title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2024-05 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Metabolite analysis reveals flavonoids accumulation during flower development in Rhododendron pulchrum sweet (Ericaceae) link: https://peerj.com/articles/17325 last-modified: 2024-05-31 description: The azalea (Rhododendron simsii Planch.) is an important ornamental woody plant with various medicinal properties due to its phytochemical compositions and components. However little information on the metabolite variation during flower development in Rhododendron has been provided. In our study, a comparative analysis of the flavonoid profile was performed in Rhododendron pulchrum sweet at three stages of flower development, bud (stage 1), partially open flower (stage 2), and full bloom (stage 3). A total of 199 flavonoids, including flavone, flavonol, flavone C-glycosides, flavanone, anthocyanin, and isoflavone were identified. In hierarchical clustering analysis (HCA) and principal component analysis (PCA), the accumulation of flavonoids displayed a clear development stage variation. During flower development, 78 differential accumulated metabolites (DAMs) were identified, and most were enriched to higher levels at the full bloom stage. A total of 11 DAMs including flavone (chrysin, chrysoeriol O-glucuronic acid, and chrysoeriol O-hexosyl-O-pentoside), isoflavone (biochanin A), and flavonol (3,7-di-O-methyl quercetin and isorhamnetin) were significantly altered at three stages. In particular, 3,7-di-O-methyl quercetin was the top increased metabolite during flower development. Furthermore, integrative analyses of metabolomic and transcriptomic were conducted, revealing that the contents of isoflavone, biochanin A, glycitin, and prunetin were correlated with the expression of 2-hydroxyisoflavanone dehydratase (HIDH), which provide insight into the regulatory mechanism that controls isoflavone biosynthesis in R. pulchrum. This study will provide a new reference for increasing desired metabolites effectively by more accurate or appropriate genetic engineering strategies. creator: Qiaofeng Yang creator: Zhiliang Li creator: Yuting Ma creator: Linchuan Fang creator: Yan Liu creator: Xinyu Zhu creator: Hongjin Dong creator: Shuzhen Wang uri: https://doi.org/10.7717/peerj.17325 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Yang et al. title: Association between yoga and related contextual factors with moderate-to-vigorous physical activity among children and youth aged 5 to 17 years across five Indian states link: https://peerj.com/articles/17369 last-modified: 2024-05-31 description: Physical inactivity is one of the four key preventable risk factors, along with unhealthy diet, tobacco use, and alcohol consumption, underlying most noncommunicable diseases. Promoting physical activity is particularly important among children and youth, whose active living behaviours often track into adulthood. Incorporating yoga, an ancient practice that originated in India, can be a culturally-appropriate strategy to promote physical activity in India. However, there is little evidence on whether yoga practice is associated with moderate-to-vigorous physical activity (MVPA) accumulation. Thus, this study aims to understand how yoga practice is associated with MVPA among children and youth in India. Data for this study were obtained during the coronavirus disease lockdown in 2021. Online surveys capturing MVPA, yoga practice, contextual factors, and sociodemographic characteristics, were completed by 5 to 17-year-old children and youth in partnership with 41 schools across 28 urban and rural locations in five states. Linear regression analyses were conducted to assess the association between yoga practice and MVPA. After controlling for age, gender, and location, yoga practice was significantly associated with MVPA among children and youth (β = 0.634, p < 0.000). These findings highlight the value of culturally-appropriate activities such as yoga, to promote physical activity among children and youth. Yoga practice might have a particularly positive impact on physical activity among children and youth across the world, owing to its growing global prevalence. creator: Jamin Patel creator: Sheriff Ibrahim creator: Jasmin Bhawra creator: Anuradha Khadilkar creator: Tarun Reddy Katapally uri: https://doi.org/10.7717/peerj.17369 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Patel et al. title: Current and future scenarios of suitability and expansion of cassava brown streak disease, Bemisia tabaci species complex, and cassava planting in Africa link: https://peerj.com/articles/17386 last-modified: 2024-05-31 description: Cassava (Manihot esculenta) is among the most important staple crops globally, with an imperative role in supporting the Sustainable Development Goal of ‘Zero hunger’. In sub-Saharan Africa, it is cultivated mainly by millions of subsistence farmers who depend directly on it for their socio-economic welfare. However, its yield in some regions has been threatened by several diseases, especially the cassava brown streak disease (CBSD). Changes in climatic conditions enhance the risk of the disease spreading to other planting regions. Here, we characterise the current and future distribution of cassava, CBSD and whitefly Bemisia tabaci species complex in Africa, using an ensemble of four species distribution models (SDMs): boosted regression trees, maximum entropy, generalised additive model, and multivariate adaptive regression splines, together with 28 environmental covariates. We collected 1,422 and 1,169 occurrence records for cassava and Bemisia tabaci species complex from the Global Biodiversity Information Facility and 750 CBSD occurrence records from published literature and systematic surveys in East Africa. Our results identified isothermality as having the highest contribution to the current distribution of cassava, while elevation was the top predictor of the current distribution of Bemisia tabaci species complex. Cassava harvested area and precipitation of the driest month contributed the most to explain the current distribution of CBSD outbreaks. The geographic distributions of these target species are also expected to shift under climate projection scenarios for two mid-century periods (2041–2060 and 2061–2080). Our results indicate that major cassava producers, like Cameron, Ivory Coast, Ghana, and Nigeria, are at greater risk of invasion of CBSD. These results highlight the need for firmer agricultural management and climate-change mitigation actions in Africa to combat new outbreaks and to contain the spread of CBSD. creator: Geofrey Sikazwe creator: Rosita Endah epse Yocgo creator: Pietro Landi creator: David M. Richardson creator: Cang Hui uri: https://doi.org/10.7717/peerj.17386 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sikazwe et al. title: Gut microbiota alterations in postmenopausal women with osteoporosis and osteopenia from Shanghai, China link: https://peerj.com/articles/17416 last-modified: 2024-05-31 description: BackgroundThe importance of the gut microbiota in maintaining bone homeostasis has been increasingly emphasized by recent research. This study aimed to identify whether and how the gut microbiome of postmenopausal women with osteoporosis and osteopenia may differ from that of healthy individuals.MethodsFecal samples were collected from 27 individuals with osteoporosis (OP), 44 individuals with osteopenia (ON), and 23 normal controls (NC). The composition of the gut microbial community was analyzed by 16S rRNA gene sequencing.ResultsNo significant difference was found in the microbial composition between the three groups according to alpha and beta diversity. At the phylum level, Proteobacteria and Fusobacteriota were significantly higher and Synergistota was significantly lower in the ON group than in the NC group. At the genus level, Roseburia, Clostridia_UCG.014, Agathobacter, Dialister and Lactobacillus differed between the OP and NC groups as well as between the ON and NC groups (p < 0.05). Linear discriminant effect size (LEfSe) analysis results showed that one phylum community and eighteen genus communities were enriched in the NC, ON and OP groups, respectively. Spearman correlation analysis showed that the abundance of the Dialister genus was positively correlated with BMD and T score at the lumbar spine (p < 0.05). Functional predictions revealed that pathways relevant to amino acid biosynthesis, vitamin biosynthesis, and nucleotide metabolism were enriched in the NC group. On the other hand, pathways relevant to metabolites degradation and carbohydrate metabolism were mainly enriched in the ON and OP groups respectively.ConclusionsOur findings provide new epidemiologic evidence regarding the relationship between the gut microbiota and postmenopausal bone loss, laying a foundation for further exploration of therapeutic targets for the prevention and treatment of postmenopausal osteoporosis (PMO). creator: Jiaqing Ji creator: Zhengrong Gu creator: Na Li creator: Xin Dong creator: Xiong Wang creator: Qiang Yao creator: Zhongxiao Zhang creator: Li Zhang creator: Liehu Cao uri: https://doi.org/10.7717/peerj.17416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ji et al. title: Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan link: https://peerj.com/articles/17420 last-modified: 2024-05-31 description: Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore’s Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research. creator: Khush Bakhat Samreen creator: Farkhanda Manzoor uri: https://doi.org/10.7717/peerj.17420 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Samreen and Manzoor title: New records of non-indigenous species from the eastern Mediterranean Sea (Crustacea, Mollusca), with a revision of genus Isognomon (Mollusca: Bivalvia) link: https://peerj.com/articles/17425 last-modified: 2024-05-31 description: We report new data on non-indigenous invertebrates from the Mediterranean Sea (four ostracods and 20 molluscs), including five new records for the basin: the ostracods Neomonoceratina iniqua, Neomonoceratina aff. mediterranea, Neomonoceratina cf. entomon, Loxoconcha cf. gisellae (Arthropoda: Crustacea)–the first records of non-indigenous ostracods in the Mediterranean–and the bivalve Striarca aff. symmetrica (Mollusca). Additionally, we report for the first time Electroma vexillum from Israel, and Euthymella colzumensis, Joculator problematicus, Hemiliostraca clandestina, Pyrgulina nana, Pyrgulina microtuber, Turbonilla cangeyrani, Musculus aff. viridulus and Isognomon bicolor from Cyprus. We also report the second record of Fossarus sp. and of Cerithiopsis sp. cf. pulvis in the Mediterranean Sea, the first live collected specimens of Oscilla galilae from Cyprus and the northernmost record of Gari pallida in Israel (and the Mediterranean). Moreover, we report the earliest records of Rugalucina angela, Ervilia scaliola and Alveinus miliaceus in the Mediterranean Sea, backdating their first occurrence in the basin by 3, 5 and 7 years, respectively. We provide new data on the presence of Spondylus nicobaricus and Nudiscintilla aff. glabra in Israel. Finally, yet importantly, we use both morphological and molecular approaches to revise the systematics of the non-indigenous genus Isognomon in the Mediterranean Sea, showing that two species currently co-occur in the basin: the Caribbean I. bicolor, distributed in the central and eastern Mediterranean, and the Indo-Pacific I. aff. legumen, at present reported only from the eastern Mediterranean and whose identity requires a more in-depth taxonomic study. Our work shows the need of taxonomic expertise and investigation, the necessity to avoid the unfounded sense of confidence given by names in closed nomenclature when the NIS belong to taxa that have not enjoyed ample taxonomic work, and the necessity to continue collecting samples–rather than relying on visual censuses and bio-blitzes–to enable accurate detection of non-indigenous species. creator: Paolo G. Albano creator: Yuanyuan Hong creator: Jan Steger creator: Moriaki Yasuhara creator: Stefano Bartolini creator: Cesare Bogi creator: Marija Bošnjak creator: Marina Chiappi creator: Valentina Fossati creator: Mehmet Fatih Huseyinoglu creator: Carlos Jiménez creator: Hadas Lubinevsky creator: Arseniy R. Morov creator: Simona Noè creator: Magdalene Papatheodoulou creator: Vasilis Resaikos creator: Martin Zuschin creator: Tamar Guy-Haim uri: https://doi.org/10.7717/peerj.17425 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Albano et al. title: De novo assembly and characterization of the transcriptome of Morchella esculenta growth with selenium supplementation link: https://peerj.com/articles/17426 last-modified: 2024-05-31 description: Although Morchella esculenta (L.) Pers. is an edible and nutritious mushroom with significant selenium (Se)-enriched potential, its biological response to selenium stimuli remains unclear. This study explored the effect of selenium on mushroom growth and the global gene expression profiles of M. esculenta. While 5 µg mL−1selenite treatment slightly promoted mycelia growth and mushroom yield, 10 µg mL−1significantly inhibited growth. Based on comparative transcriptome analysis, samples treated with 5 µg mL−1 and 10 µg mL−1 of Se contained 16,061 (452 upregulated and 15,609 downregulated) and 14,155 differentially expressed genes (DEGs; 800 upregulated and 13,355 downregulated), respectively. Moreover, DEGs were mainly enriched in the cell cycle, meiosis, aminoacyl-tRNA biosynthesis, spliceosome, protein processing in endoplasmic reticulum pathway, and mRNA surveillance pathway in both selenium-treated groups. Among these, MFS substrate transporter and aspartate aminotransferase genes potentially involved in Se metabolism and those linked to redox homeostasis were significantly upregulated, while genes involved in isoflavone biosynthesis and flavonoid metabolism were significantly downregulated. Gene expression levels increased alongside selenite treatment concentration, suggesting that high Se concentrations promoted M. esculenta detoxification. These results can be used to thoroughly explain the potential detoxification and Se enrichment processes in M. esculenta and edible fungi. creator: Mengxiang Du creator: Shengwei Huang creator: Zihan Huang creator: Lijuan Qian creator: Yang Gui creator: Jing Hu creator: Yujun Sun uri: https://doi.org/10.7717/peerj.17426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Du et al. title: A geometric morphometric protocol to correct postmortem body arching in fossil fishes link: https://peerj.com/articles/17436 last-modified: 2024-05-31 description: Postmortem body curvature introduces error in fish morphometric data. Compared to living fish, the causes of such body curvature in fossils may be due to additive taphonomic processes that have been widely studied. However, a protocol that helps to correct its effect upon morphometric data remains unexplored. Here, we test two different mathematical approaches (multivariate regression and the so-called ‘unbending functions’) available to tackle fish geometric morphometric data in two exceptionally preserved gonorynchiformes fossil fishes, Rubiesichthys gregalis and Gordichthys conquensis, from the Las Hoyas deposits (Early Cretaceous, Spain). Although both methods successfully correct body curvature (i.e., removing misleading geometric variation), our results show that traditional approaches applied in living fishes might not be appropriate to fossil ones, because of the additional anatomical alterations. Namely, the best result for 2D fossil fishes is achieved by correcting the arching of the specimens (mathematically “unbending” them). Ultimately, the effect of body curvature on morphometric data is largely taxon independent and morphological diversity mitigates its effect, but size is an important factor to take into account (because larger individuals tend to be less curved). creator: Carla San Román creator: Hugo Martín-Abad creator: Jesús Marugán-Lobón uri: https://doi.org/10.7717/peerj.17436 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 San Román et al. title: EvatCrop: a novel hybrid quasi-fuzzy artificial neural network (ANN) model for estimation of reference evapotranspiration link: https://peerj.com/articles/17437 last-modified: 2024-05-31 description: Reference evapotranspiration (ET0 ) is a significant parameter for efficient irrigation scheduling and groundwater conservation. Different machine learning models have been designed for ET0 estimation for specific combinations of available meteorological parameters. However, no single model has been suggested so far that can handle diverse combinations of available meteorological parameters for the estimation of ET0. This article suggests a novel architecture of an improved hybrid quasi-fuzzy artificial neural network (ANN) model (EvatCrop) for this purpose. EvatCrop yielded superior results when compared with the other three popular models, decision trees, artificial neural networks, and adaptive neuro-fuzzy inference systems, irrespective of study locations and the combinations of input parameters. For real-field case studies, it was applied in the groundwater-stressed area of the Terai agro-climatic region of North Bengal, India, and trained and tested with the daily meteorological data available from the National Centres for Environmental Prediction from 2000 to 2014. The precision of the model was compared with the standard Penman-Monteith model (FAO56PM). Empirical results depicted that the model performances remarkably varied under different data-limited situations. When the complete set of input parameters was available, EvatCrop resulted in the best values of coefficient of determination (R2 = 0.988), degree of agreement (d = 0.997), root mean square error (RMSE = 0.183), and root mean square relative error (RMSRE = 0.034). creator: Gouravmoy Banerjee creator: Uditendu Sarkar creator: Sanway Sarkar creator: Indrajit Ghosh uri: https://doi.org/10.7717/peerj.17437 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Banerjee et al. title: Effect of GnRH agonist down-regulation combined with hormone replacement treatment on reproductive outcomes of frozen blastocyst transfer cycles in women of different ages link: https://peerj.com/articles/17447 last-modified: 2024-05-31 description: ObjectiveTo investigate the effect of GnRH agonist (GnRH-a) down-regulation prior to hormone replacement treatment (HRT) to prepare the endometrium in frozen embryo transfer (FET) cycles in women of different ages.MethodsThis was a retrospective study, and after excluding patients with adenomyosis, endometriosis, severe endometrial adhesions, polycystic ovary syndrome (PCOS), and repeated embryo implantation failures, a total of 4,091 HRT cycles were collected. Patients were divided into group A (<35 years old) and group B (≥35 years old), and each group was further divided into HRT and GnRHa-HRT groups. The clinical outcomes were compared between groups.ResultsThere was no statistically significant difference in clinical outcomes between the HRT and GnRHa-HRT groups among women aged <35 years. In women of advanced age, higher rates of clinical pregnancy and live birth were seen in the GnRHa-HRT group. Logistic regression analysis showed that female age and number of embryos transferred influenced the live birth rate in FET cycles, and in women aged ≥ 35 years, the use of GnRH-a down-regulation prior to HRT improved pregnancy outcomes.ConclusionsIn elderly woman without adenomyosis, endometriosis, PCOS, severe uterine adhesions, and RIF, hormone replacement treatment with GnRH agonist for pituitary suppression can improve the live birth rate of FET cycles. creator: Jianghuan Xie creator: Jieqiang Lu creator: Huina Zhang uri: https://doi.org/10.7717/peerj.17447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xie et al. title: Public transit mobility as a leading indicator of COVID-19 transmission in 40 cities during the first wave of the pandemic link: https://peerj.com/articles/17455 last-modified: 2024-05-31 description: BackgroundThe rapid global emergence of the COVID-19 pandemic in early 2020 created urgent demand for leading indicators to track the spread of the virus and assess the consequences of public health measures designed to limit transmission. Public transit mobility, which has been shown to be responsive to previous societal disruptions such as disease outbreaks and terrorist attacks, emerged as an early candidate.MethodsWe conducted a longitudinal ecological study of the association between public transit mobility reductions and COVID-19 transmission using publicly available data from a public transit app in 40 global cities from March 16 to April 12, 2020. Multilevel linear regression models were used to estimate the association between COVID-19 transmission and the value of the mobility index 2 weeks prior using two different outcome measures: weekly case ratio and effective reproduction number.ResultsOver the course of March 2020, median public transit mobility, measured by the volume of trips planned in the app, dropped from 100% (first quartile (Q1)–third quartile (Q3) = 94–108%) of typical usage to 10% (Q1–Q3 = 6–15%). Mobility was strongly associated with COVID-19 transmission 2 weeks later: a 10% decline in mobility was associated with a 12.3% decrease in the weekly case ratio (exp(β) = 0.877; 95% confidence interval (CI): [0.859–0.896]) and a decrease in the effective reproduction number (β = −0.058; 95% CI: [−0.068 to −0.048]). The mobility-only models explained nearly 60% of variance in the data for both outcomes. The adjustment for epidemic timing attenuated the associations between mobility and subsequent COVID-19 transmission but only slightly increased the variance explained by the models.DiscussionOur analysis demonstrated the value of public transit mobility as a leading indicator of COVID-19 transmission during the first wave of the pandemic in 40 global cities, at a time when few such indicators were available. Factors such as persistently depressed demand for public transit since the onset of the pandemic limit the ongoing utility of a mobility index based on public transit usage. This study illustrates an innovative use of “big data” from industry to inform the response to a global pandemic, providing support for future collaborations aimed at important public health challenges. creator: Jean-Paul R. Soucy creator: Shelby L. Sturrock creator: Isha Berry creator: Duncan J. Westwood creator: Nick Daneman creator: David Fisman creator: Derek R. MacFadden creator: Kevin A. Brown uri: https://doi.org/10.7717/peerj.17455 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Soucy et al. title: A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus) link: https://peerj.com/articles/17482 last-modified: 2024-05-31 description: BackgroundPrevious work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups.MethodsA chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison.ResultsTwelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa.DiscussionThis study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions. creator: Robert S. Cornman uri: https://doi.org/10.7717/peerj.17482 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy link: https://peerj.com/articles/17486 last-modified: 2024-05-31 description: Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in the pig industry but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. The present study aims to identify obese-specific biomarkers and key pathways correlated with ASFD in pigs. The ASF-related mRNA expression dataset GSE136754 was retrieved from the Gene Expression Omnibus (GEO) database and systematically analyzed using a comprehensive bioinformatics method. A total of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in the p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network, consisting of 540 nodes and 1,065 edges, was constructed, and the top ten genes with the highest degree scores—ABL1, HDAC1, CDC42, HDAC2, MRPS5, MRPS10, MDM2, JUP, RPL7L1 and UQCRFS1—were identified as hub genes in the whole PPI network. Especially HDAC1, MDM2, MRPS10 and RPL7L1 were identified as potential robust obese-specific biomarkers due to their significant differences in single gene expression levels and high ROC area; this was further verified by quantitative real-time PCR (qRT-PCR) on abdominal subcutaneous fat samples from obese-type (Saba) and lean-type (Large White) pigs. Additionally, a mRNA-miRNA-lncRNA ceRNA network consisting of four potential biomarkers, 15 miRNAs and 51 lncRNAs was established, and two targeted lncRNAs with more connections, XIST and NEAT1, were identified as potentially important regulatory factors. The findings of this study may provide novel insights into the molecular mechanism involved in ASFD. creator: Yongli Yang creator: Xiaoyi Wang creator: Mingli Li creator: Shuyan Wang creator: Huiyu Wang creator: Qiang Chen creator: Shaoxiong Lu uri: https://doi.org/10.7717/peerj.17486 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Anti-BIRC5 autoantibody serves as a valuable biomarker for diagnosing AFP-negative hepatocellular carcinoma link: https://peerj.com/articles/17494 last-modified: 2024-05-31 description: BackgroundAutoantibodies targeting tumor-associated antigens (TAAbs) have emerged as promising biomarkers for early cancer detection. This research aimed to assess the diagnostic capacity of anti-BIRC5 autoantibody in detecting AFP-negative hepatocellular carcinoma (ANHCC).MethodsThis research was carried out in three stages (discovery phase, validation phase, and evaluation phase) and included a total of 744 participants. Firstly, the anti-BIRC5 autoantibody was discovered using protein microarray, exhibiting a higher positive rate in ANHCC samples (ANHCCs) compared to normal control samples (NCs). Secondly, the anti-BIRC5 autoantibody was validated through enzyme-linked immunosorbent assay (ELISA) in 85 ANHCCs and 85 NCs from two clinical centers (Zhengzhou and Nanchang). Lastly, the diagnostic usefulness of the anti-BIRC5 autoantibody for hepatocellular carcinoma (HCC) was evaluated by ELISA in a cohort consisting of an additional 149 AFP-positive hepatocellular carcinoma samples (APHCCs), 95 ANHCCs and 244 NCs. The association of elevated autoantibody to high expression of BIRC5 in HCC was further explored by the database from prognosis, immune infiltration, DNA methylation, and gene mutation level.ResultsIn the validation phase, the area under the ROC curve (AUC) of anti-BIRC5 autoantibody to distinguish ANHCCs from NCs in Zhengzhou and Nanchang centers was 0.733 and 0.745, respectively. In the evaluation phase, the AUCs of anti-BIRC5 autoantibody for identifying ANHCCs and HCCs from NCs were 0.738 and 0.726, respectively. Furthermore, when combined with AFP, the AUC for identifying HCCs from NCs increased to 0.914 with a sensitivity of 77.5% and specificity of 91.8%. High expression of BIRC5 gene is not only correlated with poor prognosis of HCCs, but also significantly associated with infiltration of immune cells, DNA methylation, and gene mutation.ConclusionThe findings suggest that the anti-BIRC5 autoantibody could serve as a potential biomarker for ANHCC, in addition to its supplementary role alongside AFP in the diagnosis of HCC. Next, we can carry out specific verification and explore the function of anti-BIRC5 autoantibody in the occurrence and development of HCC. creator: Qing Li creator: Haiyan Liu creator: Han Wang creator: Wenzhuo Xiong creator: Liping Dai creator: Xiuzhi Zhang creator: Peng Wang creator: Hua Ye creator: Jianxiang Shi creator: Zhihao Fang creator: Keyan Wang uri: https://doi.org/10.7717/peerj.17494 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Identifying risk zones and landscape features that affect common leopard depredation link: https://peerj.com/articles/17497 last-modified: 2024-05-31 description: Human-wildlife conflict (HWC) is a pressing issue worldwide but varies by species over time and place. One of the most prevalent forms of HWC in the mid-hills of Nepal is human-common-leopard conflict (HLC). Leopard attacks, especially in forested areas, can severely impact villagers and their livestock. Information on HLC in the Gorkha district was scarce, thus making it an ideal location to identify high-risk zones and landscape variables associated with such events. Registered cases were collected and reviewed from the Division Forest Office (DFO) during 2019-2021. Claims from DFO records were confirmed with herders and villagers via eight focus group discussions. To enhance modeling success, researchers identified a total of 163 leopard attack locations on livestock, ensuring a minimum distance of at least 100 meters between locations. Using maximum entropy (MaxEnt) and considering 13 environmental variables, we mapped common leopard attack risk zones. True Skill Statistics (TSS) and area under receiver-operator curve (AUC) were used to evaluate and validate the Output. Furthermore, 10 replications, 1,000 maximum iterations, and 1000 background points were employed during modeling. The average AUC value for the model, which was 0.726 ± 0.021, revealed good accuracy. The model performed well, as indicated by a TSS value of 0.61 ± 0.03. Of the total research area (27.92 km2), about 74% was designated as a low-risk area, 19% as a medium-risk area, and 7% as a high-risk area. Of the 13 environmental variables, distance to water (25.2%) was the most significant predictor of risk, followed by distance to road (16.2%) and elevation (10.7%). According to response curves, the risk of common leopard is highest in the areas between 1.5 to 2 km distances from the water sources, followed by the closest distance from a road and an elevation of 700 to 800 m. Results suggest that managers and local governments should employ intervention strategies immediately to safeguard rural livelihoods in high-risk areas. Improvements include better design of livestock corrals, insurance, and total compensation of livestock losses. Settlements near roads and water sources should improve the design and construction of pens and cages to prevent livestock loss. More studies on the characteristics of victims are suggested to enhance understanding of common leopard attacks, in addition to landscape variables. Such information can be helpful in formulating the best management practices. creator: Thakur Silwal creator: Bijaya Neupane creator: Nirjala Raut creator: Bijaya Dhami creator: Binaya Adhikari creator: Amit Adhikari creator: Aakash Paudel creator: Shalik Ram Kandel creator: Mahamad Sayab Miya uri: https://doi.org/10.7717/peerj.17497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Silwal et al. title: Effectiveness of in-group versus individually administered pain neuroscience education on clinical and psychosocial outcomes in patients with chronic low back pain: randomized controlled study protocol link: https://peerj.com/articles/17507 last-modified: 2024-05-31 description: Objective(1) This trial will compare the clinical and psychosocial effectiveness of in-group and individually pain neuroscience education (PNE) in patients with chronic low back pain (CLBP). In addition, (2) the influence of social determinants of health on post-treatment results will be analyzed.MethodsA three-arm randomized controlled trial will be conducted. Sixty-nine participants with CLBP will be recruited in a 1:1:1 ratio. Participants, assessor, and statistician will be blinded to group assignment. The PNE intervention will be adapted to the context of the participants. An experimental group (n = 33) will receive PNE in an in-group modality, the other experimental group (n = 33) will receive PNE in an individually modality and the control group (n = 33) will continue with usual care. Additionally, participants will be encouraged to stay active by walking for 20–30 min 3–5 times per week and will be taught an exercise to improve transversus abdominis activation (bracing or abdominal following). The outcome measures will be fear avoidance and beliefs, pressure pain threshold, pain self-efficacy, catastrophizing, pain intensity, and treatment expectation. Outcome measures will be collected at one-week before intervention, immediately post-intervention, and four-weeks post-intervention.ConclusionThe innovative approach of PNE oriented to fear beliefs proposed in this study could broaden the application strategies of this educational therapeutic modality. Impact. Contextualized PNE delivered by physical therapist could be essential to achieve a good cost-effectiveness ratio of this intervention to improve the clinical condition of people with CLBP. creator: Joaquín Salazar-Méndez creator: Iván Cuyul-Vásquez creator: Felipe Ponce-Fuentes creator: Rodrigo Núñez-Cortés creator: Guillermo Mendez-Rebolledo creator: Jorge Fuentes uri: https://doi.org/10.7717/peerj.17507 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Salazar-Méndez et al. title: Impacts of forest age on soil characteristics and fertility quality of Populus simonii shelter forest at the southern edge of the Horqin Sandy Land, China link: https://peerj.com/articles/17512 last-modified: 2024-05-31 description: The sand fixing shelter forests in the Horqin Sandy Land are a key area in the “3-North” Shelter Forest Program in China, which has a history of over 50 years of artificial afforestation. Populus simonii Carr is one of the most dominant silvicultural species in the region. The aim of this study is to understand the soil characteristics and soil fertility of Populus simonii shelter forests at different growth stages and to establish a scientific basis for soil nutrient regulation and sustainable management of Populus simonii shelter forests at the southern edge of the Horqin Sandy Land. Sample plots were selected for young (≤15 a), middle-aged (16–25 a), near-mature (26–30 a), mature (31–40 a), and over-mature (≥41 a) forests. Each forest studied was in a state of natural restoration with uniform stand conditions and no artificial fertilizer was applied. These sites were selected to study changes in the soil characteristics in soil depths of 0–20, 20–40, and 40–60 cm. In order to avoid the problem of multicollinearity between soil variables and to reduce redundancy, principal component analysis (PCA), Pearson’s correlation analysis, and Norm value calculation were used to select the least correlated indicators with the highest factor loadings. This was used to establish the minimum data set. The soil fertility quality of these shelterbelts in different forest ages was quantified using the soil quality index (SQI). In the growth stage from young to nearly mature forests, the soil bulk weight and pH decreased with increasing forest age. Soil capillary porosity, noncapillary porosity, total porosity, water content, field water holding capacity, and organic carbon content increased with increasing forest age and soil nutrient content gradually improved. At the stage of near-mature to over-mature forests, the effect of forest age on soil bulk density was not significant and all other soil characteristics decreased to varying degrees as the forest age increased. The soil also developed from alkaline to neutral. The SQI of the total data set and the SQI of the minimum data set consistently showed that near-mature forests (NMF) > middle-aged forests (MAF) > mature forests (MF) > over-mature forests (OMF) > young forests (YF). The results of the two evaluation systems showed a significant positive correlation (P < 0.05, R 2 = 0.8263) indicating that it is feasible to use the minimum data set to evaluate the soil fertility of shelter forests of different forest ages. The age of the forest has an obvious effect on the soil characteristics and overall soil fertility of shelter forests. The Populus simonii shelter forests on the southern edge of the Horqin Sandy Land have great soil development at the early stage of afforestation and the soil nutrient content gradually increases. The soil fertility reaches a peak when the forest is nearly mature and the soil fertility declines after the age of the forest reaches 30 years. creator: Xinyu Guo creator: Guang Yang creator: Ji Wu creator: Shi Qiao creator: Li Tao uri: https://doi.org/10.7717/peerj.17512 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Guo et al. title: Nrf2 pathway activation promotes the expression of genes related to glutathione metabolism in alcohol-exposed astrocytes link: https://peerj.com/articles/17541 last-modified: 2024-05-31 description: IntroductionOxidative and antioxidant pathways play essential roles in the development of alcohol-induced brain injury. The Nrf2 pathway is an endogenous antioxidant response pathway, but there has been little research on the role of Nrf2 in alcohol-related diseases. Thus, we examined the effects of alcohol and an Nrf2 agonist (TBHQ) on astrocyte function, mRNA expression, and metabolite content to further explore the protective mechanisms of Nrf2 agonists in astrocytes following alcohol exposure.MethodsCTX TNA2 astrocytes were cultured with alcohol and TBHQ and then subjected to transcriptome sequencing, LC-MS/MS analysis, quantitative reverse transcription polymerase chain reaction (qRT-PCR), and malondialdehyde (MDA) and superoxide dismutase (SOD) activity assays.ResultsAlcohol exposure significantly increased malondialdehyde (MDA) levels while decreasing superoxide dismutase (SOD) levels in astrocytes. Treatment with TBHQ effectively reversed these effects, demonstrating its protective role against oxidative stress induced by alcohol. Transcriptome sequencing and qRT-PCR analysis revealed that TBHQ specifically upregulates genes involved in glutathione metabolism, including a notable increase in the expression of the glutathione S-transferase A5 (GSTA5) gene, which was suppressed by alcohol exposure. Additionally, metabolomic analysis showed that TBHQ regulates key components of ether lipid metabolism in alcohol-exposed astrocytes, with significant reductions in the levels of lysophosphatidylcholine (18:0) (LysoPC (18:0)) and 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine, both of which are critical markers in the ether lipid metabolic pathway.DiscussionThe findings underscore the role of TBHQ as an Nrf2 agonist in mitigating alcohol-induced oxidative damage in astrocytes by modulating glutathione metabolism and ether lipid metabolism. The regulation of GSTA5 gene expression emerges as a key mechanism through which Nrf2 agonists confer neuroprotection against oxidative stress and lipid oxidation. These insights pave the way for potential therapeutic strategies targeting the Nrf2 pathway to protect astrocytes from alcohol-induced damage. creator: Congyan Li creator: Jingxin Fan creator: Guangtao Sun creator: Huiying Zhao creator: Xiaogang Zhong creator: Xinyan Huang creator: Xiaofeng Zhu creator: Xunzhong Qi uri: https://doi.org/10.7717/peerj.17541 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Differences in visuospatial cognition among table tennis players of different skill levels: an event-related potential study link: https://peerj.com/articles/17295 last-modified: 2024-05-30 description: This study aimed to examine the influence of sport skill levels on behavioural and neuroelectric performance in visuospatial attention and memory visuospatial tasks were administered to 54 participants, including 18 elite and 18 amateur table tennis players and 18 nonathletes, while event-related potentials were recorded. In all the visuospatial attention and memory conditions, table tennis players displayed faster reaction times than nonathletes, regardless of skill level, although there was no difference in accuracy between groups. In addition, regardless of task conditions, both player groups had a greater P3 amplitude than nonathletes, and elite players exhibited a greater P3 amplitude than amateurs players. The results of this study indicate that table tennis players, irrespective of their skill level, exhibit enhanced visuospatial capabilities. Notably, athletes at the elite level appear to benefit from an augmented allocation of attentional resources when engaging in visuospatial tasks. creator: Kuan-Fu Chen creator: Ting-Yu Chueh creator: Tsung-Min Hung uri: https://doi.org/10.7717/peerj.17295 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris) link: https://peerj.com/articles/17365 last-modified: 2024-05-30 description: The saturniid moth genus Automeris includes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru. Automeris moths are cryptically colored, with forewings that resemble dead leaves, and conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships within Automeris and between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny of Automeris to date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera, Pseudautomeris and Leucanella, as well as a morphologically distinct genus, Molippa. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to assemble a high-quality dataset for phylogenetic analysis. The resulting phylogeny supports Automeris as a paraphyletic genus, with Leucanella and Pseudautomeris nested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects of Automeris biology, including geographical distribution patterns, potential drivers of speciation, and ecological adaptations such as antipredator defense mechanisms. creator: Chelsea Skojec creator: Chandra Earl creator: Christian D. Couch creator: Paul Masonick creator: Akito Y. Kawahara uri: https://doi.org/10.7717/peerj.17365 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Skojec et al. title: Zoonotic spillover and viral mutations from low and middle-income countries: improving prevention strategies and bridging policy gaps link: https://peerj.com/articles/17394 last-modified: 2024-05-30 description: The increasing frequency of zoonotic spillover events and viral mutations in low and middle-income countries presents a critical global health challenge. Contributing factors encompass cultural practices like bushmeat consumption, wildlife trade for traditional medicine, habitat disruption, and the encroachment of impoverished settlements onto natural habitats. The existing “vaccine gap” in many developing countries exacerbates the situation by allowing unchecked viral replication and the emergence of novel mutant viruses. Despite global health policies addressing the root causes of zoonotic disease emergence, there is a significant absence of concrete prevention-oriented initiatives, posing a potential risk to vulnerable populations. This article is targeted at policymakers, public health professionals, researchers, and global health stakeholders, particularly those engaged in zoonotic disease prevention and control in low and middle-income countries. The article underscores the importance of assessing potential zoonotic diseases at the animal-human interface and comprehending historical factors contributing to spillover events. To bridge policy gaps, comprehensive strategies are proposed that include education, collaborations, specialized task forces, environmental sampling, and the establishment of integrated diagnostic laboratories. These strategies advocate simplicity and unity, breaking down barriers, and placing humanity at the forefront of addressing global health challenges. Such a strategic and mental shift is crucial for constructing a more resilient and equitable world in the face of emerging zoonotic threats. creator: Zulfqarul Haq creator: Junaid Nazir creator: Tasaduq Manzoor creator: Afnan Saleem creator: H. Hamadani creator: Azmat Alam Khan creator: Sahar Saleem Bhat creator: Priyanka Jha creator: Syed Mudasir Ahmad uri: https://doi.org/10.7717/peerj.17394 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Haq et al. title: The COVID-19 pandemic “anthropause” decreased plastic ingestion in neotropic cormorants Nannopterum brasilianus in Lima, Peru link: https://peerj.com/articles/17407 last-modified: 2024-05-30 description: BackgroundThe anthropause during the recent COVID-19 pandemic provided a unique opportunity to examine the impact of human activity on seabirds. Lockdowns in Peru prevented people from visiting coastal areas, thereby reducing garbage disposal on beaches and the movement of microplastics into the ocean. This cessation of activities likely led to a temporary decrease in plastic pollution in coastal regions. We aimed to investigate this phenomenon in inshore-feeding neotropic cormorants (Nannopterum brasilianus) along the Circuito de Playas Costa Verde (CPCV), situated on the coastal strip of Lima, Peru (∼ 11 million people).MethodsWe collected and analyzed fresh pellets along the CPCV before (over 11 months) and during the pandemic lockdowns (over 8 months).ResultsOur findings revealed a significant reduction in the occurrence of plastic in pellets during the pandemic period (% Oc = 2.47, n = 647 pellets) compared to pre-pandemic conditions (% Oc = 7.13, n = 800 pellets). The most common plastic debris item found in the pellets was threadlike microplastic. Additionally, our study highlights the direct correlation between human presence on beaches and the quantity of microplastics (mainly threadlike) found in cormorant pellets. We suggest that the reintroduction of these materials into the sea, previously accumulated on the coast, is likely facilitated by the movement and activity of beachgoers toward the ocean. creator: Laura Catalina Porras-Parra creator: Carlos B. Zavalaga creator: Alvaro Rios uri: https://doi.org/10.7717/peerj.17407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Porras-Parra et al. title: Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats link: https://peerj.com/articles/17412 last-modified: 2024-05-30 description: Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics. creator: Mariette Viladomat Jasso creator: Manuel García-Ulloa creator: Icoquih Zapata-Peñasco creator: Luis E. Eguiarte creator: Valeria Souza uri: https://doi.org/10.7717/peerj.17412 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Viladomat Jasso et al. title: Seasonal dynamics and environmental drivers of tissue and mucus microbiomes in the staghorn coral Acropora pulchra link: https://peerj.com/articles/17421 last-modified: 2024-05-30 description: BackgroundRainfall-induced coastal runoff represents an important environmental impact in near-shore coral reefs that may affect coral-associated bacterial microbiomes. Shifts in microbiome community composition and function can stress corals and ultimately cause mortality and reef declines. Impacts of environmental stress may be site specific and differ between coral microbiome compartments (e.g., tissue versus mucus). Coastal runoff and associated water pollution represent a major stressor for near-shore reef-ecosystems in Guam, Micronesia.MethodsAcropora pulchra colonies growing on the West Hagåtña reef flat in Guam were sampled over a period of 8 months spanning the 2021 wet and dry seasons. To examine bacterial microbiome diversity and composition, samples of A. pulchra tissue and mucus were collected during late April, early July, late September, and at the end of December. Samples were collected from populations in two different habitat zones, near the reef crest (farshore) and close to shore (nearshore). Seawater samples were collected during the same time period to evaluate microbiome dynamics of the waters surrounding coral colonies. Tissue, mucus, and seawater microbiomes were characterized using 16S DNA metabarcoding in conjunction with Illumina sequencing. In addition, water samples were collected to determine fecal indicator bacteria (FIB) concentrations as an indicator of water pollution. Water temperatures were recorded using data loggers and precipitation data obtained from a nearby rain gauge. The correlation structure of environmental parameters (temperature and rainfall), FIB concentrations, and A. pulchra microbiome diversity was evaluated using a structural equation model. Beta diversity analyses were used to investigate spatio-temporal trends of microbiome composition.ResultsAcropora pulchra microbiome diversity differed between tissues and mucus, with mucus microbiome diversity being similar to the surrounding seawater. Rainfall and associated fluctuations of FIB concentrations were correlated with changes in tissue and mucus microbiomes, indicating their role as drivers of A. pulchra microbiome diversity. A. pulchra tissue microbiome composition remained relatively stable throughout dry and wet seasons; tissues were dominated by Endozoicomonadaceae, coral endosymbionts and putative indicators of coral health. In nearshore A. pulchra tissue microbiomes, Simkaniaceae, putative obligate coral endosymbionts, were more abundant than in A. pulchra colonies growing near the reef crest (farshore). A. pulchra mucus microbiomes were more diverse during the wet season than the dry season, a distinction that was also associated with drastic shifts in microbiome composition. This study highlights the seasonal dynamics of coral microbiomes and demonstrates that microbiome diversity and composition may differ between coral tissues and the surface mucus layer. creator: Therese C. Miller creator: Bastian Bentlage uri: https://doi.org/10.7717/peerj.17421 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Miller and Bentlage title: The unexpected effect of the compound microbial agent NP-M2 on microbial community dynamics in a nonylphenol-contaminated soil: the self-stability of soil ecosystem link: https://peerj.com/articles/17424 last-modified: 2024-05-30 description: BackgroundNonylphenol (NP) is widely recognized as a crucial environmental endocrine-disrupting chemical and persistent toxic substance. The remediation of NP-contaminated sites primarily relies on biological degradation. Compound microbial products, as opposed to pure strains, possess a greater variety of metabolic pathways and can thrive in a wider range of environmental conditions. This characteristic is believed to facilitate the synergistic degradation of pollutants. Limited research has been conducted to thoroughly examine the potential compatibility of compound microbial agents with indigenous microflora, their ability to function effectively in practical environments, their capacity to enhance the dissipation of NP, and their potential to improve soil physicochemical and biological characteristics.MethodsIn order to efficiently eliminate NP in contaminated soil in an eco-friendly manner, a simulation study was conducted to investigate the impact of bioaugmentation using the functional compound microbial agent NP-M2 at varying concentrations (50 and 200 mg/L) on the dynamics of the soil microbial community. The treatments were set as follows: sterilized soil with 50 mg/kg NP (CK50) or 200 mg/kg NP (CK200); non-sterilized soil with 50 mg/kg NP (TU50) or 200 mg/kg NP (TU200); non-sterilized soil with the compound microbial agent NP-M2 at 50 mg/kg NP (J50) or 200 mg/kg NP (J200). Full-length 16S rRNA analysis was performed using the PacBio Sequel II platform.ResultsBoth the indigenous microbes (TU50 and TU200 treatments) and the application of NP-M2 (J50 and J200 treatments) exhibited rapid NP removal, with removal rates ranging from 93% to 99%. The application of NP-M2 further accelerated the degradation rate of NP for a subtle lag period. Although the different treatments had minimal impacts on the soil bacterial α-diversity, they significantly altered the β-diversity and composition of the bacterial community. The dominant phyla were Proteobacteria (35.54%–44.14%), Acidobacteria (13.55%–17.07%), Planctomycetes (10.78%–11.42%), Bacteroidetes (5.60%–10.74%), and Actinobacteria (6.44%–8.68%). The core species were Luteitalea_pratensis, Pyrinomonas_methylaliphatogenes, Fimbriiglobus_ruber, Longimicrobium_terrae, and Massilia_sp003590855. The bacterial community structure and taxon distribution in polluted soils were significantly influenced by the activities of soil catalase, sucrase, and polyphenol oxidase, which were identified as the major environmental factors. Notably, the concentration of NP and, to a lesser extent, the compound microbial agent NP-M2 were found to cause major shifts in the bacterial community. This study highlights the importance of conducting bioremediation experiments in conjunction with microbiome assessment to better understand the impact of bioaugmentation/biostimulation on the potential functions of complex microbial communities present in contaminated soils, which is essential for bioremediation success. creator: Zhaoliang Chen creator: Juanqin Zhang creator: Weiguang Lv creator: Hanlin Zhang creator: Shuangxi Li creator: Haiyun Zhang creator: Yue Shen creator: Chunnu Geng creator: Naling Bai uri: https://doi.org/10.7717/peerj.17424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Sucrose rinse modulates the salivary behavior of carbonic anhydrase VI and its buffering capacity: a longitudinal study in 4 to 6.5-year-old children link: https://peerj.com/articles/17429 last-modified: 2024-05-30 description: BackgroundCarbonic anhydrase VI (CA VI) is crucial in regulating oral pH and predicting susceptibility to dental caries. The hypothesis posits that caries activity may alter the CA VI function, diminishing its capacity to regulate pH effectively and potentially exacerbating cariogenic challenges. This 1-year cohort study sought to investigate the enzymatic activity of salivary CA VI and buffering capacity following a 20% sucrose rinse in 4 to 6.5-year-old children.MethodThis research involved 46 volunteers categorized into three groups based on their caries status after follow-up: caries-free (CFee), arrested caries (CArrested), and caries active (CActive). Children underwent visible biofilm examination and saliva collection for salivary flow rate, buffering capacity, and CA VI analyses before and after a 20% sucrose rinse.ResultsA reduction in the buffering capacity was observed after sucrose rinse in all groups. The CA VI activity decreased significantly in CFee and CArrested groups after sucrose rinse, although it did not change in the CActive group. An improvement in the buffering capacity and salivary flow rate was found at follow-up when compared with the baseline. After 1-year follow-up, buffering capacity and salivary flow rate increased in all groups, whilst the CA VI activity reduced only in CFree and CArrested children.ConclusionSucrose rinse universally reduces the salivary buffering capacity, while caries activity may disrupt CA VI activity response during a cariogenic challenge. After a year, increased salivary flow enhances buffering capacity but not CA VI activity in caries-active children. creator: Thayse Rodrigues de Souza creator: Bruna Raquel Zancope creator: Emerson Tavares de Sousa creator: Thais Manzano Parisotto creator: Marcelo Rocha Marques creator: Marinês Nobre dos Santos uri: https://doi.org/10.7717/peerj.17429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Souza et al. title: Crizotinib inhibits the metabolism of tramadol by non-competitive suppressing the activities of CYP2D1 and CYP3A2 link: https://peerj.com/articles/17446 last-modified: 2024-05-30 description: ObjectivesTo investigate the interaction between tramadol and representative tyrosine kinase inhibitors, and to study the inhibition mode of drug-interaction.MethodsLiver microsomal catalyzing assay was developed. Sprague-Dawley rats were administrated tramadol with or without selected tyrosine kinase inhibitors. Samples were prepared and ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) was used for analysis. Besides, liver, kidney, and small intestine were collected and morphology was examined by hematoxyline-eosin (H&E) staining. Meanwhile, liver microsomes were prepared and carbon monoxide differential ultraviolet radiation (UV) spectrophotometric quantification was performed.ResultsAmong the screened inhibitors, crizotinib takes the highest potency in suppressing the metabolism of tramadol in rat/human liver microsome, following non-competitive inhibitory mechanism. In vivo, when crizotinib was co-administered, the AUC value of tramadol increased compared with the control group. Besides, no obvious pathological changes were observed, including cell morphology, size, arrangement, nuclear morphology with the levels of alanine transaminase (ALT) and aspartate transaminase (AST) increased after multiple administration of crizotinib. Meanwhile, the activities of CYP2D1 and CYP3A2 as well as the total cytochrome P450 abundance were found to be decreased in rat liver of combinational group.ConclusionsCrizotinib can inhibit the metabolism of tramadol. Therefore, this recipe should be vigilant to prevent adverse reactions. creator: Nanyong Gao creator: Xiaoyu Xu creator: Feng Ye creator: Xin-yue Li creator: Chengqi Lin creator: Xiu-wei Shen creator: Jianchang Qian uri: https://doi.org/10.7717/peerj.17446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: Analysis of rotational grazing management for sheep in mixed grassland link: https://peerj.com/articles/17453 last-modified: 2024-05-30 description: Sown mixed grassland is rarely used for livestock raising and grazing; however, different forages can provide various nutrients for livestock, which may be beneficial to animal health and welfare. We established a sown mixed grassland and adopted a rotational grazing system, monitored the changes in aboveground biomass and sheep weights during the summer grazing period, measured the nutrients of forage by near-infrared spectroscopy, tested the contents of medium- and long-chain fatty acids by gas chromatography, and explored an efficient sheep fattening system that is suitable for agro-pastoral interlacing areas. The results showed that the maximum forage supply in a single grazing paddock was 4.6 kg DM/d, the highest dry matter intake (DMI) was 1.80 kg DM/ewe/d, the average daily weight gain (ADG) was 193.3 g, the DMI and ADG were significantly correlated (P < 0.05), and the average feed weight gain ratio (F/G) reached 8.02. The average crude protein and metabolizable energy intake by sheep were 286 g/ewe/d and 18.5 MJ/ewe/d respectively, and the n-6/n-3 ratio of polyunsaturated fatty acids in mutton was 2.84. The results indicated that the sheep fattening system had high feed conversion efficiency, could improve the yield and quality of sheep, and could be promoted in suitable regions. creator: Zongyong Tong creator: Xianlin Dai creator: Yu Wang creator: Xianglin Li creator: Feng He creator: Guomei Yin uri: https://doi.org/10.7717/peerj.17453 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tong et al. title: Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses link: https://peerj.com/articles/17462 last-modified: 2024-05-30 description: Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress. creator: Rasmieh Hamid creator: Feba Jacob creator: Zahra Ghorbanzadeh creator: Mojtaba Khayam Nekouei creator: Mehrshad Zeinalabedini creator: Mohsen Mardi creator: Akram Sadeghi creator: Sushil Kumar creator: Mohammad Reza Ghaffari uri: https://doi.org/10.7717/peerj.17462 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hamid et al. title: Regulation of dye-decolorizing peroxidase gene expression in Pleurotus ostreatus grown on glycerol as the carbon source link: https://peerj.com/articles/17467 last-modified: 2024-05-30 description: Dye-decolorizing peroxidases (DyPs) (E.C. 1.11.1.19) are heme peroxidases that catalyze oxygen transfer reactions similarly to oxygenases. DyPs utilize hydrogen peroxide (H2O2) both as an electron acceptor co-substrate and as an electron donor when oxidized to their respective radicals. The production of both DyPs and lignin-modifying enzymes (LMEs) is regulated by the carbon source, although less readily metabolizable carbon sources do improve LME production. The present study analyzed the effect of glycerol on Pleurotus ostreatus growth, total DyP activity, and the expression of three Pleos-dyp genes (Pleos-dyp1, Pleos-dyp2 and Pleos-dyp4), via real-time RT-qPCR, monitoring the time course of P. ostreatus cultures supplemented with either glycerol or glucose and Acetyl Yellow G (AYG) dye. The results obtained indicate that glycerol negatively affects P. ostreatus growth, giving a biomass production of 5.31 and 5.62 g/L with respective growth rates (micra; m) of 0.027 and 0.023 h−1 for fermentations in the absence and presence of AYG dye. In contrast, respective biomass production levels of 7.09 and 7.20 g/L and growth rates (μ) of 0.033 and 0.047 h−1 were observed in equivalent control fermentations conducted with glucose in the absence and presence of AYG dye. Higher DyP activity levels, 4,043 and 4,902 IU/L, were obtained for fermentations conducted on glycerol, equivalent to 2.6-fold and 3.16-fold higher than the activity observed when glucose is used as the carbon source. The differential regulation of the DyP-encoding genes in P. ostreatus were explored, evaluating the carbon source, the growth phase, and the influence of the dye. The global analysis of the expression patterns throughout the fermentation showed the up- and down- regulation of the three Pleos-dyp genes evaluated. The highest induction observed for the control media was that found for the Pleos-dyp1 gene, which is equivalent to an 11.1-fold increase in relative expression (log2) during the stationary phase of the culture (360 h), and for the glucose/AYG media was Pleos-dyp-4 with 8.28-fold increase after 168 h. In addition, glycerol preferentially induced the Pleos-dyp1 and Pleos-dyp2 genes, leading to respective 11.61 and 4.28-fold increases after 144 h. After 360 and 504 h of culture, 12.86 and 4.02-fold increases were observed in the induction levels presented by Pleos-dyp1 and Pleos-dyp2, respectively, in the presence of AYG. When transcription levels were referred to those found in the control media, adding AYG led to up-regulation of the three dyp genes throughout the fermentation. Contrary to the fermentation with glycerol, where up- and down-regulation was observed. The present study is the first report describing the effect of a less-metabolizable carbon source, such as glycerol, on the differential expression of DyP-encoding genes and their corresponding activity. creator: Jorge Cuamatzi-Flores creator: Soley Nava-Galicia creator: Edgardo Ulises Esquivel-Naranjo creator: Agustin Lopez Munguia creator: Analilia Arroyo-Becerra creator: Miguel Angel Villalobos-López creator: Martha Bibbins-Martínez uri: https://doi.org/10.7717/peerj.17467 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cuamatzi-Flores et al. title: Exogenous silicon induces aluminum tolerance in white clover (Trifolium repens) by reducing aluminum uptake and enhancing organic acid secretion link: https://peerj.com/articles/17472 last-modified: 2024-05-30 description: Excessive aluminum (Al) in acidic soils is a primary factor that hinders plant growth. The objective of the present study was to investigate the effect and physiological mechanism of exogenous silicon (Si) in alleviating aluminum toxicity. Under hydroponic conditions, 4 mM Al significantly impeded the growth of white clover; however, pretreatments with 1 mM Si mitigated this inhibition, as evidenced by notable changes in growth indicators and physiological parameters. Exogenous silicon notably increased both shoot and root length of white clover and significantly decreased electrolyte leakage (EL) and malondialdehyde (MDA) content compared to aluminum treatments. This positive effect was particularly evident in the roots. Further analysis involving hematoxylin staining, scanning electron microscopy (SEM), and examination of organic acids (OAs) demonstrated that silicon relieved the accumulation of bioactive aluminum and ameliorated damage to root tissues in aluminum-stressed plants. Additionally, energy-dispersive X-ray (EDX) analysis revealed that additional silicon was primarily distributed in the root epidermal and cortical layers, effectively reducing the transport of aluminum and maintaining the balance of exchangeable cations absorption. These findings suggest that gradual silicon deposition in root tissues effectively prevents the absorption of biologically active aluminum, thereby reducing the risk of mineral nutrient deficiencies induced by aluminum stress, promoting organic acids exudation, and compartmentalizing aluminum in the outer layer of root tissues. This mechanism helps white clover alleviate the damage caused by aluminum toxicity. creator: Weiqiang Yang creator: Huahao Feng creator: Jianzhen Zhou creator: Tong Jia creator: Tao Tang creator: Han Zhang creator: Yan Peng uri: https://doi.org/10.7717/peerj.17472 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Yang et al. title: Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida) link: https://peerj.com/articles/17480 last-modified: 2024-05-30 description: BackgroundBarbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae.MethodsNext-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method.ResultsThe full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae. creator: Yingkui Liu creator: Xinxin Fu creator: Yu Wang creator: Jing Liu creator: Yong Liu creator: Chong Li creator: Jiajia Dong uri: https://doi.org/10.7717/peerj.17480 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Reassessment of pore occlusion in some diatom taxa with re-evaluation of Placoneis Mereschkowsky (Bacillariophyceae: Cymbellales) and description of two new genera link: https://peerj.com/articles/17278 last-modified: 2024-05-29 description: In this article, the history and taxonomy of Placoneis gastrum, the type species of the genus Placoneis, was discussed. We investigated the structure of pore occlusions in Placoneis and related genera. As a result, we propose a new classification for tectulum-like types of pore occlusions. The new classification is congruent with previously-published and newly-constructed phylogenies based on molecular data. Based on the different structures of the pore occlusions, species of Placoneis are transferred to Witkowskia gen. nov. Hence, 168 new combinations are introduced. A new diatom species, with a similar morphology to Placoneis flabellata, was discovered in Bắc Kạn Province, Vietnam. It is described in this article as Chudaevia densistriata sp. nov. Placoneis flabellata is transferred to Chudaevia gen. nov. We also illustrate Placoneis flabellata herein and compare it to Chudaevia densistriata sp. nov. An unknown diatom, similar to Placoneis coloradensis, was discovered in Chukotka, Russia. It is introduced as Placoneis elinae sp. nov. below. Additionally, we discuss the distribution of some species of Witkowskia gen. nov. and Chudaevia gen. nov. creator: Andrei Mironov creator: Anton Glushchenko creator: Yevhen Maltsev creator: Sergey Genkal creator: Irina Kuznetsova creator: John Patrick Kociolek creator: Yan Liu creator: Maxim Kulikovskiy uri: https://doi.org/10.7717/peerj.17278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mironov et al. title: Investigating molecular markers linked to acute myocardial infarction and cuproptosis: bioinformatics analysis and validation in the AMI mice model link: https://peerj.com/articles/17280 last-modified: 2024-05-29 description: Cuproptosis-related key genes play a significant role in the pathological processes of acute myocardial infarction (AMI). However, a complete understanding of the molecular mechanisms behind this participation remains elusive. This study was designed to identify genes and immune cells critical to AMI pathogenesis. Based on the GSE48060 dataset (31 AMI patients and 21 healthy persons, GPL570-55999), we identified genes associated with dysregulated cuproptosis and the activation of immune responses between normal subjects and patients with a first myocardial attack. Two molecular clusters associated with cuproptosis were defined in patients with AMI. Immune infiltration analysis showed that there was significant immunity heterogeneity among different clusters. Multiple immune responses were closely associated with Cluster2-specific differentially expressed genes (DEGs). The generalized linear model machine model presented the best discriminative performance with relatively lower residual and root mean square error, and a higher area under the curve (AUC = 0.870). A final two-gene-based generalized linear model was constructed, exhibiting satisfactory performance in two external validation datasets (AUC = 0.719, GSE66360 and AUC = 0.856, GSE123342). Column graph, calibration curve, and decision curve analyses also proved the accuracy of AMI prediction. We also constructed a mouse C57BL/6 model of AMI (3 h, 48 h, and 1 week) and used qRT-PCR and immunofluorescence to detect the expression changes of CBLB and ZNF302. In this study, we present a systematic analysis of the complex relationship between cuproptosis and a first AMI attack, and provide new insights into the diagnosis and treatment of AMI. creator: Bingyu Wang creator: Jianqing Zhou creator: Ning An uri: https://doi.org/10.7717/peerj.17280 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Genome-wide identification and expression analysis of the WRKY gene family in Rhododendron henanense subsp. lingbaoense link: https://peerj.com/articles/17435 last-modified: 2024-05-29 description: BackgroundThis work explored the characteristics of the WRKY transcription factor family in Rhododendron henanense subsp. lingbaoense (Rhl) and the expression patterns of these genes under abiotic stress by conducting bioinformatics and expression analyses.MethodsRhlWRKY genes were identified from a gene library of Rhl. Various aspects of these genes were analyzed, including genetic structures, conserved sequences, physicochemical properties, cis-acting elements, and chromosomal location. RNA-seq was employed to analyze gene expression in five different tissues of Rhl: roots, stems, leaves, flowers, and hypocotyls. Additionally, qRT-PCR was used to detect changes in the expression of five RhlWRKY genes under abiotic stress.ResultA total of 65 RhlWRKY genes were identified and categorized into three subfamilies based on their structural characteristics: Groups I, II, and III. Group II was further divided into five subtribes, with shared similar genetic structures and conserved motifs among members of the same subtribe. The physicochemical properties of these proteins varied, but the proteins are generally predicted to be hydrophilic. Most proteins are predicted to be in the cell nucleus, and distributed across 12 chromosomes. A total of 84 cis-acting elements were discovered, with many related to responses to biotic stress. Among the identified RhlWRKY genes, there were eight tandem duplicates and 97 segmental duplicates. The majority of duplicate gene pairs exhibited Ka/Ks values <1, indicating purification under environmental pressure. GO annotation analysis indicated that WRKY genes regulate biological processes and participate in a variety of molecular functions. Transcriptome data revealed varying expression levels of 66.15% of WRKY family genes in all five tissue types (roots, stems, leaves, flowers, and hypocotyls). Five RhlWRKY genes were selected for further characterization and there were changes in expression levels for these genes in response to various stresses.ConclusionThe analysis identified 65 RhlWRKY genes, among which the expression of WRKY_42 and WRKY_17 were mainly modulated by the drought and MeJA, and WRKY_19 was regulated by the low-temperature and high-salinity conditions. This insight into the potential functions of certain genes contributes to understanding the growth regulatory capabilities of Rhl. creator: Xiangmeng Guo creator: Xinyu Yan creator: Yonghui Li uri: https://doi.org/10.7717/peerj.17435 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guo et al. title: Effects of high-intensity sprint exercise on neuromuscular function in sprinters: the countermovement jump as a fatigue assessment tool link: https://peerj.com/articles/17443 last-modified: 2024-05-29 description: BackgroundHigh-intensity sprint exercises (HIS) are central to sprinter training and require careful monitoring of athlete muscle fatigue to improve performance and prevent injury. While the countermovement jump (CMJ) may be used to monitor neuromuscular fatigue (NMF), little is known about the specific effects from HIS. The purpose of this study is to investigate the effects of HIS on the CMJ to assess its utility for assessing NMF following HIS.MethodsTen male collegiate 400 m sprinters completed a 400 m sprint fatigue protocol and underwent five CMJ-testing sessions (baseline, 3 minutes, 10 minutes, 1 hour and 24 hours) over two days. Three CMJ trials, performed on a force plate, were completed each trial, with rating of perceived exertion (RPE) recorded as a subjective fatigue measure. Changes in RPE, CMJ variables, force-time and power-time curves at baseline and post fatigue were assessed.ResultsSignificant changes were observed in most variables following the fatigue protocol. In particular, concentric mean power remained significantly lower after 24 hours compared to baseline. In addition, the force-time curves exhibited a significant reduction in all conditions following the fatigue protocol. This decline was most pronounced within 50–75%of the concentric phase relative to baseline measurements. Conclusion. Results indicate that the CMJ may be a useful tool for monitoring fatigue in at least 400 m sprinters. These data also indicate that HIS may disproportionately reduce force output in during concentric movement. These insights may improve training prescriptions and injury prevention strategies for sprint athletes. creator: Takahiro Hasegawa creator: Kotaro Muratomi creator: Yuki Furuhashi creator: Jun Mizushima creator: Hirohiko Maemura uri: https://doi.org/10.7717/peerj.17443 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hasegawa et al. title: Dose-response relationship between weekly physical activity level and the frequency of colds in Chinese middle-aged and elderly individuals link: https://peerj.com/articles/17459 last-modified: 2024-05-29 description: BackgroundEngaging in appropriate physical activity can significantly lower the risk of various diseases among middle-aged and older adults. Investigating optimal levels of physical activity (PA) is crucial for enhancing the health of this demographic. This study aims to explore the dose–response relationship between weekly PA levels and the frequency of colds among Chinese middle-aged and elderly individuals, identifying the necessary PA level to effectively diminish the risk of colds.MethodsWe conducted a cross-sectional study using a web-based survey targeting individuals aged 40 and older (n = 1, 683) in China. The survey collected information on PA and the frequency of colds. Data was analyzed using Kruskal–Wallis test and the χ2 test. We explored the dose–response relationship between weekly PA and cold frequency over the past year through an ordered multivariate logistic regression model and a restricted cubic spline model.Results(1) Brisk walking emerged as the preferred physical exercise for those over 40. The findings suggest that engaging in moderate (odds ratio (OR) = 0.64, P < 0.001, 95% confidence interval (CI) [0.50–0.81]) and high (OR = 0.64, P < 0.001, 95% CI [0.51–0.79]) levels of PA weekly significantly reduces the risk of catching a cold. Individuals with one (OR = 1.47, P < 0.001, 95% CI [1.20–1.80]) or multiple chronic diseases (OR = 1.56, P < 0.001, 95% CI [1.21–2.00]) were at increased risk. Those residing in central (OR = 1.64, P < 0.001, 95% CI [1.33–02.01]) and western China (OR = 1.49, P = 0.008, 95% CI [1.11–02.00]) faced a higher risk compared to their counterparts in eastern China. (2) According to the restricted cubic spline model, adults who experienced one cold in the past year had a weekly PA level of 537.29 metabolic equivalent-minutes per week (MET-min/wk) with an OR value of 1. For those reporting two or more colds, the PA level was 537.76 MET-min/wk with an OR of 1.Conclusions(1) Brisk walking is the most favored exercise among the Chinese middle-aged and elderly, with the prevalence of colds being affected by the number of chronic diseases and the geographic location. (2) Regular, moderate exercise is linked to a lower risk of colds. To effectively reduce cold frequency, it is recommended that middle-aged and elderly Chinese individuals engage in a minimum of 538 MET-min/wk of exercise. creator: Xiaona Tang creator: Yichao Yu creator: Xiaoxue Wu creator: Chengru Xu creator: Zhao Zhang creator: Yifan Lu uri: https://doi.org/10.7717/peerj.17459 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tang et al. title: Effect of SlSAHH2 on metabolites in over-expressed and wild-type tomato fruit link: https://peerj.com/articles/17466 last-modified: 2024-05-29 description: BackgroundTomato (Solanum lycopersicum) is an annual or perennial herb that occupies an important position in daily agricultural production. It is an essential food crop for humans and its ripening process is regulated by a number of genes. S-adenosyl-l-homocysteine hydrolase (AdoHcyase, EC 3.3.1.1) is widespread in organisms and plays an important role in regulating biological methylation reactions. Previous studies have revealed that transgenic tomato that over-express SlSAHH2 ripen earlier than the wild-type (WT). However, the differences in metabolites and the mechanisms driving how these differences affect the ripening cycle are unclear.ObjectiveTo investigate the effects of SlSAHH2 on metabolites in over-expressed tomato and WT tomato.MethodsSlSAHH2 over-expressed tomato fruit (OE-5# and OE-6#) and WT tomato fruit at the breaker stage (Br) were selected for non-targeted metabolome analysis.ResultsA total of 733 metabolites were identified by mass spectrometry using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Human Metabolome database (HMDB). The metabolites were divided into 12 categories based on the superclass results and a comparison with the HMDB. The differences between the two databases were analyzed by PLS-DA. Based on a variable important in projection value >1 and P < 0.05, 103 differential metabolites were found between tomato variety OE-5# and WT and 63 differential metabolites were found between OE-6# and WT. These included dehydrotomatine, L-serine, and gallic acid amongst others. Many metabolites are associated with fruit ripening and eight common metabolites were found between the OE-5# vs. WT and OE-6# vs. WT comparison groups. The low L-tryptophan expression in OE-5# and OE-6# is consistent with previous reports that its content decreases with fruit ripening. A KEGG pathway enrichment analysis of the significantly different metabolites revealed that in the OE-5# and WT groups, up-regulated metabolites were enriched in 23 metabolic pathways and down-regulated metabolites were enriched in 11 metabolic pathways. In the OE-6# and WT groups, up-regulated metabolites were enriched in 29 pathways and down-regulated metabolites were enriched in six metabolic pathways. In addition, the differential metabolite changes in the L-serine to flavonoid transformation metabolic pathway also provide evidence that there is a