title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2024-04 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny—a case study on dwarf chameleons link: https://peerj.com/articles/17076 last-modified: 2024-04-30 description: Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work. creator: Devon C. Main creator: Jody M. Taft creator: Anthony J. Geneva creator: Bettine Jansenvan Vuuren creator: Krystal A. Tolley uri: https://doi.org/10.7717/peerj.17076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Main et al. title: Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities link: https://peerj.com/articles/17091 last-modified: 2024-04-30 description: Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe. creator: Alice J. Clark creator: Sophie R. Atkinson creator: Valentina Scarponi creator: Tim Cane creator: Nathan R. Geraldi creator: Ian W. Hendy creator: J. Reuben Shipway creator: Mika Peck uri: https://doi.org/10.7717/peerj.17091 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Clark et al. title: Pollen thermotolerance of a widespread plant, Lotus corniculatus, in response to climate warming: possible local adaptation of populations from different elevations link: https://peerj.com/articles/17148 last-modified: 2024-04-30 description: One of the most vulnerable phases in the plant life cycle is sexual reproduction, which depends on effective pollen transfer, but also on the thermotolerance of pollen grains. Pollen thermotolerance is temperature-dependent and may be reduced by increasing temperature associated with global warming. A growing body of research has focused on the effect of increased temperature on pollen thermotolerance in crops to understand the possible impact of temperature extremes on yield. Yet, little is known about the effects of temperature on pollen thermotolerance of wild plant species. To fill this gap, we selected Lotus corniculatus s.l. (Fabaceae), a species common to many European habitats and conducted laboratory experiments to test its pollen thermotolerance in response to artificial increase in temperature. To test for possible local adaptation of pollen thermal tolerance, we compared data from six lowland (389–451 m a.s.l.) and six highland (841–1,030 m a.s.l.) populations. We observed pollen germination in vitro at 15 °C, 25 °C, 30 °C, and 40 °C. While lowland plants maintained a stable germination percentage across a broad temperature range (15–30 °C) and exhibited reduced germination only at extremely high temperatures (40 °C), highland plants experienced reduced germination even at 30 °C–temperatures commonly exceeded in lowlands during warm summers. This suggests that lowland populations of L. corniculatus may be locally adapted to higher temperature for pollen germination. On the other hand, pollen tube length decreased with increasing temperature in a similar way in lowland and highland plants. The overall average pollen germination percentage significantly differed between lowland and highland populations, with highland populations displaying higher germination percentage. On the other hand, the average pollen tube length was slightly smaller in highland populations. In conclusion, we found that pollen thermotolerance of L. corniculatus is reduced at high temperature and that the germination of pollen from plant populations growing at higher elevations is more sensitive to increased temperature, which suggests possible local adaptation of pollen thermotolerance. creator: Karolína Jackwerth creator: Paolo Biella creator: Jan Klečka uri: https://doi.org/10.7717/peerj.17148 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jackwerth et al. title: Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease link: https://peerj.com/articles/17186 last-modified: 2024-04-30 description: Pulmonary hypertension (PH), a common complication in dogs affected by degenerative mitral valve disease (DMVD), is a progressive disorder characterized by increased pulmonary arterial pressure (PAP) and pulmonary vascular remodeling. Phosphorylation of proteins, impacting vascular function and cell proliferation, might play a role in the development and progression of PH. Unlike gene or protein studies, phosphoproteomic focuses on active proteins that function as end-target proteins within signaling cascades. Studying phosphorylated proteins can reveal active contributors to PH development. Early diagnosis of PH is crucial for effective management and improved clinical outcomes. This study aimed to identify potential serum biomarkers for diagnosing PH in dogs affected with DMVD using a phosphoproteomic approach. Serum samples were collected from healthy control dogs (n = 28), dogs with DMVD (n = 24), and dogs with DMVD and PH (n = 29). Phosphoproteins were enriched from the serum samples and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Data analysis was performed to identify uniquely expressed phosphoproteins in each group and differentially expressed phosphoproteins among groups. Phosphoproteomic analysis revealed nine uniquely expressed phosphoproteins in the serum of dogs in the DMVD+PH group and 15 differentially upregulated phosphoproteins in the DMVD+PH group compared to the DMVD group. The phosphoproteins previously implicated in PH and associated with pulmonary arterial remodeling, including small nuclear ribonucleoprotein G (SNRPG), alpha-2-macroglobulin (A2M), zinc finger and BTB domain containing 42 (ZBTB42), hemopexin (HPX), serotransferrin (TRF) and complement C3 (C3), were focused on. Their unique expression and differential upregulation in the serum of DMVD dogs with PH suggest their potential as biomarkers for PH diagnosis. In conclusion, this phosphoproteomic study identified uniquely expressed and differentially upregulated phosphoproteins in the serum of DMVD dogs with PH. Further studies are warranted to validate the diagnostic utility of these phosphoproteins. creator: Siriwan Sakarin creator: Anudep Rungsipipat creator: Sittiruk Roytrakul creator: Janthima Jaresitthikunchai creator: Narumon Phaonakrop creator: Sawanya Charoenlappanit creator: Siriwan Thaisakun creator: Sirilak Surachetpong uri: https://doi.org/10.7717/peerj.17186 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sakarin et al. title: Interactions between chaperone and energy storage networks during the evolution of Legionella pneumophila under heat shock link: https://peerj.com/articles/17197 last-modified: 2024-04-30 description: Waterborne transmission of the bacterium Legionella pneumophila has emerged as a major cause of severe nosocomial infections of major public health impact. The major route of transmission involves the uptake of aerosolized bacteria, often from the contaminated hot water systems of large buildings. Public health regulations aimed at controlling the mesophilic pathogen are generally concerned with acute pasteurization and maintaining high temperatures at the heating systems and throughout the plumbing of hot water systems, but L. pneumophila is often able to survive these treatments due to both bacterium-intrinsic and environmental factors. Previous work has established an experimental evolution system to model the observations of increased heat resistance in repeatedly but unsuccessfully pasteurized L. pneumophila populations. Here, we show rapid fixation of novel alleles in lineages selected for resistance to heat shock and shifts in mutational profile related to increases in the temperature of selection. Gene-level and nucleotide-level parallelisms between independently-evolving lineages show the centrality of the DnaJ/DnaK chaperone system in the heat resistance of L. pneumophila. Inference of epistatic interactions through reverse genetics shows an unexpected interaction between DnaJ/DnaK and the polyhydroxybutyrate-accumulation energy storage mechanism used by the species to survive long-term starvation in low-nutrient environments. creator: Jeffrey Liang creator: Sebastien P. Faucher uri: https://doi.org/10.7717/peerj.17197 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liang and Faucher title: The low survival rate of European hare leverets in arable farmland: evidence from the predation experiment link: https://peerj.com/articles/17235 last-modified: 2024-04-30 description: The low survival rate of leverets may significantly contribute to steep population declines and slow recovery of European hares (Lepus europaeus). However, the leveret survival rate in farmlands with different landscape structures is poorly understood, and the existing evidence comes mainly from Western Europe. In this study, we explored the survival of leveret hare dummies along linear semi-natural habitats in homogeneous Central European arable farmland during the main part of the European hare reproduction period (March–April) in 2019 and 2020. The survival rate of hare leverets during the 14-day period was only 22.2%, and all predation events were recorded during the first six days of the experiment. Mammalian predators were responsible for 53.1% of predation events, avian predators for 40.8%, and agricultural operations for 6.1%. The red fox (Vulpes vulpes) was the dominant predator in our study area and was the primary cause of leveret dummy mortality (32.7%), but it also had the highest use-intensity and visit frequency of all of the study plots. Predation by avian predators was associated with patches of lower vegetation height and cover (such as plowed fields) and during daylight hours, whereas the opposite was true for mammalian predators. We propose that improving the habitat quality of arable landscapes by increasing the proportion and quality of extensively used non-farmed habitats (e.g., set-asides, wildflower areas, extensive meadows, fallow land, and semi-natural habitats on arable land) providing cover and shelter for leverets could be an effective management measure for reducing predation risk on leverets. creator: Jan Cukor creator: Jan Riegert creator: Aleksandra Krivopalova creator: Zdeněk Vacek creator: Martin Šálek uri: https://doi.org/10.7717/peerj.17235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cukor et al. title: Cystatin C: immunoregulation role in macrophages infected with Porphyromonas gingivalis link: https://peerj.com/articles/17252 last-modified: 2024-04-30 description: BackgroundPeriodontitis is a chronic infectious disease, characterized by an exacerbated inflammatory response and a progressive loss of the supporting tissues of the teeth. Porphyromonas gingivalis is a key etiologic agent in periodontitis. Cystatin C is an antimicrobial salivary peptide that inhibits the growth of P. gingivalis. This study aimed to evaluate the antimicrobial activity of this peptide and its effect on cytokine production, nitric oxide (NO) release, reactive oxygen species (ROS) production, and programmed cell death in human macrophages infected with P. gingivalis.MethodsMonocyte-derived macrophages generated from peripheral blood were infected with P. gingivalis (MOI 1:10) and stimulated with cystatin C (2.75 µg/ml) for 24 h. The intracellular localization of P. gingivalis and cystatin C was determined by immunofluorescence and transmission electron microscopy (TEM). The intracellular antimicrobial activity of cystatin C in macrophages was assessed by counting Colony Forming Units (CFU). ELISA assay was performed to assess inflammatory (TNFα, IL-1β) and anti-inflammatory (IL-10) cytokines. The production of nitrites and ROS was analyzed by Griess reaction and incubation with 2′,7′-dichlorodihydrofluorescein diacetate (H2DCFDA), respectively. Programmed cell death was assessed with the TUNEL assay, Annexin-V, and caspase activity was also determined.ResultsOur results showed that cystatin C inhibits the extracellular growth of P. gingivalis. In addition, this peptide is internalized in the infected macrophage, decreases the intracellular bacterial load, and reduces the production of inflammatory cytokines and NO. Interestingly, peptide treatment increased ROS production and substantially decreased bacterial-induced macrophage apoptosis.ConclusionsCystatin C has antimicrobial and immuno-regulatory activity in macrophages infected with P. gingivalis. These findings highlight the importance of understanding the properties of cystatin C for its possible therapeutic use against oral infections such as periodontitis. creator: Blanca Esther Blancas-Luciano creator: Ingeborg Becker-Fauser creator: Jaime Zamora-Chimal creator: Luis Jiménez-García creator: Reyna Lara-Martínez creator: Armando Pérez-Torres creator: Margarita González del Pliego creator: Elsa Liliana Aguirre-Benítez creator: Ana María Fernández-Presas uri: https://doi.org/10.7717/peerj.17252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Blancas-Luciano et al. title: Analysis of drought and heat stress response genes in rice using co-expression network and differentially expressed gene analyses link: https://peerj.com/articles/17255 last-modified: 2024-04-30 description: Studies on Oryza sativa (rice) are crucial for improving agricultural productivity and ensuring global sustenance security, especially considering the increasing drought and heat stress caused by extreme climate change. Currently, the genes and mechanisms underlying drought and heat resistance in rice are not fully understood, and the scope for enhancing the development of new strains remains considerable. To accurately identify the key genes related to drought and heat stress responses in rice, multiple datasets from the Gene Expression Omnibus (GEO) database were integrated in this study. A co-expression network was constructed using a Weighted Correlation Network Analysis (WGCNA) algorithm. We further distinguished the core network and intersected it with differentially expressed genes and multiple expression datasets for screening. Differences in gene expression levels were verified using quantitative real-time polymerase chain reaction (PCR). OsDjC53, MBF1C, BAG6, HSP23.2, and HSP21.9 were found to be associated with the heat stress response, and it is also possible that UGT83A1 and OsCPn60a1, although not directly related, are affected by drought stress. This study offers significant insights into the molecular mechanisms underlying stress responses in rice, which could promote the development of stress-tolerant rice breeds. creator: Gaohui Cao creator: Hao Huang creator: Yuejiao Yang creator: Bin Xie creator: Lulu Tang uri: https://doi.org/10.7717/peerj.17255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cao et al. title: Structural equation models of health behaviour, psychological well-being, symptom severity and quality of life in abdominal bloating link: https://peerj.com/articles/17265 last-modified: 2024-04-30 description: BackgroundThe objective of this study was to investigate the inter-relationship between psychosocial variables and their impact on symptom severity and quality of life (QoL) concerning abdominal bloating.MethodsThe study adopted a cross-sectional design with purposive sampling. Participants who consented and met the criteria for bloating based on the Rome IV classification completed designated questionnaires. Independent variables comprised health beliefs, intentions, health-promoting behaviors, social support, depression, and anxiety, while dependent variables included bloating severity (general and within 24 h) and QoL. Structural Equation Modeling (SEM) was conducted utilizing Mplus 8.0 to analyze the relationships between these factors.ResultsA total of 323 participants, with a mean age of 27.69 years (SD = 11.50), predominantly females (64.7%), volunteered to participate in the study. The final SEM model exhibited good fit based on various indices (CFI = 0.922, SRMR = 0.064, RMSEA (95% CI) = 0.048 (0.041–0.054), p-value = 0.714), with 15 significant path relationships identified. The model explained 12.0% of the variance in severity within 24 h, 6% in general severity, and 53.8% in QoL.ConclusionThe findings underscore the significant influence of health beliefs, intentions, behaviors, social support, depression, and anxiety on symptom severity and QoL in individuals experiencing abdominal bloating. creator: Nurzulaikha Abdullah creator: Yee Cheng Kueh creator: Garry Kuan creator: Mung Seong Wong creator: Vincent Tee creator: Tengku Ahmad Iskandar Tengku Alang creator: Nurhazwani Hamid creator: Yeong Yeh Lee uri: https://doi.org/10.7717/peerj.17265 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Abdullah et al. title: Photoactivated disinfection procedure for denture stomatitis in diabetic rats link: https://peerj.com/articles/17268 last-modified: 2024-04-30 description: ObjectiveTo study the efficacy of PADTM Plus-based photoactivated disinfection (PAD) for treating denture stomatitis (DS) in diabetic rats by establishing a diabetic rat DS model.MethodsThe diabetic rat DS model was developed by randomly selecting 2-month-old male Sprague-Dawley rats and dividing them into four groups. The palate and denture surfaces of rats in the PAD groups were incubated with 1 mg/mL toluidine blue O for 1 min each, followed by a 1-min exposure to 750-mW light-emitting diode light. The PAD-1 group received one radiation treatment, and the PAD-2 group received three radiation treatments over 5 days with a 1-day interval. The nystatin (NYS) group received treatment for 5 days with a suspension of NYS of 100,000 IU. The infection group did not receive any treatment. In each group, assessments included an inflammation score of the palate, tests for fungal load, histological evaluation, and immunohistochemical detection of interleukin-17 (IL-17) and tumor necrosis factor (TNF-α) conducted 1 and 7 days following the conclusion of treatment.ResultsOne day after treatment, the fungal load on the palate and dentures, as well as the mean optical density values of IL-17 and TNF-α, were found to be greater in the infection group than in the other three treatment groups (P < 0.05). On the 7th day after treatment, these values were significantly higher in the infection group than in the PAD-2 and NYS groups (P < 0.05). Importantly, there were no differences between the infection and PAD-1 groups nor between the PAD-2 and NYS groups (P > 0.05).ConclusionsPAD effectively reduced the fungal load and the expressions of IL-17 and TNF-α in the palate and denture of diabetic DS rats. The efficacy of multiple-light treatments was superior to that of single-light treatments and similar to that of NYS. creator: Xiao Zhang creator: Zirui Zhao creator: Ruiqi Zhang creator: Juan Liu creator: Zhijiao Guo creator: Qiaoyu Hu creator: Na Liu creator: Qing Liu uri: https://doi.org/10.7717/peerj.17268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Gradual pollen presentation in Vaccinium corymbosum ‘Bluecrop’: an adaptive mechanism to improve pollination efficiency and outcrossing link: https://peerj.com/articles/17273 last-modified: 2024-04-30 description: Gradual pollen presentation is a plant reproductive mechanism to improve pollination efficiency and accuracy and promote outcrossing. Vaccinium corymbosum ‘Bluecrop’ has a typical gradual pollen presentation mechanism. ‘Bluecrop’ exhibits an inverted bell-shaped flower with a white coloration. By investigating the flower syndrome, pollination characteristics, pollination efficiency, and breeding system of ‘Bluecrop’, this study aims to explore the adaptive significance of these traits. The results showed ‘Bluecrop’ released pollen gradually through anther poricidal dehiscence. Among different pollinators, Apis mellifera and Bombus can pollinate effectively, and the mechanism of gradual pollen presentation significantly improved the efficiency of pollen transfer. This characteristic limits the amount of pollen removed by the pollinators and prolongs pollen presentation, thus attracting more pollinators and thereby increasing male fitness. The nectar secretion of ‘Bluecrop’ is gradual, with a large nectar production and a long phase of nectar secretion, enhance visitation frequencies and the chances of successful pollination. At the same time, campanulate corolla can protect pollen as well as nectar from waste due to environmental factors and other effects. The breeding system of ‘Bluecrop’ relies mainly on outcrossing because of its low affinity for self-fertilization and good interaction with pollinating insects. Thus, the special floral syndrome and the mechanism of secondary pollen presentation are significant in improving pollination efficiency and promoting the reproductive success of ‘Bluecrop’ by outcrossing. It can provide a certain theoretical basis for the future propagation breeding of ‘Bluecrop’. creator: Chunzhi Zhou creator: Yalong Yu creator: Yuwei Liu creator: Shanlin Yang creator: Yanfeng Chen uri: https://doi.org/10.7717/peerj.17273 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic link: https://peerj.com/articles/17277 last-modified: 2024-04-30 description: BackgroundSquamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups.MethodsWe used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found.ResultsIncorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further. creator: Ian V. Wilenzik creator: Benjamin B. Barger creator: R. Alexander Pyron uri: https://doi.org/10.7717/peerj.17277 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wilenzik et al. title: The impact of skeletal muscle index at the third lumbar spine on nosocomial deterioration and short-term prognosis in acute pancreatitis: a retrospective observational study link: https://peerj.com/articles/17283 last-modified: 2024-04-30 description: ObjectiveTo investigate the impact of the third lumbar skeletal muscle index (L3-SMI) assessed by CT on the in-hospital severity and short-term prognosis of acute pancreatitis.MethodsA total of 224 patients with severe acute pancreatitis admitted to Yantaishan Hospital from January 2021 to June 2022 were selected as the subjects. Based on the in-hospital treatment outcomes, they were divided into a mortality group of 59 cases as well as a survival group of 165 cases. Upon admission, general information such as the Acute Physiology and Chronic Health Evaluation II (APACHE II) score, along with the abdominal CT images of each patient, were analyzed. The L3-SMI was calculated, and the Modified CT Severity Index (MCTSI) and Balthazar CT grade were used to assess the severity of in-hospital complications of acute pancreatitis. The evaluation value of L3-SMI for the prognosis of severe acute pancreatitis was analyzed, as well as the factors influencing the prognosis of severe acute pancreatitis.ResultsNo statistically significant differences in gender, age, BMI, etiology, duration of anti-inflammatory drug use, and proportion of surgical patients between the survival and mortality groups were observed. But the mortality group showed higher proportions of patients with an elevated APACHE II score upon admission, mechanical ventilation, and renal replacement therapy, compared to the survival group, with statistically significant differences (P < 0.001). Furthermore, the mortality group had higher MCTSI scores (6.42 ± 0.69) and Balthazar CT grades (3.78 ± 0.45) than the survival group, with statistically significant differences (P < 0.001). The mortality group also had a lower L3-SMI (39.68 ± 3.25) compared to the survival group (42.71 ± 4.28), with statistically significant differences (P < 0.001). L3-SMI exhibited a negative correlation with MCTSI scores and Balthazar CT grades (r = −0.889, −0.790, P < 0.001). Logistic regression analysis, with mortality of acute pancreatitis patients as the dependent variable and MCTSI scores, Balthazar CT grades, L3-SMI, APACHE II score upon admission, mechanical ventilation, and renal replacement therapy as independent variables, revealed that MCTSI scores and L3-SMI were risk factors for mortality in acute pancreatitis patients (P < 0.001). Logistic regression analysis using the same variables confirmed that all these factors were risk factors for mortality in acute pancreatitis patients.ConclusionThis study confirmed that diagnosing muscle depletion using L3-SMI is a valuable radiological parameter for predicting in-hospital severity and short-term prognosis in patients with acute pancreatitis. creator: Chuntao Lin creator: Junyuan Zhang creator: Chunye Wang creator: Wei Lian creator: Yicong Liu uri: https://doi.org/10.7717/peerj.17283 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: Expressing banana transcription factor MaERFVII3 in Arabidopsis confers enhanced waterlogging tolerance and root growth link: https://peerj.com/articles/17285 last-modified: 2024-04-30 description: BackgroundWaterlogging poses a significant threat to plant growth and yield worldwide. Identifying the genes responsible for mitigating waterlogging stress is crucial. Ethylene-responsive factors (ERFs) are transcriptional regulators that respond to various biotic and abiotic stresses in plants. However, their roles and involvement in responding to waterlogging stress remain largely unexplored. Hence, this study aimed to elucidate the role of ERFs in enhancing banana plant resilience to waterlogging.MethodsWe hypothesized that introducing a group VII ERF transcription factor in Arabidopsis could enhance waterlogging stress tolerance. To test this hypothesis, we isolated MaERFVII3 from banana roots, where it exhibited a significant induction in response to waterlogging stress. The isolated MaERFVII3 was introduced into Arabidopsis plants for functional gene studies.ResultsCompared with wild-type plants, the MaERFVII3-expressing Arabidopsis showed increased survival and biomass under waterlogging stress. Furthermore, the abundance of transcripts related to waterlogging and hypoxia response showed an elevation in transgenic plants but a decrease in wild-type and empty vector plants when exposed to waterlogging stress. Our results demonstrate the significant contribution of MaERFVII3 to waterlogging tolerance in Arabidopsis, providing baseline data for further exploration and potentially contributing to crop improvement programs. creator: Ee Yang Teoh creator: Chee How Teo creator: Nadiya Akmal Baharum creator: Boon Chin Tan uri: https://doi.org/10.7717/peerj.17285 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Teoh et al. title: Improvement of morphophysiological and anatomical attributes of plants under abiotic stress conditions using plant growth-promoting bacteria and safety treatments link: https://peerj.com/articles/17286 last-modified: 2024-04-30 description: Drought and salinity are the major abiotic stress factors negatively affecting the morphophysiological, biochemical, and anatomical characteristics of numerous plant species worldwide. The detrimental effects of these environmental factors can be seen in leaf and stem anatomical structures including the decrease in thickness of cell walls, palisade and spongy tissue, phloem and xylem tissue. Also, the disintegration of grana staking, and an increase in the size of mitochondria were observed under salinity and drought conditions. Drought and salt stresses can significantly decrease plant height, number of leaves and branches, leaf area, fresh and dry weight, or plant relative water content (RWC%) and concentration of photosynthetic pigments. On the other hand, stress-induced lipid peroxidation and malondialdehyde (MDA) production, electrolyte leakage (EL%), and production of reactive oxygen species (ROS) can increase under salinity and drought conditions. Antioxidant defense systems such as catalase, peroxidase, glutathione reductase, ascorbic acid, and gamma-aminobutyric acid are essential components under drought and salt stresses to protect the plant organelles from oxidative damage caused by ROS. The application of safe and eco-friendly treatments is a very important strategy to overcome the adverse effects of drought and salinity on the growth characteristics and yield of plants. It is shown that treatments with plant growth-promoting bacteria (PGPB) can improve morphoanatomical characteristics under salinity and drought stress. It is also shown that yeast extract, mannitol, proline, melatonin, silicon, chitosan, α-Tocopherols (vitamin E), and biochar alleviate the negative effects of drought and salinity stresses through the ROS scavenging resulting in the improvement of plant attributes and yield of the stressed plants. This review discusses the role of safety and eco-friendly treatments in alleviating the harmful effects of salinity and drought associated with the improvement of the anatomical, morphophysiological, and biochemical features in plants. creator: Wasimah Buraykan Alshammari creator: Kholoud Alshammery creator: Salwa Lotfi creator: Haya Altamimi creator: Abeer Alshammari creator: Nadi Awad Al-Harbi creator: Dragana Jakovljević creator: Mona Hajed Alharbi creator: Moustapha Eid Moustapha creator: Diaa Abd El-Moneim creator: Khaled Abdelaal uri: https://doi.org/10.7717/peerj.17286 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Alshammari et al. title: Spatial distribution of settlement of Diadema antillarum around Saba, Dutch Caribbean link: https://peerj.com/articles/17291 last-modified: 2024-04-30 description: The mass mortality event of the herbivorous sea urchin Diadema antillarum in 1983–1984 has been a major contributor to the diminished resilience of coral reefs throughout the Caribbean. The reduction in grazing pressure resulted in algae proliferation, which inhibited coral recruitment after disturbances such as disease, hurricanes, pollution and climatic change induced marine heat waves. Natural recovery of D. antillarum after the 1983–1984 die-off has been slow. However, the few locations with recovered populations exhibit signs of improvement in coral reef health, prompting interest in D. antillarum restoration. Current restoration strategies include translocation of wild individuals, the restocking of juveniles that are either cultured from gametes or collected as settlers and head-started in a nursery, and assisted natural recovery by providing suitable settlement substrate. Both the collection of wild settlers and assisted natural recovery necessitate an understanding of the local, spatiotemporal trends in settlement. In this study, which was carried out on the Dutch Caribbean Island of Saba, artificial turf settlement collectors were deployed at nine locations around the island and monitored from June 2019 till July 2020 (13 months). The primary objective was to identify trends in larval settlement in space and time, to be able to optimize restoration efforts. Additionally, the small size of Saba allowed us to deploy settlement collectors around the island and compare D. antillarum settlement between windward and leeward sides. Our study showed that on Saba, D. antillarum settlement peaked in June and July, following similar seasonal trends observed around other islands in the Northeastern Caribbean. By far the most settlement occurred at the leeward side of the island, suggesting that hydrodynamic forces entrained D. antillarum larvae in the lee of Saba and/or calmer waters facilitated settlement. Limited settlement occurred on the more exposed windward locations. The identified high settlement locations are candidates for settler collection and restoration attempts. Continued monitoring of D. antillarum settlement, especially in light of the 2022 D. antillarum die-off, holds significance as it can provide insights into the potential of natural recovery. creator: Oliver J. Klokman creator: Alwin Hylkema uri: https://doi.org/10.7717/peerj.17291 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Klokman and Hylkema title: Seeing the impossible: the impact of watching magic on positive emotions, optimism, and wellbeing link: https://peerj.com/articles/17308 last-modified: 2024-04-30 description: Watching a magic trick is a unique experience in which seemingly impossible events appear possible but without any suspension of disbelief. Unfortunately, relatively little work has examined the psychological impact of this fascinating experience. In the current study, participants first completed a measure of the degree to which they disliked magic (Loathing of Legerdemain Scale: LOLS) and then watched a video that either contained a series of magic tricks (magic video) or carefully matched non-magic tricks (control video). Participants then rated the degree to which they experienced positive epistemic emotions (Epistemically Related Emotion Scale: ERES), their belief about impossible events being possible in the future (Modal Judgment Task: MJT), general optimism (State Optimism Measure: SOM) and subjective wellbeing (Satisfaction With Life Scale: SWLS). Compared to participants who watched the control video, those who saw the magic video reported more positive epistemic emotions on the ERES. There were no significant differences on the MJT, SOM and SWLS. Participants’ LOLS scores were negatively correlated with the ERES, SOM and SWLS, suggesting that those who like magic are more likely to experience positive epistemic emotions, have higher levels of general optimism, and express greater satisfaction with their lives. These findings are discussed within the context of short-term and long-term exposure to magic, along with recommendations for future work. creator: Richard Wiseman creator: Caroline Watt uri: https://doi.org/10.7717/peerj.17308 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wiseman and Watt title: Circulating HMGB1 in acute ischemic stroke and its association with post-stroke cognitive impairment link: https://peerj.com/articles/17309 last-modified: 2024-04-30 description: BackgroundIschemic stroke frequently leads to a condition known as post-stroke cognitive impairment (PSCI). Timely recognition of individuals susceptible to developing PSCI could facilitate the implementation of personalized strategies to mitigate cognitive deterioration. High mobility group box 1 (HMGB1) is a protein released by ischemic neurons and implicated in inflammation after stroke. Circulating levels of HMGB1 could potentially serve as a prognostic indicator for the onset of cognitive impairment following ischemic stroke.ObjectiveTo investigate the predictive value of circulating HMGB1 concentrations in the acute phase of ischemic stroke for the development of cognitive dysfunction at the 3-month follow-up.MethodsA total of 192 individuals experiencing their initial episode of acute cerebral infarction were prospectively recruited for this longitudinal investigation. Concentrations of circulating HMGB1 were quantified using an enzyme-linked immunosorbent assay (ELISA) technique within the first 24 hours following hospital admission. Patients underwent neurological evaluation including NIHSS scoring. Neuropsychological evaluation was conducted at the 3-month follow-up after the cerebrovascular event, employing the Montreal Cognitive Assessment (MoCA) as the primary tool for assessing cognitive performance. Multivariable logistic regression models were employed to investigate the relationship between circulating HMGB1 concentrations and cognitive dysfunction following stroke, which was operationalized as a MoCA score below 26, while controlling for potential confounders including demographic characteristics, stroke severity, vascular risk factors, and laboratory parameters.ResultsOf 192 patients, 84 (44%) developed PSCI. Circulating HMGB1 concentrations were significantly elevated in individuals who developed cognitive dysfunction following stroke compared to those who maintained cognitive integrity (8.4 ± 1.2 ng/mL vs 4.6 ± 0.5 ng/mL, respectively; p < 0.001). The prevalence of PSCI showed a dose-dependent increase with higher HMGB1 quartiles. After controlling for potential confounders such as demographic factors (age, gender, and education), stroke severity, vascular risk factors, and laboratory parameters in a multivariable logistic regression model, circulating HMGB1 concentrations emerged as a significant independent predictor of cognitive dysfunction following stroke (regression coefficient = 0.236, p < 0.001).ConclusionCirculating HMGB1 concentrations quantified within the first 24 hours following acute cerebral infarction are significantly and independently correlated with the likelihood of developing cognitive dysfunction at the 3-month follow-up, even after accounting for potential confounding factors. HMGB1 may be a novel biomarker to identify patients likely to develop post-stroke cognitive impairment for targeted preventive interventions. creator: Zhenbao Liu creator: Weixia Yang creator: Jianxin Chen creator: Qian Wang uri: https://doi.org/10.7717/peerj.17309 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Cortical activity associated with the maintenance of balance during unstable stances link: https://peerj.com/articles/17313 last-modified: 2024-04-30 description: BackgroundHumans continuously maintain and adjust posture during gait, standing, and sitting. The difficulty of postural control is reportedly increased during unstable stances, such as unipedal standing and with closed eyes. Although balance is slightly impaired in healthy young adults in such unstable stances, they rarely fall. The brain recognizes the change in sensory inputs and outputs motor commands to the musculoskeletal system. However, such changes in cortical activity associated with the maintenance of balance following periods of instability require further clarified.MethodsIn this study, a total of 15 male participants performed two postural control tasks and the center of pressure displacement and electroencephalogram were simultaneously measured. In addition, the correlation between amplitude of center of pressure displacement and power spectral density of electroencephalogram was analyzed.ResultsThe movement of the center of pressure was larger in unipedal standing than in bipedal standing under both eye open and eye closed conditions. It was also larger under the eye closed condition compared with when the eyes were open in unipedal standing. The amplitude of high-frequency bandwidth (1–3 Hz) of the center of pressure displacement was larger during more difficult postural tasks than during easier ones, suggesting that the continuous maintenance of posture was required. The power spectral densities of the theta activity in the frontal area and the gamma activity in the parietal area were higher during more difficult postural tasks than during easier ones across two postural control tasks, and these correlate with the increase in amplitude of high-frequency bandwidth of the center of pressure displacement.ConclusionsTaken together, specific activation patterns of the neocortex are suggested to be important for the postural maintenance during unstable stances. creator: Shoma Ue creator: Kakeru Nakahama creator: Junpei Hayashi creator: Tomohiro Ohgomori uri: https://doi.org/10.7717/peerj.17313 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ue et al. title: The representation of contextual cue is stimulus-specific yet its expression is flexible link: https://peerj.com/articles/17318 last-modified: 2024-04-30 description: BackgroundContextual cueing refers to the phenomenon in which individuals utilize frequently encountered environmental contexts, comprised of distractors, as cues to expedite a target search. Due to the conflict between the widespread occurrence of contextual cue transfer and the observed impact of changing the identity of distractors on contextual cue learning, the content of contextual cue representations remains contentious. Considering the independent nature of contextual cue learning and expression, our proposition is twofold: (1) Contextual cue representations are stimulus-specific, and (2) their expression is highly flexible.MethodsTo validate the model, two experiments were conducted. Experiment 1 aimed to confirm the hypothesis that contextual cue representations are stimulus-specific. We manipulated the identity consistency of distractors within repeated scenes during contextual cue learning. Difficulty in contextual cue learning under the identity-changing