias (i.e., Deconstructed PCR, or DePCR) that also provides empirical data regarding primer-template interactions during the first two cycles of PCR amplification. We systematically examined interactions between primers and templates using synthetic DNA templates and varying primer pools, amplified using standard PCR and DePCR protocols. We observed that in simple primer-template systems, perfect match primer-template interactions are favored, particularly when mismatches are close to the 3′ end of the primer. In more complex primer-template systems that better represent natural samples, mismatch amplifications can dominate, and heavily degenerate primer pools can improve representation of input templates. When employing the DePCR methodology, mismatched primer-template annealing led to amplification of source templates with significantly lower distortion relative to standard PCR. We establish here a quantitative experimental system for interrogating primer-template interactions and demonstrate the efficacy of DePCR for amplification of complex template mixtures with complex primer pools. creator: Jeremy Kahsen creator: Sonia K. Sherwani creator: Ankur Naqib creator: Trisha Jeon creator: Lok Yiu Ashley Wu creator: Stefan J. Green uri: https://doi.org/10.7717/peerj.17787 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kahsen et al. title: The clinical value of KL-6 for predicting the occurrence and severity of connective tissue disease-associated interstitial lung disease is not affected by CTD type or treatment link: https://peerj.com/articles/17792 last-modified: 2024-08-08 description: ObjectiveThe aim of this study was to explore the potential values of Krebs von den Lungen-6 (KL-6), neutrophil to lymphocyte ratio (NLR), systemic immune inflammation (SII), platelet to lymphocyte ratio (PLR), monocyte to lymphocyte ratio (MLR) and red blood cell distribution width (RDW) in the diagnosis and evaluation of the severity of connective tissue disease-associated interstitial lung disease (CTD-ILD).MethodsA total of 140 connective tissue disease (CTD) patients and 85 CTD-ILD patients were recruited for this study at Shanxi Provincial People’s Hospital from May 2022 to May 2023. Patients were divided into subgroups based on medication history and CTD subtypes to compare and analyze the clinical data and laboratory parameters of CTD-ILD patients and CTD patients. The receiver operating characteristic curve (ROC) was used to evaluate the diagnostic efficacy of KL-6, NLR, SII, PLR, MLR, and RDW in identifying CTD-ILD patients from CTD patients. A Spearman correlation analysis was conducted to elucidate the correlations between these markers and the lung function parameters of forced vital capacity (FVC, %), forced expired volume in one second (FEV1, %), and diffusing capacity of carbon monoxide (DLCO, %). Finally, binary logistic regression analysis was applied to discern the independent risk factors for CTD-ILD.ResultsNLR, SII, MLR, RDW, and KL-6 displayed significant statistical differences in the experimental groups. In both untreated and treated subgroups, KL-6 displayed higher values for CTD-ILD than CTD among all CTD subtypes. In untreated subgroups, there were significant differences in MLR levels between rheumatoid arthritis (RA) and RA-ILD patients and in NLR levels between Sjögren syndrome (SjS) and SjS-ILD patients. There were also significant differences in RDW-SD between the “other CTD” and “other CTD-ILD” groups. In treated subgroups, there were significant differences in both RDW-SD and RDW-CV between RA and RA-ILD patients and in NLR, SII, MLR, PLR, and RDW-SD between “other CTD” and “other CTD-ILD” groups. ROC revealed that KL-6 emerged as the most effective predictor for CTD-ILD in both treated and untreated groups. The multivariate logistic regression analysis results showed that both KL-6 and age were independent risk factors for CTD-ILD. NLR, SII, and PLR were negatively correlated with DLCO (%) in the untreated CTD-ILD group, and KL-6 was negatively correlated with various lung function parameters in both treated and untreated CTD-ILD groups.ConclusionKL-6 emerged as the most promising biomarker for diagnosing CTD-ILD and assessing its severity. The diagnostic value of KL-6 was unaffected by medication interference and surpassed the value of other parameters, such as NLR, SII, MLR, and RDW. The diagnostic value of RDW-SD was higher than that of RDW-CV in CTD-ILD patients. NLR, SII, MLR, and PLR have potential value in diagnosing the different types of CTD-ILD. creator: Huifang Xing creator: Hongping Liang uri: https://doi.org/10.7717/peerj.17792 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Xing and Liang title: Testing intra-species variation in allocation to growth and defense in rubber tree (Hevea brasiliensis) link: https://peerj.com/articles/17877 last-modified: 2024-08-08 description: BackgroundPlants allocate resources to growth, defense, and stress resistance, and resource availability can affect the balance between these allocations. Allocation patterns are well-known to differ among species, but what controls possible intra-specific trade-offs and if variation in growth vs. defense potentially evolves in adaptation to resource availability.MethodsWe measured growth and defense in a provenance trial of rubber trees (Hevea brasiliensis) with clones originating from the Amazon basin. To test hypotheses on the allocation to growth vs. defense, we relate biomass growth and latex production to wood and leaf traits, to climate and soil variables from the location of origin, and to the genetic relatedness of the Hevea clones.ResultsContrary to expectations, there was no trade-off between growth and defense, but latex yield and biomass growth were positively correlated, and both increased with tree size. The absence of a trade-off may be attributed to the high resource availability in a plantation, allowing trees to allocate resources to both growth and defense. Growth was weakly correlated with leaf traits, such as leaf mass per area, intrinsic water use efficiency, and leaf nitrogen content, but the relative investment in growth vs. defense was not associated with specific traits or environmental variables. Wood and leaf traits showed clinal correlations to the rainfall and soil variables of the places of origin. These traits exhibited strong phylogenetic signals, highlighting the role of genetic factors in trait variation and adaptation. The study provides insights into the interplay between resource allocation, environmental adaptations, and genetic factors in trees. However, the underlying drivers for the high variation of latex production in one of the commercially most important tree species remains unexplained. creator: Kanin Rungwattana creator: Poonpipope Kasemsap creator: Thitaporn Phumichai creator: Ratchanee Rattanawong creator: Peter Hietz uri: https://doi.org/10.7717/peerj.17877 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rungwattana et al. title: Where have I got to? Associations of age at marriage with marital household assets in educated and uneducated women in lowland Nepal link: https://peerj.com/articles/17671 last-modified: 2024-08-07 description: BackgroundWomen’s underage marriage (<18 years) is associated with adverse maternal and child health outcomes. Poverty in the natal household has been widely considered to be a key risk factor for underage marriage, but the evidence base is unreliable. When investigating this issue, most studies use marital wealth inappropriately, as a proxy for wealth in the natal household. In contrast, we investigated whether the timing of women’s marriage was associated with the wealth of the households they marry into, and how this may vary by women’s education level. This approach allows us to explore a different set of research questions which help to understand the economic value placed on the timing of women’s marriage.MethodsWe used data on 3,102 women aged 12–34 years, surveyed within 1 year of marriage, from the cluster-randomized Low Birth Weight South Asia Trial in lowland rural Nepal. Linear mixed-effects regression models investigated independent associations of women’s marriage age and education level with marital household wealth, and their interactive effects. Models adjusted for marital household traits. We analysed the full sample, and then only the uneducated women, who comprised a substantial proportion in our sample.ResultsIn the full sample, we found that each later year of women’s marriage was associated with 1.5% lower asset score for those with primary education, and with 0.3% and 1.3% higher asset score for those with lower secondary or secondary/higher education, respectively. For uneducated women, relative to marrying ≤14 years, marrying at 15, 16, 17 and ≥18 years was associated with 1.5%, 4.4%, 2.4% and 6.2% greater marital asset score respectively.ConclusionOn average, marrying ≥18 years was associated with greater marital assets for secondary-educated women. There were only very modest benefits in terms of marital household wealth for delaying marriage beyond 16 years for uneducated women or those with low education. These findings elucidate potential trade-offs faced by