phenotypic explanation for the changes in transgenic tomato.DiscussionThe metabolomic mechanism controlling SlSAHH2 promotion of tomato fruit ripening has been further elucidated. creator: Lu Yang creator: Yue Teng creator: Sijia Bu creator: Ben Ma creator: Shijia Guo creator: Mengxiao Liang creator: Lifen Huang uri: https://doi.org/10.7717/peerj.17466 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: The impact of history of depression and access to weapons on suicide risk assessment: a comparison of ChatGPT-3.5 and ChatGPT-4 link: https://peerj.com/articles/17468 last-modified: 2024-05-29 description: The aim of this study was to evaluate the effectiveness of ChatGPT-3.5 and ChatGPT-4 in incorporating critical risk factors, namely history of depression and access to weapons, into suicide risk assessments. Both models assessed suicide risk using scenarios that featured individuals with and without a history of depression and access to weapons. The models estimated the likelihood of suicidal thoughts, suicide attempts, serious suicide attempts, and suicide-related mortality on a Likert scale. A multivariate three-way ANOVA analysis with Bonferroni post hoc tests was conducted to examine the impact of the forementioned independent factors (history of depression and access to weapons) on these outcome variables. Both models identified history of depression as a significant suicide risk factor. ChatGPT-4 demonstrated a more nuanced understanding of the relationship between depression, access to weapons, and suicide risk. In contrast, ChatGPT-3.5 displayed limited insight into this complex relationship. ChatGPT-4 consistently assigned higher severity ratings to suicide-related variables than did ChatGPT-3.5. The study highlights the potential of these two models, particularly ChatGPT-4, to enhance suicide risk assessment by considering complex risk factors. creator: Shiri Shinan-Altman creator: Zohar Elyoseph creator: Inbar Levkovich uri: https://doi.org/10.7717/peerj.17468 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shinan-Altman et al. title: SlZIP11 mediates zinc accumulation and sugar storage in tomato fruits link: https://peerj.com/articles/17473 last-modified: 2024-05-29 description: BackgroundZinc (Zn) is a vital micronutrient essential for plant growth and development. Transporter proteins of the ZRT/IRT-like protein (ZIP) family play crucial roles in maintaining Zn homeostasis. Although the acquisition, translocation, and intracellular transport of Zn are well understood in plant roots and leaves, the genes that regulate these pathways in fruits remain largely unexplored. In this study, we aimed to investigate the function of SlZIP11 in regulating tomato fruit development.MethodsWe used Solanum lycopersicum L. ‘Micro-Tom’ SlZIP11 (Solanum lycopersicum) is highly expressed in tomato fruit, particularly in mature green (MG) stages. For obtaining results, we employed reverse transcription-quantitative polymerase chain reaction (RT-qPCR), yeast two-hybrid assay, bimolecular fluorescent complementation, subcellular localization assay, virus-induced gene silencing (VIGS), SlZIP11 overexpression, determination of Zn content, sugar extraction and content determination, and statistical analysis.ResultsRT-qPCR analysis showed elevated SlZIP11 expression in MG tomato fruits. SlZIP11 expression was inhibited and induced by Zn deficiency and toxicity treatments, respectively. Silencing SlZIP11 via the VIGS technology resulted in a significant increase in the Zn content of tomato fruits. In contrast, overexpression of SlZIP11 led to reduced Zn content in MG fruits. Moreover, both silencing and overexpression of SlZIP11 caused alterations in the fructose and glucose contents of tomato fruits. Additionally, SlSWEEET7a interacted with SlZIP11. The heterodimerization between SlSWEET7a and SlZIP11 affected subcellular targeting, thereby increasing the amount of intracellularly localized oligomeric complexes. Overall, this study elucidates the role of SlZIP11 in mediating Zn accumulation and sugar transport during tomato fruit ripening. These findings underscore the significance of SlZIP11 in regulating Zn levels and sugar content, providing insights into its potential implications for plant physiology and agricultural practices. creator: Jiaqi Sun creator: Manning Wang creator: Xinsheng Zhang creator: Xin Liu creator: Jing Jiang uri: https://doi.org/10.7717/peerj.17473 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sun et al. title: Neoadjuvant chemotherapy efficacy and prognosis in HER2-low and HER2-zero breast cancer patients by HR status: a retrospective study in China link: https://peerj.com/articles/17492 last-modified: 2024-05-29 description: BackgroundThe promising efficacy of novel anti-HER2 antibody-drug conjugates (ADC) in HER2-low breast cancer has made HER2-low a research hotspot. However, controversy remains regarding the neoadjuvant chemotherapy (NAC) efficacy, prognosis, and the relationship with hormone receptor (HR) status of HER2-low.MethodsA retrospective analysis was conducted on 975 patients with HER2-negative breast cancer undergoing NAC at Tianjin Medical University Cancer Institute and Hospital, evaluating pathological complete response (pCR) rate and prognosis between HER2-low and HER2-zero in the overall cohort and subgroups.ResultsOverall, 579 (59.4%) and 396 (40.6%) patients were HER2-low and HER2-zero disease, respectively. Compared with HER2-zero, the HER2-low cohort consists of more postmenopausal patients, with lower histological grade and higher HR positivity. In the HR-positive subgroup, HER2-low cases remain to exhibit lower histological grade, while in the HR-negative subgroup, they show higher grade. The HER2-low group had lower pCR rates than the HER2-zero group (16.4% vs. 24.0%). In the HR-positive subgroup, HER2-low consistently showed lower pCR rate (8.1% vs. 15.5%), and served as an independent suppressive factor for the pCR rate. However, no significant difference was observed in the pCR rates between HER2-low and HER2-zero in the HR-negative breast cancer. In the entire cohort and in stratified subgroups based on HR and pCR statuses, no difference in disease-free survival were observed between HER2-low and HER2-zero.ConclusionsIn the Chinese population, HER2-low breast cancer exhibits distinct characteristics and efficacy of NAC in different HR subgroups. Its reduced pCR rate in HR-positive subgroup is particularly important for clinical decisions. However, HER2-low is not a reliable factor for assessing long-term survival outcomes. creator: Shaorong Zhao creator: Yuyun Wang creator: Angxiao Zhou creator: Xu Liu creator: Yi Zhang creator: Jin Zhang uri: https://doi.org/10.7717/peerj.17492 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhao et al. title: Genome-wide identification and characterization of SPXdomain-containing genes family in eggplant link: https://peerj.com/articles/17341 last-modified: 2024-05-28 description: Phosphorus is one of the lowest elements absorbed and utilized by plants in the soil. SPX domain-containing genes family play an important role in plant response to phosphate deficiency signaling pathway, and related to seed development, disease resistance, absorption and transport of other nutrients. However, there are no reports on the mechanism of SPX domain-containing genes in response to phosphorus deficiency in eggplant. In this study, the whole genome identification and functional analysis of SPX domain-containing genes family in eggplant were carried out. Sixteen eggplant SPX domain-containing genes were identified and divided into four categories. Subcellular localization showed that these proteins were located in different cell compartments, including nucleus and membrane system. The expression patterns of these genes in different tissues as well as under phosphate deficiency with auxin were explored. The results showed that SmSPX1, SmSPX5 and SmSPX12 were highest expressed in roots. SmSPX1, SmSPX4, SmSPX5 and SmSPX14 were significantly induced by phosphate deficiency and may be the key candidate genes in response to phosphate starvation in eggplant. Among them, SmSPX1 and SmSPX5 can be induced by auxin under phosphate deficiency. In conclusion, our study preliminary identified the SPX domain genes in eggplant, and the relationship between SPX domain-containing genes and auxin was first analyzed in response to phosphate deficiency, which will provide theoretical basis for improving the absorption of phosphorus in eggplants through molecular breeding technology. creator: Li Zhuomeng creator: Tuo Ji creator: Qi Chen creator: Chenxiao Xu creator: Yuqing Liu creator: Xiaodong Yang creator: Jing Li creator: Fengjuan Yang uri: https://doi.org/10.7717/peerj.17341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhuomeng et al. title: Single-cell transcriptome reveals the heterogeneity of malignant ductal cells and the prognostic value of REG4 and SPINK1 in primary pancreatic ductal adenocarcinoma link: https://peerj.com/articles/17350 last-modified: 2024-05-28 description: BackgroundPancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related deaths, with very limited therapeutic options available. This study aims to comprehensively depict the heterogeneity and identify prognostic targets for PDAC with single-cell RNA sequencing (scRNA-seq) analysis.MethodsScRNA-seq analysis was performed on 16 primary PDAC and three adjacent lesions. A series of analytical methods were applied for analysis in cell clustering, gene profiling, lineage trajectory analysis and cell-to-cell interactions. In vitro experiments including colony formation, wound healing and sphere formation assay were performed to assess the role of makers.ResultsA total of 32,480 cells were clustered into six major populations, among which the ductal cell cluster expressing high copy number variants (CNVs) was defined as malignant cells. Malignant cells were further subtyped into five subgroups which exhibited specific features in immunologic and metabolic activities. Pseudotime trajectory analysis indicated that components of various oncogenic pathways were differentially expressed along tumor progression. Furthermore, intensive substantial crosstalk between ductal cells and stromal cells was identified. Finally, genes (REG4 and SPINK1) screened out of differentially expressed genes (DEGs) were upregulated in PDAC cell lines. Silencing either of them significantly impaired proliferation, invasion, migration and stemness of PDAC cells.ConclusionsOur findings offer a valuable resource for deciphering the heterogeneity of malignant ductal cells in PDAC. REG4 and SPINK1 are expected to be promising targets for PDAC therapy. creator: Yutian Ji creator: Qianhui Xu creator: Weilin Wang uri: https://doi.org/10.7717/peerj.17350 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ji et al. title: Multimodal sensorimotor assessment of hand and forearm asymmetries: a reliability and correlational study link: https://peerj.com/articles/17403 last-modified: 2024-05-28 description: BackgroundEffective rehabilitation of upper limb musculoskeletal disorders requires multimodal assessment to guide clinicians’ decision-making. Furthermore, a comprehensive assessment must include reliable tests. Nevertheless, the interrelationship among various upper limb tests remains unclear. This study aimed to evaluate the reliability of easily applicable upper extremity assessments, including absolute values and asymmetries of muscle mechanical properties, pressure pain threshold, active range of motion, maximal isometric strength, and manual dexterity. A secondary aim was to explore correlations between different assessment procedures to determine their interrelationship.MethodsThirty healthy subjects participated in two experimental sessions with 1 week between sessions. Measurements involved using a digital myotonometer, algometer, inclinometer, dynamometer, and the Nine-Hole Peg test. Intraclass correlation coefficients, standard error of the mean, and minimum detectable change were calculated as reliability indicators. Pearson’s correlation was used to assess the interrelationship between tests.ResultsFor the absolute values of the dominant and nondominant sides, reliability was ‘good’ to ‘excellent’ for muscle mechanical properties, pressure pain thresholds, active range of motion, maximal isometric strength, and manual dexterity. Similarly, the reliability for asymmetries ranged from ‘moderate’ to ‘excellent’ across the same parameters. Faster performance in the second session was consistently found for the Nine-Hole Peg test. No systematic inter-session errors were identified for the values of the asymmetries. No significant correlations were found between tests, indicating test independence.ConclusionThese findings indicate that the sensorimotor battery of tests is reliable, while monitoring asymmetry changes may offer a more conservative approach to effectively tracking recovery of upper extremity injuries. creator: Pablo Bellosta-López creator: Julia Blasco-Abadía creator: Lars L. Andersen creator: Jonas Vinstrup creator: Sebastian V. Skovlund creator: Víctor Doménech-García uri: https://doi.org/10.7717/peerj.17403 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bellosta-López et al. title: Gene expression and immune infiltration analysis comparing lesioned and preserved subchondral bone in osteoarthritis link: https://peerj.com/articles/17417 last-modified: 2024-05-28 description: BackgroundOsteoarthritis (OA) is a degenerative disease requiring additional research. This study compared gene expression and immune infiltration between lesioned and preserved subchondral bone. The results were validated using multiple tissue datasets and experiments.MethodsDifferentially expressed genes (DEGs) between the lesioned and preserved tibial plateaus of OA patients were identified in the GSE51588 dataset. Moreover, functional annotation and protein–protein interaction (PPI) network analyses were performed on the lesioned and preserved sides to explore potential therapeutic targets in OA subchondral bones. In addition, multiple tissues were used to screen coexpressed genes, and the expression levels of identified candidate DEGs in OA were measured by quantitative real-time polymerase chain reaction. Finally, an immune infiltration analysis was conducted.ResultsA total of 1,010 DEGs were identified, 423 upregulated and 587 downregulated. The biological process (BP) terms enriched in the upregulated genes included “skeletal system development”, “sister chromatid cohesion”, and “ossification”. Pathways were enriched in “Wnt signaling pathway” and “proteoglycans in cancer”. The BP terms enriched in the downregulated genes included “inflammatory response”, “xenobiotic metabolic process”, and “positive regulation of inflammatory response”. The enriched pathways included “neuroactive ligand–receptor interaction” and “AMP-activated protein kinase signaling”. JUN, tumor necrosis factor α, and interleukin-1β were the hub genes in the PPI network. Collagen XI A1 and leucine-rich repeat-containing 15 were screened from multiple datasets and experimentally validated. Immune infiltration analyses showed fewer infiltrating adipocytes and endothelial cells in the lesioned versus preserved samples.ConclusionOur findings provide valuable information for future studies on the pathogenic mechanism of OA and potential therapeutic and diagnostic targets. creator: Gang Zhang creator: Jinwei Qin creator: Wenbo Xu creator: Meina Liu creator: Rilige Wu creator: Yong Qin uri: https://doi.org/10.7717/peerj.17417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Lactobacillus rhamnosus GG improves cognitive impairments in mice with sepsis link: https://peerj.com/articles/17427 last-modified: 2024-05-28 description: BackgroundSurvivors of sepsis may encounter cognitive impairment following their recovery from critical condition. At present, there is no standardized treatment for addressing sepsis-associated encephalopathy. Lactobacillus rhamnosus GG (LGG) is a prevalent bacterium found in the gut microbiota and is an active component of probiotic supplements. LGG has demonstrated to be associated with cognitive improvement. This study explored whether LGG administration prior to and following induced sepsis could ameliorate cognitive deficits, and explored potential mechanisms.MethodsFemale C57BL/6 mice were randomly divided into three groups: sham surgery, cecal ligation and puncture (CLP), and CLP+LGG. Cognitive behavior was assessed longitudinally at 7-9d, 14-16d, and 21-23d after surgery using an open field test and novel object recognition test. The impact of LGG treatment on pathological changes, the expression level of brain-derived neurotrophic factor (BDNF), and the phosphorylation level of the TrkB receptor (p-TrkB) in the hippocampus of mice at two weeks post-CLP (16d) were evaluated using histological, immunofluorescence, immunohistochemistry, and western blot analyses.ResultsThe CLP surgery induced and sustained cognitive impairment in mice with sepsis for a minimum of three weeks following the surgery. Compared to mice subjected to CLP alone, the administration of LGG improved the survival of mice with sepsis and notably enhanced their cognitive functioning. Moreover, LGG supplementation significantly alleviated the decrease in hippocampal BDNF expression and p-TrkB phosphorylation levels caused by sepsis, preserving neuronal survival and mitigating the pathological changes within the hippocampus of mice with sepsis. LGG supplementation mitigates sepsis-related cognitive impairment in mice and preserves BDNF expression and p-TrkB levels in the hippocampus. creator: Linxiao Wang creator: Rui Zhao creator: Xuemei Li creator: Pei Shao creator: Jiangang Xie creator: Xiangni Su creator: Sijia Xu creator: Yang Huang creator: Shanbo Hu uri: https://doi.org/10.7717/peerj.17427 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Erector spinae plane block versus paravertebral block on postoperative quality of recovery in obese patients undergoing laparoscopic sleeve gastrectomy: a randomized controlled trial link: https://peerj.com/articles/17431 last-modified: 2024-05-28 description: PurposeTo compare the impact of erector spinae plane block (ESPB) and paravertebral block (PVB) on the quality of postoperative recovery (QoR) of patients following laparoscopic sleeve gastrectomy (LSG).MethodsA total of 110 patients who underwent elective LSG under general anesthesia were randomly assigned to receive either ultrasound-guided bilateral ESPB or PVB at T8 levels. Before anesthesia induction, 40 mL of 0.33% ropivacaine was administered. The primary outcome was the QoR-15 score at 24 hours postoperatively.ResultsAt 24 hours postoperatively, the QoR-15 score was comparable between the ESPB and PVB groups (131 (112–140) vs. 124 (111–142.5), P = 0.525). Consistently, there was no significant difference in QoR-15 scores at 48 hours postoperatively, numerical rating scale (NRS) pain scores at any postoperative time points, time to first ambulation, time to first anal exhaust, postoperative cumulative oxycodone consumption, and incidence of postoperative nausea and vomiting (PONV) between the two groups (all P > 0.05). No nerve block-related complications were observed in either group.ConclusionIn patients undergoing LSG, preoperative bilateral ultrasound-guided ESPB yields comparable postoperative recovery to preoperative bilateral ultrasound-guided PVB. creator: Guanyu Yang creator: Pengfei Wang creator: Yue Yin creator: Huan Qu creator: Xin Zhao creator: Xiaogao Jin creator: Qinjun Chu uri: https://doi.org/10.7717/peerj.17431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang et al. title: Linking patient-reported oral and general health-related quality of life link: https://peerj.com/articles/17440 last-modified: 2024-05-28 description: BackgroundThe relationship between oral and overall health is of interest to health care professionals and patients alike. This study investigated the correlation between oral health-related quality of life (OHRQoL) and health-related quality of life (HRQoL) in a general adult population.MethodsThis cross-sectional study used a convenience sample of adult participants (N = 607) attending the 2022 Minnesota County and State fairs in USA, the 5-item Oral Health Impact Profile (OHIP-5) assessed OHRQoL, and the 10-item PROMIS v.1.2 Global Health Instrument assessed HRQoL. Spearman and Pearson correlations were used to summarize the bivariable relationship between OHRQoL and HRQoL (both physical and mental health dimensions). A structural equation model determined OHRQoL-HRQoL correlations (r). Correlations’ magnitude was interpreted according to Cohen’s guidelines (r = 0.10, 0.30, and 0.50 to demarcate “small,” “medium,” and “large” effects, respectively).ResultsOHRQoL and HRQoL correlated with r = 0.52 (95% confidence interval, CI: [0.50–0.55]), indicating that the two constructs shared 27% of their information. According to Cohen, this was a “large” effect. OHRQoL, and the physical and mental HRQoL dimensions correlated with r = 0.55 (95% CI: [0.50–0.59]) and r = 0.43 (95% CI: [0.40–0.46]), respectively, indicating a “large” and a “medium” effect. OHRQoL and HRQoL were substantially correlated in an adult population.ConclusionUsing OHIP-5 to assess their dental patients’ oral health impact allows dental professionals to gain insights into patients’ overall health-related wellbeing. creator: Danna R. Paulson creator: Phonsuda Chanthavisouk creator: Mike T. John creator: Leah Feuerstahler creator: Xing Chen creator: Aparna Ingleshwar uri: https://doi.org/10.7717/peerj.17440 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Paulson et al. title: Effect of erythromycin residuals in food on the development of resistance in Streptococcus pneumoniae: an in vivo study in Galleria mellonella link: https://peerj.com/articles/17463 last-modified: 2024-05-28 description: BackgroundThe use of antimicrobials to treat food animals may result in antimicrobial residues in foodstuffs of animal origin. The European Medicines Association (EMA) and World Health Organization (WHO) define safe antimicrobial concentrations in food based on acceptable daily intakes (ADIs). It is unknown if ADI doses of antimicrobials in food could influence the antimicrobial susceptibility of human-associated bacteria.ObjectivesThis aim of this study was to evaluate if the consumption of ADI doses of erythromycin could select for erythromycin resistance in a Galleria mellonella model of Streptococcus pneumoniae infection.MethodsA chronic model of S. pneumoniae infection in G. mellonella larvae was used for the experiment. Inoculation of larvae with S. pneumoniae was followed by injections of erythromycin ADI doses (0.0875 and 0.012 μg/ml according to EMA and WHO, respectively). Isolation of S. pneumoniae colonies was then performed on selective agar plates. Minimum inhibitory concentrations (MICs) of resistant colonies were measured, and whole genome sequencing (WGS) was performed followed by variant calling to determine the genetic modifications.ResultsExposure to single doses of both EMA and WHO ADI doses of erythromycin resulted in the emergence of erythromycin resistance in S. pneumoniae. Emergent resistance to erythromycin was associated with a mutation in rplA, which codes for the L1 ribosomal protein and has been linked to macrolide resistance in previous studies.ConclusionIn our in vivo model, even single doses of erythromycin that are classified as acceptable by the WHO and EMA induced significant increases in erythromycin MICs in S. pneumoniae. These results suggest the need to include the induction of antimicrobial resistance (AMR) as a significant criterion for determining ADIs. creator: Yuliia Baranchyk creator: Zina Gestels creator: Dorien Van den Bossche creator: Saïd Abdellati creator: Basil Britto Xavier creator: Sheeba Santhini Manoharan-Basil creator: Chris Kenyon uri: https://doi.org/10.7717/peerj.17463 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Baranchyk et al. title: Impact of biological manure substitution on grain yield, nitrogen recovery efficiency, and soil biochemical properties link: https://peerj.com/articles/17475 last-modified: 2024-05-28 description: Fertilization plays a crucial role in ensuring global food security and ecological balance. This study investigated the impact of substituting innovative biological manure for chemical fertilization on rice (Oryza sativa L) productivity and soil biochemical properties based on a three-year experiment. Our results suggested rice yield and straw weight were increased under manure addition treatment. Specifically, 70% of total nitrogen (N) fertilizer substituted by biological manure derived from straw, animal waste and microbiome, led to a substantial 13.6% increase in rice yield and a remarkable 34.2% boost in straw weight. In comparison to the conventional local farmer practice of applying 165 kg N ha−1, adopting 70% of total N plus biological manure demonstrated superior outcomes, particularly in enhancing yield components and spike morphology. Fertilization treatments led to elevated levels of soil microbial biomass carbon and N. However, a nuanced comparison with local practices indicated that applying biological manure alongside urea resulted in a slight reduction in N content in vegetative and economic organs, along with decreases of 10.4%, 11.2%, and 6.1% in N recovery efficiency (NRE), respectively. Prudent N management through the judicious application of partial biological manure fertilizer in rice systems could be imperative for sustaining productivity and soil fertility in southern China. creator: Zhili Sun creator: Chengshun Wang creator: Jiabao Wang creator: Gang Wu creator: Manman Yuan creator: Haiming Zou creator: Yixiang Sun uri: https://doi.org/10.7717/peerj.17475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sun et al. title: Estimating body volumes and surface areas of animals from cross-sections link: https://peerj.com/articles/17479 last-modified: 2024-05-28 description: BackgroundBody mass and surface area are among the most important biological properties, but such information is lacking for some extant organisms and most extinct species. Numerous methods have been developed for body size estimation of animals for this reason. There are two main categories of mass-estimating approaches: extant-scaling approaches and volumetric-density approaches. Extant-scaling approaches determine the relationships between linear skeletal measurements and body mass using regression equations. Volumetric-density approaches, on the other hand, are all based on models. The models are of various types, including physical models, 2D images, and 3D virtual reconstructions. Once the models are constructed, their volumes are acquired using Archimedes’ Principle, math formulae, or 3D software. Then densities are assigned to convert volumes to masses. The acquisition of surface area is similar to volume estimation by changing math formulae or software commands. This article presents a new 2D volumetric-density approach called the cross-sectional method (CSM).MethodsThe CSM integrates biological cross-sections to estimate volume and surface area accurately. It requires a side view or dorsal/ventral view image, a series of cross-sectional silhouettes and some measurements to perform the calculation. To evaluate the performance of the CSM, two other 2D volumetric-density approaches (Graphic Double Integration (GDI) and Paleomass) are compared with it.ResultsThe CSM produces very accurate results, with average error rates around 0.20% in volume and 1.21% in area respectively. It has higher accuracy than GDI or Paleomass in estimating the volumes and areas of irregular-shaped biological structures.DiscussionMost previous 2D volumetric-density approaches assume an elliptical or superelliptical approximation of animal cross-sections. Such an approximation does not always have good performance. The CSM processes the true profiles directly rather than approximating and can deal with any shape. It can process objects that have gradually changing cross-sections. This study also suggests that more attention should be paid to the careful acquisition of cross-sections of animals in 2D volumetric-density approaches, otherwise serious errors may be introduced during the estimations. Combined with 2D modeling techniques, the CSM can be considered as an alternative to 3D modeling under certain conditions. It can reduce the complexity of making reconstructions while ensuring the reliability of the results. creator: Ruizhe Jackevan Zhao uri: https://doi.org/10.7717/peerj.17479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhao title: Epigallocatechin gallate protects MC3T3-E1 cells from cadmium-induced apoptosis and dysfunction via modulating PI3K/AKT/mTOR and Nrf2/HO-1 pathways link: https://peerj.com/articles/17488 last-modified: 2024-05-28 description: Epigallocatechin gallate (EGCG), an active constituent of tea, is recognized for its anticancer and anti-inflammatory properties. However, the specific mechanism by which EGCG protects osteoblasts from cadmium-induced damage remains incompletely understood. Here, the action of EGCG was investigated by exposing MC3T3-E1 osteoblasts to EGCG and CdCl2 and examining their growth, apoptosis, and differentiation. It was found that EGCG promoted the viability of cadmium-exposed MC3T3-E1 cells, mitigated apoptosis, and promoted both maturation and mineralization. Additionally, CdCl2 has been reported to inhibit both the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) and nuclear factor erythroid 2-related factor 2/heme oxygenase-1(Nrf2/HO-1) signaling pathways. EGCG treatment attenuated cadmium-induced apoptosis in osteoblasts and restored their function by upregulating both signaling pathways. The findings provide compelling evidence for EGCG’s role in attenuating cadmium-induced osteoblast apoptosis and dysfunction through activating the PI3K/AKT/mTOR and Nrf2/HO-1 pathways. This suggests the potential of using EGCG for treating cadmium-induced osteoblast dysfunction. creator: Fanhao Wei creator: Kai Lin creator: Binjia Ruan creator: Chaoyong Wang creator: Lixun Yang creator: Hongwei Wang creator: Yongxiang Wang uri: https://doi.org/10.7717/peerj.17488 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wei et al. title: Identification and analysis of immunoreactive proteins of Shigella flexneri in human sera and stool specimens link: https://peerj.com/articles/17498 last-modified: 2024-05-28 description: BackgroundThe method currently available to diagnose shigellosis is insensitive and has many limitations. Thus, this study was designed to identify specific antigenic protein(s) among the cell surface associated proteins (SAPs) of Shigella that would be valuable in the development of an alternative diagnostic assay for shigellosis, particularly one that could be run using a stool sample rather than serum.MethodsThe SAPs of clinical isolates of S. dysenteriae, S. boydii, Shigella flexneri, and S. sonnei were extracted from an overnight culture grown at 37 °C using acidified-glycine extraction methods. Protein profiles were observed by SDS-PAGE. To determine if antibodies specific to certain Shigella SAPs were present in both sera and stool suspensions, Western blot analysis was used to detect the presence of IgA, IgG, and IgM.ResultsImmunoblot analysis revealed that sera from patients infected with S. flexneri recognized 31 proteins. These SAP antigens are recognized by the host humoral response during Shigella infection. Specific antibodies against these antigens were also observed in intestinal secretions of shigellosis patients. Of these 31 S. flexneri proteins, the 35 kDa protein specifically reacted against IgA present in patients’ stool suspensions. Further study illustrated the immunoreactivity of this protein in S. dysenteriae, S. boydii, and S. sonnei. This is the first report that demonstrates the presence of immunoreactive Shigella SAPs in stool suspensions. The SAPSs could be very useful in developing a simple and rapid serodiagnostic assay for shigellosis directly from stool specimens. creator: Kirnpal Kaur Banga Singh creator: Mohd Zaki Salleh creator: Naveed Ahmed creator: Chan Yean Yean creator: Asma Ismail uri: https://doi.org/10.7717/peerj.17498 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Singh et al. title: Elevational variation in morphology and biomass allocation in carpathian snowbell Soldanella carpatica (Primulaceae) link: https://peerj.com/articles/17500 last-modified: 2024-05-28 description: Plants growing along wide elevation gradients in mountains experience considerable variations in environmental factors that vary across elevations. The most pronounced elevational changes are in climate conditions with characteristic decrease in air temperature with an increase in elevation. Studying intraspecific elevational variations in plant morphological traits and biomass allocation gives opportunity to understand how plants adapted to steep environmental gradients that change with elevation and how they may respond to climate changes related to global warming. In this study, phenotypic variation of an alpine plant Soldanella carpatica Vierh. (Primulaceae) was investigated on 40 sites distributed continuously across a 1,480-m elevation gradient in the Tatra Mountains, Central Europe. Mixed-effects models, by which plant traits were fitted to elevation, revealed that on most part of the gradient total leaf mass, leaf size and scape height decreased gradually with an increase in elevation, whereas dry mass investment in roots and flowers as well as individual flower mass did not vary with elevation. Unexpectedly, in the uppermost part of the elevation gradient overall plant size, including both below-and aboveground plant parts, decreased rapidly causing abrupt plant miniaturization. Despite the plant miniaturization at the highest elevations, biomass partitioning traits changed gradually across the entire species elevation range, namely, the leaf mass fraction decreased continuously, whereas the flower mass fraction and the root:shoot ratio increased steadily from the lowest to the highest elevations. Observed variations in S. carpatica phenotypes are seen as structural adjustments to environmental changes across elevations that increase chances of plant survival and reproduction at different elevations. Moreover, results of the present study agreed with the observations that populations of species from the ‘Soldanella’ intrageneric group adapted to alpine and subnival zones still maintain typical ‘Soldanella’-like appearance, despite considerable reduction in overall plant size. creator: Piotr Kiełtyk uri: https://doi.org/10.7717/peerj.17500 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kiełtyk title: Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae link: https://peerj.com/articles/17292 last-modified: 2024-05-27 description: Background & ObjectivesAmerican foulbrood (AFB), caused by the highly virulent, spore-forming bacterium Paenibacillus larvae, poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against P. larvae, a causative agent of American foulbrood disease in honey bee.MethodsWe investigated effective novel drug targets through a comprehensive in silico pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of P. larvae genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora (n > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand.ResultsProteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against P. larvae.ConclusionsComputer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry. creator: Sawsen Rebhi creator: Zarrin Basharat creator: Calvin R. Wei creator: Salim Lebbal creator: Hanen Najjaa creator: Najla Sadfi-Zouaoui creator: Abdelmonaem Messaoudi uri: https://doi.org/10.7717/peerj.17292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rebhi et al. title: The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq link: https://peerj.com/articles/17335 last-modified: 2024-05-27 description: BackgroundThe chloroplast genome has the potential to be genetically engineered to enhance the agronomic value of major crops. As a crop plant with major economic value, it is important to understand every aspect of the genetic inheritance pattern among Elaeis guineensis individuals to ensure the traceability of agronomic traits.MethodsTwo parental E. guineensis individuals and 23 of their F1 progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled de novo from the cleaned raw reads and aligned to check for variations. The sequences were compared and analyzed with programming language scripting and relevant bioinformatic softwares. Simple sequence repeat (SSR) loci were determined from the chloroplast genome.ResultsThe chloroplast genome assembly resulted in 156,983 bp, 156,988 bp, 156,982 bp, and 156,984 bp. The gene content and arrangements were consistent with the reference genome published in the GenBank database. Seventy-eight SSRs were detected in the chloroplast genome, with most located in the intergenic spacer region.The chloroplast genomes of 17 F1 progenies were exact copies of the maternal parent, while six individuals showed a single variation in the sequence. Despite the significant variation displayed by the male parent, all the nucleotide variations were synonymous. This study show highly conserve gene content and sequence in Elaeis guineensis chloroplast genomes. Maternal inheritance of chloroplast genome among F1 progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of Elaeis guineensis chloroplast genome especially among crops’ scientists who consider using chloroplast genome for agronomic trait modifications. creator: Nurul Shakina Mohd Talkah creator: Nur Afieqah Kaz Abdul Aziz creator: Muhammad Farid Abdul Rahim creator: Nurul Fatiha Farhana Hanafi creator: Mohd Azinuddin Ahmad Mokhtar creator: Ahmad Sofiman Othman uri: https://doi.org/10.7717/peerj.17335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mohd Talkah et al. title: Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas link: https://peerj.com/articles/17385 last-modified: 2024-05-27 description: BackgroundKoalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection.MethodsForaging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala’s gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection.Results and DiscussionThis research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection.ConclusionWe showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas. creator: Kotaro Kondo creator: Mirei Suzuki creator: Mana Amadaira creator: Chiharu Araki creator: Rie Watanabe creator: Koichi Murakami creator: Shinsaku Ochiai creator: Tadatoshi Ogura creator: Takashi Hayakawa uri: https://doi.org/10.7717/peerj.17385 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kondo et al. title: Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens link: https://peerj.com/articles/17410 last-modified: 2024-05-27 description: The basic helix-loop-helix (bHLH) gene family is integral to various aspects of plant development and the orchestration of stress response. This study focuses on the bHLH genes within Populus × canescens, a poplar species noted for its significant tolerance to cadmium (Cd) stress. Through our comprehensive genomic analysis, we have identified and characterized 170 bHLH genes within the P. canescens genome. These genes have been systematically classified into 22 distant subfamilies based on their evolutionary relationships. A notable conservation in gene structure and motif compositions