condition would suggest the necessity of identity within contextual cue representation, indicating the stimulus-specific nature of these representations. Experiment 2 was designed to affirm the conclusion of Experiment 1 and explore the flexibility in the expression of contextual cue representations. This experiment comprised two phases: learning and testing. During the learning phase, participants were exposed to two sets of repeated scenes in different colors under two learning conditions: load and no-load. Working memory load was introduced to interfere with the expression to prevent it from becoming automatic. In the subsequent testing phase, the colors of the two scene sets were interchanged to impede retrieval based on identity. If both load and no-load conditions demonstrate similar levels of contextual cue effects during the testing phase, it implies the flexibility in the expression of contextual cue representations and confirms the conclusion of Experiment 1.ResultsIn Experiment 1, a notable contextual cue learning effect was observed under the identity-consistent condition (p = 0.001). However, this effect was not evident under the identity-changing condition (p = 0.286). This finding strongly supports the stimulus-specific nature of contextual cue representation. In Experiment 2, the contextual cueing effect appeared but did not show a significant difference between the two conditions (t(23) = 0.02, p = 0.987, BF10 = 0.215), indicating the cognitive system’s ability to flexibly redefine retrieval cues. This adaptability aligns with our hypothesis and confirms the high flexibility in the expression process of contextual cue representations and confirms the conclusion of Experiment 1. creator: Xiaoyu Chen creator: Shuliang Bai creator: Qidan Ren creator: Yi Chen creator: Fangfang Long creator: Ying Jiang uri: https://doi.org/10.7717/peerj.17318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: A novel birnavirus identified as the causative agent of summer atrophy of pearl oyster (Pinctada fucata (Gould)) link: https://peerj.com/articles/17321 last-modified: 2024-04-30 description: The Akoya pearl oyster (Pinctada fucata (Gould)) is the most important species for pearl cultivation in Japan. Mass mortality of 0-year-old juvenile oysters and anomalies in adults, known as summer atrophy, have been observed in major pearl farming areas during the season when seawater temperatures exceed about 20 °C since 2019. In this study, we identified a novel birnavirus as the pathogen of summer atrophy and named it Pinctada birnavirus (PiBV). PiBV was first presumed to be the causative agent when it was detected specifically and frequently in the infected oysters in a comparative metatranscriptomics of experimentally infected and healthy pearl oysters. Subsequently, the symptoms of summer atrophy were reproduced by infection tests using purified PiBV. Infection of juvenile oysters with PiBV resulted in an increase in the PiBV genome followed by the atrophy of soft body and subsequent mortality. Immunostaining with a mouse antiserum against a recombinant PiBV protein showed that the virus antigen was localized mainly in the epithelial cells on the outer surface of the mantle. Although the phylogenetic analysis using maximum likelihood method placed PiBV at the root of the genus Entomobirnavirus, the identity of the bi-segmented, genomic RNA to that of known birnaviruses at the full-length amino acid level was low, suggesting that PiBV forms a new genus. The discovery of PiBV will be the basis for research to control this emerging disease. creator: Tomomasa Matsuyama creator: Satoshi Miwa creator: Tohru Mekata creator: Ikunari Kiryu creator: Isao Kuriyama creator: Takashi Atsumi creator: Tomokazu Itano creator: Hidemasa Kawakami uri: https://doi.org/10.7717/peerj.17321 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Matsuyama et al. title: Assessing the impact of two conventional wastewater treatment plants on small streams with effect-based methods link: https://peerj.com/articles/17326 last-modified: 2024-04-30 description: Sixty percent of discrete surface water bodies in Europe do not meet the requirements for good ecological and chemical status and in Germany, the situation is even worse with over 90% of surface water bodies failing to meet the threshold. In addition to hydromorphological degradation, intensive land use and invasive species, chemical pollution is primarily considered to be responsible for the inadequate ecological status of the water bodies. As a quantitatively important source of micropollutants, wastewater treatment plants (WWTPs) represent an important entry path for chemical stressors. It is therefore important to analyze the effectiveness of the WWTPs in eliminating micropollutants and other chemical stressors to mitigate the negative impacts of the treated wastewater (WW) in aquatic ecosystems. Accordingly, in this study, we evaluated the impacts of two conventional, medium-sized WWTPs on their small receiving water systems in the southwestern region of Hessen in Germany during two sampling campaigns (spring and fall) using effect-based methods (EBM). We hypothesized that due to the insufficient elimination of micropollutants, a broad spectrum of toxic effects would be detected in conventionally treated WW and also in the receiving surface waters downstream the WWTPs. As EBMs a battery of in vitro assays and active biomonitoring using two in vivo assays were applied. The results supported our hypothesis and showed that the untreated WW had a very high baseline toxicity and also high endocrine and mutagenic activities. Conventional WW treatment, consisting of mechanical and biological treatment with nitrification, denitrification and phosphate precipitation, reduced baseline toxicity by more than 90% and endocrine activities by more than 80% in both WWTPs. Despite these high elimination rates, the remaining baseline toxicity, the endocrine, dioxin-like and mutagenic activities of the conventionally treated WW were so high that negative effects on the two receiving waters were to be expected. This was confirmed in the active monitoring with the amphipod Gammarus fossarum and the mudsnail Potamopyrgus antipodarum, as mortality of both species increased downstream of the WWTPs and reproduction in P. antipodarum was also affected. These results indicate that advanced WW treatment is needed to more effectively eliminate chemical stressors to prevent negative impacts of treated WW particularly in small receiving waters. creator: Catalina Trejos Delgado creator: Andrea Dombrowski creator: Jörg Oehlmann uri: https://doi.org/10.7717/peerj.17326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Trejos Delgado et al. title: Aerobic exercise improves verbal working memory sub-processes in adolescents: behavioral evidence from an N-back task link: https://peerj.com/articles/17331 last-modified: 2024-04-30 description: BackgroundStudies on the effects of aerobic exercise on working memory (WM) have mainly concentrated on the overall effects, yet there is little knowledge on how moderate intensity aerobic exercise impacts the sub-processes of verbal WM (VWM) in adolescents. To address this gap, two experiments were conducted to explore the influence of aerobic exercise on the maintenance and updating sub-processes of VWM.MethodsIn Experiment 1, a mixed experimental design of 2 (exercise habit: high vs. low) × 3 (memory load: 0-back vs. 1-back vs. 2-back) was used to compare VWM and its sub-processes in 40 adolescents. In Experiment 2, a 2 (group: intervention vs. control) × 3 (time point: pretest vs. 1st post-test vs. 18th post-test) × 3 (memory load: 0-back vs. 1-back vs. 2-back) mixed experimental design was used to investigate the acute and long-term effects of moderate intensity aerobic exercise on VWM and its sub-processes in 24 adolescents with low exercise habits.ResultsThe results of Experiment 1 showed that VWM performance and its sub-processes in the high exercise habit group were better than those in the low exercise habit group. The results of Experiment 2 showed that the effects of the long-term exercise intervention were superior to those of the acute exercise intervention, and both were superior to the pretest. Meanwhile, it was found that aerobic exercise intervention had a greater effect size on the updating sub-process of VWM.ConclusionIn conclusion, the results indicated that moderate intensity aerobic exercise could enhance the performance of VWM and its sub-processes in adolescents, and long-term intervention showed greater improvement effects compared to acute intervention, especially in the updating sub-process of VWM. creator: Yue Li creator: Fei Wang creator: Jingfan Li creator: Xing Huo creator: Yin Zhang uri: https://doi.org/10.7717/peerj.17331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage link: https://peerj.com/articles/17345 last-modified: 2024-04-30 description: Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species’ evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). The genus Progne includes migrant and resident species, as well as geographically restricted taxa and widespread, intercontinentally distributed taxa, thus providing an ideal group in which to study the nature of niche divergence within a broad geographic mosaic. I obtained distributional information for the genus from publicly available databases and created ecological niche models for each species to create pairwise comparisons of environmental space. I combined these data with the most up-to-date phylogeny of Progne currently available to examine the patterns of niche evolution within the genus. I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, like extant basal Progne lineages, and several geographically localized descendant species occupy only portions of this larger ancestral niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages, and sheds light on the ways in which apparently divergent niches may arise through allopatry while not involving any true niche shifts through evolutionary time. Even taxa that appear unique in terms of habitat or behavior may not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa. creator: Jacob C. Cooper uri: https://doi.org/10.7717/peerj.17345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cooper title: Three new species of free-living marine nematodes of the Microlaimus genus (Nematoda: Microlaimidae) from the continental shelf off northeastern Brazil (Atlantic Ocean) link: https://peerj.com/articles/17355 last-modified: 2024-04-30 description: Three new species of the Microlaimus genus (Nematoda: Microlaimidae) are described from sample sediments collected in the South Atlantic, along the Continental Shelf break of Northeastern Brazil. Microlaimus paraundulatussp. n. possesses four setiform cephalic sensillae, a buccal cavity with three small teeth, arched and slender spicules and a wave-shaped gubernaculum. Microlaimus modestussp. n. is characterized by four small cephalic sensillae, a buccal cavity with three teeth (one large dorsal tooth), cephalated spicules and a strongly arched gubernaculum in the distal region. Microlaimus nordestinussp. n. is characterized by the following set of features: relatively long body, eight rows of hypodermal glands that extend longitudinally along the body and a funnel-shaped gubernaculum surrounding the spicules at the distal end. An amendment of the diagnosis is proposed for the genus. creator: Alex Manoel creator: Patrícia F. Neres creator: Andre M. Esteves uri: https://doi.org/10.7717/peerj.17355 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Manoel et al. title: Genome-wide analysis of bZIP transcription factors and their expression patterns in response to methyl jasmonate and low-temperature stresses in Platycodon grandiflorus link: https://peerj.com/articles/17371 last-modified: 2024-04-30 description: BackgroundPlatycodon grandiflorus belongs to the genus Platycodon and has many pharmacological effects, such as expectorant, antitussive, and anti-tumor properties. Among transcription factor families peculiar to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important, which exists widely in plants and participates in many biological processes, such as plant growth, development, and stress responses. However, genomic analysis of the bZIP gene family and related stress response genes has not yet been reported in P. grandiflorus.MethodsP. grandiflorus bZIP (PgbZIP) genes were first identified here, and the phylogenetic relationships and conserved motifs in the PgbZIPs were also performed. Meanwhile, gene structures, conserved domains, and the possible protein subcellular localizations of these PgbZIPs were characterized. Most importantly, the cis-regulatory elements and expression patterns of selected genes exposed to two different stresses were analyzed to provide further information on PgbZIPs potential biological roles in P. grandiflorus upon exposure to environmental stresses.ConclusionsForty-six PgbZIPs were identified in P. grandiflorus and divided into nine groups, as displayed in the phylogenetic tree. The results of the chromosomal location and the collinearity analysis showed that forty-six PgbZIP genes were distributed on eight chromosomes, with one tandem duplication event and eleven segmental duplication events identified. Most PgbZIPs in the same phylogenetic group have similar conserved motifs, domains, and gene structures. There are cis-regulatory elements related to the methyl jasmonate (MeJA) response, low-temperature response, abscisic acid response, auxin response, and gibberellin response. Ten PgbZIP genes were selected to study their expression patterns upon exposure to low-temperature and MeJA treatments, and all ten genes responded to these stresses. The real-time quantitative polymerase chain reaction (RT-qPCR) results suggest that the expression levels of most PgbZIPs decreased significantly within 6 h and then gradually increased to normal or above normal levels over the 90 h following MeJA treatment. The expression levels of all PgbZIPs were significantly reduced after 3 h of the low-temperature treatment. These results reveal the characteristics of the PgbZIP family genes and provide valuable information for improving P. grandiflorus’s ability to cope with environmental stresses during growth and development. creator: Jizhou Fan creator: Na Chen creator: Weiyi Rao creator: Wanyue Ding creator: Yuqing Wang creator: Yingying Duan creator: Jing Wu creator: Shihai Xing uri: https://doi.org/10.7717/peerj.17371 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fan et al. title: Bacterial community profiles within the water samples of leptospirosis outbreak areas link: https://peerj.com/articles/17096 last-modified: 2024-04-29 description: BackgroundLeptospirosis is a water-related zoonotic disease. The disease is primarily transmitted from animals to humans through pathogenic Leptospira bacteria in contaminated water and soil. Rivers have a critical role in Leptospira transmissions, while co-infection potentials with other waterborne bacteria might increase the severity and death risk of the disease.MethodsThe water samples evaluated in this study were collected from four recreational forest rivers, Sungai Congkak, Sungai Lopo, Hulu Perdik, and Gunung Nuang. The samples were subjected to next-generation sequencing (NGS) for the 16S rRNA and in-depth metagenomic analysis of the bacterial communities.ResultsThe water samples recorded various bacterial diversity. The samples from the Hulu Perdik and Sungai Lopo downstream sampling sites had a more significant diversity, followed by Sungai Congkak. Conversely, the upstream samples from Gunung Nuang exhibited the lowest bacterial diversity. Proteobacteria, Firmicutes, and Acidobacteria were the dominant phyla detected in downstream areas. Potential pathogenic bacteria belonging to the genera Burkholderiales and Serratia were also identified, raising concerns about co-infection possibilities. Nevertheless, Leptospira pathogenic bacteria were absent from all sites, which is attributable to its limited persistence. The bacteria might also be washed to other locations, contributing to the reduced environmental bacterial load.ConclusionThe present study established the presence of pathogenic bacteria in the river ecosystems assessed. The findings offer valuable insights for designing strategies for preventing pathogenic bacteria environmental contamination and managing leptospirosis co-infections with other human diseases. Furthermore, closely monitoring water sample compositions with diverse approaches, including sentinel programs, wastewater-based epidemiology, and clinical surveillance, enables disease transmission and outbreak early detections. The data also provides valuable information for suitable treatments and long-term strategies for combating infectious diseases. creator: Asmalia Md Lasim creator: Ahmad Mohiddin Mohd Ngesom creator: Sheila Nathan creator: Fatimah Abdul Razak creator: Mardani Abdul Halim creator: Wardah Mohd-Saleh creator: Kamaruddin Zainul Abidin creator: Farah Shafawati Mohd-Taib uri: https://doi.org/10.7717/peerj.17096 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Md Lasim et al. title: Italian adaptation of the Multidimensional Iowa Suggestibility Scale (MISS) link: https://peerj.com/articles/17145 last-modified: 2024-04-29 description: BackgroundSuggestibility is a personality trait that reflects a general tendency to accept messages. The Multidimensional Iowa Suggestibility Scale (MISS) is a self-report scale developed to measure the degree of individuals’ perceptions of their suggestibility. This study aimed to adapt the MISS in an Italian sample.MethodsWe conducted two studies. In the first study, 345 subjects (270 females (78%), mean age = 36.21 years ± 14.06 SD) completed the translated Italian version of the MISS, composed of five subscales (consumer suggestibility; persuadability; sensation contagion; physiological reactivity; peer conformity). We investigated the structural validity of the scale through confirmatory factor analysis (CFA) testing four measurement models (unidimensional, four-factor, hierarchical four factors, and bifactor) and explored reliability in terms of internal consistency through the McDonald’s omega. In the second study, we cross-validated the MISS on a new independent sample. We enrolled 277 participants (196 females (71%), mean age 30.56, SD = 12.58) who underwent the new version of the scale. We performed factor analyses to test structural validity and compared four measurement models. Then, we investigated reliability and conducted a latent variable analysis to explore divergent validity.ResultsThe CFA in the first study revealed a bifactor solution of the MISS. This structure was interpretable and provided an adequate fit for the data. The final version of the scale was reduced to forty-six items with globally good indices of adaptation. The scale also demonstrated acceptable reliability in terms of internal consistency through the McDonald’s Hierarchical Omega. In the second study, we found that the bifactor structure was confirmed. Factor loadings inspection revealed that there was no justification to report only the separate scores for the subscales. We also found that the scale showed good internal consistency, but mixed evidence for divergent validity.ConclusionsIn the end, the Italian version of the MISS demonstrated good psychometric properties which will be discussed in detail below. creator: Marco Tullio Liuzza creator: Eva Tolomeo creator: Giuseppe Occhiuto creator: Martina Cilurzo creator: Iolanda Martino creator: Antonio Cerasa uri: https://doi.org/10.7717/peerj.17145 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liuzza et al. title: Assessing dietary specialization to inform the conservation of the fairy pitta (Pitta nympha), an endangered vermivore link: https://peerj.com/articles/17189 last-modified: 2024-04-29 description: Quantifying the diet of endangered species is crucial for conservation, especially for diet specialists, which can be more susceptible to environmental changes. The vulnerable fairy pitta (Pitta nympha) is considered a specialist that primarily feeds its nestlings with earthworms. However, there have been few studies of the nestling diet provisioned by parents, and no assessments of earthworm proportion in the diet of adults. Our study aimed to fill these gaps, shedding light on crucial factors for conservation. Combining new observations with existing literature, we confirmed a consistent dominance of earthworms in the nestling diet, regardless of rainfall, nestling age, and time of day. We extrapolated the total earthworm consumption during a breeding event, accounting for potential variation in the availability of earthworms and their prevalence in the adult diet. We used literature-based earthworm densities in pitta habitats and our estimates of family earthworm consumption to calculate the habitat area that could provide a pitta family with the number of earthworms consumed during a breeding event. The predictions matched observed pitta home range sizes when assumed that the adult diet is comprised of approximately 70% earthworms. The results highlight the importance of earthworm-rich habitats for conservation planning of the fairy pitta. To mitigate the effects of habitat destruction, we discuss conservation practices that may involve enhancing earthworm abundance in natural habitats and providing vegetation cover for foraging pittas in adjacent anthropogenic habitats rich in earthworms. To guide conservation efforts effectively, future studies should investigate whether previously reported breeding in developed plantation habitats is due to high earthworm abundance there. Future studies should also quantify correlations between local earthworm densities, home range size, and the breeding success of the fairy pitta. creator: Jinseok Park creator: Jungmoon Ha creator: Woojoo Kim creator: Piotr G. Jablonski creator: Sang-im Lee uri: https://doi.org/10.7717/peerj.17189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Park et al. title: Alpha lipoic acid mitigates adverse impacts of drought stress on growth and yield of mungbean: photosynthetic pigments, and antioxidative defense mechanism link: https://peerj.com/articles/17191 last-modified: 2024-04-29 description: ContextExogenous use of potential organic compounds through different modes is a promising strategy for the induction of water stress tolerance in crop plants for better yield.AimsThe present study aimed to explore the potential role of alpha-lipoic acid (ALA) in inducing water stress tolerance in mungbean lines when applied exogenously through various modes.MethodsThe experiment was conducted in a field with a split-plot arrangement, having three replicates for each treatment. Two irrigation regimes, including normal and reduced irrigation, were applied. The plants allocated to reduced irrigation were watered only at the reproductive stage. Three levels of ALA (0, 0.1, 0.15 mM) were applied through different modes (seed priming, foliar or priming+foliar).Key resultsALA treatment through different modes manifested higher growth under reduced irrigation (water stress) and normal irrigation. Compared to the other two modes, the application of ALA as seed priming was found more effective in ameliorating the adverse impacts of water stress on growth and yield associated with their better content of leaf photosynthetic pigments, maintenance of plant water relations, levels of non-enzymatic antioxidants, improved activities of enzymatic antioxidants, and decreased lipid peroxidation and H2O2 levels. The maximum increase in shoot fresh weight (29% and 28%), shoot dry weight (27% and 24%), 100-grain weight (24% and 23%) and total grain yield (20% and 21%) in water-stressed mungbean plants of line 16003 and 16004, respectively, was recorded due to ALA seed priming than other modes of applications.ConclusionsConclusively, 0.1 and 0.15 mM levels of ALA as seed priming were found to reduce the adverse impact of water stress on mungbean yield that was associated with improved physio-biochemical mechanisms.ImplicationsThe findings of the study will be helpful for the agriculturalists working in arid and semi-arid regions to obtain a better yield of mungbean that will be helpful to fulfill the food demand in those areas to some extent. creator: Naima Hafeez Mian creator: Muhammad Azeem creator: Qasim Ali creator: Saqib Mahmood creator: Muhammad Sohail Akram uri: https://doi.org/10.7717/peerj.17191 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mian et al. title: Heavy metal levels and human health risk implications associated with fish consumption from the lower Omo river (Lotic) and Omo delta lake (Lentic), Ethiopia link: https://peerj.com/articles/17216 last-modified: 2024-04-29 description: This study is the first to determine the levels of heavy metals in commercially important fish species, namely Lates niloticus and Oreochromis niloticus and the potential human health risks associated with their consumption. A total of 120 fish samples were collected from the lower Omo river and Omo delta, with 60 samples from each water source. The fish tissue samples (liver and muscle) were analyzed using a flame atomic absorption spectrometer for nine heavy metals (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn). The human health risk assessment tools used were the target hazard quotient (THQ), the hazard index (HI), and the target cancer risk (TCR). The mean levels of heavy metals detected in the liver and muscle of L. niloticus from the lower Omo river generally occurred in the order Fe > Zn > Pb> Cu > Mn> Cr > Co > Ni and Pb > Cu > Mn > Co > Ni, respectively. The mean levels of metals in the muscle and liver tissues of O. niloticus were in the order Fe > Pb > Zn > Mn > Cu > Cr > Co > Ni and Pb > Zn > Mn > Fe > Cu > Co > Ni, respectively. Similarly, the mean levels of heavy metals detected in the liver and muscle of L. niloticus from Omo delta occurred in the order Fe > Zn > Pb > Cu > Mn > Cr > Co > Ni and Fe > Pb > Zn > Mn > Cu > Co > Cr > Ni, respectively. The mean levels in the muscle and liver tissues of O. niloticus from the Omo delta were in the order Fe > Pb > Zn > Mn > Cu > Cr > Co > Ni and Pb > Fe > Zn > Mn > Co > Cu > Ni, respectively. The study revealed that the THQ values were below 1, indicating that consumption of L. niloticus and O. niloticus from the studied sites does not pose a potential non-carcinogenic health risk. Although the TCR values for Pb in this study were within the tolerable range, it’s mean concentration in the muscle and liver tissues of both fish species from the two water bodies exceeded the permissible limit established by FAO/WHO. This is a warning sign for early intervention, and it emphasizes the need for regular monitoring of freshwater fish. Therefore, it is imperative to investigate the pollution levels and human health risks of heavy metals in fish tissues from lower Omo river and Omo delta for environmental and public health concerns. creator: Abiy Andemo Kotacho creator: Girma Tilahun Yimer creator: Solomon Sorsa Sota creator: Yohannes Seifu Berego uri: https://doi.org/10.7717/peerj.17216 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kotacho et al. title: Assessment of sealing efficacy, radiopacity, and surface topography of a bioinspired polymer for perforation repair link: https://peerj.com/articles/17237 last-modified: 2024-04-29 description: BackgroundRoot perforation repair presents a significant challenge in dentistry due to inherent limitations of existing materials. This study explored the potential of a novel polydopamine-based composite as a root repair material by evaluating its sealing efficacy, radiopacity, and surface topography.MethodsConfocal microscopy assessed sealing ability, comparing the polydopamine-based composite to the gold standard, mineral trioxide aggregate (MTA). Radiopacity was evaluated using the aluminium step wedge technique conforming to ISO standards. Surface roughness analysis utilized atomic force microscopy (AFM), while field emission scanning electron microscopy (FESEM) visualized morphology.ResultsThe polydopamine-based composite exhibited significantly superior sealing efficacy compared to MTA (P < 0.001). Radiopacity reached 3 mm aluminium equivalent, exceeding minimum clinical requirements. AFM analysis revealed a smooth surface topography, and FESEM confirmed successful composite synthesis.ConclusionThis study demonstrates promising properties of the polydopamine-based composite for root perforation repair, including superior sealing efficacy, clinically relevant radiopacity, and smooth surface topography. Further investigation is warranted to assess its clinical viability and potential translation to endodontic practice. creator: Lakshmi Nidhi Rao creator: Aditya Shetty creator: Neevan Dsouza creator: Heeresh Shetty uri: https://doi.org/10.7717/peerj.17237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rao et al. title: Systematics, distribution patterns and historical biogeography of the Central America wandering spider genus Kiekie Polotow & Brescovit, 2018 (Araneae: Ctenidae) link: https://peerj.com/articles/17242 last-modified: 2024-04-29 description: Kiekie Polotow & Brescovit, 2018 is a Neotropical genus of Ctenidae, with most of its species occuring in Central America. In this study, we review the systematics of Kiekie and describe five new species and the unknown females of K. barrocolorado Polotow & Brescovit, 2018 and K. garifuna Polotow & Brescovit, 2018, and the unknown male of K. verbena Polotow & Brescovit, 2018. In addition, we described the female of K. montanense which was wrongly assigned as K. griswoldi Polotow & Brescovit, 2018 (both species are sympatric). We provided a modified diagnosis for previously described species based on the morphology of the newly discovered species and in situ photographs of living specimens. We inferred a molecular phylogeny using four nuclear (histone H3, 28S rRNA, 18S rRNA and ITS-2) and three mitochondrial genes (cytochrome c oxidase subunit I or COI, 12S rRNA and 16S rRNA) to test the monophyly of the genus and the evolutionary relationships of its species. Lastly, we reconstruct the historical biogeography and map diversity and endemism distributional patterns of the different species. This study increased the number of known species of Kiekie from 13 to 18, and we describe a new genus, Eldivo which is sister lineage of Kiekie. Most of the diversity and endemism of the genus Kiekie is located in the montane ecosystems of Costa Rica followed by the lowland rainforest of the Pacific side (Limon Basin). Kiekie originated in the North America Tropical region, this genus started diversifying in the Late Miocene and spread to Lower Central America and South America. In that region, Kiekie colonized independently several times the montane ecosystems corresponding to periods of uplifting of Talamanca and Central Cordilleras. creator: Nicolas Hazzi creator: Gustavo Hormiga uri: https://doi.org/10.7717/peerj.17242 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hazzi and Hormiga title: A comprehensive dataset on biomechanics and motor control during human walking with discrete mechanical perturbations link: https://peerj.com/articles/17256 last-modified: 2024-04-29 description: BackgroundHumans have a remarkable capability to maintain balance while walking. There is, however, a lack of publicly available research data on reactive responses to destabilizing perturbations during gait.MethodsHere, we share a comprehensive dataset collected from 10 participants who experienced random perturbations while walking on an instrumented treadmill. Each participant performed six 5-min walking trials at a rate of 1.2 m/s, during which rapid belt speed perturbations could occur during the participant’s stance phase. Each gait cycle had a 17% probability of being perturbed. The perturbations consisted of an increase of belt speed by 0.75 m/s, delivered with equal probability at 10%, 20%, 30%, 40%, 50%, 60%, 70%, or 80% of the stance phase. Data were recorded using motion capture with 25 markers, eight inertial measurement units (IMUs), and electromyography (EMG) from the tibialis anterior (TA), soleus (SOL), lateral gastrocnemius (LG), rectus femoris (RF), vastus lateralis (VL), vastus medialis (VM), biceps femoris (BF), and gluteus maximus (GM). The full protocol is described in detail.ResultsWe provide marker trajectories, force plate data, EMG data, and belt speed information for all trials and participants. IMU data is provided for most participants. This data can be useful for identifying neural feedback control in human gait, biologically inspired control systems for robots, and the development of clinical applications. creator: Dana L. Lorenz creator: Antonie J. van den Bogert uri: https://doi.org/10.7717/peerj.17256 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lorenz and van den Bogert title: Contrasting effects of increasing dissolved iron on photosynthesis and O2 availability in the gastric cavity of two Mediterranean corals link: https://peerj.com/articles/17259 last-modified: 2024-04-29 description: Iron (Fe) plays a fundamental role in coral symbiosis, supporting photosynthesis, respiration, and many important enzymatic reactions. However, the extent to which corals are limited by Fe and their metabolic responses to inorganic Fe enrichment remains to be understood. We used respirometry, variable chlorophyll fluorescence, and O2 microsensors to investigate the impact of increasing Fe(III) concentrations (20, 50, and 100 nM) on the photosynthetic capacity of two Mediterranean coral species, Cladocora caespitosa and Oculina patagonica. While the bioavailability of inorganic Fe can rapidly decrease, we nevertheless observed significant physiological effects at all Fe concentrations. In C. caespitosa, exposure to 50 nM Fe(III) increased rates of respiration and photosynthesis, while the relative electron transport rate (rETR(II)) decreased at higher Fe(III) exposure (100 nM). In contrast, O. patagonica reduced respiration, photosynthesis rates, and maximum PSII quantum yield (Fv/Fm) across all iron enrichments. Both corals exhibited increased hypoxia (<50 µmol O2 L−1) within their gastric cavity at night when exposed to 50 and 100 nM Fe(III), leading to increased polyp contraction time and reduced O2 exchange with the surrounding water. Our results indicate that C. caespitosa, but not O. patagonica, might be limited in Fe for achieving maximal photosynthetic efficiency. Understanding the multifaceted role of iron in corals’ health and their response to environmental change is crucial for effective coral conservation. creator: Walter Dellisanti creator: Qingfeng Zhang creator: Christine Ferrier-Pagès creator: Michael Kühl uri: https://doi.org/10.7717/peerj.17259 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dellisanti et al. title: Exploring exercise-driven exerkines: unraveling the regulation of metabolism and inflammation link: https://peerj.com/articles/17267 last-modified: 2024-04-29 description: Exercise has many beneficial effects that provide health and metabolic benefits. Signaling molecules are released from organs and tissues in response to exercise stimuli and are widely termed exerkines, which exert influence on a multitude of intricate multi-tissue processes, such as muscle, adipose tissue, pancreas, liver, cardiovascular tissue, kidney, and bone. For the metabolic effect, exerkines regulate the metabolic homeostasis of organisms by increasing glucose uptake and improving fat synthesis. For the anti-inflammatory effect, exerkines positively influence various chronic inflammation-related diseases, such as type 2 diabetes and atherosclerosis. This review highlights the prospective contribution of exerkines in regulating metabolism, augmenting the anti-inflammatory effects, and providing additional advantages associated with exercise. Moreover, a comprehensive overview and analysis of recent advancements are provided in this review, in addition to predicting future applications used as a potential biomarker or therapeutic target to benefit patients with chronic diseases. creator: Nihong Zhou creator: Lijing Gong creator: Enming Zhang creator: Xintang Wang uri: https://doi.org/10.7717/peerj.17267 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Microbial community structure and carbon transformation characteristics of different aggregates in black soil link: https://peerj.com/articles/17269 last-modified: 2024-04-29 description: BackgroundPrevious research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification.MethodsIn this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2–5, 1–2, 0.5–1, 0.25–0.5, <0.25 mm, and bulk soil.ResultsThe relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25–0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25–0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil’s ability to fix carbon and nitrogen.DiscussionThere were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25–0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils. creator: Danqi Zhao creator: Wei Zhang creator: Juntao Cui uri: https://doi.org/10.7717/peerj.17269 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhao et al. title: Plasma-based lipidomics reveals potential diagnostic biomarkers for esophageal squamous cell carcinoma: a retrospective study link: https://peerj.com/articles/17272 last-modified: 2024-04-29 description: BackgroundEsophageal squamous cell carcinoma (ESCC) is highly prevalent and has a high mortality rate. Traditional diagnostic methods, such as imaging examinations and blood tumor marker tests, are not effective in accurately diagnosing ESCC due to their low sensitivity and specificity. Esophageal endoscopic biopsy, which is considered as the gold standard, is not suitable for screening due to its invasiveness and high cost. Therefore, this study aimed to develop a convenient and low-cost diagnostic method for ESCC using plasma-based lipidomics analysis combined with machine learning (ML) algorithms.MethodsPlasma samples from a total of 40 ESCC patients and 31 healthy controls were used for lipidomics study. Untargeted lipidomics analysis was conducted through liquid chromatography-mass spectrometry (LC-MS) analysis. Differentially expressed lipid features were filtered based on multivariate and univariate analysis, and lipid annotation was performed using MS-DIAL software.ResultsA total of 99 differential lipids were identified, with 15 up-regulated lipids and 84 down-regulated lipids, suggesting their potential as diagnostic targets for ESCC. In the single-lipid plasma-based diagnostic model, nine specific lipids (FA 15:4, FA 27:1, FA 28:7, FA 28:0, FA 36:0, FA 39:0, FA 42:0, FA 44:0, and DG 37:7) exhibited excellent diagnostic performance, with an area under the curve (AUC) exceeding 0.99. Furthermore, multiple lipid-based ML models also demonstrated comparable diagnostic ability for ESCC. These findings indicate plasma lipids as a promising diagnostic approach for ESCC. creator: Yang Chen creator: Yixuan Gu creator: Jinhua Rong creator: Luyin Xu creator: Xiancong Huang creator: Jing Zhu creator: Zhongjian Chen creator: Weimin Mao uri: https://doi.org/10.7717/peerj.17272 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Variational Bayesian phylogenies through matrix representation of tree space link: https://peerj.com/articles/17276 last-modified: 2024-04-29 description: In this article, we study the distance matrix as a representation of a phylogeny by way of hierarchical clustering. By defining a multivariate normal distribution on (a subset of) the entries in a matrix, this allows us to represent a distribution over rooted time trees. Here, we demonstrate tree distributions can be represented accurately this way for a number of published tree distributions. Though such a representation does not map to unique trees, restriction to a subspace, in particular one we call a “cube”, makes the representation bijective at the cost of not being able to represent all possible trees. We introduce an algorithm “cubeVB” specifically for cubes and show through well calibrated simulation study that it is possible to recover parameters of interest like tree height and length. Although a cube cannot represent all of tree space, it is a great improvement over a single summary tree, and it opens up exciting new opportunities for scaling up Bayesian phylogenetic inference. We also demonstrate how to use a matrix representation of a tree distribution to get better summary trees than commonly used maximum clade credibility trees. An open source implementation of the cubeVB algorithm is available from https://github.com/rbouckaert/cubevb as the cubevb package for BEAST 2. creator: Remco R. Bouckaert uri: https://doi.org/10.7717/peerj.17276 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bouckaert title: Association between passing return-to-sport testing and re-injury risk in patients after anterior cruciate ligament reconstruction surgery: a systematic review and meta-analysis link: https://peerj.com/articles/17279 last-modified: 2024-04-29 description: BackgroundInconsistent results have been obtained regarding the association between return-to-sport (RTS) testing and the risk of subsequent re-injury following anterior cruciate ligament reconstruction (ACLR). We therefore conducted a systematic review and meta-analysis to assess the potential association between passing of RTS and the risk of re-injury for patients after ACLR.MethodsThis meta-analysis was registered in INPLASY with the registration number INPLASY202360027. The electronic databases MedLine, EmBase, and the Cochrane library were systematically searched to identify eligible studies from their inception up to September 2023. The investigated outcomes included knee injury, secondary ACL, contralateral ACL injury, and graft rupture. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using the random-effects model.ResultsA total number of nine studies involving 1410 individuals were selected for the final quantitative analysis. We noted that passing RTS test was not associated with the risk of subsequent knee injury (OR: 0.95; 95% CI: 0.28–3.21; P = 0.929), secondary ACL injury (OR: 0.98; 95% CI: 0.55–1.75; P = 0.945), and contralateral ACL injury (OR: 1.53; 95% CI: 0.63–3.71; P = 0.347). However, the risk of graft rupture was significantly reduced (OR: 0.49; 95% CI: 0.33–0.75; P = 0.001).ConclusionsThis study found that passing RTS test was not associated with the risk of subsequent knee injury, secondary ACL injury, and contralateral ACL injury, while it was associated with a lower risk of graft rupture. Thus, it is recommended that patients after ACLR pass an RTS test in clinical settings. creator: Wenqi Zhou creator: Xihui Liu creator: Qiaomei Hong creator: Jingping Wang creator: Xiaobing Luo uri: https://doi.org/10.7717/peerj.17279 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhou et al. title: Anodal transcranial direct current stimulation enhances response inhibition and attention allocation in fencers link: https://peerj.com/articles/17288 last-modified: 2024-04-29 description: BackgroundThe aim of this study is to investigate the acute effects of anodal transcranial direct current stimulation (tDCS) on reaction time, response inhibition and attention in fencers.MethodsSixteen professional female fencers were recruited, and subjected to anodal tDCS and sham stimulation in the primary motor area (M1) one week apart in a randomized, crossover, single-blind design. A two-factor analysis of variance with repeated measures was used to analyze the effects of stimulation conditions (anodal stimulation, sham stimulation) and time (pre-stimulation, post-stimulation) on reaction time, response inhibition, and attention in fencers.ResultsThe study found a significant improvement in response inhibition and attention allocation from pre-stimulation to post-stimulation following anodal tDCS but not after sham stimulation. There was no statistically significant improvement in reaction time and selective attention.ConclusionsA single session of anodal tDCS could improve response inhibition, attention allocation in female fencers. This shows that tDCS has potential to improve aspects of an athlete’s cognitive performance, although we do not know if such improvements would transfer to improved performance in competition. However, more studies involving all genders, large samples, and different sports groups are needed in the future to further validate the effect of tDCS in improving the cognitive performance of athletes. creator: Jiansong Dai creator: Yang Xiao creator: Gangrui Chen creator: Zhongke Gu creator: Kai Xu uri: https://doi.org/10.7717/peerj.17288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dai et al. title: Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities link: https://peerj.com/articles/17310 last-modified: 2024-04-29 description: BackgroundOat is a dual-purpose cereal used for grain and forage. The demand of oat has been increasing as the understanding of the nutritional, ecological, and economic values of oat increased. However, the frequent lodging during the growing period severely affect the high yielding potential and the quality of the grain and forage of oat.MethodsTherefore, we used the lodging-resistant variety LENA and the lodging-sensitive variety QY2 as materials, implementing four different planting densities: 2.25×106 plants/ha (D1), 4.5×106 plants/ha (D2), 6.75×106 plants/ha (D3), and 9×106 plants/ha (D4). At the appropriate growth and development stages, we assessed agronomic traits, mechanical characteristics, biochemical compositions, yield and its components. The study investigated the impact of planting density on the growth, lodging, and yield of oat, as well as their interrelationships. Additionally, we identified the optimal planting density to establish a robust crop structure. The research aims to contribute to the high-yield and high-quality cultivation of oat.ResultsWe observed that with increasing planting density, plant height, grass and grain yields of both varieties first increased and then decreased; root fresh weight, stem diameter, stem wall thickness, stem puncture strength, breaking strength, compressive strength, lignin and crude fiber contents, and yield components decreased; whereas the lodging rate and lodging coefficient increased. Planting density affects lodging by regulating plant height, height of center of gravity, stem wall thickness, internode length, and root fresh weight of oat. Additionally, it can impact stem mechanical strength by modulating the synthesis of lignin and crude fiber, which in turn affecting lodging resistance. Plant height, height of center of gravity, stem wall thickness, internode length, root fresh weight, breaking strength, compressive strength, lignin and crude fiber content, single-plant weight, grain yield and 1,000-grain weight can serve as important indicators for evaluating oat stem lodging resistance. We also noted that planting density affected grain yield both directly and indirectly (by affecting lodging); high density increased lodging rate and decreased grain yield, mainly by reducing 1,000-grain weight. Nonetheless, there was no significant relationship between lodging and grass yield. As appropriate planting density can increase the yield while maintaining good lodging resistance, in this study, 4.5×106 plants/ha (D2) was found to be the best planting density for oat in terms of lodging resistance and grass and grain yield. These findings can be used as a reference for oat planting. creator: Lingling Liu creator: Guoling Liang creator: Wenhui Liu creator: Zeliang Ju uri: https://doi.org/10.7717/peerj.17310 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney link: https://peerj.com/articles/17316 last-modified: 2024-04-29 description: This review discusses the importance of homeostasis with a particular emphasis on the acid-base (AB) balance, a crucial aspect of pH regulation in living systems. Two primary organ systems correct deviations from the standard pH balance: the respiratory system via gas exchange and the kidneys via proton/bicarbonate secretion and reabsorption. Focusing on kidney functions, we describe the complexity of renal architecture and its challenges for experimental research. We address specific roles of different nephron segments (the proximal convoluted tubule, the loop of Henle and the distal convoluted tubule) in pH homeostasis, while explaining the physiological significance of ion exchange processes maintained by the kidneys, particularly the role of bicarbonate ions (HCO3−) as an essential buffer system of the body. The review will be of interest to researchers in the fields of physiology, biochemistry and molecular biology, which builds a strong foundation and critically evaluates existing studies. Our review helps identify the gaps of knowledge by thoroughly understanding the existing literature related to kidney acid-base homeostasis. creator: Elena Gantsova creator: Oxana Serova creator: Polina Vishnyakova creator: Igor Deyev creator: Andrey Elchaninov creator: Timur Fatkhudinov uri: https://doi.org/10.7717/peerj.17316 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gantsova et al. title: Density of cannabis outlets vs. cannabis use behaviors and prevalent cannabis use disorder: findings from a nationally-representative survey link: https://peerj.com/articles/17317 last-modified: 2024-04-29 description: BackgroundThailand recently decriminalized (de facto legalized) cannabis use and sales. However, nationally representative data are scarce with regard to cannabis use behaviors and its association with cannabis outlet density. The objectives of this study are: (1) to describe the prevalence of cannabis use behaviors and cannabis use disorder among the general adult population of Thailand; (2) to describe the extent that the density of cannabis outlets is associated with cannabis use behaviors, cannabis use disorder, and the amount of cannabis smoked per day.MethodsWe conducted a community-based cross-sectional study in 11 provinces and the Bangkok Metropolitan Area. Participants were residents of sampled communities aged 20 years or older. We requested literate participants to self-administer the questionnaire and interviewed participants who could not read. We analyzed data using descriptive statistics with sampling weight adjustments and multivariate logistic regression analyses.ResultsThe prevalence of current cannabis use was 15 percent. At a 400-m radius, participants who reported three cannabis outlets had 4.2 times higher odds of being current users than participants who reported no outlet (Adjusted OR = 4.82; 95% CI [3.04–7.63]). We found no association between outlet density and hazardous cannabis use or cannabis use disorder, nor association with the amount of cannabis use among cannabis smokers.Discussion and ConclusionThe patterns of association between outlet density and cannabis use behaviors were inconsistent. Furthermore, limitations regarding outlet density measurement and lack of temporality should be considered as caveats in the interpretation of the study findings. creator: Wit Wichaidit creator: Ilham Chapakiya creator: Aneesah Waeuseng creator: Kemmapon Chumchuen creator: Sawitri Assanangkornchai uri: https://doi.org/10.7717/peerj.17317 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wichaidit et al. title: Combining multisensor images and social network data to assess the area flooded by a hurricane event link: https://peerj.com/articles/17319 last-modified: 2024-04-29 description: In this study, multisensor remote sensing datasets were used to characterize the land use and land covers (LULC) flooded by Hurricane Willa which made landfall on October 24, 2018. The landscape characterization was done using an unsupervised K-means algorithm of a cloud-free Sentinel-2 MultiSpectral Instrument (MSI) image, acquired during the dry season before Hurricane Willa. A flood map was derived using the histogram thresholding technique over a Synthetic Aperture Radar (SAR) Sentinel-1 C-band and combined with a flood map derived from a Sentinel-2 MSI image. Both, the Sentinel-1 and Sentinel-2 images were obtained after Willa landfall. While the LULC map reached an accuracy of 92%, validated using data collected during field surveys, the flood map achieved 90% overall accuracy, validated using locations extracted from social network data, that were manually georeferenced. The agriculture class was the dominant land use (about 2,624 km2), followed by deciduous forest (1,591 km2) and sub-perennial forest (1,317 km2). About 1,608 km2 represents the permanent wetlands (mangrove, salt marsh, lagoon and estuaries, and littoral classes), but only 489 km2 of this area belongs to aquatic surfaces (lagoons and estuaries). The flooded area was 1,225 km2, with the agricultural class as the most impacted (735 km2). Our analysis detected the saltmarsh class occupied 541 km2in the LULC map, and around 328 km2 were flooded during Hurricane Willa. Since the water flow receded relatively quickly, obtaining representative imagery to assess the flood event was a challenge. Still, the high overall accuracies obtained in this study allow us to assume that the outputs are reliable and can be used in the implementation of effective strategies for the protection, restoration, and management of wetlands. In addition, they will improve the capacity of local governments and residents of Marismas Nacionales to make informed decisions for the protection of vulnerable areas to the different threats derived from climate change. creator: Rafael Hernández-Guzmán creator: Arturo Ruiz-Luna uri: https://doi.org/10.7717/peerj.17319 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hernández-Guzmán and Ruiz-Luna title: The role of environmental gradients and microclimates in structuring communities and functional groups of lizards in a rainforest-savanna transition area link: https://peerj.com/articles/16986 last-modified: 2024-04-26 description: Environmental heterogeneity poses a significant influence on the functional characteristics of species and communities at local scales. Environmental transition zones, such as at the savanna-forest borders, can act as regions of ecological tension when subjected to sharp variations in the microclimate. For ectothermic organisms, such as lizards, environmental temperatures directly influence physiological capabilities, and some species use different thermoregulation strategies that produce varied responses to local climatic conditions, which in turn affect species occurrence and community dynamics. In the context of global warming, these various strategies confer different types of vulnerability as well as risks of extinction. To assess the vulnerability of a species and understand the relationships between environmental variations, thermal tolerance of a species and community structure, lizard communities in forest-savanna transition areas of two national parks in the southwestern Amazon were sampled and their thermal functional traits were characterized. Then, we investigated how community structure and functional thermal variation were shaped by two environmental predictors (i.e., microclimates estimated locally and vegetation structure estimated from remote sensing). It was found that the community structure was more strongly predicted by the canopy surface reflectance values obtained via remote sensing than by microclimate variables. Environmental temperatures were not the most important factor affecting the occurrence of species, and the variations in ecothermal traits demonstrated a pattern within the taxonomic hierarchy at the family level. This pattern may indicate a tendency for evolutionary history to indirectly influence these functional features. Considering the estimates of the thermal tolerance range and warming tolerance, thermoconformer lizards are likely to be more vulnerable and at greater risk of extinction due to global warming than thermoregulators. The latter, more associated with open environments, seem to take advantage of their lower vulnerability and occur in both habitat types across the transition, potentially out-competing and further increasing the risk of extinction and vulnerability of forest-adapted thermoconformer lizards in these transitional areas. creator: Alan F. Souza-Oliveira creator: Gabriela Zuquim creator: Lidia F. Martins creator: Lucas N. Bandeira creator: Luisa Maria Diele-Viegas creator: Victor H.G.L. Cavalcante creator: Fabricio Baccaro creator: Guarino Rinaldi Colli creator: Hanna Tuomisto creator: Fernanda P. Werneck uri: https://doi.org/10.7717/peerj.16986 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Souza-Oliveira et al. title: Transcriptome differential expression analysis of defoliation of two different lemon varieties link: https://peerj.com/articles/17218 last-modified: 2024-04-26 description: ‘Allen Eureka’ is a bud variety of Eureka lemon with excellent fruiting traits. However, it suffers from severe winter defoliation that leads to a large loss of organic nutrients and seriously affects the tree’s growth and development as well as the yield of the following year, and the mechanism of its response to defoliation is still unclear. In order to investigate the molecular regulatory mechanisms of different leaf abscission periods in lemon, two lemon cultivars (‘Allen Eureka’ and ‘Yunning No. 1’) with different defoliation traits were used as materials. The petiole abscission zone (AZ) was collected at three different defoliation stages, namely, the pre-defoliation stage (CQ), the mid-defoliation stage (CZ), and the post-defoliation stage (CH). Transcriptome sequencing was performed to analyze the gene expression differences between these two cultivars. A total of 898, 4,856, and 3,126 differentially expressed genes (DEGs) were obtained in CQ, CZ, and CH, respectively, and the number of DEGs in CZ was the largest. GO analysis revealed that the DEGs between the two cultivars were mainly enriched in processes related to oxidoreductase, hydrolase, DNA binding transcription factor, and transcription regulator activity in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in CZ and involved plant hormone signal transduction, phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism. The expression trends of some DEGs suggested their roles in regulating defoliation in lemon. Eight gene families were obtained by combining DEG clustering analysis and weighted gene co-expression network analysis (WGCNA), including β-glucosidase, AUX/IAA, SAUR, GH3, POD, and WRKY, suggesting that these genes may be involved in the regulation of lemon leaf abscission. The above conclusions enrich the research related to lemon leaf abscission and provide reliable data for the screening of lemon defoliation candidate genes and analysis of defoliation pathways. creator: Meichao Dong creator: Tuo Yin creator: Junyan Gao creator: Hanyao Zhang creator: Fan Yang creator: Shaohua Wang creator: Chunrui Long creator: Xiaomeng Fu creator: Hongming Liu creator: Lina Guo creator: Dongguo Zhou uri: https://doi.org/10.7717/peerj.17218 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dong et al. title: Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites link: https://peerj.com/articles/17240 last-modified: 2024-04-26 description: BackgroundSchisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera?MethodsIn this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed.ResultsThe major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new opportunity to further understand the effects of microorganisms on the active secondary metabolites and provided a basis for further research on the sustainable utilization of S. sphenanthera. creator: Xiaolu Qin creator: Han Pu creator: Xilin Fang creator: Qianqian Shang creator: Jianhua Li creator: Qiaozhu Zhao creator: Xiaorui Wang creator: Wei Gu uri: https://doi.org/10.7717/peerj.17240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Qin et al. title: Influence of honey bee (Apis mellifera) breeding on wing venation in Serbia and neighbouring countries link: https://peerj.com/articles/17247 last-modified: 2024-04-26 description: In order to improve the productivity of honey bees (Apis mellifera), some of their traits are selected by breeding. On one hand, breeding is mainly based on the natural geographical variation of this species; on the other hand, mass production and distribution of artificially selected queens can significantly affect the natural geographic variation of honey bees. In this study, we have compared honey bee wings originating from breeding and non-breeding populations in Serbia. In the comparison, we have also used data from a large area of south-eastern Europe. The wings were measured using the 19 landmarks indicated on the wing images. The coordinates were analysed using the methodology of geometric morphometrics. We found that honey bees obtained from honey bee queen breeder differed in wing venation from surrounding populations, which are under natural selection. Therefore, we argue against including populations under artificial selection in the analysis of the natural geographical variation of honey bees. In our analysis of non-breeding samples, we found that in south-eastern Europe there is continuous variation in wing venation and no clear boundaries between A. m. carnica, A. m. cecropia, and A. m. macedonica. creator: Hardeep Kaur creator: Nebojša Nedić creator: Adam Tofilski uri: https://doi.org/10.7717/peerj.17247 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kaur et al. title: Genome-wide identification and analysis of ascorbate peroxidase (APX) gene family in hemp (Cannabis sativa L.) under various abiotic stresses link: https://peerj.com/articles/17249 last-modified: 2024-04-26 description: Ascorbate peroxidase (APX) plays a critical role in molecular mechanisms such as plant development and defense against abiotic stresses. As an important economic crop, hemp (Cannabis sativa L.) is vulnerable to adverse environmental conditions, such as drought, cold, salt, and oxidative stress, which lead to a decline in yield and quality. Although APX genes have been characterized in a variety of plants, members of the APX gene family in hemp have not been completely identified. In this study, we (1) identified eight members of the CsAPX gene family in hemp and mapped their locations on the chromosomes using bioinformatics analysis; (2) examined the physicochemical characteristics of the proteins encoded by these CsAPX gene family members; (3) investigated their intraspecific collinearity, gene structure, conserved domains, conserved motifs, and cis-acting elements; (4) constructed a phylogenetic tree and analyzed interspecific collinearity; and (5) ascertained expression differences in leaf tissue subjected to cold, drought, salt, and oxidative stresses using quantitative real-time-PCR (qRT-PCR). Under all four stresses, CsAPX6, CsAPX7, and CsAPX8 consistently exhibited significant upregulation, whereas CsAPX2 displayed notably higher expression levels under drought stress than under the other stresses. Taken together, the results of this study provide basic genomic information on the expression of the APX gene family and pave the way for studying the role of APX genes in abiotic stress. creator: Zixiao Liang creator: Hongguo Xu creator: Hongying Qi creator: Yiying Fei creator: Jiaying Cui uri: https://doi.org/10.7717/peerj.17249 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liang et al. title: A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer link: https://peerj.com/articles/17254 last-modified: 2024-04-26 description: BackgroundOccult lymph node metastasis (OLNM) is an essential prognostic factor for early-stage tongue cancer (cT1-2N0M0) and a determinant of treatment decisions. Therefore, accurate prediction of OLNM can significantly impact the clinical management and outcomes of patients with tongue cancer. The aim of this study was to develop and validate a multiomics-based model to predict OLNM in patients with early-stage tongue cancer.MethodsThe data of 125 patients diagnosed with early-stage tongue cancer (cT1-2N0M0) who underwent primary surgical treatment and elective neck dissection were retrospectively analyzed. A total of 100 patients were randomly assigned to the training set and 25 to the test set. The preoperative contrast-enhanced computed tomography (CT) and clinical data on these patients were collected. Radiomics features were extracted from the primary tumor as the region of interest (ROI) on CT images, and correlation analysis and the least absolute shrinkage and selection operator (LASSO) method were used to identify the most relevant features. A support vector machine (SVM) classifier was constructed and compared with other machine learning algorithms. With the same method, a clinical model was built and the peri-tumoral and intra-tumoral images were selected as the input for the deep learning model. The stacking ensemble technique was used to combine the multiple models. The predictive performance of the integrated model was evaluated for accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC-ROC), and compared with expert assessment. Internal validation was performed using a stratified five-fold cross-validation approach.ResultsOf the 125 patients, 41 (32.8%) showed OLNM on postoperative pathological examination. The integrated model achieved higher predictive performance compared with the individual models, with an accuracy of 84%, a sensitivity of 100%, a specificity of 76.5%, and an AUC-ROC of 0.949 (95% CI [0.870–1.000]). In addition, the performance of the integrated model surpassed that of younger doctors and was comparable to the evaluation of experienced doctors.ConclusionsThe multiomics-based model can accurately predict OLNM in patients with early-stage tongue cancer, and may serve as a valuable decision-making tool to determine the appropriate treatment and avoid unnecessary neck surgery in patients without OLNM. creator: Wei Han creator: Yingshu Wang creator: Tao Li creator: Yuke Dong creator: Yanwei Dang creator: Liang He creator: Lianfang Xu creator: Yuhao Zhou creator: Yujie Li creator: Xudong Wang uri: https://doi.org/10.7717/peerj.17254 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Han et al. title: The status and influencing factors of abnormal fetal pregnancy outcomes in 265 cases in China: a retrospective study link: https://peerj.com/articles/17284 last-modified: 2024-04-26 description: BackgroundWith the advancement of prenatal diagnosis technology, the detection rate of fetal abnormalities continues to increase, imposing a significant burden on both society and families. A retrospective analysis of essential information about pregnant women, such as their pregnancy history and delivery details, is crucial for understanding the primary factors that influence pregnancy outcomes in women with fetal abnormalities. This analysis is of great significance for improving the level of pregnancy management and outcomes in pregnant women with fetal abnormalities.ObjectiveTo retrospectively analyze the pregnancy outcomes of women with fetal abnormalities and explore the factors that influence these outcomes.MethodsPregnant women’s pregnancy outcomes were collected from the medical information system and through telephone follow-ups. The chi-square test and logistic regression were used to analyze the factors influencing pregnancy outcomes.ResultsAmong 265 pregnant women diagnosed with fetal abnormalities, 190 chose to continue the pregnancy, while 75 chose to terminate it. Pregnant women with multiple fetal abnormalities (OR = 3.774, 95% CI [1.640–8.683]) were more likely to choose termination of pregnancy (TOP), and pregnant women who were advised to terminate their pregnancy or make a careful choice were more likely to terminate the pregnancy (OR = 41.113, 95% CI [11.028–153.267]).ConclusionThe number of organs involved in fetal abnormalities and treatment recommendations were identified as the primary factors influencing pregnancy outcomes. Improving awareness of maternal health care during pregnancy, early pregnancy screening technology, and a multidisciplinary diagnosis and treatment approach are of great significance in assisting pregnant women in making informed decisions and improving fetal prognosis. creator: Jing Ruan creator: Xuemei Zhong creator: Jiaxuan Mai creator: Cuifen Liu creator: Huiyang Ding uri: https://doi.org/10.7717/peerj.17284 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ruan et al. title: Application of prohexadione-calcium priming affects Brassica napus L. seedlings by regulating morph-physiological characteristics under salt stress link: https://peerj.com/articles/17312 last-modified: 2024-04-26 description: Salinity stress imposes severe constraints on plant growth and development. Here, we explored the impacts of prohexadione-calcium (Pro-Ca) on rapeseed growth under salt stress. We designed a randomized block design pot experiment using two rapeseed varieties, ‘Huayouza 158R’ and ‘Huayouza 62’. We conducted six treatments, S0: non-primed + 0 mM NaCl, Pro-Ca+S0: Pro-Ca primed + 0 mM NaCl, S100: non-primed + 100 mM NaCl, Pro-Ca+S100: Pro-Ca primed + 100 mM NaCl, S150: non-primed + 150 mM NaCl, Pro-Ca+S150: Pro-Ca primed + 150 mM NaCl. The morphophysiological characteristics, and osmoregulatory and antioxidant activities were compared for primed and non-primed varieties. Our data analysis showed that salt stress induced morph-physiological traits and significantly reduced the antioxidant enzyme activities in both rapeseed varieties. The Pro-Ca primed treatment significantly improved seedlings, root, and shoot morphological traits and accumulated more dry matter biomass under salt stress. Compared to Huayouza 158R, Huayouza 62 performed better with the Pro-Ca primed treatment. The Pro-Ca primed treatment significantly enhanced chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and actual photochemical quantum efficiency (ФPSII). Furthermore, the Pro-Ca primed treatment also improved ascorbic acid (ASA) content, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) activity, and stimulated the accumulation of soluble proteins. These findings strongly suggested that the Pro-Ca primed treatment may effectively counteract the negative impacts of salinity stress by regulating the morph-physiological and antioxidant traits. creator: Peng Deng creator: Aaqil Khan creator: Hang Zhou creator: Xutong Lu creator: Huiming Zhao creator: Youwei Du creator: Yaxin Wang creator: Naijie Feng creator: Dianfeng Zheng uri: https://doi.org/10.7717/peerj.17312 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Deng et al. title: Exosomes from uterine fluid promote capacitation of human sperm link: https://peerj.com/articles/16875 last-modified: 2024-04-25 description: BackgroundExtracellular vesicles (EVs) are membrane-bound vesicles containing various proteins, lipids, and nucleic acids. EVs are found in many body fluids, such as blood and urine. The release of EVs can facilitate intercellular communication through fusion with the plasma membrane or endocytosis into the recipient cell or through internalization of the contents. Recent studies have reported that EVs isolated from human endometrial epithelial cells (EECs) promote sperm fertilization ability. EVs from uterine flushing fluid more closely resemble the physiological condition of the uterus. However, it is unclear whether EVs derived directly from uterine flushing fluid have the same effect on sperm. This study aimed to research the effect of EVs from uterine flushing fluid on sperm.MethodsEVs were isolated from the uterine flushing fluid. The presence of EVs was confirmed by nanoparticle tracking analysis (NTA), Western blot, and transmission electron microscopy (TEM). EVs were incubated with human sperm for 2 h and 4 h. The effects of EVs on sperm were evaluated by analyzing acrosome reaction, sperm motility, and reactive oxygen species (ROS).ResultsThe EVs fractions isolated from the uterine fluid were observed in cup-shaped vesicles of different sizes by TEM. All isolated vesicles contained similar numbers of vesicles in the expected size range (30–200 nm) by NTA. CD9 and CD63 were detected in EVs by western blot. Comparing the motility of the two groups incubated sperm motility significantly differed at 4 h. The acrosome reactions were promoted by incubating with EVs significantly. ROS were increased in sperm incubated with EVs.ConclusionOur results showed EVs present in the uterine fluid. Acrosome reactions and ROS levels increased in human sperm incubated with EVs. EVs from uterine fluid can promote the capacitation of human sperm. The increased capacitation after sperm interaction with EVs suggests a possible physiological effect during the transit of the uterus. creator: Renbin Deng creator: Zhao Wu creator: Chaoyong He creator: Chuncheng Lu creator: Danpeng He creator: Xi Li creator: Zhenling Duan creator: Hui Zhao uri: https://doi.org/10.7717/peerj.16875 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Deng et al. title: Natrix natrix after dark: citizen science sheds light on the common grass snake’s nightlife link: https://peerj.com/articles/17168 last-modified: 2024-04-25 description: Activity patterns in animals are often species-specific, and can be generally categorized as diurnal, crepuscular, or nocturnal. Understanding these patterns provides insight into ecological adaptations and behaviors. The common grass snake (Natrix natrix), one of the most common and widespread European snake species, is traditionally considered diurnal, with scarce evidence of its crepuscular and nocturnal activity. We aimed to document the distribution, environmental conditions, and potential phenotype associations of nighttime activity in N. natrix. We used citizen science data from iNaturalist (1992–2022), Observation.org (2012–2022), together with personal field observations (2010–2023) to collect 127 crepuscular and nocturnal activity records. Most observations occurred between May and August, coinciding with the peak activity period of grass snakes across their distribution range. Statistical analyses revealed no significant difference in mean daily temperatures between crepuscular and nocturnal observations. However, striped individuals displayed nocturnal activity at higher temperatures, consistent with their distribution in warmer regions, but failed to register any difference when tested on a geographic subsample, that accounted for sympatry of the phenotypes. Surprisingly, we found no significant impact of moon presence or moonlight on nighttime activity or age class, contrary to expectations based on other snake species’ responses. While our study reveals that nocturnal activity in the common grass snake is geographically widespread, further research is warranted to understand its drivers and ecological implications. This study highlights the value of citizen science platforms for biological and ecological research, offering unparalleled spatial and temporal coverage by their users. In conclusion, our work extends the knowledge of nocturnal behavior in N. natrix and underlines the critical role of citizen science in discovering behavioral aspects of common and widespread species. creator: Petronel Spaseni creator: Tiberiu C. Sahlean creator: Iulian Gherghel creator: Ștefan R. Zamfirescu creator: Ionuț C. Petreanu creator: Raluca Melenciuc creator: Cristina F. Alistar creator: Viorel D. Gavril creator: Alexandru Strugariu uri: https://doi.org/10.7717/peerj.17168 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Spaseni et al. title: Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador link: https://peerj.com/articles/17199 last-modified: 2024-04-25 description: Carbapenem-resistant Acinetobacter spp. is associated with nosocomial infections in intensive care unit patients, resulting in high mortality. Although Acinetobacter spp. represent a serious public health problem worldwide, there are a few studies related to the presence of carbapenemases in health care facilities and other environmental settings in Ecuador. The main aim of this study was to characterize the carbapenem-resistant Acinetobacter spp. isolates obtained from four hospitals (52) and from five rivers (27) close to Quito. We used the disc diffusion and EDTA sinergy tests to determine the antimicrobial susceptibility and the production of metallo β-lactamases, respectively. We carried out a multiplex PCR of gyrB gene and the sequencing of partial rpoB gene to bacterial species identification. We performed molecular screening of nine carbapenem-resistant genes (blaSPM, blaSIM, blaGIM, blaGES, blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, and blaOXA-143) by multiplex PCR, followed by identification using sequencing of blaOXA genes. Our findings showed that carbapenem-resistant A. baumannii were the main species found in health care facilities and rivers. Most of the clinical isolates came from respiratory tract samples and harbored blaOXA-23, blaOXA-366, blaOXA-72, blaOXA-65, blaOXA-70, and blaOXA-143-like genes. The river isolates harbored only the blaOXA-51 and probably blaOXA-259 genes. We concluded that the most predominant type of carbapenem genes among isolates were both blaOXA-23 and blaOXA-65 among A. baumannii clinical isolates. creator: Nicole Sotomayor creator: José Eduardo Villacis creator: Noela Burneo creator: Jorge Reyes creator: Sonia Zapata creator: Rosa de los Ángeles Bayas-Rea uri: https://doi.org/10.7717/peerj.17199 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sotomayor et al. title: The role of mitophagy in the development of chronic kidney disease link: https://peerj.com/articles/17260 last-modified: 2024-04-25 description: Chronic kidney disease (CKD) represents a significant global health concern, with renal fibrosis emerging as a prevalent and ultimate manifestation of this condition. The absence of targeted therapies presents an ongoing and substantial challenge. Accumulating evidence suggests that the integrity and functionality of mitochondria within renal tubular epithelial cells (RTECs) often become compromised during CKD development, playing a pivotal role in the progression of renal fibrosis. Mitophagy, a specific form of autophagy, assumes responsibility for eliminating damaged mitochondria to uphold mitochondrial equilibrium. Dysregulated mitophagy not only correlates with disrupted mitochondrial dynamics but also contributes to the advancement of renal fibrosis in CKD. While numerous studies have examined mitochondrial metabolism, ROS (reactive oxygen species) production, inflammation, and apoptosis in kidney diseases, the precise pathogenic mechanisms underlying mitophagy in CKD remain elusive. The exact mechanisms through which modulating mitophagy mitigates renal fibrosis, as well as its influence on CKD progression and prognosis, have not undergone systematic investigation. The role of mitophagy in AKI has been relatively clear, but the role of mitophagy in CKD is still rare. This article presents a comprehensive review of the current state of research on regulating mitophagy as a potential treatment for CKD. The objective is to provide fresh perspectives, viable strategies, and practical insights into CKD therapy, thereby contributing to the enhancement of human living conditions and patient well-being. creator: Kexin Yang creator: Ting Li creator: Yingpu Geng creator: Xiangyu Zou creator: Fujun Peng creator: Wei Gao uri: https://doi.org/10.7717/peerj.17260 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang et al. title: Genome‑wide analysis of the MYB gene family in pumpkin link: https://peerj.com/articles/17304 last-modified: 2024-04-25 description: The MYB gene family exerts significant influence over various biological processes and stress responses in plants. Despite this, a comprehensive analysis of this gene family in pumpkin remains absent. In this study, the MYB genes of Cucurbita moschata were identified and clustered into 33 groups (C1-33), with members of each group being highly conserved in terms of their motif composition. Furthermore, the distribution of 175 CmoMYB genes across all 20 chromosomes was found to be non-uniform. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with phytohormone responses and abiotic/biotic stress. Utilizing quantitative real-time polymerase chain reaction (qRT-PCR), the expression patterns of 13 selected CmoMYB genes were validated, particularly in response to exogenous phytohormone exposure and various abiotic stressors, including ABA, SA, MeJA, and drought treatments. Expression analysis in different tissues showed that CmoMYB genes are expressed at different levels in different tissues, suggesting that they are functionally divergent in regulating growth and abiotic stresses. These results provide a basis for future studies to characterize the function of the MYB gene family under abiotic stresses in pumpkins. creator: Minyan Xu creator: Jingjing Fu creator: Ying Ni creator: Chenchen Zhang uri: https://doi.org/10.7717/peerj.17304 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xu et al. title: Circular RNA circMAN1A2 promotes ovarian cancer progression through the microRNA-135a-3p/IL1RAP/TAK1 pathway link: https://peerj.com/articles/16967 last-modified: 2024-04-24 description: BackgroundOvarian cancer (OC) is the most lethal malignancy in women owing to its diagnosis only at the advanced stage. Elucidation of its molecular pathogenesis may help identify new tumor markers and targets for therapy. Circular RNAs (circRNAs) are stable, conserved, and functional biomolecules that can be used as effective biomarkers for various cancers.MethodsIn this study, a potential circRNA related to early diagnosis of OC, circMAN1A2, was analyzed. Overexpression/knockdown of circMAN1A2 in OC cells was used to decipher its effects on cell proliferation with a Cell Counting Kit-8, 5-ethynyl-2’-deoxyuridine (EdU), cell cycle, clone formation, and wound healing assay. RNA pull-down and Dual luciferase assay were used to explain the underlying mechanism by which circMAN1A2 regulates OC cell proliferation. In vivo, the effect of circMAN1A2 in OC was evaluated using nude mouse xenograft experiments.ResultsCircMAN1A2 was highly expressed in OC and promoted proliferation, clone formation, and tumorigenicity of OC cells. In addition, we found that circMAN1A2 acted as a sponge for microRNA (miR)-135a-3p; miR-135a-3p directly targeted the 3’ untranslated region of interleukin 1 receptor accessory protein (IL1RAP) in OC cells, thereby regulating the phosphorylation of transforming growth factor-beta activated kinase 1 (TAK1), which resulted in promotion of OC cell growth.ConclusionsCircMAN1A2 promotes OC cell proliferation by inhibiting the miR-135a-3p/IL1RAP/TAK1 axis. In conclusion, circMAN1A2 may be a biomarker for early detection of OC and a target for subsequent therapy. creator: Bo Li creator: Chuancui Hu creator: Da Zhao creator: Mingchao Nie creator: Xiaoli Wang uri: https://doi.org/10.7717/peerj.16967 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Li et al. title: Physical activity and sedentary behavior among school-going adolescents in low- and middle-income countries: insights from the global school-based health survey link: https://peerj.com/articles/17097 last-modified: 2024-04-24 description: BackgroundThe Global School Student Health Survey (GSHS) is being carried out by students in various countries across the globe to advance improved health programs for youth. However, in comparison to high-income countries, adolescents in low- and middle-income countries (LMICs) are generally at an early stage of understanding regarding physical activity (PA) and sedentary behavior (SB), often exhibiting low levels of PA and high levels of SB. Furthermore, there is limited evidence connecting PA and SB in school-going adolescents from LMICs.PurposeThe objective of this review was to synthesize the available evidence regarding PA and sedentary behavior among school-going adolescents in LMICs using data from the GSHS.MethodOn March 18, 2023, a systematic literature search was performed across four electronic databases, namely Web of Science, PubMed, ScienceDirect, and EBSCO with n odaterestrictions. Studies were eligible if they: (1) utilization of data sourced from the Global Student-based Health Survey; (2) exploration of physical activity; (3) specific focus on adolescents; (4) conducted in low- and middle-income countries; (5) study design encompassing observational; (6) published as English journal articles.ResultsAmong the 29 studies included in the analysis, the majority revealed elevated levels of sedentary behavior and diminished levels of PA in low- and middle-income countries. Furthermore, notable disparities in physical engagement and sedentary behavior were noted between male and female adolescents (p < 0.001). Augmented PA among teenagers was observed to correlate with higher consumption of vegetables and fruits (AOR = 1.30; 95% CI [1.13–1.50]; p < 0.001), decreased alcohol consumption, and a reduced prevalence of loneliness and depression (aOR 1.37, 95% CI [1.18–1.59]).ConclusionsThe results of this review affirm that in contrast to high-income countries, adolescents in low- and middle-income countries (LMICs) are in the early stages of comprehending physical activity, marked by low levels of PA. Physical activity and sedentary behavior in school-going adolescents from LMICs appear to be influenced by factors such as policies, cultural norms, socioeconomic conditions, as well as gender, and age. creator: Hui Li creator: Wenyu Zhang creator: Jin Yan uri: https://doi.org/10.7717/peerj.17097 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Rate dependent neural responses of interaural-time-difference cues in fine-structure and envelope link: https://peerj.com/articles/17104 last-modified: 2024-04-24 description: Advancements in cochlear implants (CIs) have led to a significant increase in bilateral CI users, especially among children. Yet, most bilateral CI users do not fully achieve the intended binaural benefit due to potential limitations in signal processing and/or surgical implant positioning. One crucial auditory cue that normal hearing (NH) listeners can benefit from is the interaural time difference (ITD), i.e., the time difference between the arrival of a sound at two ears. The ITD sensitivity is thought to be heavily relying on the effective utilization of temporal fine structure (very rapid oscillations in sound). Unfortunately, most current CIs do not transmit such true fine structure. Nevertheless, bilateral CI users have demonstrated sensitivity to ITD cues delivered through envelope or interaural pulse time differences, i.e., the time gap between the pulses delivered to the two implants. However, their ITD sensitivity is significantly poorer compared to NH individuals, and it further degrades at higher CI stimulation rates, especially when the rate exceeds 300 pulse per second. The overall purpose of this research thread is to improve spatial hearing abilities in bilateral CI users. This study aims to develop electroencephalography (EEG) paradigms that can be used with clinical settings to assess and optimize the delivery of ITD cues, which are crucial for spatial hearing in everyday life. The research objective of this article was to determine the effect of CI stimulation pulse rate on the ITD sensitivity, and to characterize the rate-dependent degradation in ITD perception using EEG measures. To develop protocols for bilateral CI studies, EEG responses were obtained from NH listeners using sinusoidal-amplitude-modulated (SAM) tones and filtered clicks with changes in either fine structure ITD (ITDFS) or envelope ITD (ITDENV). Multiple EEG responses were analyzed, which included the subcortical auditory steady-state responses (ASSRs) and cortical auditory evoked potentials (CAEPs) elicited by stimuli onset, offset, and changes. Results indicated that acoustic change complex (ACC) responses elicited by ITDENV changes were significantly smaller or absent compared to those elicited by ITDFS changes. The ACC morphologies evoked by ITDFS changes were similar to onset and offset CAEPs, although the peak latencies were longest for ACC responses and shortest for offset CAEPs. The high-frequency stimuli clearly elicited subcortical ASSRs, but smaller than those evoked by lower carrier frequency SAM tones. The 40-Hz ASSRs decreased with increasing carrier frequencies. Filtered clicks elicited larger ASSRs compared to high-frequency SAM tones, with the order being 40 > 160 > 80> 320 Hz ASSR for both stimulus types. Wavelet analysis revealed a clear interaction between detectable transient CAEPs and 40-Hz ASSRs in the time-frequency domain for SAM tones with a low carrier frequency. creator: Hongmei Hu creator: Stephan D. Ewert creator: Birger Kollmeier creator: Deborah Vickers uri: https://doi.org/10.7717/peerj.17104 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hu et al. title: Validation for the function of protein C in mouse models link: https://peerj.com/articles/17261 last-modified: 2024-04-24 description: ObjectivesProtein C (PC) is an anticoagulant that is encoded by the PROC gene. Validation for the function of PC was carried out in mouse models.MethodsIn this study, autosomal recessive PC deficiency (PCD) was selected as the target, and the specific mutation site was chromosome 2 2q13-q14, PROC c.1198G>A (p.Gly400Ser) which targets G399S (GGT to AGC) in mouse models. To investigate the role of hereditary PC in mice models, we used CRISPR/Cas9 gene editing technology to create a mouse model with a genetic PCD mutation.ResultsThe two F0 generation positive mice produced using the CRISPR/Cas9 gene editing technique were chimeras, and the mice in F1 and F2 generations were heterozygous. There was no phenotype of spontaneous bleeding or thrombosis in the heterozygous mice, but some of them were blind. Blood routine results showed no significant difference between the heterozygous mice and wild-type mice (P > 0.05). Prothrombin time (PT), activated partial thromboplastin time (APTT), and thrombin time (TT) were prolonged in the heterozygous mice, while the level of fibrinogen content (FIB) decreased, suggesting secondary consumptive coagulation disease. The protein C activity of heterozygous mice was significantly lower than that of wild-type mice (P < 0.001), but there was no significant difference in protein C antigen levels (P > 0.05). H&E staining showed steatosis and hydrodegeneration in the liver of heterozygous mice. Necrosis and exfoliated epithelial cells could be observed in renal tubule lumen, forming cell or granular tubules. Hemosiderin deposition was found in the spleen along with splenic hemorrhage. Immunohistochemistry demonstrated significant fibrin deposition in the liver, spleen, and kidney of heterozygous mice.ConclusionIn this study, heterozygotes of the mouse model with a PC mutation were obtained. The function of PC was then validated in a mouse model through genotype, phenotype, and PC function analysis. creator: Ya Liu creator: Maoping Cai creator: Yan Chen creator: Guocai Wu creator: Songyu Li creator: Zhanghui Chen uri: https://doi.org/10.7717/peerj.17261 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: A physical fitness–evaluation system for outstanding Chinese male boxers link: https://peerj.com/articles/17271 last-modified: 2024-04-24 description: BackgroundWe sought to create a system to evaluate the physical fitness of outstanding Chinese male boxers that included an evaluation index, fitness level criteria, and modeling. This system was then used to assess athletes’ physical fitness and development.MethodsDocumentation, expert interviews, questionnaires, measurements, and statistical analyses were used in this study.ResultsThe physical fitness evaluation system included the following three components: (1) body shape indexes (n = 4) including the backhand upper arm circumference differential, finger span height, Cottrell index, and pelvic width/shoulder width × 100; (2) body function indexes (n = 4) including relative maximum anaerobic power, relative maximal oxygen uptake, and creatine kinase and testosterone concentrations; and (3) athletic quality indexes (n = 9) including the speed strength index, the backhand straight punch strength, 3-min cumulative punching force, backhand straight punch reaction time, backhand straight punch speed, 30-m sprint, 9-min double shake jump rope, 1-min double shake jump rope, and sitting forward bend tests. A five-point grading system to evaluate physical fitness was established and an evaluation model was proposed.ConclusionsThe reference values were determined to be objective and effective using a back substitution process. Individual and differential assessments reflected the athletes’ level of physical fitness. The critical values were established under the best and worst conditions and the optimal values were found to be valid and effective. creator: Guodong Wu creator: Yuqiang Guo creator: Liqin Zhang creator: Chao Chen uri: https://doi.org/10.7717/peerj.17271 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wu et al. title: Melanella martarum sp. nov. (Gastropoda: Eulimidae): the first parasitic deep-sea snail reported for the Salas & Gomez Ridge link: https://peerj.com/articles/16932 last-modified: 2024-04-23 description: Eulimidae is a highly diverse family of gastropods that are often parasites of echinoderms. They are cosmopolitan and live from the intertidal to great depths. Despite its wide geographic and bathymetric distribution, no species of Eulimidae have been reported for the Salas & Gómez Ridge to date. In this study, we describe Melanella martarum sp. nov., which was collected during the EPIC oceanographic cruise onboard RV Mirai (JAMSTEC, Japan) in 2019. Seven specimens were collected with a modified Agassiz trawl on the summit of seamount “Pearl” (Zhemchuznaya) in the Salas & Gómez Ridge (25.59°S, 89.13°W) at 545 m depth. The morphology of M. martarum sp. nov. was compared with other Melanella species reported for the area, including Chile and Rapa Nui. DNA was extracted and partial sequences of the mitochondrial genes Cytochrome Oxidase 1 (COI) and 16S rDNA, and the nuclear gene Histone 3 (H3) were sequenced. Melanella martarum sp. nov. has morphological characteristics that separate it from other species of Melanella, such as the thickness and color of the shell, and the shape of the protoconch. In addition, M. martarum sp. nov. was genetically differentiated from other Melanella spp. sequences (uncorrected p distances from 18,1–8.6% in mitochondrial COI and 16S rDNA to 3% in nuclear H3 sequences). Although there is not much molecular data available for Eulimidae, the phylogenetic analysis confirms the results obtained by morphology, placing the species found on the Salas & Gómez Ridge within the genus Melanella. The current study advances the understanding of the poorly known benthic fauna found on seamounts in the easternmost part of the Sala & Gómez ridge, a location distinguished by a high level of endemism. creator: Leonardo Santos de Souza creator: Cynthia M. Asorey creator: Javier Sellanes uri: https://doi.org/10.7717/peerj.16932 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 de Souza et al. title: Discovery of a peculiar insular race of Ravenna nivea (Nire, 1920) (Lepidoptera: Lycaenidae) endemic to Yinggeling Mountain of Hainan, suggesting heterogeneous geological history of mountain formation of the island link: https://peerj.com/articles/17172 last-modified: 2024-04-23 description: A peculiar population of Ravenna nivea (Nire, 1920) was discovered from the Yinggeling Mountain Mass of central Hainan. Its wing pattern and COI barcode data show considerable distinction from other geographic populations of R. nivea, including that of Bawangling, approximately only 40 km away and also located in Hainan. The p-distance value of the COI barcode between the Yinggeling and Bawangling populations was 1.1%, considerably higher than the value (0.6%) between Bawangling population and populations in eastern China, where the subspecific name howarthi Saigusa, 1993 applies. The population is regarded as a distinct subspecies ngiunmoiae Lo & Hsu, subsp. nov. The distinctness and high degree of COI haplotype diversity of R. nivea found in Hainan and Taiwan suggest continental islands may serve as glacial refugees for the butterfly and other organisms during previous glaciations, and the presence of the relict populations of montane butterflies like R. nivea may provide useful clues towards a better understanding of the geological history of mountain formation within islands. creator: Yu-Feng Hsu creator: Yik Fui Philip Lo creator: Rung-Juen Lin uri: https://doi.org/10.7717/peerj.17172 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hsu et al. title: Prognosis value of galectin-3 in patients with dilated cardiomyopathy: a meta-analysis link: https://peerj.com/articles/17201 last-modified: 2024-04-23 description: BackgroundAccurate prediction and assessment of myocardial fibrosis (MF) and adverse cardiovascular events (MACEs) are crucial in patients with dilated cardiomyopathy (DCM). Several studies indicate that galectin-3 (gal-3) as a promising prognostic predictor in patients with DCM.MethodsA comprehensive search was conducted in PubMed, EMBASE, the Cochrane Library, and Web of Science for relevant studies up to August 2023. The hazard ratios (HRs) of gal-3 for MACEs in DCM patients, and for MACEs in LGE(+) versus LGE(-) groups, were evaluated. Statistical analysis was performed using STATA SE 14.0 software.ResultsSeven studies, encompassing 945 patients, met the eligibility criteria. In DCM patients, abnormally elevated gal-3 levels were indicative of an increased MACEs risk (HR = 1.10, 95% CI [1.00–1.21], I2 = 65.7%, p = 0.008). Compared with the LGE(-) group, the level of gal-3 in LGE(+) group was higher (HR = 1.12, 95% CI [1.05–1.19], I2 = 31.4%, p = 0.233), and the combination of gal-3 and LGE significantly improved the prediction of MACEs. Sensitivity analysis confirmed the robustness of all results.ConclusionsThis study’s findings suggest that elevated gal-3 levels significantly correlate with increased MACE risk in DCM, highlighting its potential as a biomarker. However, significant heterogeneity among studies necessitates further research to ascertain gal-3’s predictive and diagnostic value in DCM prognosis, particularly in conjunction with LGE.PROSPERO IDCRD42023471199. creator: Yan Xiong creator: Qing Zhang uri: https://doi.org/10.7717/peerj.17201 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xiong and Zhang title: The effects of COVID-19 on agriculture supply chain, food security, and environment: a review link: https://peerj.com/articles/17281 last-modified: 2024-04-23 description: COVID-19 has a deep impact on the economic, environmental, and social life of the global population. Particularly, it disturbed the entire agriculture supply chain due to a shortage of labor, travel restrictions, and changes in demand during lockdowns. Consequently, the world population faced food insecurity due to a reduction in food production and booming food prices. Low-income households face food security challenges because of limited income generation during the pandemic. Thus, there is a need to understand comprehensive strategies to meet the complex challenges faced by the food industry and marginalized people in developing countries. This research is intended to review the agricultural supply chain, global food security, and environmental dynamics of COVID-19 by exploring the most significant literature in this domain. Due to lockdowns and reduced industrial production, positive environmental effects are achieved through improved air and water quality and reduced noise pollution globally. However, negative environmental effects emerged due to increasing medical waste, packaging waste, and plastic pollution due to disruptions in recycling operations. There is extensive literature on the effects of COVID-19 on the environment and food security. This study is an effort to review the existing literature to understand the net effects of the pandemic on the environment and food security. The literature suggested adopting innovative policies and strategies to protect the global food supply chain and achieve economic recovery with environmental sustainability. For instance, food productivity should be increased by using modern agriculture technologies to ensure food security. The government should provide food to vulnerable populations during the pandemic. Trade restrictions should be removed for food trade to improve international collaboration for food security. On the environmental side, the government should increase recycling plants during the pandemic to control waste and plastic pollution. creator: Haider Mahmood creator: Maham Furqan creator: Gowhar Meraj creator: Muhammad Shahid Hassan uri: https://doi.org/10.7717/peerj.17281 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mahmood et al. title: Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand link: https://peerj.com/articles/17289 last-modified: 2024-04-23 description: Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system. creator: Pongrawee Nimnoi creator: Patawee Pirankham creator: Kittipong Srimuang creator: Pornthip Ruanpanun uri: https://doi.org/10.7717/peerj.17289 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Nimnoi et al. title: A comparison of the effects of two protocols of concurrent resistance and aerobic training on physical fitness in middle school students link: https://peerj.com/articles/17294 last-modified: 2024-04-23 description: ObjectiveThis study aimed to compare the effects of two concurrent training (CT) protocols on the physical fitness of middle school students.MethodA 12-week quasi-experimental pre-test/post-test study was conducted with 157 middle school students (age = 12.48 ± 0.34, n = 90 females) divided into three groups: CT group A (CT-0h) received combined resistance training (RT) and aerobic training (AT) in each physical education session, CT group B (CT-48h) received RT and AT across two separate physical education classes 48 h apart, and a control group (Con) received no training. Training occurred twice a week. Test indicators included cardiorespiratory fitness (CRF) measured by estimated VO2max and 20 m shuttle run (laps), as well as muscle strength assessed through long jump, vertical jump, and handgrip strength.ResultsThe intervention groups exhibited significant increases in estimated VO2max and muscle strength compared to their baseline values (p < 0.05). Both CT-0h and CT-48h groups demonstrated significant improvements in 20 m shuttle run (laps) (mean difference: 8.88 laps, p < 0.01; mean difference: 4.81 laps, p < 0.01, respectively), standing long jump (mean difference: 6.20 cm, p < 0.01; mean difference: 3.68 cm, p < 0.01, respectively), vertical jump (mean difference: 4.95 cm, p < 0.01; mean difference: 4.04 cm, p < 0.01, respectively), and handgrip strength (mean difference: 11.17 kg, p < 0.01; mean difference: 6.99 kg, p < 0.01, respectively). CT-0h group exhibited significantly increased estimated VO2max (mean difference: 1.47 ml/kg/min, p < 0.01) compared to the CT-48h group.ConclusionBoth CT programs effectively improved adolescents’ physical fitness indicators. However, the program that integrated RT and AT within the same physical education class demonstrated superior enhancement in adolescents’ CRF. creator: Zhen Li creator: Teng Ding creator: Yanan Gao creator: Xiaowei Han creator: Yang Liu creator: Zhixiong Zhou uri: https://doi.org/10.7717/peerj.17294 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Are women with endometriosis more likely to experience reduced physical performance compared to women without the condition? link: https://peerj.com/articles/16835 last-modified: 2024-04-22 description: BackgroundEndometriosis is a condition of the female reproductive system associated with pelvic pain. Chronic pain can affect physical performance by limiting the functional activities, thus, it is hypothesized that women with endometriosis may also present decreased functional capacity, decreased strength, and mobility. The objective of this study is to compare physical performance in women with and without endometriosis.MethodsThis is a cross-sectional study composed of 115 women equally divided into two groups: the endometriosis group (EG), composed of women with a confirmed diagnosis of the disease by magnetic resonance imaging, and the comparator group (CG), consisting of women without suspicion of the disease. Physical performance (dependent variable) was assessed using hand dynamometry, the 6-min walk test (6MWT), gait speed, and the chair stands test. CG participants performed the tests during the luteal phase of the menstrual cycle. Descriptive statistics, unpaired t-tests, and chi-square tests were used to describe and compare the groups. Multiple linear regression tested the associations adjusted for covariates (age, income, education, age at menarche, and body mass index).ResultsThe EG had worse gait speed (mean difference: −0.11; 95% CI: [−0.18 to −0.04]), weaker grip strength (mean difference: −3.32; 95% CI: [−5.30 to −1.33]), shorter distance covered in the 6MWT (mean difference: −83.46; 95% CI: [−121.38 to −45.53]), and a lower number of repetitions in the chair stands test (mean difference: −8.44; 95% CI: [−10.64 to −6.25]) than the CG, even after adjusting for covariates.ConclusionGrip strength, lower limb strength, mobility, and functional capacity were worse in women diagnosed with endometriosis. Women with endometriosis should be encouraged to engage in physical exercise, adopt healthy lifestyle habits, and participate in rehabilitation activities to control pain, with the aim of reducing functional impairments. creator: Tatiana Silva creator: Maiara Oliveira creator: Edwiges Oliveira creator: Rayllanne Macena creator: Gessica Taynara de Oliveira Silva creator: Saionara M. A. Câmara creator: Maria Micussi uri: https://doi.org/10.7717/peerj.16835 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Silva et al. title: High frequency of transition to transversion ratio in the stem region of RNA secondary structure of untranslated region of SARS-CoV-2 link: https://peerj.com/articles/16962 last-modified: 2024-04-22 description: IntroductionThe propensity of nucleotide bases to form pairs, causes folding and the formation of secondary structure in the RNA. Therefore, purine (R): pyrimidine (Y) base-pairing is vital to maintain uniform lateral dimension in RNA secondary structure. Transversions or base substitutions between R and Y bases, are more detrimental to the stability of RNA secondary structure, than transitions derived from substitutions between A and G or C and T. The study of transversion and transition base substitutions is important to understand evolutionary mechanisms of RNA secondary structure in the 5′  and 3′  untranslated (UTR) regions of SARS-CoV-2. In this work, we carried out comparative analysis of transition and transversion base substitutions in the stem and loop regions of RNA secondary structure of SARS-CoV-2.MethodsWe have considered the experimentally determined and well documented stem and loop regions of 5′ and 3′ UTR regions of SARS-CoV-2 for base substitution analysis. The secondary structure comprising of stem and loop regions were visualized using the RNAfold web server. The GISAID repository was used to extract base sequence alignment of the UTR regions. Python scripts were developed for comparative analysis of transversion and transition frequencies in the stem and the loop regions.ResultsThe results of base substitution analysis revealed a higher transition (ti) to transversion (tv) ratio (ti/tv) in the stem region of UTR of RNA secondary structure of SARS-CoV-2 reported during the early stage of the pandemic. The higher ti/tv ratio in the stem region suggested the influence of secondary structure in selecting the pattern of base substitutions. This differential pattern of ti/tv values between stem and loop regions was not observed among the Delta and Omicron variants that dominated the later stage of the pandemic. It is noteworthy that the ti/tv values in the stem and loop regions were similar among the later dominant Delta and Omicron variant strains which is to be investigated to understand the rapid evolution and global adaptation of SARS-CoV-2.ConclusionOur findings implicate the lower frequency of transversions than the transitions in the stem regions of UTRs of SARS-CoV-2. The RNA secondary structures are associated with replication, translation, and packaging, further investigations are needed to understand these base substitutions across different variants of SARS-CoV-2. creator: Madhusmita Dash creator: Preetisudha Meher creator: Aditya Kumar creator: Siddhartha Sankar Satapathy creator: Nima D. Namsa uri: https://doi.org/10.7717/peerj.16962 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dash et al. title: Shifts in dominance of benthic communities along a gradient of water temperature and turbidity in tropical coastal ecosystems link: https://peerj.com/articles/17132 last-modified: 2024-04-22 description: Tropical coastal benthic communities will change in species composition and relative dominance due to global (e.g., increasing water temperature) and local (e.g., increasing terrestrial influence due to land-based activity) stressors. This study aimed to gain insight into possible trajectories of coastal benthic assemblages in Raja Ampat, Indonesia, by studying coral reefs at varying distances from human activities and marine lakes with high turbidity in three temperature categories (<31 °C, 31–32 °C, and >32 °C). The benthic community diversity and relative coverage of major benthic groups were quantified via replicate photo transects. The composition of benthic assemblages varied significantly among the reef and marine lake habitats. The marine lakes <31 °C contained hard coral, crustose coralline algae (CCA), and turf algae with coverages similar to those found in the coral reefs (17.4–18.8% hard coral, 3.5–26.3% CCA, and 15–15.5% turf algae, respectively), while the higher temperature marine lakes (31–32 °C and >32 °C) did not harbor hard coral or CCA. Benthic composition in the reefs was significantly influenced by geographic distance among sites but not by human activity or depth. Benthic composition in the marine lakes appeared to be structured by temperature, salinity, and degree of connection to the adjacent sea. Our results suggest that beyond a certain temperature (>31 °C), benthic communities shift away from coral dominance, but new outcomes of assemblages can be highly distinct, with a possible varied dominance of macroalgae, benthic cyanobacterial mats, or filter feeders such as bivalves and tubeworms. This study illustrates the possible use of marine lake model systems to gain insight into shifts in the benthic community structure of tropical coastal ecosystems if hard corals are no longer dominant. creator: Ludi Parwadani Aji creator: Diede Louise Maas creator: Agustin Capriati creator: Awaludinnoer Ahmad creator: Christiaan de Leeuw creator: Leontine Elisabeth Becking uri: https://doi.org/10.7717/peerj.17132 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Aji et al. title: Incidence and risk factors of systemic lupus erythematosus in patients with primary immune thrombocytopenia: a systematic review and meta-analysis link: https://peerj.com/articles/17152 last-modified: 2024-04-22 description: BackgroundImmune disorders and autoantibodies has been noted in both primary immune thrombocytopenia (ITP) and systemic lupus erythematosus (SLE). Whether the two disorders are correlated is unclear. The lack of evidence on the incidence of and risk factors for SLE in primary ITP patients poses a challenge for prediction in clinical practice. Therefore, we conducted this study.MethodsThe protocol was registered with PROSPERO (CRD42023403665). Web of Science, Cochrane, PubMed, and EMBASE were searched for articles published from inception to 30 September 2023 on patients who were first diagnosed with primary ITP and subsequently developed into SLE. Furthermore, the risk factors were analyzed. Study quality was estimated using the Newcastle-Ottawa Scale. The statistical process was implemented using the R language.ResultsThis systematic review included eight articles. The incidence of SLE during the follow-up after ITP diagnosis was 2.7% (95% CI [1.3–4.4%]), with an incidence of 4.6% (95% CI [1.6–8.6%]) in females and 0 (95% CI [0.00–0.4%]) in males. Older age (OR = 6.31; 95% CI [1.11–34.91]), positive antinuclear antibody (ANA) (OR = 6.64; 95% CI [1.40–31.50]), hypocomplementemia (OR = 8.33; 95% CI [1.62–42.91]), chronic ITP (OR = 24.67; 95% CI [3.14–100.00]), organ bleeding (OR = 13.67; 95% CI [2.44–76.69]), and female (OR = 20.50; 95% CI [4.94–84.90]) were risk factors for subsequent SLE in ITP patients.ConclusionPatients with primary ITP are at higher risk of SLE. Specific follow-up and prevention strategies should be tailored especially for older females with positive ANA, hypocomplementemia, or chronic ITP. In subsequent studies, we need to further investigate the risk factors and try to construct corresponding risk prediction models to develop specific prediction strategies for SLE. creator: En-min Zhou creator: Heping Shen creator: Di Wang creator: Weiqun Xu uri: https://doi.org/10.7717/peerj.17152 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics link: https://peerj.com/articles/17181 last-modified: 2024-04-22 description: Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large. creator: Kauthar M. Omar creator: George L. Kitundu creator: Adijat O. Jimoh creator: Dorcus N. Namikelwa creator: Felix M. Lisso creator: Abiola A. Babajide creator: Seun E. Olufemi creator: Olaitan I. Awe uri: https://doi.org/10.7717/peerj.17181 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Omar et al. title: Regulation of endoplasmic reticulum stress on autophagy and apoptosis of nucleus pulposus cells in intervertebral disc degeneration and its related mechanisms link: https://peerj.com/articles/17212 last-modified: 2024-04-22 description: Intervertebral disc degeneration (IVDD) is a common and frequent disease in orthopedics, which seriously affects the quality of life of patients. Endoplasmic reticulum stress (ERS)-regulated autophagy and apoptosis play an important role in nucleus pulposus (NP) cells in IVDD. Hypoxia and serum deprivation were used to induce NP cells. Cell counting kit-8 (CCK-8) assay was used to detect cell activity and immunofluorescence (IF) was applied for the appraisement of glucose regulated protein 78 (GRP78) and green fluorescent protein (GFP)-light chain 3 (LC3). Cell apoptosis was detected by flow cytometry and the expression of LC3II/I was detected by western blot. NP cells under hypoxia and serum deprivation were induced by lipopolysaccharide (LPS), and intervened by ERS inhibitor (4-phenylbutyric acid, 4-PBA) and activator (Thapsigargin, TP). Then, above functional experiments were conducted again and western blot was employed for the evaluation of autophagy-, apoptosis and ERS-related proteins. Finally, NP cells under hypoxia and serum deprivation were stimulated by LPS and intervened using apoptosis inhibitor z-Val-Ala-DL-Asp-fluoromethyl ketone (Z-VAD-FMK) and autophagy inhibitor 3-methyladenine (3-MA). CCK-8 assay, IF, flow cytometry and western blot were performed again. Besides, the levels of inflammatory cytokines were measured with enzyme-linked immunosorbent assay (ELISA) and the protein expressions of programmed death markers were estimated with western blot. It showed that serum deprivation induces autophagy and apoptosis. ERS was significantly activated by LPS in hypoxic and serum deprivation environment, and autophagy and apoptosis were significantly promoted. Overall, ERS affects the occurrence and development of IVDD by regulating autophagy, apoptosis and other programmed death. creator: Jiuming Dai creator: Jin Liu creator: Yucheng Shen creator: Bing Zhang creator: Chaonian Li creator: Zhidong Liu uri: https://doi.org/10.7717/peerj.17212 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dai et al. title: SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity link: https://peerj.com/articles/17234 last-modified: 2024-04-22 description: BackgroundPost-translational modification by Small Ubiquitin-like MOdifier (SUMO) is an important mechanism to regulate protein activity, protein stability, and localization of substrates. Zbtb21 is a zinc finger and BTB (Broad-complex, Tram-track and Bric à brac) domain-containing transcription factor. Bioinformatic prediction suggests several putative SUMOylated sites in Zbtb21 protein.MethodsTwo evolutionarily conserved lysine residues in Zbtb21 protein were mutated alone or in combination to disrupt the binding with SUMO molecules. Western blot and co-immunoprecipitation analyses were performed to detect the SUMOylation state of wild type and mutant Zbtb21 proteins, respectively. Luciferase reporter assays were conducted to evaluate their transcription activities. Meanwhile, immunofluorescence staining was carried out to show their sub-nuclear localizations. Finally, co-immunoprecipitation was performed to detect the interaction between Zbtb21 and its partners.ResultsPhylogenetically conserved lysines 419 and 845 of zebrafish Zbtb21 protein can be conjugated with SUMO molecules. SUMOylation does not affect the subcellular localization and protein stability of Zbtb21, as well as the interaction with Zbtb14 or Zbtb21. Nevertheless, luciferase reporter assays revealed that Zbtb21 is a dual-function transcription factor which exerts activation or repression effect on different promoters, and SUMOylation can modulate the transcriptional activity of Zbtb21 in regulating downstream target genes. Hence, Zbtb21 is identified as a novel substrate of SUMOylation, which would be important for its function.ConclusionsZebrafish Zbtb21 protein can be SUMOylated on lysines 419 and 845, which is evolutionary conserved. SUMOylation affects the dual role of Zbtb21 on transcription. creator: Zhou Fang creator: Yun Deng creator: Haihong Wang creator: Jun Zhou uri: https://doi.org/10.7717/peerj.17234 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fang et al. title: Kernel density estimation of allele frequency including undetected alleles link: https://peerj.com/articles/17248 last-modified: 2024-04-22 description: Whereas undetected species contribute to estimation of species diversity, undetected alleles have not been used to estimated genetic diversity. Although random sampling guarantees unbiased estimation of allele frequency and genetic diversity measures, using undetected alleles may provide biased but more precise estimators useful for conservation. We newly devised kernel density estimation (KDE) for allele frequency including undetected alleles and tested it in estimation of allele frequency and nucleotide diversity using population generated by coalescent simulation as well as well as real population data. Contrary to expectations, nucleotide diversity estimated by KDE had worse bias and accuracy. Allele frequency estimated by KDE was also worse except when the sample size was small. These might be due to finity of population and/or the curse of dimensionality. In conclusion, KDE of allele frequency does not contribute to genetic diversity estimation. creator: Satoshi Aoki creator: Keita Fukasawa uri: https://doi.org/10.7717/peerj.17248 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Aoki and Fukasawa title: Fumaric acid production from fermented oil palm empty fruit bunches using fungal isolate K20: a comparison between free and immobilized cells link: https://peerj.com/articles/17282 last-modified: 2024-04-22 