title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2024-01 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: How reliable is metabarcoding for pollen identification? An evaluation of different taxonomic assignment strategies by cross-validation link: https://peerj.com/articles/16567 last-modified: 2024-01-31 description: Metabarcoding is a powerful tool, increasingly used in many disciplines of environmental sciences. However, to assign a taxon to a DNA sequence, bioinformaticians need to choose between different strategies or parameter values and these choices sometimes seem rather arbitrary. In this work, we present a case study on ITS2 and rbcL databases used to identify pollen collected by bees in Belgium. We blasted a random sample of sequences from the reference database against the remainder of the database using different strategies and compared the known taxonomy with the predicted one. This in silico cross-validation (CV) approach proved to be an easy yet powerful way to (1) assess the relative accuracy of taxonomic predictions, (2) define rules to discard dubious taxonomic assignments and (3) provide a more objective basis to choose the best strategy. We obtained the best results with the best blast hit (best bit score) rather than by selecting the majority taxon from the top 10 hits. The predictions were further improved by favouring the most frequent taxon among those with tied best bit scores. We obtained better results with databases containing the full sequences available on NCBI rather than restricting the sequences to the region amplified by the primers chosen in our study. Leaked CV showed that when the true sequence is present in the database, blast might still struggle to match the right taxon at the species level, particularly with rbcL. Classical 10-fold CV—where the true sequence is removed from the database—offers a different yet more realistic view of the true error rates. Taxonomic predictions with this approach worked well up to the genus level, particularly for ITS2 (5–7% of errors). Using a database containing only the local flora of Belgium did not improve the predictions up to the genus level for local species and made them worse for foreign species. At the species level, using a database containing exclusively local species improved the predictions for local species by ∼12% but the error rate remained rather high: 25% for ITS2 and 42% for rbcL. Foreign species performed worse even when using a world database (59–79% of errors). We used classification trees and GLMs to model the % of errors vs. identity and consensus scores and determine appropriate thresholds below which the taxonomic assignment should be discarded. This resulted in a significant reduction in prediction errors, but at the cost of a much higher proportion of unassigned sequences. Despite this stringent filtering, at least 1/5 sequences deemed suitable for species-level identification ultimately proved to be misidentified. An examination of the variability in prediction accuracy between plant families showed that rbcL outperformed ITS2 for only two of the 27 families examined, and that the % correct species-level assignments were much better for some families (e.g. 95% for Sapindaceae) than for others (e.g. 35% for Salicaceae). creator: Gilles San Martin creator: Louis Hautier creator: Dominique Mingeot creator: Benjamin Dubois uri: https://doi.org/10.7717/peerj.16567 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 San Martin et al. title: Understanding park visitors’ soundscape perception using subjective and objective measurement link: https://peerj.com/articles/16592 last-modified: 2024-01-31 description: Environmental noise knows no boundaries, affecting even protected areas. Noise pollution, originating from both external and internal sources, imposes costs on these areas. It is associated with adverse health effects, while natural sounds contribute to cognitive and emotional improvements as ecosystem services. When it comes to parks, individual visitors hold unique perceptions of soundscapes, which can be shaped by various factors such as their motivations for visiting, personal norms, attitudes towards specific sounds, and expectations. In this study, we utilized linear models and geospatial data to evaluate how visitors’ personal norms and attitudes, the park’s acoustic environment, visitor counts, and the acoustic environment of visitors’ neighborhoods influenced their perception of soundscapes at Muir Woods National Monument. Our findings indicate that visitors’ subjective experiences had a greater impact on their perception of the park’s soundscape compared to purely acoustic factors like sound level of the park itself. Specifically, we found that motivations to hear natural sounds, interference caused by noise, sensitivity to noise, and the sound levels of visitors’ home neighborhoods influenced visitors’ perception of the park’s soundscape. Understanding how personal factors shape visitors’ soundscape perception can assist urban and non-urban park planners in effectively managing visitor experiences and expectations. creator: Lauren A. Ferguson creator: B. Derrick Taff creator: Justine I. Blanford creator: Daniel J. Mennitt creator: Andrew J. Mowen creator: Mitchell Levenhagen creator: Crow White creator: Christopher A. Monz creator: Clinton D. Francis creator: Jesse R. Barber creator: Peter Newman uri: https://doi.org/10.7717/peerj.16592 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferguson et al. title: Association between lactic acidosis and multiple organ dysfunction syndrome after cardiopulmonary bypass link: https://peerj.com/articles/16769 last-modified: 2024-01-31 description: BackgroundThe relationship between hyperlactatemia and prognosis after cardiopulmonary bypass (CPB) is controversial, and some studies ignore the presence of lactic acidosis in patients with severe hyperlactacemia. This study explored the association between lactic acidosis (LA) and the occurrence of multiple organ dysfunction syndrome (MODS) after cardiopulmonary bypass.MethodsThis study was a post hoc analysis of patients who underwent cardiac surgery between February 2017 and August 2018 and participated in a prospective study at Taizhou Hospital. The data were collected at: ICU admission (H0), and 4, 8, 12, 24, and 48 h after admission. Blood lactate levels gradually increased after CPB, peaking at H8 and then gradually decreasing. The patients were grouped as LA, hyperlactatemia (HL), and normal control (NC) based on blood test results 8 h after ICU admission. Basic preoperative, perioperative, and postoperative conditions were compared between the three groups, as well as postoperative perfusion and oxygen metabolism indexes.ResultsThere were 22 (19%), 73 (64%), and 19 (17%) patients in the LA, HL, and NC groups, respectively. APACHE II (24h) and SOFA (24h) scores were the highest in the LA group (P < 0.05). ICU stay duration was the longest for the LA group (48.5 (42.5, 50) h), compared with the HL (27 (22, 48) h) and NC (27 (25, 46) h) groups (P = 0.012). The LA group had the highest incidence of MODS (36%), compared with the HL (14%) and NC (5%) groups (P = 0.015). In the LA group, the oxygen extraction ratio (O2ER) was lower (21.5 (17.05, 32.8)%) than in the HL (31.3 (24.8, 37.6)%) and the NC group (31.3 (29.0, 35.4) %) (P = 0.018). In the univariable analyses, patient age (OR = 1.054, 95% CI [1.003–1.109], P = 0.038), the LA group (vs. the NC group, (OR = 10.286, 95% CI [1.148–92.185], P = 0.037), and ΔPCO2 at H8 (OR = 1.197, 95% CI [1.022–1.401], P = 0.025) were risk factor of MODS after CPB.ConclusionsWe speculated that there was correlation between lactic acidosis and MODS after CPB. In addition, LA should be monitored intensively after CPB. creator: Dan Zheng creator: Guo-Liang Yu creator: Yi-Ping Zhou creator: Qiao-Min Zhang creator: Chun-Guo Wang creator: Sheng Zhang uri: https://doi.org/10.7717/peerj.16769 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zheng et al. title: Hibiscetin attenuates lipopolysaccharide-evoked memory impairment by inhibiting BDNF/caspase-3/NF-κB pathway in rodents link: https://peerj.com/articles/16795 last-modified: 2024-01-31 description: This study explores the neuroprotective potential of hibiscetin concerning memory deficits induced by lipopolysaccharide (LPS) injection in rats. The aim of this study is to evaluate the effect of hibiscetin against LPS-injected memory deficits in rats. The behavioral paradigms were conducted to access LPS-induced memory deficits. Various biochemical parameters such as acetyl-cholinesterase activity, choline-acetyltransferase, antioxidant (superoxide dismutase, glutathione transferase, catalase), oxidative stress (malonaldehyde), and nitric oxide levels were examined. Furthermore, neuroinflammatory parameters such as tumor necrosis factor-α, interleukin-1β (IL-1β), IL-6, and nuclear factor-kappa B expression and brain-derived neurotrophic factor as well as apoptosis marker i.e., caspase-3 were evaluated. The results demonstrated that the hibiscetin-treated group exhibited significant recovery in LPS-induced memory deficits in rats by using behavioral paradigms, biochemical parameters, antioxidant levels, oxidative stress, neuroinflammatory markers, and apoptosis markers. Recent research suggested that hibiscetin may serve as a promising neuroprotective agent in experimental animals and could offer an alternative in LPS-injected memory deficits in rodent models. creator: Sadaf Jamal Gilani creator: May Nasser Bin Jumah creator: Farhat Fatima creator: Fahad A. Al-Abbasi creator: Muhammad Afzal creator: Sami I. Alzarea creator: Nadeem Sayyed creator: Muhammad Shahid Nadeem creator: Imran Kazmi uri: https://doi.org/10.7717/peerj.16795 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gilani et al. title: New genera of Afrotropical Chalcidoidea (Hymenoptera: Cerocephalidae, Epichrysomallidae, Pirenidae and Pteromalidae) link: https://peerj.com/articles/16798 last-modified: 2024-01-31 description: As a preliminary step towards the development of a key to genera of several families of Afrotropical Chalcidoidea, seven new genera in four families are described: Cerocephalidae–Milokoa Mitroiu, gen. nov. (type species: Milokoa villemantae Mitroiu, sp. nov.); Epichrysomallidae–Delvareus Rasplus, Mitroiu & van Noort, gen. nov. (type species: Delvareus dicranostylae Rasplus, Mitroiu & van Noort, sp. nov.); Pirenidae–Afrothopus Mitroiu, gen. nov. (type species: Afrothopus georgei Mitroiu, sp. nov.); Pteromalidae–Kerangania Mitroiu, gen. nov. (type species: Kerangania nuda Mitroiu, sp. nov.), Pilosalis Mitroiu, Rasplus & van Noort, gen. nov. (type species: Pilosalis barbatulus Mitroiu, sp. nov.), Scrobesia Mitroiu & Rasplus, gen. nov. (type species: Scrobesia acutigaster Mitroiu & Rasplus, sp. nov.), and Spiniclava Mitroiu & Rasplus, gen. nov. (type species: Spiniclava baaiensis Mitroiu & Rasplus, sp. nov.). Additionally, the following new species are described: Pilosalis bouceki Mitroiu & Rasplus, sp. nov., Pilosalis eurys Mitroiu & van Noort, sp. nov., Pilosalis minutus Mitroiu, sp. nov., Pilosalis platyscapus Mitroiu, Rasplus & van Noort, sp. nov., Scrobesia pondo Mitroiu, sp. nov., and Spiniclava setosa Mitroiu, sp. nov. All taxa are illustrated and the relationships with similar taxa are discussed. For each non-monotypic genus a key to species is provided. creator: Mircea-Dan Mitroiu creator: Jean-Yves Rasplus creator: Simon van Noort uri: https://doi.org/10.7717/peerj.16798 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mitroiu et al. title: Circulating cell-free DNA-based methylation pattern in plasma for early diagnosis of esophagus cancer link: https://peerj.com/articles/16802 last-modified: 2024-01-31 description: With the increased awareness of early tumor detection, the importance of detecting and diagnosing esophageal cancer in its early stages has been underscored. Studies have consistently demonstrated the crucial role of methylation levels in circulating cell-free DNA (cfDNA) in identifying and diagnosing early-stage cancer. cfDNA methylation pertains to the methylation state within the genomic scope of cfDNA and is strongly associated with cancer development and progression. Several research teams have delved into the potential application of cfDNA methylation in identifying early-stage esophageal cancer and have achieved promising outcomes. Recent research supports the high sensitivity and specificity of cfDNA methylation in early esophageal cancer diagnosis, providing a more accurate and efficient approach for early detection and improved clinical management. Accordingly, this review aims to present an overview of methylation-based cfDNA research with a focus on the latest developments in the early detection of esophageal cancer. Additionally, this review summarizes advanced analytical technologies for cfDNA methylation that have significantly benefited from recent advancements in separation and detection techniques, such as methylated DNA immunoprecipitation sequencing (MeDIP-seq). Recent findings suggest that biomarkers based on cfDNA methylation may soon find successful applications in the early detection of esophageal cancer. However, large-scale prospective clinical trials are required to identify the potential of these biomarkers. creator: Rui Wang creator: Yue Yang creator: Tianyu Lu creator: Youbin Cui creator: Bo Li creator: Xin Liu uri: https://doi.org/10.7717/peerj.16802 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Insulin signaling and pharmacology in humans and in corals link: https://peerj.com/articles/16804 last-modified: 2024-01-31 description: Once thought to be a unique capability of the Langerhans islets in the pancreas of mammals, insulin (INS) signaling is now recognized as an evolutionarily ancient function going back to prokaryotes. INS is ubiquitously present not only in humans but also in unicellular eukaryotes, fungi, worms, and Drosophila. Remote homologue identification also supports the presence of INS and INS receptor in corals where the availability of glucose is largely dependent on the photosynthetic activity of the symbiotic algae. The cnidarian animal host of corals operates together with a 20,000-sized microbiome, in direct analogy to the human gut microbiome. In humans, aberrant INS signaling is the hallmark of metabolic disease, and is thought to play a major role in aging, and age-related diseases, such as Alzheimer’s disease. We here would like to argue that a broader view of INS beyond its human homeostasis function may help us understand other organisms, and in turn, studying those non-model organisms may enable a novel view of the human INS signaling system. To this end, we here review INS signaling from a new angle, by drawing analogies between humans and corals at the molecular level. creator: Meghana Hosahalli Shivananda Murthy creator: Paniz Jasbi creator: Whitney Lowe creator: Lokender Kumar creator: Monsurat Olaosebikan creator: Liza Roger creator: Jinkyu Yang creator: Nastassja Lewinski creator: Noah Daniels creator: Lenore Cowen creator: Judith Klein-Seetharaman uri: https://doi.org/10.7717/peerj.16804 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Murthy et al. title: Using molecular characteristics to distinguish multiple primary lung cancers and intrapulmonary metastases link: https://peerj.com/articles/16808 last-modified: 2024-01-31 description: ObjectivesMultiple lung cancers may present as multiple primary lung cancers (MPLC) or intrapulmonary metastasis (IPM) with variations in clinical stage, treatment, and prognosis. However, the existing differentiation criteria based on histology do not fully meet the clinical needs. Next-generation sequencing (NGS) may play an important role in assisting the identification of different pathologies. Here, we extended the relevant data by combining histology and NGS to develop detailed identification criteria for MPLC and IPM.Materials and MethodsPatients with lung cancer (each patient had ≥2 tumors) were enrolled in the training (n = 22) and validation (n = 13) cohorts. Genomic profiles obtained from 450-gene-targeted NGS were analyzed, and the new criteria were developed based on our findings and pre-existing Martini & Melamed criteria and molecular benchmarks.ResultsThe analysis of the training cohort indicated that patients identified with MPLC had no (or <2) trunk or shared mutations. However, 98.02% of mutations were branch mutations, and 69.23% of MPLC had no common mutations. In contrast, a higher percentage of trunk (33.08%) or shared (9.02%) mutations were identified in IPM, suggesting significant differences among mutated components. Subsequently, eight MPLC and five IPM cases were identified in the validation cohort, aligning with the independent imaging and pathologic distinction. Overall, the percentage of trunk and shared mutations was higher in patients with IPM than in patients with MPLC. Based on these results and the establishment of new determination criteria for MPLC and IPM, we emphasize that the type and number of shared variants based on histologic consistency assist in identification.ConclusionDetermining genetic alterations may be an effective method for differentiating MPLC and IPM, and NGS can be used as a valuable assisting tool. creator: Zhenhua Li creator: Huilai Lv creator: Fan Zhang creator: Ziming Zhu creator: Qiang Guo creator: Mingbo Wang creator: Chao Huang creator: Lijie Guo creator: Fanfei Meng creator: Ziqiang Tian uri: https://doi.org/10.7717/peerj.16808 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Neck circumference is a highly reliable anthropometric measure in older adults requiring long-term care link: https://peerj.com/articles/16816 last-modified: 2024-01-31 description: The reliability of neck circumference measurement as an assessment tool for older adults requiring long-term care remains unknown. This study aimed to evaluate the reliability of neck circumference measurement in older adults requiring long-term care, and the effect of edema on measurement error. Two physical therapists measured the neck circumference. Intraclass correlation coefficient (ICC) and Bland–Altman analyses were performed to examine the reliability of neck circumference measurement. Correlation analysis was used to evaluate the relationship between edema values (extracellular water/total body water) and neck circumference measurement difference. For inter-rater reliability of neck circumference measurement, the overall ICC (2,1) was 0.98. The upper and lower limits of the difference between examiners ranged from −0.9 to 1.2 cm. There was no association between edema values and neck circumference measurement error. Thus, measurement of the neck circumference in older adults requiring long-term care is a reliable assessment tool, with a low error rate, even in older adults with edema. creator: Ryo Sato creator: Yohei Sawaya creator: Masahiro Ishizaka creator: Lu Yin creator: Takahiro Shiba creator: Tamaki Hirose creator: Tomohiko Urano uri: https://doi.org/10.7717/peerj.16816 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sato et al. title: Static versus dynamic muscle modelling in extinct species: a biomechanical case study of the Australopithecus afarensis pelvis and lower extremity link: https://peerj.com/articles/16821 last-modified: 2024-01-31 description: The force a muscle generates is dependent on muscle structure, in which fibre length, pennation angle and tendon slack length all influence force production. Muscles are not preserved in the fossil record and these parameters must be estimated when constructing a musculoskeletal model. Here, we test the capability of digitally reconstructed muscles of the Australopithecus afarensis model (specimen AL 288-1) to maintain an upright, single-support limb posture. Our aim was to ascertain the influence that different architectural estimation methods have on muscle specialisation and on the subsequent inferences that can be extrapolated about limb function. Parameters were estimated for 36 muscles in the pelvis and lower limb and seven different musculoskeletal models of AL 288-1 were produced. These parameters represented either a ‘static’ Hill-type muscle model (n = 4 variants) which only incorporated force, or instead a ‘dynamic’ Hill-type muscle model with an elastic tendon and fibres that could vary force-length-velocity properties (n = 3 variants). Each muscle’s fibre length, pennation angle, tendon slack length and maximal isometric force were calculated based upon different input variables. Static (inverse) simulations were computed in which the vertical and mediolateral ground reaction forces (GRF) were incrementally increased until limb collapse (simulation failure). All AL 288-1 variants produced somewhat similar simulated muscle activation patterns, but the maximum vertical GRF that could be exerted on a single limb was not consistent between models. Three of the four static-muscle models were unable to support >1.8 times body weight and produced models that under-performed. The dynamic-muscle models were stronger. Comparative results with a human model imply that similar muscle group activations between species are needed to sustain single-limb support at maximally applied GRFs in terms of the simplified static simulations (e.g., same walking pose) used here. This approach demonstrated the range of outputs that can be generated for a model of an extinct individual. Despite mostly comparable outputs, the models diverged mostly in terms of strength. creator: Ashleigh L.A. Wiseman creator: James P. Charles creator: John R. Hutchinson uri: https://doi.org/10.7717/peerj.16821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wiseman et al. title: New materials of plesiacerathere (Perissodactyla, Rhinocerotidae) from the late Early Miocene of Northern China link: https://peerj.com/articles/16822 last-modified: 2024-01-31 description: As a member of Aceratheriinae, the genus Plesiaceratherium in Europe is widely distributed and highly diverse. However, only one species of Plesiaceratherium (i.e., P. gracile) exists in China with a discontinuous distribution range. Recently, we have discovered new materials of Plesiaceratherium in the lower layers of the Zhang’enbao Formation exposed in Miaoerling in Tongxin County, China. The new materials are well-preserved and can be separated from other Plesiaceratherium species by the following combination of features: the long and generally flat skull, with closed frontoparietal crests; the deep nasal notch at the level of P4; the high supraorbital margin, with its anterior margin at the level of the M1/M2 boundary; the medium-sized upper I1, with an oval abraded surface; the semi-molarized upper premolars with the protocone and hypocone joined by a lingual bridge; the strong constrictions of protocone on the upper molars; the absent buccal cingulum on upper cheek teeth; the cheek teeth are covered by cement on the buccal walls; the convex base of mandibular corpus; the inclined backward ramus; and the mandibular foramen above the teeth neck. Based on the combination of characteristics and phylogenetic analysis, we herein establish the new species as Plesiaceratherium tongxinense sp. nov. living in the late Early Miocene. Phylogenetic analysis reveals that P. tongxinense is in the basal position of the genus Plesiaceratherium, providing more detailed morphological characteristics of the plesiaceratheres. creator: Danhui Sun creator: Tao Deng creator: Shiqi Wang uri: https://doi.org/10.7717/peerj.16822 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sun et al. title: Knowledge of cardiovascular disease risk factors among caregivers of cardiology patients attending Jordan University Hospital link: https://peerj.com/articles/16830 last-modified: 2024-01-31 description: Cardiovascular disease (CVD) is an umbrella term that includes various pathologies involving the heart and the vasculature system of the body. CVD is the leading cause of death worldwide, accounting for an estimated 32% of all deaths. More than 40% of annual deaths in Jordan are due to CVD; this number is further expected to rise, particularly in the Eastern Mediterranean region where Jordan is located. Due to the chronic nature of CVD, the presence of a caregiver who can help mitigate the challenges patients face is essential, and their level of knowledge determines the quality of care they can provide. Hence, this cross-sectional study was conducted in the cardiology clinics at Jordan University Hospital (JUH). Questionnaires were distributed to 469 participants, defined in this study as the caregivers escorting patients with established coronary heart disease (CHD). The self-administered questionnaire included three sections: sociodemographic and health factors, knowledge of CVD risk factors, and CHD symptoms. The mean age of the study population was 44.38 years ± 15.92 and 54.2% of participants were males. Regarding knowledge of CVD risk factors, 84.6% of participants answered more than 70% of the questions correctly. More than 95% knew that chest pain is a symptom of an acute cardiovascular event. However, only 53.5% and 74.8% of the participants reported that jaw pain and arm pain are symptoms of an acute event, respectively. Several factors influenced the caregiver’s knowledge, such as age, income, frequent health checkups, having a history of CVD, CKD, or DM, and their relationship to the patient. This study sheds light on the importance of caregiver knowledge in patient care. By improving the caregivers’ knowledge, identifying their role in patient care, and raising CVD awareness in susceptible populations, healthcare professionals can improve the patients’ quality of life. Overall, assessing caregivers’ knowledge pertaining to CVD can provide invaluable data, which may enhance patient care by educating their caregivers. creator: Hanna Al-Makhamreh creator: Amro Alkhatib creator: Ahmed Attarri creator: Ahmad A. Toubasi creator: Aya Dabbas creator: Basel Al-Bkoor creator: Zaid Sarhan creator: Osama Alghafri uri: https://doi.org/10.7717/peerj.16830 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Al-Makhamreh et al. title: Validity and reliability of a teledentistry survey among dental practitioners in Saudi Arabia link: https://peerj.com/articles/16834 last-modified: 2024-01-31 description: BackgroundThe perception of teledentistry use among dental practitioners in various contexts was assessed using the Teledentistry Survey (the TDS-24). However, this survey’s psychometric analyses have not yet been analysed. This present study aims to examine the validity and reliability of the TDS-24 in a sample of dental practitioners in Saudi Arabia.MethodsA self-administered questionnaire, including sociodemographic characteristics and the TDS, was distributed as a cross-sectional survey to 800 current dental practitioners in Saudi Arabia recruited via convenience and snowball sampling. The construct validity and reliability of the TDS were assessed using exploratory factor analysis (EFA) and Cronbach’s alpha.ResultsThe EFA of the survey yielded 20 items supporting a four-factor structure as follows: factor I (10 items), factor II (four items), factor III (three items) and factor IV (three items). The overall Cronbach’s alpha was 0.85, while it was 0.86 for the first factor, 0.70 for the second factor, 0.52 for the third factor and 0.57 for the fourth factor.ConclusionsThe TDS-20, after excluding four items, revealed four factors with adequate psychometric properties, making it a valid and reliable tool in assessing teledentistry perceptions among dental practitioners in this study sample. creator: Alla Alsharif creator: Doaa Felemban creator: Hala Bakeer creator: Saba Kassim uri: https://doi.org/10.7717/peerj.16834 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alsharif et al. title: Evaluation of sesame (Sesamum indicum L.) varieties for drought tolerance using agromorphological traits and drought tolerance indices link: https://peerj.com/articles/16840 last-modified: 2024-01-31 description: Sesame (Sesamum indicum L.) is an important cash crop cultivated under rain-fed conditions where it contributes a significant proportion of Ethiopia’s foreign exchange earnings. However, its productivity is constrained by drought stress. The present study aimed to evaluate the agromorphological and yield performance of sesame varieties and to identify drought tolerant varieties using drought tolerance indices. The sesame varieties were evaluated under well-watered (WW) and water-stressed (WS) field conditions with a factorial design laid down in randomized complete block design in three replications. The results revealed the presence of a significant variation in agromorphological traits and drought tolerance indices due to water levels, varieties and their interactive effect. On average, a 21.8, 49.6, 48.4, 47.9 and 21.7% reduction was recorded in plant height, number of leaves per plant, leaf length, leaf width and relative growth rate (RGR), respectively under WS condition. Similarly, a significant reduction was found in shoot biomass, root biomass, biological yield, number of pods per plant and seed yield under WS condition. These traits showed an average reduction of 52.2, 72.5, 54.0, 51.9 and 52.8%, respectively compared to WW condition. The highest yield reduction was recorded from wollega under WS condition, while the lowest was from abasena. Wollega variety produced the highest seed yield (kg/ha) under WW condition, while gondar-1 and humera-1 had the highest yield in kg/ha under WS condition. Under both water levels, abasena produced the lowest yield (kg/ha). Moreover, gondar-1 and humera-1 varieties had a comparatively higher values of stress tolerance index (STI), yield stress score index (YSSI), yield potential score index (YPSI), geometric mean productivity (GMP) and mean productivity (MP) that are significantly and positively correlated with yield under WS, indicating higher yield performance under water stress. The biplot analysis clustered the varieties as low yielding (abasena) and relatively above average performing varieties (humera-1, gondar-1 and wollega). According to the rank sum of all indices, humera-1 was identified as drought tolerant, while abasena as the most susceptible and low yielding varieties. Thus, humera-1 followed by gondar-1 were found to be drought tolerant and high yielding varieties. However, further studies focusing on drought tolerance mechanisms of the varieties are recommended. creator: Getahun Yemata creator: Tewachew Bekele uri: https://doi.org/10.7717/peerj.16840 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yemata and Bekele title: Application of fenugreek in ruminant feed: implications for methane emissions and productivity link: https://peerj.com/articles/16842 last-modified: 2024-01-31 description: BackgroundHuman demand for meat and dairy products will increase as a result of economic development and population growth, and the farming of ruminants, such as cattle and sheep, will also increase. Methane (CH4) emission from the enteric fermentation of ruminant livestock is a major source of greenhouse gas emissions and a significant contributor to global warming. Meanwhile, growth performance is often limited and animals are more vulnerable to diseases in high-density, intensive farming, greatly reducing livestock productivity, so developing ways to reduce CH4 emissions and improve ruminant productivity has become a research hotspot. Studies have reported that fenugreek (Trigonella foenum-graecum L.) as feed additives have the potential to reduce ruminant methane and improve the productivity. However, systematic reviews of such studies are lacking.MethodologyIn this review, databases of Google Scholar, Web of Science, PubMed, Scopus and Science Direct were used for the literature search. The initial keywords search was fenugreek or Trigonella foenum-graecum L. For more focused search, we added terms such as methane, rumen fermentation, growth, milk production and antioxidants. All were done for ruminants. The literature that conforms to the theme of this article is selected, summarized, and finally completed this article.ResultsBy regulating the rumen microbiome (suppressing protozoans, methanogenic bacteria, and fungi), fenugreek can lower CH4 emissions according to many in vitro anaerobic fermentation experiments. Fenugreek secondary metabolites (saponins and tannins) are responsible for this impact, but it is still unclear exactly how they work. Therefore, more long-term in vivo experiments are needed to verify its efficacy. Fenugreek is also rich in alkaloids, amino acids, flavonoids, saponins and phenolic acids. These compounds have been shown to have beneficial effects on ruminant growth, lactation, and total antioxidant capacity. Therefore, fenugreek has a great opportunity to develop into a new green feed additive.ConclusionsThis review provides a summary of the effect of fenugreek and its bioactive compounds on rumen fermentation, CH4 emissions and production performance by ruminants. In addition, based on the available data, the possible biochemical pathway of fenugreek to reduce CH4 emissions in ruminants was described. Overall, the livestock feed industry has the opportunity to develop natural, environmentally-friendly feed additives based on fenugreek. creator: Xiangbiao Zeng creator: Yiwen Chen creator: Wenjuan Li creator: Shijun Liu uri: https://doi.org/10.7717/peerj.16842 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zeng et al. title: Azoramide ameliorates cadmium-induced cytotoxicity by inhibiting endoplasmic reticulum stress and suppressing oxidative stress link: https://peerj.com/articles/16844 last-modified: 2024-01-31 description: BackgroundCadmium (Cd) is hazardous to human health because of its cytotoxicity and long biological half-life. Azoramide is a small molecular agent that targets the endoplasmic reticulum (ER) and moderates the unfolded protein response. However, its role in Cd-induced cytotoxicity remains unclear. This study was performed to investigate the protective effect of azoramide against Cd-induced cytotoxicity and elucidate its underlying mechanisms.MethodsInductively coupled plasma‒mass spectrometry was used to measure Cd concentrations in each tissue of ICR male mice. The human proximal tubule epithelial cell line HK-2 and the human retinal pigment epithelial cell line ARPE-19 were used in the in vitro study. Cell apoptosis was determined by DAPI staining, JC-1 staining, and annexin V/propidium iodide double staining. Intracellular oxidative stress was detected by MitoSOX red staining, western blot, and quantitative real-time PCR. Moreover, ER stress signaling, MAPK cascades, and autophagy signaling were analyzed by western blot.ResultsThe present data showed that Cd accumulated in various organs of ICR mice, and the concentrations of Cd in the studied organs, from high to low, were as follows: liver > kidney > testis > lung > spleen > eye. Our study demonstrated that azoramide inhibited ER stress by promoting BiP expression and suppressing the PERK-eIF2α-CHOP pathway. Additionally, we also found that azoramide significantly decreased ER stress-associated radical oxidative species production, attenuated p38 MAPK and JNK signaling, and inhibited autophagy, thus suppressing apoptosis in HK-2 and ARPE-19 cells.ConclusionOur study investigated the effect of azoramide on Cd-induced cytotoxicity and revealed that azoramide may be a therapeutic drug for Cd poisoning. creator: Lingmin Zhang creator: Jianguo Zhang creator: Yingying Zhou creator: Qingqing Xia creator: Jing Xie creator: Bihong Zhu creator: Yang Wang creator: Zaixing Yang creator: Jie Li uri: https://doi.org/10.7717/peerj.16844 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Electrical stimulation promoting the angiogenesis in diabetic rat perforator flap through attenuating oxidative stress-mediated inflammation and apoptosis link: https://peerj.com/articles/16856 last-modified: 2024-01-31 description: BackgroundSkin flap transplantation is one of the effective methods to treat the diabetes-related foot ulceration, but the intrinsic damage to vessels in diabetes mellitus (DM) leads to the necrosis of skin flaps. Therefore, the discovery of a non-invasive and effective approach for promoting the survival of flaps is of the utmost importance. Electrical stimulation (ES) promotes angiogenesis and increases the proliferation, migration, and elongation of endothelial cells, thus being a potential effective method to improve flap survival.ObjectiveThe purpose of this study was to elucidate the mechanism used by ES to effectively restore the impaired function of endothelial cells caused by diabetes.MethodsA total of 79 adult male Sprague-Dawley rats were used in this study. Gene and protein expression was assessed by PCR and western blotting, respectively. Immunohistochemistry and hematoxylin-eosin staining were performed to evaluate the morphology and density of the microvessels in the flap.ResultsThe optimal duration for preconditioning the flap with ES was 7 days. The flap survival area percentage and microvessels density in the DMES group were markedly increased compared to the DM group. VEGF, MMP2, and MMP9 protein expression was significantly upregulated. ROS intensity was significantly decreased and GSH concentration was increased. The expression of IL-1β, MCP‑1, cleaved caspase-3, and Bax were downregulated in the DMES group, while TGF-β expression was upregulated.ConclusionsES improves the angiogenesis in diabetic ischemic skin flaps by attenuating oxidative stress–mediated inflammation and apoptosis, eventually increasing their viability. creator: Cong Chen creator: Xiaolu Li creator: Yong Hu creator: Yuan Chen creator: Hongrui Wang creator: Xian Li creator: Xiucun Li uri: https://doi.org/10.7717/peerj.16856 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: The serotonin blocker Ketanserin reduces coral reef fish Ctenochaetus striatus aggressive behaviour during between-species social interactions link: https://peerj.com/articles/16858 last-modified: 2024-01-31 description: A multitude of species engages in social interactions not only with their conspecifics but also with other species. Such interspecific interactions can be either positive, like helping, or negative, like aggressive behaviour. However, the physiological mechanisms of these behaviours remain unclear. Here, we manipulated the serotonin system, a well-known neurohormone for regulating intraspecific aggressive behaviour, to investigate its role in interspecific aggression. We tested whether serotonin blockade affects the aggressive behaviour of a coral reef fish species (Ctenochaetus striatus) that engages in mutualistic interactions with another species, the cleaner fish (Labroides dimidiatus). Although this mutualistic cleaning relationship may appear positive, cleaner fish do not always cooperate and remove ectoparasites from the other coral reef fish (“clients”) but tend to cheat and bite the client’s protective layer of mucus. Client fish thus often apply control mechanisms, like chasing, to deter their cleaner fish partners from cheating. Our findings show that blocking serotonin receptors 5-HT2A and 5-HT2C with ketanserin reduced the client fish’s aggressive behaviour towards cleaner fish, but in the context where the latter did not cheat. These results are evidence of the involvement of serotonin in regulating aggressive behaviour at the between-species social interactions level. Yet, the direction of effect we found here is the opposite of previous findings using a similar experimental set-up and ecological context but with a different client fish species (Scolopsis bilineatus). Together, it suggests that serotonin’s role in aggressive behaviour is complex, and at least in this mutualistic ecological context, its function is species-dependent. This warrants, to some extent, careful interpretations from single-species studies looking into the physiological mechanisms of social behaviour. creator: Virginie Staubli creator: Redouan Bshary creator: Zegni Triki uri: https://doi.org/10.7717/peerj.16858 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Staubli et al. title: Caries risk assessment by Caries Management by Risk Assessment (CAMBRA) Protocol among the general population of Pakistan–a multicenter analytical study link: https://peerj.com/articles/16863 last-modified: 2024-01-31 description: BackgroundCaries risk (CR) assessment tools are used to properly identify individuals with caries risk and to improve preventive procedures and programs. A tool such as CAMBRA determines the precise protective factors of caries and identifies an individual’s specific therapeutic intervention. The purpose of this study was to assess the caries risk using the CAMBRA protocol among the general population of Pakistan.MethodsThis multicentre analytical study was conducted in ten dental hospitals in different provinces of Pakistan and the caries risk assessment was carried out using a questionnaire that was designed using the Caries Management by Risk Assessment (CAMBRA) protocol. All 521 participants were intra-orally examined to assess oral hygiene status and the presence of disease. Multiple logistic regression test was performed for analysis.ResultsA higher number of participants (61.2%) were found to be in the moderate risk category of caries risk assessment. The males are 51% less likely to have caries compared to the females (AOR = 0.49, P = 0.081). The majority of participants (71.3%) had one or more disease indicators, with white spots and visible cavities. Those with visible, heavy plaque were 13.9 times more likely to have caries compared to those without (AOR = 13.92, P < 0.001). Those using calcium and phosphate during the last 6 months were 90% less likely to have caries compared to those not using them (AOR = 0.10, P < 0.001). There was no significant interaction between all eight risk factors retained in the final model (P > 0.05), the Hosmer and Lemeshow Test P < 0.001, classification accuracy = 87.1%, and AUC = 91.2%.ConclusionThe caries risk among the general population of Pakistan is moderate, with significant variation among age groups, education levels, and socioeconomic status. creator: Azhar Iqbal creator: Yasir Dilshad Siddiqui creator: Farooq Ahmad Chaudhary creator: Malik Zain ul Abideen creator: Talib Hussain creator: Bilal Arjumand creator: Mohammed Almuhaiza creator: Mohammed Mustafa creator: Osama Khattak creator: Reham Mohammed Attia creator: Asma Abubaker Rashed creator: Sherif Elsayed Sultan uri: https://doi.org/10.7717/peerj.16863 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Iqbal et al. title: The prognostic significance of lymph nodes in patients with pT1c33N0M0 non-small cell lung cancer: a retrospective study link: https://peerj.com/articles/16866 last-modified: 2024-01-31 description: ObjectiveThe objective of this study was to appraise the prognostic impact of lymph nodes in patients diagnosed with pT1c33N0M0 non-small cell lung cancer (NSCLC) and to delve into the prognostic significance of lymph nodes located at the N1 lymph node station in this patient cohort.MethodsA retrospective analysis of clinical data was conducted for 255 patients diagnosed with pT1c33N0M0 NSCLC. Lymph nodes were tabulated and categorized into three groups (0–10 nodes, 11–16 nodes, >16 nodes). Clinical data among these three groups of pT1c33N0M0 NSCLC patients were compared. We conducted both univariate and multivariate analyses to pinpoint the factors that impact the prognosis of patients with pT1c33N0M0 non-small cell lung cancer (NSCLC). Additionally, we employed receiver operating characteristic (ROC) curve analysis to pinpoint the optimal lymph node criteria at the N1 station for prognostic prediction in pT1c33N0M0 NSCLC patients.ResultsWithin the cohort of 255 individuals afflicted with pT1c33N0M0 non-small cell lung cancer (NSCLC), a comprehensive tally of 3,902 lymph nodes was diligently established, yielding an average of 15.3 nodes for each patient. Multivariate analysis demonstrated that tumor size, T stage, and lymph nodes were independent factors significantly impacting the prognosis of pT1c33N0M0 NSCLC patients (P < 0.05). ROC curve analysis revealed an area under the curve of 0.6982 for predicting prognosis using N1 station in pT1c33N0M0 NSCLC patients. The maximum Youden index was observed at an N1 station of 2.7 nodes. Patients with N1 station ≥ three nodes had significantly better prognoses compared to those with < 3 nodes (both P < 0.05).ConclusionLymph nodes serve as an independent prognostic factor for pT1c33N0M0 NSCLC patients. Detecting at least three or more lymph nodes at the N1 station is associated with a more favourable prognosis in pT1c33N0M0 NSCLC patients. creator: Wei Yang creator: Luyi Wang uri: https://doi.org/10.7717/peerj.16866 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang and Wang title: Establishment and validation of a heart failure risk prediction model for elderly patients after coronary rotational atherectomy based on machine learning link: https://peerj.com/articles/16867 last-modified: 2024-01-31 description: ObjectiveTo develop and validate a heart failure risk prediction model for elderly patients after coronary rotational atherectomy based on machine learning methods.MethodsA retrospective cohort study was conducted to select 303 elderly patients with severe coronary calcification as the study subjects. According to the occurrence of postoperative heart failure, the study subjects were divided into the heart failure group (n = 53) and the non-heart failure group (n = 250). Retrospective collection of clinical data from the study subjects during hospitalization. After processing the missing values in the original data and addressing sample imbalance using Adaptive Synthetic Sampling (ADASYN) method, the final dataset consists of 502 samples: 250 negative samples (i.e., patients not suffering from heart failure) and 252 positive samples (i.e., patients with heart failure). According to a 7:3 ratio, the datasets of 502 patients were randomly divided into a training set (n = 351) and a validation set (n = 151). On the training set, logistic regression (LR), extreme gradient boosting (XGBoost), support vector machine (SVM), and lightweight gradient boosting machine (LightGBM) algorithms were used to construct heart failure risk prediction models; Evaluate model performance on the validation set by calculating the area under the receiver operating characteristic curve (ROC) curve (AUC), sensitivity, specificity, positive predictive value, negative predictive value, F1-score, and prediction accuracy.ResultA total of 17.49% of 303 patients occured postoperative heart failure. The AUC of LR, XGBoost, SVM, and LightGBM models in the training set were 0.872, 1.000, 0.699, and 1.000, respectively. After 10 fold cross validation, the AUC was 0.863, 0.972, 0.696, and 0.963 in the training set, respectively. Among them, XGBoost had the highest AUC and better predictive performance, while SVM models had the worst performance. The XGBoost model also showed good predictive performance in the validation set (AUC = 0.972, 95% CI [0.951–0.994]). The Shapley additive explanation (SHAP) method suggested that the six characteristic variables of blood cholesterol, serum creatinine, fasting blood glucose, age, triglyceride and NT-proBNP were important positive factors for the occurrence of heart failure, and LVEF was important negative factors for the occurrence of heart failure.ConclusionThe seven characteristic variables of blood cholesterol, blood creatinine, fasting blood glucose, NT-proBNP, age, triglyceride and LVEF are all important factors affecting the occurrence of heart failure. The prediction model of heart failure risk for elderly patients after CRA based on the XGBoost algorithm is superior to SVM, LightGBM and the traditional LR model. This model could be used to assist clinical decision-making and improve the adverse outcomes of patients after CRA. creator: Lixiang Zhang creator: Xiaojuan Zhou creator: Jiaoyu Cao uri: https://doi.org/10.7717/peerj.16867 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: A ubiquitination-related risk model for predicting the prognosis and immunotherapy