were conserved across these subfamilies. Further analysis of the promoter regions of these genes revealed an abundance of essential cis-acting element, which are associated with plant hormonal regulation, development processes, and stress response pathway. Utilizing quantitative PCR (qPCR), we have documented the differential regulation of PcbHLHs in response to elevated Cd concentrations, with distinct expression patterns observed across various tissues. This study is poised to unravel the molecular mechanism underpinning Cd tolerance in P. canescens, offering valuable insights for the development of new cultivars with enhanced Cd accumulation capacity and tolerance. Such advancements are crucial for implementing effective phytoremediation strategies to mitigate soil pollution caused by Cd. creator: Yuneng Yao creator: Zhengquan He creator: Xinmeng Li creator: Jing Xu creator: Xiaojiao Han creator: Hongwei Liang creator: Renying Zhuo creator: Wenmin Qiu uri: https://doi.org/10.7717/peerj.17410 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Yao et al. title: Identification and analysis of novel recessive alleles for Tan1 and Tan2 in sorghum link: https://peerj.com/articles/17438 last-modified: 2024-05-27 description: BackgroundThe identification and analysis of allelic variation are important bases for crop diversity research, trait domestication and molecular marker development. Grain tannin content is a very important quality trait in sorghum. Higher tannin levels in sorghum grains are usually required when breeding varieties resistant to bird damage or those used for brewing liquor. Non-tannin-producing or low-tannin-producing sorghum accessions are commonly used for food and forage. Tan1 and Tan2, two important cloned genes, regulate tannin biosynthesis in sorghum, and mutations in one or two genes will result in low or no tannin content in sorghum grains. Even if sorghum accessions contain dominant Tan1 and Tan2, the tannin contents are distributed from low to high, and there must be other new alleles of the known regulatory genes or new unknown genes contributing to tannin production.MethodsThe two parents 8R306 and 8R191 did not have any known recessive alleles for Tan1 and Tan2, and it was speculated that they probably both had dominant Tan1 and Tan2 genotypes. However, the phenotypes of two parents were different; 8R306 had tannins and 8R191 had non-tannins in the grains, so these two parents were constructed as a RIL population. Bulked segregant analysis (BSA) was used to determine other new alleles of Tan1 and Tan2 or new Tannin locus. Tan1 and Tan2 full-length sequences and tannin contents were detected in wild sorghum resources, landraces and cultivars.ResultsWe identified two novel recessive tan1-d and tan1-e alleles and four recessive Tan2 alleles, named as tan2-d, tan2-e, tan2-f, and tan2-g. These recessive alleles led to loss of function of Tan1 and Tan2, and low or no tannin content in sorghum grains. The loss-of-function alleles of tan1-e and tan2-e were only found in Chinese landraces, and other alleles were found in landraces and cultivars grown all around the world. tan1-a and tan1-b were detected in foreign landraces, Chinese cultivars and foreign cultivars, but not in Chinese landraces.ConclusionThese results implied that Tan1 and Tan2 recessive alleles had different geographically distribution in the worldwide, but not all recessive alleles had been used in breeding. The discovery of these new alleles provided new germplasm resources for breeding sorghum cultivars for food and feed, and for developing molecular markers for low-tannin or non-tannin cultivar-assisted breeding in sorghum. creator: Lixia Zhang creator: Chunyu Wang creator: Miao Yu creator: Ling Cong creator: Zhenxing Zhu creator: Bingru Chen creator: Xiaochun Lu uri: https://doi.org/10.7717/peerj.17438 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Biodegradation of crystal violet by newly isolated bacteria link: https://peerj.com/articles/17442 last-modified: 2024-05-27 description: Confronting the environmental threat posed by textile dyes, this study highlights bioremediation as a pivotal solution to mitigate the impacts of Crystal Violet, a widely-utilized triphenylmethane dye known for its mutagenic and mitotic toxicity. We isolated and identified several bacterial strains capable of degrading Crystal Violet under various environmental conditions. Newly identified strains, including Mycolicibacterium nivoides, Chryseobacterium sp., Agrobacterium rhizogenes, Pseudomonas crudilactis, and Pseudomonas koreensis demonstrated significant decolorization activity of Crystal Violet, complementing the already known capabilities of Stenotrophomonas maltophilia. Initial experiments using crude extracts confirmed their degradation potential, followed by detailed studies that investigated the impact of different pH levels and temperatures on some strains’ degradation efficiency. Depending on the bacteria, the degree of activity change according to pH and temperature was different. At 37 °C, Chryseobacterium sp. and Stenotrophomonas maltophilia exhibited higher degradation activity compared to 25 °C, while Pseudomonas crudilactis and Mycolicibacterium nivoides did not exhibit a statistically significant difference between the two temperatures. Mycolicibacterium nivoides performed optimally at pH 8, while Pseudomonas crudilactis showed high activity at pH 5. Stenotrophomonas maltophilia’s activity remained consistent across the pH range. These findings not only underscore the effectiveness of these bacteria as agents for Crystal Violet degradation but also pave the way for their application in large-scale bioremediation processes for the treatment of textile effluents, marking them as vital to environmental sustainability efforts. creator: Soon Jun Kwak creator: Jiyul Park creator: Yuri Sim creator: Hisu Choi creator: Jein Cho creator: Young-Man Lee uri: https://doi.org/10.7717/peerj.17442 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kwak et al. title: Migraine eye: correlation between migraine and the retina link: https://peerj.com/articles/17454 last-modified: 2024-05-27 description: BackgroundActivation of the trigeminal vascular system in migraine releases vasoactive neurotransmitters, causing abnormal vasoconstriction, which may affect the ocular system, leading to retinal damage. The purpose of our study was to determine whether there are differences in each retinal layer between migraine patients and healthy subjects.MethodsA case-control study recruited 38 migraine patients and 38 age- and sex-matched controls. Optical coherence tomography was used to measure the thickness of the peripapillary and macular retinal nerve fiber layer (pRNFL and mRNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), and inner nuclear layer (INL).ResultsThe mean ages of the migraine patients and controls were 36.29 ± 9.45 and 36.45 ± 9.27 years, respectively. Thirty-four patients (89.48%) in both groups were female. The mean disability score was 19.63 ± 20.44 (indicating severe disability). The superior-outer INL of migraine patients were thicker than controls. Thickness of the GCL at temporal-outer sector and mRNFL at the superior-outer sector of the headache-side eyes was reduced. However, the INL of the headache-side-eye showed negative correlation with the disability score. This is the first study having found thinning of the GCL and mRNFL of the headache-side eyes. The INL was also thickened in migraines but showed negative correlation with the disability score.ConclusionsIncreased INL thickness in migraine patients may result from inflammation. The more severe cases with a high disability score might suffered progressive retinal neuronal loss, resulting in thinner INL than less severe cases. creator: Lunla Udomwech creator: Rini Sulastiwaty creator: Doungkamol Siriarchawawat uri: https://doi.org/10.7717/peerj.17454 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Udomwech et al. title: Exogenous application of 5-NGS increased osmotic stress resistance by improving leaf photosynthetic physiology and antioxidant capacity in maize link: https://peerj.com/articles/17474 last-modified: 2024-05-27 description: BackgroundDrought is a critical limiting factor affecting the growth and development of spring maize (Zea mays L.) seedlings in northeastern China. Sodium 5-nitroguaiacol (5-NGS) has been found to enhance plant cell metabolism and promote seedling growth, which may increase drought tolerance.MethodsIn the present study, we investigated the response of maize seedlings to foliar application of a 5-NGS solution under osmotic stress induced by polyethylene glycol (PEG-6000). Four treatment groups were established: foliar application of distilled water (CK), foliar application of 5-NGS (NS), osmotic stress + foliar application of distilled water (D), and osmotic stress + foliar application of 5-NGS (DN). Plant characteristics including growth and photosynthetic and antioxidant capacities under the four treatments were evaluated.ResultsThe results showed that under osmotic stress, the growth of maize seedlings was inhibited, and both the photosynthetic and antioxidant capacities were weakened. Additionally, there were significant increases in the proline and soluble sugar contents and a decrease in seedling relative water content (RWC). However, applying 5-NGS alleviated the impact of osmotic stress on maize seedling growth parameters, particularly the belowground biomass, with a dry mass change of less than 5% and increased relative water content (RWC). Moreover, treatment with 5-NGS mitigated the inhibition of photosynthesis caused by osmotic stress by restoring the net photosynthetic rate (Pn) through an increase in chlorophyll content, photosynthetic electron transport, and intercellular CO2 concentration (Ci). Furthermore, the activity of antioxidant enzymes in the aboveground parts recovered, resulting in an approximately 25% decrease in both malondialdehyde (MDA) and H2O2. Remarkably, the activity of enzymes in the underground parts exhibited more significant changes, with the contents of MDA and H2O2 decreasing by more than 50%. Finally, 5-NGS stimulated the dual roles of soluble sugars as osmoprotectants and energy sources for metabolism under osmotic stress, and the proline content increased by more than 30%. We found that 5-NGS played a role in the accumulation of photosynthates and the effective distribution of resources in maize seedlings.ConclusionsBased on these results, we determined that foliar application of 5-NGS may improve osmotic stress tolerance in maize seedlings. This study serves as a valuable reference for increasing maize yield under drought conditions. creator: Deguang Yang creator: Zhifeng Gao creator: Yuqi Liu creator: Qiao Li creator: Jingjing Yang creator: Yanbo Wang creator: Meiyu Wang creator: Tenglong Xie creator: Meng Zhang creator: Hao Sun uri: https://doi.org/10.7717/peerj.17474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang et al. title: Evaluation of a cadaveric wrist motion simulator using marker-based X-ray reconstruction of moving morphology link: https://peerj.com/articles/17179 last-modified: 2024-05-24 description: Surgical intervention is a common option for the treatment of wrist joint arthritis and traumatic wrist injury. Whether this surgery is arthrodesis or a motion preserving procedure such as arthroplasty, wrist joint biomechanics are inevitably altered. To evaluate effects of surgery on parameters such as range of motion, efficiency and carpal kinematics, repeatable and controlled motion of cadaveric specimens is required. This study describes the development of a device that enables cadaveric wrist motion to be simulated before and after motion preserving surgery in a highly controlled manner. The simulator achieves joint motion through the application of predetermined displacements to the five major tendons of the wrist, and records tendon forces. A pilot experiment using six wrists aimed to evaluate its accuracy and reproducibility. Biplanar X-ray videoradiography (BPVR) and X-Ray Reconstruction of Moving Morphology (XROMM) were used to measure overall wrist angles before and after total wrist arthroplasty. The simulator was able to produce flexion, extension, radioulnar deviation, dart thrower’s motion and circumduction within previously reported functional ranges of motion. Pre- and post-surgical wrist angles did not significantly differ. Intra-specimen motion trials were repeatable; root mean square errors between individual trials and average wrist angle and tendon force profiles were below 1° and 2 N respectively. Inter-specimen variation was higher, likely due to anatomical variation and lack of wrist position feedback. In conclusion, combining repeatable intra-specimen cadaveric motion simulation with BPVR and XROMM can be used to determine potential effects of motion preserving surgeries on wrist range of motion and biomechanics. creator: Joanna Glanville creator: Karl T. Bates creator: Daniel Brown creator: Daniel Potts creator: John Curran creator: Sebastiano Fichera uri: https://doi.org/10.7717/peerj.17179 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Glanville et al. title: Assessment of medical information on irritable bowel syndrome information in Wikipedia and Baidu Encyclopedia: comparative study link: https://peerj.com/articles/17264 last-modified: 2024-05-24 description: BackgroundIrritable bowel syndrome (IBS) is a functional gastrointestinal disorder (FGID) with heterogeneous clinical presentations. There are no clear testing parameters for its diagnosis, and the complex pathophysiology of IBS and the limited time that doctors have to spend with patients makes it difficult to adequately educate patients in the outpatient setting. An increased awareness of IBS means that patients are more likely to self-diagnose and self-manage IBS based on their own symptoms. These factors may make patients more likely to turn to Internet resources. Wikipedia is the most popular online encyclopedia among English-speaking users, with numerous validations. However, in Mandarin-speaking regions, the Baidu Encyclopedia is most commonly used. There have been no studies on the reliability, readability, and objectivity of IBS information on the two sites. This is an urgent issue as these platforms are accessed by approximately 1.45 billion people.ObjectiveWe compared the IBS content on Wikipedia (in English) and Baidu Baike (in Chinese), two online encyclopedias, in terms of reliability, readability, and objectivity.MethodsThe Baidu Encyclopedia (in Chinese) and Wikipedia (in English) were evaluated based on the Rome IV IBS definitions and diagnoses. All possible synonyms and derivatives for IBS and IBS-related FGIDs were screened and identified. Two gastroenterology experts evaluated the scores of articles for both sites using the DISCERN instrument, the Journal of the American Medical Association scoring system (JAMA), and the Global Quality Score (GQS).ResultsWikipedia scored higher overall with DISCERN (p < .0001), JAMA (p < .0001) and GQS (p < .05) than the Baidu Encyclopedia. Specifically, Wikipedia scored higher in DISCERN Section 1 (p < .0001), DISCERN Section 2 (p < .01), DISCERN Section 3 (p < .001), and the General DISCERN score (p < .0001) than the Baidu Encyclopedia. Both sites had low DISCERN Section 2 scores (p = .18). Wikipedia also had a larger percentage of high quality scores in total DISCERN, DISCERN Section 1, and DISCERN Section 3 (p < .0001, P < .0001, P < .0004, respectively, based on the above 3 (60%) rule).ConclusionsWikipedia provides more reliable, higher quality, and more objective IBS-related health information than the Baidu Encyclopedia. However, there should be improvements in the information quality for both sites. Medical professionals and institutions should collaborate with these online platforms to offer better health information for IBS. creator: Xi Li creator: Kexin Chen creator: Yongbin Jia creator: Fang Yin creator: Xi Wen creator: Chunhui Wang creator: Zhipeng Li creator: Hu Zhang uri: https://doi.org/10.7717/peerj.17264 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Polymorphism in the aggressive mimicry lure of the parasitic freshwater mussel Lampsilis fasciola link: https://peerj.com/articles/17359 last-modified: 2024-05-24 description: Unionoid freshwater mussels (Bivalvia: Unionidae) are free-living apart from a brief, obligately parasitic, larval stage that infects fish hosts, and gravid female mussels have evolved a spectrum of strategies to infect fish hosts with their larvae. In many North American species, this involves displaying a mantle lure: a pigmented fleshy extension that acts as an aggressive mimic of a host fish prey, thereby eliciting a feeding response that results in host infection. The mantle lure of Lampsilis fasciola is of particular interest because it is apparently polymorphic, with two distinct primary lure phenotypes. One, described as “darter-like”, has “eyespots”, a mottled body coloration, prominent marginal extensions, and a distinct “tail”. The other, described as “worm-like”, lacks those features and has an orange and black coloration. We investigated this phenomenon using genomics, captive rearing, biogeographic, and behavioral analyses. Within-brood lure variation and within-population phylogenomic (ddRAD-seq) analyses of individuals bearing different lures confirmed that this phenomenon is a true polymorphism. The relative abundance of the two morphs appears stable over ecological timeframes: the ratio of the two lure phenotypes in a River Raisin (MI) population in 2017 was consistent with that of museum samples collected at the same site six decades earlier. Within the River Raisin, four main “darter-like” lure motifs visually approximated four co-occurring darter species (Etheostoma blennioides, E. exile, E. microperca, and Percina maculata), and the “worm-like” lure resembled a widespread common leech, Macrobdella decora. Darters and leeches are typical prey of Micropterus dolomieui (smallmouth bass), the primary fish host of L. fasciola. In situ field recordings of the L. fasciola “darter” and “leech” lure display behaviors, and the lure display of co-occurring congener L. cardium, were captured. Despite having putative models in distinct phyla, both L. fasciola lure morphs have largely similar display behaviors that differ significantly from that of sympatric L. cardium individuals. Some minor differences in the behavior between the two L. fasciola morphs were observed, but we found no clear evidence for a behavioral component of the polymorphism given the criteria measured. Discovery of discrete within-brood inheritance of the lure polymorphism implies potential control by a single genetic locus and identifies L. fasciola as a promising study system to identify regulatory genes controlling a key adaptive trait of freshwater mussels. creator: Trevor L. Hewitt creator: Paul D. Johnson creator: Michael Buntin creator: Talia Y. Moore creator: Diarmaid Ó Foighil uri: https://doi.org/10.7717/peerj.17359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hewitt et al. title: Wearing surgical face mask has no significant impact on auscultation assessment link: https://peerj.com/articles/17368 last-modified: 2024-05-24 description: ObjectiveDuring the COVID-19 pandemic, universal mask-wearing became one of the main public health interventions. Because of this, most physical examinations, including lung auscultation, were done while patients were wearing surgical face masks. The aim of this study was to investigate whether mask wearing has an impact on pulmonologist assessment during auscultation of the lungs.MethodsThis was a repeated measures crossover design study. Three pulmonologists were instructed to auscultate patients with previously verified prolonged expiration, wheezing, or crackles while patients were wearing or not wearing masks (physician and patients were separated by an opaque barrier). As a measure of pulmonologists’ agreement in the assessment of lung sounds, we used Fleiss kappa (K).ResultsThere was no significant difference in agreement on physician assessment of lung sounds in all three categories (normal lung sound, duration of expiration, and adventitious lung sound) whether the patient was wearing a mask or not, but there were significant differences among pulmonologists when it came to agreement of lung sound assessment.ConclusionClinicians and health professionals are safer from respiratory infections when they are wearing masks, and patients should be encouraged to wear masks because our research proved no significant difference in agreement on pulmonologists’ assessment of auscultated lung sounds whether or not patients wore masks. creator: Ivana Folnožić creator: Marija Gomerčić Palčić creator: Matilda Sabljak creator: Ena Vučak creator: Luka Vrbanić creator: Marija Mandić Perić creator: Fanika Mrsić creator: Aljoša Šikić creator: Ivan Ivanovski uri: https://doi.org/10.7717/peerj.17368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Folnožić et al. title: Comparative evaluation of the sleep quality metrics between a cardboard bed and a camp cot: a randomized controlled crossover study link: https://peerj.com/articles/17392 last-modified: 2024-05-24 description: BackgroundHealth-beneficial emergency bedding has become increasingly important for dealing with natural disasters such as the anticipated Nankai Trough earthquake in Japan. When the Great East Japan Earthquake occurred, cardboard beds were provided to evacuees. However, there were concerns about lower back pain and sleep disturbances, as cardboard beds offer insufficient pressure distribution. This study aimed to compare the effects of cardboard beds with those of foldable camp cots on sleep quality.MethodsA randomized controlled crossover study involving 20 healthy participants aged 18–45 years was conducted between June 2022 and January 2023. Participants were asked to sleep for one night on a camp cot and for another night on a cardboard bed, with a minimum three-day washout period between the two nights. Body pressure distribution and sleep metrics obtained from polysomnography (PSG) and questionnaires were compared between the two-bed types (P < 0.05).ResultsThe camp cot exhibited better body pressure distribution than a cardboard bed, leading to improved sleep satisfaction, bedding comfort, and reduced morning sleepiness. Nevertheless, polysomnography revealed no notable differences in sleep metrics or sleep architecture between the two types of beds.ConclusionsOur findings indicate that cardboard beds have lower pressure dispersion capabilities than camp cots, leading to an increased number of position changes during sleep. Additionally, subjective sleep quality, such as alertness on waking, sleep comfort, and sleep satisfaction, was lower for cardboard beds, suggesting that camp cots might offer a more comfortable bedding option for evacuees. However, there were no discernible differences between the two-bed types in terms of objective sleep metrics derived from PSG. The potential for sleep disturbances caused by lower back pain from a hard mattress has been noted, and it is possible that a single night’s experience in healthy individuals might not be enough for sleep issues to manifest. creator: Seiji Hamanishi creator: Airi Miki creator: Shinsuke Sasaki uri: https://doi.org/10.7717/peerj.17392 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hamanishi et al. title: Using a golf specific functional movement screen to predict golf performance in collegiate golfers link: https://peerj.com/articles/17411 last-modified: 2024-05-24 description: BackgroundThis study aims to examine the relationship between functional movements and golf performance using the Golf Specific Functional Movement Screen (GSFMS).MethodsThis cross-sectional study included a total of 56 collegiate golfers (aged 20.89 ± 0.99 years, height of 174.55 ± 7.76 cm, and weight 68.48 ± 9.30 kg) who met the criteria, and were recruited from Hainan Normal University in June 2022. The participants’ golf motor skills (1-yard putt, 10-yard putt, 25-yard chip, 130/100-yard set shot, driver, and 9-hole stroke play) were tested and the GSFMS (e.g., pelvic tilt, pelvic rotation, and torso rotation) was used.ResultsThere were significant weak or moderate correlations between the variables. Furthermore, a multiple linear regression analysis found that pelvic rotation and lower-body rotation abilities can significantly predict golf skill levels, which collectively explain 31.2% of the variance in golf skill levels among collegiate golfers (Adjusted R2 = 0.312, F = 2.663, p < 0.05). Standardised β values indicate that pelvic rotation (β = 0.398) has a more substantial impact on golf skill levels than lower-body rotation (β = 0.315).ConclusionsThis study found the weak to moderate correlations between the GSFMS and golf performance, and pelvic rotation and lower-body rotation abilities, thus predicting golf skills. Our findings provide novel insights into the relationship between functional abilities and comprehensive skill performance within the context of the Gray Cook’s Movement Pyramid model, and provide theoretical support and practical reference for collegiate golf motor-skill learning and sports injury prevention. creator: Min Shi creator: Hua Wu creator: Hui Ruan creator: Dan Xu creator: Libo Deng creator: Shibo Pang uri: https://doi.org/10.7717/peerj.17411 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shi et al. title: Physical activity and self-efficacy in college students: the mediating role of grit and the moderating role of gender link: https://peerj.com/articles/17422 last-modified: 2024-05-24 description: BackgroundThere is a paucity of knowledge concerning the psychological variables that serve to facilitate the connection between physical activity and self-efficacy, and the factors capable of moderating these pathways. This study aimed to examine the relationship between physical activity and self-efficacy among college students, with a focus on the mediating effect of grit and the moderating effect of gender.MethodsThis study recruited 3,228 undergraduate students from a university in Shanghai, China. They completed the General Self-Efficacy Scale, the Short Grit Scale, and the International Physical Activity Questionnaire. Statistical analysis was conducted using SPSS 26.0 and the Process v4.0 plugin.ResultsPhysical activity had both a direct effect on self-efficacy (β = 0.07, 95% CI [0.04–0.11]) and an indirect effect through the two dimensions of grit: perseverance of effort (β = 0.06, 95% CI [0.04–0.07]) and consistency of interest (β = 0.03, 95% CI [0.02–0.04]). The mediating effect explained 53.27% of the total effect. Furthermore, gender moderated the relationship between perseverance of effort and self-efficacy, with a stronger effect observed in males (β = 0.08, t = 3.27, p < 0.01).ConclusionThe results revealed that grit is an underlying psychological mechanism that links physical activity and self-efficacy. Moreover, gender moderates the effect of perseverance of effort on self-efficacy, with a stronger effect observed in males. These findings have practical implications for educators to design tailored physical activity interventions that foster grit and self-efficacy among college students. creator: Hongyan Yu creator: Tingfei Zhu creator: Jianing Tian creator: Gang Zhang creator: Peng Wang creator: Junxiong Chen creator: Liqun Shen uri: https://doi.org/10.7717/peerj.17422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yu et al. title: Variation in fine-scale water table depth drives abundance of a unique semi-terrestrial crayfish species link: https://peerj.com/articles/17330 last-modified: 2024-05-23 description: With anthropogenic changes altering the environment and the subsequent decline of natural habitats, it can be challenging to predict essential habitats for elusive and difficult to study taxa. Primary burrowing crayfish are one such group due to the complexity in sampling their semi-terrestrial, subterranean habitat. Sampling burrows usually requires a labor-intensive, time-consuming excavation or trapping process. However, limited information on burrowing crayfish suggests that fine-scale habitat variation may drive burrowing crayfish habitat choice. This project aimed to evaluate the fine-scale habitat characteristics that influence burrowing crayfish presence and abundance at a large, restored-remnant grassland preserve in north-central Illinois. We documented burrow abundance and quadrat-specific habitat variables such as root biomass, canopy cover, apparent seasonal high-water table (water table) depth and dominant vegetation at sites with and without burrowing crayfish populations. Data was recorded at every quadrat and analyzed using generalized linear mixed models. A total of 21 models were created to determine what habitat variables affected burrow presence and abundance. We found that the water table depth was a significant driver of burrow presence and abundance. Root biomass and vegetation cover were not significant drivers, although they did show up in the final models, explaining the data. These findings demonstrate empirical support for previous observations from other burrowing crayfish research and demonstrate the influence of fine-scale habitat when modeling elusive taxa requirements. creator: Molly C. Carlson creator: Dusty A. Swedberg creator: Elizabeth A. Miernicki creator: Christopher A. Taylor uri: https://doi.org/10.7717/peerj.17330 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Carlson et al. title: Ultrastructure of the Jurassic serpulid tubes–phylogenetic and paleoecological implications link: https://peerj.com/articles/17389 last-modified: 2024-05-23 description: The ultrastructural diversity of the Middle and Late Jurassic serpulid tubes from the Polish Basin has been investigated. The inspection of 12 taxa representing the two major serpulid clades allowed for the identification of three ultrastructure types—irregularly oriented prismatic structure (IOP), spherulitic prismatic structure (SPHP), and simple prismatic structure (SP). Six of the studied species are single-layered and six species possess two distinct layers. Ultrastructural diversity corresponds to certain serpulid clades. The members of Filograninae have single-layered tube walls composed of possibly plesiomorphic, irregularly oriented prismatic structure (IOP). Two-layered tubes occur solely within the clade Serpulinae, where the external, denser layer is built of either the ordered spherulitic (SPHP) or simple prismatic microstructure (SP), and the internal layer is composed of irregularly oriented prismatic structure (IOP). Apart from phylogenetic signals provided by the tube ultrastructure, it can be used in analyzing paleoecological aspects of tube-dwelling polychaetes. Compared to the more primitive, irregularly oriented microstructures of Filograninae, the regularly oriented microstructures of Serpulinae need a higher level of biological control over biomineralization. The advent of the dense outer protective layer (DOL) in serpulids, as well as the general increase in ultrastructure diversity, was likely a result of the evolutionary importance of the tubes for serpulids. Such diversity of the tube ultrastructural fabrics allowed for maximizing functionality by utilizing a variety of morphogenetic programs. The biomineralization system of serpulids remains more complex compared to other tube-dwelling polychaetes. Physiologically more expensive tube formation allows for mechanical strengthening of the tube by building robust, strongly ornamented tubes and firm attachment to the substrate. Contrary to sabellids, which perform a fugitive strategy, an increased tube durability allows serpulids a competitive advantage over other encrusters. creator: Jakub Słowiński creator: Olev Vinn creator: Michał Zatoń uri: https://doi.org/10.7717/peerj.17389 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Słowiński et al. title: Effect of simulated clinical use and sterilization on the cyclic fatigue resistance of nickel titanium files link: https://peerj.com/articles/17418 last-modified: 2024-05-23 description: AimAssess the effect of simulated clinical use and sterilization on the cyclic fatigue resistance of Race Evo and Tia Tornado Blue nickel titanium (NiTi) files.Materials and MethodsFor this study, a total of sixty-four NiTi files were selected, with thirty-two files each from two different manufacturers. Files from each manufacturer were subdivided into four subgroups (n = 8) based on the test parameters. The control groups included files that were neither used nor sterilized. Files from the test groups were used to prepare the root canals of extracted mandibular premolars and then sterilized. This procedure was repeated once, twice, or thrice, depending on the test group. All files were then subjected to a cyclic fatigue test. Data was statistically analyzed using the Kruskal–Wallis and Mann–Whitney U tests.ResultsNo significant difference was observed in the number of cycles to failure (NCF) among the subgroups for both types of files (P = 0.869 for Tia Tornado Blue, P = 0.626 for Race Evo). Tia Tornado Blue files displayed significantly higher NCF values in the control (P = 0.021), once (P = 0.027), and thrice (P = 0.031) usage groups when compared to Race Evo files.ConclusionsRepeated clinical use and sterilization for up to three cycles did not affect the cyclic fatigue resistance of Race Evo and Tia Tornado Blue files. creator: Mohammad Alajemi creator: Ammar AbuMostafa uri: https://doi.org/10.7717/peerj.17418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Alajemi and AbuMostafa title: A murine model of hypertensive heart disease in older women link: https://peerj.com/articles/17434 last-modified: 2024-05-23 description: We propose a new mouse (C57Bl6/J) model combining several features of heart failure with preserved ejection fraction encountered in older women, including hypertension from Angiotensin II infusion (AngII), menopause, and advanced age. To mimic menopause, we delayed ovariectomy (Ovx) at 12 months of age. We also studied the effects of AngII infusion for 28 days in younger animals and the impact of losing gonadal steroids earlier in life. We observed that AngII effects on heart morphology were different in younger and adult mice (3- and 12-month-old; 20 and 19% increase in heart weight. P < 0.01 for both) than in older animals (24-month-old; 6%; not significant). Ovariectomy at 12 months restored the hypertrophic response to AngII in elderly females (23%, p = 0.0001). We performed a bulk RNA sequencing study of the left ventricle (LV) and left atrial gene expression in elderly animals, controls, and Ovx. AngII modulated (|Log2 fold change| ≥ 1) the LV expression of 170 genes in control females and 179 in Ovx ones, 64 being shared. In the left atrium, AngII modulated 235 genes in control females and 453 in Ovx, 140 shared. We observed many upregulated genes associated with the extracellular matrix regulation in both heart chambers. Many of these upregulated genes were shared between the ventricle and the atrium as well as in control and Ovx animals, namely for the most expressed Ankrd1, Nppb, Col3a1, Col1a1, Ctgf Col8a1, and Cilp. Several circadian clock LV genes were modulated differently by AngII between control and Ovx females (Clock, Arntl, Per2, Cry2, and Ciart). In conclusion, sex hormones, even in elderly female mice, modulate the heart’s hypertrophic response to AngII. Our study identifies potential new markers of hypertensive disease in aging female mice and possible disturbances of their cardiac circadian clock. creator: Audrey Morin-Grandmont creator: Elisabeth Walsh-Wilkinson creator: Sara-Ève Thibodeau creator: Dominique K. Boudreau creator: Marie Arsenault creator: Yohan Bossé creator: Jacques Couet uri: https://doi.org/10.7717/peerj.17434 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Morin-Grandmont et al. title: Abiotic processes control carbon dioxide dynamics in temperate karst lakes link: https://peerj.com/articles/17393 last-modified: 2024-05-22 description: Inland waters are crucial in the carbon cycle, contributing significantly to the global CO2 fluxes. Carbonate lakes may act as both sources and sinks of CO2 depending on the interactions between the amount of dissolved inorganic carbon (DIC) inputs, lake metabolisms, and geochemical processes. It is often difficult to distinguish the dominant mechanisms driving CO2 dynamics and their effects on CO2 emissions. This study was undertaken in three groundwater-fed carbonate-rich lakes in central Spain (Ruidera Lakes), severely polluted with nitrates from agricultural overfertilization. Diel and seasonal (summer and winter) changes in CO2 concentration (CCO2) DIC, and CO2 emissions-(FCO2)-, as well as physical and chemical variables, including primary production and phytoplanktonic chlorophyll-a were measured. In addition, δ13C-DIC, δ13C-CO2 in lake waters, and δ13C of the sedimentary organic matter were measured seasonally to identify the primary CO2 sources and processes. While the lakes were consistently CCO2 supersaturated and FCO2 was released to the atmosphere during both seasons, the highest CCO2 and DIC were in summer (0.36–2.26 µmol L–1). Our results support a strong phosphorus limitation for primary production in these lakes, which impinges on CO2 dynamics. External DIC inputs to the lake waters primarily drive the CCO2 and, therefore, the FCO2. The δ13C-DIC signatures below –12‰  confirmed the primary geogenic influence on DIC. As also suggested by the high values on the calcite saturation index, the Miller-Tans plot revealed that the CO2 source in the lakes was close to the signature provided by the fractionation of δ13C-CO2 from calcite precipitation. Therefore, the main contribution behind the CCO2 values found in these karst lakes should be attributed to the calcite precipitation process, which is temperature-dependent according to the seasonal change observed in δ13C-DIC values. Finally, co-precipitation of phosphate with calcite could partly explain the observed low phytoplankton production in these lakes and the impact on the contribution to increasing greenhouse gas emissions. However, as eutrophication increases and the soluble reactive phosphorus (SRP) content increases, the co-precipitation of phosphate is expected to be progressively inhibited. These thresholds must be assessed to understand how the CO32− ions drive lake co-precipitation dynamics. Carbonate regions extend over 15% of the Earth’s surface but seem essential in the CO2 dynamics at a global scale. creator: Mariana Vargas-Sánchez creator: Javier Alcocer creator: Eric Puche creator: Salvador Sánchez-Carrillo uri: https://doi.org/10.7717/peerj.17393 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vargas-Sánchez et al. title: Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea link: https://peerj.com/articles/17314 last-modified: 2024-05-22 description: BackgroundDespite the Caridean shrimps’ vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P.  ortmanni, P. izumiae and P. lophotes.MethodsThe complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina’s next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank.ResultsThe complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species—P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group.ConclusionsGene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus. creator: Yuman Sun creator: Jian Chen creator: Xinjie Liang creator: Jiji Li creator: Yingying