families, including decisions over how much education, if any, to provide to daughters. They may help to understand the economic rationale underpinning the timing of marriage, and why early marriage remains common despite efforts to delay it. creator: Akanksha A. Marphatia creator: Naomi M. Saville creator: Dharma S. Manandhar creator: Mario Cortina-Borja creator: Jonathan C. K. Wells uri: https://doi.org/10.7717/peerj.17671 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Marphatia et al. title: Advances in research on the main nutritional quality of daylily, an important flower vegetable of Liliaceae link: https://peerj.com/articles/17802 last-modified: 2024-08-07 description: Daylily (Hemerocallis citrina) is a perennial herb of the genus Hemerocallis of Liliaceae. It is also an economically important crop and is widely cultivated. Daylily has nutritional, medicinal and ornamental values. The research literature shows that daylily is a high-quality food raw material rich in soluble sugars, ascorbic acid, flavonoids, dietary fiber, carotenoids, mineral elements, polyphenols and other nutrients, which are effective in clearing heat and diuresis, resolving bruises and stopping bleeding, strengthening the stomach and brain, and reducing serum cholesterol levels. This article reviews the main nutrients of daylily and summarizes the drying process of daylily. In addition, due to the existence of active ingredients, daylily also has a variety of biological activities that are beneficial to human health. This article also highlights the nutritional quality of daylily, the research progress of dried vegetable rehydration technology and dried daylily. In the end, the undeveloped molecular mechanism and functional research status of daylily worldwide are introduced in order to provide reference for the nutritional quality research and dried processing industry of daylily. creator: Li-Xiang Wang creator: Ya-Hui Wang creator: Chen Chen creator: Jie-Xia Liu creator: Tong Li creator: Jing-Wen Li creator: Pei-Zhuo Liu creator: De-Bao Xu creator: Sheng Shu creator: Ai-Sheng Xiong uri: https://doi.org/10.7717/peerj.17802 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li-Xiang et al. title: Femora nutrient foramina and aerobic capacity in giant extinct xenarthrans link: https://peerj.com/articles/17815 last-modified: 2024-08-07 description: Nutrient foramina are small openings in the periosteal surface of the mid-shaft region of long bones that traverse the cortical layer and reach the medullary cavity. They are important for the delivery of nutrients and oxygen to bone tissue and are crucial for the repair and remodeling of bones over time. The nutrient foramina in the femur’s diaphysis are related to the energetic needs of the femur and have been shown to be related to the maximum metabolic rate (MMR) of taxa. Here, we investigate the relationship between nutrient foramen size and body mass as a proxy to the aerobic capacity of taxa in living and extinct xenarthrans, including living sloths, anteaters, and armadillos, as well as extinct xenarthrans such as glyptodonts, pampatheres, and ground sloths. Seventy femora were sampled, including 20 from extant taxa and 50 from extinct taxa. We obtained the blood flow rate (Q̇) based on foramina area and performed PGLS and phylogenetic ANCOVA in order to explore differences among mammalian groups. Our results show that, among mammals, taxa commonly associated with lower metabolism like living xenarthrans showed relatively smaller foramina, while the foramina of giant extinct xenarthrans like ground sloths and glyptodonts overlapped with non-xenarthran placentals. Consequently, Q̇ estimations indicated aerobic capacities comparable to other placental giant taxa like elephants or some ungulates. Furthermore, the estimation of the MMR for fossil giant taxa showed similar results, with almost all taxa showing high values except for those for which strong semi-arboreal or fossorial habits have been proposed. Moreover, the results are compatible with the diets predicted for extinct taxa, which indicate a strong consumption of grass similar to ungulates and in contrast to the folivorous or insectivorous diets of extant xenarthrans. The ancestral reconstruction of the MMR values indicated a lack of a common pattern for all xenarthrans, strongly supporting the occurrence of low metabolic rates in extant forms due to their particular dietary preferences and arboreal or fossorial habits. Our results highlight the importance of considering different evidence beyond the phylogenetic position of extinct taxa, especially when extinct forms are exceptionally different from their extant relatives. Future studies evaluating the energetic needs of giant extinct xenarthrans should not assume lower metabolic rates for these extinct animals based solely on their phylogenetic position and the observations on their extant relatives. creator: Luciano Varela creator: Sebastián Tambusso creator: Richard Fariña uri: https://doi.org/10.7717/peerj.17815 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Varela et al. title: Arbuscular mycorrhizal fungi enhance drought resistance in Bombax ceiba by regulating SOD family genes link: https://peerj.com/articles/17849 last-modified: 2024-08-07 description: The physiological activity facilitated by arbuscular mycorrhizal fungi (AMF) contributes to plants’ ability to tolerate drought. Nevertheless, it is unclear if AMF colonization affects the expression of genes in the host plant that encode antioxidant enzymes in the superoxide dismutase (SOD) family, which help alleviate drought stress in plants. Here, we conducted a pot trial to determine whether colonization by the AMF Rhizophagus irregularis improves drought resistance in Bombax ceiba. We comprehensively analyzed the SOD gene family and evaluated genome-wide expression patterns of SODs and SOD activity in AMF-colonized and non-mycorrhizal plants under simulated drought. We identified a total of 13 SODs in the genome of B. ceiba, including three FeSODs (BcFSDs), three MnSODs (BcMSDs), and seven Cu/ZnSODs (BcCSDs). Phylogenetic analysis based on binding domain revealed that SOD genes from B. ceiba and various other plant species can be divided into three separate groups, showing significant bootstrap values. Our examination of gene composition and patterns suggests that most BcSOD genes in these three subgroups are significantly conserved. Additionally, it was noted that hormones and stress-responsive cis-regulatory elements were found in all BcSOD promoters. Expression profiling by qRT-PCR demonstrated that AMF increased relative expression levels of Cu/Zn-SODs in both roots and shoots under drought stress, except for BcCSD3 in roots. Furthermore, AMF colonization increased the relative expression of BcMSD1a and BcMSD1b in roots, augmenting SOD activities and increasing ROS scavenging during drought. In general, this work offers molecular evidence in support of the beneficial effect of AMF colonization on drought tolerance in B. ceiba. It also elucidates the expression patterns of SOD genes, which will support efforts to optimize mycorrhizal seedling cultivation under stressful conditions. creator: Changxin Luo creator: Zhumei Li creator: Yumei Shi creator: Yong Gao creator: Yanguo Xu creator: Yanan Zhang creator: Honglong Chu uri: https://doi.org/10.7717/peerj.17849 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Luo et al. title: Modic changes in patients with lumbar disc herniation followed more than 1 year after lumbar discectomy: a systematic review and meta-analysis link: https://peerj.com/articles/17851 last-modified: 2024-08-07 description: BackgroundModic changes (MCs) are identified as an independent risk factor for low back pain. Different subtypes of MCs vary in their impact on postoperative pain relief. However, consensus on the transformation of postoperative MC fractions in patients with distinct MC subtypes is lacking.MethodsThis comprehensive systematic review and meta-analysis searched English-language articles in PubMed, Cochrane Library, Web of Science, and Embase databases until January 2024. Studies included focused on patients transitioning between various microcrack subtypes post-discectomy. The primary outcome measure was the transformation between different postoperative microcrack fractions.ResultsEight studies with 689 participants were analyzed. Overall, there is moderate to high-quality evidence indicating differences in the incidence of MC conversion across MC subtypes. The overall incidence of MC conversion was 27.7%, with rates of 37.0%, 20.5%, and 19.1% for MC0, MC1, and MC2 subtypes, respectively. Thus, postoperative MC type transformation, particularly from preoperative MC0 to MC1 (17.7%) or MC2 (13.1%), was more common, with MC1 transformation being predominant. Patients with preoperative comorbid MC1 types (19.0%) exhibited more postoperative transitions than those with MC2 types (12.4%).ConclusionThis study underscores the significance of analyzing post-discectomy MCs in patients with lumbar disc herniation, revealing a higher incidence of MCs post-lumbar discectomy, particularly from preoperative absence of MC to MC1 or MC2. Preoperative