response of gastric adenocarcinoma patients link: https://peerj.com/articles/16868 last-modified: 2024-01-31 description: Ubiquitination is crucial for the growth of cancer. However, the role of ubiquitination-related genes (URGs) in stomach adenocarcinoma (STAD) remains unclear. Differentially expressed URGs (DE-URGs) were examined in the whole TCGA-STAD dataset, and the prognosis-related genes were discovered from the The Cancer Genome Atlas (TCGA) training set. Prognostic genes were discovered using selection operator regression analysis and absolute least shrinkage (LASSO). A multivariate Cox analysis was further employed, and a polygene-based risk assessment system was established. Signatures were verified using the Gene Expression Omnibus (GEO) database record GSE84433 and the TCGA test set. Using the MEXPRESS dataset, a detailed analysis of gene expression and methylation was carried out. Using the DAVID database, DE-URG function and pathway enrichment was examined. The identified 163 DE-URGs were significantly associated with pathways related to protein ubiquitination, cell cycle, and cancer. A prognostic signature based on 13 DE-URGs was constructed, classifying patients into two risk groups. Compared to low-risk patients, people at high risk had considerably shorter survival times. Cox regression analyses considered prognostic parameters independent of age and risk score and were used to generate nomograms. Calibration curves show good agreement between nomogram predictions and observations. Furthermore, the results of the MEXPRESS analysis indicated that 13 prognostic DE-URGs had an intricate methylation profile. The enhanced Random Forest-based model showed greater efficacy in predicting prognosis, mutation, and immune infiltration. The in vitro validation, including CCK8, EdU, Transwell, and co-culture Transwell, proved that RNF144A was a potent oncogene in STAD and could facilitate the migration of M2 macrophages. In this research, we have created a genetic model based on URGs that can appropriately gauge a patient’s prognosis and immunotherapy response, providing clinicians with a reliable tool for prognostic assessment and supporting clinical treatment decisions. creator: Shuai Shao creator: Yang Sun creator: Dongmei Zhao creator: Yu Tian creator: Yifan Yang creator: Nan Luo uri: https://doi.org/10.7717/peerj.16868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Shao et al. title: Extending beyond individual caves: a graph theory approach broadening conservation priorities in Amazon iron ore caves link: https://peerj.com/articles/16877 last-modified: 2024-01-31 description: The Amazon is renowned worldwide for its biological significance, but it also harbors substantial mineral reserves. Among these, the ferruginous geosystems of the region are critical for iron ore extraction, accounting for 10% of Brazil’s export revenue. Additionally, this region holds a significant speleological heritage with more than 1,000 caves. However, cave conservation efforts are often in conflict with land use, necessitating mediation through environmental regulations. While conservation decisions typically consider only the caves’ characteristics, such an approach fails to account for the interactions among cave communities and their surrounding landscape. This poses a challenge to reserve design for cave conservation purposes. To address this issue, we assessed the predictors that influence the similarity among cave communities, suggesting the use of this parameter as a proxy for subterranean connectivity. Applying graph theory, we proposed a tool to aid in the selection of priority caves for conservation purposes. Our study involved the sampling of invertebrates in 69 iron ore caves and analyzing 28 environmental variables related to these subterranean habitats and adjacent landscape. Our analysis revealed that landscape and habitat characteristics are more important than geographical distance in determining patterns of similarity among caves. Our graph approach highlighted densely interconnected clusters based on similarity. However, specific caves stood out for harboring exclusive fauna and/or exhibiting habitat specificity, making them unique in the study area. Thus, we recommend prioritizing cave clusters for conservation, assembling both singular caves and others that influence them. It is crucial to note that protocols for the protection of subterranean biodiversity must consider measures that encompass both the caves and the surrounding landscape. Our methodology provides insights into the connectivity among caves, identifies existing groups, highlights singular (or unique) cavities that require preservation, and recognizes those influencing these unique habitats. This methodological advancement is crucial for the development of better conservation policies for the speleological heritage in areas under constant economic pressure. creator: Marcus P. A. Oliveira creator: Rodrigo L. Ferreira uri: https://doi.org/10.7717/peerj.16877 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Oliveira and Ferreira title: Resequencing and characterization of the first Corynebacterium pseudotuberculosis genome isolated from camel link: https://peerj.com/articles/16513 last-modified: 2024-01-30 description: BackgroundCorynebacterium pseudotuberculosis is a zoonotic Gram-positive bacterial pathogen known to cause different diseases in many mammals, including lymph node abscesses in camels. Strains from biovars equi and ovis of C. pseudotuberculosis can infect camels. Comparative genomics could help to identify features related to host adaptation, and currently strain Cp162 from biovar equi is the only one from camel with a sequenced genome.MethodsIn this work, we compared the quality of three genome assemblies of strain Cp162 that used data from the DNA sequencing platforms SOLiD v3 Plus, IonTorrent PGM, and Illumina HiSeq 2500 with an optical map and investigate the unique features of this strain. For this purpose, we applied comparative genomic analysis on the different Cp162 genome assembly versions and included other 129 genomes from the same species.ResultsSince the first version of the genome, there was an increase of 88 Kbp and 121 protein-coding sequences, a decrease of pseudogenes from 139 to 53, and two inversions and one rearrangement corrected. We identified 30 virulence genes, none associated to the camel host, and the genes rpob2 and rbpA predicted to confer resistance to rifampin. In comparison to 129 genomes of the same species, strain Cp162 has four genes exclusively present, two of them code transposases and two truncated proteins, and the three exclusively absent genes lysG, NUDIX domain protein, and Hypothetical protein. All 130 genomes had the rifampin resistance genes rpob2 and rbpA. Our results found no unique gene that could be associated with tropism to camel host, and further studies should include more genomes and genome-wide association studies testing for genes and SNPs. creator: Enrico Giovanelli Tacconi Gimenez creator: Marcus Vinicius Canário Viana creator: Thiago de Jesus Sousa creator: Flávia Aburjaile creator: Bertram Brenig creator: Artur Silva creator: Vasco Azevedo uri: https://doi.org/10.7717/peerj.16513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Giovanelli Tacconi Gimenez et al. title: Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci link: https://peerj.com/articles/16570 last-modified: 2024-01-30 description: BackgroundOil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis.MethodsA mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B).ResultsA total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1–25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS). creator: Fakhrur Razi Mohd Shaha creator: Pui Ling Liew creator: Faridah Qamaruz Zaman creator: Rosimah Nulit creator: Jakim Barin creator: Justina Rolland creator: Hui Yee Yong creator: Soo Heong Boon uri: https://doi.org/10.7717/peerj.16570 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mohd Shaha et al. title: Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals link: https://peerj.com/articles/16654 last-modified: 2024-01-30 description: Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai‘i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments. creator: Jill Ashey creator: Hailey McKelvie creator: John Freeman creator: Polina Shpilker creator: Lauren H. Zane creator: Danielle M. Becker creator: Lenore Cowen creator: Robert H. Richmond creator: Valerie J. Paul creator: Francois O. Seneca creator: Hollie M. Putnam uri: https://doi.org/10.7717/peerj.16654 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Sleep and memory complaints in long COVID: an insight into clustered psychological phenotypes link: https://peerj.com/articles/16669 last-modified: 2024-01-30 description: This study evaluated clinical features of individuals with long COVID (5–8 months after diagnosis) who reported sleep and memory problems (62 cases) compared to those without (52 controls). Both groups had a similar mean age (41 vs. 39 years). Around 86% of the participants were non-hospitalized at the time of infection, and none of them were vaccinated at that point. Subsequently, both cases and controls received the vaccine; however, the vaccination rates differed significantly between the groups (30.7% vs. 51.0%). Cases and controls had similar rates of symptoms at acute COVID phase. However, cases were more likely to experience coryza, dyspnea, headache, and nausea/vomiting during long COVID. Regarding new-onset symptoms in long COVID, 12.9% of cases had dyspnea, and 14.5% experienced nausea/vomiting, whereas in the control group there were only 1.9% and 0.0%, respectively. Cases also had a significantly higher prevalence of persistent headache (22.6% vs. 7.7%), and dyspnea (12.9% vs. 0.0). In addition, cases also showed an increased rate of mental health complaints: disability in daily activities (45.2% vs. 9.6%; P < 0.001); concentration/sustained attention difficulties (74.2% vs. 9.6%; P < 0.001); anxiety–Generalized Anxiety Disorder 2-item scale (GAD-2) ≥ 3 (66.1% vs. 34.6%; P = 0.0013); and “post-COVID sadness” (82.3% vs. 40.4%; P < 0.001). We observed a significant correlation between sadness and anxiety in cases, which was not observed in controls (P=0.0212; Spearman correlation test). Furthermore, the frequency of concomitant sadness and anxiety was markedly higher in cases compared to controls (59.7% vs. 19.2%) (P < 0.0001; Mann-Whitney test). These findings highlight a noteworthy association between sadness and anxiety specifically in cases. In conclusion, our data identified concurrent psychological phenotypes in individuals experiencing sleep and memory disturbances during long COVID. This strengthens the existing evidence that SARS-CoV-2 causes widespread brain pathology with interconnected phenotypic clusters. This finding highlights the need for comprehensive medical attention to address these complex issues, as well as major investments in testing strategies capable of preventing the development of long COVID sequelae, such as vaccination. creator: Ricardo Titze-de-Almeida creator: Pedro Henrique Araújo Lacerda creator: Edson Pereira de Oliveira creator: Mariah Eduarda Ferreira de Oliveira creator: Yngrid Sallaberry Silva Vianna creator: Amanda Machado Costa creator: Eloísa Pereira dos Santos creator: Louise Marie Coelho Guérard creator: Matheus Augusto de Miranda Ferreira creator: Isabel Cristina Rodrigues dos Santos creator: Jéssica Daniele da Silva Gonçalves creator: Gabriel Ginani Ferreira creator: Simoneide Souza Titze-de-Almeida creator: Pedro Renato de Paula Brandão creator: Helena Eri Shimizu creator: Andrezza Paula Brito Silva creator: Raimundo Nonato Delgado-Rodrigues uri: https://doi.org/10.7717/peerj.16669 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Titze-de-Almeida et al. title: Identification of fungi isolated from commercial bumblebee colonies link: https://peerj.com/articles/16713 last-modified: 2024-01-30 description: Fungi can have important beneficial and detrimental effects on animals, yet our understanding of the diversity and function of most bee-associated fungi is poor. Over 2 million bumblebee colonies are traded globally every year, but the presence and transport of viable fungi within them is unknown. Here, we explored whether any culturable fungi could be isolated from commercial bumblebee nests. We collected samples of various substrates from within 14 bumblebee colonies, including the honey, honey cup wall, egg cup wall, and frass then placed them on agar and recorded any growth. Fungal morphotypes were then subcultured and their ITS region sequenced for identification. Overall, we cultured 11 fungal species from the various nest substrates. These included both pathogenic and non-pathogenic fungi, such as Aspergillus sp., Penicillium sp., and Candida sp. Our results provide the first insights into the diversity of viable fungal communities in commercial bumblebee nests. Further research is needed to determine if these fungi are unique to commercial colonies or prevalent in wild bumblebee nests, and crucially to determine the ecological and evolutionary implications of these fungi in host colonies. creator: Lui Julie Chow creator: Miles L. Nesbit creator: Tom Hill creator: Christopher Tranter creator: Sophie E.F. Evison creator: William O.H. Hughes creator: Peter Graystock uri: https://doi.org/10.7717/peerj.16713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chow et al. title: The role of ferroptosis in central nervous system damage diseases link: https://peerj.com/articles/16741 last-modified: 2024-01-30 description: Ferroptosis is a form of cell death, i.e., programmed cell death characterized by lipid peroxidation and iron dependence, which has unique morphological and biochemical properties. This unique mode of cell death is driven by iron-dependent phospholipid peroxidation and regulated by multiple cell metabolic pathways, including redox homeostasis, iron metabolism, mitochondrial activity, and the metabolism of amino acids, lipids, and sugars. Many organ injuries and degenerative pathologies are caused by ferroptosis. Ferroptosis is closely related to central nervous system injury diseases and is currently an important topic of research globally. This research examined the relationships between ferroptosis and the occurrence and treatment of central nervous system injury diseases. Additionally, ferroptosis was assessed from the aspect of theory proposal, mechanism of action, and related signaling pathways per recent research. This review provides a relevant theoretical basis for further research on this theory, the prospect of its development, and the prevention and treatment of such diseases. creator: Mingzhu Li creator: Shengbo Jin creator: Xudong Zhu creator: Jian Xu creator: Yang Cao creator: Haozhe Piao uri: https://doi.org/10.7717/peerj.16741 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks link: https://peerj.com/articles/16773 last-modified: 2024-01-30 description: BackgroundHuman opisthorchiasis is a dangerous infectious chronic disease distributed in many Asian areas in the water-basins of large rivers, Siberia, and Europe. The gold standard for human opisthorchiasis laboratory diagnosis is the routine examination of Opisthorchis spp. eggs under a microscope. Manual detection is laborious, time-consuming, and dependent on the microscopist’s abilities and expertise. Automatic screening of Opisthorchis spp. eggs with deep learning techniques is a useful diagnostic aid.MethodsHerein, we propose a convolutional neural network (CNN) for classifying and automatically detecting O. viverrini eggs from digitized images. The image data acquisition was acquired from infected human feces and was processed using the gold standard formalin ethyl acetate concentration technique, and then captured under the microscope digital camera at 400x. Microscopic images containing artifacts and O.viverrini egg were augmented using image rotation, filtering, noising, and sharpening techniques. This augmentation increased the image dataset from 1 time to 36 times in preparation for the training and validation step. Furthermore, the overall dataset was subdivided into a training-validation and test set at an 80:20 ratio, trained with a five-fold cross-validation to test model stability. For model training, we customized a CNN for image classification. An object detection method was proposed using a patch search algorithm to detect eggs and their locations. A performance matrix was used to evaluate model efficiency after training and IoU analysis for object detection.ResultsThe proposed model, initially trained on non-augmented data of artifacts (class 0) and O. viverrini eggs (class 1), showed limited performance with 50.0% accuracy, 25.0% precision, 50.0% recall, and a 33.0% F1-score. After implementing data augmentation, the model significantly improved, reaching 100% accuracy, precision, recall, and F1-score. Stability assessments using 5-fold cross-validation indicated better stability with augmented data, evidenced by an ROC-AUC metric improvement from 0.5 to 1.00. Compared to other models such as ResNet50, InceptionV3, VGG16, DenseNet121, and Xception, the proposed model, with a smaller file size of 2.7 MB, showed comparable perfect performance. In object detection, the augmented data-trained model achieved an IoU score over 0.5 in 139 out of 148 images, with an average IoU of 0.6947.ConclusionThis study demonstrated the successful application of CNN in classifying and automating the detection of O. viverrini eggs in human stool samples. Our CNN model’s performance metrics and true positive detection rates were outstanding. This innovative application of deep learning can automate and improve diagnostic precision, speed, and efficiency, particularly in regions where O. viverrini infections are prevalent, thereby possibly improving infection sustainable control and treatment program. creator: Tongjit Thanchomnang creator: Natthanai Chaibutr creator: Wanchai Maleewong creator: Penchom Janwan uri: https://doi.org/10.7717/peerj.16773 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Thanchomnang et al. title: The impact of the route of administration on the efficacy and safety of the drug therapy for patent ductus arteriosus in premature infants: a systematic review and meta-analysis link: https://peerj.com/articles/16591 last-modified: 2024-01-29 description: BackgroundThis systematic review and meta-analysis aims to explore the potential impact of the route of administration on the efficacy of therapies and occurrence of adverse events when administering medications to premature infants with patent ductus arteriosus (PDA).MethodThe protocol for this review has been registered with PROSPERO (CRD 42022324598). We searched relevant studies in PubMed, Embase, Cochrane, and the Web of Science databases from March 26, 1996, to January 31, 2022.ResultsA total of six randomized controlled trials (RCTs) and five observational studies were included for analysis, involving 630 premature neonates in total. Among these infants, 480 were in the ibuprofen group (oral vs. intravenous routes), 78 in the paracetamol group (oral vs. intravenous routes), and 72 in the ibuprofen group (rectal vs. oral routes). Our meta-analysis revealed a significant difference in the rate of PDA closure between the the initial course of oral ibuprofen and intravenous ibuprofen groups (relative risk (RR) = 1.27, 95% confidence interval (CI) [1.13–1.44]; P < 0.0001, I2 = 0%). In contrast, the meta-analysis of paracetamol administration via oral versus intravenous routes showed no significant difference in PDA closure rates (RR = 0.86, 95% CI [0.38–1.91]; P = 0.71, I2 = 76%). However, there was no statistically significant difference in the risk of adverse events or the need for surgical intervention among various drug administration methods after the complete course of drug therapy.ConclusionThis meta-analysis evaluated the safety and effectiveness of different medication routes for treating PDA in premature infants. Our analysis results revealed that compared with intravenous administration, oral ibuprofen may offer certain advantages in closing PDA without increasing the risk of adverse events. Conversely, the use of paracetamol demonstrated no significant difference in PDA closure and the risk of adverse events between oral and intravenous administration. creator: Hanwen Luo creator: Jianghua He creator: Xiaoming Xu creator: Hongju Chen creator: Jing Shi uri: https://doi.org/10.7717/peerj.16591 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Luo et al. title: A fish can change its stripes: investigating the role of body colour and pattern in the bluelined goatfish link: https://peerj.com/articles/16645 last-modified: 2024-01-29 description: Bluelined goatfish (Upeneichthys lineatus) rapidly change their body colour from a white horizontally banded pattern to a seemingly more conspicuous vertically banded red pattern, often when foraging. Given the apparent conspicuousness of the pattern to a range of observers, it seems unlikely that this colour change is used for camouflage and instead may be used for communication/signalling. Goatfish often drive multispecies associations, and it is possible that goatfish use this colour change as a foraging success signal to facilitate cooperation, increase food acquisition, and reduce predation risk through a ‘safety in numbers’ strategy. Using a novel approach, we deployed 3D model goatfish in different colour morphs—white without bands, white with black vertical bands, and white with red vertical bands—to determine whether the red colouration is an important component of the signal or if it is only the vertical banding pattern, regardless of colour, that fish respond to as an indicator of foraging success. Use of remote underwater video allowed us to obtain information without the influence of human observers on the communities and behaviours of other fish in response to these different colours exhibited by goatfish. We found that conspecifics were more abundant around the black- and red-banded model fish when compared with the white models. Conspecifics were also more likely to forage around the models than to pass or show attraction, but this was unaffected by model colour. No difference in the abundance and behaviour of associated heterospecifics around the different models was observed, perhaps due to the static nature of the models. Some species did, however, spend more time around the red- and black-banded fish, which suggests the change in colour may indicate benefits in addition to food resources. Overall, the results suggest that the body colour/pattern of U. lineatus is likely a signalling tool but further work is required to explore the benefits to both conspecifics and heterospecifics and to further determine the behavioural functions of rapid colour change in U. lineatus. creator: Louise Tosetto creator: Nathan S. Hart creator: Jane E. Williamson uri: https://doi.org/10.7717/peerj.16645 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tosetto et al. title: Do you even exercise, ref? Exploring habits of Spanish basketball referees during practice and matches link: https://peerj.com/articles/16742 last-modified: 2024-01-29 description: BackgroundBasketball referees are a vital part of the organised competition system, although they remain an “outgroup” in sport. While physical development and fitness programming are deemed necessary for basketball officiating excellence, there is a paucity of literature exploring strategies for physical fitness management in this population.MethodsThis research was a nationwide cross-sectional, self-administered online survey conducted in 2021. A sample of 628 (531 males, 97 females) referees from 18 regional referee organisations in Spain provided individual responses to gather information on demographic details, level of participation in refereeing, physical fitness practices, and match-day exercise-based regimens. The data were described using summary statistics, and the associations of the assessed variables were subsequently calculated using contingency tables.ResultsOur findings reveal that a large fraction of the Spanish basketball referee population focuses on aerobic (83%) and strength (73.6%) activities, while less attention is paid to speed (36.9%) and flexibility (23.2%), and agility, coordination, and balance tasks are somewhat overlooked. No significant differences were observed among the referee categories regarding weekly training days or session duration, with most training for 15–60 min per session. Elite referees were more likely to hire personal trainers and engage in strength and flexibility exercises. Sub-elite referees showed a higher tendency to perform stretching and joint mobility activities post-match, while regional referees did so less frequently. Approximately 30.7% of referees across all competitive levels engaged in re-warm-up (RW-U) activities, with stretching and joint mobility being the most prevalent.ConclusionsSpanish basketball referees participate in routine physical exercise and fitness practices, irrespective of their competition level. While warm-up activities are prevalent, some sub-elite and regional referees do not consistently perform them, and re-warm-up routines are not extensively embraced. creator: David Suárez-Iglesias creator: Daniel González-Devesa creator: Carlos Ayán creator: Alberto Sánchez-Sixto creator: Alejandro Vaquera uri: https://doi.org/10.7717/peerj.16742 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Suárez-Iglesias et al. title: Mesenchymal stem cells alleviate sepsis-induced acute lung injury by blocking neutrophil extracellular traps formation and inhibiting ferroptosis in rats link: https://peerj.com/articles/16748 last-modified: 2024-01-29 description: Acute lung injury (ALI) is one of the most serious complications of sepsis, characterized by high morbidity and mortality rates. Ferroptosis has recently been reported to play an essential role in sepsis-induced ALI. Excessive neutrophil extracellular traps (NETs) formation induces exacerbated inflammation and is crucial to the development of ALI. In this study, we explored the effects of ferroptosis and NETs and observed the therapeutic function of mesenchymal stem cells (MSCs) on sepsis-induced ALI. First, we produced a cecal ligation and puncture (CLP) model of sepsis in rats. Ferrostain-1 and DNase-1 were used to inhibit ferroptosis and NETs formation separately, to confirm their effects on sepsis-induced ALI. Next, U0126 was applied to suppress the MEK/ERK signaling pathway, which is considered to be vital to NETs formation. Finally, the therapeutic effect of MSCs was observed on CLP models. The results demonstrated that both ferrostain-1 and DNase-1 application could improve sepsis-induced ALI. DNase-1 inhibited ferroptosis significantly in lung tissues, showing that ferroptosis could be regulated by NETs formation. With the inhibition of the MEK/ERK signaling pathway by U0126, NETs formation and ferroptosis in lung tissues were both reduced, and sepsis-induced ALI was improved. MSCs also had a similar protective effect against sepsis-induced ALI, not only inhibiting MEK/ERK signaling pathway-mediated NETs formation, but also alleviating ferroptosis in lung tissues. We concluded that MSCs could protect against sepsis-induced ALI by suppressing NETs formation and ferroptosis in lung tissues. In this study, we found that NETs formation and ferroptosis were both potential therapeutic targets for the treatment of sepsis-induced ALI, and provided new evidence supporting the clinical application of MSCs in sepsis-induced ALI treatment. creator: TieNan Wang creator: Zheng Zhang creator: Zhizhao Deng creator: Weiqi Zeng creator: Yingxin Gao creator: Ziqing Hei creator: Dongdong Yuan uri: https://doi.org/10.7717/peerj.16748 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Navigating the complexities of the forest land sharing vs sparing logging dilemma: analytical insights through the governance theory of social-ecological systems dynamics link: https://peerj.com/articles/16809 last-modified: 2024-01-29 description: This study addresses the ongoing debate on forest land-sparing vs land-sharing, aiming to identify effective strategies for both species conservation and timber exploitation. Previous studies, guided by control theory, compared sharing and sparing by optimizing logging intensity along a presumed trade-off between timber yield and ecological outcomes. However, the realism of this trade-off assumption is questioned by ecological and governance theories. This article introduces a mathematical model of Social-Ecological System (SES) dynamics, distinguishing selective logging intensification between sharing and sparing, with associated governance requirements. The model assumes consistent rules for logging, replanting, conservation support, access regulation, socio-economic, soil and climate conditions. Actors, each specialized in sustainable logging and replanting of a single species, coexist with various tree species in the same space for land sharing, contrasting with separate actions on monospecific stands for sparing. In sharing scenarios, a gradient of intensification is created from 256 combinations of selective logging for a forest with eight coexisting tree species. This is compared with eight scenarios of monospecific stands adjacent to a spared eight-species forest area safeguarded from logging. Numerical projections over 100 years rank sparing and sharing options based on forest-level tree biodiversity, carbon storage, and timber yield. The findings underscore the context-specific nature of the problem but identify simple heuristics to optimize both sparing and sharing practices. Prioritizing the most productive tree species is effective when selecting sparing, especially when timber yield and biodiversity are benchmarks. Conversely, sharing consistently outperforms sparing when carbon storage and biodiversity are main criteria. Sharing excels across scenarios considering all three criteria, provided a greater diversity of actors access and coexist in the shared space under collective rules ensuring independence and sustainable logging and replanting. The present model addresses some limitations in existing sparing-sharing theory by aligning with established ecological theories exploring the intricate relationship between disturbance practices, productivity and ecological outcomes. The findings also support a governance hypothesis from the 2009 Nobel Prize in Economics (E. Ostrom) regarding the positive impact on biodiversity and productivity of increasing polycentricity, i.e., expanding the number of independent species controllers’ channels (loggers/replanters/supporters/regulators). This hypothesis, rooted in Ashby’s law of requisite variety from control theory, suggests that resolving the sharing/sparing dilemma may depend on our ability to predict the yield-ecology performances of sparing (in heterogeneous landscapes) vs of sharing (in the same space) from their respective levels of “polycentric requisite variety”. creator: Jean-Baptiste Pichancourt uri: https://doi.org/10.7717/peerj.16809 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pichancourt title: Biology, ecology, and biogeography of eremic praying mantis Blepharopsis mendica (Insecta: Mantodea) link: https://peerj.com/articles/16814 last-modified: 2024-01-29 description: BackgroundBlepharopsis mendica (Fabricius, 1775) is a large mantid species found from the Canary Islands across North Africa, the Middle East, and Pakistan. Research on this species has been limited, especially in Iran, despite the country’s potential significance for studying its biology and distribution. Adults of this species are easily recognizable by their marble-white pattern and rhomboidal leaf-like pronotum. They are sit-and-wait predators that inhabit various open environments.MethodsField observations were conducted across various regions of the Egyptian Flower mantis (Blepharopsis mendica) global distribution, with a focus on Morocco, Tunisia, and Iran. Distribution data for B. mendicawere gathered from fieldwork, museum collections, online biodiversity databases, and publications, totaling 593 occurrence points. Ecological niche modeling was performed using environmental data, and various models were evaluated for suitability. Phylogeographic analyses involved DNA sequencing and construction of a haplotype network to examine genetic relationships between populations. Divergence time estimation and biogeographical range expansion models were applied to explore historical distribution shifts of the species across different regions. The study provided comprehensive insights into the biology, distribution, and genetic history of B. mendica.ResultsWe provide information on the life cycle, ootheca, defense behavior, habitat, and biogeography of the Egyptian Flower mantis Blepharopsis mendica. This mantid is an overwintering univoltine species with nymphs emerging in summer and becoming adults in spring. In the wild, females start oviposition in April and can lay their first ootheca within a week after mating. The species is distributed from the Canary Islands to Pakistan in the dry belt. Thus, its distribution is associated with xeric areas or desert and semi-desert habitats. Phylogeographic analyses revealed three major genetic lineages, (i) in the Maghreb, (ii) from Egypt via Arabia to Iran (with internal substructures), and (iii) likely in Pakistan; the estimated onset of differentiation into these lineages is of Pleistocene age. Defense behavior involves flying away or extending wings broadly and lifting forelegs. Performing laboratory breeding, we documented life cycle and color changes from first instar to adulthood. Due to overwintering, the last larval instar needs considerably longer than the others. At 25 °C (±2), average adult life span was 118 days (±6 SD) for females (range: 100–124) and 46 days (±5 SD) for males (range: 39–55), with a significant difference among sexes. On average, oothecae contained 32.3 eggs (±10.1 SD) and the mean incubation period was 36.8 days (±2.9 SD). We did not find evidence of parthenogenesis. In general, the biology of B. mendica shows a variety of adaptations to its often extreme and little predictable type of habitat. creator: Zohreh Mirzaee creator: Marianna V.P. Simões creator: Roberto Battiston creator: Saber Sadeghi creator: Martin Wiemers creator: Thomas Schmitt uri: https://doi.org/10.7717/peerj.16814 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mirzaee et al. title: Phylogenetic analysis of Microdochium spp. associated with turfgrass and their pathogenicity in cereals link: https://peerj.com/articles/16837 last-modified: 2024-01-29 description: Turfgrass is frequently used today in the arrangement and aesthetic beautification of grounds in parks, gardens, median strips, recreation and sports areas. In this study, surveys were conduct in turfgrass areas in the three provinces of Türkiye. As a result of isolations from the collected samples, 44 Microdochium isolates obtained belonging to five different species including M. bolleyi, M. majus, M. nivale, M. paspali and M. sorghi which have different virulences. Identification of the isolates were performed by rDNA-ITS sequence analyzes. According to the pathogenicity tests results, the most virulent species was M. nivale M62 with a disease severity value of 91.93%. This was followed by M. bolleyi M1584 and M. majus M63, with disease severity values of 91.12% and 91.08%, respectively. The virulence of M. bolleyi isolates varied among the species. Only 13 of the 31 M. bolleyi species were found to be virulent in turfgrass, M. paspali was less virulent than the others in Poa pratensis. The most virulent isolate of each Microdochium species was tested on four different cereal varieties. M. sorghi and M. paspali had low virulence values in barley and oat than the other Microdochium species, while the other three species showed high virulence in turfgrass, wheat and barley, other than oat. In the phylogenetic neighboor-joining tree belonging to 44 Microdochium isolates clearly demonstrated that the isolates were grouped into five distinct clusters. M. nivale and M. majus were considered genetically close isolates. creator: Filiz Ünal uri: https://doi.org/10.7717/peerj.16837 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ünal title: Screening of salt tolerance of maize (Zea mays L.) lines using membership function value and GGE biplot analysis link: https://peerj.com/articles/16838 last-modified: 2024-01-29 description: Soil salinization is a widely recognized global environmental concern that has a significant impact on the sustainable development of agriculture at a global scale. Maize, a major crop that contributes to the global agricultural economy, is particularly vulnerable to the adverse effects of salt stress, which can hinder its growth and development from germination to the seedling stage. This study aimed to screen highly salt-tolerant maize varieties by using four NaCl concentrations of 0, 60, 120, and 180 mMol/L. Various agronomic traits and physiological and biochemical indices associated with salt tolerance were measured, and salt tolerance was evaluated using principal component analysis, membership function method, and GGE biplot analysis. A total of 41 local maize varieties were assessed based on their D values. The results show that stem thickness, germ length, radicle length, leaf area, germination rate, germination index, salt tolerance index, and seed vigor all decreased as salt concentration increased, while electrical conductivity and salt injury index increased with the concentration of saline solution. Under the stress of 120 mMol/L and 180 mMol/L NaCl, changes in antioxidant enzymes occurred, reflecting the physiological response mechanisms of maize under salt stress. Principal component analysis identified six major components including germination vigor, peroxidase (POD), plant height, embryo length, SPAD chlorophyll and proline (PRO) factors. After calculating the comprehensive index (D value) of each variety’s performance in different environments using principal component analysis and the membership function method, a GGE biplot analysis was conducted to identify maize varieties with good salt tolerance stability: Qun Ce 888, You Qi 909, Ping An 1523, Xin Nong 008, Xinyu 66, and Hong Xin 990, as well as varieties with poor salt tolerance: Feng Tian 14, Xi Meng 668, Ji Xing 218, Gan Xin 2818, Hu Xin 712, and Heng Yu 369. Furthermore, it was determined that a 120 mMol/L NaCl concentration was suitable for screening maize varieties during germination and seedling stages. This study further confirmed the reliability of GGE biplot analysis in germplasm selection, expanded the genetic resources of salt-tolerant maize, and provided theoretical references and germplasm utilization for the introduction of maize in saline-alkali areas. These research findings contribute to a better understanding of maize salt tolerance and promote its cultivation in challenging environments. creator: Huijuan Tian creator: Hong Liu creator: Dan Zhang creator: Mengting Hu creator: Fulai Zhang creator: Shuqi Ding creator: Kaizhi Yang uri: https://doi.org/10.7717/peerj.16838 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tian et al. title: Clinical value of serum DJ-1 in lung adenocarcinoma link: https://peerj.com/articles/16845 last-modified: 2024-01-29 description: ObjectiveDJ-1 is an oncoprotein secreted by cancer cells. However, the physiological and pathological significance of DJ-1 secretion is not clearly understood. This study investigated the clinical value of serum DJ-1 in lung adenocarcinoma (LUAD).MethodsThe study involved 224 LUAD patients, 110 patients with benign pulmonary disease and 100 healthy controls from the First Affiliated Hospital of Nanjing Medical University. We detected the expression of DJ-1 in lung cell lines in vitro. Meanwhile, serum concentrations of DJ-1, carcinoembryonic antigen (CEA), neuron-specific enolase (NSE), and cytokeratin 19 fragment (CYFRA21-1) were measured. The diagnostic performance of LUAD was obtained using receiver operating characteristic (ROC) curves. Kaplan–Meier, univariate and multivariate Cox regression analyses were performed for progression-free survival (PFS).ResultsDJ-1 was highly expressed in LUAD cell lines. Serum DJ-1 levels were significantly higher in the LUAD group compared to the benign pulmonary disease group (5.04 vs. 3.66 ng/mL, P < 0.001) and healthy controls (5.04 vs. 3.51 ng/mL, P < 0.001). DJ-1 levels were associated with gender (P = 0.002), smoking history (P = 0.042) and lymph node metastasis (P = 0.040). ROC curve analysis of DJ-1 revealed an area under the curve (AUC) of 0.758 (95% CI [0.714–0.803], P < 0.001) with a sensitivity of 63.8% and specificity of 78.6% at a cutoff value of 4.62 ng/mL for the detection of LUAD. Univariate and multivariate analyses confirmed that the preoperative serum DJ-1 level, tumor stage and smoking history were independent prognostic factors of PFS.ConclusionOur study is the first to explore the clinical value of serum DJ-1 in LUAD comprehensively. Serum DJ-1 could be a potential diagnostic and prognostic biomarker for LUAD. creator: Lin Wang creator: Li Wei creator: Shuxian Miao creator: Wei Zhang uri: https://doi.org/10.7717/peerj.16845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: A retrospective study investigating the clinical significance of body mass index in acute pancreatitis link: https://peerj.com/articles/16854 last-modified: 2024-01-29 description: BackgroundAcute pancreatitis is an unpredictable and potentially fatal condition for which no definitive cure is currently available. Our research focused on exploring the connection between body mass index, a frequently overlooked risk factor, and both the onset and progression of acute pancreatitis.Material/MethodsA total of 247 patients with acute pancreatitis admitted to Jiangsu Provincial Hospital of Chinese Medicine from January 2021 to February 2023 were retrospectively reviewed. After screening, 117 patients with complete height and body weight data were selected for detailed assessment. Additionally, 85 individuals who underwent physical examinations at our hospital during this period were compiled to create a control group. The study received ethical approval from the ethics committee of Jiangsu Province Hospital of Chinese Medicine (Ref: No.2022NL-114-02) and was conducted in accordance with the China Good Clinical Practice in Research guidelines.ResultsA significant difference in body mass index (BMI) was observed between the healthy group and acute pancreatitis (AP) patients (p < 0.05), with a more pronounced disparity noted in cases of hyperlipidemic acute pancreatitis (p < 0.01). A potential risk for AP was identified at a BMI greater than 23.56 kg/m2 (AUC = 0.6086, p < 0.05). Being in the obese stage I (95%CI, [1.11–1.84]) or having a BMI below 25.4 kg/m2 (95%CI, [1.82–6.48]) are identified as risk factors for adverse AP progression. Moreover, BMI effectively predicts the onset of acute edematous pancreatitis and acute necrotizing pancreatitis (AUC = 0.7893, p < 0.001, cut-off value = 25.88 kg/m2). A higher BMI correlates with increased recurrence rates within a short timeframe (r = 0.7532, p < 0.01).ConclusionsElevated BMI is a risk factor for both the occurrence and progression of AP, and underweight status may similarly contribute to poor disease outcomes. BMI is crucial for risk prediction and stratification in AP and warrants ongoing monitoring and consideration. creator: Yuanzhen Bai creator: Guanwen Gong creator: Reziya Aierken creator: Xingyu Liu creator: Wei Cheng creator: Junjie Guan creator: Zhiwei Jiang uri: https://doi.org/10.7717/peerj.16854 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bai et al. title: Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean (Vigna radiata L. Wilczek) using genotyping by sequencing approach link: https://peerj.com/articles/16653 last-modified: 2024-01-26 description: Yellow mosaic disease (YMD) remains a major constraint in mungbean (Vigna radiata (L.)) production; while short-duration genotypes offer multiple crop cycles per year and help in escaping terminal heat stress, especially during summer cultivation. A comprehensive genotyping by sequencing (GBS)-based genome-wide association studies (GWAS) analysis was conducted using 132 diverse mungbean genotypes for traits like flowering time, YMD resistance, soil plant analysis development (SPAD) value, trichome density, and leaf area. The frequency distribution revealed a wide range of values for all the traits. GBS studies identified 31,953 high-quality single nucleotide polymorphism (SNPs) across all 11 mungbean chromosomes and were used for GWAS. Structure analysis revealed the presence of two genetically distinct populations based on ΔK. The linkage disequilibrium (LD) varied throughout the chromosomes and at r2 = 0.2, the mean LD decay was estimated as 39.59 kb. Two statistical models, mixed linear model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) identified 44 shared SNPs linked with various candidate genes. Notable candidate genes identified include FPA for flowering time (VRADI10G01470; chr. 10), TIR-NBS-LRR for mungbean yellow mosaic India virus (MYMIV) resistance (VRADI09G06940; chr. 9), E3 ubiquitin-protein ligase RIE1 for SPAD value (VRADI07G28100; chr. 11), WRKY family transcription factor for leaf area (VRADI03G06560; chr. 3), and LOB domain-containing protein 21 for trichomes (VRADI06G04290; chr. 6). In-silico validation of candidate genes was done through digital gene expression analysis using Arabidopsis orthologous (compared with Vigna radiata genome). The findings provided valuable insight for marker-assisted breeding aiming for the development of YMD-resistant and early-maturing mungbean varieties. creator: Manju Kohli creator: Hina Bansal creator: Gyan Prakash Mishra creator: Harsh Kumar Dikshit creator: Shashidhar B. Reddappa creator: Anirban Roy creator: Subodh Kumar Sinha creator: K.M. Shivaprasad creator: Nikki Kumari creator: Atul Kumar creator: Ranjeet R. Kumar creator: Ramakrishnan Madhavan Nair creator: Muraleedhar Aski uri: https://doi.org/10.7717/peerj.16653 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kohli et al. title: Collecting whales: processes and biases in Nordic museum collections link: https://peerj.com/articles/16794 last-modified: 2024-01-26 description: Whales are unique museum objects that have entered collections in many ways and for different reasons. This work studies three Nordic natural history museum collections in Norway and Denmark with more than 2,500 whale specimens in total, and gathers the available biological and collection data on the specimens, which include skeletal elements, foetuses and organs preserved in ethanol or formalin, and a few dry-preserved organs. It finds that influx of specimens, which were mainly locally common species that were hunted, to the collections, mainly happened in the latest 1800s and earliest 1900s, fuelled by research trends, nation building, local whaling, and colonial mechanisms. Norway was a major whaling nation, but the largest hunt for whales in the Southern Ocean in the mid-1900s is not reflected in the Norwegian museum collections, probably because of the commercial focus of the whaling industry and logistical challenges, combined with limited research interest in zoological specimens at that time. The results demonstrate that it is important to understand these processes and the resulting biases for future research, outreach, and conservation. creator: Lene Liebe Delsett uri: https://doi.org/10.7717/peerj.16794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Delsett title: Effect of dynamic taping on neck pain, disability, and quality of life in patients with chronic non-specific neck pain: a randomized sham-control trial link: https://peerj.com/articles/16799 last-modified: 2024-01-26 description: BackgroundIn 2020, 203 million people experienced neck pain, with a higher prevalence in women. By 2050, it is predicted that neck pain will affect 269 million people, representing a 32.5% increase. Physical