Ye creator: Kaida Xu uri: https://doi.org/10.7717/peerj.17314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sun et al. title: The nematode Caenorhabditis elegans enhances tolerance to landfill leachate stress by increasing trehalose synthesis link: https://peerj.com/articles/17332 last-modified: 2024-05-22 description: The burgeoning issue of landfill leachate, exacerbated by urbanization, necessitates evaluating its biological impact, traditionally overshadowed by physical and chemical assessments. This study harnesses Caenorhabditis elegans, a model organism, to elucidate the physiological toxicity of landfill leachate subjected to different treatment processes: nanofiltration reverse osmosis tail water (NFRO), membrane bioreactor (MBR), and raw leachate (RAW). Our investigation focuses on the modulation of sugar metabolism, particularly trehalose—a disaccharide serving dual functions as an energy source and an anti-adversity molecule in invertebrates. Upon exposure, C. elegans showcased a 60–70% reduction in glucose and glycogen levels alongside a significant trehalose increase, highlighting an adaptive response to environmental stress by augmenting trehalose synthesis. Notably, trehalose-related genes in the NFRO group were up-regulated, contrasting with the MBR and RAW groups, where trehalose synthesis genes outpaced decomposition genes by 20–30 times. These findings suggest that C. elegans predominantly counters landfill leachate-induced stress through trehalose accumulation. This research not only provides insights into the differential impact of leachate treatment methods on C. elegans but also proposes a molecular framework for assessing the environmental repercussions of landfill leachate, contributing to the development of novel strategies for pollution mitigation and environmental preservation. creator: Yuru Chen creator: Binsong Jin creator: Jie Yu creator: Liangwei Wu creator: Yingying Wang creator: Bin Tang creator: Huili Chen uri: https://doi.org/10.7717/peerj.17332 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Determining the plant-pollinator network in a culturally significant food and medicine garden in the Great Lakes region link: https://peerj.com/articles/17401 last-modified: 2024-05-22 description: Understanding the interactions between plants and pollinators within a system can provide information about pollination requirements and the degree to which species contribute to floral reproductive success. Past research has focused largely on interactions within monocultured agricultural systems and only somewhat on wild pollination networks. This study focuses on the culturally significant Three Sisters Garden, which has been grown and tended by many Indigenous peoples for generations in the Great Lakes Region. Here, the plant-pollinator network of the traditional Three Sisters Garden with the inclusion of some additional culturally significant plants was mapped. Important visitors in this system included the common eastern bumble bee, Bombus impatiens Cresson (Hymenoptera: Apidae), and the hoary squash bee, Xenoglossa pruinosa (Say) (Hymenoptera: Apidae), as determined by their abundances and pollinator service index (PSI) values. Understanding the key pollinators in the Three Sisters Garden links biological diversity to cultural diversity through the pollination of culturally significant plants. Further, this information could be of use in supporting Indigenous food sovereignty by providing knowledge about which wild pollinators could be supported to increase fruit and seed set within the Three Sisters Garden. Our findings can also lead to more effective conservation of important wild pollinator species. creator: Shelby D. Gibson creator: Thomas M. Onuferko creator: Lisa Myers creator: Sheila R. Colla uri: https://doi.org/10.7717/peerj.17401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gibson et al. title: Temperature-size responses during ontogeny are independent of progenitors’ thermal environments link: https://peerj.com/articles/17432 last-modified: 2024-05-22 description: BackgroundWarming generally induces faster developmental and growth rates, resulting in smaller asymptotic sizes of adults in warmer environments (a pattern known as the temperature-size rule). However, whether temperature-size responses are affected across generations, especially when thermal environments differ from one generation to the next, is unclear. Here, we tested temperature-size responses at different ontogenetic stages and in two consecutive generations using two soil-living Collembola species from the family Isotomidae: Folsomia candida (asexual) and Proisotoma minuta (sexually reproducing).MethodsWe used individuals (progenitors; F0) from cultures maintained during several generations at 15 °C or 20 °C, and exposed their offspring in cohorts (F1) to various thermal environments (15 °C, 20 °C, 25 °C and 30 °C) during their ontogenetic development (from egg laying to first reproduction; i.e., maturity). We measured development and size traits in the cohorts (egg diameter and body length at maturity), as well as the egg diameters of their progeny (F2). We predicted that temperature-size responses would be predominantly determined by within-generation plasticity, given the quick responsiveness of growth and developmental rates to changing thermal environments. However, we also expected that mismatches in thermal environments across generations would constrain temperature-size responses in offspring, possibly due to transgenerational plasticity.ResultsWe found that temperature-size responses were generally weak in the two Collembola species, both for within- and transgenerational plasticity. However, egg and juvenile development were especially responsive at higher temperatures and were slightly affected by transgenerational plasticity. Interestingly, plastic responses among traits varied non-consistently in both Collembola species, with some traits showing plastic responses in one species but not in the other and vice versa. Therefore, our results do not support the view that the mode of reproduction can be used to explain the degree of phenotypic plasticity at the species level, at least between the two Collembola species used in our study. Our findings provide evidence for a general reset of temperature-size responses at the start of each generation and highlight the importance of measuring multiple traits across ontogenetic stages to fully understand species’ thermal responses. creator: Gerard Martínez-De León creator: Micha Fahrni creator: Madhav P. Thakur uri: https://doi.org/10.7717/peerj.17432 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Martínez-De León et al. title: Dental pulp stem cells ameliorate D-galactose-induced cardiac ageing in rats link: https://peerj.com/articles/17299 last-modified: 2024-05-21 description: BackgroundAgeing is a key risk factor for cardiovascular disease and is linked to several alterations in cardiac structure and function, including left ventricular hypertrophy and increased cardiomyocyte volume, as well as a decline in the number of cardiomyocytes and ventricular dysfunction, emphasizing the pathological impacts of cardiomyocyte ageing. Dental pulp stem cells (DPSCs) are promising as a cellular therapeutic source due to their minimally invasive surgical approach and remarkable proliferative ability.AimThis study is the first to investigate the outcomes of the systemic transplantation of DPSCs in a D-galactose (D-gal)-induced rat model of cardiac ageing. Methods. Thirty 9-week-old Sprague-Dawley male rats were randomly assigned into three groups: control, ageing (D-gal), and transplanted groups (D-gal + DPSCs). D-gal (300 mg/kg/day) was administered intraperitoneally daily for 8 weeks. The rats in the transplantation group were intravenously injected with DPSCs at a dose of 1 × 106 once every 2 weeks.ResultsThe transplanted cells migrated to the heart, differentiated into cardiomyocytes, improved cardiac function, upregulated Sirt1 expression, exerted antioxidative effects, modulated connexin-43 expression, attenuated cardiac histopathological alterations, and had anti-senescent and anti-apoptotic effects.ConclusionOur results reveal the beneficial effects of DPSC transplantation in a cardiac ageing rat model, suggesting their potential as a viable cell therapy for ageing hearts. creator: Gehan El-Akabawy creator: Sherif Othman Fathy El-Kersh creator: Ahmed Othman Fathy Othman El-Kersh creator: Shaimaa Nasr Amin creator: Laila Ahmed Rashed creator: Noha Abdel Latif creator: Ahmed Elshamey creator: Mohamed Abdallah Abd El Megied Abdallah creator: Ibrahim G. Saleh creator: Zaw Myo Hein creator: Ibrahim El-Serafi creator: Nabil Eid uri: https://doi.org/10.7717/peerj.17299 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 El-Akabawy et al. title: Awareness and attitudes towards eye donation among medical and allied health students in Jeddah, Saudi Arabia link: https://peerj.com/articles/17334 last-modified: 2024-05-21 description: BackgroundMany national studies in Saudi Arabia have revealed a lack of knowledge about eye donation. The current study assessed awareness and attitudes towards eye donation among health faculty students in Jeddah, Saudi Arabia. It aims to increase their awareness as future healthcare providers are expected to raise general awareness to attain more local corneal donations.MethodsA cross-sectional study including 1,060 health faculty students was conducted at King Abdulaziz University. Data were collected through an online questionnaire that covered participants’ demographics, academic year, knowledge, and attitudes regarding eye donation.ResultsThirty-five percent of students had heard about eye donation, with the most common sources of information being social media (29%) and health workers (24%). Most respondents, 61% (n = 643), indicated willingness to donate their eyes after death. Of these respondents, 93% (n = 986), 6.8% (n = 72), and 0.2% (n = 2) had poor, fair, and good knowledge levels, respectively. A total of 66% (n = 696) and 34% (n = 364) had negative and positive attitudes, respectively.ConclusionStudents in this study showed low levels of knowledge and negative attitudes about eye donation. Students should be adequately educated about the significance of eye donation. creator: Mahmood Showail creator: Turki A. AlAmoudi creator: Esraa Basalem creator: Khalid Alshebl creator: Nawaf Meshal Almalki creator: Abdullah Al Matrafi creator: Mohammed Ashour uri: https://doi.org/10.7717/peerj.17334 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Showail et al. title: Estimates on age, growth, and mortality of Leuciscus chuanchicus (Kessler 1876) in the Ningxia section of the upper reaches of the Yellow River, China link: https://peerj.com/articles/17351 last-modified: 2024-05-21 description: To investigate the age structure, growth pattern, mortality and exploitation rates of Leuciscus chuanchicus in the upstream Ningxia section of the Yellow River, four sampling surveys were conducted between 2022 and 2023. A total of 472 individuals were measured for their total length (TL) and body weight (W). Age determination was performed using otoliths. The collected samples had a range of total lengths from 4.52 to 37.45 cm, body weights ranging from 0.68 to 552.43 g, and ages ranging from 1 to 7 years old. The relationship between total length and body weight was expressed as W = 0.0052 L3.19 for all samples, which indicates that the growth of L. chuanchicus adheres to allometry. The Von Bertalanffy growth equation revealed that the fish had an asymptotic total length (L∞) of approximately 37.9 cm with a growth coefficient (K) value of approximately 0.461 yr−1. Using the age-based catch curve method, the calculated total instantaneous mortality rate (Z) for all samples was determined as being equal to approximately 1.1302 yr−1. Additionally, three methods were used to estimate the average instantaneous rate of natural mortality (M), resulting in an approximate value of 0.7167 yr−1 for all samples. Furthermore, the instantaneous rate of fishing mortality (F) for all samples was calculated as 0.4134 yr−1, leading us to determine that the exploitation rate (E) is 0.3658. It was concluded that the growth rate of L. chuanchicus in the upstream of the Yellow River is relatively fast, and L. chuanchicus has not been subjected to excessive exploitation, yet its relatively high natural mortality rate underscores the need for targeted management measures aimed at preserving its habitat. creator: Shuhan Xiong creator: Jiacheng Liu creator: Peilun Li creator: Yanbin Liu creator: Kai Liu creator: Yongjie Wang creator: Jilong Wang uri: https://doi.org/10.7717/peerj.17351 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xiong et al. title: Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs link: https://peerj.com/articles/17358 last-modified: 2024-05-21 description: Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals. creator: Ross Cunning creator: Elizabeth A. Lenz creator: Peter J. Edmunds uri: https://doi.org/10.7717/peerj.17358 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cunning et al. title: Pseudotargeted lipidomics analysis of scoparone on glycerophospholipid metabolism in non-alcoholic steatohepatitis mice by LC-MRM-MS link: https://peerj.com/articles/17380 last-modified: 2024-05-21 description: As the inflammatory subtype of nonalcoholic fatty liver disease (NAFLD), the progression of nonalcoholic steatohepatitis (NASH) is associated with disorders of glycerophospholipid metabolism. Scoparone is the major bioactive component in Artemisia capillaris which has been widely used to treat NASH in traditional Chinese medicine. However, the underlying mechanisms of scoparone against NASH are not yet fully understood, which hinders the development of effective therapeutic agents for NASH. Given the crucial role of glycerophospholipid metabolism in NASH progression, this study aimed to characterize the differential expression of glycerophospholipids that is responsible for scoparone’s pharmacological effects and assess its efficacy against NASH. Liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS) was performed to get the concentrations of glycerophospholipids, clarify mechanisms of disease, and highlight insights into drug discovery. Additionally, pathologic findings also presented consistent changes in high-fat diet-induced NASH model, and after scoparone treatment, both the levels of glycerophospholipids and histopathology were similar to normal levels, indicating a beneficial effect during the observation time. Altogether, these results refined the insights on the mechanisms of scoparone against NASH and suggested a route to relieve NASH with glycerophospholipid metabolism. In addition, the current work demonstrated that a pseudotargeted lipidomic platform provided a novel insight into the potential mechanism of scoparone action. creator: Qi Song creator: Ziyi Zhao creator: Hu Liu creator: Jinling Zhang creator: Zhiqiang Wang creator: Yunqi Zhang creator: Guowei Ma creator: Shaoqin Ge uri: https://doi.org/10.7717/peerj.17380 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Song et al. title: Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.) link: https://peerj.com/articles/17388 last-modified: 2024-05-21 description: The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes. creator: Peiqi Ye creator: Xiaoliang Che creator: Yang Liu creator: Ming Zeng creator: Wenbing Guo creator: Yongbin Long creator: Tianyi Liu creator: Zhe Wang uri: https://doi.org/10.7717/peerj.17388 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ye et al. title: Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network link: https://peerj.com/articles/17396 last-modified: 2024-05-21 description: Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants. creator: Weihan Zhang creator: Ping Zhang creator: Weicheng Sun creator: Jinsheng Xu creator: Liao Liao creator: Yunpeng Cao creator: Yuepeng Han uri: https://doi.org/10.7717/peerj.17396 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: CircCamsap1 is dispensable for male fertility in mice link: https://peerj.com/articles/17399 last-modified: 2024-05-21 description: BackgroundCircular RNAs (circRNAs) are a large class of RNAs present in mammals. Among these, circCamsap1 is a well-acknowledged circRNA with significant implications, particularly in the development and progression of diverse tumors. However, the potential consequences of circCamsap1 depletion in vivo on male reproduction are yet to be thoroughly investigated.MethodsThe presence of circCamsap1 in the mouse testes was confirmed, and gene expression analysis was performed using reverse transcription quantitative polymerase chain reaction. CircCamsap1 knockout mice were generated utilizing the CRISPR/Cas9 system. Phenotypic analysis of both the testes and epididymis was conducted using histological and immunofluorescence staining. Additionally, fertility and sperm motility were assessed.ResultsHere, we successfully established a circCamsap1 knockout mouse model without affecting the expression of parental gene. Surprisingly, male mice lacking circCamsap1 (circCamsap1−/−) exhibited normal fertility, with no discernible differences in testicular and epididymal histology, spermatogenesis, sperm counts or sperm motility compared to circCamsap1+/+ mice. These findings suggest that circCamsap1 may not play an essential role in physiological spermatogenesis. Nonetheless, this result also underscores the complexity of circRNA function in male reproductive biology. Therefore, further research is necessary to elucidate the precise roles of other circRNAs in regulating male fertility. creator: Shu Zhang creator: Haojie Li creator: Wei Jiang creator: Xia Chen creator: Han Zhou creator: Chang Wang creator: Hao Kong creator: Yichao Shi creator: Xiaodan Shi uri: https://doi.org/10.7717/peerj.17399 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: No benefit of higher protein dosing in critically ill patients: a systematic review and meta-analysis of randomized controlled trials link: https://peerj.com/articles/17433 last-modified: 2024-05-21 description: PurposeThe optimal range of protein dosage and effect of high-dose protein on critically ill patients remain controversial. We conducted a meta-analysis to compare higher and lower doses of protein supplementation for nutritional support in critically ill patients.MethodsWe searched the PubMed, Embase, Scopus, and Cochrane Library databases for randomized controlled trials that compared higher (≥1.2 g/kg per day) versus lower (<1.2 g/kg per day) doses of protein supplementation among critically ill adult patients. This search spanned from the inception of relevant databases to November 20, 2023. Our primary endpoint of interest was overall mortality, while secondary endpoints included length of stay in the intensive care unit, length of hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury.ResultsSeventeen studies including 2,965 critically ill patients were included in our meta-analysis. The pooled analyses showed no significant difference in overall mortality (RR 1.03, 95%CI [0.92–1.15], P = 0.65, I2 = 0%), length of intensive care unit stay (MD 0.19, 95%CI [−0.67 to 1.04], P = 0.66, I2 = 25%), length of hospital stay (MD 0.73, 95%CI [−1.59 to 3.04], P = 0.54, I2 = 27%), duration of mechanical ventilation (MD −0.14, 95%CI [−0.83 to 0.54], P = 0.68, I2 = 8%), and incidence of acute kidney injury (RR 1.11, 95%CI [0.87–1.41], P = 0.38, I2 = 0%) between critically ill patients receiving higher or lower doses of protein supplementation.ConclusionsFor critically ill patients, the protein supplementation dose had no significant effect on clinical outcomes, including overall mortality, length of intensive care unit and hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury. creator: Yonggen Qin creator: Jian Huang creator: Xiaofeng Ping creator: Hui Zheng creator: Kai Zhang creator: Xiaoya Xu creator: Jiuqing Yu uri: https://doi.org/10.7717/peerj.17433 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Qin et al. title: Exploring the influence of self-identification on perceptual judgments of physical and social causality link: https://peerj.com/articles/17449 last-modified: 2024-05-21 description: People tend to overestimate the causal contribution of the self to the observed outcome in various situations, a cognitive bias known as the ‘illusion of control.’ This study delves into whether this cognitive bias impacts causality judgments in animations depicting physical and social causal interactions. In two experiments, participants were instructed to associate themselves and a hypothetical stranger identity with two geometrical shapes (a circle and a square). Subsequently, they viewed animations portraying these shapes assuming the roles of agent and patient in causal interactions. Within one block, the shape related to the self served as the agent, while the shape associated with the stranger played the role of the patient. Conversely, in the other block, the identity-role association was reversed. We posited that the perception of the self as a causal agent might influence explicit judgments of physical and social causality. Experiment 1 demonstrated that physical causality ratings were solely shaped by kinematic cues. In Experiment 2, emphasising social causality, the dominance of kinematic parameters was confirmed. Therefore, contrary to the hypothesis anticipating diminished causality ratings with specific identity-role associations, results indicated negligible impact of our manipulation. The study contributes to understanding the interplay between kinematic and non-kinematic cues in human causal reasoning. It suggests that explicit judgments of causality in simple animations primarily rely on low-level kinematic cues, with the cognitive bias of overestimating the self’s contribution playing a negligible role. creator: Michele Vicovaro creator: Francesca Squadrelli Saraceno creator: Mario Dalmaso uri: https://doi.org/10.7717/peerj.17449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Vicovaro et al. title: Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum link: https://peerj.com/articles/17376 last-modified: 2024-05-20 description: BackgroundCondyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA.MethodsHigh-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA.ResultsThe results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue.ConclusionsOur study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA. creator: Xiaoyan Liu creator: Bo Xie creator: Su Wang creator: Yinhua Wu creator: Yu Zhang creator: Liming Ruan uri: https://doi.org/10.7717/peerj.17376 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: PTX3 mediates PI3K/AKT/mTOR signaling to downregulate apoptosis and autophagy to attenuate myocardial injury in sepsis link: https://peerj.com/articles/17263 last-modified: 2024-05-20 description: BackgroundThis study aimed to investigate the effect and mechanism of Pentraxin 3 (PTX3) on myocardial injury in sepsis.MethodsThirty male C57BL/6 mice were randomly assigned to Groups A, B, or C. Mice in Groups A and B were injected with unloaded lentivirus, while mice in Group C were injected with lentivirus encoding PTX3 overexpression. Seven days after injection, septic myocardial injury mouse models were constructed following intraperitoneal injection with LPS in Groups B and C, and mice in Group A were intraperitoneally injected with normal saline. Cardiac function was examined using echocardiography; pathological variation of myocardial cells was measured through HE staining, transmission electron microscopy, and TUNEL staining; and Western blot was used to measure the expression of PI3K/AKT/mTOR pathway-related, autophagy-related, and apoptosis-related proteins in mice myocardial cells.ResultsPTX3 significantly improved cardiac function and structure in sepsis-stricken mice, and PTX3 alleviated cardiac damage caused by sepsis. PTX3 reduced the relative protein expression of p-PI3K, p-AKT, mTOR, LC3I/II, Beclin, ATG5, Bax, Caspase-3, and Caspase-9 in septic mouse cardiomyocytes and increased the relative protein expression of Bcl-2.ConclusionPTX3 can attenuate myocardial injury in sepsis due to the down-regulation of apoptosis and autophagy induced by the PI3K/AKT/mTOR pathway. creator: Na Cui creator: Zhi Chen creator: Zhanbiao Yu creator: Xiaowei Lv creator: Zhenjie Hu uri: https://doi.org/10.7717/peerj.17263 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cui et al. title: Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil link: https://peerj.com/articles/17306 last-modified: 2024-05-20 description: BackgroundSalmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil’s relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses.MethodsAnalyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries.ResultswgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes.ConclusionThe results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred. creator: Felipe P. Vilela creator: Andrei G. Felice creator: Amanda A. Seribelli creator: Dália P. Rodrigues creator: Siomar C. Soares creator: Marc W. Allard creator: Juliana P. Falcão uri: https://doi.org/10.7717/peerj.17306 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vilela et al. title: Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex link: https://peerj.com/articles/17324 last-modified: 2024-05-20 description: Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services. creator: Anna-Maria Vafeiadou creator: Kevin Geldhof creator: Wissam Barhdadi creator: Jan M. Baetens creator: Bernard De Baets creator: Tom Moens creator: Aisling J. Daly uri: https://doi.org/10.7717/peerj.17324 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vafeiadou et al. title: A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026 link: https://peerj.com/articles/17336 last-modified: 2024-05-20 description: BackgroundUrinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75–95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs.AimTo analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins.MethodsThe frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools.ResultsThe ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 but not in all the clinical isolates. Strain UMN026 had antibacterial activity against UPEC clinical isolate 4014 (ECUMN−) and E. faecalis but not against isolate 4012 (ECUMN+). Bioinformatics analysis suggested that the ECUMN genes encode a chaperone/effector/immunity system.ConclusionsThe ECUMN genes are conserved in clinical isolates from symptomatic and asymptomatic patients and are not related to UTI symptoms. However, these genes encode a putative chaperone/effector/immunity system that seems to be involved in the antibacterial activity of strain UMN026. creator: América Casiano González creator: Arantxa Pacheco Villanueva creator: Natividad Castro-Alarcón creator: Julio Méndez creator: Ricardo Oropeza creator: Verónica I. Martínez-Santos uri: https://doi.org/10.7717/peerj.17336 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Casiano González et al. title: Identification of YUC genes associated with leaf wrinkling trait in Tacai variety of Chinese cabbage link: https://peerj.com/articles/17337 last-modified: 2024-05-20 description: Chinese cabbage (Brassica campestris L. ssp. chinensis (L.) Makino) stands as a widely cultivated leafy vegetable in China, with its leaf morphology significantly influencing both quality and yield. Despite its agricultural importance, the precise mechanisms governing leaf wrinkling development remain elusive. This investigation focuses on ‘Wutacai’, a representative cultivar of the Tacai variety (Brassica campestris L. ssp. chinensis var. rosularis Tsen et Lee), renowned for its distinct leaf wrinkling characteristics. Within the genome of ‘Wutacai’, we identified a total of 18 YUCs, designated as BraWTC_YUCs, revealing their conservation within the Brassica genus, and their close homology to YUCs in Arabidopsis. Expression profiling unveiled that BraWTC_YUCs in Chinese Cabbage exhibited organ-specific and leaf position-dependent variation. Additionally, transcriptome sequencing data from the flat leaf cultivar ‘Suzhouqing’ and the wrinkled leaf cultivar ‘Wutacai’ revealed differentially expressed genes (DEGs) related to auxin during the early phases of leaf development, particularly the YUC gene. In summary, this study successfully identified the YUC gene family in ‘Wutacai’ and elucidated its potential function in leaf wrinkling trait, to provide valuable insights into the prospective molecular mechanisms that regulate leaf wrinkling in Chinese cabbage. creator: Xuelian Ye creator: Ji Sun creator: Yuan Tian creator: Jingwen Chen creator: Xiangtan Yao creator: Xinhua Quan creator: Li Huang uri: https://doi.org/10.7717/peerj.17337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ye et al. title: Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis link: https://peerj.com/articles/17349 last-modified: 2024-05-20 description: BackgroundAntibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis.MethodsAmpicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL−1, and in combination at 50 µg mL−1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones.ResultsUnder most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments.DiscussionAntibiotics resulted in a significant increase to settlement time of N. vectensis larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals. creator: Quinton Krueger creator: Britney Phippen creator: Adam Reitzel uri: https://doi.org/10.7717/peerj.17349 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Krueger et al. title: Machine learning approaches to debris flow susceptibility analyses in the Yunnan section of the Nujiang River Basin link: https://peerj.com/articles/17352 last-modified: 2024-05-20 description: BackgroundThe Yunnan section of the Nujiang River (YNR) Basin in the alpine-valley area is one of the most critical areas of debris flow in China.MethodsWe analyzed the applicability of three machine learning algorithms to model of susceptibility to debris flow—Random Forest (RF), the linear kernel support vector machine (Linear SVM), and the radial basis function support vector machine (RBFSVM)—and compared 20 factors to determine the dominant controlling in debris flow occurrence in the region.ResultsWe found that (1) RF outperformed RBFSVM and Linear SVM in terms of accuracy, (2) topographic conditions were prerequisites, and geology, precipitation, vegetation, and anthropogenic influence were critical to forming debris flows. Also, the relative elevation difference was the most prominent evaluation factor of debris flow susceptibility, and (3) susceptibility maps based on RF’s debris flow susceptibility (DFS) showed that zones with very high susceptibility were distributed along the mainstream of the Nujiang River. These findings provide methodological guidance and reference for improvement of DFS assessment. It enriches the content of DFS studies in the alpine-valley areas. creator: Jingyi Zhou creator: Jiangcheng Huang creator: Zhengbao Sun creator: Qi Yi creator: Aoyang He uri: https://doi.org/10.7717/peerj.17352 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Terrestrial wildlife as indicators of microplastic pollution in western Thailand link: https://peerj.com/articles/17384 last-modified: 2024-05-20 description: Plastic pollution in terrestrial wildlife represents a new conservation challenge, with research in this area, especially within protected areas (PAs), being scant. This study documents the accumulation of microplastics (MPs) in terrestrial wildlife both inside and outside PAs in western Thailand. Carcasses of road-killed vertebrates in good condition, as well as live tadpoles, were collected to examine their exposure to plastic pollution. The digestive tracts of the vertebrate carcasses and the entire bodies of tadpoles were analyzed for MPs, which were identified if they measured over 50 µm. A total of 136 individuals from 48 vertebrate species were examined. The sample comprised snakes (44.12%), birds (11.03%), lizards (5.15%), tadpoles (32.25%), amphibians (5.88%), and mammals (1.47%). In total, 387 MPs were found in 44 species (91.67%), with an average occurrence of 3.25 ± 3.63 MPs per individual or 0.05 ± 0.08 MPs per gram of body weight. The quantities of MPs significantly varied among the animal groups, both in terms of number per individual (p < 0.05) and number per gram of body weight (p < 0.01). Furthermore, a significant difference in MP quantities was observed between specimens collected inside and outside PAs on an individual basis (p < 0.05), but not on a body weight basis (p = 0.07). Most MPs were fibers (77%), followed by fragments (22.22%), with only a minimal presence of film (0.52%) and foam (0.26%). Of all the MPs identified, 36.84% were confirmed as plastics or fibers made from natural materials, and 31.58% were plastics, including Polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), Polyvinylidene chloride (PVDC), and polyester (PES). Additionally, fibers made of cotton, and those containing polyurethane (PU), rayon, PES, and combinations of rayon and PU, were identified. The quantities of MPs were significantly influenced by animal body weight, factors associated with human settlement/activity, and land use types. Our findings highlight the prevalence of plastic pollution in terrestrial vertebrates within Thai PAs. Further toxicological studies are required to establish plastic pollution standards. It is proposed that snakes, obtained from road kills, could serve as a non-invasive method for monitoring plastic pollution, thus acting as an indicator of the pollution threat to species within terrestrial ecosystems. There is an urgent need for the standardization of solid waste management at garbage dump sites in remote areas, especially within PAs. Conservation education focusing on MP occurrence, potential sources, and impacts could enhance awareness, thereby influencing changes in behaviors and attitudes toward plastic waste management at the household level. creator: Jiraporn Teampanpong creator: Prateep Duengkae uri: https://doi.org/10.7717/peerj.17384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Teampanpong and Duengkae title: Systematic evaluation and meta-analysis of the prognosis of down-staging human papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma using cetuximab combined with radiotherapy instead of cisplatin combined with radiotherapy link: https://peerj.com/articles/17391 last-modified: 2024-05-20 description: ObjectiveTo evaluate the efficacy and safety of cetuximab instead of cisplatin in combination with downstaging radiotherapy for papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC).DesignMeta-analysis and systematic evaluation.Data sourcesThe PubMed, Embase, Web of Science, and Cochrane library databases were searched up to June 8, 2023, as well as Clinicaltrials.gov Clinical Trials Registry, China Knowledge Network, Wanfang Data Knowledge Service Platform, and Wiprojournal.com.Eligibility criteria for selecting studiesRandomized controlled trials reporting results of standard regimens of cetuximab + radiotherapy vs cisplatin + radiotherapy in treating HPV+ OPSCC were included. The primary outcomes of interest were overall survival (OS), progression-free survival (PFS), local regional failure rate (LRF), distant metastasis rate (DM), and adverse events (AE).Data extraction and synthesisTwo reviewers independently extracted data and assessed the risk of bias of the included studies. The HR and its 95% CI were used as the effect analysis statistic for survival analysis, while the OR and its 95% CI were used as the effect analysis statistic for dichotomous variables. These statistics were extracted by the reviewers and aggregated using a fixed-effects model to synthesise the data.ResultsA total of 874 relevant papers were obtained from the initial search, and five papers that met the inclusion criteria were included; a total of 1,617 patients with HPV+ OPSCC were enrolled in these studies. Meta-analysis showed that OS and PFS were significantly shorter in the cetuximab + radiotherapy group of patients with HPV+ OPSCC compared with those in the conventional cisplatin + radiotherapy group (HR = 2.10, 95% CI [1.39–3.15], P = 0.0004; HR = 1.79, 95% CI [1.40–2.29], P < 0.0001); LRF and DM were significantly increased (HR = 2.22, 95% CI [1.58–3.11], P < 0.0001; HR = 1.66, 95% CI [1.07–2.58], P = 0.02), but there was no significant difference in overall grade 3 to 4, acute and late AE overall (OR = 0.86, 95% CI [0.65–1.13], P = 0.28).ConclusionsCisplatin + radiotherapy remains the standard treatment for HPV+ OPSCC. According to the 7th edition AJCC/UICC criteria, low-risk HPV+ OPSCC patients with a smoking history of ≤ 10 packs/year and non-pharyngeal tumors not involved in lymphatic metastasis had similar survival outcomes with cetuximab/cisplatin + radiotherapy. However, further clinical trials are necessary to determine whether cetuximab + radiotherapy can replace cisplatin + radiotherapy for degraded treatment in individuals who meet the aforementioned characteristics, particularly those with platinum drug allergies.Prospero registration numberCRD42023445619. creator: Qiong Hu creator: Feng Li creator: Kai Yang uri: https://doi.org/10.7717/peerj.17391 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hu et al. title: The effect of rehabilitation time on functional recovery after arthroscopic rotator cuff repair: a systematic review and meta-analysis link: https://peerj.com/articles/17395 last-modified: 2024-05-20 description: ObjectiveWe compared the effects of early and delayed rehabilitation on the function of patients after rotator cuff repair by meta-analysis to find effective interventions to promote the recovery of shoulder function.MethodsThis meta-analysis was registered in PROSPERO (CRD42023466122). We manually searched the randomized controlled trials (RCTs) in the Cochrane Library, Pubmed, Cochrane Library, EMBASE, the China National Knowledge Infrastructure (CNKI), the China VIP Database (VIP), and the Wanfang Database to evaluate the effect of early and delayed rehabilitation after arthroscopic shoulder cuff surgery on the recovery of shoulder joint function. Review Manager 5.3 software was used to analyze the extracted data. Then, the PEDro scale was employed to appraise the methodological quality of the included research.ResultsThis research comprised nine RCTs and 830 patients with rotator cuff injuries. According to the findings of the meta-analysis, there was no discernible difference between the early rehabilitation group and the delayed rehabilitation group at six and twelve months after the surgery in terms of the VAS score, SST score, follow-up rotator cuff healing rate, and the rotator cuff retear rate at the final follow-up. There was no difference in the ASES score between the early and delayed rehabilitation groups six months after the operation. However, although the ASES score in the early rehabilitation group differed significantly from that in the delayed rehabilitation group twelve months after the operation, according to the analysis of the minimal clinically important difference (MCID), the results have no clinical significance.ConclusionsThe improvement in shoulder function following arthroscopic rotator cuff surgery does not differ clinically between early and delayed rehabilitation. When implementing rehabilitation following rotator cuff repair, it is essential to consider the paradoxes