MC0 types were more likely to undergo postoperative MC transformation than combined MC1 or MC2 types. These findings are crucial for enhancing surgical outcomes and postoperative care. creator: Xiangyu Feng creator: Sunqi Nian creator: Jiayu Chen creator: Na Li creator: Pingguo Duan uri: https://doi.org/10.7717/peerj.17851 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Feng et al. title: Assessment and phenotypic identification of millet germplasm (Setaria italica L.) in Liaoning, China link: https://peerj.com/articles/17871 last-modified: 2024-08-07 description: AimsThis study evaluated millet germplasms in Liaoning Province to support the collection, preservation and innovation of millet germplasm resources.MethodsThe study was conducted from 2018 to 2020, involved the selection of 105 millet germplasm resources from the Germplasm Bank of the Liaoning Academy of Agricultural Sciences (LAAS), the observation and recording of 31 traits, and the application of multivariate analysis methods to assess phenotypic diversity.ResultsFrom the diversity analysis and correlation analysis, it was found that the tested traits had abundant diversity and complex correlations among them. Principal component analysis (PCA) comprehensively analyzed all quantitative traits and extracted seven principal components. Grey relational analysis (GRA) highlighted the varied contributions of different traits to yield. Through systematic cluster analysis (SCA), the resources were categorized into six groups at Euclidean distance of 17.09. K-mean cluster analysis determined the distribution interval and central value of each trait, then identified resources with desirable traits.ConclusionThe results revealed resources that possess characteristics such as upthrow seedling leaves, more tillers and branches, larger and well-formed ears, and lodging resistance prefer to higher grain yield. It was also discovered that the subear internode length (SIL) could be an indicator for maturity selection. Four specific resources, namely, Dungu No. 1, Xiao-li-xiang, Basen Shengu, and Yuhuanggu No. 1, were identified for further breeding and practical applications. creator: Xintong Li creator: Weifeng He creator: Honghao Wang creator: Min Xu uri: https://doi.org/10.7717/peerj.17871 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Cognitive expertise in esport experts: a three-level model meta-analysis link: https://peerj.com/articles/17857 last-modified: 2024-08-07 description: ObjectivesThe cognitive expertise of experts has been an intriguing theme; there has been rapid growth in cognitive research related to esports. Given the close association between esports activities and cognition, esports holds promise in offering new perspectives for understanding cognitive expertise. This meta-analysis aims at quantitatively delineating the cognitive disparities between esports experts and amateurs.MethodsThe expert group comprised professional video game players and high-ranking players (top 1%), while amateurs were assigned to the control group. Research studies published between January 2000 and December 2023 were systematically searched in databases. A three-level model with cluster-robust variance estimation was used to calculate the overall effect size. The moderating variables included professional level, cognitive abilities, dependent variable type, game genre, gender and age.ResultsA total of 15 studies containing 142 effect sizes and 1085 participants were included in this meta-analysis. The results indicated that, compared to amateurs, video game experts demonstrated superior cognitive abilities with a small effect size (Hedges’ g = 0.373, 95% CI [0.055–0.691], p = .012). The differences between experts and amateur players mainly manifest in spatial cognition and attention. Sensitivity analysis, risk of bias, and publication bias results indicated the reliability of these findings.ConclusionsThis meta-analysis confirms that esports experts possess superior cognitive abilities compared to amateurs, particularly in aspects of spatial cognition and attention. These can provide an effective reference for future selection and training in esports. creator: Haofei Miao creator: Hao He creator: Xianyun Hou creator: Jinghui Wang creator: Lizhong Chi uri: https://doi.org/10.7717/peerj.17857 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Miao et al. title: Effects of strength training on repeated sprint ability in team sports players: a systematic review link: https://peerj.com/articles/17756 last-modified: 2024-08-06 description: ObjectiveThis systematic review was conducted to analyze the existing evidence on the effects of strength training (ST) and complex/contrast training (CCT) on repeated sprint ability (RSA) in team sports players.MethodsA systematic review of the literature was performed following the PRISMA statement. PubMed, Web of Science, and Scopus databases were used. Original full-text articles were analyzed, without date restriction until May 26, 2024, written in English, peer-reviewed, and for eligibility must have included (1) male or female team sports players, amateur or professional category, without age restriction (2) lower extremity ST and/or CCT program (3) active control group (4) running RSA test (e.g., repeated shuttle sprint ability test or straight-line repeated sprint ability test) before and after the intervention period (5) controlled trial.ResultsA total of 3,376 studies were identified and screened. Finally, 10 articles were included based on the inclusion and exclusion criteria, all with moderate methodological quality according to the PEDro scale. The best time, mean time, and total time presented significant pre and post-test changes, using ST in 3, 2, and 1 experimental groups, respectively, and using CCT in 1, 1, and 1 experimental groups, respectively, with almost no differences in the percentage decrement most commonly reported in RSA tests. There were no changes in the control groups.ConclusionTogether, ST performed in a range of maximal power provides benefits in the best time and mean time and performed between 80 to 95% of 1 repetition maximum (RM) provides benefits in the best time, mean time, and total time in RSA tests. CCT performed between 75 to 90% of 1 RM combined with jumps and sprints provides benefits in the best time, mean time, and total time in RSA test, but no unaltered percentage decrement in ST and CCT in elite and semi-professional team sport players. creator: Andrés Osses-Rivera creator: Rodrigo Yáñez-Sepúlveda creator: Sebastián Jannas-Vela creator: Jeppe F. Vigh-Larsen creator: Matías Monsalves-Álvarez uri: https://doi.org/10.7717/peerj.17756 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Osses-Rivera et al. title: Prediction of PM2.5 concentration based on a CNN-LSTM neural network algorithm link: https://peerj.com/articles/17811 last-modified: 2024-08-06 description: Fine particulate matter (PM2.5) is a major air pollutant affecting human survival, development and health. By predicting the spatial distribution concentration of PM2.5, pollutant sources can be better traced, allowing measures to protect human health to be implemented. Thus, the purpose of this study is to predict and analyze the PM2.5 concentration of stations based on the integrated deep learning of a convolutional neural network long short-term memory (CNN-LSTM) model. To solve the complexity and nonlinear characteristics of PM2.5 time series data problems, we adopted the CNN-LSTM deep learning model. We collected the PM2.5data of Qingdao in 2020 as well as meteorological factors such as temperature, wind speed and air pressure for pre-processing and characteristic analysis. Then, the CNN-LSTM deep learning model was integrated to capture the temporal and spatial features and trends in the data. The CNN layer was used to extract spatial features, while the LSTM layer was used to learn time dependencies. Through comparative experiments and model evaluation, we found that the CNN-LSTM model can achieve excellent PM2.5 prediction performance. The results show that the coefficient of determination (R2) is 0.91, and the root mean square error (RMSE) is 8.216 µg/m3. The CNN-LSTM model achieves better prediction accuracy and generalizability compared with those of the CNN and LSTM models (R2 values of 0.85 and 0.83, respectively, and RMSE values of 11.356 and 14.367, respectively). Finally, we analyzed and explained the predicted results. We also found that some meteorological factors (such as air temperature, pressure, and wind speed) have significant effects on the PM2.5 concentration at ground stations in Qingdao. In summary, by using deep learning methods, we obtained better prediction performance and revealed the association between PM2.5 concentration and meteorological factors. These findings are of great significance for improving the quality of the atmospheric environment and protecting public health. creator: Xuesong Bai creator: Na Zhang creator: Xiaoyi Cao creator: Wenqian Chen uri: https://doi.org/10.7717/peerj.17811 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bai et al. title: Study on the relationship between net primary productivity and site quality in