rehabilitation is often employed for the treatment of chronic non-specific neck pain (CNSNP) and the associated functional loss. Taping is frequently used as an adjunct treatment alongside primary physical rehabilitation. Unlike kinesio tape (KT), the therapeutic benefits of dynamic tape (DT) have not been thoroughly explored and documented in non-athletic conditions. Therefore, the aim of this trial was to determine the effects of DT on pain, disability, and overall well-being in individuals experiencing CNSNP.MethodsA prospective parallel-group active controlled trial was conducted at a single center, involving 136 patients with CNSNP, randomly allocated in a 1:1 ratio. The sham taping group (STC) received standard physiotherapy care (n = 67) alongside DT without tension, while the dynamic taping group (DTC) (n = 69) underwent standard cervical offloading technique with appropriate tension in addition to standard physiotherapy care. Demographic information and three patient-reported outcome measures (PROMs), namely the Neck Disability Index (NDI), Visual Analogue Scale (VAS), and the World Health Organization—Five Well-Being Index (WHO-5), were collected for each participant at three time points (baseline, four weeks post-taping, and four weeks follow-up).ResultsAt baseline, no significant differences were observed between the STC and DTC for any outcome measure. Notably, all three PROMs exhibited a significant improvement from baseline to four weeks post-intervention, with moderate to small effect sizes (NDI ηp2 = 0.21, VAS ηp2 = 0.23, and WHO-55 ηp2 = 0.05). The WHO-5 scores for both groups demonstrated improvement from baseline through follow-up (p < 0.001). The NDI and VAS scores ameliorated from baseline to the four weeks post-taping period, with marginal improvements observed during the four weeks follow-up.ConclusionThe incorporation of DT as an adjunct to standard physiotherapy care yielded enhancements in pain levels, functional disability, and well-being among patients with CNSNP when compared to the sham group. However, the sustainability of these improvements beyond the taping period lacks statistical significance and warrants further validation. creator: Mohammad Sidiq creator: Aksh Chahal creator: Balamurugan Janakiraman creator: Faizan Kashoo creator: Sharad Kumar Kedia creator: Neha Kashyap creator: Richa Hirendra Rai creator: Neha Vyas creator: T.S. Veeragoudhaman creator: Krishna Reddy Vajrala creator: Megha Yadav creator: Shahiduz Zafar creator: Sanghamitra Jena creator: Monika Sharma creator: Shashank Baranwal creator: Mshari Alghadier creator: Abdullah Alhusayni creator: Abdullah Alzahrani creator: Vijay Selvan Natarajan uri: https://doi.org/10.7717/peerj.16799 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sidiq et al. title: Prevalence of intestinal parasites and comparison of detection techniques for soil-transmitted helminths among newly arrived expatriate labors in Jeddah, Saudi Arabia link: https://peerj.com/articles/16820 last-modified: 2024-01-26 description: BackgroundDiversity in clinical signs and symptoms are associated with soil transmitted diseases (STD), which are spread to humans by intestinal worms and transmitted in a variety of ways. There is a need for the present study, which aimed to investigate the prevalence of intestinal parasites and to compare between the common detection techniques for soil-transmitted helminths (STHs) among newly arrived expatriate labors in Jeddah, Saudi Arabia.MethodsA total of 188 stool samples were analyzed by macroscopic examination, and microscopic examination using direct iodine smear and the formal ether sedimentation technique. Trichrome and modified Kinyoun’s stains were used to confirm the morphology of any detected protozoa stages and oocyst of Cryptosporidium, respectively. A chromatographic immunoassay kit was used for Entamoeba histolytica, Giardia lamblia and Cryptosporidium. In addition, real-time PCR was employed only to identify various STHs.ResultsOut of 188, several types of parasites were detected in 35 samples (18.62%), of which some with multiple infections. Nine samples (4.79%) were positive for Entamoeba coli, seven samples (3.72%) for Trichuris trichiura, six samples (3.19%) for Necator americanus, four samples (2.13%) for Strongyloides stercoralis, four samples (2.13%) for Ascaris lumbricoides, four samples (2.13%) for E. histolytica, three samples (1.60%) for Blastocystis hominis and two samples (1.06%) for Ancylostoma duodenale. In comparison between laboratory techniques for STHs, real-time PCR was able to detect the DNA of 19 samples (10.1%) followed by Ritchie sedimentation technique (18, 9.6%), and direct smear (7, 3.7%) (p > 0.05).ConclusionThe high rate of newly arrived foreign workers infected with intestinal parasites could lead to a risk to society. Continuous and regular surveys are needed to deal with the occurrence of intestinal parasitic infections including STHs. To improve the identification of these infections, we recommend a supporting infrastructure for the application of concentration methods and molecular assays. creator: Mohammad F. Al-Refai creator: Majed H. Wakid uri: https://doi.org/10.7717/peerj.16820 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Al-Refai and Wakid title: Immortalization of American miniature horse-derived fibroblast by cell cycle regulator with normal karyotype link: https://peerj.com/articles/16832 last-modified: 2024-01-26 description: Immortalized cells serve as a crucial research tool that capitalizes on their robust proliferative properties for functional investigations of an organism. Establishing an immortalized American miniature horse cell line could yield valuable insights into these animals’ genetic and physiological characteristics and susceptibility to health issues. To date, immortalized small horse cells with normal karyotypes have not been established. In this study, we successfully established primary and immortalized fibroblast cell lines through the combined expression of human-derived mutant cyclin-dependent kinase 4 (CDK4R24C), cyclin D1, and Telomerase Reverse Transcriptase (TERT), although CDK4R24C and cyclin D1, SV40T and TERT did not result in successful immortalization. Our comparison of the properties of these immortalized cells demonstrated that K4DT immortalized cells maintain a normal karyotype. Ultimately, our findings could pave the way for the development of targeted interventions to enhance the health and well-being of American miniature horses. creator: Tetsuya Tani uri: https://doi.org/10.7717/peerj.16832 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tani title: A vertebra of a small species of Pachycetus from the North Sea and its inner structure and vascularity compared with other basilosaurid vertebrae from the same site link: https://peerj.com/articles/16541 last-modified: 2024-01-25 description: In the Western Scheldt Estuary near the Belgian-Dutch border, middle to late Eocene strata crop out at the current seafloor. Most vertebrae of large Eocene basilosaurid taxa from this area were previously described in several papers. They represent three morphotypes: elongated vertebrae of a large species of Pachycetus (Morphotype 1b), a not-elongated vertebra of a large ‘dorudontid’ basilosaurid (Morphotype 2) and ‘shortened’ vertebrae of a new, unnamed taxon (Morphotype 3). This article deals with a still undescribed, smaller vertebra, NMR-16642, from this site. Our first aim was to date it by dinoflagellate cysts in adhering sediments. Yielding an age of about 38 Ma, it is one of the very few remains of basilosaurids from Europe, of which the age could be assessed with reasonable certainty. The vertebra, Morphotype 1a, is assigned to a small species of Pachycetus. High-quality CT scans are used to differentiate between NMR-16642, Morphotype 1a, and the large species of Pachycetus, Morphotype 1b. Another aim of this paper is to investigate the inner structure and vascularity of the study vertebra and that of the other morphotypes (1b, 2, 3) from this area by using high-quality CT scans. Notwithstanding differences in size, shape and compactness, the vertebral inner structure with a multi-layered cortex of periosteal bone, surrounding two cones of endosteal bone appears to be basically similar in all morphotypes. Apparently, this inner structure reflects the ontogenetic vertebral growth. An attempt to reconstruct the vascularity of the vertebrae reveals a remarkable pattern of interconnected vascular systems. From the dorsal and, if present, ventral foramina, vascular canals are running to a central vascular node. From this node a system of vascular canals goes to the epiphyseal ends, giving rise to separate systems for cortex and cones. It is the first time that the vascularity of vertebrae of archaeocetes is investigated. creator: Henk Jan van Vliet creator: Mark E.J. Bosselaers creator: Dirk K. Munsterman creator: Marcel L. Dijkshoorn creator: Jeffrey Joël de Groen creator: Klaas Post uri: https://doi.org/10.7717/peerj.16541 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 van Vliet et al. title: Evaluation of P5CS and ProDH activity in Paulownia tomentosa (Steud.) as an indicator of oxidative changes induced by drought stress link: https://peerj.com/articles/16697 last-modified: 2024-01-25 description: The aim of the study was to investigate changes in proline metabolism in seedlings of tree species during drought stress. One month old Paulownia tomentosa seedlings were exposed to moisture conditions at various levels (irrigation at 100, 75, 50 and 25% of field capacity), and then the material (leaves and roots) was collected three times at 10-day intervals. The activity of enzymes involved in proline metabolism was closely related to drought severity; however, proline content was not directly impacted. The activity of pyrroline-5-carboxylate synthetase (P5CS), which catalyzes proline biosynthesis, increased in response to hydrogen peroxide accumulation, which was correlated with soil moisture. In contrast, the activity of proline dehydrogenase (ProDH), which catalyzes proline catabolism, decreased. Compared to proline, the activity of these enzymes may be a more reliable biochemical marker of stress-induced oxidative changes. The content of proline is dependent on numerous additional factors, i.e., its degradation is an important alternative energy source. Moreover, we noted tissue-specific differences in this species, in which roots appeared to be proline biosynthesis sites and leaves appeared to be proline catabolism sites. Further research is needed to examine a broader view of proline metabolism as a cycle regulated by multiple mechanisms and differences between species. creator: Joanna Kijowska-Oberc creator: Mikołaj K. Wawrzyniak creator: Liliana Ciszewska creator: Ewelina Ratajczak uri: https://doi.org/10.7717/peerj.16697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kijowska-Oberc et al. title: Gpr149 is involved in energy homeostasis in the male mouse link: https://peerj.com/articles/16739 last-modified: 2024-01-25 description: GPR149 is an orphan receptor about which little is known. Accordingly, in the present study, we mapped the tissue expression of Gpr149 in mice using three complementary approaches: quantitative PCR, in situ hybridization, and a newly generated Gpr149-Cre reporter mouse model. The strongest expressions of Gpr149 were observed in neurons of the islands of Calleja, the ventromedial hypothalamus, and the rostral interpeduncular nucleus. Moderate-to-low expression was also observed in the basal forebrain, striatum, hypothalamus, brainstem, and spinal cord. Some Gpr149 expression was also detected in the primary afferent neurons, enteric neurons, and pituitary endocrine cells. This expression pattern is consistent with the involvement of GPR149 signaling in the regulation of energy balance. To explore the physiological function of GPR149 in vivo, we used CRISPR-Cas9 to generate a global knockout allele with mice lacking Gpr149 exon 1. Preliminary metabolic findings indicated that Gpr149−/− mice partially resist weight gain when fed with a high-fat diet and have greater sensitivity to insulin than control mice. In summary, our data may serve as a resource for future in vivo studies on GPR149 in the context of diet-induced obesity. creator: Steven Wyler creator: Surbhi creator: Newton Cao creator: Warda Merchant creator: Angie Bookout creator: Laurent Gautron uri: https://doi.org/10.7717/peerj.16739 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wyler et al. title: Water deprivation-induced hypoxia and oxidative stress physiology responses in respiratory organs of the Indian stinging fish in near coastal zones link: https://peerj.com/articles/16793 last-modified: 2024-01-25 description: BackgroundWater deprivation-induced hypoxia stress (WDIHS) has been extensively investigated in numerous fish species due to their adaptation with accessory respiratory organs to respire air but this has not been studied in Indian stinging fish Heteropneustes fossilis. Data regarding WDIHS-induced metabolism in accessory respiratory organ (ARO) and gills and its relationship with oxidative stress (OS) in respiratory organs of air-breathing fish H. fossilis, are limited. So, this study aimed to investigate the effects of WDIHS (0, 3, 6, 12, and 18 h) on hydrogen peroxide (H2O2) as reactive oxygen species (ROS), OS, redox regulatory enzymes, and electron transport enzymes (ETC) in ARO and gills of H. fossilis.MethodsFish were exposed to air for different hours (up to 18 h) against an appropriate control, and ARO and gills were sampled. The levels of oxygen saturation in the body of the fish were assessed at various intervals during exposure to air. Protein carbonylation (PC) and thiobarbituric acid reactive substances (TBARS) were used as OS markers, H2O2 as ROS marker, and various enzymatic activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione reductase (GR), along with the assessment of complex enzymes (I, II, III, and V) as well as the levels of ascorbic acid (AA) and the reduced glutathione (GSH) were quantified in both the tissues.ResultsDiscriminant function analyses indicate a clear separation of the variables as a function of the studied parameters. The gills exhibited higher levels of GSH and H2O2 compared to ARO, while ARO showed elevated levels of PC, TBARS, AA, SOD, CAT, and GPx activities compared to the gills. The activities of GR and ETC enzymes exhibited similar levels in both the respiratory organs, namely the gills, and ARO. These organs experienced OS due to increased H2O2, TBARS, and PC levels, as observed during WDIHS. Under WDIHS conditions, the activity/level of CAT, GPx, GR, and GSH decreased in ARO, while SOD activity, along with GR, GSH, and AA levels decreased in gills. However, the activity/level of SOD and AA in ARO and CAT in gills was elevated under WDIHS. Complex II exhibited a positive correlation with WDIHS, while the other ETC enzymes (complex I, III, and V) activities had negative correlations with the WDIHS.DiscussionThe finding suggests that ARO is more susceptible to OS than gills under WDIHS. Despite both organs employ distinct redox regulatory systems to counteract this stress, their effectiveness is hampered by the inadequacy of small redox regulatory molecules and the compromised activity of the ETC, impeding their ability to effectively alleviate the stress induced by the water-deprivation condition. creator: Samar Gourav Pati creator: Falguni Panda creator: Abhipsa Bal creator: Biswaranjan Paital creator: Dipak Kumar Sahoo uri: https://doi.org/10.7717/peerj.16793 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pati et al. title: Numerical and biomass growth study of Bulimulus bonariensis (Rafinesque, 1833) (Gastropoda: Bulimulidae) under laboratory conditions link: https://peerj.com/articles/16803 last-modified: 2024-01-25 description: Bulimulus bonariensis is considered a species of relevance to agribusiness, having been declared a pest with indirect damage because of its negative effects on several crops such as soybeans, chickpeas, and corn in central and northern Argentina. The objective of this work was to analyze the growth pattern of a population born under laboratory conditions, to explore population aspects such as survival and mortality, to estimate the age and size at gonadal maturity and first reproduction, and to contribute to the knowledge of the reproductive biology of this gastropod. From the clutches obtained, the basic biologic parameters were calculated and the individuals hatched under laboratory conditions counted and measured every two weeks. The clutches contained an average of 44 eggs, which took about 13.7 days to hatch at a birth rate of 41.82%. The growth pattern in the five clutches was analyzed individually, and the logistic model used was the one with the highest degree of fit to that observed growth pattern, followed by the Gompertz model, and finally the von Bertalanffy model. In addition, the models were applied to the 102 specimens analyzed together as a cohort, where the best fitting model was also proved to be the logistic growth model. A concave type III survival curve was obtained from the horizontal life table. The cohort was reduced by 48% during the first 50 days after birth. Beyond one month of hatching, life expectancy gradually increased and remained high between 65–302 days of life. After day 330, life expectancy decreased and only 13.72% exceeded one year of birth, with an average length of 16.68 mm. The last specimen died after 23 months at a total length of 20.24 mm, and the life expectancy was estimated at almost three years. In addition, it was inferred that gonadal maturity, when these gastropods reach 12 mm of total shell length, is reached after 200 days of life. Therefore, the individuals that are born are able to reproduce for the first time a year after birth, when they have the approximate size of 16.68 mm. creator: Ana Carolina Díaz creator: Stella Maris Martin uri: https://doi.org/10.7717/peerj.16803 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Díaz and Martin title: Factors influencing space-use and kill distribution of sympatric lion prides in a semi-arid savanna landscape link: https://peerj.com/articles/16749 last-modified: 2024-01-24 description: Understanding lions’ (Panthera leo) space-use is important for the management of multi-species wildlife systems because lions can have profound impacts on ecosystem-wide ecological processes. Semi-arid savanna landscapes are typically heterogeneous with species space-use driven by the availability and distribution of resources. Previous studies have demonstrated that lions select areas close to water as encounter rates with prey are higher and hunting success is greater in these regions. Where multiple lion prides exist, landscape partitioning is expected to follow a despotic distribution in which competitively superior prides occupy high-quality areas while subordinates select poorer habitats. In this study, Global Positioning System collar data and logistic regression were used to investigate space-use and hunting success among 50% of lion prides at Malilangwe Wildlife Reserve, Zimbabwe. Our findings show that lion space-use was driven by surface water availability and that home range selection was socially hierarchical with the dominant pride occupying habitat in which water was most abundant. In addition, we found that the effect of shrub cover, clay content and soil depth on kill probability was area specific and not influenced by hierarchical dominance. Where multiple lion prides are studied, we recommend treating prides as individual units because pooling data may obscure site and pride specific response patterns. creator: Allan Tarugara creator: Bruce W. Clegg creator: Sarah B. Clegg uri: https://doi.org/10.7717/peerj.16749 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tarugara et al. title: Retrospective study of BRAFV600E mutation and CT features of papillary thyroid carcinoma link: https://peerj.com/articles/16810 last-modified: 2024-01-24 description: ObjectiveThis study aimed to examine the correlation between BRAFV600E status and computed tomography (CT) imaging characteristics in papillary thyroid carcinoma (PTC) and determine if suspicious CT imaging features could predict BRAFV600E status.MethodsThis retrospective study included patients with pathologically confirmed PTC at the Department of Thyroid Surgery of Zhongshan Hospital, Xiamen University, between July 2020 and June 2022. We compared the clinicopathologic factors and CT findings of nodules with and without the mutation, and the multiple logistical regression test was used to determine independent parameters of the BRAFV600E mutation.ResultsThis study included 381 patients with PTC, among them, BRAFV600E mutation was detected in 314 patients (82.4%). Multivariate logistic regression analysis showed that gender (OR = 0.542, 95% CI [0.296–0.993], P = 0.047) and shape (OR = 0.510, 95% CI [0.275–0.944], P = 0.032) were associated with BRAFV600E mutation.ConclusionsCompared to BRAFV600E mutation-negative, BRAFV600E-positive PTC lesions were more likely to be found in female patients and were characterized by irregular shape. However, the CT imaging finding is not enough to predict BRAFV600E status, but an indication. creator: Xiaoquan Hong creator: Juxiang Li creator: Shaoyin Duan creator: Youkuang You uri: https://doi.org/10.7717/peerj.16810 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hong et al. title: Diosgenin biosynthesis pathway and its regulation in Dioscorea cirrhosa L. link: https://peerj.com/articles/16702 last-modified: 2024-01-23 description: Dioscorea cirrhosa L. (D. cirrhosa) tuber is a traditional medicinal plant that is abundant in various pharmacological substances. Although diosgenin is commonly found in many Dioscoreaceae plants, its presence in D. cirrhosa remained uncertain. To address this, HPLC-MS/MS analysis was conducted and 13 diosgenin metabolites were identified in D. cirrhosa tuber. Furthermore, we utilized transcriptome data to identify 21 key enzymes and 43 unigenes that are involved in diosgenin biosynthesis, leading to a proposed pathway for diosgenin biosynthesis in D. cirrhosa. A total of 3,365 unigenes belonging to 82 transcription factor (TF) families were annotated, including MYB, AP2/ERF, bZIP, bHLH, WRKY, NAC, C2H2, C3H, SNF2 and Aux/IAA. Correlation analysis revealed that 22 TFs are strongly associated with diosgenin biosynthesis genes (—r2— > 0.9, P < 0.05). Moreover, our analysis of the CYP450 gene family identified 206 CYP450 genes (CYP450s), with 40 being potential CYP450s. Gene phylogenetic analysis revealed that these CYP450s were associated with sterol C-22 hydroxylase, sterol-14-demethylase and amyrin oxidase in diosgenin biosynthesis. Our findings lay a foundation for future genetic engineering studies aimed at improving the biosynthesis of diosgenin compounds in plants. creator: Yan Lin creator: Qiuyan Hu creator: Qiang Ye creator: Haohua Zhang creator: Ziyu Bao creator: Yongping Li creator: Luo Jian Mo uri: https://doi.org/10.7717/peerj.16702 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Seventeen-year study reveals fluctuations in key ecological indicators on two reef crests in Cuba link: https://peerj.com/articles/16705 last-modified: 2024-01-23 description: Reef crests in the Caribbean have lost approximately 80% of the foundational habitat-forming coral Acropora palmata (Lamarck, 1816), with declines registered as early as the 1950s mainly from anthropogenic causes. We studied two reef crests in the northwestern region of Cuba over 17 years (2005 to 2021) to evaluate temporal changes in coral cover, dominated by A. palmata, and their potential drivers. The density of A. palmata generally showed a negative trend at both reefs, with the lowest density recorded in 2021 at 0.2 ± 0.05 col. m−2 at Playa Baracoa and 1.0 ± 0.1 col. m−2 at Rincon de Guanabo. The mean size of the colonies in the two reefs also decreased over time. In Playa Baracoa, the mean diameter of A. palmata colonies decreased from 2012 at 67 ± 5.9 cm to 2013 at 34 ± 2.2 cm, whereas in Rincon de Guanabo, a change in diameter was evident from 2015 at 44.3 ± 2.3 to 2021 at 21.6 ± 0.9 cm. Adult colonies (10 cm–50 cm diameter) predominated in most years on both reefs. The populations of A. palmata on both reefs were healthy, with an average of 70% colonies in good condition during the study period. However, A. palmata cover decreased by almost half by 2021, to 8.6% in Playa Baracoa and 16.8% in Rincon de Guanabo. By contrast, macroalgal cover increased two-fold to 87.1% in Playa Baracoa and four-fold to 77.2% in Rincon de Guanabo. The density of the sea urchin Diadema antillarum was higher in Playa Baracoa than in Rincon de Guanabo. The highest densities were 2.8 ± 0.2 ind. m−2 in Playa Baracoa in 2005 and 0.1 ± 0.03 ind. m−2 in Rincon de Guanabo in 2008. Although our results show an overall decline of A. palmata (density and percent cover) and an increase in macroalgae, these two reef crests are in better condition than most reefs in the Caribbean in terms of the density and health of A. palmata populations, and the density of D. antillarum at Playa Baracoa. Our results are important in establishing a management plan to ensure the condition of these reef crests does not degrade further. creator: Amanda Ramos creator: Patricia González-Díaz creator: Anastazia T. Banaszak creator: Orlando Perera creator: Fredy Hernandez Delgado creator: Sandra Delfín de León creator: Patricia Vicente Castro creator: Gabriela Caridad Aguilera Pérez creator: Alain Duran uri: https://doi.org/10.7717/peerj.16705 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ramos et al. title: A dynamic nomogram for predicting 28-day mortality in septic shock: a Chinese retrospective cohort study link: https://peerj.com/articles/16723 last-modified: 2024-01-23 description: BackgroundSeptic shock is a severe life-threatening disease, and the mortality of septic shock in China was approximately 37.3% that lacks prognostic prediction model. This study aimed to develop and validate a prediction model to predict 28-day mortality for Chinese patients with septic shock.MethodsThis retrospective cohort study enrolled patients from Intensive Care Unit (ICU) of the Second Affiliated Hospital, School of Medicine, Zhejiang University between December 2020 and September 2021. We collected patients’ clinical data: demographic data and physical condition data on admission, laboratory data on admission and treatment method. Patients were randomly divided into training and testing sets in a ratio of 7:3. Univariate logistic regression was adopted to screen for potential predictors, and stepwise regression was further used to screen for predictors in the training set. Prediction model was constructed based on these predictors. A dynamic nomogram was performed based on the results of prediction model. Using receiver operator characteristic (ROC) curve to assess predicting performance of dynamic nomogram, which were compared with Sepsis Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation II (APACHE II) systems.ResultsA total of 304 patients with septic shock were included, with a 28-day mortality of 25.66%. Systolic blood pressure, cerebrovascular disease, Na, oxygenation index (PaO2/FiO2), prothrombin time, glucocorticoids, and hemodialysis were identified as predictors for 28-day mortality in septic shock patients, which were combined to construct the predictive model. A dynamic nomogram (https://zhijunxu.shinyapps.io/DynNomapp/) was developed. The dynamic nomogram model showed a good discrimination with area under the ROC curve of 0.829 in the training set and 0.825 in the testing set. Additionally, the study suggested that the dynamic nomogram has a good predictive value than SOFA and APACHE II.ConclusionThe dynamic nomogram for predicting 28-day mortality in Chinese patients with septic shock may help physicians to assess patient survival and optimize personalized treatment strategies for septic shock. creator: Zhijun Xu creator: Man Huang uri: https://doi.org/10.7717/peerj.16723 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Xu et al. title: β-sitosterol isolated from the leaves of Trema orientalis (Cannabaceae) promotes viability and proliferation of BF-2 cells link: https://peerj.com/articles/16774 last-modified: 2024-01-23 description: Trema orientalis is a pioneer species in the cannabis family (Cannabaceae) that is widely distributed in Thai community forests and forest edges. The mature leaves are predominantly used as an anti-parasite treatment and feed for local freshwater fish, inspiring investigation of their phytochemical composition and bioactivity. The purpose of this work was to investigate the bioactive compounds in T. orientalis leaf extract and their cytotoxicity in the BF-2 fish cell line (ATCC CCL-91). Flash column chromatography was used to produce 25 mL fractions with a mixture solvent system comprised of hexane, diethyl ether, methanol, and acetone. All fractions were profiled with HPLC-DAD (mobile phase methanol:aqueous buffer, 60:40 v/v) and UV detection (wavelengths 256 and 365 nm). After drying, a yellowish powder was isolated from lipophilic leaf extract with a yield of 280 µg/g dry weight. Structure elucidation by nuclear magnetic resonance (NMR) indicated it to consist of pure β-sitosterol. The lipophilic extract and pure compound were evaluated for cytotoxicity using BF-2 cells. MTT assays showed both leaf extract and pure compound at 1 µg/mL to increase cell viability after 24 h treatment. The respective half maximal inhibitory concentration (IC50) values of leaf extract and β-sitosterol were 7,027.13 and 86.42 µg/ml, indicating a lack of toxicity in the BF-2 cell line. Hence, T. orientalis can serve as a source of non-toxic natural lipophilic compounds that can be useful as bioactive ingredients in supplement feed development. creator: Amita Mekarunothai creator: Markus Bacher creator: Raveevatoo Buathong creator: Saraphorn Intarasam creator: Ngampuk Tayana creator: Sumet Kongkiatpaiboon creator: Theppanya Charoenrat creator: Tiwtawat Napiroon uri: https://doi.org/10.7717/peerj.16774 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mekarunothai et al. title: Comparison design and evaluation power in cohort and self-controlled case series designs for post-authorization vaccine safety studies link: https://peerj.com/articles/16780 last-modified: 2024-01-23 description: BackgroundPost-authorization safety studies (PASSs) of vaccines are important. PASSs enable the evaluation of association between vaccination and adverse events following immunization through common study designs. Clinical trials during vaccine development typically include a few thousand to 10,000 participants while a PASS might aim to detect a few adverse events per 100,000 vaccine recipients. While all available data may be utilized, prior consideration of power analyses are nonetheless crucial for interpretation in cases where statistically significant differences are not found.MethodsThis research primarily examined cohort study design and self-controlled case series (SCCS) design, estimating the power of a PASS under plausible conditions.ResultsBoth the cohort study and SCCS designs necessitated large sample sizes or high event counts to guarantee adequate power. The SCCS design is particularly suited to evaluating rare adverse events. However, extremely rare events may not yield sufficient occurrences, thereby resulting in low power. Although the SCCS design can more efficiently control for time-invariant confounding in principle, it solely estimates relative measures. A cohort study design might be preferred if confounding can be adequately managed as it also estimates absolute measures. It may be an easy decision to use all the data at hand for either design. We found it necessary to estimate the sample size and number of events to be used in the study based on a priori information and anticipated results. creator: Shuntaro Sato creator: Yurika Kawazoe creator: Tomohiro Katsuta creator: Haruhisa Fukuda uri: https://doi.org/10.7717/peerj.16780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sato et al. title: Predicting repeat power ability through common field assessments: is repeat power ability a unique physical quality? link: https://peerj.com/articles/16788 last-modified: 2024-01-23 description: BackgroundThe repeat power ability (RPA) assessment is used to test the ability to repeatedly produce maximal ballistic efforts with an external load. The underpinning physical qualities influencing RPA are undetermined. This study aimed to gain further insight into the physical qualities that determine RPA by analysing the association between physical qualities and an assessment of RPA.Materials and methodsTen well-trained male field hockey players performed an RPA assessment consisting of 20 repetitions of loaded countermovement jumps (LCMJ20), with a percent decrement score of peak power output calculated. Over a two-week period, each participant performed the YoYo Intermittent Recovery Test 2 (IRT2), a repeated speed ability assessment incorporating a 180° change of direction (RSA180), a 40-meter linear speed test (40 mST), an isometric mid-thigh pull (IMTP), a countermovement jump (CMJ), and a 3-repetition maximum half squat (HS) assessment. Pearson’s correlation analysis was used to determine the strength of relationships between each assessment variable and the LCMJ20. The assessment variables with the strongest relationships within each assessment were used in a stepwise multiple linear regression analysis to determine the best predictor model of LCMJ20.ResultsRSA180percent decrement score (RSA180% had a very strong, significant relationship with LCMJ20 (r = 0.736: p < 0.05). HS relative strength (HSrel) was found to have a significant and very strong, negative relationship with LCMJ20 (r =  − 0.728: p < 0.05). Stepwise multiple linear regression analysis showed RSA180 to explain 48.4% of LCMJ20 variance (Adjusted R2 = 0.484) as the only covariate included in the model.ConclusionThe findings indicate that RSA180 as a repeated high intensity effort (RHIE) task is strongly related to LCMJ20 and is also the best predictor of LCMJ20. This may suggest that RPA can provide practitioners with information on RHIE performance. The variance between assessment methods indicates that RPA may be a distinct physical quality, future research should assess other physical capacities to better understand the factors contributing to RPA. creator: Alex O. Natera creator: Dale W. Chapman creator: Neil D. Chapman creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.16788 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Natera et al. title: A peptide encoded by the circular form of the SHPRH gene induces apoptosis in neuroblastoma cells link: https://peerj.com/articles/16806 last-modified: 2024-01-23 description: BackgroundCircular RNAs (circRNAs) and their derived peptides represent largely unchartered areas in cellular biology, with many potential roles yet to be discovered. This study aimed to elucidate the role and molecular interactions of circSHPRH and its peptide derivative SHPRH-146aa in the pathogenesis of neuroblastoma (NB).MethodsNB samples in the GSE102285 dataset were analyzed to measure circSHPRH expression, followed by in vitro experiments for validation. The role of SHPRH-146aa in NB cell proliferation, migration, and invasion was then examined, and luciferase activity assay was performed after SHPRH-146aa and RUNX1 transfection. Finally, the regulation of NB cell apoptosis by SHPRH-146aa combined with NFKBIA was tested.ResultsThe GSE102285 dataset indicated overexpression of circSHPRH in NB samples, further supported by in vitro findings. Overexpression of circ-SHPRH and SHPRH-146aa inhibited proliferation, migration, and invasion of NB cells. A significant increase in apoptosis was observed, with upregulation of Caspase-3 and downregulation of Bcl-2. Furthermore, the peptide derivative SHPRH-146aa, derived from circSHPRH, suppressed NB cell malignancy traits, suggesting its role as a therapeutic target. A direct interaction between SHPRH-146aa and the transcription factor RUNX1 was identified, subsequently leading to increased NFKBIA expression. Notably, NFKBIA knockdown inhibited the pro-apoptotic effect of SHPRH-146aa on NB cells.ConclusionThe study demonstrates that circ-SHPRH and SHPRH-146aa play significant roles in inhibiting the malignant progression of NB. They induce apoptosis primarily by modulating key apoptotic proteins Caspase-3 and Bcl-2, a process that appears to be regulated by NFKBIA. The SHPRH-146aa-RUNX1 interaction further elucidates a novel pathway in the regulation of apoptosis in NB. These findings indicate that circ-SHPRH and its derived peptide SHPRH-146aa could be potential therapeutic targets for NB treatment. creator: Jingjing Gao creator: Hong Pan creator: Jie Li creator: Jun Jiang creator: Wenxian Wang uri: https://doi.org/10.7717/peerj.16806 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gao et al. title: Vegetation restoration improved aggregation stability and aggregated-associated carbon preservation in the karst areas of Guizhou Province, southwest China link: https://peerj.com/articles/16699 last-modified: 2024-01-22 description: BackgroundThe change in the soil carbon bank is closely related to the carbon dioxide in the atmosphere, and the vegetation litter input can change the soil organic carbon content. However, due to various factors, such as soil type, climate, and plant species, the effects of vegetation restoration on the soil vary. Currently, research on aggregate-associated carbon has focused on single vegetation and soil surface layers, and the changes in soil aggregate stability and carbon sequestration under different vegetation restoration modes and in deeper soil layers remain unclear. Therefore, this study aimed to explore the differences and relationships between stability and the carbon preservation capacity (CPC) under different vegetation restoration modes and to clarify the main influencing factors of aggregate carbon preservation.MethodsGrassland (GL), shrubland (SL), woodland (WL), and garden plots (GP) were sampled, and they were compared with farmland (FL) as the control. Soil samples of 0–40 cm were collected. The soil aggregate distribution, aggregate-associated organic carbon concentration, CPC, and stability indicators, including the mean weight diameter (MWD), fractal dimension (D), soil erodibility (K), and geometric mean diameter (GMD), were measured.ResultsThe results showed that at 0–40 cm, vegetation restoration significantly increased the >2 mm aggregate proportions, aggregate stability, soil organic carbon (SOC) content, CPC, and soil erosion resistance. The >2 mm fractions of the GL and SL were at a significantly greater proportion at 0–40 cm than that of the other vegetation types but the CPC was only significantly different between 0 and 10 cm when compared with the other vegetation types (P < 0.05). The >2 mm aggregates showed a significant positive correlation with the CPC, MWD, and GMD (P < 0.01), and there was a significant negative correlation with the D and K (P < 0.05). The SOC and CPC of all the vegetation types were mainly distributed in the 0.25–2 mm and <0.25 mm aggregate fractions. The MWD, GMD, SOC, and CPC all gradually decreased with increasing soil depth. Overall, the effects of vegetation recovery on soil carbon sequestration and soil stability were related to vegetation type, aggregate particle size, and soil depth, and the GL and SL restoration patterns may be more suitable in this study area. Therefore, to improve the soil quality and the sequestration of organic carbon and reduce soil erosion, the protection of vegetation should be strengthened and the policy of returning farmland to forest should be prioritized. creator: Hui Yang creator: Hui Long creator: Xuemei Li creator: Xiulong Luo creator: Yuanhang Liao creator: Changmin Wang creator: Hua Cai creator: Yingge Shu uri: https://doi.org/10.7717/peerj.16699 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang et al. title: Regulation of lipid metabolism by APOE4 in intrahepatic cholangiocarcinoma via the enhancement of ABCA1 membrane expression link: https://peerj.com/articles/16740 last-modified: 2024-01-22 description: Intrahepatic cholangiocarcinoma (ICC) is a malignancy with a dismal prognosis, thus the discovery of promising diagnostic markers and treatment targets is still required. In this study, 1,852 differentially expressed genes (DEGs) were identified in the GSE45001 dataset for weighted gene co-expression network analysis (WGCNA), and the turquoise module was confirmed as the key module. Next, the subnetworks of the 1,009 genes in the turquoise module analyzed by MCODE, MCC, and BottleNeck algorithms identified nine overlapping genes (CAT, APOA1, APOC2, HSD17B4, EHHADH, APOA2, APOE4, ACOX1, AGXT), significantly associated with lipid metabolism pathways, such as peroxisome and cholesterol metabolism. Among them, APOE4 exhibited a potential tumor-suppressive role in ICC and high diagnostic value for ICC in both GSE45001 and GSE32879 datasets. In vitro experiments demonstrated Apolipoprotein E4 (APOE4) overexpression suppressed ICC cell proliferation, migration, and invasion, knockdown was the opposite trend. And in ICC modulated lipid metabolism, notably decreasing levels of TG, LDL-C, and HDL-C, while concurrently increasing the expressions of TC. Further, APOE4 also downregulated lipid metabolism-related genes, suggesting a key regulatory role in maintaining cellular homeostasis, and regulating the expression of the membrane protein ATP-binding cassette transporter A1 (ABCA1). These findings highlighted the coordinated regulation of lipid metabolism by APOE4 and ABCA1 in ICC progression, providing new insights into ICC mechanisms and potential therapeutic strategies. creator: Liqiang Qian creator: Gang Wang creator: Bin Li creator: Haoyuan Su creator: Lei Qin uri: https://doi.org/10.7717/peerj.16740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Qian et al. title: Association between aluminum and iron exposure in maternal blood and umbilical cord blood and congenital heart defects in children link: https://peerj.com/articles/16755 last-modified: 2024-01-22 description: BackgroundCongenital heart disease (CHDs) is the major cause of mortality from birth defects, affecting up to 1% of live births worldwide. However, the relationship between aluminum (Al) and iron (Fe) levels and the risk of CHDs has yielded inconsistent results.MethodsWe conducted a pair-matched case–control study that included 97 CHDs and 194 non-CHDs to investigate the association and interaction between Al/Fe exposure and the risk of CHDs in a birth cohort study in Lanzhou, China.ResultsHigher concentrations of cord blood Al were associated with a greater risk of total CHDs (aOR = 2.826, 95% CI [1.009–7.266]) and isolated CHDs (aOR = 10.713, 95% CI [1.017–112.851]) compared to the lowest Al level. Both in maternal blood and cord blood, a significant dose-effect was observed between Al level and total CHDs (Ptrend < 0.05), but a similar pattern was not observed for Fe. High Al in addition to high Fe appeared to elicit a stronger association with CHDs than both lowest tertile of Al and Fe level in umbilical cord blood, particularly for multiple CHDs, septal defects and patent ductus arteriosus.ConclusionsOur study suggests that exposure to Al during pregnancy (≥2,408 μg/L) is significantly associated with an increased risk of CHDs in offspring, especially septal defects, and that high levels of Al and Fe are strongly correlated with fetal heart development. Further research is needed to understand the underlying mechanisms. creator: Jing Li creator: Chunhua Zhang creator: Baohong Mao creator: Qian Liu creator: Yanxia Wang creator: Bin Yi creator: Qing Liu uri: https://doi.org/10.7717/peerj.16755 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Genome-wide identification of the MADS-box gene family in Avena sativa and its role in photoperiod-insensitive oat link: https://peerj.com/articles/16759 last-modified: 2024-01-22 description: BackgroundTraditional spring-summer sown oat is a typical long-day crop that cannot head under short-day conditions. The creation of photoperiod-insensitive oats overcomes this limitation. MADS-box genes are a class of transcription factors involved in plant flowering signal transduction regulation. Previous transcriptome studies have shown that MADS-box genes may be related to the oat photoperiod.MethodsPutative MADS-box genes were identified in the whole genome of oat. Bioinformatics methods were used to analyze their classification, conserved motifs, gene structure, evolution, chromosome localization, collinearity and cis-elements. Ten representative genes were further screened via qRT‒PCR analysis under short days.ResultsIn total, sixteen AsMADS genes were identified and grouped into nine subfamilies. The domains, conserved motifs and gene structures of all AsMADS genes were conserved. All members contained light-responsive elements. Using the photoperiod-insensitive oat MENGSIYAN4HAO (MSY4) and spring-summer sown oat HongQi2hao (HQ2) as materials, qRT‒PCR analysis was used to analyze the AsMADS gene at different panicle differentiation stages under short-day conditions. Compared with HQ2, AsMADS3, AsMADS8, AsMADS11, AsMADS13, and AsMADS16 were upregulated from the initial stage to the branch differentiation stage in MSY4, while AsMADS12 was downregulated. qRT‒PCR analysis was also performed on the whole panicle differentiation stages in MSY4 under short-day conditions, the result showed that the expression levels of AsMADS9 and AsMADS11 gradually decreased. Based on the subfamily to which these genes belong, the above results indicated that AsMADS genes, especially SVP, SQUA and Mα subfamily members, regulated panicle development in MSY4 by responding to short-days. This work provides a foundation for revealing the function of the AsMADS gene family in the oat photoperiod pathway. creator: Jinsheng Nan creator: Jianghong An creator: Yan Yang creator: Guofen Zhao creator: Xiaohong Yang creator: Huiyan Liu creator: Bing Han uri: https://doi.org/10.7717/peerj.16759 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Nan et al. title: Virtual screening of flavonoids as potential RIPK1 inhibitors for neurodegeneration therapy link: https://peerj.com/articles/16762 last-modified: 2024-01-22 description: BackgroundGlobal prevalence of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease is increasing gradually, whereas approvals of successful therapeutics for central nervous system disorders are inadequate. Accumulating evidence suggests pivotal roles of the receptor-interacting serine/threonine-protein kinase 1 (RIPK1) in modulating neuroinflammation and necroptosis. Discoveries of potent small molecule inhibitors for RIPK1 with favorable pharmacokinetic properties could thus address the unmet medical needs in treating neurodegeneration.MethodsIn a structure-based virtual screening, we performed site-specific molecular docking of 4,858 flavonoids against the kinase domain of RIPK1 using AutoDock Vina. We predicted physicochemical descriptors of the top ligands using the SwissADME webserver. Binding interactions of the best ligands and the reference ligand L8D were validated using replicated 500-ns Gromacs molecular dynamics simulations and free energy calculations.ResultsFrom Vina docking, we shortlisted the top 20 flavonoids with the highest binding affinities, ranging from −11.7 to −10.6 kcal/mol. Pharmacokinetic profiling narrowed down the list to three orally bioavailable and blood-brain-barrier penetrant flavonoids: Nitiducarpin, Pinocembrin 7-O-benzoate, and Paratocarpin J. Next, trajectories of molecular dynamics simulations of the top protein-ligand complexes were analyzed for binding interactions. The root-mean-square deviation (RMSD) was 1.191 Å (±0.498 Å), 1.725 Å (±0.828 Å), 1.923 Å (±0.942 Å), 0.972 Å (±0.155 Å) for Nitiducarpin, Pinocembrin 7-O-benzoate, Paratocarpin J, and L8D, respectively. The radius of gyration (Rg) was 2.034 nm (±0.015 