surrounding shoulder range of motion and tendon anatomic healing. A program that allows for flexible progression based on the patient’s ability to meet predetermined clinical goals or criteria may be a better option. creator: Yang Chen creator: Hui Meng creator: Yuan Li creator: Hui Zong creator: Hongna Yu creator: HaiBin Liu creator: Shi Lv creator: Liang Huai uri: https://doi.org/10.7717/peerj.17395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: USP22 as a key regulator of glycolysis pathway in osteosarcoma: insights from bioinformatics and experimental approaches link: https://peerj.com/articles/17397 last-modified: 2024-05-20 description: BackgroundOsteosarcoma is the most common primary malignant bone tumor, but its pathogenesis remains unclear. Ubiquitin-specific processing peptidase 22 (USP22) is reported to be highly expressed and associated with tumor malignancy and prognosis in cancers. However, the role and mechanism of USP22 in osteosarcoma is not fully understood. This study aims to investigate the function and potential mechanism of USP22 in osteosarcoma using bioinformatics analysis combined with experimental validation.MethodsWe first integrated transcriptomic datasets and clinical information of osteosarcoma from GEO and TCGA databases to assess the expression and prognostic value of USP22 in osteosarcoma. Then, differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify USP22-related co-expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the biological functions and signaling pathways of USP22 co-expressed genes. To validate the accuracy of bioinformatics analyses, we downregulated USP22 expression in osteosarcoma cell line Sao-2 using siRNA and assessed its effect on cell proliferation, migration, invasion, apoptosis, and regulation of key signaling pathways.ResultsWe found that USP22 was highly expressed in osteosarcoma tissues and correlated with poor prognosis in osteosarcoma patients. USP22 also showed potential as a diagnostic marker for osteosarcoma. In addition, 344 USP22-related co-expressed genes were identified, mainly involved in signaling pathways such as glycolysis, oxidative phosphorylation, spliceosome, thermogenesis, and cell cycle. The in vitro experiments confirmed the accuracy and reliability of bioinformatics analyses. We found that downregulation of USP22 could inhibit Sao-2 cell proliferation, migration, invasion, and induce apoptosis. Furthermore, downregulation of USP22 significantly reduced aerobic glycolysis levels in Sao-2 cells and inhibited the expression of key enzymes and transporters in aerobic glycolysis pathways such as HK2, PKM2, and GLUT1.ConclusionsUSP22 plays a critical role in the occurrence, development, and prognosis of osteosarcoma. USP22 could influence Sao-2 cell proliferation, apoptosis, migration, and invasion by regulating the glycolysis pathway, thereby promoting osteosarcoma progression. Therefore, USP22 may be a potential therapeutic target for the treatment of osteosarcoma. creator: Qiao Zhang creator: Jinwei Zhu creator: Jian Xie creator: Yurong Gu creator: Lu Chen uri: https://doi.org/10.7717/peerj.17397 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Vaccine refusal in pregnant women in Kahramanmaraş: a community-based study from Türkiye link: https://peerj.com/articles/17409 last-modified: 2024-05-20 description: BackgroundThe global health landscape is increasingly challenged by the rejection of childhood vaccines. This study investigates vaccination reservations and refusal among pregnant women.MethodsA cross-sectional study was conducted in Kahramanmaraş, Türkiye, spanning January to March 2019, entailing face to face interviews with 938 pregnant women. The questionnaire collected sociodemographic data and probed vaccination attitudes. The decision to vaccinate the baby was treated as the dependent variable, analyzed alongside sociodemographic factors and other variables. Data underwent evaluation via descriptive analysis, the Chi-square test, and binary logistic regression.ResultsParticipants had a mean age of 27.6 years. Among them 20 (2.1%) expressed intent to either abstain from or partially vaccinate their babies, with 70% citing apprehensions regarding potential vaccine-related harm. Statistical analysis unveiled that higher economic income, elevated parental education level, fewer than two children, reliance on the Internet for vaccination information, and a lack of trust in physicians significantly correlated with vaccine refusal among pregnant women (p < 0.05).ConclusionsThe study concludes that dissemination of vaccination information by the healthcare professionals, complemented by the enactment of pro-vaccine internet policies holds promise in shaping vaccination behavior. creator: Ramazan Azim Okyay creator: Erhan Kaya creator: Ayşegül Erdoğan uri: https://doi.org/10.7717/peerj.17409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Okyay et al. title: Clinical value of serum polyunsaturated fatty acids in patients with gastric polyps link: https://peerj.com/articles/17413 last-modified: 2024-05-20 description: Polyunsaturated fatty acids (PUFAs) are vital nutrients in human physiology and are implicated in various chronic diseases. However, the relationship between PUFAs and gastric polyps remains unclear. This study employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to assess PUFA levels in the serum of 350 patients, along with analyzing the ω-6 to ω-3 ratio. The results revealed significant differences in the levels of C16:1, C18:1, C18:2, α-C18:3, γ-C18:3, C20:1, C20:4, C20:5, ω-3-C22:5, ω-6-C22:5, and C22:6, as well as ω-6 to ω-3 ratio between the control and gasteic polyp groups. Moreover, setting the threshold for ω-6: ω-3 at 10 revealed a close correlation between polyp occurrence and this ratio. These findings suggest that PUFAs and the ω-6 to ω-3 ratio hold promise as potential early screening markers for gastric polyps. However, further research is imperative to elucidate the underlying mechanisms and therapeutic potential of PUFAs in managing gastric polyps. creator: Nan Li creator: Qiliu Qian creator: Jun Ouyang creator: Mingyue Hu creator: Juan Liu creator: Hailu Wu creator: Ruihua Shi creator: Shiya Zheng uri: https://doi.org/10.7717/peerj.17413 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Nucleolin myocardial-specific knockout exacerbates glucose metabolism disorder in endotoxemia-induced myocardial injury link: https://peerj.com/articles/17414 last-modified: 2024-05-20 description: BackgroundSepsis-induced myocardial injury, as one of the important complications of sepsis, can significantly increase the mortality of septic patients. Our previous study found that nucleolin affected mitochondrial function in energy synthesis and had a protective effect on septic cardiomyopathy in mice. During sepsis, glucose metabolism disorders aggravated myocardial injury and had a negative effect on septic patients.ObjectivesWe investigated whether nucleolin could regulate glucose metabolism during endotoxemia-induced myocardial injury.MethodsThe study tested whether the nucleolin cardiac-specific knockout in the mice could affect glucose metabolism through untargeted metabolomics, and the results of metabolomics were verified experimentally in H9C2 cells. The ATP content, lactate production, and oxygen consumption rate (OCR) were evaluated.ResultsThe metabolomics results suggested that glycolytic products were increased in endotoxemia-induced myocardial injury, and that nucleolin myocardial-specific knockout altered oxidative phosphorylation-related pathways. The experiment data showed that TNF-α combined with LPS stimulation could increase the lactate content and the OCR values by about 25%, and decrease the ATP content by about 25%. However, interference with nucleolin expression could further decrease ATP content and OCR values by about 10–20% and partially increase the lactate level in the presence of TNF-α and LPS. However, nucleolin overexpression had the opposite protective effect, which partially reversed the decrease in ATP content and the increase in lactate level.ConclusionDown-regulation of nucleolin can exacerbate glucose metabolism disorders in endotoxemia-induced myocardial injury. Improving glucose metabolism by regulating nucleolin was expected to provide new therapeutic ideas for patients with septic cardiomyopathy. creator: Yuting Tang creator: Leijing Yin creator: Ludong Yuan creator: Xiaofang Lin creator: Bimei Jiang uri: https://doi.org/10.7717/peerj.17414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tang et al. title: Unpredictable soil conditions can affect the prevalence of a microbial symbiosis link: https://peerj.com/articles/17445 last-modified: 2024-05-20 description: The evolution of symbiotic interactions may be affected by unpredictable conditions. However, a link between prevalence of these conditions and symbiosis has not been widely demonstrated. We test for these associations using Dictyostelium discoideum social amoebae and their bacterial endosymbionts. D. discoideum commonly hosts endosymbiotic bacteria from three taxa: Paraburkholderia, Amoebophilus and Chlamydiae. Three species of facultative Paraburkholderia endosymbionts are the best studied and give hosts the ability to carry prey bacteria through the dispersal stage to new environments. Amoebophilus and Chlamydiae are obligate endosymbiont lineages with no measurable impact on host fitness. We tested whether the frequency of both single infections and coinfections of these symbionts were associated with the unpredictability of their soil environments by using symbiont presence-absence data from D. discoideum isolates from 21 locations across the eastern United States. We found that symbiosis across all infection types, symbiosis with Amoebophilus and Chlamydiae obligate endosymbionts, and symbiosis involving coinfections were not associated with any of our measures. However, unpredictable precipitation was associated with symbiosis in two species of Paraburkholderia, suggesting a link between unpredictable conditions and symbiosis. creator: Trey J. Scott creator: Calum J. Stephenson creator: Sandeep Rao creator: David C. Queller creator: Joan E. Strassmann uri: https://doi.org/10.7717/peerj.17445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Scott et al. title: Influence of purple non-sulfur bacterial augmentation on soil nutrient dynamics and rice (Oryza sativa) growth in acidic saline-stressed environments link: https://peerj.com/articles/16943 last-modified: 2024-05-17 description: The aim of the current study was to assess the potency of the exopolymeric substances (EPS)-secreting purple non-sulfur bacteria (PNSB) on rice plants on acidic salt-affected soil under greenhouse conditions. A two-factor experiment was conducted following a completely randomized block design. The first factor was the salinity of the irrigation, and the other factor was the application of the EPS producing PNSB (Luteovulum sphaeroides EPS18, EPS37, and EPS54), with four replicates. The result illustrated that irrigation of salt water at 3–4‰ resulted in an increase in the Na+ accumulation in soil, resulting in a lower rice grain yield by 12.9–22.2% in comparison with the 0‰ salinity case. Supplying the mixture of L. sphaeroides EPS18, EPS37, and EPS54 increased pH by 0.13, NH4+ by 2.30 mg NH4+ kg−1, and available P by 8.80 mg P kg−1, and decreased Na+ by 0.348 meq Na+ 100 g−1, resulting in improvements in N, P, and K uptake and reductions in Na uptake, in comparison with the treatment without bacteria. Thus, the treatments supplied with the mixture of L. sphaeroides EPS18, EPS37, and EPS54 resulted in greater yield by 27.7% than the control treatment. creator: Nguyen Quoc Khuong creator: Nguyen Minh Nhat creator: Le Thi My Thu creator: Le Vinh Thuc uri: https://doi.org/10.7717/peerj.16943 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Khuong et al. title: TPX2 upregulates MMP13 to promote the progression of lipopolysaccharide-induced osteoarthritis link: https://peerj.com/articles/17032 last-modified: 2024-05-17 description: PurposeThis study seeks to identify potential clinical biomarkers for osteoarthritis (OA) using bioinformatics and investigate OA mechanisms through cellular assays.MethodsDifferentially Expressed Genes (DEGs) from GSE52042 (four OA samples, four control samples) were screened and analyzed with protein-protein interaction (PPI) analysis. Overlapping genes in GSE52042 and GSE206848 (seven OA samples, and seven control samples) were identified and evaluated using Gene Set Enrichment Analysis (GSEA) and clinical diagnostic value analysis to determine the hub gene. Finally, whether and how the hub gene impacts LPS-induced OA progression was explored by in vitro experiments, including Western blotting (WB), co-immunoprecipitation (Co-IP), flow cytometry, etc.ResultBioinformatics analysis of DEGs (142 up-regulated and 171 down-regulated) in GSE52042 identified two overlapping genes (U2AF2, TPX2) that exhibit significant clinical diagnostic value. These genes are up-regulated in OA samples from both GSE52042 and GSE206848 datasets. Notably, TPX2, which AUC = 0.873 was identified as the hub gene. In vitro experiments have demonstrated that silencing TPX2 can alleviate damage to chondrocytes induced by lipopolysaccharide (LPS). Furthermore, there is a protein interaction between TPX2 and MMP13 in OA. Excessive MMP13 can attenuate the effects of TPX2 knockdown on LPS-induced changes in OA protein expression, cell growth, and apoptosis.ConclusionIn conclusion, our findings shed light on the molecular mechanisms of OA and suggested TPX2 as a potential therapeutic target. TPX2 could promote the progression of LPS-induced OA by up-regulating the expression of MMP13, which provides some implications for clinical research. creator: Jingtao Yu creator: Weiqi Wang creator: Zenghui Jiang creator: Huashun Liu uri: https://doi.org/10.7717/peerj.17032 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu et al. title: Changes in the concentration of bone turnover markers in men after maximum intensity exercise link: https://peerj.com/articles/17258 last-modified: 2024-05-17 description: BackgroundPhysical activity is an important factor in modelling the remodelling and metabolism of bone tissue. The aim of the study was to evaluate the changes in indices demonstrating bone turnover in men under the influence of maximum-intensity exercise.MethodsThe study involved 33 men aged 20–25, divided into two groups: experimental (n = 15) and control (n = 18). People training medium- and long-distance running were assigned to the experimental group, and non-training individuals to the control. Selected somatic, physiological and biochemical indices were measured. The level of aerobic fitness was determined using a progressively increasing graded test (treadmill test for subjective fatigue). Blood samples for determinations were taken before the test and 60 minutes after its completion. The concentration of selected bone turnover markers was assessed: bone fraction of alkaline phosphatase (b-ALP), osteoclacin (OC), N-terminal cross-linked telopeptide of the alpha chain of type I collagen (NTx1), N-terminal propeptide of type I progolagen (PINP), osteoprotegerin (OPG). In addition, the concentration of 25(OH)D3 prior to the stress test was determined. Additionally, pre and post exercise, the concentration of lactates in the capillary blood was determined.ResultsWhen comparing the two groups, significant statistical differences were found for the mean level of: 25(OH)D3 (p = 0.025), b-ALP (p < 0.001), OC (p = 0.004) and PINP (p = 0.029) prior to the test. On the other hand, within individual groups, between the values pre and post the stress test, there were statistically significant differences for the average level of: b-ALP (p < 0.001), NTx1 (p < 0.001), OPG (p = 0.001) and PINP (p = 0.002).ConclusionA single-session maximum physical effort can become an effective tool to initiate positive changes in bone turnover markers. creator: Małgorzata Bagińska creator: Łukasz Marcin Tota creator: Małgorzata Morawska-Tota creator: Justyna Kusmierczyk creator: Tomasz Pałka uri: https://doi.org/10.7717/peerj.17258 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bagińska et al. title: Orbicularis oculi muscle activity during computer reading under different degrees of artificially-induced aniseikonia link: https://peerj.com/articles/17293 last-modified: 2024-05-17 description: BackgroundAniseikonia is a binocular vision disorder that has been associated with asthenopic symptoms. However, asthenopia has been evaluated with subjective tests that make difficult to determine the level of aniseikonia. This study aims to objectively evaluate the impact of induced aniseikonia at different levels on visual fatigue by measuring the orbicularis oculi muscle activity in the dominant and non-dominant eyes while performing a reading task.MethodsTwenty-four collegiate students (24.00 ± 3.86 years) participated in this study. Participants read a passage for 7 minutes under four degrees of aniseikonia (0%, 3%, 5% and 10%) at 50 cm. Orbicularis oculi muscle activity of the dominant and non-dominant eye was recorded by surface electromyography. In addition, visual discomfort was assessed after each task by completing a questionnaire.ResultsOrbicularis oculi muscle activity increased under induced aniseikonia (i.e., greater values for the 10% condition in comparison to 0%, and 3% conditions (p = 0.034 and p = 0.023, respectively)). No statistically significant differences were observed in orbicularis oculi muscle activity for the time on task and between the dominant and non-dominant eyes. Additionally, higher levels of subjective visual discomfort were observed for lower degrees of induced aniseikonia.ConclusionInduced aniseikonia increases visual fatigue at high aniseikonia degrees as measured by the orbicularis oculi muscle activity, and at low degrees as measured with subjective questionnaires. These findings may be of relevance to better understand the visual symptomatology of aniseikonia. creator: Beatriz Redondo creator: Jesus Vera creator: Rubén Molina creator: Alejandro Molina-Molina creator: Raimundo Jiménez uri: https://doi.org/10.7717/peerj.17293 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Redondo et al. title: Bacteriogenic synthesis of morphologically diverse silver nanoparticles and their assessment for methyl orange dye removal and antimicrobial activity link: https://peerj.com/articles/17328 last-modified: 2024-05-17 description: Nanotechnology and nanoparticles have gained massive attention in the scientific community in recent years due to their valuable properties. Among various AgNPs synthesis methods, microbial approaches offer distinct advantages in terms of cost-effectiveness, biocompatibility, and eco-friendliness. In the present research work, investigators have synthesized three different types of silver nanoparticles (AgNPs), namely AgNPs-K, AgNPs-M, and AgNPs-E, by using Klebsiella pneumoniae (MBC34), Micrococcus luteus (MBC23), and Enterobacter aerogenes (MBX6), respectively. The morphological, chemical, and elemental features of the synthesized AgNPs were analyzed by using UV-Vis spectroscopy (UV-Vis), Fourier transform-infrared spectroscopy (FTIR), X-ray diffraction (XRD), field emission scanning electron microscope (FESEM) and energy-dispersive spectroscopy (EDX). UV-Vis absorbance peaks were obtained at 475, 428, and 503 nm for AgNPs-K, AgNPs-M, and AgNPs-E, respectively. The XRD analysis confirmed the crystalline nature of the synthesized AgNPs, having peaks at 26.2°, 32.1°, and 47.2°. At the same time, the FTIR showed bands at 599, 963, 1,693, 2,299, 2,891, and 3,780 cm−1 for all the types of AgNPs indicating the presence of bacterial biomolecules with the developed AgNPs. The size and morphology of the AgNPs varied from 10 nm to several microns and exhibited spherical to porous sheets-like structures. The percentage of Ag varied from 37.8% (wt.%) to 61.6%, i.e., highest in AgNPs-K and lowest in AgNPs-M. Furthermore, the synthesized AgNPs exhibited potential for environmental remediation, with AgNPs-M exhibiting the highest removal efficiency (19.24% at 120 min) for methyl orange dye in simulated wastewater. Further, all three types of AgNPs were evaluated for the removal of methyl orange dye from the simulated wastewater, where the highest dye removal percentage was 19.24% at 120 min by AgNPs-M. Antibacterial potential of the synthesized AgNPs assessment against both Gram-positive (GPB) Bacillus subtilis (MBC23), B. cereus (MBC24), and Gram-negative bacteria Enterococcus faecalis (MBP13) revealed promising results, with AgNPs-M, exhibiting the largest zone of inhibition (12 mm) against GPB B. megaterium. Such investigation exhibits the potential of the bacteria for the synthesis of AgNPs with diverse morphology and potential applications in environmental remediation and antibacterial therapy-based synthesis of AgNPs. creator: Bhakti Patel creator: Virendra Kumar Yadav creator: Reema Desai creator: Shreya Patel creator: Abdelfattah Amari creator: Nisha Choudhary creator: Haitham Osman creator: Rajat Patel creator: Deepak Balram creator: Kuang-Yow Lian creator: Dipak Kumar Sahoo creator: Ashish Patel uri: https://doi.org/10.7717/peerj.17328 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Patel et al. title: Leeches Baicalobdella torquata feed on hemolymph but have a low effect on the cellular immune response of amphipod Eulimnogammarus verrucosus from Lake Baikal link: https://peerj.com/articles/17348 last-modified: 2024-05-17 description: Lake Baikal is one of the largest and oldest freshwater reservoirs on the planet with a huge endemic diversity of amphipods (Amphipoda, Crustacea). These crustaceans have various symbiotic relationships, including the rarely described phenomenon of leech parasitism on amphipods. It is known that leeches feeding on hemolymph of crustacean hosts can influence their physiology, especially under stressful conditions. Here we show that leeches Baicalobdella torquata (Grube, 1871) found on gills of Eulimnogammarus verrucosus (Gerstfeldt, 1858), one of the most abundant amphipods in the Baikal littoral zone, indeed feed on the hemolymph of their host. However, the leech infection had no effect on immune parameters such as hemocyte concentration or phenoloxidase activity and also did not affect glycogen content. The intensity of hemocyte reaction to foreign bodies in a primary culture was identical between leech-free and leech-infected animals. Artificial infection with leeches also had only a subtle effect on the course of a model microbial infection in terms of hemocyte concentration and composition. Despite we cannot fully exclude deleterious effects of the parasites, our study indicates a low influence of a few leeches on E. verrucosus and shows that leech-infected amphipods can be used at least for some types of ecophysiological experiments. creator: Anna Nazarova creator: Andrei Mutin creator: Denis Skafar creator: Nadezhda Bolbat creator: Sofya Sedova creator: Polina Chupalova creator: Vasiliy Pomazkin creator: Polina Drozdova creator: Anton Gurkov creator: Maxim Timofeyev uri: https://doi.org/10.7717/peerj.17348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Nazarova et al. title: Comparing trophic position estimates using bulk and compound specific stable isotope analyses: applying new approaches to mackerel icefish Champsocephalus gunnari link: https://peerj.com/articles/17372 last-modified: 2024-05-17 description: Quantifying the tropic position (TP) of an animal species is key to understanding its ecosystem function. While both bulk and compound-specific analyses of stable isotopes are widely used for this purpose, few studies have assessed the consistency between and within such approaches. Champsocephalus gunnari is a specialist teleost that predates almost exclusively on Antarctic krill Euphausia superba. This well-known and nearly constant trophic relationship makes C. gunnari particularly suitable for assessing consistency between TP methods under field conditions. In the present work, we produced and compared TP estimates for C. gunnari and its main prey using a standard bulk and two amino acid-specific stable isotope approaches (CSI-AA). One based on the difference between glutamate and phenylalanine (TPGlx-Phe), and the other on the proline-phenylalanine difference (TPPro-Phe). To do that, samples from C. gunnari, E. superba and four other pelagic invertebrate and fish species, all potential prey for C.gunnari, were collected off the South Orkney Islands between January and March 2019, analyzed using standard isotopic ratio mass spectrometry methods and interpreted following a Bayesian approach. Median estimates (CI95%) for C. gunnari were similar between TPbulk (3.6; CI95%: 3.0-4.8) and TPGlx-Phe(3.4; CI95%:3.2-3.6), and lower for TPPro-Phe (3.1; CI95%:3.0-3.3). TP differences between C. gunnari and E. superba were 1.4, 1.1 and 1.2, all compatible with expectations from the monospecific diet of this predator (ΔTP=1). While these results suggest greater accuracy for Glx-Phe and Pro-Phe, differences observed between both CSI-AA approaches suggests these methods may require further validation before becoming a standard tool for trophic ecology. creator: Jose Antonio Canseco creator: Edwin J. Niklitschek creator: Claudio Quezada-Romegialli creator: Chris Yarnes creator: Chris Harrod uri: https://doi.org/10.7717/peerj.17372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Canseco et al. title: Occurrence patterns of sympatric forest wallabies: assessing the influence of structural habitat attributes on the coexistence of Thylogale thetis and T. stigmatica link: https://peerj.com/articles/17383 last-modified: 2024-05-17 description: BackgroundWe studied the occurrence of two sympatric wallabies, the red-necked pademelon (Thylogale thetis) and the red-legged pademelon (T. stigmatica) in northeastern New South Wales, Australia in relation to structural habitat attributes. At our study site, both species inhabit closed forest environments and have overlapping distributions, but T. thetis leaves the forest at night to graze adjacent grassy forest edges whereas T. stigmatica remains within the forest and browses forest vegetation. The objectives of the study were to investigate how structural attributes of two forest types, wet sclerophyll forest and rainforest, relate to the fine-scale occurrence of these two wallaby species within the forested environment.MethodsWe gathered occurrence data from 48 camera trap stations divided equally between rainforest and wet sclerophyll forest. At each camera point, we also measured a range of structural habitat attributes to determine habitat affiliations for the two Thylogale species. Principal component analyses were used to describe major trends in habitat, and generalised linear models were used to describe the efficacy of the variables in predicting habitat occurrence of each species.ResultsThe number of occurrences of Thylogale thetis was significantly greater than occurrences of T. stigmatica, which was driven by significantly greater occurrences of T. thetis in wet sclerophyll forest. There was both spatial and temporal partitioning between the two species; there was a significant difference in the occurrences of the two species at individual cameras and T. stigmatica had a different activity schedule than T. thetis in wet sclerophyll forest, where the latter reached its greatest rate of occurrence. At a finer (camera station) scale, occurrences of T. thetis increased with proximity to roads and grassy edges and at sites that were less rocky and less steep. T. stigmatica occurrence increased in the presence of rainforest elements like vines, palms and ferns, more ground-level cover and tree-fall gaps and at sites with fewer emergent eucalypts.ConclusionOur findings have implications for managing these pademelons and their habitats. T. thetis is a common species that was encountered more often than T. stigmatica, and it responded positively to human disturbance like roadsides and grassy edges, presumably because these areas provided good grazing opportunities. By comparison, T. stigmatica is a threatened species, and it responded to natural disturbance like tree-fall gaps where lateral cover was greater, and where rainforest food plants may be more abundant. Our results suggest, therefore, that conservation of the threatened T. stigmatica requires the preservation of intact rainforest. creator: Lucy E.V. Smith creator: Nigel R. Andrew creator: Karl Vernes uri: https://doi.org/10.7717/peerj.17383 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Smith et al. title: Validity and reliability of My Jump 2® app to measure the vertical jump on elite women beach volleyball players link: https://peerj.com/articles/17387 last-modified: 2024-05-17 description: PurposeThe aim of this study was to assess the reliability and validity of the My Jump 2® app in measuring jump height, flight time, and peak power among elite women beach volleyball players on sand surfaces.MethodsEleven elite female beach volleyball players (aged 23.6 ± 6.2 years; weight 66.3 ± 5.8 kg; height 174.4 ± 5.8 cm; with 8.4 ± 4.8 years of professional experience) participated in this study. Each player performed six countermovement jumps in a wooden box filled with sand on a force platform while simultaneously recording a video for subsequent analysis using the My Jump 2® app.ResultsWe found excellent agreement for flight time, jump height and peak power between observers (ICC = 0.92, 0.91 and 0.97, respectively). No significant differences between force platform and My Jump 2® app were detected in the values obtained for the three variables (P > 0.05). For the force platform and the My Jump 2® app, we found a good agreement measuring jump height and flight time (ICC = 0.85 and 0.85, respectively). However, we only found a moderate agreement for peak power (ICC = 0.64). The difference in jump height showed a limit of agreement between −4.10 and 4.74 cm in Bland-Altman, indicating a high level of agreement between the two measurement tools.ConclusionBased on our findings, the My Jump 2® app reveals a valid tool for measuring jump height and flight time of CMJ on sand surfaces. However, more caution is needed when measuring peak power. creator: Alexandre Igor Araripe Medeiros creator: Geovani Messias da Silva creator: Francisco Oliveira Neto creator: Mário Simim creator: Túlio Banja creator: Victor S. Coswig creator: José Afonso creator: Ana Ramos creator: Isabel Mesquita uri: https://doi.org/10.7717/peerj.17387 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Medeiros et al. title: Seasonal occurrence and individual variability of bull sharks, Carcharhinus leucas, in a marine reserve of the southwestern Gulf of California link: https://peerj.com/articles/17192 last-modified: 2024-05-16 description: BackgroundStudying how the bull sharks aggregate and how they can be driven by life history traits such as reproduction, prey availability, predator avoidance and social interaction in a National Park such as Cabo Pulmo, is key to understand and protect the species.MethodsThe occurrence variability of 32 bull sharks tracked with passive acoustic telemetry were investigated via a hierarchical logistic regression model, with inference conducted in a Bayesian framework, comparing sex, and their response to temperature and chlorophyll.ResultsBased on the fitted model, occurrence probability varied by sex and length. Juvenile females had the highest values, whereas adult males the lowest. A strong seasonality or day of the year was recorded, where sharks were generally absent during September–November. However, some sharks did not show the common pattern, being detected just for a short period. This is one of the first studies where the Bayesian framework is used to study passive acoustic telemetry proving the potential to be used in further studies. creator: Frida Lara-Lizardi creator: Eleazar Castro creator: Vianey Leos Barajas creator: Juan Manuel Morales creator: Edgar Mauricio Hoyos-Padilla creator: James Ketchum uri: https://doi.org/10.7717/peerj.17192 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lara-Lizardi et al. title: Balance performance, falls-efficacy and social participation in patients with type 2 diabetes mellitus with and without vestibular dysfunction link: https://peerj.com/articles/17287 last-modified: 2024-05-16 description: BackgroundThe performance of balance is an important factor to perform activities. The complications of type 2 diabetes mellitus (T2DM), especially vestibular dysfunction (VD), could decrease balance performance and falls-efficacy (FE) which consequently impacts social participation and quality of life (QoL).PurposeThis study aimed to compare balance performance, FE, social participation and QoL between individuals with T2DM with and without VD.MethodsThe participants comprised 161 T2DM with VD and 161 without VD. Three clinical tests used for confirming VD included the Head Impulse Test (HIT), the Dix Hallpike Test (DHT) and the Supine Roll Test (SRT). The scores of static and dynamic balances, FE, social participation and QoL were compared between groups.ResultsThe balance performance, FE, social participation and QoL were lower in the group with VD. The number of patients who had severe social restriction was higher in T2DM with VD than without VD (58.4% vs 48.4%). Moreover, all domains of QoL (physical, psychological, social relationships and environmental) were lower in T2DM with VD than without VD.ConclusionThe presence of VD in T2DM patients was associated with decreased physical balance performances and increased social and QoL disengagement. Comprehensive management related to balance and FE, as well as the monitoring to support social participation and QoL, should be emphasized in patients with T2DM with VD. creator: Dwi Rosella Komalasari creator: Mantana Vongsirinavarat creator: Vimonwan Hiengkaew creator: Nantinee Nualnim uri: https://doi.org/10.7717/peerj.17287 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Komalasari et al. title: Environmental awareness and sustainable consumption behaviours of Turkish nursing students link: https://peerj.com/articles/17366 last-modified: 2024-05-16 description: ObjectivesThis study aims to determine the environmental awareness and sustainable consumption behaviours of nursing students.MethodsThis cross-sectional study was conducted with 380 undergraduate nursing students studying at Faculty of Nursing, Ege University, Türkiye. The Personal Information Form, Environmental Awareness Scale (EAS), and Sustainable Consumption Behaviours Scale (SCBS) were used to collect the research data. Number, percentage, mean, Kolmogorov-Smirnov Z test, t-test, one-way analysis of variance, Pearson’s correlation test, and linear regression analysis were used in statistical evaluation.ResultsThe mean total score on the EAS was 46.12 (SD = 6.60), and the mean total score of the SCBS was 61.83 (SD = 9.10). A significant, moderate, and positive correlation was found between students’ environmental awareness and sustainable consumption behaviours. Moreover, students’ gender and the people they lived with caused statistically significant differences in the EAS score. The people students lived with, the place where they lived for the longest time, and their perceived income level caused statistically significant differences in the SCBS score.ConclusionsNursing students had high environmental awareness and moderate to good sustainable consumption behaviours. It is necessary to include the contribution of sustainable practices to the environment and the effects of these practices on human health in curricula for nurses and thus provide environmental awareness to students. creator: Renginar Öztürk Dönmez creator: Eda Yardımcı uri: https://doi.org/10.7717/peerj.17366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dönmez and Yardımcı title: Effects of extreme meteorological factors and high air pollutant concentrations on the incidence of hand, foot and mouth disease in Jining, China link: https://peerj.com/articles/17163 last-modified: 2024-05-15 description: BackgroundThe evidence on the effects of extreme meteorological conditions and high air pollution levels on incidence of hand, foot and mouth disease (HFMD) is limited. Moreover, results of the available studies are inconsistent. Further investigations are imperative to elucidate the specific issue.MethodsData on the daily cases of HFMD, meteorological factors and air pollution were obtained from 2017 to 2022 in Jining City. We employed distributed lag nonlinear model (DLNM) incorporated with Poisson regression to explore the impacts of extreme meteorological conditions and air pollution on HFMD incidence.ResultsWe found that there were nonlinear relationships between temperature, wind speed, PM2.5, SO2, O3 and HFMD. The cumulative risk of extreme high temperature was higher at the 95th percentile (P95th) than at the 90th percentile(P90th), and the RR values for both reached their maximum at 10-day lag (P95th RR = 1.880 (1.261–2.804), P90th RR = 1.787 (1.244–2.569)), the hazardous effect of extreme low temperatures on HFMD is faster than that of extreme high temperatures. The cumulative effect of extreme low wind speeds reached its maximum at 14-day lag (P95th RR = 1.702 (1.389-2.085), P90th RR = 1.498(1.283–1.750)). The cumulative effect of PM2.5 concentration at the P90th was largest at 14-day lag (RR = 1.637 (1.069–2.506)), and the cumulative effect at the P95th was largest at 10-day lag (RR = 1.569 (1.021–2.411)). High SO2 concentration at the P95th at 14-day lag was associated with higher risk for HFMD (RR: 1.425 (1.001–2.030)).ConclusionOur findings suggest that high temperature, low wind speed, and high concentrations of PM2.5 and SO2 are associated with an increased risk of HFMD. This study not only adds insights to the understanding of the impact of extreme meteorological conditions and high levels of air pollutants on HFMD incidence but also holds practical significance for the development and enhancement of an early warning system for HFMD. creator: Haoyue Cao creator: Rongrong Xu creator: Yongmei Liang creator: Qinglin Li creator: Wenguo Jiang creator: Yudi Jin creator: Wenjun Wang creator: Juxiang Yuan uri: https://doi.org/10.7717/peerj.17163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cao et al. title: Retrospective analysis of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2), Ki67 changes and their clinical significance between primary breast cancer and metastatic tumors link: https://peerj.com/articles/17377 last-modified: 2024-05-15 description: ObjectiveTo explore the relationship between receptor heterogeneity and clinicopathological characteristics in 166 patients with invasive breast cancer during metastasis.MethodsWe conducted a retrospective analysis of 166 patients diagnosed with metastatic breast cancer through biopsy, who were admitted to our hospital from January 2018 to December 2022. Statistical analysis was employed to assess the heterogeneity of receptors in both primary and metastatic lesions, including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2), Ki67, as well as their association with clinicopathological features such as tumor size, lymph node metastasis, treatment regimen, and disease-free survival.ResultsThe discordant expression rates of ER, PR, HER2, Ki-67 and Luminal classification between primary and metastatic lesions were 21.7%, 41.6%, 8.9%, 34.4% and 36.8%, respectively. There