Japanese larch plantations in mountainous areas of eastern Liaoning link: https://peerj.com/articles/17820 last-modified: 2024-08-06 description: Plantation forests enhance carbon storage in terrestrial ecosystems in China. Larix kaempferi (Lamb.) Carrière (Lamb.) (Larix olgensis Henry) is the main species for afforestation in the eastern Liaoning Province. Therefore, it is important to understand the correlation between the site class and carbon sink potential of Larix kaempferi plantations in Liaoning Province for afforestation and carbon sink in this area. The model was fitted using three classical theoretical growth equations: the Richards model, the Korf model, and the Hossfeld model. This study used the forest resource inventory data for management in Liaoning Province in 2011 to build six dynamic height-age models for a Larix kaempferi plantation in Dandong City regardless of base-age. The optimal model derived by the generalized algebraic difference approach (GADA) method was compared with the model derived by the algebraic difference approach (ADA) method. The superiority of GADA was demonstrated by comparison. The Levenberg-Marquardt algorithm was used to fit the model. The statistical and biological characteristics were considered synthetically when comparing the models. The best model was screened out by statistical analysis and graphic analysis. The results show that the differential height-age model derived from Richards equation can well explain the growth process of Larix kaempferi in Dandong City, Liaoning Province under different conditions. The site index model based on Richards equation and derived by GADA was used to calculate the site class of a Larix kaempferi plantation in Dandong City. The net primary productivity (NPP) value from the past ten years was extracted from the MOD17A3HGF data set. Spearman correlation analysis and Kendall correlation analysis were used to show that there is a significant positive correlation between NPP value and site class of Larix kaempferi plantation in Dandong City. Among them, the highest growth occurred in 2016; NPP increased by about 3.914 gC/m2/year for every two increases in height-age grade; the lowest increase in NPP was in 2014; NPP increased by about 2.113 gC/m2/year for every two increases in height-age grade; and for every two increases in height-age grade in the recent ten years, the average NPP value increased by about 2.731 gC/m2/year. creator: Wenlong Chang creator: JingHao Li creator: Jinwei Wu creator: Jian Zhang creator: Yang Yu creator: Huiwen Sun creator: Yibo Wen uri: https://doi.org/10.7717/peerj.17820 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chang et al. title: Localization of potato browning resistance genes based on BSA-seq technology link: https://peerj.com/articles/17831 last-modified: 2024-08-06 description: Browning is a common problem that occurs during potato processing; it is typically resolved by adding chemicals during the production process. However, there is a need to develop potato varieties that are resistant to browning due to a growing consumer interest in healthier diets. This study initially identified 275 potato varieties that are resistant to browning; these were narrowed down to eight varieties, with four of them being highly resistant. A hybrid population was developed by crossing the highly resistant CIP395109.29 with the easily browned Kexin 23. Bulked segregant analysis (BSA) was conducted, which identified 21 potato genes associated with anti-browning properties through sequencing data analysis and organization. The findings of this study lay a solid groundwork for future research on breeding potatoes with anti-browning traits, offer molecular markers for identifying anti-browning varieties, and serve as a valuable reference for further investigations into potato browning mechanisms. creator: Haiyan Wang creator: Ze Pang creator: Lichun Wang creator: Guokui Tian creator: Fengyun Li creator: Yang Pan creator: Kaixin Ding uri: https://doi.org/10.7717/peerj.17831 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Bayesian multistate models for measuring invasive carp movement and evaluating telemetry array performance link: https://peerj.com/articles/17834 last-modified: 2024-08-06 description: Understanding the movement patterns of an invasive species can be a powerful tool in designing effective management and control strategies. Here, we used a Bayesian multistate model to investigate the movement of two invasive carp species, silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), using acoustic telemetry. The invaded portions of the Illinois and Des Plaines Rivers, USA, are a high priority management zone in the broader efforts to combat the spread of invasive carps from reaching the Laurentian Great Lakes. Our main objective was to characterize the rates of upstream and downstream movements by carps between river pools that are maintained by navigation lock and dam structures. However, we also aimed to evaluate the efficacy of the available telemetry infrastructure to monitor carp movements through this system. We found that, on a monthly basis, most individuals of both species remained within their current river pools: averaging 76.2% of silver carp and 75.5% of bighead carp. Conversely, a smaller proportion of silver carp, averaging 14.2%, and bighead carp, averaging 13.9%, moved to downstream river pools. Movements towards upstream pools were the least likely for both species, with silver carp at an average of 6.7% and bighead carp at 7.9%. The highest probabilities for upstream movements were for fish originating from the three most downstream river pools, where most of the population recruitment occurs. However, our evaluation of the telemetry array’s effectiveness indicated low probability to detect fish in this portion of the river. We provide insights to enhance the placement and use of these monitoring tools, aiming to deepen our comprehension of these species’ movement patterns in the system. creator: Jessica C. Stanton creator: Marybeth K. Brey creator: Alison A. Coulter creator: David R. Stewart creator: Brent Knights uri: https://doi.org/10.7717/peerj.17834 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2024 Stanton et al. title: Ferroptosis-related gene transferrin receptor protein 1 expression correlates with the prognosis and tumor immune microenvironment in cervical cancer link: https://peerj.com/articles/17842 last-modified: 2024-08-06 description: BackgroundFerroptosis is a non-apoptotic iron-dependent form of cell death implicated in various cancer pathologies. However, its precise role in tumor growth and progression of cervical cancer (CC) remains unclear. Transferrin receptor protein 1 (TFRC), a key molecule associated with ferroptosis, has been identified as influencing a broad range of pathological processes in different cancers. However, the prognostic significance of TFRC in CC remains unclear. The present study utilized bioinformatics to explore the significance of the ferroptosis-related gene TFRC in the progression and prognosis of CC.MethodsWe obtained RNA sequencing data and corresponding clinical information on patients with CC from The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx) and Gene Expression Omnibus (GEO) databases. Using least absolute shrinkage and selection operator (LASSO) Cox regression, we then generated a multigene signature of five ferroptosis-related genes (FRGs) for the prognostic prediction of CC. We investigated the relationship between TFRC gene expression and immune cell infiltration by employing single-sample GSEA (ssGSEA) analysis. The potential functional role of the TFRC gene was evaluated through gene set enrichment analysis (GSEA). Immunohistochemistry and qPCR was employed to assess TFRC mRNA and protein expression in 33 cases of cervical cancer. Furthermore, the relationship between TFRC mRNA expression and overall survival (OS) was investigated in patients.ResultsCC samples had significantly higher TFRC gene expression levels than normal tissue samples. Higher TFRC gene expression levels were strongly associated with higher cancer T stages and OS events. The findings of multivariate analyses illustrated that the OS in CC patients with high TFRC expression is shorter than in patients with low TFRC expression. Significant increases were observed in the levels of TFRC mRNA and protein expression in patients diagnosed with CC.ConclusionIncreased TFRC expression in CC was associated with disease progression, an unfavorable prognosis, and dysregulated immune cell infiltration. In addition, it highlights ferroptosis as a promising therapeutic target for CC. creator: Xiujuan Shang creator: Hongdong Wang creator: Jin Gu creator: Xiaohui Zhao creator: Jing Zhang creator: Bohao Sun creator: Xinming Zhu uri: https://doi.org/10.7717/peerj.17842 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shang et al. title: Chemical composition and egg production capacity throughout bloom development of ctenophore Mnemiopsis leidyi in the northern Adriatic Sea link: https://peerj.com/articles/17844 last-modified: 2024-08-06 description: High abundances of gelatinous zooplankton (GZ) can significantly