nm), 2.0.39 nm (± 0.025 nm), 2.053 nm (±0.021 nm), 2.037 nm (±0.016 nm) for Nitiducarpin, Pinocembrin 7-O-benzoate, Paratocarpin J, and L8D, respectively. The solvent accessible surface area (SASA) was 159.477 nm2 (±3.021 nm2), 159.661 nm2 (± 3.707 nm2), 160.755 nm2 (±4.252 nm2), 156.630 nm2 (±3.521 nm2), for Nitiducarpin, Pinocembrin 7-O-benzoate, Paratocarpin J, and L8D complexes, respectively. Therefore, lower RMSD, Rg, and SASA values demonstrated that Nitiducarpin formed the most stable complex with the target protein among the best three ligands. Finally, 2D protein-ligand interaction analysis revealed persistent hydrophobic interactions of Nitiducarpin with the critical residues of RIPK1, including the catalytic triads and the activation loop residues, implicated in the kinase activity and ligand binding.ConclusionOur target-based virtual screening identified three flavonoids as strong RIPK1 inhibitors, with Nitiducarpin exhibiting the most potent inhibitory potential. Future in vitro and in vivo studies with these ligands could offer new hope for developing effective therapeutics and improving the quality of life for individuals affected by neurodegeneration. creator: Asim Kumar Bepari creator: Swakkhar Shatabda creator: Hasan Mahmud Reza uri: https://doi.org/10.7717/peerj.16762 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bepari et al. title: Single-cell data revealed CD14-type and FCGR3A-type macrophages and relevant prognostic factors for predicting immunotherapy and prognosis in stomach adenocarcinoma link: https://peerj.com/articles/16776 last-modified: 2024-01-22 description: BackgroundStomach adenocarcinoma (STAD) exhibits profound tumor heterogeneity and represents a great therapeutic challenge. Single-cell sequencing technology is a powerful tool to identify characteristic cell types.MethodsSingle-cell sequencing data (scRNA-seq) GSE167297 and bulk RNA-seq data from TCGA, GTEx, GSE26901 and GSE15459 database were included in this study. By downscaling and annotating the cellular data in scRNA-seq, critical cell types in tumor progression were identified by AUCell score. Relevant gene modules were then identified by weighted gene co-expression network analysis (WGCNA). A prognostic scoring system was constructed by identifying prognostic factors in STAD by Least absolute shrinkage and selection operator (LASSO) COX model. The prognosis and model performance in the RiskScore groups were measured by Kaplan-Meier (K-M) curves and Receiver operating characteristic (ROC) curves. Nomogram was drawn based on RiskScore and prognosis-related clinical factors. In addition, we evaluated patient’s feedback on immunotherapy in the RiskScore groups by TIMER, ESTIMATE and TIDE analysis. Finally, the expression levels of prognostic factors were verified in gastric cancer cell lines (MKN7 and MKN28) and human normal gastric mucosal epithelial cells (GES-1), and the effects of prognostic factors on the viability of gastric cancer cells were examined by the CCK8 assay and cell cycle.ResultsscRNA-seq analysis revealed that 11 cell types were identified, and macrophages exhibited relatively higher AUCell scores and specifically expressed CD14 and FCGR3A. High macrophage scores worsened the prognosis of STAD patients. We intersected the specifically expressed genes in macrophages subgroups (670) and macrophage module genes (2,360) obtained from WGCNA analysis. Among 86 common genes, seven prognostic factors (RGS2, GNAI2, ANXA5, MARCKS, CD36, NRP1 and PDE4A) were identified and composed a RiskScore model. Patients in low Risk group showed a better survival advantage. Nomogram also provided a favorable prediction for survival at 1, 3 and 5 years in STAD patients. Besides, we found positive feedback to immunotherapy in patients with low RiskScore. The expression tendency of the seven prognostic factors in MKN7 and MKN28 was consistent with that in the RNA-seq data in addition to comparison of protein expression levels in the public HPA (The Human Protein Atlas) database. Further functional exploration disclosed that MARCKS was an important prognostic factor in regulating cell viability in STAD.ConclusionThis study preliminary uncovered a single cell atlas for STAD patients, and Macrophages relevant gene signature and nomogram displayed favorable immunotherapy and prognostic prediction ability. Collectively, our work provides a new insight into the molecular mechanisms and therapeutic approach for LUAD patients. creator: Mengling Li creator: Ming Lu creator: Jun Li creator: Qingqing Gui creator: Yibin Xia creator: Chao Lu creator: Hongchun Shu uri: https://doi.org/10.7717/peerj.16776 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Gaining more from doing less? The effects of a one-week deload period during supervised resistance training on muscular adaptations link: https://peerj.com/articles/16777 last-modified: 2024-01-22 description: BackgroundBased on emerging evidence that brief periods of cessation from resistance training (RT) may re-sensitize muscle to anabolic stimuli, we aimed to investigate the effects of a 1-week deload interval at the midpoint of a 9-week RT program on muscular adaptations in resistance-trained individuals.MethodsThirty-nine young men (n = 29) and women (n = 10) were randomly assigned to 1 of 2 experimental, parallel groups: An experimental group that abstained from RT for 1 week at the midpoint of a 9-week, high-volume RT program (DELOAD) or a traditional training group that performed the same RT program continuously over the study period (TRAD). The lower body routines were directly supervised by the research staff while upper body training was carried out in an unsupervised fashion. Muscle growth outcomes included assessments of muscle thickness along proximal, mid and distal regions of the middle and lateral quadriceps femoris as well as the mid-region of the triceps surae. Adaptions in lower body isometric and dynamic strength, local muscular endurance of the quadriceps, and lower body muscle power were also assessed.ResultsResults indicated no appreciable differences in increases of lower body muscle size, local endurance, and power between groups. Alternatively, TRAD showed greater improvements in both isometric and dynamic lower body strength compared to DELOAD. Additionally, TRAD showed some slight psychological benefits as assessed by the readiness to train questionnaire over DELOAD.ConclusionIn conclusion, our findings suggest that a 1-week deload period at the midpoint of a 9-week RT program appears to negatively influence measures of lower body muscle strength but has no effect on lower body hypertrophy, power or local muscular endurance. creator: Max Coleman creator: Ryan Burke creator: Francesca Augustin creator: Alec Piñero creator: Jaime Maldonado creator: James P. Fisher creator: Michael Israetel creator: Patroklos Androulakis Korakakis creator: Paul Swinton creator: Douglas Oberlin creator: Brad J. Schoenfeld uri: https://doi.org/10.7717/peerj.16777 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Coleman et al. title: Prevalence of type 2 diabetes mellitus and impaired fasting glucose, and their associated lifestyle factors among teachers in the CLUSTer cohort link: https://peerj.com/articles/16778 last-modified: 2024-01-22 description: BackgroundTeachers are responsible for educating future generations and therefore play an important role in a country’s education system. Teachers constitute about 2.6% of all employees in Malaysia, making it one of the largest workforces in the country. While health and well-being are crucial to ensuring teachers’ work performance, reports on non-communicable diseases such as type 2 diabetes mellitus (T2DM) among Malaysian teachers are scarce. Hence, this study focused on the prevalence of T2DM, undiagnosed diabetes mellitus (DM), impaired fasting glucose (IFG), and underlying lifestyle factors associated with these outcomes among Malaysian teachers.MethodsThis is a cross-sectional study from the CLUSTer cohort. There were 14144 teachers from the Peninsular Malaysia included in this study. The teachers’ sociodemographic and lifestyle characteristics were described using a weighted complex analysis. A matched age group comparison was carried out between teachers and the Malaysian general population on T2DM, undiagnosed DM, and IFG status. Next, the researchers examined the association of lifestyle factors with T2DM and IFG using multivariable logistic regression.ResultsThe prevalence of T2DM, undiagnosed DM, and IFG among the Malaysian teachers were 4.1%, 5.1%, and 5.6%, respectively. The proportions of teachers with T2DM (both diagnosed and undiagnosed) and the IFG increased linearly with age. Teachers had a lower weighted prevalence of T2DM (known and undiagnosed) than the general population. However, teachers were more inclined to have IFG than the general population, particularly those aged 45 years and older. Among all lifestyle indicators, only waist circumference (aOR: 1.14, 95% CI: 1.08, 1.20) was found to be associated with T2DM, whereas waist circumference (aOR: 1.10, 95% CI: 1.05, 1.15) and physical activity [moderately active = (aOR: 0.71, 95% CI: 0.52, 0.98); highly active = (aOR: 0.56, 95% CI: 0.40, 0.80)] were associated with IFG.ConclusionsModifiable lifestyle factors such as abdominal obesity and physical activity were associated with T2DM and IFG. Intervention programs targeting these factors could help reduce future treatment costs and increase productivity. creator: Yit Han Ng creator: Foong Ming Moy creator: Noran Naqiah Hairi creator: Awang Bulgiba uri: https://doi.org/10.7717/peerj.16778 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ng et al. title: Altered O-linked glycosylation in benign and malignant meningiomas link: https://peerj.com/articles/16785 last-modified: 2024-01-22 description: BackgroundChanges in protein glycosylation have been reported in various diseases, including cancer; however, the consequences of altered glycosylation in meningiomas remains undefined. We established two benign meningioma cell lines—SUT-MG12 and SUT-MG14, WHO grade I—and demonstrated the glycan and glycosyltransferase profiles of the mucin-type O-linked glycosylation in the primary benign meningioma cells compared with two malignant meningioma cell lines—HKBMM and IOMM-Lee, WHO grade III. Changes in O-linked glycosylation profiles in malignant meningiomas were proposed.MethodsPrimary culture technique, morphological analysis, and immunocytochemistry were used to establish and characterize two benign meningioma cell lines. The glycan profiles of the primary benign and malignant meningiomas cell lines were then analyzed using lectin cytochemistry. The gene expression of O-linked glycosyltransferases, mucins, sialyltransferases, and fucosyltransferases were analyzed in benign and malignant meningioma using the GEO database (GEO series GSE16581) and quantitative-PCR (qPCR).ResultsLectin cytochemistry revealed that the terminal galactose (Gal) and N-acetyl galactosamine (GalNAc) were highly expressed in primary benign meningioma cells (WHO grade I) compared to malignant meningioma cell lines (WHO grade III). The expression profile of mucin types O-glycosyltransferases in meningiomas were observed through the GEO database and gene expression experiment in meningioma cell lines. In the GEO database, C1GALT1-specific chaperone (COSMC) and mucin 1 (MUC1) were significantly increased in malignant meningiomas (Grade II and III) compared with benign meningiomas (Grade I). Meanwhile, in the cell lines, Core 2 β1,6-N-acetylglucosaminyltransferase-2 (C2GNT2) was highly expressed in malignant meningiomas. We then investigated the complex mucin-type O-glycans structures by determination of sialyltransferases and fucosyltransferases. We found ST3 β-galactoside α-2,3-sialyltransferase 4 (ST3GAL4) was significantly decreased in the GEO database, while ST3GAL1, ST3GAL3, α1,3 fucosyltransferases 1 and 8 (FUT1 and FUT8) were highly expressed in malignant meningioma cell lines—(HKBMM)—compared to primary benign meningioma cells—(SUT-MG12 and SUT-MG14).ConclusionOur findings are the first to demonstrate the potential glycosylation changes in the O-linked glycans of malignant meningiomas compared with benign meningiomas, which may play an essential role in the progression, tumorigenesis, and malignancy of meningiomas. creator: Chutima Talabnin creator: Thanawat Trasaktaweesakul creator: Pitchanun Jaturutthaweechot creator: Pundit Asavaritikrai creator: Dusit Kongnawakun creator: Atit Silsirivanit creator: Norie Araki creator: Krajang Talabnin uri: https://doi.org/10.7717/peerj.16785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Talabnin et al. title: Deteriorated sleep quality and associate factors in patients with type 2 diabetes mellitus complicated with diabetic peripheral neuropathy link: https://peerj.com/articles/16789 last-modified: 2024-01-22 description: ObjectivesTo understand the sleep quality and its influencing factors in patients with type 2 diabetes mellitus (T2DM) who suffered diabetic peripheral neuropathy (DPN), and provide evidence for clinicians to carry out comprehensive intervention measures to improve the sleep quality of patients.MethodsPatients who were admitted to the Endocrinology Department of Affiliated Hospital of Zunyi Medical University were recruited from May to December 2022, and the investigation were conducted by face-to-face interview. The questionnaires included PSQI questionnaire and influencing factors, such as lifestyle and health status.ResultsAmong the 193 patients, 40.4% of the patients never took physical examination, 56.5% of the patients had duration of illness greater than 5 years, 61.7% of the patients had had an operation, 10.4% of the patients had bad dietary status, and 55.4% of the patients had physical pain. In addition, the PSQI general score was 8.34 ± 3.98, the occurrence rate of poor sleep quality (PSQI ≥ 8) was 54.4%, and the results showed that sleep quality of the physical pain group was worse than the no pain group. Moreover, the results of multivariate analysis revealed that the factors affecting sleep quality were lower frequency of exercise, bad dietary status, lower frequency of physical examination, longer duration of illness, and smoking, and the OR and 95% CI were [1.40, 1.04∼1.89], [3.42, 1.86∼6.29], [1.49, 1.01∼2.20], [1.78, 1.09∼2.92], [2.38, 1.17∼4.88], respectively. ConclusionPatients with DPN have higher risk of poor sleep quality. Moreover, there were many risk factors associated with poor sleep quality, clinicians and health policymakers should timely detect and effectively intervene in these factors to improve the sleep quality, which is important to enhance the quality of life of T2DM patients complicated with DPN. creator: Lin Fu creator: Liping Zhong creator: Xin Liao creator: Lingrui Wang creator: Youyi Wang creator: Xiuquan Shi creator: Yanna Zhou uri: https://doi.org/10.7717/peerj.16789 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fu et al. title: Four new complete mitochondrial genomes of Gobioninae fishes (Teleostei: Cyprinidae) and their phylogenetic implications link: https://peerj.com/articles/16632 last-modified: 2024-01-19 description: The subfamily Gobioninae is one of the most diverse fish groups within Cyprinidae. Their taxonomy and phylogenetic relationships are not completely resolved. In this study, the complete mitochondrial genomes (mitogenome) of four Gobioninae species (Microphysogobio elongatus, Microphysogobio chinssuensis, Gobio rivuloides and Rhinogobio nasutus) were sequenced and compared. The mitogenomes of four species ranges from 16603 bp to 16609 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Most PCGs had significant codon usage bias. Except for the tRNASer (GCT), all the nucleotide substitutions of tRNA loops higher than the stems could fold into a stable secondary structure. The nucleotide compositions of Gobioninae mitogenome were biased toward A/T, and NAD4 was subjected to low purification selection and had a faster evolution rate among 13 PCGs. Bayesian inference and maximum likelihood phylogenetic analyses showed the consistent results. The four sequenced species clustered together with their congener species. However, more samples and mitogenome data are needed to untangle the phylogenetic relationships among genera Microphysogobio, Romanogobio, Hugobio, Biwia and Platysmacheilus. creator: Yongtao Tang creator: Wenwen Ma creator: Xin Chen creator: Guoxing Nie creator: Chuanjiang Zhou uri: https://doi.org/10.7717/peerj.16632 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tang et al. title: Study of miRNA and lymphocyte subsets as potential biomarkers for the diagnosis and prognosis of gastric cancer link: https://peerj.com/articles/16660 last-modified: 2024-01-19 description: ObjectiveThe aim of this study was to identify the expression of miRNA and lymphocyte subsets in the blood of gastric cancer (GC) patients, elucidate their clinical significance in GC, and establish novel biomarkers for the early diagnosis and prognosis of GC.MethodsThe expression of miRNAs in the serum of GC patients was screened using second-generation sequencing and detected using qRT-PCR. The correlation between miRNA expression and clinicopathological characteristics of GC patients was analyzed, and molecular markers for predicting cancer were identified. Additionally, flow cytometry was used to detect the proportion of lymphocyte subsets in GC patients compared to healthy individuals. The correlations between differential lymphocyte subsets, clinicopathological features of GC patients, and their prognosis were analyzed statistically.ResultsThe study revealed that hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were expressed at lower levels in the blood of GC patients, which is consistent with miRNA-seq findings. The AUC values of hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were found to be effective predictors of GC occurrence. Additionally, hsa-miR-296-5p was found to be negatively correlated with CA724. Furthermore, hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were found to be associated with the stage of the disease and were closely linked to the clinical pathology of GC. The lower the levels of these miRNAs, the greater the clinical stage of the tumor and the worse the prognosis of gastric cancer patients. Finally, the study found that patients with GC had lower absolute numbers of CD3+ T cells, CD4+ T cells, CD8+ T cells, CD19+ B cells, and lymphocytes compared to healthy individuals. The quantity of CD4+ T lymphocytes and the level of the tumor marker CEA were shown to be negatively correlated. The ROC curve and multivariate logistic regression analysis demonstrated that lymphocyte subsets can effectively predict gastric carcinogenesis and prognosis.ConclusionThese miRNAs such as hsa-miR-1306-5p, hsa-miR-3173-5p, hsa-miR-296-5p and lymphocyte subsets such as the absolute numbers of CD3+ T cells, CD4+ T cells, CD8+ T cells, CD19+ B cells, lymphocytes are down-regulated in GC and are closely related to the clinicopathological characteristics and prognosis of GC patients. They may serve as new molecular markers for predicting the early diagnosis and prognosis of GC patients. creator: Jinpeng Li creator: Zixi Chen creator: Qian Li creator: Rongrong Liu creator: Jin Zheng creator: Qing Gu creator: Fenfen Xiang creator: Xiaoxiao Li creator: Mengzhe Zhang creator: Xiangdong Kang creator: Rong Wu uri: https://doi.org/10.7717/peerj.16660 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Unidirectional hybridization between American paddlefish Polyodon spathula (Walbaum, 1792) and sterlet Acipenser ruthenus (Linnaeus, 1758) link: https://peerj.com/articles/16717 last-modified: 2024-01-19 description: Interspecific hybridizations among sturgeon species are feasible and often bidirectional. The American paddlefish (Polyodon spathula) from Family Polyodontidae and sturgeon species from Family Acipenseridae were reported capable of hybridization, but viable hybrids have been described only in crosses with the American paddlefish as paternal parents. In the reciprocal cross, the hybrids were not viable however embryos start to develop and reach late gastrula and early neurula stages. The goal of this study was to examine the hybridization between the sterlet sturgeon (Acipenser ruthenus) and the American paddlefish. Hybrid and purebred crosses were produced by artificial fertilization. Viable hybrid offspring were harvested (three month old) and verified in the families produced by female sterlet crossing with male American paddlefish. In the reciprocal hybrid crosses with female American paddlefish and male sterlet, the embryos development did not pass over 120 h post fertilization, indicating the unidirectional hybridization between American paddlefish and sterlet. Chromosome counting showed for the same ploidy level of viable hybrid and parent species. Analysis of three microsatellite markers confirmed the unidirectional hybridization between the American paddlefish and the sterlet species. Overall, the inferred genetic cause suggests that unidirectional hybridization between American paddlefish and sterlet may be the case not only for these two species but likely also between American paddlefish and other sturgeon species. creator: Jenő Káldy creator: Georgina Fazekas creator: Balázs Kovács creator: Mariann Molnár creator: Bence Lázár creator: Nóra Pálinkás-Bodzsár creator: Uroš Ljubobratović creator: Gyöngyvér Fazekas creator: Gyula Kovács creator: Eszter Várkonyi uri: https://doi.org/10.7717/peerj.16717 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Káldy et al. title: SCUBE1 promotes pulmonary artery smooth muscle cell proliferation and migration in acute pulmonary embolism by modulating BMP7 link: https://peerj.com/articles/16719 last-modified: 2024-01-19 description: ObjectivesAfter an episode of acute pulmonary embolism (APE), activated platelets have the ability to release various bioactive factors that can stimulate both proliferation and migration of pulmonary artery smooth muscle cells (PASMCs). SCUBE1 has been previously reported to engage in platelet-platelet interactions, potentially contributing to the activation of platelets in early onset thrombi. The purpose of this study was to examine the alterations in SCUBE1 expression in PASMCs after APE, as well as understand the mechanism behind these changes.MethodsThe platelet-rich plasma samples of both APE patients and healthy individuals were collected. A hyperproliferative model of PASMCs was established by using platelet-derived growth factor (PDGF) as a stimulator and various assays were used to investigate how SCUBE1-mediated BMP7 can regulate PDGF-induced PASMC proliferation and migration.ResultsElevated level of SCUBE1 were observed in platelet-rich plasma from patients with APE and in PASMCs induced by PDGF. SCUBE1 interference ameliorated PDGF-driven cell proliferation and migration, and also downregulated PCNA expression. Additionally, mechanistic studies demonstrated that SCUBE1 could directly bind to bone morphogenetic protein 7 (BMP7) and enhance BMP7 expression, which completely abolished the impact of SCUBE1 silencing on proliferation and migration ability of PASMCs after PDGF treatment.ConclusionIn the PDGF-induced proliferation of PASMCs, the expression of SCUBE1 and BMP7 was upregulated. Silencing of SCUBE1 impeded PDGF-induced proliferation and migration of PASMCs by restraining BMP7. creator: Xiaoya Qu creator: Dongmei Huang creator: Xiaomin Zhou creator: Wenwen Ruan uri: https://doi.org/10.7717/peerj.16719 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Qu et al. title: Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids link: https://peerj.com/articles/16728 last-modified: 2024-01-19 description: BackgroundAs hybridization can reduce biodiversity or cause extinction, it is important to identify both purebred parental species and their hybrids prior to conserving them. The Suwon tree frog, Dryophytes suweonensis, is an endangered wildlife species in Korea that shares its habitat and often hybridizes with the Japanese tree frog, D. japonicus. In particular, D. suweonensis, D. japonicus, and their hybrids often have abnormal ovaries and gonads, which are known causes that could threaten their existence.MethodsWe collected 57 individuals from six localities where D. suweonensis is known to be present. High-resolution melting curve (HRM) analysis of the mitochondrial 12S ribosomal RNA gene was performed to determine the maternal species. Thereafter, the DNA sequences of five nuclear genes (SIAH, TYR, POMC, RAG1, and C-MYC) were analyzed to determine their parental species and hybrid status.ResultsThe HRM analysis showed that the melting temperature of D. suweonensis was in the range of 79.0–79.3 °C, and that of D. japonicus was 77.7–78.0 °C, which clearly distinguished the two tree frog species. DNA sequencing of the five nuclear genes revealed 37 single-nucleotide polymorphism (SNP) sites, and STRUCTURE analysis showed a two-group structure as the most likely grouping solution. No heterozygous position in the purebred parental sequences with Q values ≥ 0.995 were found, which clearly distinguished the two treefrog species from their hybrids; 11 individuals were found to be D. suweonensis, eight were found to be D. japonicus, and the remaining 38 individuals were found to be hybrids.ConclusionThus, it was possible to unambiguously identify the parental species and their hybrids using HRM analysis and DNA sequencing methods. This study provided fundamental information for D. suweonensis conservation and restoration research. creator: Nakyung Yoo creator: Ju-Duk Yoon creator: Jeongwoo Yoo creator: Keun-Yong Kim creator: Jung Soo Heo creator: Keun-Sik Kim uri: https://doi.org/10.7717/peerj.16728 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yoo et al. title: Validity and reliability of a repeated multi-changes of direction agility test in senior soccer players link: https://peerj.com/articles/16753 last-modified: 2024-01-19 description: BackgroundThis study aimed to evaluate the validity, reliability, and sensitivity of repeated multi-changes of direction agility test (rMCOD) compared to a soccer-specific field test of repeated sprint ability (S-RSA) and repeated sprint ability test (RSA).MethodsThirty-five healthy male soccer players (age: 18.4 ± 1.3 years) from Tunisan national soccer league (elite and sub-elite) took part in this study. They performed the tests in a randomized order over five sessions interspaced by at least 72 h. The construct, predictive and discriminant validity, relative and absolute reliability, and sensitivity of the tests were analyzed. The total and best time of the test (the sum for all trials and the trial with the lowest duration on nine, six, and seven attempts for rMCOD, RSA, and S-RSA, respectively), fatigue index, rating of perceived exertion (RPE), and lactate concentration were recorded.ResultsrMCOD correlated with both, S-RSA and RSA in total time (r = 0.85 and r = 0.52, respectively) and fatigue index (r = 0.74 and r = 0.83, respectively). Receiver operator characteristics were not able to discriminate between group levels (elite and sub-elite). When comparing training levels, only the fatigue index in S-RSA showed a difference between groups. Fatigue index, total time, and the best time in rMCOD showed excellent reliability, as well as the minimal change detectable (MCD = 0.89, MCD = 0.63, and MCD = 0.11, respectively) was higher than the standard error of the mean (SEM = 0.32, SEM = 0.23, and 0.04, respectively).ConclusionrMCOD showed large to very large predictive validity compared with the S-RSA and RSA, being a reliable test for the following parameters: the best time and total time to perform the test. Nevertheless, this study design cannot ensure whether or not this test is able to detect real changes in performance in response to training since it did not include a training intervention; besides, rMCOD could not distinguish between elite and sub-elite players, which is a limitation. creator: Mehdi Ben Brahim creator: Adrián García-Valverde creator: Hussain Yasin creator: Alejandro Sal-de-Rellán uri: https://doi.org/10.7717/peerj.16753 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Brahim et al. title: Nitrogen addition enhances seed yield by improving soil enzyme activity and nutrients link: https://peerj.com/articles/16791 last-modified: 2024-01-19 description: Nitrogen (N) addition is a simple and effective field management approach to enhancing plant productivity. Nonetheless, the regulatory mechanisms governing nitrogen concentrations and their effect on soil enzyme activity, nutrient levels, and seed yield in the Festuca kirilowii seed field have yet to be elucidated. Therefore, this study sought to investigate the effect of N fertilizer application on soil enzyme activities, soil nutrients, and seed yield of F. kirilowii Steud cv. Huanhu, the only domesticated variety in the Festuca genus of the Poaceae family, was investigated based on two-year field experiments in the Qinghai–Tibet Plateau (QTP). Results showed that N input significantly affected soil nutrients (potential of hydrogen, total nitrogen, organic matter, and total phosphorus). In addition, soil enzyme activities (urease, catalase, sucrase, and nitrate reductase) significantly increased in response to varying N concentrations, inducing changes in soil nutrient contents. Introducing N improved both seed yield and yield components (number of tillers and number of fertile tillers). These findings suggest that the introduction of different concentrations of N fertilizers can stimulate soil enzyme activity, thus hastening nutrient conversion and increasing seed yield. The exhaustive evaluation of the membership function showed that the optimal N fertilizer treatment was N4 (75 kg·hm−2) for both 2022 and 2023. This finding provides a practical recommendation for improving the seed production of F. kirilowii in QTP. creator: Wenbo Mi creator: Feng Luo creator: Wenhui Liu creator: Yan Qin creator: Yongchao Zhang creator: Kaiqiang Liu creator: Wen Li uri: https://doi.org/10.7717/peerj.16791 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mi et al. title: The significance of information variables in polydrug use by adolescents: insights from a cross-sectional study in Tarragona (Spain) link: https://peerj.com/articles/16801 last-modified: 2024-01-19 description: Substance use, especially among adolescents, is a significant public health concern, with profound implications for physical and psychological development. This study aimed to evaluate the quantity and sources of information available to adolescents regarding polydrug use. A cross-sectional survey was conducted in Tarragona involving adolescents with an average age of 16.44 years. This study assessed the number of substances used (alcohol, cigarettes, and cannabis) in the past month, along with information sources related to substance use. Monitored sources (e.g., schools, parents, and mass media) and unmonitored sources (e.g., peers, siblings, internet) were distinguished. In addition, four individual and four environmental control variables were considered. Multinomial logistic regression analysis revealed that incorporating variables related to adolescents’ substance use information and its sources enhanced the explanatory model, surpassing control variables. The degree of information about substance use did not significantly explain consumption patterns, but the number of information sources, both monitored and unmonitored, did. The unmonitored sources were associated with increased polydrug use. Conversely, greater reliance on supervised sources for information was linked to reduced single-substance and polydrug use. This protective effect increased with an increase in the number of substances used. In conclusion, information obtained from monitored sources acts as a deterrent to substance consumption, consistent with findings suggesting that greater health literacy among adolescents discourages substance use. Conversely, this study suggests that information from more informal sources may encourage heavier polydrug use, aligning with reports indicating that adolescents with a more comprehensive understanding of substance use consequences tend to engage in heavier drug use. creator: Jorge de Andrés-Sánchez creator: Angel Belzunegui-Eraso creator: Francesc Valls-Fonayet uri: https://doi.org/10.7717/peerj.16801 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 de Andrés-Sánchez et al. title: Resource partitioning among bat species in Peninsular Malaysia rice fields link: https://peerj.com/articles/16657 last-modified: 2024-01-18 description: Resource partitioning among tropical bats in agricultural areas of Peninsular Malaysia remains unclear. This study was conducted to evaluate resource partitioning among bats by examining their fecal samples. The main bat species sampled included: Rhinolophus coelophyllus, Rhinolophus malayanus, Rhinolophus pusillus, Rhinolophus refulgens, Taphozous melanopogon and Hipposideros larvatus. Two harp traps were set at different elevations on a hilltop (Gunung Keriang) and two high nets were used in neighboring rice fields at three sites, for three consecutive nights per sampling from April 2021 to February 2022. A total of 301 bats and 1,505 pellets were analyzed using a conventional approach which examined the fecal sample under the microscope. All of the bat species within the study had insects from the order Coleoptera, Lepidoptera, Diptera and Hemiptera in their diet. Larger bats exhibited a greater variety of prey consumption. Male individuals were observed to be generalists while female individuals were specialists, particularly during pregnancy and lactating reproductive stages. Bat species and insect order had a significant impact on the percentage fragment frequency of the insects consumed. Rhinolophus coelophyllus specialized in feeding on Coleoptera and Diptera, H. larvatus fed on Coleoptera, R. malayanus fed on Hemiptera, R. pusillus and T. melanopogon fed on Lepidoptera. Future molecular analysis can be carried out to further identify the insect pests consumed by these bats up to species level. These findings enhance our understanding of bats’ ecological roles in agricultural landscapes and contribute to conservation and pest management strategies. creator: Nur-Izzati Abdullah creator: Nurul-Ain Elias creator: Nobuhito Ohte creator: Christian Vincenot uri: https://doi.org/10.7717/peerj.16657 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Abdullah et al. title: Integrin-associated transcriptional characteristics of circulating tumor cells in breast cancer patients link: https://peerj.com/articles/16678 last-modified: 2024-01-18 description: BackgroundIntegrins enable cell communication with the basal membrane and extracellular matrix, activating signaling pathways and facilitating intracellular changes. Integrins in circulating tumor cells (CTCs) play a significant role in apoptosis evasion and anchor-independent survival. However, the link between CTCs expressing different integrin subunits, their transcriptional profile and, therefore, their functional activity with respect to metastatic potential remains unclear.MethodsSingle-cell RNA sequencing of CD45-negative cell fraction of breast cancer patients was performed. All CTCs were divided into nine groups according to their integrin profile.ResultsСTCs without the gene expression of integrins or with the expression of non-complementary α and β subunits that cannot form heterodimers prevailed. Only about 15% of CTCs expressed integrin subunits which can form heterodimers. The transcriptional profile of CTCs appeared to be associated with the spectrum of expressed integrins. The lowest potential activity was observed in CTCs without integrin expression, while the highest frequency of expression of tumor progression-related genes, namely genes of stemness, epithelial-mesenchymal transition (EMT), invasion, proinflammatory chemokines and cytokines as well as laminin subunits, were observed in CTCs co-expressing ITGA6 and ITGB4. Validation on the protein level revealed that the median of integrin β4+ CTCs was higher in patients with more aggressive molecular subtypes as well as in metastatic breast cancer patients. One can expect that CTCs with ITGA6 and ITGB4 expression will have pronounced metastatic potencies manifesting in expression of EMT and stemness-related genes, as well as potential ability to produce chemokine/proinflammatory cytokines and laminins. creator: Evgeniya Grigoryeva creator: Liubov Tashireva creator: Vladimir Alifanov creator: Olga Savelieva creator: Marina Zavyalova creator: Maxim Menyailo creator: Anna Khozyainova creator: Evgeny V. Denisov creator: Olga Bragina creator: Nataliya Popova creator: Nadezhda V. Cherdyntseva creator: Vladimir Perelmuter uri: https://doi.org/10.7717/peerj.16678 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Grigoryeva et al. title: Time-series analysis of meteorological factors and emergency department visits due to dog/cat bites in Jinshan area, China link: https://peerj.com/articles/16758 last-modified: 2024-01-18 description: BackgroundMeteorological factors play an important role in human health. Clarifying the occurrence of dog and cat bites (DCBs) under different meteorological conditions can provide key insights into the prevention of DCBs. Therefore, the objective of the study was to explore the relationship between meteorological factors and DCBs and to provide caution to avoid the incidents that may occur by DCBs.MethodsIn this study, data on meteorological factors and cases of DCBs were retrospectively collected at the Shanghai Climate Center and Jinshan Hospital of Fudan University, respectively, in 2016–2020. The distributed lag non-linear and time series model (DLNM) were used to examine the effect of meteorological elements on daily hospital visits due to DCBs.ResultsA total of 26,857 DCBs were collected ranging from 1 to 39 cases per day. The relationship between ambient temperature and DCBs was J-shaped. DCBs were positively correlated with daily mean temperature (rs = 0.588, P < 0.01). The relative risk (RR) of DCBs was associated with high temperature (RR = 1.450; 95% CI [1.220–1.722]). Female was more susceptible to high temperature than male. High temperature increased the risk of DCBs.ConclusionsThe extremely high temperature increased the risk of injuries caused by DCBs, particularly for females. These data may help to develop public health strategies for potentially avoiding the occurrence of DCBs. creator: Pei Pang creator: Xiaoyong Zhou creator: Yabin Hu creator: Yin Zhang creator: Baoshi He creator: Guoxiong Xu uri: https://doi.org/10.7717/peerj.16758 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pang et al. title: DoAP2/ERF89 activated the terpene synthase gene DoPAES in Dendrobium officinale and participated in the synthesis of β-patchoulene link: https://peerj.com/articles/16760 last-modified: 2024-01-18 description: Dendrobium officinale Kimura et Migo is a tonic plant that has both ornamental and medicinal properties. Terpenoids are significant and diverse secondary metabolites in plants, and are one of the important natural active ingredients in D. officinale. The AP2/ERF gene family plays a major role in primary and secondary metabolism. However, the AP2/ERF transcription factor family has not been identified in D. officinale, and it is unclear if it is involved in the regulation of terpenoid biosynthesis. This study identified a sesquiterpene synthetase-β-patchoulene synthase (DoPAES) using transcriptome and terpenic metabolic profile analyses. A total of 111 members of the AP2/ERF family were identified through the whole genome of D. officinale. The tissue-specific expression and gene co-expression pattern of the DoAP2/ERF family members were analyzed. The results showed that the expression of DoPAES was highly correlated with the expression of DoAP2/ERF89 and DoAP2/ERF47. The yeast one-hybrid (Y1H) assays and dual-luciferase experiments demonstrated that DoAP2/ERF89 and DoAP2/ERF47 could regulate the expression of DoPAES. The transcriptional regulatory effects were examined using homologous transient expression of DoAP2/ERF89 in protocorms of D. officinale. DoAP2/ERF89 positively regulated the biosynthesis of β-patchoulene. This study showed that DoAP2/ERF89 can bind to the promoter region of DoPAES to control its expression and further regulate the biosynthesis of β-patchoulene in D. officinale. These results provide new insights on the regulation of terpenoid biosynthesis. creator: Decong Li creator: Lin Liu creator: Xiaohong Li creator: Guo Wei creator: Yongping Cai creator: Xu Sun creator: Honghong Fan uri: https://doi.org/10.7717/peerj.16760 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: A systematic review of conference papers presented at two large Japanese psychology conferences in 2013 and 2018: did Japanese social psychologists selectively report p < 0.05 results without peer review? link: https://peerj.com/articles/16763 last-modified: 2024-01-18 description: We conducted a systematic review of conference papers in social psychology at two large psychology conferences in Japan: the Japanese Psychological Association and the Japanese Society for Social Psychology. The conference papers were effectively not subjected to peer review; hence, they were suitable for testing if psychologists selectively reported statistically significant findings without pressure from journal editors and reviewers. We investigated the distributions of z-values converted from the p-values reported in the articles presented at the 2013 and 2018 conferences. The z-curve analyses suggest the existence of selective reporting by the authors in 2013. The expected discovery rate (EDR) was much lower than the observed discovery rate (ODR; 7% vs. 76%, respectively), and the 95% confidence interval (CI) did not include the ODR. However, this does not mean that the set of studies completely lacked evidential value. The expected replication rate (ERR) was 31%; this is significantly higher than 5%, which was expected under the null hypothesis of no effect. Changes were observed between 2013 and 2018. The ERR increased (31% to 44%), and the EDR almost doubled (7% to 13%). However, the estimation of the maximum false discovery rate (FDR; 68% in 2013 and 35% in 2018) suggested that a substantial proportion of the reported findings were false positives. Overall, while social psychologists in Japan engaged in selective reporting, this does not mean that the entire field was covered with false positives. In addition, slight signs of improvement were observed in how they reported their findings. Still, the evidential value of the target studies was weak, even in 2018, allowing for no optimism. creator: Kai Hiraishi creator: Asako Miura creator: Masataka Higuchi creator: Yoshitsugu Fujishima creator: Daiki Nakamura creator: Masaki Suyama uri: https://doi.org/10.7717/peerj.16763 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hiraishi et al. title: Relationship between perceptual and mechanical markers of fatigue during bench press and bench pull exercises: impact of inter-set rest period length link: https://peerj.com/articles/16754 last-modified: 2024-01-17 description: This study aimed to explore whether the relationship between perceptual (rating of perceived exertion; RPE) and mechanical (maximal number of repetitions completed [MNR], fastest set velocity, and mean velocity decline) variables is affected by the length of inter-set rest periods during resistance training sets not leading to failure. Twenty-three physically active individuals (15 men and eight women) randomly completed 12 testing sessions resulting from the combination of two exercises (bench press and bench pull), three inter-set rest protocols (1, 3, and 5 min), and two minimal velocity thresholds (farther from muscular failure [MVT0.45 for bench press and MVT0.65 for bench pull] and closer to muscular failure [MVT0.35 for bench press and MVT0.55 for bench pull]). The duration of inter-set rest periods did not have a significant impact on RPE values (p ranged from 0.061 to 0.951). Higher proximities to failure, indicated by lower MVTs, were associated with increased RPE values (p < 0.05 in 19 out of 24 comparisons). Moreover, as the number of sets increased, an upward trend in RPE values was observed (p < 0.05 in seven out of 12 comparisons). Finally, while acknowledging some inconsistencies, it was generally observed that higher magnitudes of the mechanical variables, especially MNR (rs < −0.55 in three out of four comparisons), were associated with lower RPE values. These results, which were comparable for the bench press and bench pull exercises, suggest that post-set RPE values are affected by the fatigue experienced at both the beginning and end of the set. creator: Danica Janicijevic creator: Sergio Miras-Moreno creator: Maria Dolores Morenas-Aguilar creator: Pablo Jiménez-Martínez creator: Carlos Alix-Fages creator: Amador García-Ramos uri: https://doi.org/10.7717/peerj.16754 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Janicijevic et al. title: Transcriptome analysis of green and purple fruited pepper provides insight into novel regulatory genes in anthocyanin biosynthesis link: https://peerj.com/articles/16792 last-modified: 2024-01-17 description: BackgroundPepper (Capsicum annuum L.) is a valuable horticultural crop with economic significance, and its purple fruit color is attributed to anthocyanin, a phytonutrient known for its health-promoting benefits. However, the mechanisms regulating anthocyanin biosynthesis in pepper have yet to be fully elucidated.MethodsRNA sequencing (RNA-seq) was utilized to analyze the transcriptome of fruits from three purple-fruited varieties (HN191, HN192, and HN005) and one green-fruited variety (EJT) at various developmental stages. To determine the relationships between samples, Pearson correlation coefficients (PCC) and principal component analysis (PCA) were calculated. Differential expression analysis was performed using the DESeq2 package to identify genes that were expressed differently between two samples. Transcription factors (TF) were predicted using the iTAK program. Heatmaps of selected genes were generated using Tbtools software.ResultsThe unripe fruits of HN191, HN192, and HN005, at the stages of 10, 20, and 30 days after anthesis (DAA), display a purple color, whereas the unripe fruits of variety EJT remain green. To understand the molecular basis of this color difference, five transcriptome comparisons between green and purple fruits were conducted: HN191-10 vs EJT-10, HN191-20 vs EJT-20, HN191-30 vs EJT-30, HN192-30 vs EJT-30, and HN005-30 vs EJT-30. Through this analysis, 503 common differentially expressed genes (DEGs) were identified. Among these DEGs, eight structural genes related to the anthocyanin biosynthesis pathway and 24 transcription factors (TFs) were detected. Notably, one structural gene (MSTRG.12525) and three TFs (T459_25295, T459_06113, T459_26036) exhibited expression patterns that suggest they may be novel candidate genes involved in anthocyanin biosynthesis. These results provide new insights into the regulation of anthocyanin biosynthesis in purple pepper fruit and suggest potential candidate genes for future genetic improvement of pepper germplasm with enhanced anthocyanin accumulation. creator: Huaqiang Tan creator: Liping Li creator: Manman Tie creator: Ronghai Lu creator: Shaokun Pan creator: Youwan Tang uri: https://doi.org/10.7717/peerj.16792 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tan et al. title: Prognostic significance of integrating total metabolic tumor volume and EGFR mutation status in patients with lung adenocarcinoma link: https://peerj.com/articles/16807 last-modified: 2024-01-17 description: BackgroundThe objective of this study was to investigate the prognostic significance of total metabolic tumor volume (TMTV) derived from baseline 18F-2-fluoro-2-deoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT), in conjunction with epidermal growth factor receptor (EGFR) mutation status, among patients with lung adenocarcinoma (LUAD).MethodsWe