description: This study investigated the potential of using steam-exploded oil palm empty fruit bunches (EFB) as a renewable feedstock for producing fumaric acid (FA), a food additive widely used for flavor and preservation, through a separate hydrolysis and fermentation process using the fungal isolate K20. The efficiency of FA production by free and immobilized cells was compared. The maximum FA concentration (3.25 g/L), with 0.034 g/L/h productivity, was observed after incubation with the free cells for 96 h. Furthermore, the production was scaled up in a 3-L air-lift fermenter using oil palm EFB-derived glucose as the substrate. The FA concentration, yield, and productivity from 100 g/L initial oil palm EFB-derived glucose were 44 g/L, 0.39 g/g, and 0.41 g/L/h, respectively. The potential for scaling up the fermentation process indicates favorable results, which could have significant implications for industrial applications. creator: Antika Boondaeng creator: Jureeporn Keabpimai creator: Chanaporn Trakunjae creator: Nanthavut Niyomvong uri: https://doi.org/10.7717/peerj.17282 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Boondaeng et al. title: Predicting central cervical lymph node metastasis in papillary thyroid carcinoma with Hashimoto’s thyroiditis: a practical nomogram based on retrospective study link: https://peerj.com/articles/17108 last-modified: 2024-04-19 description: BackgroundIn papillary thyroid carcinoma (PTC) patients with Hashimoto’s thyroiditis (HT), preoperative ultrasonography frequently reveals the presence of enlarged lymph nodes in the central neck region. These nodes pose a diagnostic challenge due to their potential resemblance to metastatic lymph nodes, thereby impacting the surgical decision-making process for clinicians in terms of determining the appropriate surgical extent.MethodsLogistic regression analysis was conducted to identify independent risk factors associated with central lymph node metastasis (CLNM) in PTC patients with HT. Then a prediction model was developed and visualized using a nomogram. The stability of the model was assessed using ten-fold cross-validation. The performance of the model was further evaluated through the use of ROC curve, calibration curve, and decision curve analysis.ResultsA total of 376 HT PTC patients were included in this study, comprising 162 patients with CLNM and 214 patients without CLNM. The results of the multivariate logistic regression analysis revealed that age, Tg-Ab level, tumor size, punctate echogenic foci, and blood flow grade were identified as independent risk factors associated with the development of CLNM in HT PTC. The area under the curve (AUC) of this model was 0.76 (95% CI [0.71–0.80]). The sensitivity, specificity, accuracy, and positive predictive value of the model were determined to be 88%, 51%, 67%, and 57%, respectively.ConclusionsThe proposed clinic-ultrasound-based nomogram in this study demonstrated a favorable performance in predicting CLNM in HT PTCs. This predictive tool has the potential to assist clinicians in making well-informed decisions regarding the appropriate extent of surgical intervention for patients. creator: Lirong Wang creator: Lin Zhang creator: Dan Wang creator: Jiawen Chen creator: Wenxiu Su creator: Lei Sun creator: Jue Jiang creator: Juan Wang creator: Qi Zhou uri: https://doi.org/10.7717/peerj.17108 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Magnification in preclinical procedures: effect on muscle activity and angular deviations of the neck and trunk link: https://peerj.com/articles/17188 last-modified: 2024-04-19 description: ObjectivesThis study aimed to assess the effects of different magnification systems on the angular deviations of the neck and trunk and the muscle activities of the upper back and neck during preclinical cavity preparation.MethodsThis was an experimental laboratory study, with the angular deviations from the neutral positions of the neck and trunk and the activities of the bilateral upper back (the descending and ascending trapezius) and neck (sternocleidomastoid) muscles as the dependent variables. The independent variables were the different magnification systems used (Simple, Galilean, and Keplerian loupes, with direct vision as the control) and prepared teeth (teeth 16, 26, 36, and 46). A dental mannequin phantom head with artificial resin teeth was used, and Class I cavity preparations for composite resin were performed on teeth 16, 26, 36, and 46 using a 1012 round diamond bur at low speed. To analyze the angular deviations, the postures adopted during the procedure were recorded using a tripod-mounted camera positioned to provide a lateral view of the operator. A trained researcher measured the angular deviations using the software entitled “Software for Postural Assessment”—SAPO (version 0.69). Bilateral muscle activity was assessed using surface electromyography. Descriptive statistical analysis was performed, and after verifying the assumptions of normality and homoscedasticity, two-way analysis of variance and the Tukey and Games-Howell post-hoc tests were used to compare the data (α=0.05).ResultsThe angular deviation from the neutral position of the neck was found to be significantly higher during cavity preparations performed with the naked eye and the Simple loupe, irrespective of the prepared tooth. With regard to tooth location, the angular deviation of the neck was significantly greater during cavity preparation on teeth 16 and 26, and the angular deviation of the trunk was significantly greater during cavity preparation on tooth 26, regardless of the magnification system used. There were significant differences in right sternocleidomastoid muscle activity between the Simple, Galilean, and Keplerian loupes, with activity being the lowest for the Galilean loupe (p = 0.008). There were no significant differences in left sternocleidomastoid muscle activity between the loupes, regardless of the prepared tooth (p = 0.077). The activities of the bilateral descending trapezius and the right ascending trapezius muscles were significantly lower when the Galilean loupe was used (p < 0.010).ConclusionThese results suggest that the Galilean loupe resulted in lower muscle activity in the neck and back regions and that the Galilean and Keplerian loupes resulted in less angular deviations of the neck and trunk during cavity preparation. creator: Júlia Margato Pazos creator: Ana Flávia Ribeiro Monteiro Fernandes creator: Edson Donizetti Verri creator: Guilherme Gallo Costa Gomes creator: Simone Cecílio Hallak Regalo creator: Patricia Petromilli Nordi Sasso Garcia uri: https://doi.org/10.7717/peerj.17188 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pazos et al. title: Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients link: https://peerj.com/articles/17208 last-modified: 2024-04-19 description: BackgroundStroke is a disease with high morbidity, disability, and mortality. Immune factors play a crucial role in the occurrence of ischemic stroke (IS), but their exact mechanism is not clear. This study aims to identify possible immunological mechanisms by recognizing immune-related biomarkers and evaluating the infiltration pattern of immune cells.MethodsWe downloaded datasets of IS patients from GEO, applied R language to discover differentially expressed genes, and elucidated their biological functions using GO, KEGG analysis, and GSEA analysis. The hub genes were then obtained using two machine learning algorithms (least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE)) and the immune cell infiltration pattern was revealed by CIBERSORT. Gene-drug target networks and mRNA-miRNA-lncRNA regulatory networks were constructed using Cytoscape. Finally, we used RT-qPCR to validate the hub genes and applied logistic regression methods to build diagnostic models validated with ROC curves.ResultsWe screened 188 differentially expressed genes whose functional analysis was enriched to multiple immune-related pathways. Six hub genes (ANTXR2, BAZ2B, C5AR1, PDK4, PPIH, and STK3) were identified using LASSO and SVM-RFE. ANTXR2, BAZ2B, C5AR1, PDK4, and STK3 were positively correlated with neutrophils and gamma delta T cells, and negatively correlated with T follicular helper cells and CD8, while PPIH showed the exact opposite trend. Immune infiltration indicated increased activity of monocytes, macrophages M0, neutrophils, and mast cells, and decreased infiltration of T follicular helper cells and CD8 in the IS group. The ceRNA network consisted of 306 miRNA-mRNA interacting pairs and 285 miRNA-lncRNA interacting pairs. RT-qPCR results indicated that the expression levels of BAZ2B, C5AR1, PDK4, and STK3 were significantly increased in patients with IS. Finally, we developed a diagnostic model based on these four genes. The AUC value of the model was verified to be 0.999 in the training set and 0.940 in the validation set.ConclusionOur research explored the immune-related gene expression modules and provided a specific basis for further study of immunomodulatory therapy of IS. creator: Lin Cong creator: Yijie He creator: Yun Wu creator: Ze Li creator: Siwen Ding creator: Weiwei Liang creator: Xingjun Xiao creator: Huixue Zhang creator: Lihua Wang uri: https://doi.org/10.7717/peerj.17208 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cong et al. title: Exogenous Hemin enhances the antioxidant defense system of rice by regulating the AsA-GSH cycle under NaCl stress link: https://peerj.com/articles/17219 last-modified: 2024-04-19 description: Abiotic stress caused by soil salinization remains a major global challenge that threatens and severely impacts crop growth, causing yield reduction worldwide. In this study, we aim to investigate the damage of salt stress on the leaf physiology of two varieties of rice (Huanghuazhan, HHZ, and Xiangliangyou900, XLY900) and the regulatory mechanism of Hemin to maintain seedling growth under the imposed stress. Rice leaves were sprayed with 5.0 μmol·L−1 Hemin or 25.0 μmol·L−1 ZnPP (Zinc protoporphyrin IX) at the three leaf and one heart stage, followed by an imposed salt stress treatment regime (50.0 mmol·L−1 sodium chloride (NaCl)). The findings revealed that NaCl stress increased antioxidant enzymes activities and decreased the content of nonenzymatic antioxidants such as ascorbate (AsA) and glutathione (GSH). Furthermore, the content of osmoregulatory substances like soluble proteins and proline was raised. Moreover, salt stress increased reactive oxygen species (ROS) content in the leaves of the two varieties. However, spraying with Hemin increased the activities of antioxidants such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) and accelerated AsA-GSH cycling to remove excess ROS. In summary, Hemin reduced the effect of salt stress on the physiological characteristics of rice leaves due to improved antioxidant defense mechanisms that impeded lipid peroxidation. Thus, Hemin was demonstrated to lessen the damage caused by salt stress. creator: Fengyan Meng creator: Naijie Feng creator: Dianfeng Zheng creator: Meiling Liu creator: Hang Zhou creator: Rongjun Zhang creator: XiXin Huang creator: Anqi Huang uri: https://doi.org/10.7717/peerj.17219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Meng et al. title: Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma link: https://peerj.com/articles/17222 last-modified: 2024-04-19 description: Targeting tumor angiogenesis is an important approach in advanced tumor therapy. Here we investigated the effect of the suppressor of variegation 3–9 homolog 1 (SUV39H1) on tumor angiogenesis in oral squamous cell carcinoma (OSCC). The GEPIA database was used to analyze the expression of SUV39H1 in various cancer tissues. The expression of SUV39H1 in OSCC was detected by immunohistochemistry, and the correlation between SUV39H1 and Notch1 and microvascular density (MVD) was analyzed. The effect of SUV39H1 inhibition on OSCC was investigated in vivo by chaetocin treatment. The migration and tube formation of vascular endothelial cells by conditioned culture-medium of different treatments of oral squamous cell cells were measured. The transcriptional level of SUV39H1 is elevated in various cancer tissues. The transcription level of SUV39H1 in head and neck squamous cell carcinoma was significantly higher than that in control. Immunohistochemistry result showed increased SUV39H1 expression in OSCC, which was significantly correlated with T staging. The expression of SUV39H1 was significantly correlated with Notch1 and CD31. In vivo experiment chaetocin treatment significantly inhibit the growth of tumor, and reduce SUV39H1, Notch1, CD31 expression. The decreased expression of SUV39H1 in OSCC cells lead to the decreased expression of Notch1 and VEGF proteins, as well as the decreased migration and tube formation ability of vascular endothelial cells. Inhibition of Notch1 further enhance this effect. Our results suggest inhibition of SUV39H1 may affect angiogenesis by regulating Notch1 expression. This study provides a foundation for SUV39H1 as a potential therapeutic target for OSCC. creator: Yan Chen creator: Xiuhong Weng creator: Chuanjie Zhang creator: Simin Wang creator: Xuechen Wu creator: Bo Cheng uri: https://doi.org/10.7717/peerj.17222 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Unveiling the aesthetic secrets: exploring connections between genetic makeup, chemical, and environmental factors for enhancing/improving the color and fragrance/aroma of Chimonanthus praecox link: https://peerj.com/articles/17238 last-modified: 2024-04-19 description: Floral color and scent profiles vary across species, geographical locations, and developmental stages. The exclusive floral color and fragrance of Chimonanthus praecox is contributed by a range of endogenous chemicals that distinguish it from other flowers and present amazing ornamental value. This comprehensive review explores the intricate interplay of environmental factors, chemicals and genes shaping the flower color and fragrance of Chimonanthus praecox. Genetic and physiological factors control morpho-anatomical attributes as well as pigment synthesis, while environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Specific genes control pigment synthesis, and environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Physiological processes including plant hormone contribute to flower color and fragrance. Hormones, notably ethylene, exert a profound influence on varioustraits. Pigment investigations have spotlighted specific flavonoids, including kaempferol 3-O-rutinoside, quercetin, and rutin. Red tepals exhibit unique composition with cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside being distinctive components. Elucidating the molecular basis of tepal color variation, particularly in red and yellow varieties, involves the identification of crucial regulatory genes. In conclusion, this review unravels the mysteries of Chimonanthus praecox, providing a holistic understanding of its flower color and fragrance for landscape applications. This comprehensive review uniquely explores the genetic intricacies, chemical and environmental influences that govern the mesmerizing flower color and fragrance of Chimonanthus praecox, providing valuable insights for its landscape applications. This review article is designed for a diverse audience, including plant geneticists, horticulturists, environmental scientists, urban planners, and students, offering understandings into the genetic intricacies, ecological significance, and practical applications of Chimonanthus praecox across various disciplines. Its appeal extends to professionals and enthusiasts interested in plant biology, conservation, and industries dependent on unique floral characteristics. creator: Haoyu Zhao creator: Hafiza Ayesha Masood creator: Sher Muhammad uri: https://doi.org/10.7717/peerj.17238 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al. title: Meta-analysis of the correlation between pulmonary hypertension and echocardiographic parameters in patients with chronic kidney disease link: https://peerj.com/articles/17245 last-modified: 2024-04-19 description: ObjectiveTo investigate the correlation between pulmonary hypertension (PH) and echocardiographic parameters in patients with chronic kidney disease (CKD).MethodsPubMed, Embase, Web of Science, Cochrane, VIP, CNKI, and Wanfang databases were systematically searched for articles published from inception to 19 May 2023. Study quality was estimated using the Quality Assessment of Case-Control Studies tool. Forest plots were drawn using R language software. The “metacor” function in the “meta” package was utilized for meta-analysis of the r-values and their standard errors. Heterogeneity and sensitivity analyses were carried out, with the main outcomes as r-value, p-value, and I2 value.ResultsEleven studies were included, with 1,809 CKD patients. The correlations between 12 echocardiographic parameters and PH were analyzed. Except for FS and LVEF which were negatively correlated with CKD-PH, the other 10 parameters were positively correlated with CKD-PH. Among them, LA was highly correlated with CKD-PH (0.70 < r < 0.89); LVDD, RA, RV, LVMI, and LVDS were moderately correlated with CKD-PH (0.40 < r < 0.69); while PA, IVS, LVPW, SV, FS, and LVEF were lowly correlated with CKD-PH (0.20 < r < 0.39). The synthesized estimates were stable against heterogeneity.ConclusionCKD-PH patients may have large cardiac chambers, thickened septal tissue on both sides of the chambers, reduced pulmonary artery flow rates, and decreased left ventricular function. creator: Jiahui Jin creator: Wen Hao creator: Deqiong Xie uri: https://doi.org/10.7717/peerj.17245 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jin et al. title: The effect of obesity on the outcome of thoracic endovascular aortic repair: a systematic review and meta-analysis link: https://peerj.com/articles/17246 last-modified: 2024-04-19 description: BackgroundObesity is a well-known predictor for poor postoperative outcomes of vascular surgery. However, the association between obesity and outcomes of thoracic endovascular aortic repair (TEVAR) is still unclear. This systematic review and meta-analysis was performed to assess the roles of obesity in the outcomes of TEVAR.MethodsWe systematically searched the Web of Science and PubMed databases to obtain articles regarding obesity and TEVAR that were published before July 2023. The odds ratio (OR) or hazard ratio (HR) was used to assess the effect of obesity on TEVAR outcomes. Body mass index (BMI) was also compared between patients experiencing adverse events after TEVAR and those not experiencing adverse events. The Newcastle–Ottawa Scale was used to evaluate the quality of the enrolled studies.ResultsA total of 7,849 patients from 10 studies were included. All enrolled studies were high-quality. Overall, the risk of overall mortality (OR = 1.49, 95% CI [1.02–2.17], p = 0.04) was increased in obese patients receiving TEVAR. However, the associations between obesity and overall complications (OR = 2.41, 95% CI [0.84–6.93], p = 0.10) and specific complications were all insignificant, including stroke (OR = 1.39, 95% CI [0.56–3.45], p = 0.48), spinal ischemia (OR = 0.97, 95% CI [0.64–1.47], p = 0.89), neurological complications (OR = 0.13, 95% CI [0.01–2.37], p = 0.17), endoleaks (OR = 1.02, 95% CI [0.46–2.29], p = 0.96), wound complications (OR = 0.91, 95% CI [0.28–2.96], p = 0.88), and renal failure (OR = 2.98, 95% CI [0.92–9.69], p = 0.07). In addition, the patients who suffered from postoperative overall complications (p < 0.001) and acute kidney injury (p = 0.006) were found to have a higher BMI. In conclusion, obesity is closely associated with higher risk of mortality after TEVAR. However, TEVAR may still be suitable for obese patients. Physicians should pay more attention to the perioperative management of obese patients. creator: Jiajun Li creator: Yucong Zhang creator: Haijun Huang creator: Yongzhi Zhou creator: Jing Wang creator: Min Hu uri: https://doi.org/10.7717/peerj.17246 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Association of time-averaged serum uric acid level with clinicopathological information and long-term outcomes in patients with IgA nephropathy link: https://peerj.com/articles/17266 last-modified: 2024-04-19 description: ObjectiveWhether serum uric acid (SUA) at baseline could been identiûed as a risk factor for progression in IgA nephropathy (IgAN) patients remains unclear, therefore, long- term SUA control levels must be monitored. We aimed to investigate the relevant factors affecting time-averaged SUA (TA-SUA) and to assess the prognostic value of TA-SUA in IgAN.MethodsThis retrospective study included 152 patients with IgAN. The relationships between TA-SUA and clinicopathological features and renal outcomes (defined as the doubling of the baseline serum creatinine level or end-stage renal disease) were analyzed in groups divided by quartiles of TA-SUA levels, the presence of hyperuricemia, and sex.ResultsPatients with high TA-SUA levels had higher levels of baseline SUA, blood urea nitrogen (BUN), triglycerides, serum C3 and serum C4 and were more likely to be male and have hypertension, proteinuria, poor renal function, and pathological injuries including high grades of tubular atrophy/interstitial fibrosis (T1–T2). These patients had a poorer prognosis compared with patients with low TA-SUA levels. The TA-SUA level was positively correlated with baseline age and BUN, triglycerides, serum C3, and serum C4 levels, and negatively correlated with baseline eGFR. Survival curve analysis indicated that persistent hyperuricemia was associated with significantly poorer renal outcomes than normo-uricemia in both men and women. The TA-SUA level also was an independent predictor of renal outcome in patients with IgAN, with optimal cutoû values of 451.38 µmol/L (area under the curve (AUC) = 0.934) for men and 492.83 µmol/L (AUC = 0.768) for women.ConclusionsThe TA-SUA level is associated with triglyceride level, complement component levels, renal function, and pathological severity of IgAN, and it may be a prognostic indicator in male and female patients with IgAN. creator: Mengjie Weng creator: Binbin Fu creator: Yongjie Zhuo creator: Jiaqun Lin creator: Zhenhuan Zou creator: Yi Chen creator: Jiong Cui creator: Guifen Li creator: Caiming Chen creator: Yanfang Xu creator: Dewen Jiang creator: Jianxin Wan uri: https://doi.org/10.7717/peerj.17266 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Weng et al. title: Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults link: https://peerj.com/articles/17270 last-modified: 2024-04-19 description: BackgroundThe appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data.MethodsThis study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23–43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson’s correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions.ResultsOur study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good’s coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson’s correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius). creator: Naruemon Tunsakul creator: Lampet Wongsaroj creator: Kantima Janchot creator: Krit Pongpirul creator: Naraporn Somboonna uri: https://doi.org/10.7717/peerj.17270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tunsakul et al. title: Metabolome and transcriptome integration reveals insights into petals coloration mechanism of three species in Sect. Chrysantha chang link: https://peerj.com/articles/17275 last-modified: 2024-04-19 description: BackgroundSect. Chrysantha Chang, belonging to the Camellia genus, is one of the rare and precious ornamental plants distinguished by a distinctive array of yellow-toned petals. However, the variation mechanisms of petal color in Sect. Chrysantha Chang remains largely unclear.MethodsWe conducted an integrated analysis of metabolome and transcriptome to reveal petal coloration mechanism in three species, which have different yellow tones petals, including C. chuongtsoensis (CZ, golden yellow), C. achrysantha (ZD, light yellow), and C. parvipetala (XB, milk white).ResultsA total of 356 flavonoid metabolites were detected, and 295 differential metabolites were screened. The contents of 74 differential metabolites showed an upward trend and 19 metabolites showed a downward trend, among which 11 metabolites were annotated to the KEGG pathway database. We speculated that 10 metabolites were closely related to the deepening of the yellowness. Transcriptome analysis indicated that there were 2,948, 14,018 and 13,366 differentially expressed genes (DEGs) between CZ vs. ZD, CZ vs. XB and ZD vs. XB, respectively. Six key structural genes (CcCHI, CcFLS, CcDFR1, CcDFR2, CcDFR3, and CcCYP75B1) and five candidate transcription factors (MYB22, MYB28, MYB17, EREBP9, and EREBP13) were involved in the regulation of flavonoid metabolites. The findings indicate that flavonoid compounds influence the color intensity of yellow-toned petals in Sect. Chrysantha Chang. Our results provide a new perspective on the molecular mechanisms underlying flower color variation and present potential candidate genes for Camellia breeding. creator: Yadan Yan creator: Ye Wang creator: Yafeng Wen creator: Yu Huang creator: Minhuan Zhang creator: Jiadi Huang creator: Xinyu Li creator: Chuncheng Wang creator: Dangqing Xu uri: https://doi.org/10.7717/peerj.17275 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yan et al. title: Relationships among barodontalgia prevalence, altitude, stress, dental care frequency, and barodontalgia awareness: a survey of Turkish pilots link: https://peerj.com/articles/17290 last-modified: 2024-04-19 description: BackgroundGas expansion in body cavities due to pressure changes at high altitudes can cause barodontalgia. This condition may compromise flight safety.AimTo investigate relationships among barodontalgia awareness, dental visit frequency, and barodontalgia prevalence in civilian and military pilots operating at high altitudes.Materials and MethodsCivilian pilots from Turkish Airlines and military pilots from the Turkish Air Force, flying between November 2022 and January 2023, participated in this study. A 20-question survey was administered to 750 pilots, covering topics such as barodontalgia awareness, dental visit frequency, breaks after dental treatments, in-flight pain, and pain type and severity. The voluntary surveys were distributed by email.ResultsOf the 750 pilots, 526 completed the survey; 61% were aware of barodontalgia, and 81% of pilots who had experienced it reported pain at altitudes <2000 feet. The study revealed higher barodontalgia awareness among pilots who had experienced it, with the highest prevalence among jet pilots. Pilots with barodontalgia also showed a higher frequency of dental visits (p < 0.001). Additionally, this group reported more frequent interruption of flight due to dental treatment (IFDT), more problems experienced in flights after treatment (PFAT), and higher instances of bruxism or teeth clenching during flight, suggesting stress and anxiety (p < 0.05).ConclusionsBarodontalgia, a type of pain linked to stress, significantly impacts pilot performance, and can threaten flight safety, even at lower altitudes. Thus, there is a need to educate pilots about stress management, barodontalgia awareness, and the importance of regular dental check-ups. creator: Celalettin Topbaş creator: Dursun Ali Şirin creator: Hilal Gezeravcı creator: Fatih Özçelik creator: Yelda Erdem Hepşenoğlu creator: Şeyda Erşahan uri: https://doi.org/10.7717/peerj.17290 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Topbaş et al. title: S100A8/9 modulates perturbation and glycolysis of macrophages in allergic asthma mice link: https://peerj.com/articles/17106 last-modified: 2024-04-18 description: BackgroundAllergic asthma is the most prevalent asthma phenotype and is associated with the disorders of immune cells and glycolysis. Macrophages are the most common type of immune cells in the lungs. Calprotectin (S100A8 and S100A9) are two pro-inflammatory molecules that target the Toll-like receptor 4 (TLR4) and are substantially increased in the serum of patients with severe asthma. This study aimed to determine the effects of S100A8/A9 on macrophage polarization and glycolysis associated with allergic asthma.MethodsTo better understand the roles of S100A8 and S100A9 in the pathogenesis of allergic asthma, we used ovalbumin (OVA)-induced MH-S cells, and OVA-sensitized and challenged mouse models (wild-type male BALB/c mice). Enzyme-linked immunosorbent assay, quantitative real-time polymerase chain reaction, flow cytometry, hematoxylin-eosin staining, and western blotting were performed. The glycolysis inhibitor 3-bromopyruvate (3-BP) was used to observe changes in glycolysis in mice.ResultsWe found knockdown of S100A8 or S100A9 in OVA-induced MH-S cells inhibited inflammatory cytokines, macrophage polarization biomarker expression, and pyroptosis cell proportion, but increased anti-inflammatory cytokine interleukin (IL)-10 mRNA; also, glycolysis was inhibited, as evidenced by decreased lactate and key enzyme expression; especially, knockdown of S100A8 or S100A9 inhibited the activity of TLR4/myeloid differentiation primary response gene 88 (MyD88)/Nuclear factor kappa-B (NF-κB) signaling pathway. Intervention with lipopolysaccharides (LPS) abolished the beneficial effects of S100A8 and S100A9 knockdown. The observation of OVA-sensitized and challenged mice showed that S100A8 or S100A9 knockdown promoted respiratory function, improved lung injury, and inhibited inflammation; knockdown of S100A8 or S100A9 also suppressed macrophage polarization, glycolysis levels, and activation of the TLR4/MyD88/NF-κB signaling pathway in the lung. Conversely, S100A9 overexpression exacerbated lung injury and inflammation, promoting macrophage polarization and glycolysis, which were antagonized by the glycolysis inhibitor 3-BP.ConclusionS100A8 and S100A9 play critical roles in allergic asthma pathogenesis by promoting macrophage perturbation and glycolysis through the TLR4/MyD88/NF-κB signaling pathway. Inhibition of S100A8 and S100A9 may be a potential therapeutic strategy for allergic asthma. creator: Xiaoyi Ji creator: Chunhua Nie creator: Yuan Yao creator: Yu Ma creator: Huafei Huang creator: Chuangli Hao uri: https://doi.org/10.7717/peerj.17106 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ji et al. title: Carbon content and other soil properties of near-surface peats before and after peatland restoration link: https://peerj.com/articles/17113 last-modified: 2024-04-18 description: Peatland restoration usually aims at restarting the peatlands’ function to store carbon within peat. The soil properties of the near-surface peat can give a first understanding of this process. Therefore, we sampled pH value, total organic carbon content (TOC), total nitrogen content (TN), C/N ratio as well as dry bulk density (BD), and describe the structure of near-surface peats in six restored fens in North-East Germany before (2002–2004) and after (2019–2021) restoration. Before restoration, the study sites showed peat degradation to various extents in their near-surface peats. pH values remained relatively stable over time. Comparing the degraded peat horizons, TOC increased significantly in four study sites, ranging from 35.7% to 47.8% in 2002–2004 and from 42.5% to 54.0% in 2019–2021. TN varied from 1.5% to 3.5% in 2002–2004 and from 1.8% to 3.2% in 2019–2021, but changes were only significant in one site, showing a slight decrease. In three sites, the increase in C/N ratio was significant, indicating lower nutrient availability. BD ranged from 0.08 to 0.48 g/cm3 in 2002–2004 and from 0.10 to 0.16 g/cm3 in 2019–2021, decreasing significantly in four sites. The structure of the degraded peat horizons changed after restoration to a more homogenous, sludge mass with larger re-aggregates. In three sites, new peat moss peat layers above the degraded soil horizon were present in 2019–2021, with a mean thickness of 6.8 to 36.1 cm. The structure was comparable to typical, slightly decomposed peat moss peat. Our findings suggest that within about 17 years after fen restoration, and thereby a water table rise close to surface, TOC of the near-surface peats increased to values that are typical for undisturbed peatlands. This indicates that restoration can lead to the re-establishment of peatlands as potential carbon sinks, with TOC within the near-surface peat as one key factor in this process. Further, we assume that the decrease in nutrient availability, decrease of BD, and new, undisturbed peat layers can favor the establishment of mire-specific biodiversity and support ecosystem services similar to near-natural mires. creator: Jenny Hammerich creator: Corinna Schulz creator: Robert Probst creator: Thomas Lüdicke creator: Vera Luthardt uri: https://doi.org/10.7717/peerj.17113 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hammerich et al. title: COVID-19 and malaria co-infection: a systematic review of clinical outcomes in endemic areas link: https://peerj.com/articles/17160 last-modified: 2024-04-18 description: BackgroundCOVID-19 and malaria cause significant morbidity and mortality globally. Co-infection of these diseases can worsen their impact on public health. This review aims to synthesize literature on the clinical outcomes of COVID-19 and malaria co-infection to develop effective prevention and treatment strategies.MethodsA comprehensive literature search was conducted using MeSH terms and keywords from the start of the COVID-19 pandemic to January 2023. The review included original articles on COVID-19 and malaria co-infection, evaluating their methodological quality and certainty of evidence. It was registered in PROSPERO (CRD42023393562).ResultsOut of 1,596 screened articles, 19 met the inclusion criteria. These studies involved 2,810 patients, 618 of whom had COVID-19 and malaria co-infection. Plasmodium falciparum and vivax were identified as causative organisms in six studies. Hospital admission ranged from three to 18 days. Nine studies associated co-infection with severe disease, ICU admission, assisted ventilation, and related complications. One study reported 6% ICU admission, and mortality rates of 3%, 9.4%, and 40.4% were observed in four studies. Estimated crude mortality rates were 10.71 and 5.87 per 1,000 person-days for patients with and without concurrent malaria, respectively. Common co-morbidities included Diabetes mellitus, hypertension, cardiovascular diseases, and respiratory disorders.ConclusionMost patients with COVID-19 and malaria co-infection experienced short-term hospitalization and mild to moderate disease severity. However, at presentation, co-morbidities and severe malaria were significantly associated with higher mortality or worse clinical outcomes. These findings emphasize the importance of early detection, prompt treatment, and close monitoring of patients with COVID-19 and malaria co-infection. creator: Amal H. Mohamed creator: Ebtihal Eltyeb creator: Badria Said creator: Raga Eltayeb creator: Abdullah Algaissi creator: Didier Hober creator: Abdulaziz H. Alhazmi uri: https://doi.org/10.7717/peerj.17160 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mohamed et al. title: Hand grab or noose pole? Evaluating the least stressful practice for capture of endangered Turks and Caicos Rock Iguanas Cyclura carinata link: https://peerj.com/articles/17171 last-modified: 2024-04-18 description: As the analysis of blood metabolites has become more readily accessible thanks to the use of point-of-care analyzers, it is now possible to evaluate stress level of wild animals directly in the field. Lactate is receiving much attention as a good stress level proxy in individuals subjected to capture, manual restraint, and data sampling in the wild, and appropriate protocols to maintain lactate values low should be preferred. In this study we compare how two different capture methodologies, hand grab vs. noose pole, affect the variation of blood lactate values in Cyclura carinata iguanas when captured for sampling. We used blood lactate concentration, measured immediately upon- and 15 min after-capture, as a proxy for stress level. While the primary goal of this work is to determine the least stressful capture methodology to be favored when sampling this and other wild iguanas, we also evaluated additional baseline physiological parameters relevant to the health and disease monitoring for this species. Our results show that while initial lactate values level-out in sampled individuals after 15 min in captivity, regardless of the capture methodology, rock iguanas captured by noose pole showed significantly higher lactate concentration and increased heartbeat rate immediately after capture. While the overall health evaluation determined that all analyzed individuals were in good health, based on our results we recommend that, when possible, hand capture should be preferred over noose pole when sampling wild individuals. creator: Giuliano Colosimo creator: Gwyneth Montemuro creator: Gregory A. Lewbart creator: Gabriele Gentile creator: Glenn P. Gerber uri: https://doi.org/10.7717/peerj.17171 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Colosimo et al. title: Preliminary study on the protective effect of remazolam against sepsis-induced acute respiratory distress syndrome (ARDS) link: https://peerj.com/articles/17205 last-modified: 2024-04-18 description: BackgroundSepsis can disrupt immune regulation and lead to acute respiratory distress syndrome (ARDS) frequently. Remazolam, a fast-acting hypnotic drug with superior qualities compared to other drugs, was investigated for its potential protective effects against sepsis-induced ARDS.MethodsForty Sprague-Dawley rats were randomly divided into four groups, including the sepsis + saline group, sham operation + saline group, sham operation + remazolam group and the sepsis + remazolam group. Lung tissues of rats were extracted for HE staining to assess lung damage, and the wet weight to dry weight (W/D) ratio was calculated. The levels of proinflammatory factors, anti-inflammatory factors, CD4+ and CD8+ T cells in peripheral blood, MDA, MPO, and ATP in the lung tissue were measured by using ELISA. Western blotting was performed to determine the protein expression of HMGB1 in lung tissues.ResultsIn comparison to the sham operation + saline and sham operation + remazolam groups, the sepsis + saline group exhibited significantly higher values for W/D ratio, lung damage score, IL-1β, IL-6, TNF-α, PCT, CRP, MDP and MPO, while exhibiting lower levels of CD4+ and CD8+ T lymphocytes, PaO2, PCO2, and ATP. The rats in the sepsis + saline group displayed ruptured alveolar walls and evident interstitial lung edema. However, the rats in the sepsis + remazolam group showed improved alveolar structure. Furthermore, the HMGB1 protein expression in the sepsis + remazolam group was lower than the sepsis + saline group.ConclusionRemazolam can alleviate the inflammatory response in infected rats, thereby alleviating lung injury and improving immune function, which may be attributed to the reduction in HMGB1 protein expression. creator: Xiaoxin Gao creator: Rujun Zhang creator: Zhenzhou Wang creator: Qingan Chen creator: Zhenlin Lei creator: Yanan Yang creator: Jia Tian uri: https://doi.org/10.7717/peerj.17205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: Novel monoclonal antibodies against house dust mite allergen Der p 21 and their application to analyze allergen extracts link: https://peerj.com/articles/17233 last-modified: 2024-04-18 description: BackgroundAllergen extracts and recombinant allergens are used in allergy diagnostics and immunotherapy. Since allergen extracts from different manufacturers lack proper standardization regarding their composition, monoclonal antibodies (MAbs) against specific allergen components can be used for their identification and quantification