impact marine ecosystem by acting as both sink and source of organic matter (OM) and nutrients. The decay of GZ bloom can introduce significant amount of OM to the ocean interior, with its variability influenced by GZ life traits and environmental factors, impacting microbial communities vital to marine biogeochemical cycles. The invasive ctenophores Mnemiopsis leidyi has formed massive blooms in the northern Adriatic Sea since 2016. However, the variability in the chemical composition and egg production of blooming populations, as well as the role of environmental factors in governing this variability, remains largely unknown. Our analysis of biometry, chemical composition, and fecundity of M. leidyi sampled in the Gulf of Trieste in 2021 revealed stable carbon and nitrogen content throughout bloom development, with no significant correlation with seawater temperature, salinity, oxygen, and chlorophyll a concentration. Although the studied population exhibited homogeneity in terms of biometry and chemical composition, the number of produced eggs varied substantially, showing no clear correlation with environmental variables and being somewhat lower than previously reported for the study area and other Mediterranean areas. We observed a positive correlation between the wet weight of individuals and the percentage of hatched eggs, as well as a significant positive correlation between the percentage of hatched eggs and ambient seawater temperature. Additionally, we noted that the speed of hatching decreased with decreasing seawater temperature in autumn, corresponding to the end of M. leidyi bloom. creator: Kevin Rečnik creator: Katja Klun creator: Lovrenc Lipej creator: Alenka Malej creator: Tinkara Tinta uri: https://doi.org/10.7717/peerj.17844 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Rečnik et al. title: Associations of 24-hour movement guidelines adherence with fruit and vegetable intake in university students link: https://peerj.com/articles/17875 last-modified: 2024-08-06 description: BackgroundUnhealthy eating habits, such as low vegetable and fruit intake, are associated with many health problems. 24-h movement behaviors have been reported to be positively associated with numerous health-related outcomes. Despite the importance of these two modifiable lifestyle behaviors in building healthy habits in university students, there is a paucity of relevant research in this population. Therefore, this study aims to examine the correlation between compliance with 24-h movement guideline (24-h MG) and intake of fruits and vegetables (IFV) in Chinese university students.MethodsThis study investigated the relationship between the compliance with 24-h MG and IFV in 1,793 Chinese university students using a convenience sampling method online. Physical activity (PA) and sedentary behavior (SB) were assessed by the International Physical Activity Questionnaire-Short Form, while sleep was measured using the Pittsburgh Sleep Quality Index. The Chinese version of the Health Promoting Lifestyle Profile II was used to measure IFV. Generalized linear models were applied to examine the correlation between compliance with the 24-h MG and eating habits.ResultsThe proportion of participants who routinely consumed vegetables and fruits was 24.6% and 43.1%, respectively, while the proportion of meeting the three 24-h MG and a combination of any two guidelines was 27.8% and 40.1%, respectively. Meeting all three guidelines was associated with a greater IFV intake compared to not meeting either guideline. Meeting all three guidelines (OR = 2.42 [1.63, 3.58]) and the combination of moderate to vigorous PA (MVPA) and sleep (OR = 2.06 [1.37, 3.10]) were positively associated with the frequency of vegetable consumption (p < 0.05). As well, meeting all three guidelines (OR = 2.06 [1.37, 3.10]), the combination of MVPA and sleep (OR = 1.72 [1.04, 2.84]), and sleep only (OR = 1.88 [1.21, 2.92]) were positively associated with fruits consumption (p < 0.05).ConclusionAlmost a third of the university students met the three 24-h MG, and compliance with all three guidelines was associated with a higher frequency of IFV. Furthermore, meeting the sleep guideline alone or in conjunction with the PA, and meeting the entire 24-h MG was associated with greater consumption of fruits. creator: Yao Zhang creator: Xingyi Yang creator: Zhen Yang creator: Xinli Chi creator: Sitong Chen uri: https://doi.org/10.7717/peerj.17875 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Modelling take-off moment arms in an ornithocheiraean pterosaur link: https://peerj.com/articles/17678 last-modified: 2024-08-05 description: Take-off is a vital part of powered flight which likely constrains the size of birds, yet extinct pterosaurs are known to have reached far larger sizes. Three different hypothesised take-off motions (bipedal burst launching, bipedal countermotion launching, and quadrupedal launching) have been proposed as explanations for how pterosaurs became airborne and circumvented this proposed morphological limit. We have constructed a computational musculoskeletal model of a 5 m wingspan ornithocheiraean pterosaur, reconstructing thirty-four key muscles to estimate the muscle moment arms throughout the three hypothesised take-off motions. Range of motion constrained hypothetical kinematic sequences for bipedal and quadrupedal take-off motions were modelled after extant flying vertebrates. Across our simulations we did not find higher hindlimb moment arms for bipedal take-off motions or noticeably higher forelimb moment arms in the forelimb for quadrupedal take-off motions. Despite this, in all our models we found the muscles utilised in the quadrupedal take-off have the largest total launch applicable moment arms throughout the entire take-off sequences and for the take-off pose. This indicates the potential availability of higher leverage for a quadrupedal take-off than hypothesised bipedal motions in pterosaurs pending further examination of muscle forces. creator: Benjamin W. Griffin creator: Elizabeth Martin-Silverstone creator: Rodrigo V. Pêgas creator: Erik Anthony Meilak creator: Fabiana R. Costa creator: Colin Palmer creator: Emily J. Rayfield uri: https://doi.org/10.7717/peerj.17678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Griffin et al. title: Genome sequencing and CAZymes repertoire analysis of Diaporthe eres P3-1W causing postharvest fruit rot of ‘Hongyang’ kiwifruit in China link: https://peerj.com/articles/17715 last-modified: 2024-08-05 description: Postharvest rot caused by various fungal pathogens is a damaging disease affecting kiwifruit production and quality, resulting in significant annual economic losses. This study focused on isolating the strain P3-1W, identified as Diaporthe eres, as the causal agent of ‘Hongyang’ postharvest rot disease in China. The investigation highlighted cell wall degrading enzymes (CWDEs) as crucial pathogenic factors. Specially, the enzymatic activities of cellulase, β-galactosidase, polygalacturonase, and pectin methylesterases peaked significantly on the second day after infection of D. eres P3-1W. To gain a comprehensive understanding of these CWDEs, the genome of this strain was sequenced using PacBio and Illumina sequencing technologies. The analysis revealed that the genome of D. eres P3-1W spans 58,489,835 bp, with an N50 of 5,939,879 bp and a GC content of 50.7%. A total of 15,407 total protein-coding genes (PCGs) were predicted and functionally annotated. Notably, 857 carbohydrate-active enzymes (CAZymes) were identified in D. eres P3-1W, with 521 CWDEs consisting of 374 glycoside hydrolases (GHs), 108 carbohydrate esterase (CEs) and 91 polysaccharide lyases (PLs). Additionally, 221 auxiliary activities (AAs), 91 glycosyltransferases (GTs), and 108 carbohydrate binding modules (CBMs) were detected. These findings offer valuable insights into the CAZymes of D. eres P3-1W. creator: Li-Zhen Ling creator: Ling-Ling Chen creator: Zhen-Zhen Liu creator: Lan-Ying Luo creator: Si-Han Tai creator: Shu-Dong Zhang uri: https://doi.org/10.7717/peerj.17715 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ling et al. title: Within-host adaptive speciation of commensal yoyo clams leads to ecological exclusion, not co-existence link: https://peerj.com/articles/17753 last-modified: 2024-08-05 description: Symbionts dominate planetary diversity and three primary symbiont diversification processes have been proposed: co-speciation with hosts, speciation by host-switching, and within-host speciation. The last mechanism is prevalent among members of an extraordinary marine symbiosis in the Indian River Lagoon, Florida, composed of a host mantis shrimp, Lysiosquilla scabricauda, and seven host-specific commensal vasconielline “yoyo” clams (Galeommatoidea) that collectively occupy two distinct niches: burrow-wall-attached, and host-attached/ectocommensal. This within-host symbiont radiation provides a natural experiment to test how symbiont coexistence patterns are regulated in a common ancestral habitat. The competitive exclusion principle predicts that sister taxa produced by adaptive speciation (with distinct morphologies and within-burrow niches) are most likely to