performed a retrospective analysis on 141 patients with LUAD (74 males, 67 females, median age 67 (range 34–86)) who underwent 18F-FDG PET/CT and had their EGFR mutation status determined. Optimal cutoff points for TMTV were determined using time-dependent receiver operating characteristic curve analysis. The survival difference was compared using Cox regression analysis and Kaplan‒Meier curves.ResultsThe EGFR mutant patients (n = 79, 56.0%) exhibited significantly higher 2-year progression-free survival (PFS) and overall survival (OS) rates compared to those with EGFR wild-type (n = 62, 44.0%), with rates of 74.2% vs 69.2% (P = 0.029) and 86.1% vs 67.7% (P = 0.009), respectively. The optimal cutoff values of TMTV were 36.42 cm3 for PFS and 37.51 cm3 for OS. Patients with high TMTV exhibited significantly inferior 2-year PFS and OS, with rates of 22.4% and 38.1%, respectively, compared to those with low TMTV, who had rates of 85.8% and 95.0% (both P < 0.001). In both the EGFR mutant and wild-type groups, patients exhibiting high TMTV demonstrated significantly inferior 2-year PFS and OS compared to those with low TMTV. In multivariate analysis, EGFR mutation status (hazard ratio, HR, 0.41, 95% confidence interval, CI [0.18–0.94], P = 0.034) and TMTV (HR 8.08, 95% CI [2.34–28.0], P < 0.001) were independent prognostic factors of OS, whereas TMTV was also an independent prognosticator of PFS (HR 2.59, 95% CI [1.30–5.13], P = 0.007).ConclusionOur study demonstrates that the integration of TMTV on baseline 18F-FDG PET/CT with EGFR mutation status improves the accuracy of prognostic evaluation for patients with LUAD. creator: Maoqing Jiang creator: Xiuyu Guo creator: Ping Chen creator: Xiaohui Zhang creator: Qiaoling Gao creator: Jingfeng Zhang creator: Jianjun Zheng uri: https://doi.org/10.7717/peerj.16807 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jiang et al. title: Carotenoid-dependent singlet oxygen photogeneration in light-harvesting complex 2 of Ectothiorhodospira haloalkaliphila leads to the formation of organic hydroperoxides and damage to both pigments and protein matrix link: https://peerj.com/articles/16615 last-modified: 2024-01-16 description: Earlier, it was suggested that carotenoids in light-harvesting complexes 2 (LH2) can generate singlet oxygen, further oxidizing bacteriochlorophyll to 3-acetyl-chlorophyll. In the present work, it was found that illumination of isolated LH2 preparations of purple sulfur bacterium Ectothiorhodospira haloalkaliphila with light in the carotenoid absorption region leads to the photoconsumption of molecular oxygen, which is accompanied by the formation of hydroperoxides of organic molecules in the complexes. Photoformation of two types of organic hydroperoxides were revealed: highly lipophilic (12 molecules per one LH2) and relatively hydrophobic (68 per one LH2). It has been shown that illumination leads to damage to light-harvesting complexes. On the one hand, photobleaching of bacteriochlorophyll and a decrease in its fluorescence intensity are observed. On the other hand, the photoinduced increase in the hydrodynamic radius of the complexes, the reduction in their thermal stability, and the change in fluorescence intensity indicate conformational changes occurring in the protein molecules of the LH2 preparations. Inhibition of the processes described above upon the addition of singlet oxygen quenchers (L-histidine, Trolox, sodium L-ascorbate) may support the hypothesis that carotenoids in LH2 preparations are capable of generating singlet oxygen, which, in turn, damage to protein molecules. creator: Denis Yanykin creator: Mark Paskhin creator: Aleksandr Aleksandrovich Ashikhmin creator: Maxim Alexandrovich Bolshakov uri: https://doi.org/10.7717/peerj.16615 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yanykin et al. title: Effects of fertilizer application on the growth of Stranvaesia davidiana D. seedlings link: https://peerj.com/articles/16721 last-modified: 2024-01-16 description: Wild plants represent a potential source of urban landscape trees. Stranvaesia davidiana Dcne. is a member of the Stranvaesia Lindl. Genus, which belongs to family Rosaceae Juss. It has great ornamental value. It can contribute to urban color foliage and fruit species. However, the most effective fertilizer application strategy required for its cultivation is unknown. Therefore, we conducted an orthogonal experiment to investigate the fertilizer type and level (pure nitrogen) using ten experimental groups, including an untreated control group. Pot experiments were used to determine the growth indices of seedlings, including plant height, basal diameter, and chlorophyll content post-fertilizer treatment. This study explored the most appropriate fertiler application model for the growth of S. davidiana seedlings. The results revealed that enhanced seedling growth depended on the type and amount of fertilizer used, and their interaction. Fertilizer application increased the plant height by 2.67 cm to 12.26 cm, basal diameter by 0.39 cm to 0.75 cm, and chlorophyll content by 5.66 to 19.86. Among the different types of fertilizer, organic fertilizer increased the plant height by 0.42 cm to 9.59 cm and basal diameter by 0.01 cm to 0.05 cm, compared with the control group. Organic fertilizer had the maximum effect on seedling growth, especially at medium levels. The total growth of basal diameter and chlorophyll content was 1.58 ± 0.04 cm and 39.53 ± 2.37, respectively. Basal diameter is the most critical index in seedling reproduction . The study results suggest that the application of 4.06 g of organic fertilizer per plant was the most effective, and served as a basis for further field trials. creator: Xue-Man Wang creator: Yu-Tong Zhu creator: Juan Wang creator: Shi-Hui Wang creator: Wen-Qian Bai creator: Zhi-Fei Wang creator: Wan-Qing Zeng creator: Pei-Hao Peng uri: https://doi.org/10.7717/peerj.16721 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: neo4jsbml: import systems biology markup language data into the graph database Neo4j link: https://peerj.com/articles/16726 last-modified: 2024-01-16 description: Systems Biology Markup Language (SBML) has emerged as a standard for representing biological models, facilitating model sharing and interoperability. It stores many types of data and complex relationships, complicating data management and analysis. Traditional database management systems struggle to effectively capture these complex networks of interactions within biological systems. Graph-oriented databases perform well in managing interactions between different entities. We present neo4jsbml, a new solution that bridges the gap between the Systems Biology Markup Language data and the Neo4j database, for storing, querying and analyzing data. The Systems Biology Markup Language organizes biological entities in a hierarchical structure, reflecting their interdependencies. The inherent graphical structure represents these hierarchical relationships, offering a natural and efficient means of navigating and exploring the model’s components. Neo4j is an excellent solution for handling this type of data. By representing entities as nodes and their relationships as edges, Cypher, Neo4j’s query language, efficiently traverses this type of graph representing complex biological networks. We have developed neo4jsbml, a Python library for importing Systems Biology Markup Language data into a Neo4j database using a user-defined schema. By leveraging Neo4j’s graphical database technology, exploration of complex biological networks becomes intuitive and information retrieval efficient. Neo4jsbml is a tool designed to import Systems Biology Markup Language data into a Neo4j database. Only the desired data is loaded into the Neo4j database. neo4jsbml is user-friendly and can become a useful new companion for visualizing and analyzing metabolic models through the Neo4j graphical database. neo4jsbml is open source software and available at https://github.com/brsynth/neo4jsbml. creator: Guillaume Gricourt creator: Thomas Duigou creator: Sandra Dérozier creator: Jean-Loup Faulon uri: https://doi.org/10.7717/peerj.16726 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gricourt et al. title: Reversal of cholestatic liver disease by the inhibition of sphingosine 1-phosphate receptor 2 signaling link: https://peerj.com/articles/16744 last-modified: 2024-01-16 description: AimsThe objective of this study is to examine the impact of inhibiting Sphingosine 1-phosphate receptor 2 (S1PR2) on liver inflammation, fibrogenesis, and changes of gut microbiome in the context of cholestasis-induced conditions.MethodsThe cholestatic liver injury model was developed by common bile duct ligation (CBDL). Sprague-Dawley rats were randomly allocated to three groups, sham operation, CBDL group and JTE-013 treated CBDL group. Biochemical and histological assessments were conducted to investigate the influence of S1PR2 on the modulation of fibrogenic factors and inflammatory infiltration. We conducted an analysis of the fecal microbiome by using 16S rRNA sequencing. Serum bile acid composition was evaluated through the utilization of liquid chromatography-mass spectrometry techniques.ResultsIn the BDL rat model, the study findings revealed a significant increase in serum levels of conjugated bile acids, accompanied by an overexpression of S1PR2. Treatment with the specific inhibitor of S1PR2, known as JTE-013, resulted in a range of specific effects on the BDL rats. These effects included the improvement of liver function, reduction of liver inflammation, inhibition of hepatocyte apoptosis, and suppression of NETosis. These effects are likely mediated through the TCA/S1PR2/NOX2/NLRP3 pathway. Furthermore, the administration of JTE-013 resulted in an augmentation of the diversity of the bacterial community’s diversity, facilitating the proliferation of advantageous species while concurrently inhibiting the prevalence of detrimental bacteria.ConclusionsThe results of our study suggest that the administration of JTE-013 may have a beneficial effect in alleviating cholestatic liver disease and restoring the balance of intestinal flora. creator: Huiling Cao creator: Lin Chen creator: Ziyang Zeng creator: Xianfeng Wu creator: Yuhao Lei creator: Wen Jia creator: Guang Yue creator: Bin Yi creator: Yu-jie Li creator: Yuan Shi uri: https://doi.org/10.7717/peerj.16744 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cao et al. title: Effects of restoration years on soil nitrogen and phosphorus in inland salt marshes link: https://peerj.com/articles/16766 last-modified: 2024-01-16 description: Inland salt marsh wetlands have very important ecological functions in semi-arid areas. However, degradation and soil desertification have impacted these areas, making it necessary to study the impact of wetland restoration years on the soil quality of salt marsh wetland. We used remote sensing methods, field surveys, and inquiries to examine the seasonal profile effects of two-, four-, and six-year restoration periods on total nitrogen (TN), total phosphorus (TP) and the ratio of nitrogen to phosphorus (N:P) in P. australis and S. triqueter wetland natural states. Our results showed that soil TN in P. australis wetland in restored conditions was higher than that in natural conditions. The average soil TP of the S. triqueter wetlands at 0–10 cm, 10–20 cm, 20–30 cm, and 30–40 cm layers was 0.36 g/kg, 0.31 g/kg, 0.21 g/kg, and 0.17 g/kg s in September, respectively. The soil TP of the S. triqueter wetland increased slightly over the entire growing season. The restoration years had a great influence on the soil TP of the S. triqueter wetland from May to July. The soil TN in the P. australis wetland was almost restored to its natural condition in each layer during the six-year restoration period. The soil TP of the S. triqueter wetland was higher in the restored two-year period and showed a decreasing trend with an increased soil depth. Our conclusions can significantly guide the restoration of inland salt marsh wetlands. creator: Dandan Zhao creator: Daiji Wan creator: Jian Yang creator: Jiping Liu creator: Zhicheng Yong creator: Chongya Ma uri: https://doi.org/10.7717/peerj.16766 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al. title: GSDMD suppresses keratinocyte differentiation by inhibiting FLG expression and attenuating KCTD6-mediated HDAC1 degradation in atopic dermatitis link: https://peerj.com/articles/16768 last-modified: 2024-01-16 description: BackgroundRecent studies have shown that activated pyroptosis in atopic dermatitis (AD) switches inflammatory processes and causes abnormal cornification and epidermal barrier dysfunction. Little research has focused on the interaction mechanism between pyroptosis-related genes and human keratinocyte differentiation.MethodsThe AD dataset from the Gene Expression Omnibus (GEO) was used to identify differently expressed pyroptosis-related genes (DEPRGs). Hub genes were identified and an enrichment analysis was performed to select epithelial development-related genes. Lesions of AD patients were detected via immunohistochemistry (IHC) to verify the hub gene. Human keratinocytes cell lines, gasdermin D (GSDMD) overexpression, Caspase1 siRNA, Histone Deacetylase1 (HDAC1) siRNA, and HDAC1 overexpression vectors were used for gain-and-loss-of-function experiments. Regulation of cornification protein was determined by qPCR, western blot (WB), immunofluorescence (IF), dual-luciferase reporter assay, co-immunoprecipitation (Co-IP), and chromatin immunoprecipitation (ChIP).ResultsA total of 27 DEPRGs were identified between either atopic dermatitis non-lesional skin (ANL) and healthy control (HC) or atopic dermatitis lesional skin (AL) and HC. The enrichment analysis showed that these DEPRGs were primarily enriched in the inflammatory response and keratinocytes differentiation. Of the 10 hub genes identified via the protein-protein interaction network, only GSDMD was statistically and negatively associated with the expression of epithelial tight junction core genes. Furthermore, GSDMD was upregulated in AD lesions and inhibited human keratinocyte differentiation by reducing filaggrin (FLG) expression. Mechanistically, GSDMD activated by Caspase1 reduced FLG expression via HDAC1. HDAC1 decreased FLG expression by reducing histone acetylation at the FLG promoter. In addition, GSDMD blocked the interaction of Potassium Channel Tetramerization Domain Containing 6 (KCTD6) and HDAC1 to prohibit HDAC1 degradation.ConclusionThis study revealed that GSDMD was upregulated in AD lesions and that GSDMD regulated keratinocytes via epigenetic modification, which might provide potential therapeutic targets for AD. creator: Yi Zhong creator: Taoyuan Huang creator: Xiaoli Li creator: Peiyi Luo creator: Bingjun Zhang uri: https://doi.org/10.7717/peerj.16768 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhong et al. title: Transcriptome analysis of Chinese mitten crabs (Eriocheir sinensis) gills in response to ammonia stress link: https://peerj.com/articles/16786 last-modified: 2024-01-16 description: The Chinese mitten crab (Eriocheir sinensis) is an important commercial species in China. E. sinensis is typically farmed in rice-crab symbiosis, as an important ecological farming model. However, E. sinensis is often exposed to a high ammonia environment due to the application of nitrogen fertilizers essential for rice growth. We investigated the molecular mechanisms in the gills of E. sinensis exposed to high ammonia at transcriptional and histological levels. We randomly assigned E. sinensis to two groups (control group, CG; ammonia stress group, AG), and gill samples were excised from the CG and AG groups for histopathological and transcriptome analyses. The histopathological evaluation revealed that ammonia stress damaged the gills of E. sinensis. The transcriptome analysis showed that some essential genes, including Xanthine dehydrogenase (XDH), Ubiquitin C-terminal hydrolase-L3 (UCHL3), O-linked N-acetylglucosamine transferase (OGT), Cathepsin B (CTSB), and Ubiquitin-conjugating enzyme E2 W (UBE2W) changed significantly during ammonia exposure. These genes are related to ammonia detoxification, the immune response, and apoptosis. This study demonstrated the molecular response mechanism of E. sinensis gills to ammonia stress at the transcriptional and histological levels. This study provides insight for further study on the molecular mechanism of ammonia stress in crustaceans and supplies technical support for rice crab symbiosis. creator: Zhengfei Wang creator: Yue Wang creator: Yayun Guan creator: Zhuofan Chen creator: Yaotong Zhai creator: Ya Wu creator: Ying Zhou creator: Jinghao Hu creator: Lulu Chen uri: https://doi.org/10.7717/peerj.16786 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: A novel non-invasive nociceptive monitoring approach fit for intracerebral surgery: a retrospective analysis link: https://peerj.com/articles/16787 last-modified: 2024-01-16 description: BackgroundMeasuring depth of anesthesia during intracerebral surgery is an important task to guarantee patient safety, especially while the patient is fixated in a Mayfield-clamp. Processed electro-encephalography measurements have been established to monitor deep sedation. However, visualizing nociception has not been possible until recently and has not been evaluated for the neurosurgical setting. In this single-center, retrospective observational analysis, we routinely collected the nociceptive data via a nociception level monitor (NOL®) of 40 patients undergoing intracerebral tumor resection and aimed to determine if this monitoring technique is feasible and delivers relevant values to potentially base therapeutic decisions on.MethodsForty patients (age 56 ± 18 years) received total intravenous anesthesia and were non-invasively connected to the NOL®via a finger clip as well as a bispectral-index monitoring (BIS®) to confirm deep sedation. The measured nociception levels were retrospectively evaluated at specific time points of nociceptive stress (intubation, Mayfield-positioning, incision, extubation) and compared to standard vital signs.ResultsNociceptive measurements were successfully performed in 35 patients. The largest increase in nociceptive stimulation occurred during intubation (NOL® 40 ± 16) followed by Mayfield positioning (NOL® 39 ± 16) and incision (NOL® 26 ± 12). Correlation with BIS measurements confirmed a sufficiently deep sedation during all analyzed time points (BIS 45 ± 13). Overall, patients showed an intraoperative NOL® score of 10 or less in 56% of total intervention time.ConclusionsNociceptive monitoring using the NOL® system during intracerebral surgery is feasible and might yield helpful information to support therapeutic decisions. This could help to reduce hyperanalgesia, facilitating shorter emergence periods and less postoperative complications. Prospective clinical studies are needed to further examine the potential benefits of this monitoring approach in a neurosurgical context.Trial registrationGerman trial registry, registration number DRKS00029120. creator: Robert Ruemmler creator: Veselina Moravenova creator: Sandy Al-Butmeh creator: Kimiko Fukui-Dunkel creator: Eva-Verena Griemert creator: Alexander Ziebart uri: https://doi.org/10.7717/peerj.16787 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ruemmler et al. title: XYA-2: a marine-derived compound targeting apoptosis and multiple signaling pathways in pancreatic cancer link: https://peerj.com/articles/16805 last-modified: 2024-01-16 description: BackgroundPancreatic cancer is a highly aggressive and fatal disease with limited treatment options and poor prognosis for patients. This study aimed to investigate the impact of XYA-2 {N-(3,7-dimethyl-2,6-octadienyl)-2-aza-2-deoxychaetoviridin A}, a nitrogenated azaphilon previously reported from a deep-sea-derived fungus on the progression of pancreatic cancer cells.MethodsThe inhibitory effects of XYA-2 on cell proliferation, clonogenic potential, cell cycle progression, apoptosis, migration, and invasion were assessed using various assays. The CCK-8 assay, clone formation assay, flow cytometry assay, wound healing assay, and transwell assay were employed to evaluate cell proliferation, clonogenic potential, cell cycle progression, apoptosis, migration, and invasion, respectively. Moreover, we employed RNA-seq and bioinformatics analyses to uncover the underlying mechanism by which XYA-2 influences pancreatic cancer cells. The revealed mechanism was subsequently validated through qRT-PCR.ResultsOur results demonstrated that XYA-2 dose-dependently inhibited the proliferation of pancreatic cancer cells and induced cell cycle arrest and apoptosis. Additionally, XYA-2 exerted a significant inhibitory effect on the invasion and migration of cancer cells. Moreover, XYA-2 was found to regulate the expression of genes involved in multiple cancer-related pathways based on our RNA-seq and bioinformatics analysis.ConclusionThese findings highlight the potential of XYA-2 as a promising therapeutic option for the treatment of pancreatic cancer. creator: Xiaoqing Guan creator: Yun Li creator: Xiaodan Guan creator: Linfei Fan creator: Jieer Ying uri: https://doi.org/10.7717/peerj.16805 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guan et al. title: Growth type and relative condition factor as a function of the body shape of deep-water crustaceans in the Colombian Caribbean Sea link: https://peerj.com/articles/16583 last-modified: 2024-01-15 description: Length-weight relationships (LWR) and relative condition factor were described for species of deep-water crustaceans caught with bottom trawls in a depth range between 150 and 535 m during August and December of 2009, and March and May of 2010 in the Colombian Caribbean Sea. A linear regression was performed using the logarithmically transformed data to calculate the a and b coefficients of the LWR for 22 crustacean species corresponding to 13 families and 19 genera and three types of crustaceans (shrimp, crab, lobster). Six crustacean species showed a maximum total length greater than that reported in SeaLifeBase: Garymunida longipes (77.00 mm), Eunephrops bairdii (220.00 mm), Metanephrops binghami (197.46 mm), Penaeopsis serrata (149.00 mm), Polycheles typhlops (196.27 mm) and Pleoticus robustus (240.00 mm). A total of 11 species (50.0%) exhibited isometric growth, five species (22.7%) negative allometric and six species (27.3%) positive allometric. This study shows the first estimates of LWR for 12 species of deep-water crustaceans in the Colombian Caribbean Sea. We demonstrate for the first time that the growth parameters (intercept and slope) of the LWR varying significantly as a function of the body shape of crabs, lobsters and shrimps in deep-water crustaceans. creator: Jorge Paramo creator: Alfredo Rodriguez creator: Camilo Quintana uri: https://doi.org/10.7717/peerj.16583 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Paramo et al. title: Impact of online learning on physical activity during COVID-19 lockdown period among female undergraduate students in Saudi Arabia: a cross-sectional study link: https://peerj.com/articles/16579 last-modified: 2024-01-15 description: BackgroundDuring early 2020, because of the COVID-19 pandemic and related lockdown, most education systems—including universities—shifted from face-to-face classes to online learning. In Saudi Arabia, this might have contributed to a decreased level of physical activity (PA) and a concurrent increase in sedentary behaviour among young adults. This study aimed to investigate the impact of online learning on PA during the COVID-19 lockdown period among female undergraduate students in Saudi Arabia.MethodsData were collected through an online survey administered to participants. It consisted of three sections including demographic information, participants’ perception towards online learning and PA, and PA level using the self-reported active-questionnaire survey tool. The association between online learning and PA was measured using linear regression. The statistical significance was set at P < 0.05.ResultsA total of 197 female undergraduate students were included; 95.4% of them were aged 18–24 years old, and 59.9% were in the normal body mass index range (18.5–24.9 kg/m2). In terms of PA level, 55.3% were highly active, 33.5% were moderately active and 10.1% were low-active. In terms of students’ perception of engaging in PA, 53.3% of students reported that engaging in PA definitely affected their psychological status. Moreover, compared with those attending <25 hours/week of online learning, those who attended >30 hours/week had lower PA (r =  − 363.24; 95% confidence interval (CI) −593.97, −132.50), followed by those attending 25–30 hours/week (r =  − 277.66; 95% CI −484.65, −70.66).ConclusionOnline learning has negatively affected the PA level of female undergraduate students in Saudi Arabia during the COVID-19 lockdown period, in a dose-dependent manner. Moreover, this might affect their phycological status. Nevertheless, future studies are warranted to further investigate the relationship between PA level and psychological status. creator: Rania Almeheyawi creator: Alaa Alsini creator: Bayadir Aljadrawi creator: Layan Alshehri creator: Rawan Algethami creator: Razan Althobaiti creator: Ahlam Alrubeai creator: Hosam Alzahrani creator: Fahad Alshehri creator: Yousef Alshehre uri: https://doi.org/10.7717/peerj.16579 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Almeheyawi et al. title: Distribution and demographics of mysids (Crustacea: Mysida) as prey for gray whales (Eschrichtius robustus) in northwest Washington state link: https://peerj.com/articles/16587 last-modified: 2024-01-15 description: BackgroundThe movement and distribution of gray whales (Eschrichtius robustus) during the feeding season is likely dependent on the quality of foraging opportunities and the distribution of prey species. These dynamics are especially important to understand for the Pacific Coast Feeding Group (PCFG) of gray whales which spend the feeding season along the coast from northern California, USA through northern British Columbia, Canada. In Washington state, no previous work has been done to describe available gray whale prey. The main goal of this research was to initiate studies on an important gray whale prey item in northwest Washington, mysid shrimp (Mysida), by establishing a baseline understanding of mysid swarm demographics in the area and investigating patterns in gray whale and mysid presence.MethodsPrey samples were collected during June through November 2019 and June through September 2020 using a vertically-towed plankton net at seven sites in the Strait of Juan de Fuca and seven sites in the Pacific Ocean in areas where gray whales were known to feed. Mysids collected in the samples were counted and the sex, length, species, maturity, and gravidity were documented. Patterns in gray whale and mysid co-occurrence were explored through data visualization.ResultsSeven species of mysids were observed in the survey area. In 2019, the number of mysids per tow increased steadily through the season, the most abundant species of mysids were Holmesimysis sculpta and Neomysis rayii, and sampled mysids averaged 4.7 mm in length. In 2020, mysids were abundant in tow samples in June and July but were not abundant in the remaining months of the sampling season. The average length of mysids in 2020 was 13.3 mm, and a large portion were sexually mature males and brooded females identified as H. sculpta. Throughout the survey area, the majority of whale sightings occurred later in the season in 2019 and earlier in the season in 2020, coinciding with the trends of sampled mysids.DiscussionThis study provides the first description of mysid swarm composition and temporal variation in northwest Washington. Tows were dominated by a similar assemblage of mysid species as what is observed in other areas of the PCFG range. The differences in sampled mysid assemblages between years, and the presence of whales in the survey area in times and at sites where samples with high mysid counts were collected, suggest evidence for interesting predator-prey dynamics that warrant further investigation. creator: Elizabeth Marina Allyn creator: Jonathan J. Scordino creator: Adrianne M. Akmajian uri: https://doi.org/10.7717/peerj.16587 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Allyn et al. title: Antimalarial target vulnerability of the putative Plasmodium falciparum methionine synthase link: https://peerj.com/articles/16595 last-modified: 2024-01-15 description: BackgroundPlasmodium falciparum possesses a cobalamin-dependent methionine synthase (MS). MS is putatively encoded by the PF3D7_1233700 gene, which is orthologous and syntenic in Plasmodium. However, its vulnerability as an antimalarial target has not been assessed.MethodsWe edited the PF3D7_1233700 and PF3D7_0417200 (dihydrofolate reductase-thymidylate synthase, DHFR-TS) genes and obtained transgenic P. falciparum parasites expressing epitope-tagged target proteins under the control of the glmS ribozyme. Conditional loss-of-function mutants were obtained by treating transgenic parasites with glucosamine.ResultsDHFR-TS, but not MS mutants showed a significant proliferation defect over 96 h, suggesting that P. falciparum MS is not a vulnerable antimalarial target. creator: Nirut Leela creator: Parichat Prommana creator: Sumalee Kamchonwongpaisan creator: Tana Taechalertpaisarn creator: Philip J. Shaw uri: https://doi.org/10.7717/peerj.16595 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Leela et al. title: A simulation study evaluating how population survival and genetic diversity in a newly established population can be affected by propagule size, extinction rates, and initial heterozygosity link: https://peerj.com/articles/16628 last-modified: 2024-01-15 description: The introduction and establishment of invasive species in regions outside their native range, is one of the major threats for the conservation of ecosystems, affecting native organisms and the habitat where they live in, causing substantial biological and monetary losses worldwide. Due to the impact of invasive species, it is important to understand what makes some species more invasive than others. Here, by simulating populations using a forward-in-time approach combining ecological and single polymorphic nucleotides (SNPs) we evaluated the relation between propagule size (number of individuals = 2, 10, 100, and 1,000), extinction rate (with values 2%, 5%, 10%, and 20%), and initial heterozygosity (0.1, 0.3, and 0.5) on the population survival and maintenance of the heterozygosity of a simulated invasive crab species over 30 generations assuming a single introduction. Our results revealed that simulated invasive populations with initial propagule sizes of 2–1,000 individuals experiencing a high extinction rate (10–20% per generation) were able to maintain over 50% of their initial heterozygosity during the first generations and that under scenarios with lower extinction rates invasive populations with initial propagule sizes of 10–1,000 individuals can survive up to 30 generations and maintain 60–100% of their initial heterozygosity. Our results can help other researchers better understand, how species with small propagule sizes and low heterozygosities can become successful invaders. creator: Iván Vera-Escalona creator: Antonio Brante uri: https://doi.org/10.7717/peerj.16628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vera-Escalona and Brante title: Biochemical, anatomical, and histochemical characterization of cachichín (Oecopetalum mexicanum Greenm. & C.H. Thomps: Metteniusaceae) seeds exposed to different thermal treatments link: https://peerj.com/articles/16663 last-modified: 2024-01-15 description: BackgroundCachichín (Oecopetalum mexicanum Greenm. & C.H. Thomps: Metteniusaceae) is an arboreal species native to the Misantla mountain range, Veracruz, Mexico, whose fruit contains an edible seed with potential nutraceutical properties. Basic biochemical analyses have been performed, though the effects of thermal treatments on the concentration of vital molecules, the seed structure and the histochemistry have yet to be elicited. Herewith we determined the effect of different thermal treatments on the concentrations of total sugars; glucose and fructose; proteins; and amino acids; as well as the impact of such treatments on the anatomy and histochemistry of seeds.MethodsBiochemical, anatomical, and histochemical characterizations of the cachichín seed were carried out in raw form (T1) and under three thermal treatments: boiled (T2), commercial toasting (T3), and controlled toasting (T4). The biochemical variables evaluated were total and reducing sugars, total proteins, and total amino acids. Observations of the seed structure were performed by scanning electron microscopy (SEM), while histochemical staining was carried out to identify starch, lipids, tannins, polysaccharides and proteins under compound light microscopy.ResultsConcentration of total sugars was reduced in boiled (T2) and commercial toasting (T3) seeds as compared to raw (T1) and controlled toasting (T4) seeds; boiled seeds (T3) displayed the lowest concentration of total sugars. An increase in the concentrations of glucose and fructose was observed in T4. As compared to T1, all other treatments did not change protein concentrations in the seed; the only significant difference observed was between T2 and T3, with commercial toasting displaying the highest mean for this variable. Amino acid concentrations decreased in T3 and T4 compared to T1, while in T2 the concentration of these molecules increased. The anatomic analysis of (T1) revealed a well-organized structure, compared to applied thermal treatments, where degradation of anatomical structures was observed. In general, the thermal treatments tested modified the concentrations and distribution of starch, lipids, tannins, polysaccharides and proteins as compared to raw seeds. The raw cachichín seed has a well-defined anatomical and cellular compartmental organization, while the application of the thermal treatments caused a loss of its structural organization and degradation of vital biomolecules.ConclusionThe cachichín seed can be considered a good source of proteins and lipids. Thermal treatments can improve its organoleptic properties, though they negatively impact its nutritional value and anatomical structure. Among thermal treatments tested, the controlled toasting can maintain or even improve some nutraceutical properties with a few structural and biochemical modifications. creator: Alejandro Esli Hernández-Mora creator: Libia Iris Trejo-Téllez creator: Hilda Araceli Zavaleta-Mancera creator: José Andrés Herrera-Corredor creator: María Magdalena Crosby-Galván creator: Fernando Carlos Gómez-Merino uri: https://doi.org/10.7717/peerj.16663 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hernández-Mora et al. title: Analysis of biogas production from sewage sludge combining BMP experimental assays and the ADM1 model link: https://peerj.com/articles/16720 last-modified: 2024-01-15 description: The Anaerobic Digestion Model No. 1 (ADM1) was employed to simulate methane (CH4) production in an anaerobic reactor (AR), and the associated bench-scale biochemical methane potential (BMP) assay, having sewage sludge (SWS) from a municipal wastewater treatment plant (WWTP) as feedstock. The SWS presented the following physical-chemical characteristics: pH (7.4–7.6), alkalinity (2,382 ± 100 mg CaCO3 L−1), tCOD (21,903 ± 1,000 mg L−1), TOC (895 ± 100 mg L−1), TS, TVS, and VSS (2.0%, 1.1%, and 0.8%, respectively). The BMP assay was conducted in six replicates under anaerobic mesophilic conditions (37 ± 0.1°C) for 11 days with a CH4 yield registered of 137.6 ± 6.39 NmL CH4 or 124 ± 6.72 CH4 g−1 VS−1. When the results obtained with the BMP bench-scale reactors were compared to the output generated with computational data by the ADM1 model having as input data the same initial sewage tCOD, similar cumulative CH4 production curves were obtained, indicating the accuracy of the ADM1 model. This approach allowed the characterization of the sludge and estimation of its biogas production potential. The combination of BMP assays, experimental data, and ADM1 model simulations provided a framework for studying anaerobic digestion (AD) processes. creator: Mariana Erthal Rocha creator: Thais Carvalho Lazarino creator: Gabriel Oliveira creator: Lia Teixeira creator: Marcia Marques creator: Norberto Mangiavacchi uri: https://doi.org/10.7717/peerj.16720 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rocha et al. title: The distribution and conservation of areas with microendemic species in a biodiversity hotspot: a multi-taxa approach link: https://peerj.com/articles/16779 last-modified: 2024-01-15 description: BackgroundMicroendemic species are species with very small geographic distributions (ranges). Their presence delimitates areas with microendemic species (AMs), denoting a spatial unit comprising at least one population of at least one microendemic species. AMs are assumed to be distributed distinctively and associated with specific ecological, historical, and anthropogenic attributes. However, the level of influence of these factors remains unclear. Thus, we studied the distribution patterns of microendemic species within the Brazilian Atlantic Forest to (a) identify the region’s AMs; (b) evaluate whether ecological (latitude, altitude, distance from the coastline), historical (climate stability), and anthropogenic (ecological integrity) attributes distinguish AMs from non-AMs; and (c) assess the conservation status of the Atlantic Forest’s AMs.MethodsWe mapped the ranges of 1,362 microendemic species of angiosperms, freshwater fishes, and terrestrial vertebrates (snakes, passerine birds, and small mammals) to identify the region’s AMs. Further, spatial autoregressive logit regression models were used to evaluate whether latitude, altitude, distance from the coastline, Climate Stability Index, and ecological integrity can be used to discern AMs from non-AMs. Moreover, the AMs’ conservation status was assessed by evaluating the region’s ecological integrity and conservation efforts (measured as the proportion of AMs in protected areas).ResultsWe identified 261 AMs for angiosperm, 205 AMs for freshwater fishes, and 102 AMs for terrestrial vertebrates in the Brazilian Atlantic Forest, totaling 474 AMs covering 23.8% of the region. The Brazilian Atlantic Forest is a large and complex biogeographic mosaic where AMs represent islands or archipelagoes surrounded by transition areas with no microendemic species. All local attributes help to distinguish AMs from non-AMs, but their impacts vary across taxonomic groups. Around 69% of AMs have low ecological integrity and poor conservation efforts, indicating that most microendemic species are under threat. This study provides insights into the biogeography of one of the most important global biodiversity hotspots, creating a foundation for comparative studies using other tropical forest regions. creator: Helder F. P. de Araujo creator: Célia C. C. Machado creator: José Maria Cardoso da Silva uri: https://doi.org/10.7717/peerj.16779 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Araujo et al. title: Proteomic detection of COX-2 pathway-related factors in patients with adenomyosis link: https://peerj.com/articles/16784 last-modified: 2024-01-15 description: BackgroundInvestigating the relationship between cyclooxygenase-2 (COX-2) pathway-related factors and clinical features in patients with adenomyosis by proteomics could provide potential therapeutic targets.MethodsThis study recruited 40 patients undergoing surgical hysterectomy and pathological diagnosis of adenomyosis, collected ectopic endometrial specimens, and recorded clinical data. The expression levels of COX-2 in ectopic uterus lesions were detected using the immunohistochemical (IHC) SP method. The 40 samples were then divided into a COX-2 low or high expression group. Five samples with the most typical expression levels were selected from each of the two groups and the differential proteins between the two groups were identified using label-free quantitative proteomics. WW domain-binding protein 2 (WBP2), interferon induced transmembrane protein 3 (IFITM3), and secreted frizzled-related protein 4 (SFRP4) were selected for further verification, and their relationships with COX-2 and clinical characteristics were analyzed.ResultsThere were statistically significant differences in the expression of WBP2, IFITM3, and SFRP4 between the COX-2 low and high expression groups (P < 0.01). The expressions of COX-2, IFITM3, and SFRP4 were significantly correlated with dysmenorrhea between the two groups (P < 0.05), but not with uterine size or menstrual volume (P > 0.05). However, there was no significant correlation between the expression of WBP2 and dysmenorrhea, uterine size, and menstruation volume in both the high expression and low expression groups (P > 0.05).ConclusionsCOX-2, IFITM3, SFRP4, and WBP2 may be involved in the pathogenesis of adenomyosis. COX-2, IFITM3, and SFRP4 may serve as potential molecular biomarkers or therapeutic targets in dysmenorrhea in patients with early adenomyosis. creator: Jihua Zhang creator: Luying Shi creator: Jingya Duan creator: Minmin Li creator: Canyu Li uri: https://doi.org/10.7717/peerj.16784 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Advances in macrophage and T cell metabolic reprogramming and immunotherapy in the tumor microenvironment link: https://peerj.com/articles/16825 last-modified: 2024-01-15 description: Macrophages and T cells in the tumor microenvironment (TME) play an important role in tumorigenesis and progression. However, TME is also characterized by metabolic reprogramming, which may affect macrophage and metabolic activity of T cells and promote tumor escape. Immunotherapy is an approach to fight tumors by stimulating the immune system in the host, but requires support and modulation of cellular metabolism. In this process, the metabolic roles of macrophages and T cells become increasingly important, and their metabolic status and interactions play a critical role in the success of immunotherapy. Therefore, understanding the metabolic state of T cells and macrophages in the TME and the impact of metabolic reprogramming on tumor therapy will help optimize subsequent immunotherapy strategies. creator: Hua Cheng creator: Yongbin Zheng uri: https://doi.org/10.7717/peerj.16825 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cheng and Zheng title: Space-time mapping relationships in sensorimotor communication during asymmetric joint action link: https://peerj.com/articles/16764 last-modified: 2024-01-12 description: BackgroundSensorimotor communication is frequently observed in complex joint actions and social interactions. However, it remains challenging to explore the cognitive foundations behind sensorimotor communication.MethodsThe present study extends previous research by introducing a single-person baseline condition and formulates two distinct categories of asymmetric joint action tasks: distance tasks and orientation tasks. This research investigates the action performance of 65 participants under various experimental conditions utilizing a 2 (cooperative intention: Coop, No-coop) × 2 (task characteristic: distance, orientation) × 4 (target: T1, T2, T3, T4) repeated-measures experimental design to investigate the cognitive mechanisms underlying sensorimotor communication between individuals.ResultsThe results showed that (1) target key dwell time, motion time, total motion time, and maximum motion height in the Coop condition are more than in the No-coop condition. (2) In the distance task without cooperative intention, the dwell time of T4 is smaller than T1, T2, T3, and its variability of T1, T2, T3, and T4 were no different. In the distance task with cooperative intention, the dwell time and its variability of T1, T2, T3, and T4 displayed an increasing trend. (3) In the orientation task without cooperative intention, the dwell time of T1 is smaller than T2, T3, T4, and variability of the target keys T1, T2, T3, and T4 had no difference. In the orientation task with cooperative intention, the dwell time and variability of the target keys T1, T2, T3, and T4 had increasing trends.ConclusionsThose findings underscore the importance of cooperative intention for sensorimotor communication. In the distance task with cooperative intention, message senders establish a mapping relationship characterized by “near-small, far-large” between the task distance and the individual’s action characteristics through sensorimotor experience. In the orientation task with cooperative intention, message senders combined sensorimotor experience and verbal metaphors to establish a mapping relationship between task orientation and action characteristics, following the sequence of “left-up, right-up, left-down, right-down” to transmit the message to others. creator: Ke Zhang creator: Xin Tong creator: Shaofeng Yang creator: Ying Hu creator: Qihan Zhang creator: Xuejun Bai uri: https://doi.org/10.7717/peerj.16764 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Investigating Escherichia coli habitat transition from sediments to water in tropical urban lakes link: https://peerj.com/articles/16556 last-modified: 2024-01-11 description: BackgroundEscherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.MethodsThis study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.ResultsThe abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g–1, and was about one order higher than in the water column (1 to 2,300 cfu mL–1). The habitat transition rates ranged from 0.03 to 0.41 h–1. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h−1. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.DiscussionOur study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column. creator: Boyu Liu creator: Choon Weng Lee creator: Chui Wei Bong creator: Ai-Jun Wang uri: https://doi.org/10.7717/peerj.16556 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Plant height variation and genetic diversity between Prunus ledebouriana (Schlecht.) YY Yao and Prunus tenella Batsch based on using SSR markers in East Kazakhstan link: https://peerj.com/articles/16735 last-modified: 2024-01-11 description: BackgroundGenetic differences between isolated endemic populations of plant species and those with widely known twin species are relevant for conserving the biological diversity of our planet’s flora. Prunus ledebouriana (Schlecht.) YY Yao is an endangered and endemic species of shrub almond from central Asia. Few studies have explored this species, which is closely related and morphologically similar to the well-known Prunus tenella Batsch. In this article, we present a comparative analysis of studies of three P. ledebouriana populations and one close population of P. tenella in Eastern Kazakhstan in order to determine the particular geographic mutual replacement of the two species.MethodsThe populations were collected from different ecological niches, including one steppe population near Ust-Kamenogorsk (P. tenella) and three populations (P. ledebouriana) in the mountainous area. Estimation of plant height using a t-test suggested a statistically significant difference between the populations and the two species (P < 0.0001). DNA simple sequence repeat (SSR) markers were applied to study the two species’ genetic diversity and population structure.ResultsA total of 19 polymorphic SSR loci were analyzed, and the results showed that the population collected in mountainous areas had a lower variation level than steppe populations. The highest level of Nei’s genetic diversity index was demonstrated in the 4-UK population (0.622) of P. tenella. The lowest was recorded in population 3-KA (0.461) of P. ledebouriana, collected at the highest altitude of the four populations (2,086 meters above sea level). The total genetic variation of P. ledebouriana was distributed 73% within populations and 27% between populations. STRUCTURE results showed that two morphologically similar species diverged starting at step K = 3, with limited population mixing. The results confirmed the morphological and genetic differences between P. tenella and P. ledebouriana and described the level of genetic variation for P. ledebouriana. The study’s results proved that the steppe zone and mountain altitude factor between P. tenella and isolated mountain samples of P. ledebouriana. creator: Aidyn Orazov creator: Moldir Yermagambetova creator: Anar Myrzagaliyeva creator: Nashtay Mukhitdinov creator: Shynar Tustubayeva creator: Yerlan Turuspekov creator: Shyryn Almerekova uri: https://doi.org/10.7717/peerj.16735 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Orazov et al. title: Responsiveness of monopodal postural stability tests in recreational athletes link: https://peerj.com/articles/16765 last-modified: 2024-01-11 description: BackgroundStabilometry, the modified Star Excursion Balance Test (mSEBT) or the Emery balance test (EBT) are reported in the literature to reflect changes after an intervention in monopodal postural stability. Even so, the responsiveness of those tests has not been evaluated after an instability training programme or analysed using multiple statistical indicators of responsiveness. The main aim of this study was to analyse the responsiveness of the stabilometry, mSEBT or EBT.MethodsThirty healthy recreational athletes performed a 4-week programme with three weekly sessions of instability training of the dominant lower limb and were evaluated using stabilometry, mSEBT, and EBT tests. Responsiveness was quantified based on internal and external responsiveness.ResultsEBT and all parameters in mSEBT for the dominant lower limb showed large internal responsiveness (SRM > 0.8). Furthermore, mSEBT values for the non-dominant lower limb (except anterior displacement) also experienced significant changes with an associated large internal responsiveness. None of the stabilometry platform parameters showed a significant change after the intervention. The ability of the EBT to discriminate between the dominant and non-dominant lower limb (i.e., trained vs untrained, respectively) was generally acceptable (AUCs = 0.708). However, none of the parameters of the mSEBT test showed an acceptable AUC.ConclusionsEBT showed a positive responsiveness after instability training compared to mSEBT, which only showed internal responsiveness, or stabilometry platform measures, whose none of the parameters could identify these changes. creator: Mª Piedad Sánchez Martínez creator: Mariana Sánchez-Barbadora creator: Noemi Moreno-Segura creator: Patricia Beltrá creator: Adrian Escriche-Escuder creator: Rodrigo Martín-San Agustín uri: https://doi.org/10.7717/peerj.16765 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sánchez Martínez et al. title: Species composition, relative abundance, and habitat association of birds in Dodola dry evergreen afro-montane forest and sub-afro-alpine scrubland vegetation, southeast Ethiopia link: https://peerj.com/articles/16775 last-modified: 2024-01-11 description: BackgroundBirds’ functional groups are useful for maintaining fundamental ecological processes, ecosystem services, and economic benefits. Negative consequences of loss of functional groups are substantial. Birds are usually found at a high trophic level in food webs and are relatively sensitive to environmental change.MethodsThe first surveillance bird study was carried out southeast of Ethiopia adjacent to Bale Mountain National Park aimed at investigating the composition, relative abundance, and distribution of Aves. Using regular systematic point transact sampling, the density and species composition were analyzed through the mark recapture distance sampling engine assisted by R statistical software.ResultsThis study recorded a total of seventy-eight bird species over two distinct seasons. Among these, fifteen species were exclusive to Erica habitats, twenty-six were found in natural forest habitats, and three were specific to plantation forest habitats. The study also discovered three endemic species. Based on the 2018 IUCN Red List categories, six of the species are globally threatened, three are near threatened, and the remaining sixty-nine are classified as least concern. The relative abundance of birds did not significantly differ across habitats and seasons, but variations were observed among blocks. Bird density was found to fluctuate across the three habitats and two seasons; however, these habitat differences were not influenced by seasonal changes.ConclusionThe findings of this study reveal that the differences in composition and relative abundance are not merely seasonal changes in the forest and Erica habitats. Instead, these habitats create microclimates that cater to specific bird species. However, this localized endemism also presents challenges. The concentration of endemic species and potential resource constraints could pose a threat to these habitat-specialist birds. creator: Zenebe Ageru Yilma creator: Girma Mengesha creator: Zerihun Girma uri: https://doi.org/10.7717/peerj.16775 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yilma et al. title: The effect of high-intensity plyometric training on anaerobic performance parameters: a pilot study in U17 elite A league link: https://peerj.com/articles/16648 last-modified: 2024-01-10 description: The aim of this study was to examine the effects of high-intensity plyometric training (HIPT) on some parameters in elite soccer players in the U17. Volunteer soccer players were randomly divided into two groups according to their positions: the regular training (RT) group (age: 16.71 ± 0.47 years; stature: 163.46 ± 3.31 cm; body weight: 61.04 ± 1.59 kg) and the HIPT group (age: 16.64 ± 0.50 years; stature: 165.60 ± 3.03 cm; body weight: 59.76 ± 1.92 kg), and each group included five defenders, five midfielders, and four attackers. While the RT group did only routine soccer training, the HIPT group performed high-intensity plyometric training three days a week in addition to routine soccer training. In the study, body weight, stature, sprint (10 m, 30 m, and 40 m), jump (standing long jump, right and left-limb triple hop) and 5-0-5 change of direction speed test measurements of the soccer players were taken. Skewness and Kurtosis values obtained from the pre-test and post-test measurements were calculated to test whether the normality assumption of the study was met. A mixed measure two-way ANOVA test was used to determine the difference between the pre-test and post-test. The significance was set as p < 0.05. The results indicated that 8-week high- intensity plyometric training provided more improvement in measured performance parameters than routine soccer training. As a result, when the data obtained is examined, it can be said that HIPT had better values in sprint, jump, and change of direction parameters, so plyometric training was more beneficial for anaerobic parameters than routine soccer training in children. It is recommended that the trainers make their plans considering these results. creator: Mehmet Söyler creator: Raif Zileli creator: Yunus Emre Çingöz creator: Gökmen Kılınçarslan creator: İdris Kayantaş creator: Tolga Altuğ creator: Selim Asan creator: Musa Şahin creator: Alper Cenk Gürkan uri: https://doi.org/10.7717/peerj.16648 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Söyler et al. title: Response of conventional sunflower cultivars to drift rates of synthetic auxin herbicides link: https://peerj.com/articles/16729 last-modified: 2024-01-10 description: The agrochemical industry has launched several new synthetic auxin herbicides in rice to combat increasing numbers of herbicide resistant weeds to other modes of action. Excessive or inappropriate use of these herbicides has resulted in unintended consequences near the sites of application, such as herbicide drift. This study was conducted to determine the impact of drift of quinclorac and florpyrauxifen-benzyl+penoxsulam (FBP) on the yield and yield components of two sunflower cultivars. In a growth chamber experiment, quinclorac and FBP were applied to 2–4 true leaf stages at rates ranging from 2.93 to 93.75 and from 0.51 to 16.25 g ai ha−1, respectively. Nonlinear regression analyses indicated that the cultivar Bosfora was more sensitive to quinclorac and FBP than the cultivar Tunca. In field experiments, these sunflower cultivars were treated with drift rates of quinclorac (<375 g ai ha−1) and FBP (<65 g ai ha−1) when they were at the 8-10 true leaf stage. Quinclorac and FBP drift rates resulted in up to 52-61% and 85–100% injury and 82-88% and 100% yield loss, respectively. Crop injury and yield data clearly showed that cultivar Bosfora was more sensitive to FBP and quinclorac rates than cultivar Tunca, and both cultivars were more sensitive to FBP than quinclorac. In our work, we also found that plant height reduction caused by quinclorac at early growth stages may be a valuable indicator to evaluate crop injury and yield loss. creator: Ahmet Tansel Serim creator: Eric L. Patterson uri: https://doi.org/10.7717/peerj.16729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Serim et al. title: Chromatin accessibility complex subunit 1 enhances tumor growth by regulating the oncogenic transcription of YAP in breast and cervical cancer link: https://peerj.com/articles/16752 last-modified: 2024-01-10 description: BackgroundAs a component of chromatin remodeling complex, chromatin accessibility complex subunit 1 (CHRAC1) is critical in transcription and DNA replication. However, the significance of CHRAC1 in cancer progression has not been investigated extensively. This research aimed to determine the function of CHRAC1 in breast and cervical cancer and elucidate the molecular mechanism.MethodsThe Bio-ID method was used to identify the interactome of transcriptional activator Yes-associated protein (YAP) and the binding between YAP and CHRAC1 was verified by immunofluorescence. CCK8, colony formation and subcutaneous xenograft assays were conducted to explore the function of CHRAC1 in cancer cell proliferation. RNA-seq analysis and RT-PCR were used to analyze the transcription program change after CHRAC1 ablation. The diagnostic value of CHRAC1 was analyzed by TCGA database and further validated by immunohistochemistry staining.ResultsIn the current study, we found that the chromatin remodeler CHRAC1 was a potential YAP interactor. CHRAC1 depletion suppressed breast and cervical cancer cell proliferation and tumor growth. The potential mechanism may be that CHRAC1 interacts with YAP to facilitate oncogenic transcription of YAP target genes in Hippo pathway, thereby promoting tumorigenesis. CHRAC1 was elevated in cervical and breast cancer biopsies and the upregulation correlated with shorter survival, poor pathological stages and metastasis of cancer patients. Moreover, CHRAC1 expression was statistically associated with YAP in breast and cervical cancer biopsies.ConclusionsThese findings highlight that CHRAC1 contributes to cancer progression through regulating the oncogenic transcription of YAP, which makes it a potential therapeutic target for cancer treatment. creator: Shasha Li creator: Lulu Wang creator: Jing Shi creator: Yi Chen creator: Ang Xiao creator: Bingyue Huo creator: Wenjing Tian creator: Shilu Zhang creator: Gang Yang creator: Wensheng Gong creator: Huixia Zhang uri: https://doi.org/10.7717/peerj.16752 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Research insights into the chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM): their roles in various tumors link: https://peerj.com/articles/16757 last-modified: 2024-01-10 description: The chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing (CMTM) family includes CMTM1–8 and CKLF, and they play key roles in the hematopoietic, immune, cardiovascular, and male reproductive systems, participating in the physiological functions, cancer, and other diseases associated with these systems. CMTM family members activate and chemoattract immune cells to affect the proliferation and invasion of tumor cells through a similar mechanism, the structural characteristics typical of chemokines and transmembrane 4 superfamily (TM4SF). In this review, we discuss each CMTM family member’s chromosomal location, involved signaling pathways, expression patterns, and potential roles, and mechanisms of action in pancreatic, breast, gastric and liver cancers. Furthermore, we discuss several clinically applied tumor therapies targeted at the CMTM family, indicating that CMTM family members could be novel immune checkpoints and potential targets effective in tumor treatment. creator: Sai-Li Duan creator: Yingke Jiang creator: Guo-Qing Li creator: Weijie Fu creator: Zewen Song creator: Li-Nan Li creator: Jia Li uri: https://doi.org/10.7717/peerj.16757 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Duan et al. title: Classification and selection of the main features for the identification of toxicity in Agaricus and Lepiota with machine learning algorithms link: https://peerj.com/articles/16501 last-modified: 2024-01-09 description: The occurrence of fungi is cosmopolitan, and while some mushroom species are beneficial to human health, others can be toxic and cause illness problems. This study aimed to analyze the organoleptic, ecological, and morphological characteristics of a group of fungal specimens and identify the most significant features to develop models for fungal toxicity classification using genetic algorithms and LASSO regression. The results of the study indicated that odor, spore print color, and habitat were the most significant characteristics identified by the genetic algorithm GALGO. Meanwhile, odor, gill size, stalk shape, and twelve other features were the relevant characteristics identified by LASSO regression. The importance score of the odor variable was 99.99%, gill size obtained 73.7%, stalk shape scored 39.9%, and the remaining variables did not score higher than 18%. Logistic regression, k-nearest neighbor (KNN), and XG-Boost classification algorithms were used to develop models using the features selected by both GALGO and LASSO. The models were evaluated using sensitivity, specificity, and accuracy metrics. The models with the highest AUC values were XGBoost, with a maximum value of 0.99 using the features selected by LASSO, followed by KNN with a maximum value of 0.99. The GALGO selection resulted in a maximum AUC of 0.98 in KNN and XGBoost. The models developed in this study have the potential to aid in the accurate identification of toxic fungi, which can prevent health problems caused by their consumption. creator: Jacqueline S. Ortiz-Letechipia creator: Carlos E. Galvan-Tejada creator: Jorge I. Galván-Tejada creator: Manuel A. Soto-Murillo creator: Erika Acosta-Cruz creator: Hamurabi Gamboa-Rosales creator: José María Celaya Padilla creator: Huizilopoztli Luna-García uri: https://doi.org/10.7717/peerj.16501 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ortiz-Letechipia et al. title: A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade link: https://peerj.com/articles/16693 last-modified: 2024-01-09 description: BackgroundArvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group.MethodsHere we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data.ResultsOur results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary. creator: Charles B. Withnell creator: Simon G. Scarpetta uri: https://doi.org/10.7717/peerj.16693 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Withnell and Scarpetta title: Clinical impact of heterogeneously distributed tumor-infiltrating lymphocytes on the prognosis of colorectal cancer link: https://peerj.com/articles/16747 last-modified: 2024-01-09 description: BackgroundTumor-infiltrating lymphocytes (TILs) exist in various malignancies, and have been viewed as a promising biomarker to predict the efficacy and outcome of treatment. However, the marked inter- and intra-tumor heterogeneity of TILs has resulted in some confusion regarding their impact on the prognosis of colorectal cancer (CRC).MethodsIn this study, 78 CRC patients were enrolled and the CD3+ and CD8+ TILs densities at the tumor center (TC), the invasive margin (IM) and the tumor stroma (TS) were assessed by immunohistochemical staining. Their associations with clinicopathological features and progression free survival (PFS) were analyzed to evaluate the predictive and prognostic values of TILs.ResultsTILs were mainly distributed along the invasive margin. High density of TILs in tumor center and invasive margin was associated with smaller tumor size (CD3+TILsIM), reduced tumor invasion (CD3+TILsIM), absence of lymph node metastasis (CD3+TILsIM and CD8+TILsTC), earlier stage (CD3+TILsIM and CD8+TILsIM), and lower tumor grade (CD3+TILsIM and CD8+TILsTC). However, stromal TILs were not associated with any clinicopathological features. Kaplan–Meier survival analysis revealed that high densities of TILs always correlated with prolonged patient survival. The pathological N stage, CD3+ TILsIM and CD8+ TILsTC were found to be independent prognostic indicators. Additionally, early-stage CRC patients who developed recurrence after surgery, showed a higher CD3+/CD8+ TILs ratio in invasive margin. In the present study, it was clarified that CD3+ and CD8+ TILs were heterogeneously distributed in tumor tissues of CRC. The increase in intratumoral and peritumoral TILs had been shown to be strongly predictive of improved clinical outcome. More importantly, the immune signatures enabled to stratify early-stage CRC patients with high risk of recurrence, highlighting the prognostic power of TILs. creator: Lu Liu creator: Meiling Long creator: Shengyuan Su creator: Lijun Wang creator: Jintao Liu uri: https://doi.org/10.7717/peerj.16747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Transfemoral limb loss modestly increases the metabolic cost of optimal control simulations of walking link: https://peerj.com/articles/16756 last-modified: 2024-01-09 description: BackgroundIn transtibial limb loss, computer simulations suggest that the maintenance of muscle strength between pre- and post-limb loss can maintain the pre-limb loss metabolic cost. These results are consistent with comparable costs found experimentally in select cases of high functioning military service members with transtibial limb loss. It is unlikely that similar results would be found with transfemoral limb loss, although the theoretical limits are not known. Here we performed optimal control simulations of walking with and without an above-knee prosthesis to determine if transfemoral limb loss per se increases the metabolic cost of walking.MethodsOpenSim Moco was used to generate optimal control simulations of walking in 15 virtual “subjects” that minimized the weighted sum of (i) deviations from average able-bodied gait mechanics and (ii) the gross metabolic cost of walking, pre-limb loss in models with two intact biological limbs, and post-limb loss with one of the limbs replaced by a prosthetic knee and foot. No other changes were made to the model. Metabolic cost was compared between pre- and post-limb loss simulations in paired t-tests.ResultsMetabolic cost post-limb loss increased by 0.7–9.3% (p < 0.01) depending on whether cost was scaled by total body mass or biological body mass and on whether the prosthetic knee was passive or non-passive.ConclusionsGiven that the post-limb loss model had numerous features that predisposed it to low metabolic cost, these results suggest transfemoral limb loss per se increases the metabolic cost of walking. However, the large differences above able-bodied peers of ∼20–45% in most gait analysis experiments may be avoidable, even when minimizing deviations from able-bodied gait mechanics. Portions of this text were previously published as part of a preprint (https://www.biorxiv.org/content/10.1101/2023.06.26.546515v2.full.pdf). creator: Ross H. Miller creator: Elizabeth M. Bell creator: Elizabeth Russell Esposito uri: https://doi.org/10.7717/peerj.16756 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2024 Miller et al. title: Biocontrol potential of endophytic bacterium Bacillus altitudinis GS-16 against tea anthracnose caused by Colletotrichum gloeosporioides link: https://peerj.com/articles/16761 last-modified: 2024-01-09 description: BackgroundAs one of the main pathogens causing tea anthracnose disease, Colletotrichum gloeosporioides has brought immeasurable impact on the sustainable development of agriculture. Given the adverse effects of chemical pesticides to the environment and human health, biological control has been a focus of the research on this pathogen. Bacillus altitudinis GS-16, which was isolated from healthy tea leaves, had exhibited strong antagonistic activity against tea anthracnose disease.MethodsThe antifungal mechanism of the endophytic bacterium GS-16 against C. gloeosporioides 1-F was determined by dual-culture assays, pot experiments, cell membrane permeability, cellular contents, cell metabolism, and the activities of the key defense enzymes.ResultsWe investigated the possible mechanism of strain GS-16 inhibiting 1-F. In vitro, the dual-culture assays revealed that strain GS-16 had significant antagonistic activity (92.03%) against 1-F and broad-spectrum antifungal activity in all tested plant pathogens. In pot experiments, the disease index decreased to 6.12 after treatment with GS-16, indicating that strain GS-16 had a good biocontrol effect against tea anthracnose disease (89.06%). When the PE extract of GS-16 treated mycelial of 1-F, the mycelial appeared deformities, distortions, and swelling by SEM observations. Besides that, compared with the negative control, the contents of nucleic acids, protein, and total soluble sugar of GS-16 group were increased significantly, indicating that the PE extract of GS-16 could cause damage to integrity of 1-F. We also found that GS-16 obviously destroyed cellular metabolism and the normal synthesis of cellular contents. Additionally, treatment with GS-16 induced plant resistance by increasing the activities of the key defense enzymes PPO, SOD, CAT, PAL, and POD.ConclusionsWe concluded that GS-16 could damage cell permeability and integrity, destroy the normal synthesis of cellular contents, and induce plant resistance, which contributed to its antagonistic activity. These findings indicated that strain GS-16 could be used as an efficient microorganism for tea anthracnose disease caused by C. gloeosporioides. creator: Youzhen Wu creator: Yumei Tan creator: Qiuju Peng creator: Yang Xiao creator: Jiaofu Xie creator: Zhu Li creator: Haixia Ding creator: Hang Pan creator: Longfeng Wei uri: https://doi.org/10.7717/peerj.16761 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wu et al. title: Identification of a necroptosis-related gene signature for making clinical predictions of the survival of patients with lung adenocarcinoma link: https://peerj.com/articles/16616 last-modified: 2024-01-08 description: BackgroundLung adenocarcinoma (LUAD) is a major pathological subtype of malignant lung cancer with a poor prognosis. Necroptosis is a caspase-independent programmed cell death mode that plays a pivotal role in cancer oncogenesis and metastasis. Here, we explore the prognostic values of different necroptosis-related genes (NRGs) in LUAD.MethodsmRNA expression data and related clinical information for LUAD samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. NRGs were identified using the GeneCards database. Least absolute shrinkage and selection operator Cox regression and multivariate Cox analysis were used to construct a prognostic risk model. Time-dependent receiver-operating characteristic curves and a nomogram were constructed to validate the predictive values of the prognostic signatures. A necroptosis-related protein–protein interaction network was visualised using the STRING database and Cytoscape software. Functional analyses, including Gene Ontology, Kyoto Encyclopaedia of Genes and Genomes pathway enrichment, gene set enrichment, and gene set variation analyses, were conducted to explore the underlying molecular mechanisms. Finally, the mRNA expression of the prognostic signatures in LUAD cell lines was assessed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis.ResultsA prognostic model was established for eight NRGs (CALM1, DDX17, FPR1, OGT, PGLYRP1, PRDX1, TUFM, and CPSF3) based on TCGA-cohort data and validated with the GSE68465 cohort. Patients with low-risk scores had better survival outcomes than those with high-risk scores (p = 0.00013). The nomogram was used to predict the prognosis of patients with LUAD. The prediction curves for 1-, 3-, and 5-year OS showed good predictive performance and the accuracy of the nomograms increased over time. RT-qPCR results demonstrated that these eight genes, especially CALM1, PRDX1, and PGLYRP1, were differentially expressed in LUAD cells.ConclusionWe constructed a reliable eight-NRG signature that provides new insights for guiding clinical practice in the prognosis and treatment of LUAD. creator: Xiaoping Zhou creator: Ming Zhao creator: Yingzi Fan creator: Ying Xu uri: https://doi.org/10.7717/peerj.16616 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Microparticle-associated tissue factor activity correlates with the inflammatory response in septic disseminated intravascular coagulation patients link: https://peerj.com/articles/16636 last-modified: 2024-01-08 description: BackgroundSepsis is often accompanied by the formation of disseminated intravascular coagulation (DIC). Microparticles can exert their procoagulant and proinflammatory properties in a variety of ways. The purpose of this study was to investigate the relationship between microparticle-associated tissue factor activity (TF+-MP activity) and the inflammatory response.MethodsData from a total of 31 DIC patients with sepsis and 31 non-DIC patients with sepsis admitted to the ICU of the First Affiliated Hospital of Harbin Medical University from December 2017 to March 2019 were collected. Blood samples were collected and DIC scores were calculated on the day of enrollment. The hospital’s clinical laboratory completed routine blood, procalcitonin, and C-reactive protein tests. TF+-MP activity was measured using a tissue factor-dependent FXa generation assay. Interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) levels were determined using ELISA kits.ResultsCompared with the non-DIC group, the DIC group had higher levels of leukocytes, neutrophils, procalcitonin, C-reactive protein, IL-1β, and TNF-α, and more severe inflammatory reactions. TF+-MP activity in the DIC group was higher than that in the non-DIC group. In sepsis patients, TF+-MP activity was strongly correlated with inflammatory response indices and DIC scores.ConclusionTF+-MP activity may play a major role in promoting inflammatory response in septic DIC. creator: Shishuai Meng creator: Bin Xu creator: Wei Yang creator: Mingyan Zhao uri: https://doi.org/10.7717/peerj.16636 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Meng et al. title: Age, growth, reproduction and mortality of Xenocypris argentea (Günther,1868) in the lower reaches of the Tangwang River, China link: https://peerj.com/articles/16673 last-modified: 2024-01-08 description: To investigate various population biological parameters of Xenocypris argentea in the lower reaches of the Tangwang River (China), a comprehensive study was conducted for the first time. A total of 1,003 samples were collected from April to November 2022. The collected samples revealed that female X. argentea had total lengths ranging from 12.4 cm to 25.7 cm (weighing 15.86 g to 159.55 g), and male X. argentea had total lengths ranging from 10.8 cm to 23.9 cm (weighing 9.27 g to 121.06 g). The age of the samples was determined using otolith analysis, indicating that the ages ranged from 1 to 5 years old in both females and males. The length-weight relationships were further analyzed, uncovering the allometric growth index (b) was 3.1296 for females, indicating a positive allometric growth pattern. Differently, males exhibited a b value of 3.0274, suggesting an isometric growth pattern. Furthermore, the von Bertalanffy growth formula provided insights into the growth characteristics of X. argentea, revealing an asymptotic total length (L∞) of 36.096 cm and a growth coefficient (K) of 0.121. The analysis of the gonadal somatic index (GSI) and ovarian development period indicated that the spawning period occurred from April to July, with peak spawning in June. The study also explored fecundity-related traits, finding that individual absolute fecundity (FA) ranged from 11,364 eggs to 56,377 eggs, while eviscerated body weight relative fecundity (FW) ranged from 209 eggs/g to 823 eggs/g. The exploitation rate (E) for X. argentea was calculated as 0.574, suggesting that the population of X. argentea has been overexploited. By revealing previously unknown data on the key life history traits of X. argentea, this study has provided valuable insights that are crucial for the development of conservation strategies and policies. creator: Peilun Li creator: Jiacheng Liu creator: Wanqiao Lu creator: Shuyang Sun creator: Jilong Wang uri: https://doi.org/10.7717/peerj.16673 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny link: https://peerj.com/articles/16706 last-modified: 2024-01-08 description: Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson–Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless’ consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal. creator: Felipe Francisco Barbosa creator: José Ricardo M. Mermudes creator: Claudia A. M. Russo uri: https://doi.org/10.7717/peerj.16706 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Francisco Barbosa et al. title: COVID-19 related messaging, beliefs, information sources, and mitigation behaviors in Virginia: a cross-sectional survey in the summer of 2020 link: https://peerj.com/articles/16714 last-modified: 2024-01-08 description: BackgroundConflicting messages and misleading information related to the coronavirus (COVID-19) pandemic (SARS-CoV-2) have hindered mitigation efforts. It is important that trust in evidence-based public health information be maintained to effectively continue pandemic mitigation strategies. Officials, researchers, and the public can benefit from exploring how people receive information they believe and trust, and how their beliefs influence their behaviors.MethodsTo gain insight and inform effective evidence-based public health messaging, we distributed an anonymous online cross-sectional survey from May to July, 2020 to Virginia residents, 18 years of age or older. Participants were surveyed about their perceptions of COVID-19, risk mitigation behaviors, messages and events they felt influenced their beliefs and behaviors, and where they obtained information that they trust. The survey also collected socio-demographic information, including gender, age, race, ethnicity, level of education, income, employment status, occupation, changes in employment due to the pandemic, political affiliation, sexual orientation, and zip code. Analyses included specific focus on the most effective behavioral measures: wearing a face mask and distancing in public.ResultsAmong 3,488 respondents, systematic differences were observed in information sources that people trust, events that impacted beliefs and behaviors, and how behaviors changed by socio-demographics, political identity, and geography within Virginia. Characteristics significantly associated (p < 0.025) with not wearing a mask in public included identifying as non-Hispanic white, male, Republican political identity, younger age, lower income, not trusting national science and health organizations, believing one or more non-evidence-based messages, and residing in Southwest Virginia in logistic regression. Similar, lesser in magnitude correlations, were observed for distancing in public.ConclusionsThis study describes how information sources considered trustworthy vary across different populations and identities, and how these differentially correspond to beliefs and behaviors. This study can assist decision makers and the public to improve and effectively target public health messaging related to the ongoing COVID-19 pandemic and future public health challenges in Virginia and similar jurisdictions. creator: Rachel A. Silverman creator: Danielle Short creator: Sophie Wenzel creator: Mary Ann Friesen creator: Natalie E. Cook uri: https://doi.org/10.7717/peerj.16714 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Silverman et al. title: A nonlinear total variation based computed tomography (CT) image reconstruction method using gradient reinforcement link: https://peerj.com/articles/16715 last-modified: 2024-01-08 description: Compressed sensing-based reconstruction algorithms have been proven to be more successful than analytical or iterative methods for sparse computed tomography (CT) imaging by narrowing down the solution set thanks to its ability to seek a sparser solution. Total variation (TV), one of the most popular sparsifiers, exploits spatial continuity of features by restricting variation between two neighboring pixels in each direction as using partial derivatives. When the number of projections is much fewer than the one in conventional CT, which results in much less sampling rate than the minimum required one, TV may not provide satisfactory results. In this study, a new regularizer is proposed which seeks for a sparser solution by reinforcing the gradient of TV and empowering the spatial continuity of features. The experiments are done by using both analitical phantom and real human CT images and the results are compared with conventional, four-directional, and directional TV algorithms by using contrast-to-noise ratio (CNR), signal-to-noise ratio (SNR) and Structural Similarity Index (SSIM) metrics. Both quantitative and visual evaluations show that the proposed method is promising for sparse CT image reconstruction by reducing the background noise while preserving the features and edges. creator: Metin Ertas uri: https://doi.org/10.7717/peerj.16715 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ertas title: Didymium arenosum, a myxomycete new to science from the confluence of deserts in northwestern China link: https://peerj.com/articles/16725 last-modified: 2024-01-08 description: A new myxomycete species, Didymium arenosum, was described based on morphological evidence and phylogenetic analyses. The species was discovered in the arid region at the confluence of the Badain Jaran desert and Tengger desert on the leaves of Betula platyphylla and was cultivated in a moist chamber culture. Morphologically, the species is distinguished by the greenish-yellow calcium carbonate crystals on the surface and the spores covered with small warts, some of which are connected into a short line. A phylogenetic analysis of D. arenosum strongly supports its classification as a separate clade. The spore to spore agar culture of D. arenosum requires 23 days, and this study provides a detailed description of its life cycle. creator: Shuwei Wei creator: Shu Li creator: Pu Liu creator: Bao Qi creator: Qi Wang creator: Yu Li uri: https://doi.org/10.7717/peerj.16725 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wei et al. title: Geographical distribution of two major quarantine fruit flies (Bactrocera minax Enderlein and Bactrocera dorsalis Hendel) in Sichuan Basin based on four SDMs link: https://peerj.com/articles/16745 last-modified: 2024-01-08 description: Both Bactrocera minax and Bactrocera dorsalis are phytophagous insects, and their larvae are latent feeders, which cause great damage and economic losses to agriculture production and trade. This study aimed to provide a scientific reference for researching and developing the feasible countermeasures against these two pests. Based on the distribution data of B. minax and B. dorsalis in China, obtained from the Chinese herbaria, investigation and literature. Four niche models (Garp, Bioclim, Domain, and Maxent) were used to analyze the key environmental factors affecting the distribution of both pests and to build prediction models of the potential distribution in Sichuan Basin. Combined with two statistical standards, area under the receiver operating characteristic curve (AUC) and Kappa, the validity of prediction models were analyzed and compared. The results show that: the average AUC values of the four models are all above 0.90, and the average Kappa values are all above 0.75, indicating that the four models are suitable for predicting the potential distribution area of B. minax and B. dorsalis. The annual range of temperature, the mean temperature in the driest quarter, the mean temperature in the warmest quarter, the annual precipitation, and the precipitation in driest month are the key environmental factors affecting the distribution of B. minax, while the mean diurnal temperature range, the mean temperature in the driest quarter, the seasonal temperature variations and the precipitation in driest month affect the potential distribution of B. dorsalis. The suitable areas for B. minax are mainly concentrated in the eastern of Sichuan Basin, while the suitable areas for B. dorsalis are concentrated in the southeastern. Except for the Bioclim model, the highly-suitable area for both pests predicted by the other three models are all greater than 15.94 × 104 km2 and the moderately-suitable areas are greater than 13.57 × 104 km2. In conclusion, the suitable areas for both pests in Sichuan Basin are quite wide. Therefore, the relevant authorities should be given strengthened monitoring of both pests, especially in areas with high incursion rates. creator: Yanli Xia creator: Jinpeng Zhao creator: Jian Ding creator: Ke Xu creator: Xianjian Zhou creator: Mian Xiang creator: Huiling Xue creator: Huan Wang creator: Rulin Wang creator: Yuxia Yang uri: https://doi.org/10.7717/peerj.16745 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xia et al. title: phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things) link: https://peerj.com/articles/16505 last-modified: 2024-01-05 description: Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software. creator: Liam J. Revell uri: https://doi.org/10.7717/peerj.16505 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Revell title: Determinants of asthma among adults in Tigray, Northern Ethiopia: a facility-based case-control study link: https://peerj.com/articles/16530 last-modified: 2024-01-05 description: BackgroundAsthma is a public health concern affecting millions of productive age groups. Several studies were conducted on the determinants of asthma in children. However, little is known about the determinants of asthma among adults in Ethiopia. Understanding the determinants of asthma among adults can help reduce its burden. This study was aimed at identifying determinant factors for developing asthma among adults in Tigray hospitals.MethodsA facility-based, unmatched case-control study design was conducted from January 1 to April 26, 2019. A total of 698 participants (228 cases and 470 controls) completed their guided interviews using structured and pretested questionnaires by trained data collectors. A modified standard questionnaire from the European Community Respiratory Health Survey II (ECRHS II) was used to collect the data. The case definition was patients having asthma, and the control definition was patients without asthma. Data were entered and cleaned using Epi Data Manager Version 3.1 software and imported to statistical packages for social sciences Version 25 software for analysis. To identify asthma determinants, bivariate and multivariable logistic regression models were fitted.ResultsThe response rate for both cases and controls was 95.9%. The odds of developing asthma was nearly twice higher among those who resided in urban (AOR = 1.68; 95% CI [1.13–2.50]), more than twice higher among those who have income less than 1000 ETB (AOR = 2.3; 95% CI [1.17–4.56]), twice higher among those who had history of skin allergy (AOR = 2.09; 95% CI [1.14–3.86]), over four times higher among those with family history of asthma (AOR = 4.26; 95% CI [2.63–6.91]), three times higher among those having house dust or smoke exposure (AOR = 3.01; 95% CI [1.96–4.64]), over five times higher among those lifetime firewood users (AOR = 5.39; 95% CI [3.34–8.72]), door opening while cooking (AOR = 0.35; 95% CI [0.26–0.55]), nearly two times higher among those having house dampness (AOR = 1.98; 95% CI [1.069–3.68]), over seven times higher among pet owners (AOR = 7.46; 95% CI [4.04–13] and almost twice higher among those who were physically inactive (AOR = 1.75; 95% CI [1.11–2.85]).ConclusionAsthma has been associated with urbanization, low income, a history of allergic diseases, indoor smoke or dust, firewood use, pet ownership, and a sedentary lifestyle. The community should be informed about the known risks and implement preventive steps like opening a door while cooking to lower the risk of asthma. creator: Tirhas G. Gebresillasie creator: Alemayehu Worku creator: Ahmed Ali Ahmed creator: Negussie Deyessa Kabeta uri: https://doi.org/10.7717/peerj.16530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gebresillasie et al. title: The usefulness of balance test in preseason evaluation of injuries in amputee football players: a pilot prospective observational study link: https://peerj.com/articles/16573 last-modified: 2024-01-05 description: BackgroundLow balance ability is generally associated with an increased risk of ligament injuries. It seems that assessing the level of stability in amputee football players can help evaluate the accompanying risk of sports injuries. Thus, the study aimed to examine the usefulness of the balance test in preseason evaluation by calculating between-group differences in stability parameters between injured and non-injured amputee players.MethodsThe study was designed as a pilot prospective observational study. Twenty-five elite amputee football players representing the Polish National Team and the highest division in Polish League completed one-leg preseason balance tests on the Biodex Balance System before the start of the football season. All players in this study were male, with an average age of 29 years (SD = 7.9), a stature of 174.2 cm (SD 5.2) and a body mass of 80.1 kg (SD = 13.1). Then, players were prospectively observed over one football season, and lower leg injury data were prospectively collected through the nine months. The between-group differences were tested using the non-parametric Mann-Whitney U test for players who sustained an injury (yes) and those who did not within the analysed season (no). Overall (OSI), medial-lateral (MLSI), and anterior-posterior stability index (APSI) were analysed as primary outcomes.ResultsThe preseason values of the balance tests were not predictive (p > 0.05) regarding sustaining an injury during the season. No between-group differences were noted for any analysed outcomes (p values ranged from 0.093 to 0.453).ConclusionsAlthough static balance tasks offer a chance to make a preliminary assessment of injury prediction in amputee footballers, in overall, the balance test results cannot be regarded as the sole predictive injury risk factor in amputee football. creator: Zofia Kasińska creator: Tomasz Tasiemski creator: Teresa Zwierko creator: Piotr Lesiakowski creator: Monika Grygorowicz uri: https://doi.org/10.7717/peerj.16573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kasińska et al. title: Development of a new control rule for managing anthropogenic removals of protected, endangered or threatened species in marine ecosystems link: https://peerj.com/articles/16688 last-modified: 2024-01-05 description: Human activities in the oceans are increasing and can result in additional mortality on many marine Protected, Endangered or Threatened Species (PETS). It is necessary to implement ambitious measures that aim to restore biodiversity at all nodes of marine food webs and to manage removals resulting from anthropogenic activities. We developed a stochastic surplus production model (SPM) linking abundance and removal processes under the assumption that variations in removals reflect variations in abundance. We then consider several ‘harvest’ control rules, included two candidate ones derived from this SPM (which we called ‘Anthropogenic Removals Threshold’, or ART), to manage removals of PETS. The two candidate rules hinge on the estimation of a stationary removal rate. We compared these candidate rules to other existing control rules (e.g. potential biological removal or a fixed percentage rule) in three scenarios: (i) a base scenario whereby unbiased but noisy data are available, (ii) scenario whereby abundance estimates are overestimated and (iii) scenario whereby abundance estimates are underestimated. The different rules were tested on a simulated set of data with life-history parameters close to a small-sized cetacean species of conservation interest in the North-East Atlantic, the harbour porpoise (Phocoena phocoena), and in a management strategy evaluation framework. The effectiveness of the rules were assessed by looking at performance metrics, such as time to reach the conservation objectives, the removal limits obtained with the rules or temporal autocorrelation in removal limits. Most control rules were robust against biases in data and allowed to reach conservation objectives with removal limits of similar magnitude when averaged over time. However, one of the candidate rule (ART) displayed greater alignment with policy requirements for PETS such as minimizing removals over time. creator: Fanny Ouzoulias creator: Nicolas Bousquet creator: Mathieu Genu creator: Anita Gilles creator: Jérôme Spitz creator: Matthieu Authier uri: https://doi.org/10.7717/peerj.16688 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Ouzoulias et al. title: The effects of different rootstocks on aroma components, activities and genes expression of aroma-related enzymes in oriental melon fruit link: https://peerj.com/articles/16704 last-modified: 2024-01-05 description: Grafting is widely applied in the cultivation of melon. In this study, ‘Qinmi No.1’ (Cucumis melo L.