in allergen extracts. This study aimed to generate MAbs against allergen Der p 21 of Dermatophagoides pteronyssinus for the analysis of allergen extracts.MethodsRecombinant Der p 21 was expressed in E. coli and purified using affinity chromatography. MAbs against Der p 21 were generated using hybridoma technology. House dust mite (HDM) allergen extracts were analyzed using the newly developed sandwich enzyme-linked immunosorbent assay, Western blotting and microarray immunoassay.ResultsMAbs raised against recombinant Der p 21 were characterized in detail and proven to be reactive with natural Der p 21. Highly specific sandwich enzyme-linked immunosorbent assay for the quantification of Der p 21 was developed and optimized. The allergen was detected and its concentration was determined in only three of six analyzed HDM allergen extracts from different manufacturers.ConclusionHDM analysis by MAb-based immunoassays shows their differences in allergen composition. The results demonstrate the importance of allergen-specific MAbs as a tool for the characterization of allergen extracts and the need for their appropriate standardization before their use for allergy diagnostics or immunotherapy. creator: Vytautas Rudokas creator: Laimis Silimavicius creator: Indre Kucinskaite-Kodze creator: Aiste Sliziene creator: Milda Pleckaityte creator: Aurelija Zvirbliene uri: https://doi.org/10.7717/peerj.17233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rudokas et al. title: Transcriptome analysis during 4-vinylcyclohexene diepoxide exposure-induced premature ovarian insufficiency in mice link: https://peerj.com/articles/17251 last-modified: 2024-04-18 description: The occupational chemical 4-Vinylcyclohexene diepoxide (VCD) is a reproductively toxic environmental pollutant that causes follicular failure, leading to premature ovarian insufficiency (POI), which significantly impacts a woman’s physical health and fertility. Investigating VCD’s pathogenic mechanisms can offer insights for the prevention of ovarian impairment and the treatment of POI. This study established a mouse model of POI through intraperitoneal injection of VCD into female C57BL/6 mice for 15 days. The results were then compared with those of the control group, including a comparison of phenotypic characteristics and transcriptome differences, at two time points: day 15 and day 30. Through a comprehensive analysis of differentially expressed genes (DEGs), key genes were identified and validated some using RT-PCR. The results revealed significant impacts on sex hormone levels, follicle number, and the estrous cycle in VCD-induced POI mice on both day 15 and day 30. The DEGs and enrichment results obtained on day 15 were not as significant as those obtained on day 30. The results of this study provide a preliminary indication that steroid hormone synthesis, DNA damage repair, and impaired oocyte mitosis are pivotal in VCD-mediated ovarian dysfunction. This dysfunction may have been caused by VCD damage to the primordial follicular pool, impairing follicular development and aggravating ovarian damage over time, making it gradually difficult for the ovaries to perform their normal functions. creator: Yi Li creator: Ruifen He creator: Xue Qin creator: Qinying Zhu creator: Liangjian Ma creator: Xiaolei Liang uri: https://doi.org/10.7717/peerj.17251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Cytokine profiles of mild-to-moderate SARS-CoV-2 infected and recovered pre-vaccinated individuals residing in Indonesia link: https://peerj.com/articles/17257 last-modified: 2024-04-18 description: BackgroundAccumulating evidence suggests the involvement of cytokine-mediated inflammation, in clinical severity and death related to SARS-CoV-2 infection, especially among pre-vaccinated individuals. An increased risk of death was also described among SARS-CoV-2 recovered individuals, which might be correlated with prolonged inflammatory responses. Despite being among the countries with the highest cumulative deaths due to COVID-19, evidence regarding cytokine profiles among SARS-CoV-2 infected and recovered pre-vaccinated individuals in Indonesia is scarce. Thus, this study aimed to describe the cytokines profiles of pre-vaccinated individuals residing in Indonesia, with mild-to-moderate SARS-CoV-2 infection and those who recovered.MethodsSixty-one sera from 24 hospitalized patients with mild-to-moderate SARS-CoV-2 infection, 24 individuals recovered from asymptomatic-to-moderate SARS-CoV-2 infection, and 13 healthy controls unexposed to SARS-CoV-2 were used in this study. Quantification of serum cytokine levels, including IL-6, IL-8, IP-10, TNF-α, CCL-2, CCL-3, CCL-4, and CXCL-13, was performed using a Luminex multi-analyte-profiling (xMAP)-based assay.ResultsThe levels of IL-8 along with CCL-2 and CCL-4, were significantly higher (p ≤ 0.01) in hospitalized patients with mild-to-moderate SARS-CoV-2 infection and recovered individuals compared to healthy controls. However, no significant difference was observed in these cytokine levels between infected and recovered individuals. On the other hand, there were no significant differences in several other cytokine levels, including IL-6, IL-10, TNF-α, CCL-3, and CXCL-13, among all groups.ConclusionIL-8, CCL-2, and CCL-4 were significantly elevated in pre-vaccinated Indonesian individuals with mild-to-moderate SARS-CoV-2 infection and those who recovered. The cytokine profiles described in this study might indicate inflammatory responses not only among SARS-CoV-2 infected, but also recovered individuals. creator: Ni Luh Ayu Megasari creator: Siti Qamariyah Khairunisa creator: Radita Yuniar Arizandy creator: I. Komang Evan Wijaksana creator: Citrawati Dyah Kencono Wungu uri: https://doi.org/10.7717/peerj.17257 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Megasari et al. title: Citizen science initiatives document biodiversity baselines at an urban lake link: https://peerj.com/articles/17209 last-modified: 2024-04-17 description: Changes to biodiversity from urbanization are occurring worldwide, and baseline data is vital to document the magnitude and direction of these alterations. We set out to document the biodiversity of an urban lake in Eastern Iowa that was devoid of baseline data prior to a renovation project that will convert the site into a major area for human recreation. Throughout the course of one year, we studied the biodiversity at Cedar Lake utilizing the citizen-science application iNaturalist coupled with semi-structured BioBlitz events, which we compared to previous opportunistic observations at the site. From a semi-structured approach to document biodiversity with citizen science, our analyses revealed more diverse community metrics over a shorter period compared to more than a decade of prior observations. creator: Alyssah Ahern creator: Daniel F. Hughes uri: https://doi.org/10.7717/peerj.17209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ahern and Hughes title: Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis link: https://peerj.com/articles/17182 last-modified: 2024-04-16 description: BackgroundCorallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives.MethodsWe used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum.ResultsOur histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21–31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion.DiscussionTranscriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum, providing insight into its gene expression patterns. This study highlights the importance of using both de novo and reference-based assembly methods. Functional enrichment analysis showed that females exhibited enrichment in cell proliferation and reproduction pathways, while males exhibited enrichment in cell adhesion pathways. To the best of our knowledge, this is the first report on the gene expressions of each sex during the spawning season. Our findings offer valuable insights into the physiological ecology of incompletely mature red Japanese precious corals and suggest a method for identifying sex using various genes expressed in female and male individuals. In the future, techniques such as transplantation, artificial fertilization, and larval rearing may involve sex determination methods based on differences in gene expression to help conserve precious coral resources and ecosystems. creator: Ma. Marivic Capitle Pepino creator: Sam Edward Manalili creator: Satoko Sekida creator: Takuma Mezaki creator: Tomoyo Okumura creator: Satoshi Kubota uri: https://doi.org/10.7717/peerj.17182 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pepino et al. title: Bidirectional correlation between gastroesophageal reflux disease and sleep problems: a systematic review and meta-analysis link: https://peerj.com/articles/17202 last-modified: 2024-04-16 description: ObjectivesGastroesophageal reflux disease (GERD) and sleep problems are highly prevalent among the general population. Both them are associated with a variety of psychiatric disorders such as depression and anxiety, which is highlighting an underexplored connection between them. This meta-analysis aims to explore the association between sleep problems and GERD.MethodsWe conducted a comprehensive search on PubMed, Cochrane Library, Embase, and Web of Science, using Medical Subject Headings (MeSH) and keywords, covering articles from the inception of the databases until August 2023. Stata statistical software, version 14.0, was utilized for all statistical analyses. A fixed-effects model was applied when p > 0.1 and I2 ≤ 50%, while a random-effects model was employed for high heterogeneity (p < 0.1 and I2 > 50%). Funnel plots and Egger’s test were used to assess publication bias.ResultsInvolving 22 studies, our meta-analysis revealed that insomnia, sleep disturbance, or short sleep duration significantly increased the risk of GERD (OR = 2.02, 95% CI [1.64–2.49], p < 0.001; I2 = 66.4%; OR = 1.98, 95% CI [1.58–2.50], p < 0.001, I2 = 50.1%; OR = 2.66, 95% CI [2.02–3.15], p < 0.001; I2 = 62.5%, respectively). GERD was associated with an elevated risk of poor sleep quality (OR = 1.47, 95% CI [1.47–1.79], p < 0.001, I2 = 72.4%), sleep disturbance (OR = 1.47, 95% CI [1.24–1.74], p < 0.001, I2 = 71.6%), or short sleep duration (OR = 1.17, 95% CI [1.12–1.21], p < 0.001, I2 = 0).ConclusionThis meta-analysis establishes a bidirectional relationship between four distinct types of sleep problems and GERD. The findings offer insights for the development of innovative approaches in the treatment of both GERD and sleep problems. creator: Xiaolong Tan creator: Shasha Wang creator: Fengjie Wu creator: Jun Zhu uri: https://doi.org/10.7717/peerj.17202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tan et al. title: Defenses of whirligig beetles against native and invasive frogs link: https://peerj.com/articles/17214 last-modified: 2024-04-16 description: Many native insects have evolved defenses against native predators. However, their defenses may not protect them from non-native predators due to a limited shared history. The American bullfrog, Aquarana catesbeiana (Anura: Ranidae), which has been intentionally introduced to many countries, is believed to impact native aquatic animals through direct predation. Adults of whirligig beetles (Coleoptera: Gyrinidae), known for swimming and foraging on the water surface of ponds and streams, reportedly possess chemical defenses against aquatic predators, such as fish. Although whirligig beetles potentially encounter both bullfrogs and other frogs in ponds and lakes, the effectiveness of their defenses against frogs has been rarely studied. To assess whether whirligig beetles can defend against native and non-native frogs, we observed the behavioral responses of the native pond frog, Pelophylax nigromaculatus (Anura: Ranidae), and the invasive non-native bullfrog, A. catesbeiana, to native whirligig beetles, Gyrinus japonicus and Dineutus orientalis, in Japan. Adults of whirligig beetles were provided to frogs under laboratory conditions. Forty percent of G. japonicus and D.orientalis were rejected by P. nigromaculatus, while all whirligig beetles were easily consumed by A. catesbeiana. Chemical and other secondary defenses of G. japonicus and D. orientalis were effective for some individuals of P. nigromaculatus but not for any individuals of A. catesbeiana. These results suggest that native whirligig beetles suffer predation by invasive non-native bullfrogs in local ponds and lakes in Japan. creator: Shinji Sugiura creator: Masakazu Hayashi uri: https://doi.org/10.7717/peerj.17214 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sugiura and Hayashi title: Effects of soil pH on the growth, soil nutrient composition, and rhizosphere microbiome of Ageratina adenophora link: https://peerj.com/articles/17231 last-modified: 2024-04-16 description: Ageratina adenophora is an invasive weed species found in many countries. Methods to control the spread of this weed have been largely unsuccessful. Soil pH is the most important soil factor affecting the availability of nutrients for plant and impacting its growth. Understanding the mechanisms of the influence of soil pH on the growth of A. adenophora may help to develop effective control measures. In this study, we artificially changed the soil pH in pot experiments for A. adenophora. We studied the effects of acidic (pH 5.5), weakly acidic (pH 6.5), neutral (pH 7.2), and alkaline (pH 9.0) soils on the growth, availability of soil nutrients, activity of antioxidant enzymes, levels of redox markers in the leaves, and the structure and diversity of the rhizosphere microbiome. Soil with a pH 7.2 had a higher (47.8%) below-ground height versus soils of pH 5.5 at day 10; plant had a higher (11.3%) above-ground height in pH 7.2 soils than pH 9.0 soils at day 90; no differences in the fresh and dry weights of its above- and belowground parts, plant heights, and root lengths were observed in plants growing in acid, alkaline, or neutral pH soil were observed at day 180. Correspondingly, the antioxidant enzymes SOD (superoxide dismutase), POD (peroxidase), CAT (catalase) and redox markers GSH (glutathione) and MDA (malondialdehyde) were measured in the leaves. Significant differences existed in the activities of CAT and the levels of GSH between those growing in acidic and alkaline soils and those in neutral pH soil at day 90; however, only lower (36.8%) CAT activities in those grown at pH 5.5 than those grown at pH 7.2 were found at day 180. Similarly, significant differences in available P (16.89 vs 3.04 mg Kg−1) and total K (3.67 vs 0.96 mg Kg−1), total P (0.37 vs 0.25 g Kg−1) and total N (0.45 vs 1.09 g Kg−1) concentrations were found between the rhizosphere soils of A. adenophora grown at pH 9.0 and 7.2 at day 90; no such differences were seen at day 180. High throughput analyses of the 16S rRNA and ITS fragments showed that the rhizosphere microbiome diversity and composition under different soil pH conditions changed over 180 days. The rhizosphere microbiomes differed in diversity, phylum, and generic composition and population interactions under acid and alkaline conditions versus those grown in neutral soils. Soil pH had a greater impact on the diversity and composition of the prokaryotic rhizosphere communities than those of the fungal communities. A. adenophora responded successfully to pH stress by changing the diversity and composition of the rhizosphere microbiome to maintain a balanced nutrient supply to support its normal growth. The unusual pH tolerance of A. adenophora may be one crucial reason for its successful invasion. Our results suggest that attempts use soil pH to control its invasion by changing the soil pH (for example, using lime) will fail. creator: Yun Xia creator: Junna Feng creator: Hongbo Zhang creator: Deyu Xiong creator: Lingdong Kong creator: Robert Seviour creator: Yunhong Kong uri: https://doi.org/10.7717/peerj.17231 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xia et al. title: Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae) link: https://peerj.com/articles/17232 last-modified: 2024-04-16 description: The species richness in the Neotropics has been linked to environmental heterogeneity and a complex geological history. We evaluated which biogeographic processes were associated with the diversification of Monkey tree frogs, an endemic clade from the Neotropics. We tested two competing hypotheses: the diversification of Phyllomedusinae occurred either in a “south-north” or a “north-south” direction in the Neotropics. We also hypothesized that marine introgressions and Andean uplift had a crucial role in promoting their diversification. We used 13 molecular markers in a Bayesian analysis to infer phylogenetic relationships among 57 species of Phyllomedusinae and to estimate their divergence times. We estimated ancestral ranges based on 12 biogeographic units considering the landscape modifications of the Neotropical region. We found that the Phyllomedusinae hypothetical ancestor range was probably widespread throughout South America, from Western Amazon to Southern Atlantic Forest, at 29.5 Mya. The Phyllomedusines’ ancestor must have initially diverged through vicariance, generally followed by jump-dispersals and sympatric speciation. Dispersal among areas occurred mostly from Western Amazonia towards Northern Andes and the South American diagonal of dry landscapes, a divergent pattern from both "south-north" and "north-south" diversification hypotheses. Our results revealed a complex diversification process of Monkey tree frogs, occurring simultaneously with the orogeny of Northern Andes and the South American marine introgressions in the last 30 million years. creator: Diego Almeida-Silva creator: Leonardo Matheus Servino creator: Matheus Pontes-Nogueira creator: Ricardo J. Sawaya uri: https://doi.org/10.7717/peerj.17232 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Almeida-Silva et al. title: Association of rotating night shift work with tooth loss and severe periodontitis among permanent employees in Japan: a cross-sectional study link: https://peerj.com/articles/17253 last-modified: 2024-04-16 description: BackgroundThe modern 24/7 society demands night shift work, which is a possible risk factor for chronic diseases. This study aimed to examine the associations of rotating night shift work duration with tooth loss and severe periodontitis.MethodsThis cross-sectional study used data from a self-administered questionnaire survey conducted among 3,044 permanent employees aged 20–64 years through a Japanese web research company in 2023. The duration of rotating night shift work was assessed using a question from the Nurses’ Health Study. Tooth loss was assessed based on self-reported remaining natural teeth count. Severe periodontitis was assessed using a validated screening questionnaire comprising four questions related to gum disease, loose tooth, bone loss, and bleeding gums. We employed linear regression models for tooth loss and Poisson regression models for severe periodontitis, adjusting for demographic, health and work-related variables and socioeconomic status.ResultsAmong participants included, 10.9% worked in rotating night shifts for 1–5 years, while 11.0% worked in such shifts for ≥6 years. In fully adjusted models, rotating night shift work duration of 1–5 years was associated with tooth loss (beta −0.74, 95% confidence interval (CI) [−1.55 to 0.08]) and severe periodontitis (prevalence ratio 1.80, 95% CI [1.33–2.43]); however, the association with tooth loss was not statistically significant.ConclusionsThis study supports that employees who work short-term rotating night shifts may experience poor oral conditions. Further research is needed to determine whether long-term rotating night shift work is associated with deteriorated oral health. creator: Yukihiro Sato creator: Eiji Yoshioka creator: Yasuaki Saijo uri: https://doi.org/10.7717/peerj.17253 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sato et al. title: Promoting sustainable agriculture by exploiting plant growth-promoting rhizobacteria (PGPR) to improve maize and cowpea crops link: https://peerj.com/articles/16836 last-modified: 2024-04-15 description: Maize and cowpea are among the staple foods most consumed by most of the African population, and are of significant importance in food security, crop diversification, biodiversity preservation, and livelihoods. In order to satisfy the growing demand for agricultural products, fertilizers and pesticides have been extensively used to increase yields and protect plants against pathogens. However, the excessive use of these chemicals has harmful consequences on the environment and also on public health. These include soil acidification, loss of biodiversity, groundwater pollution, reduced soil fertility, contamination of crops by heavy metals, etc. Therefore, essential to find alternatives to promote sustainable agriculture and ensure the food and well-being of the people. Among these alternatives, agricultural techniques that offer sustainable, environmentally friendly solutions that reduce or eliminate the excessive use of agricultural inputs are increasingly attracting the attention of researchers. One such alternative is the use of beneficial soil microorganisms such as plant growth-promoting rhizobacteria (PGPR). PGPR provides a variety of ecological services and can play an essential role as crop yield enhancers and biological control agents. They can promote root development in plants, increasing their capacity to absorb water and nutrients from the soil, increase stress tolerance, reduce disease and promote root development. Previous research has highlighted the benefits of using PGPRs to increase agricultural productivity. A thorough understanding of the mechanisms of action of PGPRs and their exploitation as biofertilizers would present a promising prospect for increasing agricultural production, particularly in maize and cowpea, and for ensuring sustainable and prosperous agriculture, while contributing to food security and reducing the impact of chemical fertilizers and pesticides on the environment. Looking ahead, PGPR research should continue to deepen our understanding of these microorganisms and their impact on crops, with a view to constantly improving sustainable agricultural practices. On the other hand, farmers and agricultural industry players need to be made aware of the benefits of PGPRs and encouraged to adopt them to promote sustainable agricultural practices. creator: Nadège Adoukè Agbodjato creator: Olubukola Oluranti Babalola uri: https://doi.org/10.7717/peerj.16836 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Agbodjato and Babalola title: GPR27 expression correlates with prognosis and tumor progression in gliomas link: https://peerj.com/articles/17024 last-modified: 2024-04-15 description: BackgroundsGlioma is a highly aggressive type of brain tumor, and its prognosis is still poor despite recent progress in treatment strategies. G protein-coupled receptor 27 (GPR27) is a member of the G protein-coupled receptor family and has been reported to be involved in various cellular processes, including tumor progression. Nevertheless, the clinical potential and tumor-related role of GPR27 in glioma remain unknown. Here we aimed to explore the function and role of GPR27 in gliomas.MethodsIn the current study, we evaluated the expression and clinical significance of GPR27 in gliomas using data from The Cancer Genome Atlas (TCGA) datasets. We also conducted cellular experiments to evaluate the functional role of GPR27 in glioma cell growth.ResultsWe found that GPR27 expression level was closely associated with disease status of glioma. Of note, GPR27 was negatively correlated with WHO grade, with grade IV samples showing the lowest GPR27 levels, while grade II samples showed the highest levels. Patients with IDH mutation or 1p/19q co-deletion exhibited higher GPR27 levels. In addition, lower GPR27 levels were correlated with higher death possibilities. In cellular experiments, we confirmed that GPR27 inhibited glioma cell growth.ConclusionsOur results indicate that GPR27 may function as a potential prognostic biomarker and therapeutic target in gliomas. Further studies are needed to illustrate the signaling mechanism and clinical implications of GPR27 in gliomas. creator: Changcheng Cai creator: Libo Hu creator: Ke Wu creator: Yinggang Liu uri: https://doi.org/10.7717/peerj.17024 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cai et al. title: Effectiveness of gamification in nursing degree education link: https://peerj.com/articles/17167 last-modified: 2024-04-15 description: BackgroundPrevious research in nursing has found favorable results from the use of teaching methodologies alternative to lectures. One of the complementary methodologies used for university teaching is gamification, or the inclusion of game elements, creating a dynamic learning environment that allows the acquisition of knowledge and the development of other skills necessary for nursing students. The purpose of this study was to evaluate the effect of a gamification session on student satisfaction and knowledge scores in nursing students in simulated laboratory practice.MethodsA pre-post quasi-experimental study was conducted with 122 students from the nursing degree program who participated in the research. The evaluation consisted of four sessions of three hours each. In two sessions, participants were trained through a vertical methodology, by means of theoretical training provided by teaching staff, and two hours of clinical simulation, where the students were able to practice the techniques on professional simulators. At the other two sessions, participants received an explanation of the theoretical aspects of the session, one hour of clinical simulation, and one hour of gamification, in which they had to pass tests based on the performance of practical activities on the subject of the session. At the end of the gamification session, all the participants received a certificate as winners of the “nursing game”.ResultsThere was an improvement in the satisfaction and the knowledge level in the gamification sessions. Both were statistically significant (P < 0.001). There was an improvement in the items related to the development of critical thinking and the mobilizing concepts from theory to practice in the gamification sessions.ConclusionThe intervention was effective in improving the satisfaction of the sessions received and in knowledge development. creator: Sebastián Sanz-Martos creator: Cristina Álvarez-García creator: Carmen Álvarez-Nieto creator: Isabel M. López-Medina creator: María Dolores López-Franco creator: Maria E. Fernandez-Martinez creator: Lucía Ortega-Donaire uri: https://doi.org/10.7717/peerj.17167 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sanz-Martos et al. title: Cross-sectional association between 24-hour movement guidelines and depressive symptoms in Chinese university students link: https://peerj.com/articles/17217 last-modified: 2024-04-15 description: BackgroundThe world’s first 24-h movement guidelines for adults were released on 15 October 2020 in Canada, though evidence of their associations with health indicators in young adults is sparse. This study aimed to report the prevalence of meeting the 24-h movement guidelines and associations with depressive symptoms in a sample of Chinese university students.MethodsCross-sectional data from 1,793 Chinese university students (mean age = 20.7 years, 63.6% female) were used. Sociodemographic information, movement behaviors (physical activity, sedentary behavior, and sleep duration), and depressive symptoms were collected using a self-reported questionnaire.ResultsThe prevalence of meeting the 24-h movement guidelines was 27.8% in Chinese university students. Logistic regression results show that compared to those who met the 24-h movement guidelines, odds ratio (OR) for depressive symptoms in those who met fewer recommendations contained in the 24-h movement guidelines were significantly higher (OR for none = 3.4, 95% CI [2.1–5.5], p < 0.001; OR for one = 2.7, 95% CI [2.0–3.8], p < 0.001; OR for two = 1.5, 95% CI [1.1–2.1], p = 0.013).ConclusionThe prevalence of meeting the 24-h movement guidelines in Chinese university students was relatively low and should be enhanced through multiple strategies. Meeting the 24-h movement guidelines was associated with lower risk for depression in Chinese young adults. It is suggested that moving more, sitting less and sleeping well in this population may reduce the occurrence of depression. creator: Yanqing Zhang creator: Xinli Chi creator: Liuyue Huang creator: Xingyi Yang creator: Sitong Chen uri: https://doi.org/10.7717/peerj.17217 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Soil organic nitrogen variation shaped by diverse agroecosystems in a typical karst area: evidence from isotopic geochemistry link: https://peerj.com/articles/17221 last-modified: 2024-04-15 description: BackgroundSoil organic nitrogen (SON) levels can respond effectively to crop metabolism and are directly related to soil productivity. However, simultaneous comparisons of SON dynamics using isotopic tracing in diverse agroecosystems are lacking, especially in karst areas with fragile ecology.MethodsTo better understand the response of SON dynamics to environmental changes under the coupling of natural and anthropogenic disturbances, SON contents and their stable N isotope (δ15NSON) compositions were determined in abandoned cropland (AC, n = 16), grazing shrubland (GS, n = 11), and secondary forest land (SF, n = 20) from a typical karst area in southwest China.ResultsThe SON contents in the SF (mean: 0.09%) and AC (mean: 0.10%) profiles were obviously lower than those in the GS profile (mean: 0.31%). The δ15NSON values ranged from 4.35‰–7.59‰, 3.79‰–7.23‰, and 1.87‰–7.08‰ for the SF, AC, and GS profiles, respectively. Decomposition of organic matter controlled the SON variations in the secondary forest land by the covered vegetation, and that in the grazing shrubland by goat excreta. δ15NSON ranges were controlled by the covered vegetation, and the δ15NSON fractionations during SON transformation were influenced by microorganisms in all surface soil.ConclusionsThe excreta of goats that contained 15N-enriched SON induced a heavier δ15NSON composition in the grazed shrubland. Long-term cultivation consumes SON, whereas moderate grazing increases SON content to reduce the risk of soil degradation. This study suggests that optimized crop-livestock production may benefit the sustainable development of agroecosystems in karst regions. creator: Ruiyin Han creator: Qian Zhang creator: Zhifang Xu uri: https://doi.org/10.7717/peerj.17221 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Han et al. title: The rhizosphere and root selections intensify fungi-bacteria interaction in abiotic stress-resistant plants link: https://peerj.com/articles/17225 last-modified: 2024-04-15 description: The microbial communities, inhabiting around and in plant roots, are largely influenced by the compartment effect, and in turn, promote the growth and stress resistance of the plant. However, how soil microbes are selected to the rhizosphere, and further into the roots is still not well understood. Here, we profiled the fungal, bacterial communities and their interactions in the bulk soils, rhizosphere soils and roots of eleven stress-resistant plant species after six months of growth. The results showed that the root selection (from the rhizosphere soils to the roots) was stronger than the rhizosphere selection (from the bulk soils to the rhizosphere soils) in: (1) filtering stricter on the fungal (28.5% to 40.1%) and bacterial (48.9% to 68.1%) amplicon sequence variants (ASVs), (2) depleting more shared fungal (290 to 56) and bacterial (691 to 2) ASVs measured by relative abundance, and (3) increasing the significant fungi-bacteria crosskingdom correlations (142 to 110). In addition, the root selection, but not the rhizosphere selection, significantly increased the fungi to bacteria ratios (f:b) of the observed species and shannon diversity index, indicating unbalanced effects to the fungal and bacteria communities exerted by the root selection. Based on the results of network analysis, the unbalanced root selection effects were associated with increased numbers of negative interaction (140 to 99) and crosskingdom interaction (123 to 92), suggesting the root selection intensifies the negative fungi-bacteria interactions in the roots. Our findings provide insights into the complexity of crosskingdom interactions and improve the understanding of microbiome assembly in the rhizosphere and roots. creator: Feng Huang creator: Mengying Lei creator: Wen Li uri: https://doi.org/10.7717/peerj.17225 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Huang et al. title: Discovery of diverse Pectocaris species at the Cambrian series 2 Hongjingshao formation Xiazhuang section (Kunming, SW China) and its ecological, taphonomic, and biostratigraphic implications link: https://peerj.com/articles/17230 last-modified: 2024-04-15 description: Pectocaris species are intermediate- to large-sized Cambrian bivalved arthropods. Previous studies have documented Pectocaris exclusively from the Cambrian Series 2 Stage 3 Chengjiang biota in Yu’anshan Formation, Chiungchussu Stage in SW China. In this study, we report Pectocaris paraspatiosa sp. nov., and three other previously known Pectocaris from the Xiazhuang section in Kunming, which belongs to the Hongjingshao Formation and is a later phase within Cambrian Stage 3 than the Yu’anshan Formation. The new species can be distinguished from its congeners by the sparsely arranged endopodal endites and the morphologies of the abdomen, telson, and telson processes. We interpret P. paraspatiosa sp. nov. as a filter-feeder and a powerful swimmer adapted to shallow, agitated environments. Comparison among the Pectocaris species reinforces previous views that niche differentiation had been established among the congeneric species based on morphological differentiation. Our study shows the comprehensive occurrences of Pectocaris species outside the Chengjiang biota for the first time. With a review of the shared fossil taxa of Chengjiang and Xiaoshiba biotas, we identify a strong biological connection between the Yu’anshan and Hongjingshao Formations. creator: Changfei Jin creator: Hong Chen creator: Huijuan Mai creator: Xianguang Hou creator: Xianfeng Yang creator: Dayou Zhai uri: https://doi.org/10.7717/peerj.17230 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jin et al. title: Comparative analysis of Spodoptera frugiperda (J. E. Smith) (Lepidoptera, Noctuidae) corn and rice strains microbiota revealed minor changes across life cycle and strain endosymbiont association link: https://peerj.com/articles/17087 last-modified: 2024-04-12 description: BackgroundSpodoptera frugiperda (FAW) is a pest that poses a significant threat to corn production worldwide, causing millions of dollars in losses. The species has evolved into two strains (corn and rice) that differ in their genetics, reproductive isolation, and resistance to insecticides and Bacillus thuringiensis endotoxins. The microbiota plays an important role in insects’ physiology, nutrient acquisition, and response to chemical and biological controls. Several studies have been carried out on FAW microbiota from larvae guts using laboratory or field samples and a couple of studies have analyzed the corn strain microbiota across its life cycle. This investigation reveals the first comparison between corn strain (CS) and rice strain (RS) of FAW during different developmental insect stages and, more importantly, endosymbiont detection in both strains, highlighting the importance of studying both FAW populations and samples from different stages.MethodsThe composition of microbiota during the life cycle of the FAW corn and rice strains was analyzed through high-throughput sequencing of the bacterial 16S rRNA gene using the MiSeq system. Additionally, culture-dependent techniques were used to isolate gut bacteria and the Transcribed Internal Spacer-ITS, 16S rRNA, and gyrB genes were examined to enhance bacterial identification.ResultsRichness, diversity, and bacterial composition changed significantly across the life cycle of FAW. Most diversity was observed in eggs and males. Differences in gut microbiota diversity between CS and RS were minor. However, Leuconostoc, A2, Klebsiella, Lachnoclostridium, Spiroplasma, and Mucispirilum were mainly associated with RS and Colidextribacter, Pelomonas, Weissella, and Arsenophonus to CS, suggesting that FAW strains differ in several genera according to the host plant. Firmicutes and Proteobacteria were the dominant phyla during FAW metamorphosis. Illeobacterium, Ralstonia, and Burkholderia exhibited similar abundancies in both strains. Enterococcus was identified as a conserved taxon across the entire FAW life cycle. Microbiota core communities mainly consisted of Enterococcus and Illeobacterium. A positive correlation was found between Spiroplasma with RS (sampled from eggs, larvae, pupae, and adults) and Arsenophonus (sampled from eggs, larvae, and adults) with CS. Enterococcus mundtii was predominant in all developmental stages. Previous studies have suggested its importance in FAW response to B. thuringensis. Our results are relevant for the characterization of FAW corn and rice strains microbiota to develop new strategies for their control. Detection of Arsenophonus in CS and Spiroplasma in RS are promising for the improvement of this pest management, as these bacteria induce male killing and larvae fitness reduction in other Lepidoptera species. creator: Sandra María Marulanda-Moreno creator: Clara Inés Saldamando-Benjumea creator: Rafael Vivero Gomez creator: Gloria Cadavid-Restrepo creator: Claudia Ximena Moreno-Herrera uri: https://doi.org/10.7717/peerj.17087 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Marulanda-Moreno et al. title: Freshwater trematodes differ from marine trematodes in patterns connected with division of labor link: https://peerj.com/articles/17211 last-modified: 2024-04-12 description: BackgroundPrior research suggests that trematode rediae, a developmental stage of trematode parasites that reproduce clonally within a snail host, show evidence of division of labor (DOL). Single-species infections often have two morphologically distinct groups: small rediae, the ‘soldiers’, are active, aggressive, and do not appear to reproduce; large rediae, the ‘reproductives’, are larger, sluggish, and full of offspring. Most data supporting DOL come from trematodes infecting marine snails, while data from freshwater trematodes are more limited and generally do not supported DOL. The shorter lifespan typical of freshwater snails may partially explain this difference: defending a short-lived host at the expense of reproduction likely provides few advantages. Here, we present data from sixty-one colonies spanning twenty species of freshwater trematode exploring morphological and behavioral patterns commonly reported from marine trematodes believed to have DOL.MethodsTrematode rediae were obtained from sixty-one infected snails collected in central Vermont, USA. A portion of the COI gene was sequenced to make tentative species identifications (‘COI species’). Samples of rediae were photographed, observed, and measured to look for DOL-associated patterns including a bimodal size distribution, absence of embryos in small rediae, and pronounced appendages and enlarged pharynges (mouthparts) in small rediae. Additional rediae were used to compare activity levels and likelihood to attack heterospecific trematodes in large vs. small rediae.ResultsMany of the tests for DOL-associated patterns showed mixed results, even among colonies of the same COI species. However, we note a few consistent patterns. First, small rediae of most colonies appeared capable of reproduction, and we saw no indication (admittedly based on a small sample size and possibly insufficient attack trial methodology) that small rediae were more active or aggressive. This differs from patterns reported from most marine trematodes. Second, the small rediae of most colonies had larger pharynges relative to their body size than large rediae, consistent with marine trematodes. We also observed that colonies of three sampled COI species appear to produce a group of large rediae that have distinctly large pharynges.ConclusionsWe conclude that these freshwater species likely do not have a group of specialized non-reproductive soldiers because small rediae of at least some colonies in almost every species do appear to produce embryos. We cannot rule out the possibility that small rediae act as a temporary soldier caste. We are intrigued by the presence of rediae with enlarged pharynges in some species and propose that they may serve an adaptive role, possibly similar to the defensive role of small ‘soldier’ rediae of marine trematodes. Large-pharynx rediae have been documented in other species previously, and we encourage future efforts to study these large-pharynx rediae. creator: Allison T. Neal creator: Moira Stettner creator: Renytzabelle Ortega-Cotto creator: Daniel Dieringer creator: Lydia C. Reed uri: https://doi.org/10.7717/peerj.17211 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Neal et al. title: Efficacy of propolis extract and eye drop solutions to suppress encystation and excystation of Acanthamoeba triangularis WU19001-T4 genotype link: https://peerj.com/articles/16937 last-modified: 2024-04-11 description: BackgroundPropolis is a natural resinous product from a variety of plants and combines it with beeswax and salivary enzymes to create bee glue. Its potentials have been employed in the treatment of many diseases and conditions for centuries. This study, therefore, aims to determine the anti-Acanthamoeba properties of the propolis extract, eye drops coupled to some mechanisms such as inhibition of encystation and excystation.MethodsThe minimum inhibitory concentrations (MICs) of the most active propolis extract were assessed in trophozoites and cysts of Acanthamoeba triangularis (A. triangularis) at 0.256 and 1 mg/mL, respectively.ResultsActive eye drops inhibited trophozoites and cysts with a MIC value of 100%. At concentrations lower than their MICs values (1/2–1/16 MIC), propolis and eye drops revealed inhibition of encystation. In addition, at 1/2 MIC, both the propolis extract and eye drops showed potential inhibition of excystation. In combined sets of propolis extract and eye drops, they showed slightly increasing inhibition of encystation and excystation. Surprisingly, the MIC of chlorhexidine decreased when combined with the propolis and eye drops. SEM and TEM images displayed morphological changes in A. triangularis treated with combined sets of propolis extract and eye drops.ConclusionFrom this study, a new combined eye drop solution with propolis extract was found to be helpful in reducing encystation and excystation in A. triangularis. Therefore, this combination is an alternative for the treatment of eye diseases in early stages along with reducing the entry into the cyst stage of Acanthamoeba. The results of this study revealed new anti-Acanthamoeba inhibitors with promising combined alternative therapeutic potential for the treatment of Acanthamoeba keratitis. creator: Suthinee Sangkanu creator: Abolghasem Siyadatpanah creator: Roghayeh Norouzi creator: Julalak Chuprom creator: Watcharapong Mitsuwan creator: Sirirat Surinkaew creator: Rachasak Boonhok creator: Alok K. Paul creator: Tooba Mahboob creator: Imran Sama-ae creator: Sonia M. R. Oliveira creator: Tajudeen O. Jimoh creator: Maria de Lourdes Pereira creator: Polrat Wilairatana creator: Christophe Wiart creator: Mohammed Rahmatullah creator: Monvaris Sakolnapa creator: Veeranoot Nissapatorn uri: https://doi.org/10.7717/peerj.16937 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sangkanu et al. title: Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus) link: https://peerj.com/articles/17018 last-modified: 2024-04-11 description: The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477–0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0–0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa. creator: Declan R. Morris creator: Todd J. McWhorter creator: Wayne S. J. Boardman creator: Gregory Simpson creator: Jeanette Wentzel creator: Jannie Coetzee creator: Yoshan Moodley uri: https://doi.org/10.7717/peerj.17018 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Morris et al. title: Assessing the quality and reliability of YouTube videos as a source of information on inflammatory back pain link: https://peerj.com/articles/17215 last-modified: 2024-04-11 description: BackgroundInflammatory back pain is a chronic condition with localized pain, particularly in the axial spine and sacroiliac joints, that is associated with morning stiffness and improves with exercise. YouTube is the second most frequently used social media platform for accessing health information. This study sought to investigate the quality and reliability of YouTube videos on inflammatory back pain (IBP).MethodsThe study design was planned as cross-sectional. A search was conducted using the term “inflammatory back pain,” and the first 100 videos that met the inclusion criteria were selected on October 19, 2023. The data of the videos selected according to the inclusion and exclusion criteria in the study settings were examined. Videos with English language, with audiovisual content , had a duration >30 s, non-duplicated and primary content related to IBP were included in the study. A number of video parameters such as the number of likes, number of views, duration, and content categories were assessed. The videos were assessed for reliability using the Journal of the American Medical Association (JAMA) Benchmark criteria and the DISCERN tool. Quality was assessed using the Global Quality Score (GQS). Continuous variables were checked for normality of distribution using Shapiro–Wilk test and Kolmogorov–Smirnov test. Kruskal–Wallis test and Mann–Whitney U test were used to analyze the continuous data depending on the number of groups. Categorical data were analyzed using Pearson’s chi-square test.ResultsReliability assessment based on JAMA scores showed 21% of the videos to have high reliability. Quality assessment based on GQS results showed 19% of the videos to have high quality. JAMA, DISCERN, and GQS scores differed significantly by source of video (p < 0.001, < 0.001, and = 0.002, respectively). Video duration had a moderate positive correlation with scores from the GQS (r = 0.418, p < 0.001), JAMA (r = 0.484, p < 0.001), and modified DISCERN (r = 0.418, p < 0.001).ConclusionThe results of the present study showed that YouTube offers videos of low reliability and low quality on inflammatory back pain. Health authorities have a responsibility to protect public health and should take proactive steps regarding health information shared on social media platforms. creator: Mete Kara creator: Erkan Ozduran creator: Müge Mercan Kara creator: Volkan Hanci creator: Yüksel Erkin uri: https://doi.org/10.7717/peerj.17215 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kara et al. title: Vertical farming for lettuce production in limited space: a case study in Northern Thailand link: https://peerj.com/articles/17085 last-modified: 2024-04-10 description: BackgroundGreenhouse vertical farming under natural sunlight is an alternative farming technique that grows crops in a stacking column and extends in a vertical direction. Sunlight availability is one of the crucial factors for crop development in vertical farming. Therefore, this investigation aimed to examine the effect of sunlight availability on lettuce growth and yields at different levels of vertical shelves.MethodsSix shelves were constructed with three levels: upper, middle and lower levels. Lettuces (Lactuca sativa L.) as ‘Baby Cos’ and ‘Green Oak’ at 14 days after sowing were planted on the three levels. The photosynthetic photon flux density (PPFD) was recorded, and the PPFD values were then converted to the daily light integral (DLI). Plant height and canopy width were measured three times at 14, 21 and 28 days after transplanting. At maturity, fresh weight (FW) was directly monitored after harvest.ResultsThe results showed that the highest PPFD and DLI values were found at the upper level (PPFD 697 μmol m−2 s−1 and DLI 29 mol m−2 d−1) in comparison to the middle (PPFD 391 μmol m−2 s−1 and DLI 16 mol m−2 d−1) and lower (PPFD 322 μmol m−2 s−1 and DLI 13 mol m−2 d−1) levels. The lowest plant height and canopy width values were observed on the upper levels for both lettuce varieties during the three measurement dates. The middle (‘Baby Cos’ = 123.8 g plant−1 and ‘Green Oak’ = 190.7 g plant−1) and lower (‘Baby Cos’ = 92.9 g plant−1 and ‘Green Oak’ = 203.7 g plant−1) levels had the higher values of FW in comparison to the upper level (‘Baby Cos’ = 84.5 g plant−1 and ‘Green Oak’ = 97.3 g plant−1). The values of light use efficiency (LUE) showed an increased trend from the upper to lower levels in both varieties, with values of ‘Baby Cos’ of 0.10 g mol−1 in the upper level, 0.28 g mol−1 in the middle level and 0.26 g mol−1 in the lower level and ‘Green Oak’ of 0.12 g mol−1 in the upper level, 0.44 g mol−1 in the middle level and 0.57 g mol−1 in the lower level. The findings of the study indicated the viability of utilizing vertical shelves for lettuce production. creator: Suwimon Wicharuck creator: Nuttapon Khongdee creator: Ar Man creator: Wahyu Nurkholis Hadi Syahputra creator: Parichat Yalangkan creator: Prapaporn Chaiphak creator: Chatchawan Chaichana uri: https://doi.org/10.7717/peerj.17085 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wicharuck et al. title: Advancement in the development of single chain antibodies using phage display technology link: https://peerj.com/articles/17143 last-modified: 2024-04-10 description: Phage display technology has become an important research tool in biological research, fundamentally changing the traditional monoclonal antibody preparation process, and has been widely used in the establishment of antigen-antibody libraries, drug design, vaccine research, pathogen detection, gene therapy, antigenic epitope research, and cellular signal transduction research.The phage display is a powerful platform for technology development. Using phage display technology, single chain fragment variable (scFv) can be screened, replacing the disadvantage of the large size of traditional antibodies. Phage display single chain antibody libraries have significant biological implications. Here we describe the types of antibodies, including chimeric antibodies, bispecific antibodies, and scFvs. In addition, we describe the phage display system, phage display single chain antibody libraries, screening of specific antibodies by phage libraries and the application of phage libraries. creator: Xiaohui Zheng creator: Qi Liu creator: Yimin Liang creator: Wenzhi Feng creator: Honghao Yu creator: Chunyu Tong creator: Bocui Song uri: https://doi.org/10.7717/peerj.17143 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zheng et al. title: Association of healthy lifestyle score with control of hypertension among treated and untreated hypertensive patients: a large cross-sectional study link: https://peerj.com/articles/17203 last-modified: 2024-04-10 description: BackgroundHypertension stands as the leading single contributor to the worldwide burden of mortality and disability. Limited evidence exists regarding the association between the combined healthy lifestyle score (HLS) and hypertension control in both treated and untreated hypertensive individuals. Therefore, we aimed to investigate the association between HLS and hypertension control among adults with treated and untreated hypertension.MethodsThis cross-sectional study, including 311,994 hypertension patients, was conducted in Guangzhou using data from the National Basic Public Health Services Projects in China. The HLS was defined based on five low-risk lifestyle factors: healthy dietary habits, active physical activity, normal body mass index, never smoking, and no alcohol consumption. Controlled blood pressure was defined as systolic blood pressure <140 mmHg and diastolic blood pressure <90 mmHg. A multivariable logistic regression model was used to assess the association between HLS and hypertension control after adjusting for various confounders.ResultsThe HLS demonstrated an inverse association with hypertension control among hypertensive patients. In comparison to the low HLS group (scored 0–2), the adjusted odds ratios (95% confidence intervals) for hypertension were 0.76 (0.74, 0.78), 0.59 (0.57, 0.60), and 0.48 (0.46, 0.49) for the HLS groups scoring 3, 4, and 5, respectively (Ptrend < 0.001). Notably, an interaction was observed between HLS and antihypertensive medication in relation to hypertension control (Pinteraction < 0.001). When comparing the highest HLS (scored 5) with the lowest HLS (scored 0–2), adjusted odds ratios (95% confidence intervals) were 0.50 (0.48, 0.52, Ptrend < 0.001) among individuals who self-reported using antihypertensive medication and 0.41 (0.38, 0.44, Ptrend < 0.001) among those not using such medication. Hypertensive patients adhering to a healthy lifestyle without medication exhibited better blood pressure management than those using medication while following a healthy lifestyle.ConclusionHLS was associated with a reduced risk of uncontrolled blood pressure. creator: Ting Dong creator: Qin Zhou creator: Weiquan Lin creator: Chang Wang creator: Minying Sun creator: Yaohui Li creator: Xiangyi Liu creator: Guozhen Lin creator: Hui Liu creator: Caixia Zhang uri: https://doi.org/10.7717/peerj.17203 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dong et al. title: Representation of investigation results of microplastics on sandy beaches—accumulation rate and abundance in the entire study site link: https://peerj.com/articles/17207 last-modified: 2024-04-10 description: Long-term microplastics (MPs) environmental pollution trends cannot be understood only by investigating their presence on beaches. Without estimating MPs for the entire beach, comparisons between multiple beaches cannot be made. In this study, Nagasaki Prefecture was selected as the study site, we measured MPs accumulation rate to express the MPs pollution trend and weighted the measurement results to enable comparison of MPs content among multiple sandy beaches. The MPs accumulation rate in the study site was measured by periodic investigation at fixed spots. The average in the supratidal zone was 1.5 ± 0.9 mg-MPs/(m2-sand⋅ d) (n = 15). The weighting of the MPs content in hot spots and non-hot spots by their respective areas enabled us to obtain the representative value and the dispersion of the MPs content in the entire study site. The MPs contents in the three beaches were 298 ± 144, 1,115 ± 518, and 4,084 ± 2,243 mg-MPs/(m2-sand), respectively. Using these values, it is possible to compare the MPs contents of multiple beaches. creator: Hiroshi Asakura uri: https://doi.org/10.7717/peerj.17207 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Asakura title: Population dynamics and seasonal migration patterns of Spodoptera exigua in northern China based on 11 years of monitoring data link: https://peerj.com/articles/17223 last-modified: 2024-04-10 description: BackgroundThe beet armyworm, Spodoptera exigua (Hübner), is an important agricultural pest worldwide that has caused serious economic losses in the main crop-producing areas of China. To effectively monitor and control this pest, it is crucial to investigate its population dynamics and seasonal migration patterns in northern China.MethodsIn this study, we monitored the population dynamics of S. exigua using sex pheromone traps in Shenyang, Liaoning Province from 2012 to 2022, combining these data with amigration trajectory simulation approach and synoptic weather analysis.ResultsThere were significant interannual and seasonal variations in the capture number of S. exigua, and the total number of S. exigua exceeded 2,000 individuals in 2018 and 2020. The highest and lowest numbers of S. exigua were trapped in September and May, accounting for 34.65% ± 6.81% and 0.11% ± 0.04% of the annual totals, respectively. The average occurrence period was 140.9 ± 9.34 days during 2012–2022. In addition, the biomass of S. exigua also increased significantly during these years. The simulated seasonal migration trajectories also revealed varying source regions in different months, primarily originated from Northeast China and East China. These unique insights into the migration patterns of S. exigua will contribute to a deeper understanding of its occurrence in northern China and provide a theoretical basis for regional monitoring, early warning, and the development of effective management strategies for long-range migratory pests. creator: Hao-Tian Ma creator: Li-Hong Zhou creator: Hao Tan creator: Xian-Zhi Xiu creator: Jin-Yang Wang creator: Xing-Ya Wang uri: https://doi.org/10.7717/peerj.17223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ma et al. title: Comparative study of nasal cavity drug delivery efficiency with different nozzles in a 3D printed model link: https://peerj.com/articles/17227 last-modified: 2024-04-10 description: BackgroundNasal sprays are widely used in treating nasal and sinus diseases; however, there are very few studies on the drug delivery efficiency of nasal sprays. In this study, the drug delivery efficiency of three different nasal spray devices was evaluated in vitro using a 3D printed cast model of nasal cavity.MethodsThree nasal spray devices with different nozzles and angles of administration were used in the 3D model of the nasal cavity and paranasal sinuses. The spraying area (SA), maximal spraying distance (MSD), and spraying distribution scores on the nasal septum and lateral nasal wall were recorded.ResultsDifferent nasal spray devices have their own characteristics, including volume of each spray, SA, and plume angle. The SA of the three nozzles on the nasal septum increased with an increasing angle of administration. When the angle of administration was 50°, each nozzle reached the maximal SA. There was no statistically significant difference in MSD among the three nozzles at the three angles. The total scores for each nozzle using the three different spraying angles were as follows: nozzle A, 40° > 30° > 50°; nozzle B, 30° > 40° > 50°; and nozzle C, 30° > 40° > 50°. The total scores for different nozzles using the same angle were statistically significantly different and the scores for nozzle C were the highest. Nozzle C had the minimum plume angle. None of the three nozzles could effectively delivered drugs into the middle meatus at any angle in this model.ConclusionsThe design of the nozzle affects drug delivery efficiency of nasal spray devices. The ideal angle of administration is 50°. The nozzle with smaller plume angle has higher drug delivery efficiency. Current nasal spray devices can easily deliver drugs to most areas of the nasal cavity, such as the turbinate, nasal septum, olfactory fissure, and nasopharynx, but not the middle meatus. These findings are meaningful for nozzle selection and device improvements. creator: Shengjian Fang creator: Xiaoqing Rui creator: Yu Zhang creator: Zhangwei Yang creator: Weihua Wang uri: https://doi.org/10.7717/peerj.17227 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fang et al. title: Behind the wheel: exploring gray matter variations in experienced drivers link: https://peerj.com/articles/17228 last-modified: 2024-04-10 description: BackgroundDriving is a complex skill involving various cognitive activities. Previous research has explored differences in the brain structures related to the navigational abilities of drivers compared to non-drivers. However, it remains unclear whether changes occur in the structures associated with low-level sensory and higher-order cognitive abilities in drivers.MethodsGray matter volume, assessed via voxel-based morphometry analysis of T1-weighted images, is considered a reliable indicator of structural changes in the brain. This study employs voxel-based morphological analysis to investigate structural differences between drivers (n = 22) and non-drivers (n = 20).ResultsThe results indicate that, in comparison to non-drivers, drivers exhibit significantly reduced gray matter volume in the middle occipital gyrus, middle temporal gyrus, supramarginal gyrus, and cerebellum, suggesting a relationship with driving-related experience. Furthermore, the volume of the middle occipital gyrus, and middle temporal gyrus, is found to be marginally negative related to the years of driving experience, suggesting a potential impact of driving experience on gray matter volume. However, no significant correlations were observed between driving experiences and frontal gray matter volume.ConclusionThese findings suggest that driving skills and experience have a pronounced impact on the cortical areas responsible for low-level sensory and motor processing. Meanwhile, the influence on cortical areas associated with higher-order cognitive function appears to be minimal. creator: Jiangtao Chen creator: Xiaoyu Chen creator: Li Gong creator: Di Zhang creator: Qiang Liu uri: https://doi.org/10.7717/peerj.17228 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: The impact of chemical and hormonal treatments to improve seed germination and seedling growth of Juniperus procera Hochst. ex Endi link: https://peerj.com/articles/17236 last-modified: 2024-04-10 description: PurposeJuniper (Juniperus procera) is a common forest tree species in Saudi Arabia. The decline in many populations of J. procera in Saudi Arabia is mainly due to seed dormancy and loss of natural regeneration. This study assessed the effects of chemical and hormonal treatments on seed germination and seedling growth in juniper plants.MethodsThe seeds were subjected to either chemical scarification with 90% sulfuric acid and 20% acetic acid for 6 min or hormonal treatment by seed soaking in two concentrations (50 and 100 ppm) of three growth regulators, namely, indole acetic acid (IAA), gibberellins (GA3), and kinetin, for 72 h. A control group without any seed treatment was also prepared. The experiments were performed in an incubator maintained at room temperature and under a light and dark period of 12 h for 6 w. The germinated seeds for each treatment were counted and removed from the dishes. The selected germinated seeds from different treatments were planted in a greenhouse and irrigated with tap water for another 6 weeks. The hormone-treated seedlings were sprayed with their corresponding hormone concentrations 1 w after planting.ResultsThe highest percentage of seed germination was significantly recorded after seed soaking in 50 ppm GA3, whereas treatment with IAA (100 ppm) resulted in the best seedling growth. Seedlings treated with the three phytohormones showed a significant increase in photosynthetic pigments, total soluble sugars, proteins, percentage of oil, IAA, GA3, and kinetin contents of juniper seedlings compared with the control value, whereas abscisic acid content was decreased compared with chemical treatments.ConclusionThe investigated different treatments had an effective role in breaking seed dormancy and improving seedling growth of J. procera, which is facing a notable decline in its population worldwide. Moreover, such an effect was more pronounced in the three phytohormones that succeeded in breaking dormancy and growth of the Juniperus plant than in the other treatments. creator: Alae Ahmad Jabbour creator: Abdulaziz Alzahrani uri: https://doi.org/10.7717/peerj.17236 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jabbour and Alzahrani title: The dinosaurs that weren’t: osteohistology supports giant ichthyosaur affinity of enigmatic large bone segments from the European Rhaetian link: https://peerj.com/articles/17060 last-modified: 2024-04-09 description: Very large unidentified elongate and rounded fossil bone segments of uncertain origin recovered from different Rhaetian (Late Triassic) fossil localities across Europe have been puzzling the paleontological community since the second half of the 19th century. Different hypotheses have been proposed regarding the nature of these fossils: (1) giant amphibian bones, (2) dinosaurian or other archosaurian long bone shafts, and (3) giant ichthyosaurian jaw bone segments. We call the latter proposal the ‘Giant Ichthyosaur Hypothesis’ and test it using bone histology. In presumable ichthyosaur specimens from SW England (Lilstock), France (Autun), and indeterminate cortical fragments from Germany (Bonenburg), we found a combination of shared histological features in the periosteal cortex: an unusual woven-parallel complex of strictly longitudinal primary osteons set in a novel woven-fibered matrix type with intrinsic coarse collagen fibers (IFM), and a distinctive pattern of Haversian substitution in which secondary osteons often form within primary ones. The splenial and surangular of the holotype of the giant ichthyosaur Shastasaurus sikanniensis from Canada were sampled for comparison. The results of the sampling indicate a common osteohistology with the European specimens. A broad histological comparison is provided to reject alternative taxonomic affinities aside from ichthyosaurs of the very large bone segment. Most importantly, we highlight the occurrence of shared peculiar osteogenic processes in Late Triassic giant ichthyosaurs, reflecting special ossification strategies enabling fast growth and achievement of giant size and/or related to biomechanical properties akin to ossified tendons. creator: Marcello Perillo creator: P Martin Sander uri: https://doi.org/10.7717/peerj.17060 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Perillo and Sander title: Integration of temporal & spatial properties of dynamic functional connectivity based on two-directional two-dimensional principal component analysis for disease analysis link: https://peerj.com/articles/17078 last-modified: 2024-04-09 description: Dynamic functional connectivity, derived from resting-state functional magnetic resonance imaging (rs-fMRI), has emerged as a crucial instrument for investigating and supporting the diagnosis of neurological disorders. However, prevalent features of dynamic functional connectivity predominantly capture either temporal or spatial properties, such as mean and global efficiency, neglecting the significant information embedded in the fusion of spatial and temporal attributes. In addition, dynamic functional connectivity suffers from the problem of temporal mismatch, i.e., the functional connectivity of different subjects at the same time point cannot be matched. To address these problems, this article introduces a novel feature extraction framework grounded in two-directional two-dimensional principal component analysis. This framework is designed to extract features that integrate both spatial and temporal properties of dynamic functional connectivity. Additionally, we propose to use Fourier transform to extract temporal-invariance properties contained in dynamic functional connectivity. Experimental findings underscore the superior performance of features extracted by this framework in classification experiments compared to features capturing individual properties. creator: Feng Zhao creator: Ke Lv creator: Shixin Ye creator: Xiaobo Chen creator: Hongyu Chen creator: Sizhe Fan creator: Ning Mao creator: Yande Ren uri: https://doi.org/10.7717/peerj.17078 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al. title: Reappraisal of sauropod dinosaur diversity in the Upper Cretaceous Winton Formation of Queensland, Australia, through 3D digitisation and description of new specimens link: https://peerj.com/articles/17180 last-modified: 2024-04-09 description: Skeletal remains of sauropod dinosaurs have been known from Australia for over 100 years. Unfortunately, the classification of the majority of these specimens to species level has historically been impeded by their incompleteness. This has begun to change in the last 15 years, primarily through the discovery and description of several partial skeletons from the Cenomanian–lower Turonian (lower Upper Cretaceous) Winton Formation in central Queensland, with four species erected to date: Australotitan cooperensis, Diamantinasaurus matildae, Savannasaurus elliottorum, and Wintonotitan wattsi. The first three of these appear to form a clade (Diamantinasauria) of early diverging titanosaurs (or close relatives of titanosaurs), whereas Wintonotitan wattsi is typically recovered as a distantly related non-titanosaurian somphospondylan. Through the use of 3D scanning, we digitised numerous specimens of Winton Formation sauropods, facilitating enhanced comparison between type and referred specimens, and heretofore undescribed specimens. We present new anatomical information on the holotype specimen of Diamantinasaurus matildae, and describe new remains pertaining to twelve sauropod individuals. Firsthand observations and digital analysis enabled previously proposed autapomorphic features of all four named Winton Formation sauropod species to be identified in the newly described specimens, with some specimens exhibiting putative autapomorphies of more than one species, prompting a reassessment of their taxonomic validity. Supported by a specimen-level phylogenetic analysis, we suggest that Australotitan cooperensis is probably a junior synonym of Diamantinasaurus matildae, but conservatively regard it herein as an indeterminate diamantinasaurian, meaning that the Winton Formation sauropod fauna now comprises three (rather than four) valid diamantinasaurian species: Diamantinasaurus matildae, Savannasaurus elliottorum, and Wintonotitan wattsi, with the latter robustly supported as a member of the clade for the first time. We refer some of the newly described specimens to these three species and provide revised diagnoses, with some previously proposed autapomorphies now regarded as diamantinasaurian synapomorphies. Our newly presented anatomical data and critical reappraisal of the Winton Formation sauropods facilitates a more comprehensive understanding of the mid-Cretaceous sauropod palaeobiota of central Queensland. creator: Samantha L. Beeston creator: Stephen F. Poropat creator: Philip D. Mannion creator: Adele H. Pentland creator: Mackenzie J. Enchelmaier creator: Trish Sloan creator: David A. Elliott uri: https://doi.org/10.7717/peerj.17180 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Beeston et al. title: IGF-1 rs6218 polymorphisms modulate the susceptibility to age-related cataract link: https://peerj.com/articles/17220 last-modified: 2024-04-09 description: BackgroundSingle nucleotide polymorphisms (SNPs), as the most abundant form of DNA variation in the human genome, contribute to age-related cataracts (ARC) development. Apoptosis of lens epithelial cells (LECs) is closely related to ARC formation. Insulin-like growth factor 1 (IGF1) contributes to cell apoptosis regulation. Moreover, IGF1 was indicated to exhibit a close association with cataract formation. Afterward, an investigation was conducted to examine the correlation between polymorphisms in IGF1 and the susceptibility to ARC.MethodsThe present investigation was a case-control study. Venous blood draws were collected from the participants for DNA genotyping. Lens capsule samples were collected to detect mRNA and apoptosis. TaqMan RT-PCR was used to detect IGF1 polymorphism genotypes and qRT PCR was used to detect IGF1 mRNA levels in LECs. LEC apoptosis was evaluated through flow cytometry. The chi-square test was used to compare differences between ARCs and controls of each SNP.ResultsWe found that the G allele frequency in the IGF1-rs6218 was higher in the ARCs than in the controls. Furthermore, it was observed that the rs6218 GG genotype exhibited a positive correlation to elevated levels of IGF1 mRNA in LECs. The IGF1 mRNA in the LECs and the apoptosis of LECs in nuclear type of ARCs (ARNC) was higher than the controls.ConclusionThe susceptibility to ARC was related to IGF1-rs6218 polymorphism, and this polymorphism is associated with IGF1 expression at the mRNA level. Moreover, apoptosis in LECs of ARNCs was found to be increased. creator: Xi Zou creator: Jun Zhang creator: Yong Wang creator: Dong Zhou creator: Guohua Deng creator: Zhinan Liu uri: https://doi.org/10.7717/peerj.17220 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zou et al. title: The role of echinacoside-based cross-linker nanoparticles in the treatment of osteoporosis link: https://peerj.com/articles/17229 last-modified: 2024-04-09 description: BackgroundCurrent drugs for treating osteoporosis may lead to toxic side effects. Echinacoside (ECH) is a natural small molecule drug. This study examined and compared the therapeutic effects of cross-linker (CL)-ECH and ECH-free nanoparticles on osteoporosis.MethodsEchinocandin-based CL-ECH nanoparticles were prepared, and the nanoparticle size and drug loading were optimized and characterized by adjusting the ratio. The antioxidant effect of CL-ECH nanoparticles on bone marrow-derived macrophages (BMDMs) was analyzed using flow cytometry, immunofluorescence staining and quantitative real-time polymerase chain reaction (qRT-PCR). Bone marrow stromal cells (BMSCs)-based detection of bone-producing effects was conducted using alkaline phosphatase (ALP), Alizarin Red S (ARS) and qRT-PCR. TRAP, phalloidin staining, and qRT-PCR was performed to detect osteogenesis-inhibiting effect on BMDMs. CL-ECH nanoparticles were applied to treat an ovariectomized (OVX) mouse model at low doses.ResultsCompared to ECH, CL-ECH nanoparticles suppressed oxidative stress in BMDMs by promoting NRF-2 nuclear translocation, which inhibited the production of both reactive oxygen species (ROS) and osteoclast production through downregulating NF-κB expression, with limited effect on the osteogenesis of BMSCs. In vivo studies showed that low-dose CL-ECH nanoparticles markedly improved bone trabecular loss compared to ECH administration in the treatment of osteoporosis.ConclusionsThe current discoveries provided a solid theoretical foundation for the development of a new generation of anti-bone resorption drugs and antiosteoporosis drugs. creator: Dandan Hu creator: Chunan Cheng creator: Zhen Bian creator: Yubo Xu uri: https://doi.org/10.7717/peerj.17229 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hu et al. title: Heterogeneity of the effect of the COVID-19 pandemic on the incidence of Metabolic Syndrome onset at a Japanese campus link: https://peerj.com/articles/17013 last-modified: 2024-04-05 description: BackgroundThe coronavirus disease 2019 (COVID-19) outbreak began in China in December 2019, with the World Health Organization declaring a state of emergency in January 2020. Worldwide implementation of lockdown measures to slow the spread of the virus led to reduced physical activity, disrupted eating habits, mental health issues, and sleep disturbances, which increased the risk of lifestyle-related diseases such as metabolic syndrome (MetS). During the COVID-19 pandemic, healthcare workers, especially intensive care workers, experienced longer working hours and burnout, which further increased the risk of lifestyle-related diseases. Accordingly, it is important to identify individuals at a risk of new-onset MetS during a pandemic, which could direct preventive interventions. This study aimed to assess the heterogeneous impact of the COVID-19 pandemic on the incidence of new-onset MetS based on the conditional average treatment effect (CATE) and to identify at-risk populations.MethodsThis study analyzed health checkup data obtained from Okayama University Shikata Campus workers using paired baseline and follow-up years. Baseline data encompassed 2017 to 2019, with respective follow-up data from 2018 to 2020. Furthermore, as the COVID-19 pandemic in Japan began in January 2020, workers who underwent follow-up health checkups in 2018 to 2019 and 2020 were considered as “unexposed” and “exposed,” respectively. As the Shikata campus has several departments, comparisons among departments were made. The primary outcome was new-onset MetS at follow-up. Predictor variables included baseline health checkup results, sex, age, and department (administrative, research, medical, or intensive care department). X-learner was used to calculate the CATE.ResultsThis study included 3,572 eligible individuals (unexposed, n = 2,181; exposed, n = 1,391). Among them, 1,544 (70.8%) and 866 (62.3%) participants in the unexposed and exposed groups, respectively, were females. The mean age (±standard deviation) of the unexposed and exposed groups was 48.2 ± 8.2 and 47.8 ± 8.3 years, respectively. The COVID-19 pandemic increased the average probability of new-onset MetS by 4.4% in the overall population. According to the department, the intensive care department showed the highest CATE, with a 15.4% increase. Moreover, there was large heterogeneity according to the department. The high-CATE group was characterized by older age, urinary protein, elevated liver enzymes, higher triglyceride levels, and a history of hyperlipidemia treatment.ConclusionsThis study demonstrated that the COVID-19 pandemic increased the incidence of new-onset MetS, with this effect showing heterogeneity at a single Japanese campus. Regarding specific populations, workers in the intensive care department showed an increased risk of new-onset MetS. At-risk populations require specific preventive interventions in case the current COVID-19 pandemic persists or a new pandemic occurs. creator: Toshiharu Mitsuhashi uri: https://doi.org/10.7717/peerj.17013 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mitsuhashi title: HSP90B1 regulates autophagy via PI3K/AKT/mTOR signaling, mediating HNSC biological behaviors link: https://peerj.com/articles/17028 last-modified: 2024-04-05 description: BackgroundAutophagy, a crucial cellular mechanism, facilitates the degradation and removal of misfolded proteins and impaired organelles. Recent research has increasingly highlighted the intimate connection between autophagy and heat shock proteins (HSPs) in the context of tumor development. However, the specific role and underlying mechanisms of heat shock protein 90 beta family member 1 (HSP90B1) in modulating autophagy within head and neck squamous cell carcinoma (HNSCC) remain elusive.MethodsQuantitative real-time PCR (qRT-PCR), Western blot (WB), immunohistochemistry (IHC) were used to detect the expression in HNSC cell lines and tissues. The relationship between HSP90B1 and clinicopathologic features was explored based on TCGA (The Cancer Genome Atlas) data and IHC results. The biological functions of HSP90B1 were analyzed through in vitro and in vivo models to evaluate proliferation, migration, invasion, and autophagy. The mechanisms of HSP90B1 were studied using bioinformatics and WB.ResultsHSP90B1 was upregulated in HNSC cells and tissues. High HSP90B1 levels were associated with T-stage, M-stage, clinical stage, and poor prognosis in HNSC patients. Functionally, HSP90B1 promotes HNSC cell proliferation, migration, invasion and inhibits apoptosis. We discovered that HSP90B1 obstructs autophagy and advances HNSC progression through the PI3K/Akt/mTOR pathway.ConclusionOur study demonstrates that HSP90B1 is highly expressed in HNSC. Furthermore, HSP90B1 may regulate autophagy through the PI3K/Akt/mTOR pathway, mediating HNSC cell biological behaviors. These provide new insights into potential biomarkers and targets for HNSC therapy. creator: Chao Li creator: Xiaoyu Lin creator: Jiping Su uri: https://doi.org/10.7717/peerj.17028 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Recombinant hirudin attenuates pulmonary hypertension