coexist whereas the neutral theory predicts no difference among adaptive and non-adaptive sister taxa co-occurrence. To test these predictions, we engaged in (1) field-censusing commensal species assemblages; (2) trophic niche analyses; (3) laboratory behavioral observations. Although predicted by both models, the field census found no mixed-niche commensal assemblages: multi-species burrows were exclusively composed of burrow-wall commensals. Their co-occurrence matched random assembly process expectations, but presence of the single ectocommensal species had a highly significant negative effect on recruitment of all burrow-wall commensal species (P < 0.001), including on its burrow-wall commensal sister species (P < 0.001). Our stable isotope data indicated that commensals are suspension feeders and that co-occurring burrow-wall commensals may exhibit trophic niche differentiation. The artificial burrow behavioral experiment yielded no evidence of spatial segregation among burrow-wall commensals, and it was terminated by a sudden breakdown of the host-commensal relationship resulting in a mass mortality of all commensals unattached to the host. This study system appears to contain two distinct, superimposed patterns of commensal distribution: (1) all burrow-wall commensal species; (2) the ectocommensal species. Burrow-wall commensals (the plesiomorphic condition) broadly adhere to neutral theory expectations of species assembly but the adaptive evolution of ectocommensalism has apparently led to ecological exclusion rather than coexistence, an inverse outcome of theoretical expectations. The ecological factors regulating the observed burrow-wall/ectocommensal exclusion are currently obscure but potentially include differential recruitment to host burrows and/or differential survival in “mixed” burrow assemblages, the latter potentially due to changes in host predatory behavior. Resampling host burrows during commensal recruitment peak periods and tracking burrow-wall commensal survival in host burrows with and without added ectocommensals could resolve this outstanding issue. creator: Teal A. Harrison creator: Ryutaro Goto creator: Jingchun Li creator: Diarmaid Ó Foighil uri: https://doi.org/10.7717/peerj.17753 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Harrison et al. title: The effectiveness of different attentional foci on the acquisition of sport-specific motor skills in healthy adults: a systematic review with network meta-analysis link: https://peerj.com/articles/17799 last-modified: 2024-08-05 description: BackgroundThe acquisition of motor skills is a key element in many sports. A motor learning principle, which is frequently used to support skill acquisition is the application of different attentional foci. The effectiveness of different attentional foci on performance and the learning of motor skills has been investigated in various sports using randomised controlled trials. The aim of the present study was to investigate the effectiveness of different attentional foci (such as external (EFA) and internal attentional foci (IFA), but also holistic and switching foci) on the performance and learning of a sport-specific motor task in healthy individuals.MethodsThis study was a systematic review with network meta-analysis. We followed the Prisma reporting guideline and the Cochrane handbook for systematic reviews. Cinahl, Embase, Medline and Cochrane Central were searched for eligible studies. Network meta-analyses were performed for the post-acquisition, retention and transfer test endpoints.ResultsTwelve studies were included in the review. At post-acquisition an EFA was the most effective intervention compared to the control intervention (SMD: 0.9855; 95% CI [0.4–1.57]; p: 0.001). At the retention and transfer test endpoints, a holistic focus of attention had the highest effectiveness compared to an IFA (SMD 0.75; 95% CI [−0.1 to 1.6]; p: 0.09) and (SMD 1.16; 95% CI [0.47–1.86]; p: 0.001).DiscussionFor all three endpoints, we analysed a greater effectiveness of an EFA and holistic focus compared to an IFA. Several promising different attentional focus interventions were identified. The largest effects were analysed for a holistic focus. However, only one study used this intervention and therefore there remains uncertainty about the effectiveness. With regard to the inconsistency observed, the analysis at post-acquisition should be interpreted with caution. Modified versions of the EFA were the imagined and the dynamic EFA. Both were only explored in single studies and should therefore be investigated in further follow-up studies that directly compare them. creator: Emmanuel Favre-Bulle creator: Siri Nyfeler creator: Chloé Schorderet creator: Gaia Risso creator: Michela Bassolino creator: Karl Martin Sattelmayer uri: https://doi.org/10.7717/peerj.17799 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Favre-Bulle et al. title: Research progress on the effects of postharvest storage methods on melon quality link: https://peerj.com/articles/17800 last-modified: 2024-08-05 description: BackgroundAs an important global agricultural cash crop, melon has a long history of cultivation and a wide planting area. The physiological metabolism of melon after harvest is relatively strong; if not properly stored, melon is easily invaded by external pathogens during transportation, resulting in economic losses and greatly limiting its production, development and market supply. Therefore, the storage and freshness of melon are the main challenges in realizing the annual supply of melon, so postharvest storage has received increasing amounts of attention from researchers.MethodsThis study used academic, PubMed, and Web of Science resources to retrieve keywords related to postharvest storage and melon quality; read, refined, classified, and sorted the retrieved literature; sorted and summarized the relevant research results; and finally completed this article.ResultsThis article reviews the mechanism and effects of physical, chemical and biological preservation techniques on the sensory quality, compound contents and respiratory physiological activities of different varieties of melon fruits. When maintaining normal metabolism and not producing physiological disorders, melon inhibits cell wall metabolism, reactive oxygen species metabolism and the ethylene biosynthesis pathway, etc., to the greatest extent during postharvest storage, thereby reducing the material consumption of fruits, delaying the ripening and senescence process, and prolonging the postharvest life and shelf life.ConclusionThe literature provides a theoretical basis for postharvest preservation technology in the melon industry in the future and provides corresponding guidance for the development of the melon industry. creator: Haofei Wang creator: Jiayi Cui creator: Rui Bao creator: Hui Zhang creator: Zi Zhao creator: Xuanye Chen creator: Zhangfei Wu creator: Chaonan Wang uri: https://doi.org/10.7717/peerj.17800 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: A glycolysis-related signature to improve the current treatment and prognostic evaluation for breast cancer link: https://peerj.com/articles/17861 last-modified: 2024-08-05 description: BackgroundAs a heterogeneous malignancy, breast cancer (BRCA) shows high incidence and mortality. Discovering novel molecular markers and developing reliable prognostic models may improve the survival of BCRA.MethodsThe RNA-seq data of BRCA patients were collected from the training set The Cancer Genome Atlas (TCGA)-BRCA and validation set GSE20685 in the Gene Expression Omnibus (GEO) databases. The “GSVA” R package was used to calculate the glycolysis score for each patient, based on which all the patients were divided into different glycolysis groups. The “limma” package was employed to perform differentially expression genes (DEGs) analysis. Key signature genes were selected by performing un/multivariate and least absolute shrinkage and selection operator (LASSO) C regression and used to develop a RiskScore model. The ESTIMATE and MCP-Counter algorithms were used for quantifying immune infiltration level. The functions of the genes were validated using Western blot, colony formation, transwell and wound-healing assay.ResultsThe glycolysis score and prognostic analysis showed that high glycolysis score was related to tumorigenesis pathway and a poor prognosis in BRCA as overactive glycolysis inhibited the normal functions of immune cells. Subsequently, we screened five key prognostic genes using the LASSO Cox regression analysis and used them to establish a RiskScore with a high classification efficiency. Based on the results of the RiskScore, it was found that patients in the high-risk group had significantly unfavorable immune infiltration and prognostic outcomes. A nomogram integrating the RiskScore could well predict the prognosis for BRCA patients. Knockdown of PSCA suppressed cell proliferation, invasion and migration of BRCA cells.ConclusionThis study developed a glycolysis-related signature with five genes to distinguish between high-risk and low-risk BRCA patients. A nomogram developed on the basis of the RiskScore was reliable to predict BRCA survival. Our