(QG)) and ‘Ribenxuesong’ (Cucurbita maxima Duch. (RG)) were used as rootstocks for ‘Qingxin Yangjiaocui’ (Cucumis melo L.). The results showed that grafting with muskmelon rootstocks had no significant effect on fruit aroma, but grafting with pumpkin rootstocks significantly reduced the odor intensity and odor preference scores of melon fruits. Compared with the fruits from self-grafted plants (SG), four new aromatic volatiles with a sweet smell were detected, the alcohol dehydrogenase (ADH) activity was significantly decreased at 30 DAP, but unaffected at 42 DAP in QG fruits. There was no difference for alcohol acetyltransferase (AAT) activity between QG and SG fruits. The expression level of CmADH2 was significantly higher at 30 DAP and 42 DAP, but CmAAT2 was significantly lower at 42 DAP in QG fruits compared with SG fruits. In RG fruits, the main aroma compounds including butanoic acid ethyl ester, 2-methyl-2-butene-1-al, and 2-methylheptan-1-al were absent, while the volatile compounds with unpleasant odor characteristics including trans, cis-2,6-nonadien-1-ol, (E,E)-2,4-heptadienal, octanoic acid, and styrene were detected. Compared with SG fruits, 1-nonanol and 1-heptanol with green odor characteristics were significantly increased, but eucalyptol and farnesene with fruity aroma characteristics were significantly decreased in RG fruits. The ADH activity of RG fruits was significantly lower than that of SG fruits at 30 DAP and the AAT activity was significantly lower than that of SG fruits at 42 DAP. In addition, the expression levels of CmADH and CmAAT homologs in RG fruits were significantly lower than those in SG or QG fruits. These results show that grafting with pumpkin rootstocks affected the main aroma components, reduced ADH and AAT activities, and down-regulated the expression levels of CmADHs and CmAATs in the melon fruits. This study reveals the mechanism of different rootstocks on melon fruit aroma quality, and lays a theoretical foundation for the selection of rootstocks in melon production. Future studies using overexpression or CRISPR/CAS system to obtain stable transgenic lines of genes encoding key aromatic volatiles, would be promising to effectively improve the flavor quality of melon. creator: Kedong Guo creator: Jiateng Zhao creator: Siyu Fang creator: Qian Zhang creator: Lanchun Nie creator: Wensheng Zhao uri: https://doi.org/10.7717/peerj.16704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Guo et al. title: Assessment of functional fitness impacted by hospital rehabilitation in post-stroke patients who additionally contracted COVID-19 link: https://peerj.com/articles/16710 last-modified: 2024-01-05 description: BackgroundThe aim of the study was to assess the effects of rehabilitation in post-stroke patients, or post-stroke patients with simultaneous COVID-19 infection, in relation to: improved locomotion efficiency, improved balance, reduced risk of falling as well as the patients’ more effective performance in everyday activities.MethodsThe study involved 60 patients in the early period (2–3 months) after a stroke. Group I consisted of 18 patients (30.0%) who, in addition to a stroke, also contracted COVID-19. Group II consisted of 42 patients (70%) post-stroke, with no SARS-CoV2 infection. The effects were assessed on the basis of: Tinetti test, Timed Up & Go test and Barthel scale.ResultsBoth groups achieved a statistically significant improvement in their Barthel score after therapy (p < 0.001). The Tinetti test, assessing gait and balance, showed that participants in Group I improved their score by an average of 4.22 points. ±4.35, and in Group II, on average, by 3.48 points ± 3.45 points. In the Timed Up & Go test over a distance of 3 m, significant improvement was achieved in both groups, as well but the effect was higher in Group I (p < 0.001).ConclusionsHospital rehabilitation in the early period after stroke improved locomotion efficiency and balance, and reduced the risk of falls in post-stroke patients, both with and without COVID-19 infection. creator: Justyna Leszczak creator: Joanna Pyzińska creator: Joanna Baran creator: Rafał Baran creator: Krzysztof Bylicki creator: Teresa Pop uri: https://doi.org/10.7717/peerj.16710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Leszczak et al. title: Neutrophil extracellular traps in central nervous system (CNS) diseases link: https://peerj.com/articles/16465 last-modified: 2024-01-04 description: Excessive induction of inflammatory and immune responses is widely considered as one of vital factors contributing to the pathogenesis and progression of central nervous system (CNS) diseases. Neutrophils are well-studied members of inflammatory and immune cell family, contributing to the innate and adaptive immunity. Neutrophil-released neutrophil extracellular traps (NETs) play an important role in the regulation of various kinds of diseases, including CNS diseases. In this review, current knowledge on the biological features of NETs will be introduced. In addition, the role of NETs in several popular and well-studied CNS diseases including cerebral stroke, Alzheimer’s disease, multiple sclerosis, amyotrophic lateral sclerosis (ALS), and neurological cancers will be described and discussed through the reviewing of previous related studies. creator: Bo-Zong Shao creator: Jing-Jing Jiang creator: Yi-Cheng Zhao creator: Xiao-Rui Zheng creator: Na Xi creator: Guan-Ren Zhao creator: Xiao-Wu Huang creator: Shu-Ling Wang uri: https://doi.org/10.7717/peerj.16465 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Shao et al. title: Relationships among cost, citation, and access in journal publishing by an ecology and evolutionary biology department at a U.S. university link: https://peerj.com/articles/16514 last-modified: 2024-01-04 description: BackgroundOptimizing access to high-quality scientific journals has become an important priority for academic departments, including the ability to read the scientific literature and the ability to afford to publish papers in those journals. In this contribution, we assess the question of whether institutional investment in scientific journals aligns with the journals where researchers send their papers for publication, and where they serve as unpaid reviewers and editors.MethodsWe assembled a unique suite of information about the publishing habits of our Department of Ecology and Evolutionary Biology, including summaries of 3,540 journal publications by 35 faculty members. These data include economic costs of journals to institutions and to authors, benefits to authors in terms of journal prestige and citation rates, and considerations of ease of reading access for individuals both inside and outside the university. This dataset included data on institutional costs, including subscription pricing (rarely visible to scholars), and “investment” by scholars in supporting journals, such as time spent as editors and reviewers.ResultsOur results highlighted the complex set of relationships between these factors, and showed that institutional costs often do not match well with payoffs in terms of benefits to researchers (e.g., citation rate, prestige of journal, ease of access). Overall, we advocate for greater cost-benefit transparency to help compare different journals and different journal business models; such transparency would help both researchers and their institutions in investing wisely the limited resources available to academics. creator: A. Townsend Peterson creator: Marlon E. Cobos creator: Ben Sikes creator: Jorge Soberon creator: Luis Osorio-Olvera creator: Josh Bolick creator: Ada Emmett uri: https://doi.org/10.7717/peerj.16514 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Peterson et al. title: Utilization and transformation of Chrysotila dentata-derived dissolved organic matter by phycosphere bacteria Marinobacter hydrocarbonoclasticus and Bacillus firmus link: https://peerj.com/articles/16552 last-modified: 2024-01-04 description: The dissolved organic matter (DOM) released from the cocoolithophores (Chrysotila dentata) was studied in laboratory experiments after co-culturing C. dentata with bacteria. Marinobacter hydrocarbonoclasticus (CA6)-γ-Proteobacteria and Bacillus firmus (CF2) were used to investigate the utilization and processing of the DOM derived from C. dentata, utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC), while measuring algal abundance and photosynthetic parameters. The experimental groups consisted of axenic C. dentata groups, filter cultured with bacteria (CA6 or CF2) groups, C. dentata co-cultured with bacteria (CA6 or CF2) groups and axenic bacteria (CA6 or CF2) groups. We then evaluated the processing of DOM by determining four fluorescence indices. The number of C. dentata cells and the photosynthetic capacity of microalgae were enhanced by CA6 and CF2. The main known fluorophores, including humic-like components and protein-like components, were present in all sample. The protein-like component of algal-bacterial co-cultures was effectively utilized by CA6 and CF2. The humic-like components increased at the end of the culture time for all cultures. Meanwhile, the average fluorescence intensity of protein-like in CA6 co-culture with algae was lower than that in CF2 co-culture with algae over time. On the other hand, the average fluorescence intensity of humic-like in CA6 was higher than CF2. However, the total change in fluorescence in humic-like and protein-like of axenic CF2 cultures was lower than that of CA6. Hence, the ability of CA6 to transform microalgal-derived DOM was superior to that of CF2, and CF2’s ability to consume bacterial-derived DOM was superior to that of CA6. creator: Xueru Wang creator: Chenjuan Fan creator: Jun Sun uri: https://doi.org/10.7717/peerj.16552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: The expression and clinical significance of serine hydroxymethyltransferase2 in gastric cancer link: https://peerj.com/articles/16594 last-modified: 2024-01-04 description: BackgroundGastric cancer (GC) is one of the most common malignant tumours in the digestive system. Serine hydroxymethyltransferase 2 (SHMT2) is one of the key enzymes associated with serine metabolism. However, the prognostic role of SHMT2 in GC carcinogenesis has yet to be studied.MethodsThe expression of SHMT2 in human tumors and normal tissues was detected by the Assistant for Clinical Bioinformatics and Immunohistochemistry (IHC). The relationship of the expression of SHMT2 with clinical characteristics and survival data was analysed by the chi-square test, survival analysis and online databases. Finally, the correlation between SHMT2 expression and associated signalling channels, and molecules was analysed by online databases.ResultsSHMT2 was strongly expressed in numerous human cancers. The expression rate of SHMT2 was 56.44% in GC (P = 0.018). The survival analysis indicated that patients with high expression of SHMT2 had the worse overall survival (OS; log-rank P = 0.007). The expression of SHMT2 was correlated with tumour size (P = 0.034) and, TNM stage (P = 0.042). In particular, SHMT2, vessel invasion and M stage were independent factors for OS in GC (P = 0.044, P < 0.001, P < 0.001). The SHMT2 gene was substantially correlated with cell signalling pathways.ConclusionsSHMT2 is highly expressed in GC and is associated with a poor prognosis. The exploration of its mechanism may be related to tumour proliferation, DNA repair and replication. SHMT2 is an independent prognostic risk factor and a potential biomarker for the diagnosis and treatment of GC. creator: Yiming Shan creator: Dongdong Liu creator: Yingze Li creator: Chu Wu creator: Yanwei Ye uri: https://doi.org/10.7717/peerj.16594 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shan et al. title: Ticagrelor alleviates pyroptosis of myocardial ischemia reperfusion-induced acute lung injury in rats: a preliminary study link: https://peerj.com/articles/16613 last-modified: 2024-01-04 description: Pulmonary infection is highly prevalent in patients with acute myocardial infarction undergoing percutaneous coronary intervention. However, the potential mechanism is not well characterized. Myocardial ischemia-reperfusion injury (MIRI) induces acute lung injury (ALI) related to pulmonary infection and inflammation. Recent studies have shown that pyroptosis mediates ALI in several human respiratory diseases. It is not known whether MIRI induces pyroptosis in the lungs. Furthermore, ticagrelor is a clinically approved anti-platelet drug that reduces ALI and inhibits the expression levels of several pyroptosis-associated proteins, but the effects of ticagrelor on MIRI-induced ALI have not been reported. Therefore, we investigated whether ticagrelor alleviated ALI in the rat MIRI model, and its effects on pyroptosis in the lungs. Sprague-Dawley rats were randomly divided into four groups: control, MIRI, MIRI plus low ticagrelor (30 mg/kg), and MIRI plus high ticagrelor (100 mg/kg). Hematoxylin and Eosin (HE) staining was performed on the lung sections, and the HE scores were calculated to determine the extent of lung pathology. The wet-to-dry ratio of the lung tissues were also determined. The expression levels of pyroptosis-related proteins such as NLRP3, ASC, and Cleaved caspase-1 were estimated in the lung tissues using the western blot. ELISA was used to estimate the IL-1β levels in the lungs. Immunohistochemistry was performed to determine the levels of MPO-positive neutrophils as well as the total NLRP3-positive and Cleaved caspase-1-positive areas in the lung tissues. The lung tissues from the MIRI group rats showed significantly higher HE score, wet-to-dry ratio, and the MPO-positive area compared to the control group, but these effects were attenuated by pre-treatment with ticagrelor. Furthermore, lung tissues of the MIRI group rats showed significantly higher expression levels of pyroptosis-associated proteins, including NLRP3 (2.1-fold, P < 0.05), ASC (3.0-fold, P < 0.01), and Cleaved caspase-1 (9.0-fold, P < 0.01). Pre-treatment with the high-dose of ticagrelor suppressed MIRI-induced upregulation of NLRP3 (0.46-fold, P < 0.05), ASC (0.64-fold, P < 0.01), and Cleaved caspase-1 (0.80-fold, P < 0.01). Immunohistochemistry results also confirmed that pre-treatment with ticagrelor suppressed MIRI-induced upregulation of pyroptosis in the lungs. In summary, our data demonstrated that MIRI induced ALI and upregulated pyroptosis in the rat lung tissues. Pre-treatment with ticagrelor attenuated these effects. creator: Yi-Ning Dai creator: Li-Tao Wang creator: Ye-Shen Zhang creator: Ling Xue creator: Peng-Cheng He creator: Ning Tan creator: Yuan-Hui Liu uri: https://doi.org/10.7717/peerj.16613 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dai et al. title: Temporal trends of land-use favourability for the strongly declining little bustard: assessing the role of protected areas link: https://peerj.com/articles/16661 last-modified: 2024-01-04 description: The little bustard (Tetrax tetrax) is a steppe bird strongly and negatively influenced by agricultural intensification in Europe. Here, we use the little bustard as a model species to examine how favourability (relative occurrence likelihood of a species based on environmental characteristics, such as habitat availability) varies regionally with degree of protection in north-western Spain. The Natura2000 network is one of the main biodiversity conservation tools of the European Union, aiming to protect areas hosting species of conservation concern from unfavourable land-use changes. The network covers many landscapes across the continent, including farmland. Additionally, we examine the relationship between trends in land-use favourability and little bustard population trends over a decade in the Nature Reserve of Lagunas de Villafáfila, a protected area also in the Natura2000 network where active and intense management focused on steppe bird conservation is carried out. Favourability was much greater in Villafáfila than in both protected areas with lower degree of protection and in non-protected areas. Land-use favourability increased slightly between 2011 and 2020 both in and out of protected areas, whereas little bustard populations declined sharply in that period, even in Villafáfila. Spatial variations in little bustard abundance within Villafáfila depended on social attraction (increasing with the number of neighbouring males) but not significantly on small-scale variations in land-use favourability. These results suggest that land-use management in Natura2000 areas needs to be more conservation-focused, favouring natural and seminatural habitats and traditional farming practices to improve land-use favourability for little bustards and other steppe birds. Additional factors, such as field-level agricultural management or social interaction variables that may cause an Allee effect, should be incorporated in little bustard favourability models to improve their use in conservation planning. creator: David González del Portillo creator: Manuel B. Morales creator: Beatriz Arroyo uri: https://doi.org/10.7717/peerj.16661 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 González del Portillo et al. title: Vertical distribution characteristics of soil organic carbon and vegetation types under different elevation gradients in Cangshan, Dali link: https://peerj.com/articles/16686 last-modified: 2024-01-04 description: BackgroundThe Cangshan National Nature Reserve of Dali City was adopted as the research object to clarify the vertical distribution characteristics of soil organic carbon (SOC) and vegetation types at different elevations in western Yunnan.MethodsThe contents of SOC, light fraction organic carbon (LFOC), heavy fraction organic carbon (HFOC), and water-soluble organic carbon (WSOC) in the 0–30 cm soil layer at different elevations (2,400, 2,600, 2,800, 3,000, 3,200, 3,400, and 3,600 m) were determined, and the above-ground vegetation types at different elevations were investigated.ResultsResults showed that the SOC content was the highest in 0–20 cm surface soil and gradually decreased with the deepening of the soil layer. It increased then decreased with the increase in elevation, and it peaked at 3,000 m. The LFOC content was between 1.28 and 7.3515 g kg−1. It exhibited a decreasing trend and little change in profile distribution. The HFOC content ranged between 12.9727 and 23.3708 g kg−1; it increased then decreased with the increase in profile depth. The WSOC content was between 235.5783 and 392.3925 mg kg−1, and the response sensitivity to elevation change was weak. With the increase in elevation, WSOC/SOC and LFOC/SOC showed a similar trend, whereas HFOC presented an opposite trend. This observation indicates that the active organic carbon content at 3,600 m was lower than that at 2,400 m, and the middle elevation was conducive to the storage of active organic carbon. Meanwhile, the physical and chemical properties of soil affected the distribution of organic carbon to a certain extent. The vegetation type survey showed that the above-ground dominant species within 2,400–2,800 m were Pinus yunnanensis and Pinus armandii. Many evergreen and mixed coniferous broadleaf forests were distributed from 3,000 m to 3,200 m. Species of Abies delavayi were mainly distributed from 3,400 m to 3,600 m. This research serves as a reference for the study of forest soil carbon stability in high-elevation areas and plays an important role in formulating reasonable land use management policies, protecting forest soil, reducing organic carbon loss, and investigating the carbon sequestration stability of forest ecosystems. creator: Xue Yang creator: Jianhong Xu creator: Huifang Wang creator: Hong Quan creator: Huijuan Yu creator: Junda Luan creator: Dishan Wang creator: Yuancheng Li creator: Dongpeng Lv uri: https://doi.org/10.7717/peerj.16686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang et al. title: Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements link: https://peerj.com/articles/16695 last-modified: 2024-01-04 description: Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools. creator: Jesse J. Kerkvliet creator: Alex Bossers creator: Jannigje G. Kers creator: Rodrigo Meneses creator: Rob Willems creator: Anita C. Schürch uri: https://doi.org/10.7717/peerj.16695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kerkvliet et al. title: The influence of management practices on plant diversity: a comparative study of three urban wetlands in an expanding city in eastern China link: https://peerj.com/articles/16701 last-modified: 2024-01-04 description: Rapid urbanization has drawn some aquatic environments into the urban texture from the outskirts of cities, and the composition and distribution of plant species in urban wetlands along the urban gradient have changed. Understanding the drivers of these changes will help in the conservation and utilization of urban wetlands. This study investigated the differences in plant diversity and associated influencing factors in three wetlands, Xixi wetland, Tongjian Lake wetland, and Qingshan Lake wetland, which are located in a core area, fringe area, and suburban area of Hangzhou City, respectively. The results showed that a total of 104 families, 254 genera, and 336 species of plants were recorded in the Xixi wetland; 179 species, 150 genera, and 74 families were found in the Qingshan Lake wetland; and 112 species, 96 genera, and 57 families were collected in the Tongjian Lake wetland. The main plant species and flora distribution of the three urban wetlands showed similarities. Indigenous spontaneous vegetation was highest in the Xixi wetland, while cultivated plant species were most abundant in the Tongjian Lake wetland. The introduction of cultivated plants decreased the distance attenuation effect of plant communities, which led to a certain degree of plant diversity convergence among the three wetlands. Eight endangered plants were preserved in the Xixi wetland by planting them in suitable habitats. Ellenberg’s indicator values showed that the proportion of heliophilous plants was higher in the Qingshan Lake wetland, while the proportion of thermophilous plants and nitrogen-loving plants in the Tongjian Lake wetland was higher than in the other two wetlands. The importance of artificial interference factors affecting the differences in plant diversity was significantly higher than that of natural environmental factors in urban wetlands. The preservation of spontaneous plants and the introduction of cultivated plants had an importance of 25.73% and 25.38%, respectively. These were the main factors influencing the plant diversity of urban wetlands. The management mode that did not interfere with spontaneous vegetation and confined maintenance to cultivated plants in the Xixi wetland was beneficial for improving wetland plant diversity. Scientific plant reintroduction can also improve wetland plant diversity. creator: Yijun Lu creator: Guofu Yang creator: Youli Zhang creator: Biao Wei creator: Qiaoyi He creator: Huifang Yu creator: Yue Wang uri: https://doi.org/10.7717/peerj.16701 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lu et al. title: Tunable theranostics: innovative strategies in combating oral cancer link: https://peerj.com/articles/16732 last-modified: 2024-01-04 description: ObjectiveThis study aims to assess and compare the potential of advanced nano/micro delivery systems, including quantum dots, carbon nanotubes, magnetic nanoparticles, dendrimers, and microneedles, as theranostic platforms for oral cancer. Furthermore, we seek to evaluate their respective advantages and disadvantages over the past decade.Materials and MethodsA comprehensive literature search was performed using Google Scholar and PubMed, with a focus on articles published between 2013 and 2023. Search queries included the specific advanced delivery system as the primary term, followed by oral cancer as the secondary term (e.g., “quantum dots AND oral cancer,” etc.).ResultsThe advanced delivery platforms exhibited notable diagnostic and therapeutic advantages when compared to conventional techniques or control groups. These benefits encompassed improved tumor detection and visualization, enhanced precision in targeting tumors with reduced harm to neighboring tissues, and improved drug solubility and distribution, leading to enhanced drug absorption and tumor uptake.ConclusionThe findings suggest that advanced nano/micro delivery platforms hold promise for addressing numerous challenges associated with chemotherapy. By enabling precise targeting of cancerous cells, these platforms have the potential to mitigate adverse effects on surrounding healthy tissues, thus encouraging the development of innovative diagnostic and therapeutic strategies for oral cancer. creator: Asmaa Uthman creator: Noor AL-Rawi creator: Musab Hamed Saeed creator: Bassem Eid creator: Natheer H. Al-Rawi uri: https://doi.org/10.7717/peerj.16732 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Uthman et al. title: Acute effects of muscle mechanical properties after 2000-m rowing in young male rowers link: https://peerj.com/articles/16737 last-modified: 2024-01-04 description: BackgroundThe mechanical properties of muscles, such as changes in muscle tone and stiffness, are related to sports performance and injuries. Rowers are at increased risk of muscle fatigue and injury during high-repetition and heavy-load cyclic muscle actions. In view of this, the aim of the present study was to investigate the acute effect on muscle tone and stiffness, as well as bilateral muscle asymmetry, in high school rowers after a 2000-meter rowing ergometer test.MethodsTwelve young male rowers (age = 17.1 ± 0.9 years, body weight = 73.5 ± 9.7 kg) were included in the study. The data of muscle tone (frequency) and stiffness of the posterior deltoids (PD), latissimus dorsi (LD), and rectus femoris (RF) (dominant and non-dominant side) before and after a 2000-m rowing ergometer test were collected using a handheld MyotonPRO device.ResultsAfter the rowing ergometer test, the muscle tone of dominant side PD, LD, and RF were significantly increased (p < 0.05). On the other hand, the muscle stiffness of the non-dominant side LD and RF, as well as the dominant side PD, LD, and RF were significantly increased after the rowing ergometer test (p < 0.05). The muscle tone and stiffness results showed that the dominant side PD, LD, and RF were all significantly higher than the non-dominant side after the rowing ergometer test (p < 0.05), where bilateral PD and RF exhibits moderate asymmetry (5% < symmetry index < 10%).ConclusionsAfter a high-intensity and high-load 2000-m rowing ergometer test, PD, LD, and RF showed increases in muscle tone and stiffness, as well as changes in the symmetry of bilateral muscle mechanical properties. creator: Chun-Hao Chang creator: Chin-Shan Ho creator: Fang Li creator: Chao-Yuan Chen creator: Hung-Chih Yeh creator: Chia-An Ho uri: https://doi.org/10.7717/peerj.16737 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chang et al. title: Effects of nanoplastics on the gut microbiota of Pacific white shrimp Litopenaeus vannamei link: https://peerj.com/articles/16743 last-modified: 2024-01-04 description: Nanoplastics (NPs) are an abundant, long-lasting, and widespread type of environmental pollution that is of increasing concern because of the serious threats they might pose to ecosystems and species. Identifying the ecological effects of plastic pollution requires understanding the effects of NPs on aquatic organisms. Here, we used the Pacific white shrimp (Litopenaeus vannamei) as a model species to investigate whether ingestion of polystyrene NPs affects gut microbes and leads to metabolic changes in L. vannamei. The abundance of Proteobacteria increased and that of Bacteroidota decreased after NPs treatment. Specifically, Vibrio spp., photobacterium spp., Xanthomarina spp., and Acinetobacter spp. increased in abundance, whereas Sulfitobacter spp. and Pseudoalteromonas spp. decreased. Histological observations showed that L. vannamei exposed to NP displayed a significantly lower intestinal fold height and damaged intestinal structures compared with the control group. Exposure to NPs also stimulated alkaline phosphatase, lysozyme, and acid phosphatase activity, resulting in an immune response in L. vannamei. In addition, the content of triglycerides, total cholesterol, and glucose were significantly altered after NP exposure. These results provided significant ecotoxicological data that can be used to better understand the biological fate and effects of NPs in L. vannamei. creator: Chenxi Zhu creator: Yiming Li creator: Guoxing Liu creator: Anisah Lee Abdullah creator: Qichen Jiang uri: https://doi.org/10.7717/peerj.16743 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhu et al. title: Volumetric comparison of mandibular condyles and mandibles in the different skeletal classes in the Saudi population link: https://peerj.com/articles/16750 last-modified: 2024-01-04 description: BackgroundAssessing the relationship between the condyle and mandible volume and the various skeletal classes is essential in orthodontic diagnosis. The current study evaluated this relationship using volumetric cone-beam computed tomography (CBCT), cephalometric methods, and the correlations between them.Materials and MethodsThe study examined 37 full-head CBCTs (74 condyles) from adults in the Saudi population. The condyle and mandible were separated from within the CBCT images. The volume of each segment was compared to measurements from multiple cephalometric analyses.ResultsThe combined total condylar volume has a moderate correlation with the maxillomandibular differential in each of the genders and in the total sample. Mandibular volume has a significant correlation with the Wits appraisal (sagittal classification) in males. It was also significantly correlated with the vertical classification using gonial angles in females and in the total sample.ConclusionThe relationship between mandible and condyle volume and cephalometric measurements is both dimensional and within the maxillomandibular complex rather than positional or related to the cranial base. Also, the correlation between the condylar and mandibular volumes and the sagittal and vertical dimensions in the orthodontic skeletal classes provides better insight into the mandibular complex. creator: Hussain Y. A. Marghalani uri: https://doi.org/10.7717/peerj.16750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Marghalani title: Evaluating the imazethapyr herbicide mediated regulation of phenol and glutathione metabolism and antioxidant activity in lentil seedlings link: https://peerj.com/articles/16370 last-modified: 2024-01-03 description: The imidazolinone group of herbicides generally work for controlling weeds by limiting the synthesis of the aceto-hydroxy-acid enzyme, which is linked to the biosynthesis of branched-chain amino acids in plant cells. The herbicide imazethapyr is from the class and the active ingredient of this herbicide is the same as other herbicides Contour, Hammer, Overtop, Passport, Pivot, Pursuit, Pursuit Plus, and Resolve. It is commonly used for controlling weeds in soybeans, alfalfa hay, corn, rice, peanuts, etc. Generally, the herbicide imazethapyr is safe and non-toxic for target crops and environmentally friendly when it is used at low concentration levels. Even though crops are extremely susceptible to herbicide treatment at the seedling stage, there have been no observations of its higher dose on lentils (Lens culinaris Medik.) at that stage. The current study reports the consequence of imazethapyr treatment on phenolic acid and flavonoid contents along with the antioxidant activity of the phenolic extract. Imazethapyr treatment significantly increased the activities of several antioxidant enzymes, including phenylalanine ammonia lyase (PAL), phenol oxidase (POD), glutathione reductase (GR), and glutathione-s-transferase (GST), in lentil seedlings at doses of 0 RFD, 0.5 RFD, 1 RFD, 1.25 RFD, 1.5 RFD, and 2 RFD. Application of imazethapyr resulted in the 3.2 to 26.31 and 4.57–27.85% increase in mean phenolic acid and flavonoid content, respectively, over control. However, the consequent fold increase in mean antioxidant activity under 2, 2- diphenylpicrylhdrazyl (DPPH) and ferric reducing antioxidant power (FRAP) assay system was in the range of 1.17–1.85 and 1.47–2.03%. Mean PAL and POD activities increased by 1.63 to 3.66 and 1.71 to 3.35-fold, respectively, in agreement with the rise in phenolic compounds, indicating that these enzyme’s activities were modulated in response to herbicide treatment. Following herbicide treatments, the mean thiol content also increased significantly in corroboration with the enhancement in GR activity in a dose-dependent approach. A similar increase in GST activity was also observed with increasing herbicide dose. creator: Rajeev Kumar creator: V. Visha Kumari creator: Ranjit Singh Gujjar creator: Mala Kumari creator: Sanjay Kumar Goswami creator: Jhuma Datta creator: Srikumar Pal creator: Sudhir Kumar Jha creator: Ashok Kumar creator: Ashwini Dutt Pathak creator: Milan Skalicky creator: Manzer H. Siddiqui creator: Akbar Hossain uri: https://doi.org/10.7717/peerj.16370 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kumar et al. title: End-point rapid detection of total and pathogenic Vibrio parahaemolyticus (tdh+ and/or trh1+ and/or trh2+) in raw seafood using a colorimetric loop-mediated isothermal amplification-xylenol orange technique link: https://peerj.com/articles/16422 last-modified: 2024-01-03 description: BackgroundVibrio parahaemolyticus is the leading cause of bacterial seafood-borne gastroenteritis in humans worldwide. To ensure seafood safety and to minimize the occurrence of seafood-borne diseases, early detection of total V. parahaemolyticus (pathogenic and non-pathogenic strains) and pathogenic V. parahaemolyticus (tdh+ and/or trh1+ and/or trh2+) is required. This study further improved a loop-mediated isothermal amplification (LAMP) assay using xylenol orange (XO), a pH sensitive dye, to transform conventional LAMP into a one-step colorimetric assay giving visible results to the naked eye. LAMP-XO targeted rpoD for species specificity and tdh, trh1, and trh2 for pathogenic strains. Multiple hybrid inner primers (MHP) of LAMP primers for rpoD detection to complement the main primer set previously reported were designed by our group to maximize sensitivity and speed.MethodsFollowing the standard LAMP protocol, LAMP reaction temperature for rpoD, tdh, trh1, and trh2 detection was first determined using a turbidimeter. The acquired optimal temperature was subjected to optimize six parameters including dNTP mix, betaine, MgSO4, Bst 2.0 WarmStart DNA polymerase, reaction time and XO dye. The last parameter was done using a heat block. The color change of the LAMP-XO result from purple (negative) to yellow (positive) was monitored visually. The detection limits (DLs) of LAMP-XO using a 10-fold serial dilution of gDNA and spiked seafood samples were determined and compared with standard LAMP, PCR, and quantitative PCR (qPCR) assays. Subsequently, the LAMP-XO assay was validated with 102 raw seafood samples and the results were compared with PCR and qPCR assays.ResultsUnder optimal conditions (65 °C for 75 min), rpoD-LAMP-XO and tdh-LAMP-XO showed detection sensitivity at 102 copies of gDNA/reaction, or 10 folds greater than trh1-LAMP-XO and trh2-LAMP-XO. This level of sensitivity was similar to that of standard LAMP, comparable to that of the gold standard qPCR, and 10-100 times higher than that of PCR. In spiked samples, rpoD-LAMP-XO, tdh-LAMP-XO, and trh2-LAMP-XO could detect V. parahaemolyticus at 1 CFU/2.5 g spiked shrimp. Of 102 seafood samples, LAMP-XO was significantly more sensitive than PCR (P < 0.05) for tdh and trh2 detection and not significantly different from qPCR for all genes determined. The reliability of tdh-LAMP-XO and trh2-LAMP-XO to detect pathogenic V. parahaemolyticus was at 94.4% and 100%, respectively.ConclusionsTo detect total and pathogenic V. parahaemolyticus, at least rpoD-LAMP-XO and trh2-LAMP-XO should be used, as both showed 100% sensitivity, specificity, and accuracy. With short turnaround time, ease, and reliability, LAMP-XO serves as a better alternative to PCR and qPCR for routine detection of V. parahaemolyticus in seafood. The concept of using a one-step LAMP-XO and MHP-LAMP to enhance efficiency of diagnostic performance of LAMP-based assays can be generally applied for detecting any gene of interest. creator: Aekarin Lamalee creator: Soithong Saiyudthong creator: Chartchai Changsen creator: Wansika Kiatpathomchai creator: Jitra Limthongkul creator: Chanita Naparswad creator: Charanyarut Sukphattanaudomchoke creator: Jarinya Chaopreecha creator: Saengchan Senapin creator: Wansadaj Jaroenram creator: Sureemas Buates uri: https://doi.org/10.7717/peerj.16422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lamalee et al. title: Evaluating the relationship between Clinical G6PD enzyme activity and gene variants link: https://peerj.com/articles/16554 last-modified: 2024-01-03 description: Glucose-6-phosphate dehydrogenase (G6PD) is a the first and rate-limiting enzyme that plays a critical role in G6PD deficiency, the most common enzyme disorder worldwide, is related to intravascular hemolysis. To determine the clinical enzyme activity level in different G6PD variants, we evaluated 15 variant from 424 clinical blood samples by using multicolor melting curve analysis and DNA sequencing. The results showed that the enzyme activities of the hemizygous deficient were 1.5–2.4 U/gHb, which was significantly lower than those of the heterozygous (P < 0.001) and the compound heterozygous variants (P < 0.05). Since the hemizygous of c.1024C > T (Chinese-5) mutation affects the kinetic parameters of G6PD and increase utilization of analogues, its enzyme activity is more than those of other mutations that mutated in the β+α region of G6PD. The heterozygous enzyme levels ranged from 6.5–20.1 U/gHb; and there was no significant difference among different heterozygous variants (P > 0.05). The enzyme activity levels of the compound heterozygous mutation were mainly in the range of 1.7–3.8 U/gHb, which was much lower than that of the heterozygous mutation (P < 0.001). In summary, our findings revealed that the enzyme activity of G6PD in blood have a significant relationship with genotype of G6PD. creator: Xinyi Zhou creator: Zheng Qiang creator: Sufen Zhang creator: Yuqiu Zhou creator: Qizhi Xiao creator: Gongjun Tan uri: https://doi.org/10.7717/peerj.16554 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Genome-wide identification of the bHLH transcription factor family in Rosa persica and response to low-temperature stress link: https://peerj.com/articles/16568 last-modified: 2024-01-03 description: BackgroundBasic helix-loop-helix (bHLH) transcription factors are involved in plant growth and development, secondary metabolism, and abiotic stress responses have been studied in a variety of plants. Despite their importance in plant biology, the roles and expression patterns of bHLH family genes in Rosa persica have not been determined.MethodsIn this study, the RbebHLH family genes were systematically analyzed using bioinformatics methods, and their expression patterns under low-temperature stress were analyzed by transcriptome and related physiological index measurements.Results In total, 142 RbebHLHs were identified in the genome of R. persica, distributed on seven chromosomes. Phylogenetic analysis including orthologous genes in Arabidopsis divided RbebHLHs into 21 subfamilies, with similar structures and motifs within a subfamily. A collinearity analysis revealed seven tandem duplications and 118 segmental duplications in R. persica and 127, 150, 151, 172, and 164 segmental duplications between R. persica and Arabidopsis thaliana, Prunus mume, Fragaria vesca, Rosa chinensis, and Prunus persica, respectively. A number of cis-regulatory elements associated with abiotic stress response and hormone response were identified in RbebHLHs, and 21 RbebHLHs have potential interactions with the CBF family. In addition, the expression results showed that part of bHLH may regulate the tolerance of R. persica to low-temperature stress through the jasmonic acid and pathway. Transcriptomic data showed that the expression levels of different RbebHLHs varied during overwintering, and the expression of some RbebHLHs was significantly correlated with relative conductivity and MDA content, implying that RbebHLHs play important regulatory roles in R. persica response to low-temperature stress. Overall, this study provides valuable insights into the study of RbebHLHs associated with low-temperature stress. creator: Yueying Zhuang creator: Lijun Zhou creator: Lifang Geng creator: Lv Jiang creator: Yunji Sui creator: Le Luo creator: Huitang Pan creator: Qixiang Zhang creator: Chao Yu uri: https://doi.org/10.7717/peerj.16568 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhuang et al. title: Combined microbiome and metabolomics analysis of Taorong-type baijiu high-temperature Daqu and medium-temperature Daqu link: https://peerj.com/articles/16621 last-modified: 2024-01-03 description: BackgroundDaqu is an essential starter for baijiu brewing in China. However, the microbial enrichment and metabolic characteristics of Daqu formed at different fermentation temperatures are still unclear.MethodsHigh-throughput sequencing technology and the non-targeted metabolomics were used to compare the microbial communities and metabolites of Taorong-type high-temperature Daqu and middle-temperature Daqu. In this study, the relationship between microorganisms and metabolites was established.ResultsThe study found that the composition and metabolites of the microbial community differed due to the difference in Daqu-making temperature. The bacterial diversity of Taorong-type high-temperature Daqu was higher than that of middle-temperature Daqu, while the fungal community diversity of Taorong-type middle-temperature Daqu was higher than that of high temperature Daqu. A total of 1,034 differential metabolites were screened from the two types of Daqu, and 76 metabolites with significant differences were detected (P < 0.001 and variable importance in projection (VIP) > 1.15). Tetraacetylethylenediamine is the metabolite with the largest differential fold among the 76 differential metabolites, which can be used as a potential marker metabolite of high-temperature Daqu.ConclusionThis study helps elucidate the microbial assembly mechanisms and functional expression under different processing conditions through a further understanding of the composition and metabolic profile differences of different types of Daqu microflora in Taorong-type baijiu. creator: Yanbo Liu creator: Junyi Wu creator: Haideng Li creator: Wenxi Liu creator: Zhenke Zhang creator: Suna Han creator: Jianguang Hou creator: Chunmei Pan uri: https://doi.org/10.7717/peerj.16621 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Enrichment of polycyclic aromatic hydrocarbon metabolizing microorganisms on the oral mucosa of tobacco users link: https://peerj.com/articles/16626 last-modified: 2024-01-03 description: Certain soil microbes resist and metabolize polycyclic aromatic hydrocarbons (PAHs). The same is true for a subset of skin microbes. In the human mouth, oral microbes have the potential to oxidize tobacco PAHs, thereby increasing these chemicals’ ability to cause cancer of adjacent epithelium. We hypothesized that we could identify, in smokers, the oral mucosal microbes that can metabolize PAH. We isolated bacteria and fungi that survived long-term in minimal media with PAHs as the sole carbon source, under aerobic conditions, from the oral mucosa in 17 of 26 smokers and two of 14 nonsmokers. Of bacteria genera that survived harsh PAH exposure in vitro, most were found at trace levels, except for Staphylococcus, Actinomyces, and Kingella, which were more abundant. Two PAH-resistant strains of Candida albicans (C. albicans) were isolated from smokers. C. albicans was a prime candidate to contribute to carcinogenesis in tobacco users as it is found orally at high levels in tobacco users on the mucosa, and some Candida species can metabolize PAHs. However, when C. albicans isolates were tested for metabolism of two model PAH substrates, pyrene and phenanthrene, they were not capable, suggesting they cannot metabolize PAH under the conditions used. In conclusion, evidence for large scale microbial degradation of tobacco PAHs under aerobic conditions on the oral mucosa remains lacking, though nonabundant PAH metabolizers are certainly present. creator: Lin Tao creator: M Paul Chiarelli creator: Sylvia Pavlova creator: Antonia Kolokythas creator: Joel Schwartz creator: James DeFrancesco creator: Benjamin Salameh creator: Stefan J. Green creator: Guy Adami uri: https://doi.org/10.7717/peerj.16626 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tao et al. title: DNA barcoding continues to identify endangered species of shark sold as food in a globally significant shark fin trade hub link: https://peerj.com/articles/16647 last-modified: 2024-01-03 description: Shark fins are a delicacy consumed throughout Southeast Asia. The life history characteristics of sharks and the challenges associated with regulating fisheries and the fin trade make sharks particularly susceptible to overfishing. Here, we used DNA barcoding techniques to investigate the composition of the shark fin trade in Singapore, a globally significant trade hub. We collected 505 shark fin samples from 25 different local seafood and Traditional Chinese Medicine shops. From this, we identified 27 species of shark, three species are listed as Critically Endangered, four as Endangered and ten as Vulnerable by the International Union for Conservation of Nature (IUCN). Six species are listed on CITES Appendix II, meaning that trade must be controlled in order to avoid utilization incompatible with their survival. All dried fins collected in this study were sold under the generic term “shark fin”; this vague labelling prevents accurate monitoring of the species involved in the trade, the effective implementation of policy and conservation strategy, and could unwittingly expose consumers to unsafe concentrations of toxic metals. The top five most frequently encountered species in this study are Rhizoprionodon acutus, Carcharhinus falciformis, Galeorhinus galeus, Sphyrna lewini and Sphyrna zygaena. Accurate labelling that indicates the species of shark that a fin came from, along with details of where it was caught, allows consumers to make an informed choice on the products they are consuming. Doing this could facilitate the avoidance of species that are endangered, and similarly the consumer can choose not to purchase species that are documented to contain elevated concentrations of toxic metals. creator: Kai-Lin Selena Shen creator: Jin Jie Cheow creator: Abigail Belle Cheung creator: Ryan Jia Rong Koh creator: Amanda Koh Xiao Mun creator: Yun Ning Lee creator: Yan Zhen Lim creator: Maya Namatame creator: Eileen Peng creator: Vladislav Vintenbakh creator: Elisa X.Y. Lim creator: Benjamin John Wainwright uri: https://doi.org/10.7717/peerj.16647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Selena Shen et al. title: Impact of Argemone mexicana L. on tomato plants infected with Phytophthora infestans link: https://peerj.com/articles/16666 last-modified: 2024-01-03 description: BackgroundFungal diseases can cause significant losses in the tomato crop. Phytophthora infestans causes the late blight disease, which considerably affects tomato production worldwide. Weed-based plant extracts are a promising ecological alternative for disease control.MethodsIn this study, we analyzed the plant extract of Argemone mexicana L. using chromatography-mass spectrometry analysis (GC-MS). We evaluated its impact on the severity of P. infestans, as well as its effect on the components of the antioxidant defense system in tomato plants.ResultsThe extract from A. mexicana contains twelve compounds most have antifungal and biostimulant properties. The findings of the study indicate that applying the A. mexicana extract can reduce the severity of P. infestans, increase tomato fruit yield, enhance the levels of photosynthetic pigments, ascorbic acid, phenols, and flavonoids, as well as decrease the biosynthesis of H2O2, malondialdehyde (MDA), and superoxide anion in the leaves of plants infected with this pathogen. These results suggest that using the extract from A. mexicana could be a viable solution to control the disease caused by P. infestans in tomato crop. creator: Iridiam Hernández-Soto creator: Yolanda González-García creator: Antonio Juárez-Maldonado creator: Alma Delia Hernández-Fuentes uri: https://doi.org/10.7717/peerj.16666 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hernández-Soto et al. title: Description of a new fossil Thelyphonida (Arachnida, Uropygi) and further record of Cratosolpuga wunderlichi Selden, in Selden and Shear, 1996 (Arachnida, Solifugae) from Crato Formation (Aptian/Albian), Araripe Basin, Brazil link: https://peerj.com/articles/16670 last-modified: 2024-01-03 description: BackgroundA new fossil species of whipscorpion, Mesoproctus rayolin. sp., is described. The specimen originates from the Crato Formation, dating to the Lower Cretaceous (Aptian/Albian) period within the Araripe Sedimentary Basin. This species has been provisionally assigned to Mesoproctus Dunlop, 1998, as it represents the sole known Thelyphonida fossil genus discovered in South America and within Araripe Lagerstätte.MethodsThe material underwent detailed description and illustration processes. Key diagnostic characters, such as body length, pedipalpal coxae apophysis, the form of the opisthosoma, and the length of leg IV, were meticulously examined. SEM methods were applied in this study.ResultsThrough the detailed analysis, comparisons and differences to Mesoproctus rowlandi Dunlop, 1998 were made possible. Additionally, a well-preserved specimen of the rare camel spider, Cratosolpuga wunderlichi Selden, in Selden and Shear, 1996, was identified from the limestones of