is a significant difference in disease-free survival between patients with consistent and inconsistent receptor status of primary and metastatic lesions, which is statistically significant. The median DFS for primary HER2(-) to metastatic HER2(+) was 84 months, which was relatively high. The Cox multivariate regression analysis revealed that the expression differences of ER, PR, HER2, and Ki67 were not influenced by endocrine therapy and chemotherapy. However, a statistically significant difference in HER2 expression was observed with targeted therapy. Tumor size was correlated with ER and Ki67 receptor status (P = 0.019, 0.016). Tumor size was not correlated with PR, and HER2 (P = 0.679, 0.440). Lymph node metastasis was not associated with changes in ER, PR, HER2, and Ki67. The discordant rates of ER, PR, HER2, and Ki-67 in patients with local recurrence were 22%, 23.7%, 5.1%, and 28.8% respectively, whereas those in patients with distant metastasis were 21.5%, 36.4%, 10.3%, and 31.8% respectively.ConclusionsThe expression levels of ER, PR, HER2, and Ki-67 in primary and metastatic breast cancer exhibit heterogeneity, which is closely associated with the prognosis and treatment outcomes of patients. creator: Gaoxiu Qi creator: Xin Zhang creator: Xiaoying Gai creator: Xiong Yan uri: https://doi.org/10.7717/peerj.17377 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Qi et al. title: The prognostic value of preoperative neoindices consisting of lymphocytes, neutrophils and albumin (LANR) in operable breast cancer: a retrospective study link: https://peerj.com/articles/17382 last-modified: 2024-05-15 description: BackgroundPreoperative inflammatory factors and nutritional status are strongly associated with the prognosis of a variety of cancers. We explored the relationship between preoperative lymphocytes, neutrophils and albumin (LANR) and progression-free survival in breast cancer patients.MethodsThe clinical and follow-up data of 200 breast cancer patients were retrospectively analyzed in this study, and the value of LANR was determined as follows: LANR, lymphocytes × albumin/neutrophils. ROC curves, COX proportional risk regression analysis and subgroup analysis were used to assess the prognostic value of LANR in progression-free survival of breast cancer patients.ResultsThe median age of the patients was 55.5 years (range 50–62 years). The median follow-up time was 46 months (range 33–55 months). In progression-free survival, the area under the LANR curve was 0.748 and the HR (95% CI) was 0.035 (0.679–0.817). LANR was associated with age (p = 0.02), positive axillary lymph nodes (p < 0.001), TNM stage (p < 0.001) and human epidermal growth factor receptor 2(p = 0.004). The results indicated that preoperative LANR may be a reliable predictor of progression-free survival in patients with operable breast cancer.ConclusionLANR may be an essential predictor for breast cancer patients and provides a therapeutic basis for clinicians and patients. creator: Yuan Wang creator: Jiaru Zhuang creator: Shan Wang creator: Yibo Wu creator: Ling Chen uri: https://doi.org/10.7717/peerj.17382 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Var3PPred: variant prediction based on 3-D structure and sequence analyses of protein-protein interactions on autoinflammatory diseases link: https://peerj.com/articles/17297 last-modified: 2024-05-14 description: We developed a pathogenicity classifier, named Var3PPred, for identifying pathogenic variants in genes associated with autoinflammatory disorders. Our comprehensive approach integrates protein-protein interaction analysis and 3D structural information. Initially, we collected a dataset of 702 missense disease-associated variants from 35 genes linked to systemic autoinflammatory diseases (SAIDs). This dataset, sourced from the Infevers database, served as the training and test sets. We used the SMOTE algorithm to balance the dataset comprising 130 benign and 572 pathogenic variations. Our approach included 3D docking analysis of protein-protein interactions, utilizing data from the STRING and Intact databases. We weighted ZDOCK and SPRINT values in accordance with HGPEC gene rank scores for robustness. Additionally, we integrated sequential and structural features, such as changes in folding free energies (ΔΔ G), accessible surface area, volume, per residue local distance difference test (pLDDT) scores, and position specific independent count (PSIC) scores. These features, calculated using PyRosetta and AF2 computed structures, provided insights into amino acid conservation at variant positions and the impact of variants on protein structure and stability. Through extensive hyperparameter tuning of six machine learning algorithms, we found the random forest classifier to be the most effective, yielding an AUROC of 99% on the test set. Var3PPred outperformed three other classifiers, SIFT, PolyPhen, and CADD, on an unseen test set of a SAID-related gene. This demonstrates its capacity for pathogenicity classification of SAID variations. The source code for Var3PPred and the predictions for all 420 missense variants of uncertain significance from the Infevers database are available on GitHub: (https://github.com/alperbulbul1/Var3PPred). creator: Alper Bülbül creator: Emel Timucin creator: Ahmet Can Timuçin creator: Osman Uğur Sezerman creator: Eda Tahir Turanli uri: https://doi.org/10.7717/peerj.17297 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bülbül et al. title: Similar and divergent responses to salinity stress of jamun (Syzygium cumini L. Skeels) genotypes link: https://peerj.com/articles/17311 last-modified: 2024-05-14 description: BackgroundGenetic variation for salt tolerance remains elusive in jamun (Syzygium cumini).MethodsEffects of gradually increased salinity (2.0–12.0 dS/m) were examined in 20 monoembryonic and 28 polyembryonic genotypes of jamun. Six genotypes were additionally assessed for understanding salt-induced changes in gas exchange attributes and antioxidant enzymes.ResultsSalt-induced reductions in leaf, stem, root and plant dry mass (PDM) were relatively greater in mono- than in poly-embryonic types. Reductions in PDM relative to control implied more adverse impacts of salinity on genotypes CSJ-28, CSJ-31, CSJ-43 and CSJ-47 (mono) and CSJ-1, CSJ-24, CSJ-26 and CSJ-27 (poly). Comparably, some mono- (CSJ-5, CSJ-18) and poly-embryonic (CSJ-7, CSJ-8, CSJ-14, CSJ-19) genotypes exhibited least reductions in PDM following salt treatment. Most polyembryonic genotypes showed lower reductions in root than in shoot mass, indicating that they may be more adept at absorbing water and nutrients when exposed to salt. The majority of genotypes did not exhibit leaf tip burn and marginal scorch despite significant increases in Na+ and Cl−, suggesting that tissue tolerance existed for storing excess Na+ and Cl− in vacuoles. Jamun genotypes were likely more efficient in Cl− exclusion because leaf, stem and root Cl− levels were consistently lower than those of Na+ under salt treatment. Leaf K+ was particularly little affected in genotypes with high leaf Na+. Lack of discernible differences in leaf, stem and root Ca2+ and Mg2+ contents between control and salt treatments was likely due to their preferential uptake. Correlation analysis suggested that Na+ probably had a greater inhibitory effect on biomass in both mono- and poly-embryonic types. Discriminant analysis revealed that while stem and root Cl− probably accounted for shared responses, root Na+, leaf K+ and leaf Cl− explained divergent responses to salt stress of mono- and poly-embryonic types. Genotypes CSJ-18 and CSJ-19 seemed efficient in fending off oxidative damage caused by salt because of their stronger antioxidant defences.ConclusionsPolyembryonic genotypes CSJ-7, CSJ-8, CSJ-14 and CSJ-19, which showed least reductions in biomass even after prolonged exposure to salinity stress, may be used as salt-tolerant rootstocks. The biochemical and molecular underpinnings of tissue tolerance to excess Na+ and Cl− as well as preferential uptake of K+, Ca2+, and Mg2+ need to be elucidated. creator: Anshuman Singh creator: Ashwani Kumar creator: Jai Prakash creator: Arvind Kumar Verma uri: https://doi.org/10.7717/peerj.17311 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Singh et al. title: Vocal complexity in the long calls of Bornean orangutans link: https://peerj.com/articles/17320 last-modified: 2024-05-14 description: Vocal complexity is central to many evolutionary hypotheses about animal communication. Yet, quantifying and comparing complexity remains a challenge, particularly when vocal types are highly graded. Male Bornean orangutans (Pongo pygmaeus wurmbii) produce complex and variable “long call” vocalizations comprising multiple sound types that vary within and among individuals. Previous studies described six distinct call (or pulse) types within these complex vocalizations, but none quantified their discreteness or the ability of human observers to reliably classify them. We studied the long calls of 13 individuals to: (1) evaluate and quantify the reliability of audio-visual classification by three well-trained observers, (2) distinguish among call types using supervised classification and unsupervised clustering, and (3) compare the performance of different feature sets. Using 46 acoustic features, we used machine learning (i.e., support vector machines, affinity propagation, and fuzzy c-means) to identify call types and assess their discreteness. We additionally used Uniform Manifold Approximation and Projection (UMAP) to visualize the separation of pulses using both extracted features and spectrogram representations. Supervised approaches showed low inter-observer reliability and poor classification accuracy, indicating that pulse types were not discrete. We propose an updated pulse classification approach that is highly reproducible across observers and exhibits strong classification accuracy using support vector machines. Although the low number of call types suggests long calls are fairly simple, the continuous gradation of sounds seems to greatly boost the complexity of this system. This work responds to calls for more quantitative research to define call types and quantify gradedness in animal vocal systems and highlights the need for a more comprehensive framework for studying vocal complexity vis-à-vis graded repertoires. creator: Wendy M. Erb creator: Whitney Ross creator: Haley Kazanecki creator: Tatang Mitra Setia creator: Shyam Madhusudhana creator: Dena J. Clink uri: https://doi.org/10.7717/peerj.17320 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Erb et al. title: Hsa_circ_0009096/miR-370-3p modulates hepatic stellate cell proliferation and fibrosis during biliary atresia pathogenesis link: https://peerj.com/articles/17356 last-modified: 2024-05-14 description: BackgroundHepatic stellate cell (HSC) activation and hepatic fibrosis mediated biliary atresia (BA) development, but the underlying molecular mechanisms are poorly understood. This study aimed to investigate the roles of circRNA hsa_circ_0009096 in the regulation of HSC proliferation and hepatic fibrosis.MethodsA cellular hepatic fibrosis model was established by treating LX-2 cells with transforming growth factor β (TGF-β1). RNaseR and actinomycin D assays were performed to detect hsa_circ_0009096 stability. Expression of hsa_circ_0009096, miR-370-3p, and target genes was detected using reverse transcription-qPCR. Direct binding of hsa_circ_0009096 to miR-370-3p was validated using dual luciferase reporter assay. Cell cycle progression and apoptosis of LX-2 cells were assessed using flow cytometry. The alpha-smooth muscle actin (α-SMA), collagen 1A1 (COL1A1), and TGF beta receptor 2 (TGFBR2) protein levels in LX-2 cells were analyzed using immunocytochemistry and western blotting.ResultsHsa_circ_0009096 exhibited more resistance to RNase R and actinomycinD digestion than UTRN mRNA. Hsa_circ_0009096 expression increased significantly in LX-2 cells treated with TGF-β1, accompanied by elevated α-SMA and COL1A1 expression. Hsa_circ_0009096 siRNAs effectively promoted miR-370-3p and suppressed TGFBR2 expression in LX-2 cells, mediated by direct association of hsa_circ_0009096 with miR-370-3p. Hsa_circ_0009096 siRNA interfered with the cell cycle progression, promoted apoptosis, and reduced α-SMA and COL1A1 expression in LX-2 cells treated with TGF-β1. MiR-370-3p inhibitors mitigated the alterations in cell cycle progression, apoptosis, and α-SMA, COL1A1, and TGFBR2 expression in LX-2 cells caused by hsa_circ_0009096 siRNA. In conclusion, hsa_circ_0009096 promoted HSC proliferation and hepatic fibrosis during BA pathogenesis by accelerating TGFBR2 expression by sponging miR-370-3p. creator: Zhouguang Wu creator: Bin Wang creator: Siqi Chen creator: Taoyan Zuo creator: Wenjie Zhang creator: Zhen Cheng creator: Jingru Fu creator: Jiafeng Gong uri: https://doi.org/10.7717/peerj.17356 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wu et al. title: A comprehensive analysis of the oncogenic and prognostic role of TBC1Ds in human hepatocellular carcinoma link: https://peerj.com/articles/17362 last-modified: 2024-05-14 description: BackgroundsTBC1D family members (TBC1Ds) are a group of proteins that contain the Tre2-Bub2-Cdc16 (TBC) domain. Recent studies have shown that TBC1Ds are involved in tumor growth, but no analysis has been done of expression patterns and prognostic values of TBC1Ds in hepatocellular carcinoma (HCC).MethodsThe expression levels of TBC1Ds were evaluated in HCC using the TIMER, UALCN and Protein Atlas databases. The correlation between the mRNA levels of TBC1Ds and the prognosis of patients with HCC in the GEPIA database was then analyzed. An enrichment analysis then revealed genes that potentially interact with TBC1Ds. The correlation between levels of TBC1Ds and tumor-infiltrating immune cells (TIICs) in HCC were studied using the TIMER 2.0 database. Finally, a series of in vitro assays verified the role of TBC1Ds in HCC progression.ResultsThis study revealed the upregulated expression of TBC1Ds in HCC and the strong positive correlation between the mRNA levels of TBC1Ds and poor prognosis of patients with HCC. The functions of TBC1Ds were mainly related to autophagy and the AMPK pathway. There was also a significant correlation between level of TBC1Ds and tumor-infiltrating immune cells (TIICs) in HCC. The promoting role of TBC1Ds in HCC progression was verified in vitro assays.ConclusionThe results of this analysis indicate that TBC1Ds may serve as new biomarkers for early diagnosis and treatment of HCC. creator: Pei Zhang creator: Lei Zhu creator: Xiaodong Pan uri: https://doi.org/10.7717/peerj.17362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Arsenic disulfide promoted the demethylation of PTPL1 in diffuse large B cell lymphoma cells link: https://peerj.com/articles/17363 last-modified: 2024-05-14 description: BackgroundPromoter hypermethylation of the tumor suppressor gene is one of the well-studied causes of cancer development. The drugs that reverse the process by driving demethylation could be a candidate for anticancer therapy. This study was designed to investigate the effects of arsenic disulfide on PTPL1 methylation in diffuse large B cell lymphoma (DLBCL).MethodsWe knocked down the expression of PTPL1 in two DLBCL cell lines (i.e., DB and SU-DHL-4 cells) using siRNA. Then the DLBCL proliferation was determined in the presence of PTPL1 knockdown. The methylation of PTPL1 in DLBCL cells was analyzed by methylation specific PCR (MSPCR). The effect of arsenic disulfide on the PTPL1 methylation was determined in DLBCL cell lines in the presence of different concentrations of arsenic disulfide (5 µM, 10 µM and 20 µM), respectively. To investigate the potential mechanism on the arsenic disulfide-mediated methylation, the mRNA expression of DNMT1, DNMT3B and MBD2 was determined.ResultsPTPL1 functioned as a tumor suppressor gene in DLBCL cells, which was featured by the fact that PTPL1 knockdown promoted the proliferation of DLBCL cells. PTPL1 was found hypermethylated in DLBCL cells. Arsenic disulfide promoted the PTPL1 demethylation in a dose-dependent manner, which was related to the inhibition of DNMTs and the increase of MBD2.ConclusionExperimental evidence shows that PTPL1 functions as a tumor suppressor gene in DLBCL progression. PTPL1 hyper-methylation could be reversed by arsenic disulfide in a dose-dependent manner. creator: Chen Chen creator: Ling Wang creator: Yan Liu creator: Shenghong Du creator: Qingliang Teng uri: https://doi.org/10.7717/peerj.17363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Non-destructive prediction of anthocyanin concentration in whole eggplant peel using hyperspectral imaging link: https://peerj.com/articles/17379 last-modified: 2024-05-14 description: Accurately detecting the anthocyanin content in eggplant peel is essential for effective eggplant breeding. The present study aims to present a method that combines hyperspectral imaging with advanced computational analysis to rapidly, non-destructively, and precisely measure anthocyanin content in eggplant fruit. For this purpose, hyperspectral images of the fruits of 20 varieties with diverse colors were collected, and the content of the anthocyanin were detected using high performance liquid chromatography (HPLC) methods. In order to minimize background noise in the hyperspectral images, five preprocessing algorithms were utilized on average reflectance spectra: standard normalized variate (SNV), autoscales (AUT), normalization (NOR), Savitzky–Golay convolutional smoothing (SG), and mean centering (MC). Additionally, the competitive adaptive reweighted sampling (CARS) method was employed to reduce the dimensionality of the high-dimensional hyperspectral data. In order to predict the cyanidin, petunidin, delphinidin, and total anthocyanin content of eggplant fruit, two models were constructed: partial least squares regression (PLSR) and least squares support vector machine (LS-SVM). The HPLC results showed that eggplant peel primarily contains three types of anthocyanins. Furthermore, there were significant differences in the average reflectance rates between 400–750 nm wavelength ranges for different colors of eggplant peel. The prediction model results indicated that the model based on NOR CARS LS-SVM achieved the best performance, with a squared coefficient of determination (R2) greater than 0.98, RMSEP and RMSEC less than 0.03 for cyanidin, petunidin, delphinidin, and total anthocyanin predication. These results suggest that hyperspectral imaging is a rapid and non-destructive technique for assessing the anthocyanin content of eggplant peel. This approach holds promise for facilitating the more effective eggplant breeding. creator: Zhiling Ma creator: Changbin Wei creator: Wenhui Wang creator: Wenqiu Lin creator: Heng Nie creator: Zhe Duan creator: Ke Liu creator: Xi Ou Xiao uri: https://doi.org/10.7717/peerj.17379 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ma et al. title: Prognostic and chemotherapeutic implications of a novel four-gene pyroptosis model in head and neck squamous cell carcinoma link: https://peerj.com/articles/17296 last-modified: 2024-05-13 description: BackgroundHead and neck squamous cell carcinoma (HNSCC) is one of the most common cancers. Chemotherapy remains one dominant therapeutic strategy, while a substantial proportion of patients may develop chemotherapeutic resistance; therefore, it is particularly significant to identify the patients who could achieve maximum benefits from chemotherapy. Presently, four pyroptosis genes are reported to correlate with the chemotherapeutic response or prognosis of HNSCC, while no study has assessed the combinatorial predicting efficacy of these four genes. Hence, this study aims to evaluate the predictive value of a multi-gene pyroptosis model regarding the prognosis and chemotherapeutic responsiveness in HNSCC.MethodsBy utilizing RNA-sequencing data from The Cancer Genome Atlas database and the Gene Expression Omnibus database, the pyroptosis-related gene score (PRGscore) was computed for each HNSCC sample by performing a Gene Set Variation Analysis (GSVA) based on four genes (Caspase-1, Caspase-3, Gasdermin D, Gasdermin E). The prognostic significance of the PRGscore was assessed through Cox regression and Kaplan–Meier survival analyses. Additionally, chemotherapy sensitivity stratified by high and low PRGscore was examined to determine the potential association between pyroptosis activity and chemosensitivity. Furthermore, chemotherapy sensitivity assays were conducted in HNSCC cell lines in vitro.ResultsAs a result, our study successfully formulated a PRGscore reflective of pyroptotic activity in HNSCC. Higher PRGscore correlates with worse prognosis. However, patients with higher PRGscore were remarkably more responsive to chemotherapy. In agreement, chemotherapy sensitivity tests on HNSCC cell lines indicated a positive association between overall pyroptosis levels and chemosensitivity to cisplatin and 5-fluorouracil; in addition, patients with higher PRGscore may benefit from the immunotherapy. Overall, our study suggests that HNSCC patients with higher PRGscore, though may have a less favorable prognosis, chemotherapy and immunotherapy may exhibit better benefits in this population. creator: Peiyang Yuan creator: Sixin Jiang creator: Qiuhao Wang creator: Yuqi Wu creator: Yuchen Jiang creator: Hao Xu creator: Lu Jiang creator: Xiaobo Luo uri: https://doi.org/10.7717/peerj.17296 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yuan et al. title: Alzheimer’s diseases in America, Europe, and Asian regions: a global genetic variation link: https://peerj.com/articles/17339 last-modified: 2024-05-13 description: BackgroundAlzheimer’s disease (AD) is one of the multifaceted neurodegenerative diseases influenced by many genetic and epigenetic factors. Genetic factors are merely not responsible for developing AD in the whole population. The studies of genetic variants can provide significant insights into the molecular basis of Alzheimer’s disease. Our research aimed to show how genetic variants interact with environmental influences in different parts of the world.MethodologyWe searched PubMed and Google Scholar for articles exploring the relationship between genetic variations and global regions such as America, Europe, and Asia. We aimed to identify common genetic variations susceptible to AD and have no significant heterogeneity. To achieve this, we analyzed 35 single-nucleotide polymorphisms (SNPs) from 17 genes (ABCA7, APOE, BIN1, CD2AP, CD33, CLU, CR1, EPHA1, TOMM40, MS4A6A, ARID5B, SORL1, APOC1, MTHFD1L, BDNF, TFAM, and PICALM) from different regions based on previous genomic studies of AD. It has been reported that rs3865444, CD33, is the most common polymorphism in the American and European populations. From TOMM40 and APOE rs2075650, rs429358, and rs6656401, CR1 is the common investigational polymorphism in the Asian population.ConclusionThe results of all the research conducted on AD have consistently shown a correlation between genetic variations and the incidence of AD in the populations of each region. This review is expected to be of immense value in future genetic research and precision medicine on AD, as it provides a comprehensive understanding of the genetic factors contributing to the development of this debilitating disease. creator: Rahni Hossain creator: Kunwadee Noonong creator: Manit Nuinoon creator: Udom Lao-On creator: Christopher M. Norris creator: Pradoldej Sompol creator: Md. Atiar Rahman creator: Hideyuki J. Majima creator: Jitbanjong Tangpong uri: https://doi.org/10.7717/peerj.17339 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hossain et al. title: A retrospective prognostic evaluation using unsupervised learning in the treatment of COVID-19 patients with hypertension treated with ACEI/ARB drugs link: https://peerj.com/articles/17340 last-modified: 2024-05-13 description: IntroductionThis study aimed to evaluate the prognosis of patients with COVID-19 and hypertension who were treated with angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor B (ARB) drugs and to identify key features affecting patient prognosis using an unsupervised learning method.MethodsA large-scale clinical dataset, including patient information, medical history, and laboratory test results, was collected. Two hundred patients with COVID-19 and hypertension were included. After cluster analysis, patients were divided into good and poor prognosis groups. The unsupervised learning method was used to evaluate clinical characteristics and prognosis, and patients were divided into different prognosis groups. The improved wild dog optimization algorithm (IDOA) was used for feature selection and cluster analysis, followed by the IDOA-k-means algorithm. The impact of ACEI/ARB drugs on patient prognosis and key characteristics affecting patient prognosis were also analysed.ResultsKey features related to prognosis included baseline information and laboratory test results, while clinical symptoms and imaging results had low predictive power. The top six important features were age, hypertension grade, MuLBSTA, ACEI/ARB, NT-proBNP, and high-sensitivity troponin I. These features were consistent with the results of the unsupervised prediction model. A visualization system was developed based on these key features.ConclusionUsing unsupervised learning and the improved k-means algorithm, this study accurately analysed the prognosis of patients with COVID-19 and hypertension. The use of ACEI/ARB drugs was found to be a protective factor for poor clinical prognosis. Unsupervised learning methods can be used to differentiate patient populations and assess treatment effects. This study identified important features affecting patient prognosis and developed a visualization system with clinical significance for prognosis assessment and treatment decision-making. creator: Liye Ge creator: Yongjun Meng creator: Weina Ma creator: Junyu Mu uri: https://doi.org/10.7717/peerj.17340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ge et al. title: Salivary interleukin-17A and interleukin-18 levels in patients with celiac disease and periodontitis link: https://peerj.com/articles/17374 last-modified: 2024-05-13 description: BackgroundAn increased level of interleukin-17A and interleukin-18 in the serum and intestinal mucosa of celiac disease patients reflecting the severity of villous atrophy and inflammation was documented. Thus, the objective of this study was to evaluate the concentrations of salivary-17A, interleukin-1 beta, and interleukin-18 in patients with celiac disease who are on a gluten-free diet, both with and without periodontitis, and to compare these levels with those in healthy individuals.MethodsThe study involved 23 participants with serologically confirmed celiac disease (CD) and 23 control subjects. The CD patients had been following a gluten-free diet (GFD) for a minimum of 1 year and had no other autoimmune disorders. The research involved collecting demographic data, conducting periodontal examinations, gathering unstimulated whole saliva, and performing enzyme-linked immunosorbent assays to measure salivary interleukin-17A, interleukin-1 beta, and interleukin-18 levels. Spearman’s correlation analysis was utilized to explore the relationships between CD markers in patients on a GFD and their periodontal clinical findings.ResultsThe periodontal findings indicated significantly lower values in celiac disease patients adhering to a gluten-free diet compared to control subjects (p = 0.001). No significant differences were found in salivary IL-17A, IL-18, and IL-1B levels between celiac disease patients and control subjects. Nevertheless, the levels of all interleukins were elevated in periodontitis patients in both the celiac and control groups. The IL-1 Beta level was significantly higher in periodontitis patients compared to non-periodontitis patients in the control group (p = 0.035). Significant negative correlations were observed between serum IgA levels and plaque index (r = −0.460, p = 0.010), as well as gingival index (r = −0.396, p = 0.030) in CD patients on a gluten-free diet.ConclusionCeliac disease patients on gluten-free diet exhibited better periodontal health compared to control subjects. However, increased levels of salivary IL-17A, IL-18 and IL-1B levels were associated with periodontitis. Additionally, serum IgA level was significantly inversely associated with periodontitis clinical manifestations and with salivary inflammatory mediators in CD patients on GFD. creator: Marwa Madi creator: Maha Abdelsalam creator: Ahmed Elakel creator: Osama Zakaria creator: Maher AlGhamdi creator: Mohammed Alqahtani creator: Luba AlMuhaish creator: Faraz Farooqi creator: Turki A. Alamri creator: Ibrahim A. Alhafid creator: Ibrahim M. Alzahrani creator: Adel H. Alam creator: Majed T. Alhashmi creator: Ibrahim A. Alasseri creator: Ahmad A. AlQuorain creator: Abdulaziz A. AlQuorain uri: https://doi.org/10.7717/peerj.17374 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Madi et al. title: Feral frogs, native newts, and chemical cues: identifying threats from and management opportunities for invasive African Clawed Frogs in Washington state link: https://peerj.com/articles/17307 last-modified: 2024-05-10 description: Invasive species threaten biodiversity globally. Amphibians are one of the most threatened vertebrate taxa and are particularly sensitive to invasive species, including other amphibians. African clawed frogs (Xenopus laevis) are native to Southern Africa but have subsequently become invasive on multiple continents—including multiple parts of North America—due to releases from the pet and biomedical trades. Despite their prevalence as a global invader, the impact of X. laevis remains understudied. This includes the Pacific Northwest of the USA, which now hosts multiple expanding X. laevis populations. For many amphibians, chemical cues communicate important information, including the presence of predators. Here, we tested the role chemical cues may play in mediating interactions between feral X. laevis and native amphibians in the Pacific Northwest. We tested whether native red-legged frog (Rana aurora) tadpoles display an antipredator response to non-native frog (X. laevis) or native newt (rough-skinned newts, Taricha granulosa) predator chemical stimuli. We found that R. aurora tadpoles exhibited pronounced anti-predator responses when exposed to chemical cues from T. granulosa but did not display anti-predator response to invasive X. laevis chemical cues. We also began experimentally testing whether T. granulosa—which produce a powerful neurotoxin tetrodotoxin (TTX)—may elicit an anti-predator response in X. laevis, that could serve to deter co-occupation. However, our short-duration experiments found that X. laevis were attracted to newt chemical stimuli rather than deterred. Our findings show that X. laevis likely poses a threat to native amphibians, and that these native species may also be particularly vulnerable to this invasive predator, compared to native predators, because toxic native newts may not limit X. laevis invasions. Our research provides some of the first indications that native Pacific Northwest species may be threatened by feral X. laevis and provides a foundation for future experiments testing potential management techniques for X. laevis. creator: David Anderson creator: Olivia Cervantez creator: Gary M. Bucciarelli creator: Max R. Lambert creator: Megan R. Friesen uri: https://doi.org/10.7717/peerj.17307 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Anderson et al. title: The effect of social anxiety on threat acquisition and extinction: a systematic review and meta-analysis link: https://peerj.com/articles/17262 last-modified: 2024-05-09 description: Although exposure-based therapy has been found to be effective at alleviating symptoms of social anxiety disorder, it often does not lead to full remission, and relapse after treatment is common. Exposure therapy is based on theoretical principles of extinction of conditioned fear responses. However, there are inconsistencies in findings across experiments that have investigated the effect of social anxiety on threat conditioning and extinction processes. This systematic review and meta-analysis aimed to examine whether elevated levels of social anxiety are associated with abnormalities in threat conditioning and extinction processes. A second aim was to examine the sensitivity of various study designs and characteristics to detect social anxiety-related differences in threat conditioning and extinction. A systematic search was conducted, which identified twenty-three experiments for inclusion in the review. The findings did not demonstrate compelling evidence that high levels of social anxiety are associated with atypical threat conditioning or extinction. Further, when systematically examining the data, there was no convincing support that the use of a particular psychophysiological measure, subjective rating, or experimental parameter yields more consistent associations between social anxiety and conditioning processes during threat acquisition or extinction. Meta-analyses demonstrated that during threat extinction, the use of anxiety ratings as a dependent variable, socially relevant unconditioned stimuli, and a higher reinforcement schedule produced more detectable effects of social anxiety on compromised extinction processes compared to any other dependent variable (subjective or physiological) or experimental parameter. Overall, the results of this study suggest that social anxiety is not reliably related to deficits in conditioning and extinction processes in the context of laboratory-based Pavlovian conditioning paradigms. creator: Shannon Wake creator: Nicholas Hedger creator: Carien M. van Reekum creator: Helen Dodd uri: https://doi.org/10.7717/peerj.17262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wake et al. title: Successful treatment of diplopia using prism correction combined with vision therapy/orthoptics improves health-related quality of life link: https://peerj.com/articles/17315 last-modified: 2024-05-09 description: BackgroundTo track improvement in diplopia symptoms with strabismus-specific health-related quality of life (HRQOL) questionnaire across a treatment consisting of prism correction followed by vision therapy/orthoptics when prism treatment alone has not succeeded.MethodsForty-eight participants with diplopia and a mean age of 62.45 were asked to complete an Adult Strabismus-20 (AS-20) questionnaire and a Diplopia Questionnaire (DQ) before and after prism correction. Inclusion criteria were diplopia reported on the DQ as “sometimes”, “often” or “always” at reading or straight-ahead distance. The prism correction was classified as successful if the participant reported “never” or “rarely” on the DQ for reading and straight-ahead distance; and unsuccessful if the perceived diplopia worsened or remained the same. For all participants, mean initial AS-20 scores were compared with mean post-prism correction scores, taking into account AS-20 subscales (reading and general functions, and self-perception and interaction). Participants in the failed prism treatment subgroup subsequently underwent a programme of vision therapy wearing their prism correction, the results of which were again determined by participants’ responses on the AS-20 questionnaire, completed before and after the vision therapy.ResultsFive of the 48 participants dropped out of the study. Prism correction was classified as successful in 22 of 43 participants (51%), and unsuccessful in 21 (49%). Those participants for whom the prism correction was classified as a success showed a statistically significant improvement (p = 0.01) in both reading and general functions. In the failed treatment subgroup, no significant change in AS-20 score was recorded for any of the domains (p = 0.1). After treatment with vision therapy/orthoptics, however, 13 of the 20 participants in the unsuccessful prism correction subgroup (one of them dropped out the study) achieved binocular vision and statistically significant improvement in reading and general functions (p = 0.01).ConclusionsAlthough effective prism correction of diplopia is correlated with enhanced HRQOL, prism correction alone is frequently not sufficient to achieve this objective. In these cases, vision therapy/orthoptics treatment as a coadjutant to prism correction is shown to improve HRQOL. creator: Juan Antonio Portela-Camino creator: Irene Sanchez creator: Cristina Gutierrez creator: Santiago Martín-González uri: https://doi.org/10.7717/peerj.17315 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Portela-Camino et al. title: Regulation of cellular and molecular markers of epithelial-mesenchymal transition by Brazilin in breast cancer cells link: https://peerj.com/articles/17360 last-modified: 2024-05-09 description: Breast cancer is the most common invasive neoplasm and the leading cause of cancer death in women worldwide. The main cause of mortality in cancer patients is invasion and metastasis, where the epithelial-mesenchymal transition (EMT) is a crucial player in these processes. Pharmacological therapy has plants as its primary source, including isoflavonoids. Brazilin is an isoflavonoid isolated from Haematoxilum brasiletto that has shown antiproliferative activity in several cancer cell lines. In this study, we evaluated the effect of Brazilin on canonical markers of EMT such as E-cadherin, vimentin, Twist, and matrix metalloproteases (MMPs). By Western blot, we evaluated E-cadherin, vimentin, and Twist expression and the subcellular localization by immunofluorescence. Using gelatin zymography, we determined the levels of secretion of MMPs. We used Transwell chambers coated with matrigel to determine the in vitro invasion of breast cancer cells treated with Brazilin. Interestingly, our results show that Brazilin increases 50% in E-cadherin expression and decreases 50% in vimentin and Twist expression, MMPs, and cell invasion in triple-negative breast cancer (TNBC) MDA-MB-231 and to a lesser extend in MCF7 ER+ breast cancer cells. Together, these findings position Brazilin as a new molecule with great potential for use as complementary or alternative treatment in breast cancer therapy in the future. creator: Lorena Cayetano-Salazar creator: Jose A. Hernandez-Moreno creator: Jorge Bello-Martinez creator: Monserrat Olea-Flores creator: Eduardo Castañeda-Saucedo creator: Monica Ramirez creator: Miguel A. Mendoza-Catalán creator: Napoleon Navarro-Tito uri: https://doi.org/10.7717/peerj.17360 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cayetano-Salazar et al. title: No sex difference in preen oil chemical composition during incubation in Kentish plovers link: https://peerj.com/articles/17243 last-modified: 2024-05-08 description: Preen oil, the secretion from the uropygial gland of birds, may have a specific function in incubation. Consistent with this, during incubation, the chemical composition of preen oil is more likely to differ between sexes in species where only one sex incubates than in species where both sexes incubate. In this study, we tested the generality of this apparent difference, by investigating sex differences in the preen oil composition of a shorebird species, the Kentish plover (Anarhynchus, formerly Charadrius, alexandrinus). As both sexes incubate in this species, we predicted the absence of sex differences in preen oil composition during incubation. In the