model provided clinical guidance for the treatment of BRCA patients. creator: Sijie Feng creator: Linwei Ning creator: Huizhen Zhang creator: Zhenhui Wang creator: Yunkun Lu uri: https://doi.org/10.7717/peerj.17861 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Feng et al. title: Spatial patterns and sociodemographic predictors of chronic obstructive pulmonary disease in Florida link: https://peerj.com/articles/17771 last-modified: 2024-08-02 description: BackgroundChronic obstructive pulmonary disease (COPD) is a chronic, inflammatory respiratory disease that obstructs airflow and decreases lung function and is a leading cause death globally. In the United States (US), the prevalence among adults is 6.2%, but increases with age to 12.8% among those 65 years or older. Florida has one of the largest populations of older adults in the US, accounting for 4.5 million adults 65 years or older. This makes Florida an ideal geographic location for investigating COPD as disease prevalence increases with age. Understanding the geographic disparities in COPD and potential associations between its disparities and environmental factors as well as population characteristics is useful in guiding intervention strategies. Thus, the objectives of this study are to investigate county-level geographic disparities of COPD prevalence in Florida and identify county-level socio-demographic predictors of COPD prevalence.MethodsThis ecological study was performed in Florida using data obtained from the US Census Bureau, Florida Health CHARTS, and County Health Rankings and Roadmaps. County-level COPD prevalence for 2019 was age-standardized using the direct method and 2020 US population as the standard population. High-prevalence spatial clusters of COPD were identified using Tango’s flexible spatial scan statistics. Predictors of county-level COPD prevalence were investigated using multivariable ordinary least squares model built using backwards elimination approach. Multicollinearity of regression coefficients was assessed using variance inflation factor. Shapiro-Wilks, Breusch Pagan, and robust Lagrange Multiplier tests were used to assess for normality, homoskedasticity, and spatial autocorrelation of model residuals, respectively.ResultsCounty-level age-adjusted COPD prevalence ranged from 4.7% (Miami-Dade) to 16.9% (Baker and Bradford) with a median prevalence of 9.6%. A total of 6 high-prevalence clusters with prevalence ratios >1.2 were identified. The primary cluster, which was also the largest geographic cluster that included 13 counties, stretched from Nassau County in north-central Florida to Charlotte County in south-central Florida. However, cluster 2 had the highest prevalence ratio (1.68) and included 10 counties in north-central Florida. Together, the primary cluster and cluster 2 covered most of the counties in north-central Florida. Significant predictors of county-level COPD prevalence were county-level percentage of residents with asthma and the percentage of current smokers.ConclusionsThere is evidence of spatial clusters of COPD prevalence in Florida. These patterns are explained, in part, by differences in distribution of some health behaviors (smoking) and co-morbidities (asthma). This information is important for guiding intervention efforts to address the condition, reduce health disparities, and improve population health. creator: Sara Howard creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.17771 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Howard and Odoi title: Evaluating the potential of retinal photography in chronic kidney disease detection: a review link: https://peerj.com/articles/17786 last-modified: 2024-08-02 description: BackgroundChronic kidney disease (CKD) is a significant global health concern, emphasizing the necessity of early detection to facilitate prompt clinical intervention. Leveraging the unique ability of the retina to offer insights into systemic vascular health, it emerges as an interesting, non-invasive option for early CKD detection. Integrating this approach with existing invasive methods could provide a comprehensive understanding of patient health, enhancing diagnostic accuracy and treatment effectiveness.ObjectivesThe purpose of this review is to critically assess the potential of retinal imaging to serve as a diagnostic tool for CKD detection based on retinal vascular changes. The review tracks the evolution from conventional manual evaluations to the latest state-of-the-art in deep learning.Survey MethodologyA comprehensive examination of the literature was carried out, using targeted database searches and a three-step methodology for article evaluation: identification, screening, and inclusion based on Prisma guidelines. Priority was given to unique and new research concerning the detection of CKD with retinal imaging. A total of 70 publications from 457 that were initially discovered satisfied our inclusion criteria and were thus subjected to analysis. Out of the 70 studies included, 35 investigated the correlation between diabetic retinopathy and CKD, 23 centered on the detection of CKD via retinal imaging, and four attempted to automate the detection through the combination of artificial intelligence and retinal imaging.ResultsSignificant retinal features such as arteriolar narrowing, venular widening, specific retinopathy markers (like microaneurysms, hemorrhages, and exudates), and changes in arteriovenous ratio (AVR) have shown strong correlations with CKD progression. We also found that the combination of deep learning with retinal imaging for CKD detection could provide a very promising pathway. Accordingly, leveraging retinal imaging through this technique is expected to enhance the precision and prognostic capacity of the CKD detection system, offering a non-invasive diagnostic alternative that could transform patient care practices.ConclusionIn summary, retinal imaging holds high potential as a diagnostic tool for CKD because it is non-invasive, facilitates early detection through observable microvascular changes, offers predictive insights into renal health, and, when paired with deep learning algorithms, enhances the accuracy and effectiveness of CKD screening. creator: Nur Asyiqin Amir Hamzah creator: Wan Mimi Diyana Wan Zaki creator: Wan Haslina Wan Abdul Halim creator: Ruslinda Mustafar creator: Assyareefah Hudaibah Saad uri: https://doi.org/10.7717/peerj.17786 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Amir Hamzah et al. title: Prognostic value of left ventricular structure and strain in chronic kidney disease patients by cardiovascular magnetic resonance imaging: a retrospective study link: https://peerj.com/articles/17853 last-modified: 2024-08-02 description: BackgroundIndividuals suffering from chronic kidney disease (CKD) frequently face a heightened likelihood of experiencing cardiovascular complications, including heart failure and cardiac mortality. Cardiovascular magnetic resonance feature tracking (CMR-FT) is utilized to assess the micro-contraction function of the myocardium. The objective of this research is to explore the relationship between the left ventricular anatomy, myocardial strain, and the clinical outcomes in patients with CKD.MethodsA total of 77 patients with late-stage CKD were enrolled in this retrospective study. They underwent cardiac magnetic resonance imaging and were followed up, with no history of significant cardiac diseases. The patients were divided into two groups: those with a left ventricular global longitudinal strain (LVGLS) ≥ −15.2% (n = 49) and those with LVGLS < −15.2% (n = 28). The clinical endpoints were defined as hospitalization for heart failure or all-cause mortality.ResultsOver an average observation period of 22 ± 9 months, 11 (14%) patients passed away and 30 (39%) were admitted to the hospital for heart failure, with eight encountering both incidents. Those with LVGLS ≥ −15.2% had markedly lower rates of event-free survival concerning heart failure admissions and overall mortality than their counterparts (log-rank P = 0.014). Cox multivariable analysis indicated that reduced LVGLS consistently predicted a higher likelihood of combined outcomes of heart failure admissions and total mortality (HR: 3.40, 95% CI [1.35–8.56], P = 0.009), even when factoring in age, diabetes, left atrial diameter, and left ventricular mass index (LVMI). However, the LVMI showed no significant correlation with the risk of heart failure admissions or overall mortality.ConclusionCompared to patients with LVGLS < −15.2%, CKD patients with LVGLS ≥ −15.2% have an increased risk of heart failure hospitalization and all-cause mortality. The prognostic role of LVMI in assessing CKD patients among the Asian population requires further investigation. creator: Wenju Zhang creator: Yi Zhong creator: Fang Zhong creator: Tianhui Zhang creator: Xinghua Zhu creator: Weixiong Fan uri: https://doi.org/10.7717/peerj.17853 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Zhang et al. title: Effect of metabolic syndrome on testosterone levels in patients with metastatic prostate cancer: a real-world retrospective study link: https://peerj.com/articles/17823 last-modified: 2024-08-01 