the Crato Formation. The newly discovered fossil specimen of Cratosolpuga wunderlichi suggests two characters not previously described: (i) a segmented tarsomere on leg IV; and (ii) a leg I with one tarsal claw. creator: William Santana creator: Allysson P. Pinheiro creator: Thiago Andrade Silva creator: Daniel Lima uri: https://doi.org/10.7717/peerj.16670 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Santana et al. title: Systematic review of residual toxicity studies of pesticides to bees and veracity of guidance on pesticide labels link: https://peerj.com/articles/16672 last-modified: 2024-01-03 description: Residues of pesticides on crops can result in mortality to foraging bees. Pesticide applicators in the U.S. encounter a statement on pesticide labels, which coarsely indicate which products dissipate over the course of an evening. There is reason to suspect that these statements may not align with residual toxicity data, given previous findings. Without a complete database of residual toxicity estimates; however, it is not possible to determine whether the residual toxicity components of statements on pesticide labels similarly diverge from published studies. We compiled 50 studies on residual toxicity trials with formulated pesticides and calculated the residual time to 25% mortality (RT25) of each assay for three different bee species (Apis mellifera, Nomia melanderi, and Megachile rotundata). Our findings were compared to a U.S. Environmental Protection Agency (EPA) published database of RT25 values. Of the RT25 values that we could compare, we found that over 90% of the values support a similar conclusion to the EPA. Next, we compared our values and the EPA’s values to the statements on 155 EPA registered pesticide product labels. Of these labels, a little less than a third presented their residual toxicity in a manner inconsistent with their calculated RT25 and current EPA labeling guidelines. Moreover, over a third of labels contained an active ingredient which was neither listed under the EPA’s RT25 database nor had a published study to estimate this value. We provide the first evidence that many pesticide labels may convey residual toxicity information to applicators that is not correct and could lead to bees being exposed to toxic residues on plants. creator: Leah Swanson creator: Andony Melathopoulos creator: Matthew Bucy uri: https://doi.org/10.7717/peerj.16672 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Swanson et al. title: Multi-omics reveals changed energy metabolism of liver and muscle by caffeine after mice swimming link: https://peerj.com/articles/16677 last-modified: 2024-01-03 description: In recent years, numerous studies have investigated the effects of caffeine on exercise, and provide convincing evidence for its ergogenic effects on exercise performance. However, the precise mechanisms underlying these ergogenic effects remain unclear. In this study, an exercise swimming model was conducted to investigate the effects of orally administered with caffeine before swimming on the alterations of proteome and energy metabolome of liver and muscle after swimming. We found proteins in liver, such as S100a8, S100a9, Gabpa, Igfbp1 and Sdc4, were significantly up-regulated, while Rbp4 and Tf decreased after swimming were further down-regulated in caffeine group. The glycolysis and pentose phosphate pathways in liver and muscle were both significantly down-regulated in caffeine group. The pyruvate carboxylase and amino acid levels in liver, including cysteine, serine and tyrosine, were markedly up-regulated in caffeine group, exhibiting a strong correlation with the increased pyruvic acid and oxaloacetate levels in muscle. Moreover, caffeine significantly decreased the lactate levels in both liver and muscle after swimming, potentially benefiting exercise performance. creator: Yang Han creator: Qian Jia creator: Yu Tian creator: Yan Yan creator: Kunlun He creator: Xiaojing Zhao uri: https://doi.org/10.7717/peerj.16677 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Han et al. title: Borneol promotes autophagic degradation of HIF-1α and enhances chemotherapy sensitivity in malignant glioma link: https://peerj.com/articles/16691 last-modified: 2024-01-03 description: BackgroundGliomas are characterized by high mortality rates and resistance. Even with conventional chemotherapy the prognosis of glioblastoma remains poor. Many medications are not optimally effective due to limited bioavailability. The bioavailability of medicine can be enhanced by borneol, a monoterpenoid substance. In this study, we investigated the effect of borneol, a commonly used Chinese medicine, on chemosensitivity in C6 glioma and U251 human glioma cell lines and elucidated its therapeutic molecular targets.MethodsThe chemosensitivity-inducing effects of borneol in C6 and U251 cells were examined using CCK8 and clonal formation assays. The mechanism underlying the effect of borneol was evaluated through immunohistochemistry and western blotting assays. Further, the number of autophagosomes was determined via transmission electron microscopy. Finally, the chemical sensitization effect of borneol was evaluated in SD rats after C6 orthotopic tumor transplantation.ResultsBorneol increased cytotoxicity in C6 and U251 cells in response to temozolomide (TMZ). In addition, through transmission electron microscopy, western blotting, and immunohistochemical tests, we found that borneol combined with TMZ significantly increased the level of autophagy and that hypoxia inducible factor-1(HIF-1α) is a candidate target through which borneol enhances the cytotoxic effect of TMZ. Borneol’s ability to enhance HIF-1α degradation was counteracted following the administration of autophagy inhibitors. In vivo, borneol treatment was found to enhance the anticancer effect of TMZ and delay tumor progression, and this effect was closely related to its ability to promote the autophagic degradation of HIF-1α.ConclusionsHIF-1α might be a valid therapeutic target of borneol, which can be potentially applied as a chemosensitizing drug used for glioma treatment. creator: Luting Lin creator: Jingming Luo creator: Zeng Wang creator: Xinjun Cai uri: https://doi.org/10.7717/peerj.16691 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Polymethoxylated flavonoids in citrus fruits: absorption, metabolism, and anticancer mechanisms against breast cancer link: https://peerj.com/articles/16711 last-modified: 2024-01-03 description: Polymethoxylated flavonoids (PMFs) are a subclass of flavonoids found in citrus fruits that have shown multifunctional biological activities and potential anticancer effects against breast cancer. We studied the absorption, metabolism, species source, toxicity, anti-cancer mechanisms, and molecular targets of PMFs to better utilize their anticancer activity against breast cancer. We discuss the absorption and metabolism of PMFs in the body, including the methylation, demethylation, and hydroxylation processes. The anticancer mechanisms of PMFs against breast cancer were also reviewed, including the estrogen activity, cytochrome P-450 enzyme system, and arylhydrocarbon receptor (AhR) inhibition, along with various molecular targets and potential anticancer effects. Although PMFs may be advantageous in the prevention and treatment for breast cancer, there is a lack of clinical evidence and data to support their efficacy. Despite their promise, there is still a long way to go before PMFs can be applied clinically. creator: Yiyu Wang creator: Yuan Mou creator: Senlin Lu creator: Yuhua Xia creator: Bo Cheng uri: https://doi.org/10.7717/peerj.16711 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Experimental trials of species-specific bat flight responses to an ultrasonic deterrent link: https://peerj.com/articles/16718 last-modified: 2024-01-03 description: Unintended consequences of increasing wind energy production include bat mortalities from wind turbine blade strikes. Ultrasonic deterrents (UDs) have been developed to reduce bat mortalities at wind turbines. Our goal was to experimentally assess the species-specific effectiveness of three emission treatments from the UD developed by NRG Systems. We conducted trials in a flight cage measuring approximately 60 m × 10 m × 4.4 m (length × width × height) from July 2020 to May 2021 in San Marcos, Texas, USA. A single UD was placed at either end of the flight cage, and we randomly selected one for each night of field trials. Trials focused on a red bat species group (Lasiurus borealis and Lasiurus blossevillii; n = 46) and four species: cave myotis (Myotis velifer; n = 57), Brazilian free-tailed bats (Tadarida brasiliensis; n = 73), evening bats (Nycteceius humeralis; n = 53), and tricolored bats (Perimyotis subflavus; n = 17). The trials occurred during three treatment emissions: low (emissions from subarrays at 20, 26, and 32 kHz), high (emissions from subarrays at 38, 44, and 50 kHz), and combined (all six emission frequencies). We placed one wild-captured bat into the flight cage for each trial, which consisted of an acclimation period, a control period with the UD powered off, and the three emission treatments (order randomly selected), each interspersed with a control period. We tracked bat flight using four thermal cameras placed outside the flight cage. We quantified the effectiveness of each treatment by comparing the distances each bat flew from the UD during each treatment vs. the control period using quantile regression. Additionally, we conducted an exploratory analysis of differences between sex and season and sex within season using analysis of variance. Broadly, UDs were effective at altering the bats’ flight paths as they flew farther from the UD during treatments than during controls; however, results varied by species, sex, season, and sex within season. For the red bat group, bats flew farther from the UD during all treatments than during the control period at all percentiles (p < 0.001), and treatments were comparable in effectiveness. For cave myotis, all percentile distances were farther from the UD during each of the treatments than during the control, except the 90th percentile distance during high, and low was most effective. For evening bats and Brazilian free-tailed bats, results were inconsistent, but high and low were most effective, respectively. For tricolored bats, combined and low were significant at the 10th–75th percentiles, high was significant at all percentiles, and combined was most effective. Results suggest UDs may be an effective means of reducing bat mortalities due to wind turbine blade strikes. We recommend that continued research on UDs focus on low emission treatments, which have decreased sound attenuation and demonstrated effectiveness across the bat species evaluated in this study. creator: Sarah Rebecah Fritts creator: Emma Elizabeth Guest creator: Sara P. Weaver creator: Amanda Marie Hale creator: Brogan Page Morton creator: Cris Daniel Hein uri: https://doi.org/10.7717/peerj.16718 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fritts et al. title: Fall risk prediction ability in rehabilitation professionals: structural equation modeling using time pressure test data for Kiken-Yochi Training link: https://peerj.com/articles/16724 last-modified: 2024-01-03 description: BackgroundFalls occur frequently during rehabilitation for people with disabilities. Fall risk prediction ability (FRPA) is necessary to prevent falls and provide safe, high-quality programs. In Japan, Kiken Yochi Training (KYT) has been introduced to provide training to improve this ability. Time Pressure-KYT (TP-KYT) is an FRPA measurement specific to fall risks faced by rehabilitation professionals. However, it is unclear which FRPA factors are measured by the TP-KYT; as this score reflects clinical experience, a model can be hypothesized where differences between rehabilitation professionals (licensed) and students (not licensed) can be measured by this tool.AimsTo identify the FRPA factors included in the TP-KYT and verify the FRPA factor model based the participants’ license status.MethodsA total of 402 participants, with 184 rehabilitation professionals (physical and occupational therapists) working in 12 medical facilities and three nursing homes, and 218 rehabilitation students (physical and occupational therapy students) from two schools participated in this study. Participant characteristics (age, gender, job role, and years of experience and education) and TP-KYT scores were collected. The 24 TP-KYT items were qualitatively analyzed using an inductive approach based on content, and FRPA factors were extracted. Next, the correction score (acquisition score/full score: 0–1) was calculated for each extracted factor, and an observation variable for the job role (rehabilitation professional = 1, rehabilitation student = 0) was set. To verify the FRPA factors associated with having or not having a rehabilitation professional license, FRPA as a latent variable and the correction score of factors as an observed variable were set, and structural equation modeling was performed by drawing a path from the job role to FRPA.ResultsThe results of the qualitative analysis aggregated patient ability (PA), physical environment (PE), and human environment (HE) as factors. The standardized coefficients of the model for participants with or without a rehabilitation professional license and FRPA were 0.85 (p < 0.001) for FRPA from job role, 0.58 for PA, 0.64 for PE, and 0.46 for HE from FRPA to each factor (p < 0.001). The model showed a good fit, with root mean square error of approximation < 0.001, goodness of fit index (GFI) = 0.998, and adjusted GFI = 0.990.ConclusionOf the three factors, PA and PE were common components of clinical practice guidelines for fall risk assessment, while HE was a distinctive component. The model’s goodness of fit, which comprised three FRPA factors based on whether participants did or did not have rehabilitation professional licenses, was good. The system suggested that rehabilitation professionals had a higher FRPA than students, comprising three factors. To provide safe and high-quality rehabilitation for patients, professional training to increase FRPA should incorporate the three factors into program content. creator: Ryohei Kishita creator: Hideki Miyaguchi creator: Tomoko Ohura creator: Katsuhiko Arihisa creator: Wataru Matsushita creator: Chinami Ishizuki uri: https://doi.org/10.7717/peerj.16724 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Kishita et al. title: COVID-19 and diet: efforts towards a balanced diet and sustainable nutrition among university students in Pakistan link: https://peerj.com/articles/16730 last-modified: 2024-01-03 description: Nutrition is an important aspect of a healthy lifestyle for all individuals, including adolescents. The objective of this cross-sectional descriptive survey study was to investigate university students’ awareness of immunity enhancing foods, food nutritive values, and eating practices during the COVID-19 pandemic. A total of 839 university students from four different universities in Pakistan participated in the study from October 2021 to January 2022, 397 of which were male and 442 were female. A total of 419 students were studying in medical disciplines while 420 were non-medical students. The students had significant knowledge (p < 0.05) about COVID-19, and nutritional habits were seen in both medical and non-medical students. Results showed that medical students (n-201) were slightly more aware of immunity-enhancing foods and the nutritive values of foods compared to engineering students (n-79). However, eating practices were generally poorly adopted by all of the university students. Male and female students were not significantly different in their mean replies to questions on the nutritive value of food or in their eating habits. Healthy eating practices will aid university students in preventing illnesses connected to nutrition as well as enhancing their immune systems and nutritional well-being both during and post-pandemic. In light of these results, suggestions and implications for nutritional advice and education were explored. creator: Zeshan Ali creator: Lienda Bashier Eltayeb creator: Sndos Z.A. Fattiny creator: Iftikhar Younis Mallhi creator: Farah Javed creator: Ali Abdullah Alyousef creator: Qandeel Ijaz creator: Shoaib Younas creator: Ishrat Khan creator: Zahra Batool creator: Muhammad Ahmad uri: https://doi.org/10.7717/peerj.16730 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ali et al. title: A survey of researchers’ methods sharing practices and priorities link: https://peerj.com/articles/16731 last-modified: 2024-01-03 description: Missing or inaccessible information about the methods used in scientific research slows the pace of discovery and hampers reproducibility. Yet little is known about how, why, and under what conditions researchers share detailed methods information, or about how such practices vary across social categories like career stage, field, and region. In this exploratory study, we surveyed 997 active researchers about their attitudes and behaviors with respect to methods sharing. The most common approach reported by respondents was private sharing upon request, but a substantial minority (33%) had publicly shared detailed methods information independently of their research findings. The most widely used channels for public sharing were connected to peer-reviewed publications, while the most significant barriers to public sharing were found to be lack of time and lack of awareness about how or where to share. Insofar as respondents were moderately satisfied with their ability to accomplish various goals associated with methods sharing, we conclude that efforts to increase public sharing may wish to focus on enhancing and building awareness of existing solutions—even as future research should seek to understand the needs of methods users and the extent to which they align with prevailing practices of sharing. creator: Marcel LaFlamme creator: James Harney creator: Iain Hrynaszkiewicz uri: https://doi.org/10.7717/peerj.16731 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 LaFlamme et al. title: Chemical and spectroscopic characterization of (Artemisinin/Querctin/ Zinc) novel mixed ligand complex with assessment of its potent high antiviral activity against SARS-CoV-2 and antioxidant capacity against toxicity induced by acrylamide in male rats link: https://peerj.com/articles/15638 last-modified: 2024-01-02 description: A novel Artemisinin/Quercetin/Zinc (Art/Q/Zn) mixed ligand complex was synthesized, tested for its antiviral activity against coronavirus (SARS-CoV-2), and investigated for its effect against toxicity and oxidative stress induced by acrylamide (Acy), which develops upon cooking starchy foods at high temperatures. The synthesized complex was chemically characterized by performing elemental analysis, conductance measurements, FT-IR, UV, magnetic measurements, and XRD. The morphological surface of the complex Art/Q/Zn was investigated using scanning and transmission electron microscopy (SEM and TEM) and energy dispersive X-ray analysis (XRD). The in vitro antiviral activity of the complex Art/Q/Zn against SARS-CoV-2 and its in vivo activity against Acy-induced toxicity in hepatic and pulmonary tissues were analyzed. An experimental model was used to evaluate the beneficial effects of the novel Art/Q/Zn novel complex on lung and liver toxicities of Acy. Forty male rats were randomly divided into four groups: control, Acy (500 mg/Kg), Art/Q/Zn (30 mg/kg), and a combination of Acy and Art/Q/Zn. The complex was orally administered for 30 days. Hepatic function and inflammation marker (CRP), tumor necrosis factor, interleukin-6 (IL-6), antioxidant enzyme (CAT, SOD, and GPx), marker of oxidative stress (MDA), and blood pressure levels were investigated. Histological and ultrastructure alterations and caspase-3 variations (immunological marker) were also investigated. FT-IR spectra revealed that Zn (II) is able to chelate through C=O and C-OH (Ring II) which are the carbonyl oxygen atoms of the quercetin ligand and carbonyl oxygen atom C=O of the Art ligand, forming Art/Q/Zn complex with the chemical formula [Zn(Q)(Art)(Cl)(H2O)2]⋅3H2O. The novel complex exhibited a potent anti-SARS-CoV-2 activity even at a low concentration (IC50 = 10.14 µg/ml) and was not cytotoxic to the cellular host (CC50 = 208.5 µg/ml). Art/Q/Zn may inhibit the viral replication and binding to the angiotensin-converting enzyme-2 (ACE2) receptor and the main protease inhibitor (MPro), thereby inhibiting the activity of SARS-CoV-2 and this proved by the molecular dynamics simulation. It alleviated Acy hepatic and pulmonary toxicity by improving all biochemical markers. Therefore, it can be concluded that the novel formula Art/Q/Zn complex is an effective antioxidant agent against the oxidative stress series, and it has high inhibitory effect against SARS-CoV-2. creator: Samy M. El-Megharbel creator: Safa H. Qahl creator: Bander Albogami creator: Reham Z. Hamza uri: https://doi.org/10.7717/peerj.15638 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 El-Megharbel et al. title: Evolution of protein domain repertoires of CALHM6 link: https://peerj.com/articles/16063 last-modified: 2024-01-02 description: Calcium (Ca2 +) homeostasis is essential in conducting various cellular processes including nerve transmission, muscular movement, and immune response. Changes in Ca2 + concentration in the cytoplasm are significant in bringing about various immune responses such as pathogen clearance and apoptosis. Various key players are involved in calcium homeostasis such as calcium binders, pumps, and channels. Sequence-based evolutionary information has recently been exploited to predict the biophysical behaviors of proteins, giving critical clues about their functionality. Ion channels are reportedly the first channels developed during evolution. Calcium homeostasis modulator protein 6 (CALHM6) is one such channel. Comprised of a single domain called Ca_hom_mod, CALHM6 is a stable protein interacting with various other proteins in calcium regulation. No previous attempt has been made to trace the exact evolutionary events in the domain of CALHM6, leaving plenty of room for exploring its evolution across a wide range of organisms. The current study aims to answer the questions by employing a computational-based strategy that used profile Hidden Markov Models (HMMs) to scan for the CALHM6 domain, integrated the data with a time-calibrated phylogenetic tree using BEAST and Mesquite, and visualized through iTOL. Around 4,000 domains were identified, and 14,000 domain gain, loss, and duplication events were observed at the end which also included various protein domains other than CALHM6. The data were analyzed concerning CALHM6 evolution as well as the domain gain, loss, and duplication of its interacting partners: Calpain, Vinculin, protein S100-A7, Thioredoxin, Peroxiredoxin, and Calmodulin-like protein 5. Duplication events of CALHM6 near higher eukaryotes showed its increasing complexity in structure and function. This in-silico phylogenetic approach applied to trace the evolution of CALHM6 was an effective approach to get a better understanding of the protein CALHM6. creator: Aneela Javed creator: Sabahat Habib creator: Aaima Ayub uri: https://doi.org/10.7717/peerj.16063 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Javed et al. title: Exogenous applications of brassinosteroids promote secondary xylem differentiation in Eucalyptus grandis link: https://peerj.com/articles/16250 last-modified: 2024-01-02 description: Brassinosteroids (BRs) play many pivotal roles in plant growth and development, especially in cell elongation and vascular development. Although its biosynthetic and signal transduction pathway have been well characterized in model plants, their biological roles in Eucalyptus grandis, a major hardwood tree providing fiber and energy worldwide, remain unclear. Here, we treated E. grandis plantlets with 24-epibrassinolide (EBL), the most active BR and/or BR biosynthesis inhibitor brassinazole. We recorded the plant growth and analyzed the cell structure of the root and stem with histochemical methods; then, we performed a secondary growth, BR synthesis, and signaling-related gene expression analysis. The results showed that the BRs dramatically increased the shoot length and diameter, and the exogenous BR increased the xylem area of the stem and root. In this process, EgrBRI1, EgrBZR1, and EgrBZR2 expression were induced by the BR treatment, and the expressions of HD-ZIPIII and cellulose synthase genes were also altered. To further verify the effect of BRs in secondary xylem development in Eucalyptus, we used six-month-old plants as the material and directly applied EBL to the xylem and cambium of the vertical stems. The xylem area, fiber cell length, and cell numbers showed considerable increases. Several key BR-signaling genes, secondary xylem development-related transcription factor genes, and cellulose and lignin biosynthetic genes were also considerably altered. Thus, BR had regulatory roles in secondary xylem development and differentiation via the BR-signaling pathway in this woody plant. creator: Fangping Zhou creator: Bing Hu creator: Juan Li creator: Huifang Yan creator: Qianyu Liu creator: Bingshan Zeng creator: Chunjie Fan uri: https://doi.org/10.7717/peerj.16250 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhou et al. title: Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches link: https://peerj.com/articles/16453 last-modified: 2024-01-02 description: Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments. creator: Ann E. Holmes creator: Melinda R. Baerwald creator: Jeff Rodzen creator: Brian M. Schreier creator: Brian Mahardja creator: Amanda J. Finger uri: https://doi.org/10.7717/peerj.16453 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Holmes et al. title: Improving maize carbon and nitrogen metabolic pathways and yield with nitrogen application rate and nitrogen forms link: https://peerj.com/articles/16548 last-modified: 2024-01-02 description: Reduced fertilizer efficiency caused by excessive use of nitrogen (N) fertilizer is a major problem in agriculture and a hot topic of research. Most studies have focused on the effect of N application rate on N efficiency, whereas there are limited studies on changing the N form to improve N yield and efficiency. Here, the effects of different N application rates and nitrate-to-ammonium N ratios on post-anthesis carbon (C) and N metabolism and maize yield under shallow-buried drip irrigation were investigated. Two rates of N application (210 kg·ha−1 (NA1) and 300 kg·ha−1 (NA2)) and three nitrate-to-ammonium N ratios (2:1 (NF1), 3:1 (NF2), and 4:1 (NF3)) were utilized. Post-anthesis photosynthetic characteristics, activities of key enzymes in photosynthetic C and N metabolism, nonstructural carbohydrate content, post-anthesis N accumulation and transportation, yield, and N-use efficiency were determined. At both N application rates, NF2 treatment enhanced photosynthetic activity in the ear-leaf at silking stage and promoted key enzyme activities of C and N metabolic pathways, compared with NF1 and NF3. Furthermore, NF2 significantly increased nonstructural carbohydrate accumulation (4.00–64.71%), post-anthesis N accumulation and transportation (11.00–38.00%), and grain yield (2.60–13.08%). No significant differences between NA1 and NA2 were observed under NF2 in most of the measured variables; however, NA1 had higher N-use efficiency. Thus, the optimal treatment under shallow-buried drip irrigation was a N application rate of 210 kg ha−1 and a nitrate-to-ammonium N ratio of 3:1. These findings provide theoretical guidance on appropriate N applications for high-yield maize production. creator: Fanhao Meng creator: Ruifu Zhang creator: Yuqin Zhang creator: Weimin Li creator: Yushan Zhang creator: Mingwei Zhang creator: Xuezhen Yang creator: Hengshan Yang uri: https://doi.org/10.7717/peerj.16548 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Meng et al. title: Diagnostic value of artificial intelligence based on computed tomography (CT) density in benign and malignant pulmonary nodules: a retrospective investigation link: https://peerj.com/articles/16577 last-modified: 2024-01-02 description: ObjectiveTo evaluate the diagnostic value of artificial intelligence (AI) in the detection and management of benign and malignant pulmonary nodules (PNs) using computed tomography (CT) density.MethodsA retrospective analysis was conducted on the clinical data of 130 individuals diagnosed with PNs based on pathological confirmation. The utilization of AI and physicians has been employed in the diagnostic process of distinguishing benign and malignant PNs. The CT images depicting PNs were integrated into AI-based software. The gold standard for evaluating the accuracy of AI diagnosis software and physician interpretation was the pathological diagnosis.ResultsOut of 226 PNs screened from 130 patients diagnosed by AI and physician reading based on CT, 147 were confirmed by pathology. AI had a sensitivity of 94.69% and radiologists had a sensitivity of 85.40% in identifying PNs. The chi-square analysis indicated that the screening capacity of AI was superior to that of physician reading, with statistical significance (p < 0.05). 195 of the 214 PNs suggested by AI were confirmed pathologically as malignant, and 19 were identified as benign; among the 29 PNs suggested by AI as low risk, 13 were confirmed pathologically as malignant, and 16 were identified as benign. From the physician reading, 193 PNs were identified as malignant, 183 were confirmed malignant by pathology, and 10 appeared benign. Physician reading also identified 30 low-risk PNs, 19 of which were pathologically malignant and 11 benign. The physician readings and AI had kappa values of 0.432 and 0.547, respectively. The physician reading and AI area under curves (AUCs) were 0.814 and 0.798, respectively. Both of the diagnostic techniques had worthy diagnostic value, as indicated by their AUCs of >0.7.ConclusionIt is anticipated that the use of AI-based CT diagnosis in the detection of PNs would increase the precision in early detection of lung carcinoma, as well as yield more precise evidence for clinical management. creator: Wei Fan creator: Huitong Liu creator: Yan Zhang creator: Xiaolong Chen creator: Minggang Huang creator: Bingqiang Xu uri: https://doi.org/10.7717/peerj.16577 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fan et al. title: Speeding up iterative applications of the BUILD supertree algorithm link: https://peerj.com/articles/16624 last-modified: 2024-01-02 description: The Open Tree of Life (OToL) project produces a supertree that summarizes phylogenetic knowledge from tree estimates published in the primary literature. The supertree construction algorithm iteratively calls Aho’s Build algorithm thousands of times in order to assess the compatability of different phylogenetic groupings. We describe an incrementalized version of the Build algorithm that is able to share work between successive calls to Build. We provide details that allow a programmer to implement the incremental algorithm BuildInc, including pseudo-code and a description of data structures. We assess the effect of BuildInc on our supertree algorithm by analyzing simulated data and by analyzing a supertree problem taken from the OpenTree 13.4 synthesis tree. We find that BuildInc provides up to 550-fold speedup for our supertree algorithm. creator: Benjamin D. Redelings creator: Mark T. Holder uri: https://doi.org/10.7717/peerj.16624 license: https://creativecommons.org/licenses/by/4.0/ rights: 2024 Redelings and Holder title: Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone link: https://peerj.com/articles/16664 last-modified: 2024-01-02 description: BackgroundThe niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron.MethodsWe split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds’ niches converge.ResultsOur findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region. creator: Viridiana Lizardo creator: Erick Alejandro García Trejo creator: Juan J. Morrone uri: https://doi.org/10.7717/peerj.16664 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lizardo et al. title: A successful method to restore seagrass habitats in coastal areas affected by consecutive natural events link: https://peerj.com/articles/16700 last-modified: 2024-01-02 description: BackgroundSeagrass meadows, known for providing essential ecosystem services like supporting fishing, coastline protection from erosion, and acting as carbon sinks to mitigate climate change effects, are facing severe degradation. The current deteriorating state can be attributed to the combination of anthropogenic activities, biological factors (i.e., invasive species), and natural forces (i.e., hurricanes). Indeed, the global seagrass cover is diminishing at an alarming mean rate of 7% annually, jeopardizing the health of these vital ecosystems. However, in the Island Municipality of Culebra, Puerto Rico, losses are occurring at a faster pace. For instance, hurricanes have caused over 10% of cover seagrass losses, and the natural recovery of seagrasses across Culebra’s coast has been slow due to the low growth rates of native seagrasses (Thalassia testudinum and Syringodium filiforme) and the invasion of the invasive species Halophila stipulacea. Restoration programs are, thus, necessary to revitalize the native seagrass communities and associated fauna while limiting the spread of the invasive species.MethodsHere, we present the results of a seagrass meadow restoration project carried out in Punta Melones (PTM), Culebra, Puerto Rico, in response to the impact of Hurricanes Irma and María during 2017. The restoration technique used was planting propagation units (PUs), each with an area of 900 cm2 of native seagrasses Thalassia testudinum and Syringodium filiforme, planted at a depth between 3.5 and 4.5 m. A total of 688 PUs were planted between August 2021 and August 2023, and a sub-sample of 88 PUs was monitored between August 2021 and April 2023.ResultsPUs showed over 95% of the seagrass survived, with Hurricane Fiona causing most of the mortalities potentially due to PUs burial by sediment movement and uplifting by wave energy. The surface area of the planting units increased by approximately 200% (i.e., 2,459 cm2), while seagrass shoot density increased by 168% (i.e., 126 shoots by PU). Additionally, flowering and fruiting were observed in multiple planting units, indicating 1) that the action taken did not adversely affect the PUs units and 2) that the project was successful in revitalizing seagrass populations. The seagrass restoration project achieved remarkable success, primarily attributed to the substantial volume of each PUs. Likely this high volume played a crucial role in facilitating the connection among roots, shoots, and microfauna while providing a higher number of undamaged and active rhizome meristems and short shoots. These factors collectively contributed to the enhanced growth and survivorship of the PUs, ultimately leading to the favorable outcome observed in the seagrass restoration project. creator: Claudia Patricia Ruiz-Diaz creator: Carlos Toledo-Hernández creator: Juan Luis Sánchez-González creator: Alex E. Mercado-Molina uri: https://doi.org/10.7717/peerj.16700 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ruiz-Diaz et al. title: Quercetin alleviates PM2.5-induced chronic lung injury in mice by targeting ferroptosis link: https://peerj.com/articles/16703 last-modified: 2024-01-02 description: BackgroundPM2.5 is a well-known harmful air pollutant that can lead to acute exacerbation and aggravation of respiratory diseases. Although ferroptosis is involves in the pathological process of pulmonary disease, the potential mechanism of ferroptosis in PM2.5-caused lung inflammation and fibrosis need to be further clarified. Quercetin is a phenolic compound that can inhibit ferroptosis in various diseases. Hence, this study explores the role of ferroptosis in lung injury induced by PM2.5 in order to further elucidate the beneficial effect of quercetin and its underlying mechanism.MethodsC57BL/6J mice were treated with either saline or PM2.5 by intratracheal instillation 20 times (once every two days). Additionally, PM2.5-treated mice were supplemented with two doses of quercetin. Lung injury, lipid peroxidation, iron content and ferroptosis marker protein expression and the Nrf2 signaling pathway were evaluated. In vitro, cell experiments were applied to verify the mechanisms underlying the links between Nrf2 signaling pathway activation and ferroptosis as well as between ferroptosis and inflammation.ResultsIn vivo, PM2.5 increased lung inflammation and caused lung fibrosis and increased lipid peroxidation contents, iron contents and ferroptosis markers in lung tissues; these effects were significantly reversed by quercetin. Additionally, quercetin upregulated the nuclear Nrf2 expression and downregulated Keap1 expression in lung tissues of PM2.5-exposed mice. Quercetin decreased lipid peroxidation products, iron contents and ferroptosis levels and increased the nuclear translocation of Nrf2 and the degradation of Keap1 in PM2.5-exposed BEAS-2B cells. Moreover, we found that quercetin and dimethyl fumarate markedly decreased lipid peroxidation production and ferroptosis by activating the Nrf2-Keap1 pathway in PM2.5-exposed cells. Furthermore, quercetin reduced inflammatory cytokines and TGF-β1 in PM2.5-exposed cells.ConclusionOur data suggested that Nrf2 is involved in ferroptosis in PM2.5-induced lung injury, and quercetin can alleviate these adverse effects via activating Nrf2-Keap1 signaling pathway. creator: Shibin Ding creator: Jinjin Jiang creator: Yang Li uri: https://doi.org/10.7717/peerj.16703 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ding et al. title: Identification and characterization of biomarkers associated with endoplasmic reticulum protein processing in cerebral ischemia-reperfusion injury link: https://peerj.com/articles/16707 last-modified: 2024-01-02 description: BackgroundCerebral ischemia (CI), ranking as the second leading global cause of death, is frequently treated by reestablishing blood flow and oxygenation. Paradoxically, this reperfusion can intensify tissue damage, leading to CI-reperfusion injury. This research sought to uncover biomarkers pertaining to protein processing in the endoplasmic reticulum (PER) during CI-reperfusion injury.MethodsWe utilized the Gene Expression Omnibus (GEO) dataset GSE163614 to discern differentially expressed genes (DEGs) and single out PER-related DEGs. The functions and pathways of these PER-related DEGs were identified via Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Core genes were pinpointed through protein-protein interaction (PPI) networks. Subsequent to this, genes with diagnostic relevance were distinguished using external validation datasets. A single-sample gene-set enrichment analysis (ssGSEA) was undertaken to pinpoint genes with strong associations to hypoxia and apoptosis, suggesting their potential roles as primary inducers of apoptosis in hypoxic conditions during ischemia-reperfusion injuries.ResultsOur study demonstrated that PER-related genes, specifically ADCY5, CAMK2A, PLCB1, NTRK2, and DLG4, were markedly down-regulated in models, exhibiting a robust association with hypoxia and apoptosis.ConclusionThe data indicates that ADCY5, CAMK2A, PLCB1, NTRK2, and DLG4 could be pivotal genes responsible for triggering apoptosis in hypoxic environments during CI-reperfusion injury. creator: Liang-da Li creator: Yue Zhou creator: Shan-fen Shi uri: https://doi.org/10.7717/peerj.16707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Proteomics-based screening of AKR1B1 as a therapeutic target and validation study for sepsis-associated acute kidney injury link: https://peerj.com/articles/16709 last-modified: 2024-01-02 description: BackgroundSepsis and sepsis-associated acute kidney injury (SA-AKI) pose significant global health challenges, necessitating the development of innovative therapeutic strategies. Dysregulated protein expression has been implicated in the initiation and progression of sepsis and SA-AKI. Identifying potential protein targets and modulating their expression is crucial for exploring alternative therapies.MethodWe established an SA-AKI rat model using cecum ligation perforation (CLP) and employed differential proteomic techniques to identify protein expression variations in kidney tissues. Aldose reductase (AKR1B1) emerged as a promising target. The SA-AKI rat model received treatment with the aldose reductase inhibitor (ARI), epalrestat. Blood urea nitrogen (BUN) and creatinine (CRE) levels, as well as IL-1β, IL-6 and TNF-α levels in the serum and kidney tissues, were monitored. Hematoxylin-eosin (H-E) staining and a pathological damage scoring scale assessed renal tissue damage, while protein blotting determined PKC (protein kinase C)/NF-κB pathway protein expression.ResultDifferential proteomics revealed significant downregulation of seven proteins and upregulation of 17 proteins in the SA-AKI rat model renal tissues. AKR1B1 protein expression was notably elevated, confirmed by Western blot. ARI prophylactic administration and ARI treatment groups exhibited reduced renal injury, low BUN and CRE levels and decreased IL-1β, IL-6 and TNF-α levels compared to the CLP group. These changes were statistically significant (P < 0.05). AKR1B1, PKC-α, and NF-κB protein expression levels were also lowered in the ARI prophylactic administration and ARI treatment groups compared to the CLP group (P < 0.05).ConclusionsEpalrestat appeared to inhibit the PKC/NF-κB inflammatory pathway by inhibiting AKR1B1, resulting in reduced inflammatory cytokine levels in renal tissues and blood. This mitigated renal tissue injuries and improved the systemic inflammatory response in the severe sepsis rat model. Consequently, AKR1B1 holds promise as a target for treating sepsis-associated acute kidney injuries. creator: Lei Li creator: Zaiqin Ling creator: Xingsheng Wang creator: Xinxin Zhang creator: Yun Li creator: Guangsheng Gao uri: https://doi.org/10.7717/peerj.16709 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: The role of TRIF protein in regulating the proliferation and antigen presentation ability of myeloid dendritic cells through the ERK1/2 signaling pathway in chronic low-grade inflammation of intestinal mucosa mediated by flagellin-TLR5 complex signal link: https://peerj.com/articles/16716 last-modified: 2024-01-02 description: ObjectiveThe objective is to explore whether the flagellin-TLR5 complex signal can enhance the antigen presentation ability of myeloid DCs through the TRIF-ERK1/2 pathway, and the correlation between this pathway and intestinal mucosal inflammation response.MethodsMouse bone marrow-derived DC line DC2.4 was divided into four groups: control group (BC) was DC2.4 cells cultured normally; flagellin single signal stimulation group (DC2.4+CBLB502) was DC2.4 cells stimulated with flagellin derivative CBLB502 during culture; TLR5-flagellin complex signal stimulation group (ov-TLR5-DC2.4+CBLB502) was flagellin derivative CBLB502 stimulated ov-TLR5-DC2.4 cells with TLR5 gene overexpression; TRIF signal interference group (ov-TLR5-DC2.4+CBLB502+Pepinh-TRIFTFA) was ov-TLR5-DC2.4 cells with TLR5 gene overexpression stimulated with flagellin derivative CBLB502 and intervened with TRIF-specific inhibitor Pepinh-TRIFTFA. WB was used to detect the expression of TRIF and p-ERK1/2 proteins in each group of cells; CCK8 was used to detect cell proliferation in each group; flow cytometry was used to detect the expression of surface molecules MHCI, MHCII, CD80, 86 in each group of cells; ELISA was used to detect the levels of IL-12 and IL-4 cytokines in each group.ResultsCompared with the BC group, DC2.4+CBLB502 group, and ov-TLR5-DC2.4+CBLB502+Pepinh-TRIFTFA group, the expression of TRIF protein and p-ERK1/2 protein in ov-TLR5-DC2.4+CBLB502 group was significantly upregulated (TRIF: p = 0.02,  = 0.007,  = 0.048) (ERK1: p < 0.001, =0.0003,  = 0.0004; ERK2:p = 0.0003,  = 0.0012,  = 0.0022). The cell proliferation activity in ov-TLR5-DC2.4+CBLB502 group was enhanced compared with the other groups (p = 0.0001, p < 0.0001, p = 0.0015); at the same time, the expression of surface molecules MHCI, MHCII, CD80, 86 on DCs was upregulated (p < 0.05); and the secretion of IL-12 and IL-4 cytokines was increased, with significant differences (IL-12: p < 0.0001, p < 0.0001, p = 0.0005; IL-4: p =  < 0.0001, p =  < 0.0001, p = 0.0001). However, the ov-TLR5-DC2.4+CBLB502+Pepinh-TRIFTFA group, which was treated with TRIF signal interference, showed a decrease in intracellular TRIF protein and p-ERK1/2 protein, as well as a decrease in cell proliferation ability and surface stimulation molecules, and a decrease in the secretion of IL-12 and IL-4 cytokines (p < 0.05).ConclusionAfter stimulation of flagellin protein-TLR5 complex signal, TRIF protein and p-ERK1/2 protein expression in myeloid dendritic cells were significantly up-regulated, accompanied by increased proliferation activity and maturity of DCs, enhanced antigen presentation function, increased secretion of pro-inflammatory cytokines IL-12 and IL-4. This process can be inhibited by the specific inhibitor of TRIF signal, suggesting that the TLR5-TRIF-ERK1/2 pathway may play an important role in abnormal immune response and mucosal chronic inflammation infiltration mediated by flagellin protein in DCs, which can provide a basis for our subsequent animal experiments. creator: Zhaomeng Zhuang creator: Yi Chen creator: Juanhong Zheng creator: Shuo Chen uri: https://doi.org/10.7717/peerj.16716 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhuang et al. title: Differences in external load among indoor and beach volleyball players during elite matches link: https://peerj.com/articles/16736 last-modified: 2024-01-02 description: The aim of this cross-sectional study was to examine relationships of external load variables between beach and indoor volleyball amongst individual positions on the team. The movements of eight beach and fourteen indoor female volleyball players were recorded during elite playoff matches; in total, 2,336 three-dimensional trajectories were analyzed. Time-outs and intervals between rallies or sets were excluded from active play time. In both beach and indoor volleyball, 80% of rallies lasted up to 10 s, and players covered 4.5 to 10 m of court during 60% of rally play. Differences in dependent variables of external load were found between independent variables of sports and player positions (p < 0.05). The distance covered in beach volleyball rallies and Player Load™ parameters was significantly higher by up to 23%. The unstable court surface with sand in beach volleyball elevated explosive Player Load™ (accelerations in all three orthogonal planes of motion higher than 3.5 m/s3) in beach volleyball players compared to those of players on stable flooring in indoor. While beach volleyball blocker and defender positions showed no significant difference in parameters between each other, they differed in all parameters when compared to player positions in indoor volleyball. Indoor blocker and libero reached higher loads than setter, outside and opposite positions in various parameters. Factors that influence external load include the larger relative court areas covered by each player in beach volleyball, complexity of players’ roles, and game strategy. This data adds to the knowledge of elite match demands in female volleyball. Specified agility-drill distances and times are essential for training optimization and must be supported by scientific observation. Researchers, coaches, and conditioning specialists should find this helpful for achieving a higher degree of training regulation. creator: Mikulas Hank creator: Lee Cabell creator: Frantisek Zahalka creator: Petr Miřátský creator: Bohuslav Cabrnoch creator: Lucia Mala creator: Tomas Maly uri: https://doi.org/10.7717/peerj.16736 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hank et al.