field, we sampled preen oil from nine females and 11 males during incubation, which we analysed with gas chromatography–mass spectrometry (GC–MS). Consistent with predictions, we found no sex difference in preen oil composition, neither in beta diversity (Bray-Curtis dissimilarities) nor in alpha diversity (Shannon index and number of substances). Based on these results, we cannot conclude whether preen oil has a function during incubation in Kentish plovers. Still, we discuss hypothetical roles, such as olfactory crypsis, protection against ectoparasites or olfactory intraspecific communication, which remain to be tested. creator: Marc Gilles creator: András Kosztolányi creator: Afonso D. Rocha creator: Innes C. Cuthill creator: Tamás Székely creator: Barbara A. Caspers uri: https://doi.org/10.7717/peerj.17243 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gilles et al. title: Interactive effects of drought and deforestation on multitrophic communities and aquatic ecosystem functions in the Neotropics—a test using tank bromeliads link: https://peerj.com/articles/17346 last-modified: 2024-05-08 description: BackgroundTogether with the intensification of dry seasons in Neotropical regions, increasing deforestation is expected to exacerbate species extinctions, something that could lead to dramatic shifts in multitrophic communities and ecosystem functions. Recent studies suggest that the effects of habitat loss are greater where precipitation has decreased. Yet, experimental studies of the pure and interactive effects of drought and deforestation at ecosystem level remain scarce.MethodsHere, we used rainshelters and transplantation from rainforest to open areas of natural microcosms (the aquatic ecosystem and microbial-faunal food web found within the rainwater-filled leaves of tank bromeliads) to emulate drought and deforestation in a full factorial experimental design. We analysed the pure and interactive effects of our treatments on functional community structure (including microorganisms, detritivore and predatory invertebrates), and on leaf litter decomposition in tank bromeliad ecosystems.ResultsDrought or deforestation alone had a moderate impact on biomass at the various trophic level, but did not eliminate species. However, their interaction synergistically reduced the biomass of all invertebrate functional groups and bacteria. Predators were the most impacted trophic group as they were totally eliminated, while detritivore biomass was reduced by about 95%. Fungal biomass was either unaffected or boosted by our treatments. Decomposition was essentially driven by microbial activity, and did not change across treatments involving deforestation and/or drought.ConclusionsOur results suggest that highly resistant microorganisms such as fungi (plus a few detritivores) maintain key ecosystem functions in the face of drought and habitat change. We conclude that habitat destruction compounds the problems of climate change, that the impacts of the two phenomena on food webs are mutually reinforcing, and that the stability of ecosystem functions depends on the resistance of a core group of organisms. Assuming that taking global action is more challenging than taking local-regional actions, policy-makers should be encouraged to implement environmental action plans that will halt habitat destruction, to dampen any detrimental interactive effect with the impacts of global climate change. creator: Marie Séguigne creator: Céline Leroy creator: Jean-François Carrias creator: Bruno Corbara creator: Tristan Lafont Rapnouil creator: Régis Céréghino uri: https://doi.org/10.7717/peerj.17346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Séguigne et al. title: Global marine phytoplankton dynamics analysis with machine learning and reanalyzed remote sensing link: https://peerj.com/articles/17361 last-modified: 2024-05-08 description: Phytoplankton are the world’s largest oxygen producers found in oceans, seas and large water bodies, which play crucial roles in the marine food chain. Unbalanced biogeochemical features like salinity, pH, minerals, etc., can retard their growth. With advancements in better hardware, the usage of Artificial Intelligence techniques is rapidly increasing for creating an intelligent decision-making system. Therefore, we attempt to overcome this gap by using supervised regressions on reanalysis data targeting global phytoplankton levels in global waters. The presented experiment proposes the applications of different supervised machine learning regression techniques such as random forest, extra trees, bagging and histogram-based gradient boosting regressor on reanalysis data obtained from the Copernicus Global Ocean Biogeochemistry Hindcast dataset. Results obtained from the experiment have predicted the phytoplankton levels with a coefficient of determination score (R2) of up to 0.96. After further validation with larger datasets, the model can be deployed in a production environment in an attempt to complement in-situ measurement efforts. creator: Subhrangshu Adhikary creator: Surya Prakash Tiwari creator: Saikat Banerjee creator: Ashutosh Dhar Dwivedi creator: Syed Masiur Rahman uri: https://doi.org/10.7717/peerj.17361 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Adhikary et al. title: Effects of harvest height and time on hay yield and quality of some sweet sorghum and sorghum Sudangrass hybrid varieties link: https://peerj.com/articles/17274 last-modified: 2024-05-07 description: BackgroundThis experiment was conducted in the Research and Application Field of Canakkale Onsekiz Mart University, Faculty of Agriculture, during the 2020 and 2021 summer period. The objective of this experiment was to determine the effects of different harvesting heights on forage yields and crude ash, fat, protein, and carbon and nitrogen content of leaves and stalks of sweet sorghum (SS) and sorghum sudangrass hybrid (SSH) cultivars.MethodsNutri Honey and Nutrima varieties of SSH and the M81-E and Topper-76 varieties of SS were used in this study. The experiment was conducted using the randomized complete block design with four replications. The main plots each included two early and late varieties of SS and SSH cultivars, while the subplots were used to test different harvesting heights (30, 60, 90, 120, 150 cm) and physiological parameters of each crop.ResultsThe results of this study showed that dry forage yields increased with plant growth, with the amount of forage produced at the end of the growth cycle increasing 172.2% compared to the early growth stages. Carbon (C) content of leaves decreased by 6.5%, nitrogen (N) by 46%, crude protein (CP) by 54%, crude fat (CF) by 34%, while crude ash (CA) content increased by 6% due to the increase in plant height harvest. At the same time, in parallel with the increase in plant height at harvest, the nitrogen content of the stems of the plants decreased by 87%, crude protein by 65%, crude ash by 33% and crude fat by 41%, while the carbon content increased by 4%. As plant height at harvest increased, hay yield increased but nutrient contents of the hay decreased. However, the Nutrima, Nutri Honey and M81-E sorghum cultivars, harvested three times at heights of 90 to 120 cm, are recommended for the highest yield. creator: Fırat Alatürk uri: https://doi.org/10.7717/peerj.17274 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alatürk title: The relationship between the living environment and remote working: an analysis using the SHEL model link: https://peerj.com/articles/17301 last-modified: 2024-05-07 description: ObjectiveThis study investigates the relationship of living environment factors with satisfaction, work engagement, perceived productivity, and stress among teleworkers.BackgroundGiven the increase in telecommuting since the onset of the pandemic, the study aims to identify how to create an optimum environment for telecommuting workers.MethodsBy examining the relationships among these factors via multiple regression analysis, a comprehensive investigation of the telecommuting working environment is conducted, encompassing physical aspects and facilities as well as lifestyle rhythms and relationships with housemates. In doing so, the author identifies measures to create a more favorable living environment. The work environment of remote workers is examined from various perspectives using the framework of the SHEL model: Software (work content, lifestyle, etc.), Hardware (furniture, equipment, etc.), Environment (indoor environment), and Liveware (relationships with family members who reside with the worker).ResultsThe results suggest that positive factors, such as satisfaction and work engagement, are strongly influenced by the degree of job autonomy and the availability of a workspace dedicated to personal use. Negative aspects, such as stress, are significantly impacted by environmental noise, interruptions due to household tasks, and the use of ergonomic furniture. creator: Toshihisa Doi uri: https://doi.org/10.7717/peerj.17301 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Doi title: Effect of iron saturation of bovine lactoferrin on the inhibition of hepatitis B virus in vitro link: https://peerj.com/articles/17302 last-modified: 2024-05-07 description: BackgroundHepatitis B virus (HBV) infection poses a major public health problem worldwide. Bovine lactoferrin (bLf) is a natural product that can inhibit HBV, but the effect of iron saturation on its resistance to HBV is unknown.AimsThe purpose of this study is to investigate the impact of iron saturation of bLf against HBV.MethodsHepG2 cells were cultured in DMEM high glucose containing 10% inactivated fetal calf serum, at 37 °C, in 5% CO2. MTT method was used to detect the cytotoxicity of bLf to HepG2 cells. Apo-bLf and holo-bLf were prepared from bLf. Iron saturation of these proteins was determined by atomic absorption spectrophotometry. Non-cytotoxic concentrations of candidate proteins were used in anti-HBV tests. Fluorescent quantitative polymerase chain reaction was used to detect HBV-DNA.ResultsThe TC50 and TC0of bLf were 54.570 mg/ml and 1.997 mg/ml, respectively. The iron saturation of bLf, apo-bLf and holo-bLf were 10.29%, 8.42% and 85.32%, respectively. In this study, four non-cytotoxic concentrations of candidate proteins (1.5, 1.0, 0.5, and 0.1 mg/ml, respectively) were used to inhibit HBV in HepG2 cells. The results showed that 1.5 mg/ml bLf and 0.1 mg/ml holo-bLf effectively impaired the HBV-DNA amplification in HBV-infected HepG2 cells (P < 0.05). However, apo-bLf, and Fe3+ did not show the anti-HBV effects.ConclusionA total of 1.5 mg/ml bLf and 0.1 mg/ml holo-bLf could inhibit HBV-DNA in HepG2 cells. Complete bLf structure, appropriate concentration and iron saturation of bLf are necessary conditions for anti-HBV effects. creator: Haibo Zhou creator: Yiwei Zhu creator: Ning Liu creator: Wencui Zhang creator: Jianchun Han uri: https://doi.org/10.7717/peerj.17302 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhou et al. title: Use of digital strategies in the diagnosis of oral squamous cell carcinoma: a scoping review link: https://peerj.com/articles/17329 last-modified: 2024-05-07 description: Telediagnosis uses information and communication technologies to support diagnosis, shortening geographical distances. It helps make decisions about various oral lesions. The objective of this scoping review was to map the existing literature on digital strategies to assist in the diagnosis of oral squamous cell carcinoma. this review was structured based on the 5-stage methodology proposed by Arksey and O’Malley, the Joanna Briggs Institute Manual for Evidence Synthesis and followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews. The methods were registered on the Open Science Framework. The research question was: What digital strategies have been used to assist in the diagnosis of oral squamous cell carcinoma? The search was conducted on PubMed/MEDLINE, Scopus, Web of Science, Embase, and ScienceDirect. Inclusion criteria comprised studies on telediagnosis, teleconsultation or teleconsultation mediated by a professional and studies in English, without date restrictions. The search conducted in June 2023 yielded 1,798 articles, from which 16 studies were included. Telediagnosis was reported in nine studies, involving data screening through applications, clinical images from digital cameras, mobile phones or artificial intelligence. Histopathological images were reported in four studies. Both, telediagnosis and teleconsultation, were mentioned in seven studies, utilizing images and information submission services to platforms, WhatsApp or applications. One study presented teleconsultations involving slides and another study introduced teleconsultation mediated by a professional. Digital strategies telediagnosis and teleconsultations enable the histopathological diagnosis of oral cancer through clinical or histopathological images. The higher the observed diagnostic agreement, the better the performance of the strategy. creator: Rebeka Thiara Nascimento dos Santos creator: Caroline Augusta Belo Faria creator: Nathalya Fedechen Martins creator: Luiz Gustavo de Sousa Duda Júnior creator: Ana Beatriz Fernandes Azevêdo creator: Weslay Rodrigues da Silva creator: Ana Paula Veras Sobral uri: https://doi.org/10.7717/peerj.17329 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Combination administration of alprazolam and N-Ethylmaleimide synergistically enhances sleep behaviors in mice with no potential CNS side effects link: https://peerj.com/articles/17342 last-modified: 2024-05-07 description: BackgroundN-Ethylmaleimide (NEM), an agonist of the potassium chloride cotransporters 2 (KCC2) receptor, has been correlated with neurosuppressive outcomes, including decreased pain perception and the prevention of epileptic seizures. Nevertheless, its relationship with sleep-inducing effects remains unreported.ObjectiveThe present study aimed to investigate the potential enhancement of NEM on the sleep-inducing properties of alprazolam (Alp).MethodsThe test of the righting reflex was used to identify the appropriate concentrations of Alp and NEM for inducing sleep-promoting effects in mice. Total sleep duration and sleep quality were evaluated through EEG/EMG analysis. The neural mechanism underlying the sleep-promoting effect was examined through c-fos immunoreactivity in the brain using immunofluorescence. Furthermore, potential CNS-side effects of the combination Alp and NEM were assessed using LABORAS automated home-cage behavioral phenotyping.ResultsCombination administration of Alp (1.84 mg/kg) and NEM (1.0 mg/kg) significantly decreased sleep latency and increased sleep duration in comparison to administering 1.84 mg/kg Alp alone. This effect was characterized by a notable increase in REM duration. The findings from c-fos immunoreactivity indicated that NEM significantly suppressed neuron activation in brain regions associated with wakefulness. Additionally, combination administration of Alp and NEM showed no effects on mouse neural behaviors during automated home cage monitoring.ConclusionsThis study is the first to propose and demonstrate a combination therapy involving Alp and NEM that not only enhances the hypnotic effect but also mitigates potential CNS side effects, suggesting its potential application in treating insomnia. creator: Siqing Zhu creator: Jingjing Shi creator: Yi Zhang creator: Xuejun Chen creator: Tong Shi creator: Liqin Li uri: https://doi.org/10.7717/peerj.17342 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhu et al. title: Pathological caudal skeleton of an ichthyodectiform fish from the Upper Cretaceous Niobrara Formation of western Kansas, USA link: https://peerj.com/articles/17353 last-modified: 2024-05-07 description: A series of 12 contiguous caudal vertebrae of an ichthyodectiform fish from the Smoky Hill Chalk Member of the Niobrara Formation is described. The vertebral centra exhibit extensive overgrowth of pathological bone and there is additional pathological bone within the centra and intervertebral spaces, which together resulted in the coossification of most centra. The extent of the pathology is greatest on preural vertebrae 1-3 and decreases anteriorly, which suggests that the pathology began posteriorly and progressed anteriorly. In addition to the pathological overgrowth on bones, the specimen preserves features interpreted as calcified and/or ossified soft tissues associated with the neural and haemal canals. The pathologies are unlike previously described examples of bony pathologies in fish, and it is suggested that they resulted from combined bacterial and fungal infections. As the pathologies developed, they would have adversely impacted the fish’s swimming and feeding abilities, and presumably eventually led to the fish’s death. creator: S Christopher Bennett uri: https://doi.org/10.7717/peerj.17353 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bennett title: Identification and characterization of the CRK gene family in the wheat genome and analysis of their expression profile in response to high temperature-induced male sterility link: https://peerj.com/articles/17370 last-modified: 2024-05-07 description: Cysteine-rich receptor-like kinases (CRKs) play many important roles during plant development, including defense responses under both biotic and abiotic stress, reactive oxygen species (ROS) homeostasis, callose deposition and programmed cell death (PCD). However, there are few studies on the involvement of the CRK family in male sterility due to heat stress in wheat (Triticum aestivum L.). In this study, a genome-wide characterization of the CRK family was performed to investigate the structural and functional attributes of the wheat CRKs in anther sterility caused by heat stress. A total of 95 CRK genes were unevenly distributed on 18 chromosomes, with the most genes distributed on chromosome 2B. Paralogous homologous genes with Ka/Ks ratios less than 1 may have undergone strong purifying selection during evolution and are more functionally conserved. The collinearity analysis results of CRK genes showed that wheat and Arabidopsis (A. thaliana), foxtail millet, Brachypodium distachyon (B. distachyon), and rice have three, 12, 15, and 11 pairs of orthologous genes, respectively. In addition, the results of the network interactions of genes and miRNAs showed that five miRNAs were in the hub of the interactions map, namely tae-miR9657b-5p, tae-miR9780, tae-miR9676-5p, tae-miR164, and tae-miR531. Furthermore, qRT-PCR validation of the six TaCRK genes showed that they play key roles in the development of the mononuclear stage anthers, as all six genes were expressed at highly significant levels in heat-stressed male sterile mononuclear stage anthers compared to normal anthers. We hypothesized that the TaCRK gene is significant in the process of high-temperature-induced sterility in wheat based on the combination of anther phenotypes, paraffin sections, and qRT-PCR data. These results improve our understanding of their relationship. creator: Hongzhan Liu creator: Xiaoyi Li creator: Zehui Yin creator: Junmin Hu creator: Liuyong Xie creator: Huanhuan Wu creator: Shuying Han creator: Bing Li creator: Huifang Zhang creator: Chaoqiong Li creator: Lili Li creator: Fuli Zhang creator: Guangxuan Tan uri: https://doi.org/10.7717/peerj.17370 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Caffeoylquinic acid profiling: comparative analysis in yerba mate, Indian camphorweed, and stevia extracts with emphasis on the influence of brewing conditions and cold storage in yerba mate infusion link: https://peerj.com/articles/17250 last-modified: 2024-05-06 description: Herbal infusions exhibit diverse pharmacological effects, such as antioxidant, anti-inflammatory, anticancer, antihypertensive, and antineurodegenerative activities, which can be attributed to the high content of phenolic compounds (e.g., caffeoylquinic acids (CQAs)). In this study, we used ultraperformance liquid chromatography to determine the content of CQAs in the methanolic extracts of model herbs, namely, yerba mate (Ilex paraguariensis), stevia (Stevia rebaudiana), and Indian camphorweed (Pluchea indica (L.) Less.). The results revealed that yerba mate had the highest total CQA content (108.05 ± 1.12 mg/g of dry weight). Furthermore, we evaluated the effect of brewing conditions and storage at 4 °C under dark and light conditions on the antioxidant property and total phenolic and CQA contents of a yerba mate infusion. The analysis of the yerba mate infusions prepared with different steeping times, dried leaf weights, and water temperatures revealed that the amount of extracted CQAs was maximized (∼175 mg/150 mL) when 6 g of dried leaves were steeped in hot water for 10 min. A total of 10-day refrigerated storage resulted in no significant changes in the antioxidant activity and total phenolic and CQA contents of an infusion kept in a brown container (dark). However, the antioxidant properties and total phenolic and CQA contents were negatively affected when kept in a clear container, suggesting the detrimental effect of light exposure. Our study provides practical recommendations for improving the preparation and storage of herbal infusions, thus catering to the needs of consumers, food scientists, and commercial producers. Moreover, it is the first study of the influence of light exposure on the content of crucial quality attributes within plant-based beverages. creator: Gholamreza Khaksar creator: Nantachaporn Chaichana creator: Kitipong Assatarakul creator: Supaart Sirikantaramas uri: https://doi.org/10.7717/peerj.17250 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Khaksar et al. title: XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent link: https://peerj.com/articles/17323 last-modified: 2024-05-06 description: The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield. creator: Nan Zhang creator: Xiaoou Dong creator: Rashmi Jain creator: Deling Ruan creator: Artur Teixeira de Araujo Junior creator: Yan Li creator: Anna Lipzen creator: Joel Martin creator: Kerrie Barry creator: Pamela C. Ronald uri: https://doi.org/10.7717/peerj.17323 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Synergistic effect of seaweed extract and boric acid and/or calcium chloride on productivity and physico-chemical properties of Valencia orange link: https://peerj.com/articles/17378 last-modified: 2024-05-06 description: Many citrus species and cultivars are grown successfully in tropical and subtropical countries, as well as in arid and semi-arid regions with low levels of organic matter and low cation exchange, resulting in lower nutrient uptake by the plant. The essential nutrients needed for citrus flowering and fruit set are limited in winter due to a reduction in transpiration rate, negatively effecting vegetative growth, flowering, yield, and fruit quality. The present investigation was carried out to assess the nutritional status, fruit yield parameters, and fruit quality of Valencia orange trees after foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations in the 2020/2021 and 2021/2022 seasons. The treatments were arranged in a split-plot design (three levels spraying seaweed extract × four levels spraying calcium chloride and boric acid and their combinations × four replicates × one tree/replicate). The results indicated that all of the characteristics measured, including leaf chlorophyll, leaf mineral contents, fruit yield parameters, fruit physical properties, and fruit chemical properties, were significantly affected by the foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations. Although all treatments increased the productivity and the physical and chemical properties of Valencia orange fruits compared to the control, a treatment of 10 g/L SW combined with 0.5 g/L boric acid and 1 g/L calcium chloride produced superior results. This ratio of SW, boric acid, and calcium chloride is therefore recommended to enhance productivity and improve the physico-chemical properties of Valencia orange for greater fruit yield. creator: Abdullah Alebidi creator: Mahmoud Abdel-Sattar uri: https://doi.org/10.7717/peerj.17378 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alebidi and Abdel-Sattar title: Whole-genome analysis of Escherichia coli isolated from wild Amur tiger (Panthera tigris altaica) and North China leopard (Panthera pardus japonensis) link: https://peerj.com/articles/17381 last-modified: 2024-05-06 description: BackgroundEscherichia coli is an important intestinal flora, of which pathogenic E. coli is capable of causing many enteric and extra-intestinal diseases. Antibiotics are essential for the treatment of bacterial infections caused by pathogenic E. coli; however, with the widespread use of antibiotics, drug resistance in E. coli has become particularly serious, posing a global threat to human, animal, and environmental health. While the drug resistance and pathogenicity of E. coli carried by tigers and leopards in captivity have been studied intensively in recent years, there is an extreme lack of information on E. coli in these top predators in the wild environment.MethodsWhole genome sequencing data of 32 E. coli strains collected from the feces of wild Amur tiger (Panthera tigris altaica, n = 24) and North China leopard (Panthera pardus japonensis, n = 8) were analyzed in this article. The multi-locus sequence types, serotypes, virulence and resistance genotypes, plasmid replicon types, and core genomic SNPs phylogeny of these isolates were studied. Additionally, antimicrobial susceptibility testing (AST) was performed on these E. coli isolates.ResultsAmong the E. coli isolates studied, 18 different sequence types were identified, with ST939 (21.9%), ST10 (15.6%), and ST3246 (9.4%) being the most prevalent. A total of 111 virulence genes were detected, averaging about 54 virulence genes per sample. They contribute to invasion, adherence, immune evasion, efflux pump, toxin, motility, stress adaption, and other virulence-related functions of E. coli. Sixty-eight AMR genes and point mutations were identified. Among the detected resistance genes, those belonging to the efflux pump family were the most abundant. Thirty-two E. coli isolates showed the highest rate of resistance to tetracycline (14/32; 43.8%), followed by imipenem (4/32; 12.5%), ciprofloxacin (3/32; 9.4%), doxycycline (2/32; 6.3%), and norfloxacin (1/32; 3.1%).ConclusionsOur results suggest that E. coli isolates carried by wild Amur tigers and North China leopards have potential pathogenicity and drug resistance. creator: Hongjia Li creator: Tianming Lan creator: Hao Zhai creator: Mengchao Zhou creator: Denghui Chen creator: Yaxian Lu creator: Lei Han creator: Jinpu Wei creator: Shaochun Zhou creator: Haitao Xu creator: Lihong Tian creator: Guangshun Jiang creator: Zhijun Hou uri: https://doi.org/10.7717/peerj.17381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: A comparison of five methods to maximize RNA and DNA isolation yield from adipose tissue link: https://peerj.com/articles/17071 last-modified: 2024-05-03 description: Adipose tissue in the human body occurs in various forms with different functions. It is an energy store, a complex endocrine organ, and a source of cells used in medicine. Many molecular analyses require the isolation of nucleic acids, which can cause some difficulties connected with the large amount of lipids in adipocytes. Ribonucleic acid isolation is particularly challenging due to its low stability and easy degradation by ribonucleases. The study aimed to compare and evaluate five RNA and DNA isolation methods from adipose tissue. The tested material was subcutaneous porcine adipose tissue subjected to different homogenization methods and RNA or DNA purification. A mortar and liquid nitrogen or ceramic beads were used for homogenization. The organic extraction (TriPure Reagent), spin columns with silica-membrane (RNeasy Mini Kit or High Pure PCR Template Preparation Kit), and the automatic MagNA Pure system were used for the purification. Five combinations were compared for RNA and DNA isolation. Obtained samples were evaluated for quantity and quality. The methods were compared in terms of yield (according to tissue mass), purity (A260/280 and A260/230), and nucleic acid degradation (RNA Integrity Number, RIN; DNA Integrity Number, DIN). The results were analyzed statistically. The average RNA yield was highest in method I, which used homogenization with ceramic beads and organic extraction. Low RNA concentration didn’t allow us to measure degradation for all samples in method III (homogenization with ceramic beads and spin-column purification). The highest RNA quality was achieved with method IV using homogenization in liquid nitrogen and spin column purification, which makes it the most effective for RNA isolation from adipose tissue. Required values of DNA yield, purity, and integrity were achieved only with spin column-based methods (III and IV). The most effective method for DNA isolation from adipose tissue is method III, using spin-columns without additional homogenization. creator: Pawel Dabrowski creator: Marta Rasmus creator: Arkadiusz Jundzill creator: Tomasz Drewa creator: Marta Pokrywczynska uri: https://doi.org/10.7717/peerj.17071 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dabrowski et al. title: Are incremental exercise relationships between rating of perceived exertion and oxygen uptake or heart rate reserve valid during steady-state exercises? link: https://peerj.com/articles/17158 last-modified: 2024-05-03 description: BackgroundRating of perceived exertion (RPE) is considered a valid method for prescribing prolonged aerobic steady-state exercise (SSE) intensity due to its association with physiological indicators of exercise intensity, such as oxygen uptake (V̇O2) or heart rate (HR). However, these associations between psychological and physiological indicators of exercise intensity were found during graded exercise tests (GXT) but are currently used to prescribe SSE intensity even though the transferability and validity of the relationships found during GXT to SSE were not investigated. The present study aims to verify whether (a) RPE-HR or RPE-V̇O2 relations found during GXTs are valid during SSEs, and (b) the duration and intensity of SSE affect these relations.MethodsEight healthy and physically active males (age 22.6 ± 1.2 years) were enrolled. On the first visit, pre-exercise (during 20 min standing) and maximal (during a GXT) HR and V̇O2 values were measured. Then, on separate days, participants performed 4 SSEs on the treadmill by running at 60% and 80% of the HR reserve (HRR) for 15 and 45 min (random order). Individual linear regressions between GXTs’ RPE (dependent variable) and HRR and V̇O2 reserve (V̇O2R) values (computed as the difference between maximal and pre-exercise values) were used to predict the RPE associated with %HRR (RPEHRR) and %V̇O2R (RPEV̇O2R) during the SSEs. For each relation (RPE-%HRR and RPE-%V̇O2R), a three-way factorial repeated measures ANOVA (α = 0.05) was used to assess if RPE (dependent variable) was affected by exercise modality (i.e., RPE recorded during SSE [RPESSE] or GXT-predicted), duration (i.e., 15 or 45 min), and intensity (i.e., 60% or 80% of HRR).ResultsThe differences between RPESSE and GXT-predicted RPE, which were assessed by evaluating the effect of modality and its interactions with SSE intensity and duration, showed no significant differences between RPESSE and RPEHRR. However, when RPESSE was compared with RPEV̇O2R, although modality or its interactions with intensity were not significant, there was a significant (p = 0.020) interaction effect of modality and duration yielding a dissociation between changes of RPESSE and RPEV̇O2R over time. Indeed, RPESSE did not change significantly (p = 0.054) from SSE of 15 min (12.1 ± 2.0) to SSE of 45 min (13.5 ± 2.1), with a mean change of 1.4 ± 1.8, whereas RPEV̇O2R decreased significantly (p = 0.022) from SSE of 15 min (13.7 ± 3.2) to SSE of 45 min (12.4 ± 2.8), with a mean change of −1.3 ± 1.5.ConclusionThe transferability of the individual relationships between RPE and physiological parameters found during GXT to SSE should not be assumed as shown by the results of this study. Therefore, future studies modelling how the exercise prescription method used (e.g., RPE, HR, or V̇O2) and SSE characteristics (e.g., exercise intensity, duration, or modality) affect the relationships between RPE and physiological parameters are warranted. creator: Carlo Ferri Marini creator: Lorenzo Micheli creator: Tommaso Grossi creator: Ario Federici creator: Giovanni Piccoli creator: Luca Zoffoli creator: Luca Correale creator: Stefano Dell’Anna creator: Carlo Alberto Naldini creator: Francesco Lucertini creator: Matteo Vandoni uri: https://doi.org/10.7717/peerj.17158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferri Marini et al. title: A new species of Languidipes Hubbard (Ephemeroptera, Polymitarcyidae) from Borneo link: https://peerj.com/articles/17327 last-modified: 2024-05-03 description: The genus Languidipes is currently represented by three species distributed in southeastern Asia, India, and Sri Lanka. Languidipes corporaali is the most widely distributed species, and both, male and female imagos, as well as nymphs, are known. In contrast, the other species, L. taprobanes and L. lithophagus, are only known from nymphs. Here, we describe a new species, Languidipes janae sp nov, based on male imagos collected from Borneo, Indonesia. This new species is characterized by the presence of ommation on mesonotum, and penis almost completely divided, with sub-quadrate base and a small outer projection basal to the long and slender distal arms. This constitutes the first record of the genus for Borneo. A cladistic analysis of the subfamily Asthenopodinae supports its taxonomic status. creator: Guillermo Eduardo Hankel creator: Carlos Molineri uri: https://doi.org/10.7717/peerj.17327 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hankel and Molineri title: Significance of NKX2-1 as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma link: https://peerj.com/articles/17338 last-modified: 2024-05-01 description: BackgroundThis study was performed to determine the biological processes in which NKX2-1 is involved and thus its role in the development of lung squamous cell carcinoma (LUSC) toward improving the prognosis and treatment of LUSC.MethodsRaw RNA sequencing (RNA-seq) data of LUSC from The Cancer Genome Atlas (TCGA) were used in bioinformatics analysis to characterize NKX2-1 expression levels in tumor and normal tissues. Survival analysis of Kaplan–Meier curve, the time-dependent receiver operating characteristic (ROC) curve, and a nomogram were used to analyze the prognosis value of NKX2-1 for LUSC in terms of overall survival (OS) and progression-free survival (PFS). Then, differentially expressed genes (DEGs) were identified, and Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) were used to clarify the biological mechanisms potentially involved in the development of LUSC. Moreover, the correlation between the NKX2-1 expression level and tumor mutation burden (TMB), tumor microenvironment (TME), and immune cell infiltration revealed that NKX2-1 participates in the development of LUSC. Finally, we studied the effects of NKX2-1 on drug therapy. To validate the protein and gene expression levels of NKX2-1 in LUSC, we employed immunohistochemistry(IHC) datasets, The Gene Expression Omnibus (GEO) database, and qRT-PCR analysis.ResultsNKX2-1 expression levels were significantly lower in LUSC than in normal lung tissue. It significantly differed in gender, stage and N classification. The survival analysis revealed that high expression of NKX2-1 had shorter OS and PFS in LUSC. The multivariate Cox regression hazard model showed the NKX2-1 expression as an independent prognostic factor. Then, the nomogram predicted LUSC prognosis. There are 51 upregulated DEGs and 49 downregulated DEGs in the NKX2-1 high-level groups. GO, KEGG and GSEA analysis revealed that DEGs were enriched in cell cycle and DNA replication.The TME results show that NKX2-1 expression was positively associated with mast cells resting, neutrophils, monocytes, T cells CD4 memory resting, and M2 macrophages but negatively associated with M1 macrophages. The TMB correlated negatively with NKX2-1 expression. The pharmacotherapy had great sensitivity in the NKX2-1 low-level group, the immunotherapy is no significant difference in the NKX2-1 low-level and high-level groups. The analysis of GEO data demonstrated concurrence with TCGA results. IHC revealed NKX2-1 protein expression in tumor tissues of both LUAD and LUSC. Meanwhile qRT-PCR analysis indicated a significantly lower NKX2-1 expression level in LUSC compared to LUAD. These qRT-PCR findings were consistent with co-expression analysis of NKX2-1.ConclusionWe conclude that NKX2-1 is a potential biomarker for prognosis and treatment LUSC. A new insights of NKX2-1 in LUSC is still needed further research. creator: Huiyue Lin creator: Juyong Wang creator: Qing Shi creator: Minmin Wu uri: https://doi.org/10.7717/peerj.17338 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: The Chronic Time Pressure Inventory: further assessment of factorial structure and validity link: https://peerj.com/articles/17373 last-modified: 2024-05-01 description: BackgroundChronic time pressure represents a prevalent concern within modern society, and effective measurement is crucial for research advancement. The Chronic Time Pressure Inventory (CTPI) has thus far demonstrated adequate psychometric properties. However, only two studies have examined the measure and evidence of its validity is limited. Accordingly, the current investigation, via two independent studies, assessed the factorial composition and validity (convergent/discriminant) of the CTPI.MethodsStudy 1 (N = 398) examined competing factorial models and validity in relation to the Big Five personality traits (Extraversion, Agreeableness, Conscientiousness, Neuroticism, Openness). Study 2 (N = 358) replicated the analysis of factor structure and assessed validity in comparison with five time perspectives (Past Negative, Present Fatalistic, Future, Past Positive, Present Hedonistic). Participants across both studies completed standardized self-report measures capturing the variables.ResultsComparison of confirmatory factor analysis (CFA) and exploratory structural equation modelling (ESEM) factor solutions indicated that an ESEM bifactor model provided the strongest data-model fit. This included a general chronic time pressure component alongside specific subfactors of Feeling Harried and Cognitive Awareness of Time Shortage. All scale items reflected the general factor; however, some items loaded weakly on the intended specific factor. The CTPI is thus a robust indicator of chronic time pressure but needs refinement as a measure of the specific factors. Convergent/discriminant validity analyses inferred that the CTPI captured chronic time pressure as a related, but distinct, construct to perceived stress, and evidenced a relationship with theoretically associated constructs (Big Five personality traits and time perspective). Overall, the CTPI is a sound measure of chronic time pressure and has the potential to further cohesive research efforts on the contribution of this construct to various life domains. creator: Andrew Denovan creator: Neil Dagnall creator: Ken Drinkwater uri: https://doi.org/10.7717/peerj.17373 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Denovan et al.