description: BackgroundMetabolic syndrome (MetS) has been shown to have a negative impact on prostate cancer (PCa). However, there is limited research on the effects of MetS on testosterone levels in metastatic prostate cancer (mPCa).ObjectiveThis study aims to investigate the influence of MetS, its individual components, and composite metabolic score on the prognosis of mPCa patients, as well as the impact on testosterone levels. Additionally, it seeks to identify MetS-related risk factors that could impact the time of decline in testosterone levels among mPCa patients.MethodsA total of 212 patients with mPCa were included in the study. The study included 94 patients in the Non-MetS group and 118 patients in the combined MetS group. To analyze the relationship between MetS and testosterone levels in patients with mPCa. Additionally, the study aimed to identify independent risk factors that affect the time for testosterone levels decline through multifactor logistic regression analysis. Survival curves were plotted by the Kaplan-Meier method.ResultsCompared to the Non-MetS group, the combined MetS group had a higher proportion of patients with high tumor burden, T stage ≥ 4, and Gleason score ≥ 8 points (P < 0.05). Patients in the combined MetS group also had higher lowest testosterone values and it took longer for their testosterone to reach the lowest level (P < 0.05). The median progression-free survival (PFS) time for patients in the Non-MetS group was 21 months, while for those in the combined MetS group it was 18 months (P = 0.001). Additionally, the median overall survival (OS) time for the Non-MetS group was 62 months, whereas for the combined MetS group it was 38 months (P < 0.001). The median PFS for patients with a composite metabolic score of 0–2 points was 21 months, 3 points was 18 months, and 4–5 points was 15 months (P = 0.002). The median OS was 62 months, 42 months, and 29 months respectively (P < 0.001). MetS was found to be an independent risk factor for testosterone levels falling to the lowest value for more than 6 months. The risk of testosterone levels falling to the lowest value for more than 6 months in patients with MetS was 2.157 times higher than that of patients with Non-MetS group (P = 0.031). Patients with hyperglycemia had a significantly higher lowest values of testosterone (P = 0.015). Additionally, patients with a BMI ≥ 25 kg/m2 exhibited lower initial testosterone levels (P = 0.007). Furthermore, patients with TG ≥ 1.7 mmol/L experienced a longer time for testosterone levels to drop to the nadir (P = 0.023). The lowest value of testosterone in the group with a composite metabolic score of 3 or 4–5 was higher than that in the 0–2 group, and the time required for testosterone levels to decrease to the lowest value was also longer (P < 0.05).ConclusionWhen monitoring testosterone levels in mPCa patients, it is important to consider the impact of MetS and its components, and make timely adjustments to individualized treatment strategies. creator: Tao Zhuo creator: Xiangyue Yao creator: Yujie Mei creator: Hudie Yang creator: Abudukeyoumu Maimaitiyiming creator: Xin Huang creator: Zhuang Lei creator: Yujie Wang creator: Ning Tao creator: Hengqing An uri: https://doi.org/10.7717/peerj.17823 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhuo et al. title: Translation and validation of the Bahasa Malaysia version of the Nasal Obstruction Symptom Evaluation scale (M-NOSE) link: https://peerj.com/articles/17825 last-modified: 2024-08-01 description: BackgroundThe Nasal Obstruction Symptom Evaluation (NOSE) is a questionnaire to assess patients with nasal obstruction. The aim of this study was to translate and validate NOSE to the Malay version NOSE (M-NOSE).MethodsThe NOSE questionnaire was translated to Malay language and back to English. Psychometric properties consisting of reliability, reproducibility, validity, responsiveness were appraised in patients with nasal obstruction due to deviated nasal septum and healthy asymptomatic controls.ResultsA total of 126 participants were recruited. There was significant difference between patients and controls for all items and the total score (all p < 0.001). The correlation was moderate to strong between all items and total score (r = 0.71 to 0.8) and fair to moderate for the inter-items correlations (r= 0.31 to 0.70). Internal consistency for M-NOSE was good (α = 0.81). The test–retest for each item demonstrated no significant difference. There was significant difference of the pre- and post-operative mean for each item and total score (all p < 0.001) with good response sensitivity (effect size, d = 4.91).ConclusionsThe M-NOSE has satisfactory reliability, internal consistency, reproducibility and responsiveness. It is a valid and convenient tool in the assessment of the impact and treatment outcome of nasal obstruction. creator: Addina Mohd Baki creator: Suzina Sheikh Ab Hamid creator: Rosli Mohd Noor creator: Baharudin Abdullah uri: https://doi.org/10.7717/peerj.17825 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mohd Baki et al. title: Soil organic carbon estimation using remote sensing data-driven machine learning link: https://peerj.com/articles/17836 last-modified: 2024-08-01 description: Soil organic carbon (SOC) is a crucial component of the global carbon cycle, playing a significant role in ecosystem health and carbon balance. In this study, we focused on assessing the surface SOC content in Shandong Province based on land use types, and explored its spatial distribution pattern and influencing factors. Machine learning methods including random forest (RF), extreme gradient boosting (XGBoost), and support vector machine (SVM) were employed to estimate the surface SOC content in Shandong Province using diverse data sources like sample data, remote sensing data, socio-economic data, soil texture data, topographic data, and meteorological data. The results revealed that the SOC content in Shandong Province was 8.78 g/kg, exhibiting significant variation across different regions. Comparing the model error and correlation coefficient, the XGBoost model showed the highest prediction accuracy, with a coefficient of determination (R²) of 0.7548, root mean square error (RMSE) of 7.6792, and relative percentage difference (RPD) of 1.1311. Elevation and Clay exhibited the highest explanatory power in clarifying the surface SOC content in Shandong Province, contributing 21.74% and 13.47%, respectively. The spatial distribution analysis revealed that SOC content was higher in forest-covered mountainous regions compared to cropland-covered plains and coastal areas. In conclusion, these findings offer valuable scientific insights for land use planning and SOC conservation. creator: Qi Chen creator: Yiting Wang creator: Xicun Zhu uri: https://doi.org/10.7717/peerj.17836 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Creation of complex reef structures through coral restoration does not affect associated fish populations on a remote, well-protected, Caribbean reef link: https://peerj.com/articles/17855 last-modified: 2024-08-01 description: Coral reef ecosystems are facing severe degradation due to anthropogenic activities at both local and global scales. In response, extensive restoration efforts are underway, aiming to bolster coral cover and enhance reef fish communities to foster facilitation between fish and corals. This reciprocal relationship is anticipated to improve overall restoration efficacy and enhance coral reef resilience in the face of global warming. Here, we investigate the impact of coral restoration using out-planted Acropora cervicornis colonies attached to raised domes on the associated fish community on the isolated, well-protected reef of Little Cayman Island in the Central Caribbean. Surveys were conducted immediately preceding out-planting, five days later, and 85 days later to capture temporal changes in the fish community. After 85 days of out-planting, there were no changes in fish biomass, abundance, or species richness for the entire fish community. This pattern was consistent for selected fish functional groups. Additionally, no significant differences were observed in the fish community before outplanting, five days after out-planting, or 85 days after out-planting of restoration domes. Our results underscore the limited impact of coral restoration for influencing fish communities in the isolated and highly protected reef of Little Cayman over an 85-day period. Consequently, our findings have implications for using coral restoration as a mechanism to enhance fish populations, particularly in marginally disturbed regions where structural complexity has not been lost. Future restoration programs should therefore incorporate local knowledge of environmental history and restoration needs along with an increased data-driven understanding of the intricate interaction between fish and coral populations to be successful. creator: Jack V. Johnson creator: John F. Bruno creator: Lucas Le Gall creator: Matthew Louis Doherty creator: Alex Chequer creator: Gretchen Goodbody Gringley uri: https://doi.org/10.7717/peerj.17855 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Johnson et al.