and thrombosis in acute pulmonary embolism rat model link: https://peerj.com/articles/17039 last-modified: 2024-04-05 description: BackgroundAcute pulmonary embolism (APE) is classified as a subset of diseases that are characterized by lung obstruction due to various types of emboli. Current clinical APE treatment using anticoagulants is frequently accompanied by high risk of bleeding complications. Recombinant hirudin (R-hirudin) has been found to have antithrombotic properties. However, the specific impact of R-hirudin on APE remains unknown.MethodsSprague-Dawley (SD) rats were randomly assigned to five groups, with thrombi injections to establish APE models. Control and APE group rats were subcutaneously injected with equal amounts of dimethyl sulfoxide (DMSO). The APE+R-hirudin low-dose, middle-dose, and high-dose groups received subcutaneous injections of hirudin at doses of 0.25 mg/kg, 0.5 mg/kg, and 1.0 mg/kg, respectively. Each group was subdivided into time points of 2 h, 6 h, 1 d, and 4 d, with five animals per point. Subsequently, all rats were euthanized, and serum and lung tissues were collected. Following the assessment of right ventricular pressure (RVP) and mean pulmonary artery pressure (mPAP), blood gas analysis, enzyme-linked immunosorbnent assay (ELISA), pulmonary artery vascular testing, hematoxylin-eosin (HE) staining, Terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) staining, immunohistochemistry, and Western blot experiments were conducted.ResultsR-hirudin treatment caused a significant reduction of mPAP, RVP, and Malondialdehyde (MDA) content, as well as H2O2 and myeloperoxidase (MPO) activity, while increasing pressure of oxygen (PaO2) and Superoxide Dismutase (SOD) activity. R-hirudin also decreased wall area ratio and wall thickness to diameter ratio in APE rat pulmonary arteries. Serum levels of endothelin-1 (ET-1) and thromboxaneB2 (TXB2) decreased, while prostaglandin (6-K-PGF1α) and NO levels increased. Moreover, R-hirudin ameliorated histopathological injuries and reduced apoptotic cells and Matrix metalloproteinase-9 (MMP9), vascular cell adhesion molecule-1 (VCAM-1), p-Extracellular signal-regulated kinase (ERK)1/2/ERK1/2, and p-P65/P65 expression in lung tissues.ConclusionR-hirudin attenuated pulmonary hypertension and thrombosis in APE rats, suggesting its potential as a novel treatment strategy for APE. creator: Xiang Wei creator: Yanfen Zou creator: Shunli Dong creator: Yi Chen creator: Guoping Li creator: Bin Wang uri: https://doi.org/10.7717/peerj.17039 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wei et al. title: Self-reported side effects of COVID-19 vaccines among health professions students in India link: https://peerj.com/articles/17083 last-modified: 2024-04-05 description: Studies focusing on the safety and common side effects of vaccines play a crucial role in enhancing public acceptance of vaccination. Research is scarce regarding the usage of COVID-19 vaccines and the side effects experienced by health professions students in India and other countries. This study aimed to document self-reported side effects associated with COVID-19 vaccination among medical and dental students of six medical and dental colleges and teaching hospitals in four states (Tamil Nadu, Madhya Pradesh, Gujarat, and West Bengal) of India. A cross-sectional survey using purposive sampling of medical and dental students was conducted from 26 April to 26 May 2021. Data was collected using a Google Forms questionnaire capturing information regarding receiving COVID-19 vaccines, side effects and symptoms, onset and duration of symptoms, use of treatment to alleviate symptoms, awareness of haematologic risks associated with vaccination, and side effects from previous (non-COVID-19) vaccinations. The majority (94.5%) of participants received both doses of the Covishield/AstraZeneca COVID-19 vaccine. Among participants (n = 492), 45.3% (n = 223) reported one or more side effects. The most frequently reported side effects were soreness of the injected arm (80.3%), tiredness (78.5%), fever (71.3%), headache (64.1%), and hypersomnia (58.7%). The two most common severe symptoms were fever (14.8%) and headache (13%). Most side effects appeared on the day of vaccination: soreness of the injection site (57%), fever (43.1%), and tiredness (42.6%). Most reported symptoms persisted for one to three days–soreness of the injection site (53%), fever (47.1%), and headache (42.6%). Logistic regression showed that women were almost 85% less likely to report side effects. The study’s findings corroborate the safety of the Covishield/AstraZeneca vaccine’s first dose, evidenced by the relatively minor and transient nature of the side effects. However, the study underscores the necessity for ongoing research to assess the long-term impacts of COVID-19 vaccines, especially in the context of booster doses, thereby contributing to the global understanding of vaccine safety and efficacy. creator: Md Anwarul Azim Majumder creator: Ambadasu Bharatha creator: Santosh Kumar creator: Madhuri Chatterjee creator: Subir Gupta creator: Heather Harewood creator: Keerti Singh creator: WMS Johnson creator: Archana Rajasundaram creator: Sudeshna Banerjee Dutta creator: Sangishetti Vijay Prasad creator: Sayeeda Rahman creator: Russell Kabir creator: Ali Davod Parsa creator: Uma Gaur creator: Ahbab Mohammad Fazle Rabbi creator: Kandamaran Krishnamurthy creator: Shegufta Mohammad creator: Vikram Chode creator: Mainul Haque creator: Michael H. Campbell uri: https://doi.org/10.7717/peerj.17083 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Majumder et al. title: Exogenous melatonin improves germination rate in buckwheat under high temperature stress by regulating seed physiological and biochemical characteristics link: https://peerj.com/articles/17136 last-modified: 2024-04-05 description: The germinations of three common buckwheat (Fagopyrum esculentum) varieties and two Tartary buckwheat (Fagopyrum tataricum) varieties seeds are known to be affected by high temperature. However, little is known about the physiological mechanism affecting germination and the effect of melatonin (MT) on buckwheat seed germination under high temperature. This work studied the effects of exogenous MT on buckwheat seed germination under high temperature. MT was sprayed. The parameters, including growth, and physiological factors, were examined. The results showed that exogenous MT significantly increased the germination rate (GR), germination potential (GP), radicle length (RL), and fresh weight (FW) of these buckwheat seeds under high-temperature stress and enhanced the content of osmotic adjustment substances and enzyme activity. Comprehensive analysis revealed that under high-temperature stress during germination, antioxidant enzymes play a predominant role, while osmotic adjustment substances work synergistically to reduce the extent of damage to the membrane structure, serving as the primary key indicators for studying high-temperature resistance. Consequently, our results showed that MT had a positive protective effect on buckwheat seeds exposed to high temperature stress, providing a theoretical basis for improving the ability to adapt to high temperature environments. creator: Zemiao Tian creator: Mengyu Zhao creator: Junzhen Wang creator: Qian Yang creator: Yini Ma creator: Xinlei Yang creator: Luping Ma creator: Yongzhi Qi creator: Jinbo Li creator: Muriel Quinet creator: BaoSheng Shi creator: Yu Meng uri: https://doi.org/10.7717/peerj.17136 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tian et al. title: The comparative plastisphere microbial community profile at Kung Wiman beach unveils potential plastic-specific degrading microorganisms link: https://peerj.com/articles/17165 last-modified: 2024-04-05 description: BackgroundPlastic waste is a global environmental issue that impacts the well-being of humans, animals, plants, and microorganisms. Microplastic contamination has been previously reported at Kung Wiman Beach, located in Chanthaburi province along with the Eastern Gulf of Thailand. Our research aimed to study the microbial population of the sand and plastisphere and isolate microorganisms with potential plastic degradation activity.MethodsPlastic and sand samples were collected from Kung Wiman Beach for microbial isolation on agar plates. The plastic samples were identified by Fourier-transform infrared spectroscopy. Plastic degradation properties were evaluated by observing the halo zone on mineral salts medium (MSM) supplemented with emulsified plastics, including polystyrene (PS), polylactic acid (PLA), polyvinyl chloride (PVC), and bis (2-hydroxyethyl) terephthalate (BHET). Bacteria and fungi were identified by analyzing nucleotide sequence analysis of the 16S rRNA and internal transcribed spacer (ITS) regions, respectively. 16S and ITS microbiomes analysis was conducted on the total DNA extracted from each sample to assess the microbial communities.ResultsOf 16 plastic samples, five were identified as polypropylene (PP), four as polystyrene (PS), four as polyethylene terephthalate (PET), two as high-density polyethylene (HDPE), and one sample remained unidentified. Only 27 bacterial and 38 fungal isolates were found to have the ability to degrade PLA or BHET on MSM agar. However, none showed degradation capabilities for PS or PVC on MSM agar. Notably, Planococcus sp. PP5 showed the highest hydrolysis capacity of 1.64 ± 0.12. The 16S rRNA analysis revealed 13 bacterial genera, with seven showing plastic degradation abilities: Salipiger, Planococcus, Psychrobacter, Shewanella, Jonesia, Bacillus, and Kocuria. This study reports, for the first time of the BHET-degrading properties of the genera Planococcus and Jonesia. Additionally, The ITS analysis identified nine fungal genera, five of which demonstrated plastic degradation abilities: Aspergillus, Penicillium, Peacilomyces, Absidia, and Cochliobolus. Microbial community composition analysis and linear discriminant analysis effect size revealed certain dominant microbial groups in the plastic and sand samples that were absent under culture-dependent conditions. Furthermore, 16S and ITS amplicon microbiome analysis revealed microbial groups were significantly different in the plastic and sand samples collected.ConclusionsWe reported on the microbial communities found on the plastisphere at Kung Wiman Beach and isolated and identified microbes with the capacity to degrade PLA and BHET. creator: Nutsuda Chaimusik creator: Natthaphong Sombuttra creator: Yeampon Nakaramontri creator: Penjai Sompongchaiyakul creator: Chawalit Charoenpong creator: Bungonsiri Intra creator: Jirayut Euanorasetr uri: https://doi.org/10.7717/peerj.17165 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chaimusik et al. title: The role of CXCL10 as a biomarker for immunological response among patients with leprosy: a systematic literature review link: https://peerj.com/articles/17170 last-modified: 2024-04-05 description: IntroductionInvolvement of a chemokine known as C-X-C motif chemokine ligand 10 or CXCL10 in the immunopathology of leprosy has emerged as a possible immunological marker for leprosy diagnosis and needed to be investigate further. The purpose of this systematic review is to assess CXCL10’s potential utility as a leprosy diagnostic tool and evaluation of therapy.MethodsThis systematic review is based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020. A thorough search was carried out to find relevant studies only in English and limited in humans published up until September 2023 using PubMed, Scopus, Science Direct, and Wiley Online Library database with keywords based on medical subject headings (MeSH) and no exclusion criteria. The Newcastle-Ottawa Scale (NOS) was utilized for quality assessment, while the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS) was utilized for assessing the risk of bias. Additionally, a narrative synthesis was conducted to provide a comprehensive review of the results.ResultsWe collected a total of 115 studies using defined keywords and 82 studies were eliminated after titles and abstracts were screened. We assessed the eligibility of the remaining 26 reports in full text and excluded four studies due to inappropriate study design and two studies with incomplete outcome data. There were twenty included studies in total with total of 2.525 samples. The included studies received NOS quality evaluation scores ranging from 6 to 8. The majority of items in the risk bias assessment, using RoBANS, across all included studies yielded low scores. However, certain items related to the selection of participants and confounding variables showed variations. Most of studies indicate that CXCL10 may be a helpful immunological marker for leprosy diagnosis, particularly in leprosy reactions as stated in seven studies. The results are better when paired with other immunological markers. Its effectiveness in field-friendly diagnostic tools makes it one of the potential biomarkers used in diagnosing leprosy patients. Additionally, CXCL10 may be utilized to assess the efficacy of multidrug therapy (MDT) in leprosy patients as stated in three studies.ConclusionThe results presented in this systematic review supports the importance of CXCL10 in leprosy diagnosis, particularly in leprosy responses and in tracking the efficacy of MDT therapy. Using CXCL10 in clinical settings might help with leprosy early diagnosis. Yet the findings are heterogenous, thus more investigation is required to determine the roles of CXCL10 in leprosy while taking into account for additional confounding variables. creator: Flora Ramona Sigit Prakoeswa creator: Nabila Haningtyas creator: Listiana Masyita Dewi creator: Ellen Josephine Handoko creator: Moch. Tabriz Azenta creator: Muhana Fawwazy Ilyas uri: https://doi.org/10.7717/peerj.17170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Prakoeswa et al. title: Selective concentration of iron, titanium, and zirconium substrate minerals within Gregory’s diverticulum, an organ unique to derived sand dollars (Echinoidea: Scutelliformes) link: https://peerj.com/articles/17178 last-modified: 2024-04-05 description: Gregory’s diverticulum, a digestive tract structure unique to a derived group of sand dollars (Echinoidea: Scutelliformes), is filled with sand grains obtained from the substrate the animals inhabit. The simple methods of shining a bright light through a specimen or testing response to a magnet can reveal the presence of a mineral-filled diverticulum. Heavy minerals with a specific gravity of >2.9 g/cm3 are selectively concentrated inside the organ, usually at concentrations one order of magnitude, or more, greater than found in the substrate. Analyses of diverticulum content for thirteen species from nine genera, using optical mineralogy, powder X-ray diffraction, scanning electron microscopy and energy dispersive X-ray spectroscopy, as well as micro-computed tomography shows the preference for selection of five major heavy minerals: magnetite (Fe3O4), hematite (Fe2O3), ilmenite (FeTiO3), rutile (TiO2), and zircon (ZrSiO4). Minor amounts of heavy or marginally heavy amphibole, pyroxene and garnet mineral grains may also be incorporated. In general, the animals exhibit a preference for mineral grains with a specific gravity of >4.0 g/cm3, although the choice is opportunistic and the actual mix of mineral species depends on the mineral composition of the substrate. The animals also select for grain size, with mineral grains generally in the range of 50 to 150 μm, and do not appear to alter this preference during ontogeny. A comparison of analytical methods demonstrates that X-ray attenuation measured using micro-computed tomography is a reliable non-destructive method for heavy mineral quantification when supported by associated analyses of mineral grains extracted destructively from specimens or from substrate collected together with the specimens. Commonalities in the electro-chemical surface properties of the ingested minerals suggest that such characteristics play an important role in the selection process. creator: Louis G. Zachos creator: Alexander Ziegler uri: https://doi.org/10.7717/peerj.17178 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zachos and Ziegler title: Carnivore coexistence without competition: giant otters are more nocturnal around dens than sympatric neotropical otters link: https://peerj.com/articles/17244 last-modified: 2024-04-05 description: Nocturnal activity of tropical otters is rarely reported. To date no studies have documented den use by sympatric giant (Pteronura brasiliensis) and neotropical otters (Lontra longicaudis). We used camera-traps to monitor den use by sympatric otters along an equatorial Amazonian river. Camera-traps provided evidence that giant otters were more nocturnal around dens than sympatric neotropical otters. Nocturnal activity was recorded in 11% of giant otter photos (n = 14 of 125 photos), but was recorded only once for neotropical otters. Den use by giant and neotropical otters overlapped spatially and temporally but not concurrently. We hypothesize that previously reported nocturnal activity in neotropical otters is facilitated by the absence or low density of giant otters. Our results also underscore the need to use complementary techniques together with den counts for monitoring otters as sympatric species can use the same dens. creator: Darren Norris creator: Fernanda Michalski uri: https://doi.org/10.7717/peerj.17244 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Norris and Michalski title: Morphometric and taxonomic approach to describe Heterospio variabilis (Annelida, Longosomatidae), a new species with three size-dependent morphotypes, from the Gulf of California, Eastern Pacific link: https://peerj.com/articles/17093 last-modified: 2024-04-04 description: The Longosomatidae, a poorly known polychaete family, includes only 23 recognized species; in this study, based on morphometric and taxonomic analyses, we describe a new species with three morphotypes: Heterospio variabilis from the Gulf of California, Mexico. The specimens examined exhibit large morphological variations but were clearly separated from close species due to a unique combination of morphological characters: chaetiger 9 as the first elongated chaetiger, four to eight branchial pairs; chaetae from chaetiger 10 forming rings in two rows, posterior row with thin and robust capillaries, anterior row with subuluncini, aristate spines, acicular spines and thick acicular spines. With the discriminant analysis, carried out on 11 morphometric characters, the presence of three morphological groups were recognized (Wilks’ lambda= 0.093, p = 0.0001). However, the variables selected to discriminate the specimens (partial Wilks’ lambda > 0.57) were correlated to their size: number of branchiae, body width, prostomium width, rate length CH9/CH1-CH8, length CH1-CH8 and length CH9 (r > 0.5). So, we concluded that they belong to a single species with three morphotypes: morpho A with eight branchial pairs, morpho B with 5–6–7 pairs and morpho C with 4 pairs. No correlations between the distribution of the distinct morphotypes along the eastern gulf shelf and the environmental conditions where they settle were detected. creator: Pablo Hernández-Alcántara creator: Vivianne Solis-Weiss uri: https://doi.org/10.7717/peerj.17093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hernández-Alcántara and Solis-Weiss title: Atherosclerosis, gut microbiome, and exercise in a meta-omics perspective: a literature review link: https://peerj.com/articles/17185 last-modified: 2024-04-04 description: BackgroundCardiovascular diseases are the leading cause of death worldwide, significantly impacting public health. Atherosclerotic cardiovascular diseases account for the majority of these deaths, with atherosclerosis marking the initial and most critical phase of their pathophysiological progression. There is a complex relationship between atherosclerosis, the gut microbiome’s composition and function, and the potential mediating role of exercise. The adaptability of the gut microbiome and the feasibility of exercise interventions present novel opportunities for therapeutic and preventative approaches.MethodologyWe conducted a comprehensive literature review using professional databases such as PubMed and Web of Science. This review focuses on the application of meta-omics techniques, particularly metagenomics and metabolomics, in studying the effects of exercise interventions on the gut microbiome and atherosclerosis.ResultsMeta-omics technologies offer unparalleled capabilities to explore the intricate connections between exercise, the microbiome, the metabolome, and cardiometabolic health. This review highlights the advancements in metagenomics and metabolomics, their applications in research, and examines how exercise influences the gut microbiome. We delve into the mechanisms connecting these elements from a metabolic perspective. Metagenomics provides insight into changes in microbial strains post-exercise, while metabolomics sheds light on the shifts in metabolites. Together, these approaches offer a comprehensive understanding of how exercise impacts atherosclerosis through specific mechanisms.ConclusionsExercise significantly influences atherosclerosis, with the gut microbiome serving as a critical intermediary. Meta-omics technology holds substantial promise for investigating the gut microbiome; however, its methodologies require further refinement. Additionally, there is a pressing need for more extensive cohort studies to enhance our comprehension of the connection among these element. creator: Haotian Tang creator: Yanqing Huang creator: Didi Yuan creator: Junwen Liu uri: https://doi.org/10.7717/peerj.17185 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tang et al. title: Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host link: https://peerj.com/articles/17206 last-modified: 2024-04-04 description: Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates. creator: Dennis Carhuaricra-Huaman creator: Irys H.L. Gonzalez creator: Patricia L. Ramos creator: Aline M. da Silva creator: Joao C. Setubal uri: https://doi.org/10.7717/peerj.17206 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Carhuaricra-Huaman et al. title: Preparation and characterization of vitamin E/calcium/soy protein isolate nanoparticles for soybean milk beverage fortification link: https://peerj.com/articles/17007 last-modified: 2024-04-03 description: Soybean milk is a rich plant-based source of protein, and phenolic compounds. This study compared the nutritional value of soybean milk, flour, soy protein isolate (SPI) and evaluated the impact of prepared vitamin E/calcium salt/soy protein isolate nanoparticles (ECSPI-NPs) on fortification of developed soybean milk formulations. Results indicated that soybean flour protein content was 40.50 g/100 g, that fulfills 81% of the daily requirement (DV%), the unsaturated fatty acids (USFs), oleic and linoleic content was 21.98 and 56.7%, respectively, of total fatty acids content. In soybean milk, essential amino acids, threonine, leucine, lysine achieved 92.70, 90.81, 77.42% of amino acid scores (AAS) requirement values respectively. Ferulic acid was the main phenolic compound in soybean flour, milk and SPI (508.74, 13.28, 491.78 µg/g). Due to the moisture content of soybean milk (88.50%) against (7.10%) in soybean flour, the latest showed higher nutrients concentrations. The prepared calcium (20 mM/10 g SPI) and vitamin E (100 mg/g SPI) nanoparticles (ECSPI-NPs) exhibited that they were effectively synthesized under transmission electron microscope (TEM), stability in the zeta sizer analysis and safety up to IC50 value (202 ug/mL) on vero cell line. ECSPI-NPs fortification (NECM) enhanced significantly phenolic content (149.49 mg/mL), taste (6.10), texture (6.70) and consumer overall acceptance (6.54). Obtained results encourage the application of the prepared ECSPI-NPs for further functional foods applications. creator: Heba A. I. M. Taha creator: Neveen F. M. Agamy creator: Tarek N. Soliman creator: Nashwa M. Younes creator: Hesham Ali El-Enshasy creator: Amira M. G. Darwish uri: https://doi.org/10.7717/peerj.17007 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Taha et al. title: Tailoring transcranial alternating current stimulation based on endogenous event-related P3 to modulate premature responses: a feasibility study link: https://peerj.com/articles/17144 last-modified: 2024-04-03 description: BackgroundTranscranial alternating current stimulation (tACS) is a brain stimulation method for modulating ongoing endogenous oscillatory activity at specified frequency during sensory and cognitive processes. Given the overlap between event-related potentials (ERPs) and event-related oscillations (EROs), ERPs can be studied as putative biomarkers of the effects of tACS in the brain during cognitive/sensory task performance.ObjectiveThis preliminary study aimed to test the feasibility of individually tailored tACS based on individual P3 (latency and frequency) elicited during a cued premature response task. Thus, tACS frequency was individually tailored to match target-P3 ERO for each participant. Likewise, the target onset in the task was adjusted to match the tACS phase and target-P3 latency.MethodsTwelve healthy volunteers underwent tACS in two separate sessions while performing a premature response task. Target-P3 latency and ERO were calculated in a baseline block during the first session to allow a posterior synchronization between the tACS and the endogenous oscillatory activity. The cue and target-P3 amplitudes, delta/theta ERO, and power spectral density (PSD) were evaluated pre and post-tACS blocks.ResultsTarget-P3 amplitude significantly increased after activetACS, when compared to sham. Evoked-delta during cue-P3 was decreased after tACS. No effects were found for delta ERO during target-P3 nor for the PSD and behavioral outcomes.ConclusionThe present findings highlight the possible effect of phase synchronization between individualized tACS parameters and endogenous oscillatory activity, which may result in an enhancement of the underlying process (i.e., an increase of target-P3). However, an unsuccessful synchronization between tACS and EEG activity might also result in a decrease in the evoked-delta activity during cue-P3. Further studies are needed to optimize the parameters of endogenous activity and tACS synchronization. The implications of the current results for future studies, including clinical studies, are further discussed since transcranial alternating current stimulation can be individually tailored based on endogenous event-related P3 to modulate responses. creator: Augusto J. Mendes creator: Alberto Lema creator: Sandra Carvalho creator: Jorge Leite uri: https://doi.org/10.7717/peerj.17144 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mendes et al. title: Relationship between intended force and actual force: comparison between athletes and non-athletes link: https://peerj.com/articles/17156 last-modified: 2024-04-03 description: This cross-sectional study aimed to investigate whether athletes (ATHL) and non-athletes (NON-ATHL) individuals had similar accuracy in matching intended to actual force during ballistic (BAL) and tonic (TON) isometric contractions. In this cross-sectional study, the subjects were divided into ATHL (n = 20; 22.4 ± 2.3 yrs; 73.2 ± 15.7 kg; 1.76 ± 0.08 m) and NON-ATHL (n = 20; 24.6 ± 2.4 yrs; 68.2 ± 15.0 kg; 1.73 ± 0.1 m) groups. The isometric quadriceps strength was measured with a load cell applied to a custom-built chair. For each condition, subjects performed at first three maximal voluntary isometric contractions (MVIC) as reference. Then, subjects had to match three intended force intensities expressed in percentage of the MVIC (i.e., 25%, 50%, and 75%) without any external feedback. Subjects performed three trials for each force intensity. The accuracy (AC) was calculated as the absolute difference in percentage between the intended and the actual force. A Likert scale was administered for each trial to assess the subjective matching between the intended and the actual force. Statistical analysis showed that the ATHL group was more accurate (p < 0.001) than the NON-ATHL group. In contrast, the AC (p < 0.001) was lower when the force intensities increased independently from the group. Moreover, significantly higher AC (p < 0.001) and lower aggregate Likert scores (p < 0.001) were found in BAL than TON conditions. These results suggest that (i) sports practice could enhance muscle recruitment strategies by increasing the AC in the isometric task; (ii) differences between intended and actual force appeared to be intensity-dependent with lower AC at high force intensities; (iii) different control systems act in modulating BAL and TON contractions. creator: Alex Rizzato creator: Giovanni Cantarella creator: Elisa Basso creator: Antonio Paoli creator: Luca Rotundo creator: Patrizia Bisiacchi creator: Giuseppe Marcolin uri: https://doi.org/10.7717/peerj.17156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rizzato et al. title: Investigating mortality salience as a potential causal influence and moderator of responses to laboratory pain link: https://peerj.com/articles/17204 last-modified: 2024-04-03 description: BackgroundBecause pain can have profound ramifications for quality of life and daily functioning, understanding nuances in the interplay of psychosocial experiences with pain perception is vital for effective pain management. In separate lines of research, pain resilience and mortality salience have emerged as potentially important psychological correlates of reduced pain severity and increased tolerance of pain. However, to date, there has been a paucity of research examining potentially interactive effects of these factors on pain perception. To address this gap, the present experiment investigated mortality salience as a causal influence on tolerance of laboratory pain and a moderator of associations between pain resilience and pain tolerance within a Chinese sample.MethodsParticipants were healthy young Chinese adults (86 women, 84 men) who first completed a brief initial cold pressor test (CPT) followed by measures of demographics and pain resilience. Subsequently, participants randomly assigned to a mortality salience (MS) condition completed two open-ended essay questions in which they wrote about their death as well as a death anxiety scale while those randomly assigned to a control condition completed analogous tasks about watching television. Finally, all participants engaged in a delay task and a second CPT designed to measure post-manipulation pain tolerance and subjective pain intensity levels.ResultsMS condition cohorts showed greater pain tolerance than controls on the post-manipulation CPT, though pain intensity levels did not differ between groups. Moderator analyses indicated that the relationship between the behavior perseverance facet of pain resilience and pain tolerance was significantly stronger among MS condition participants than controls.ConclusionsThis experiment is the first to document potential causal effects of MS on pain tolerance and Ms as a moderator of the association between self-reported behavior perseverance and behavioral pain tolerance. Findings provide foundations for extensions within clinical pain samples. creator: Beibei You creator: Hongwei Wen creator: Todd Jackson uri: https://doi.org/10.7717/peerj.17204 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 You et al. title: Seasonal fluctuations of litter and soil Collembola and their drivers in rainforest and plantation systems link: https://peerj.com/articles/17125 last-modified: 2024-04-01 description: Rainforest conversion and expansion of plantations in tropical regions change local microclimate and are associated with biodiversity decline. Tropical soils are a hotspot of animal biodiversity and may sensitively respond to microclimate changes, but these responses remain unexplored. To address this knowledge gap, here we investigated seasonal fluctuations in density and community composition of Collembola, a dominant group of soil invertebrates, in rainforest, and in rubber and oil palm plantations in Jambi province (Sumatra, Indonesia). Across land-use systems, the density of Collembola in the litter was at a maximum at the beginning of the wet season, whereas in soil it generally varied little. The community composition of Collembola changed with season and the differences between land-use systems were most pronounced at the beginning of the dry season. Water content, pH, fungal and bacterial biomarkers, C/N ratio and root biomass were identified as factors related to seasonal variations in species composition of Collembola across different land-use systems. We conclude that (1) conversion of rainforest into plantation systems aggravates detrimental effects of low moisture during the dry season on soil invertebrate communities; (2) Collembola communities are driven by common environmental factors across land-use systems, with water content, pH and food availability being most important; (3) Collembola in litter are more sensitive to climatic variations than those in soil. Overall, the results document the sensitivity of tropical soil invertebrate communities to seasonal climatic variations, which intensifies the effects of the conversion of rainforest into plantation systems on soil biodiversity. creator: Winda Ika Susanti creator: Valentyna Krashevska creator: Rahayu Widyastuti creator: Christian Stiegler creator: Dodo Gunawan creator: Stefan Scheu creator: Anton M. Potapov uri: https://doi.org/10.7717/peerj.17125 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Susanti et al. title: Health and ecological risk of heavy metals in agricultural soils related to Tungsten mining in Southern Jiangxi Province, China link: https://peerj.com/articles/17200 last-modified: 2024-04-01 description: BackgroundDayu County, a major tungsten producer in China, experiences severe heavy metal pollution. This study evaluated the pollution status, the accumulation characteristics in paddy rice, and the potential ecological risks of heavy metals in agricutural soils near tungsten mining areas of Dayu County. Furthermore, the impacts of soil properties on the accumulation of heavy metals in soil were explored.MethodsThe geo-accumulation index (Igeo), the contamination factor (CF), and the pollution load index (PLI) were used to evaluate the pollution status of metals (As, Cd, Cu, Cr, Pb, Mo, W, and Zn) in soils. The ecological risk factor (RI) was used to assess the potential ecological risks of heavy metals in soil. The health risks and accumulation of heavy metals in paddy rice were evaluated using the health risk index and the translocation factor (TF), respectively. Pearson’s correlation coefficient was used to discuss the influence of soil factors on heavy metal contents in soil.ResultsThe concentrations of metals exceeded the respective average background values for soils (As: 10.4, Cd: 0.10, Cu: 20.8, Cr: 48.0, Pb: 32.1, Mo: 0.30, W: 4.93, Zn: 69.0, mg/kg). The levels of As, Cd, Mo, and tungsten(W) exceeded the risk screening values for Chinese agricultural soil contamination and the Dutch standard. The mean concentrations of the eight tested heavy metals followed the order FJ-S > QL > FJ-N > HL > CJ-E > CJ-W, with a significant distribution throughout the Zhangjiang River basin. Heavy metals, especially Cd, were enriched in paddy rice. The Igeo and CF assessment indicated that the soil was moderately to heavily polluted by Mo, W and Cd, and the PLI assessment indicated the the sites of FJ-S and QL were extremely severely polluted due to the contribution of Cd, Mo and W. The RI results indicated that Cd posed the highest risk near tungsten mining areas. The non-carcinogenic and total carcinogenic risks were above the threshold values (non-carcinogenic risk by HQ > 1, carcinogenic risks by CR > 1 × 10−4 a−1) for As and Cd. Correlation analysis indicated that K2O, Na2O, and CaO are main factors affecting the accumulation and migration of heavy metals in soils and plants. Our findings reveal significant contamination of soils and crops with heavy metals, especially Cd, Mo, and W, near mining areas, highlighting serious health risks. This emphasizes the need for immediate remedial actions and the implementation of stringent environmental policies to safeguard health and the environment. creator: Jinhu Lai creator: Yan Ni creator: Jinying Xu creator: Daishe Wu uri: https://doi.org/10.7717/peerj.17200 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lai et al. title: Spatial habitat suitability prediction of essential oil wild plants on Indonesia’s degraded lands link: https://peerj.com/articles/17210 last-modified: 2024-04-01 description: BackgroundEssential oils are natural products of aromatic plants with numerous uses. Essential oils have been traded worldwide and utilized in various industries. Indonesia is the sixth largest essential oil producing country, but land degradation is a risk to the continuing extraction and utilization of natural products. Production of essential oil plants on degraded lands is a potential strategy to mitigate this risk. This study aimed to identify degraded lands in Indonesia that could be suitable habitats for five wild native essential oil producing plants, namely Acronychia pedunculata (L.) Miq., Baeckea frutescens L., Cynometra cauliflora L., Magnolia montana (Blume) Figlar, and Magnolia sumatrana var. glauca (Blume) Figlar & Noot using various species distribution models.MethodsThe habitat suitability of these species was predicted by comparing ten species distribution models, including Bioclim, classification and regression trees (CART), flexible discriminant analysis (FDA), Maxlike, boosted regression trees (BRT), multivariate adaptive regression splines (MARS), generalized linear models (GLM), Ranger, support vector machine (SVM), and Random Forests (RF). Bioclimatic, topographic and soil variables were used as the predictors of the model habitat suitability. The models were evaluated according to their AUC and TSS metrics. Model selection was based on ranking performance. The total suitable area for five native essential oil producing plants in Indonesia’s degraded lands was derived by overlaying the models with degraded land locations.ResultsThe habitat suitability model for these species was well predicted with an AUC value >0.8 and a TSS value >0.7. The most important predictor variables affecting the habitat suitability of these species are mean temperature of wettest quarter, precipitation seasonality, precipitation of warmest quarter, precipitation of coldest quarter, cation exchange capacity, nitrogen, sand, and soil organic carbon. C. cauliflora has the largest predicted suitable area, followed by M. montana, B. frutescens, M. sumatrana var. glauca, and A. pedunculata. The overlapping area between predictive habitat suitability and degraded lands indicates that the majority of degraded lands in Indonesia’s forest areas are suitable for those species.ConclusionThe degraded lands predicted as suitable habitats for five native essential oil producing plants were widely spread throughout Indonesia, mostly in its main islands. These findings can be used by the Indonesian Government for evaluating policies for degraded land utilization and restorations that can enhance the lands’ productivity. creator: Elga Renjana creator: Elok Rifqi Firdiana creator: Melisnawati H. Angio creator: Linda Wige Ningrum creator: Intani Quarta Lailaty creator: Apriyono Rahadiantoro creator: Irfan Martiansyah creator: Rizmoon Zulkarnaen creator: Ayyu Rahayu creator: Puguh Dwi Raharjo creator: Ilham Kurnia Abywijaya creator: Didi Usmadi creator: Rosniati Apriani Risna creator: Wendell P. Cropper, Jr creator: Angga Yudaputra uri: https://doi.org/10.7717/peerj.17210 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Renjana et al.