PeerJ最新文献

{"title":"The bacterial strains JAM1^T and GP59 of the species <i>Methylophaga nitratireducenticrescens</i> differ in their expression profiles of denitrification genes in oxic and anoxic cultures.","authors":"Livie Lestin, Richard Villemur","doi":"10.7717/peerj.18361","DOIUrl":"10.7717/peerj.18361","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Strain JAM1&lt;sup&gt;T&lt;/sup&gt; and strain GP59 of the methylotrophic, bacterial species &lt;i&gt;Methylophaga nitratireducenticrescens&lt;/i&gt; were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate ( &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; ) reduction. Strain JAM1&lt;sup&gt;T&lt;/sup&gt; can reduce &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; to nitrite ( &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; ) but not &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; to nitric oxide (NO) as it lacks a NO-forming &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; reductase. Strain GP59 on the other hand can carry the complete reduction of &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; to N&lt;sub&gt;2&lt;/sub&gt;. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; reduction occurs. In strain JAM1&lt;sup&gt;T&lt;/sup&gt; cultures, &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; reduction begins immediately with accumulation of &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; . Furthermore, &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; is reduced under oxic conditions in strain JAM1&lt;sup&gt;T&lt;/sup&gt; cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Both strains were cultured under oxic conditions either with or without &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; , or under anoxic conditions with &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; . Transcript levels of selected denitrification genes (&lt;i&gt;nar1&lt;/i&gt; and &lt;i&gt;nar2&lt;/i&gt; encoding &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; reductases, &lt;i&gt;nirK&lt;/i&gt; encoding &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/math&gt; reductase, &lt;i&gt;narK12f&lt;/i&gt; encoding &lt;math&gt; &lt;msubsup&gt;&lt;mrow&gt;&lt;mi&gt;NO&lt;/mi&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mn&gt;3&lt;/mn&gt;&lt;/mrow&gt; &lt;mrow&gt;&lt;mo&gt;-&lt;/mo&gt;&lt;/mrow&gt; &lt;/msubsup&gt; &lt;/m","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of maternal serum biomarkers on maternal and neonatal outcomes in twin pregnancies: a retrospective cohort study conducted at a tertiary hospital.","authors":"Hanglin Wu, Liming Yu, Zhen Xie, Hongxia Cai, Caihe Wen","doi":"10.7717/peerj.18415","DOIUrl":"10.7717/peerj.18415","url":null,"abstract":"<p><strong>Background: </strong>Prior prediction models used for screening preeclampsia (PE) in twin pregnancies were found to be inadequate. In singleton pregnancies, various maternal biomarkers have been shown to be correlated with negative pregnancy outcomes. However, the impact of these biomarkers in twin pregnancies remained uncertain.</p><p><strong>Methods: </strong>A retrospective cohort study was carried out on 736 twin pregnancies at a tertiary hospital in Hangzhou, China. Multivariable logistic models were employed to examine the association between levels of serological markers and the likelihood of adverse pregnancy outcomes. The final logistic model was formulated as a user-friendly nomogram. The primary outcome assessed was the occurrence of PE. Results were presented as odds ratios (ORs) with corresponding 95% confidence intervals (CIs).</p><p><strong>Results: </strong>The prevalence of PE in the study was 10.3%. When comparing women diagnosed with PE to those without, it was evident that the former group experienced a significantly higher risk of unfavorable maternal and neonatal outcomes. A multivariable logistic regression analysis revealed notable associations between various factors including maternal age, parity, gestational weight gain, a family history of hypertension, as well as levels of cholesterol, albumin, and creatinine and the risk of developing PE, with a significance level of <i>P</i> < 0.05. The concordance index for the constructed nomogram was determined to be 0.792 (95% CI: [0.739-0.844]). Furthermore, an increment of 1 * 10^12/L in red blood cell (RBC) count was associated with more than a two-fold increase in the odds of experiencing adverse maternal outcomes (OR 2.247, 95% CI: [1.229-4.107]). However, no significant correlations were identified between any of the examined variables and neonatal outcomes.</p><p><strong>Conclusions: </strong>In this study, we developed a user-friendly predictive model that achieves notable detection rates by incorporating maternal serum biomarker levels alongside maternal characteristics and medical history. Our findings indicate that the probability of adverse maternal outcomes increases with elevated levels of RBCs. Obstetricians should consider intensifying surveillance for these women in clinical practice.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis.","authors":"Jiachun Sun, Shujun Zhang, Yafeng Liu, Kaijie Liu, Xinyu Gu","doi":"10.7717/peerj.18362","DOIUrl":"10.7717/peerj.18362","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to explore the heterogeneity of tumor endothelial cells (TECs) in hepatocellular carcinoma (HCC) and their role in tumor progression, with the goal of identifying new therapeutic targets and strategies to improve patient prognosis.</p><p><strong>Methods: </strong>Single-cell RNA sequencing data from nine primary liver cancer samples were analyzed, obtained from the Gene Expression Omnibus (GEO) database. Data preprocessing, normalization, dimensionality reduction, and batch effect correction were performed based on the Seurat package. HCC cell types were identified using uniform manifold approximation and projection (UMAP) and cluster analysis, and the different cell types were annotated using the CellMarker database. Pseudotime trajectory analysis was conducted with Monocle to explore the differentiation trajectory of TECs. MAPK signaling pathway activity and copy number variations (CNV) in TECs were analyzed in conjunction with data from The Cancer Genome Atlas (TCGA), the trans-well and wound healing assay was used for cell invasion and migration activity assessment.</p><p><strong>Results: </strong>Two subgroups of TECs (TECs 1 and TECs 2) were identified, exhibiting distinct functional activities and signaling pathways. Specifically, TECs 1 may be involved in tumor cell proliferation and inflammatory responses, whereas TECs 2 is not only involved in cell proliferation pathways, but also enriched in pathways such as metabolic synthesis. Pseudotime analysis revealed dynamic changes in TECs subgroups during HCC progression, correlating specific gene expressions (such as PDGFRB, PGF, JUN, and NR4A1). Subsequently, the JUN gene was predicted by performing binding sites and was shown to act as a transcription factor that may regulate the expression of the PGF gene. CNV analysis highlighted key genes and pathways in TECs that might influence HCC progression, and the PGF as key regulatory factor mediated cell proliferation and migration.</p><p><strong>Conclusion: </strong>The study revealed the heterogeneity of TECs in HCC and their potential roles in tumor progression, offering new perspectives and potential therapeutic targets for HCC molecular mechanisms. The findings emphasize the importance of further exploring TECs heterogeneity for understanding HCC pathogenesis and developing personalized treatment strategies.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part.","authors":"Yasumasa Oka, Takumi Jiroumaru, Michio Wachi, Noriyuki Kida","doi":"10.7717/peerj.18389","DOIUrl":"10.7717/peerj.18389","url":null,"abstract":"<p><strong>Background: </strong>Occupational health, grounded in occupational medicine, aims to enhance the well-being and labor productivity of the working population. Within this realm, there has been growing concern over the increasing instances of labor loss due to diminished physical capacity and the rise in musculoskeletal disorders. Chronic pain is also associated with musculoskeletal disorders. Another pressing issue related to chronic musculoskeletal pain was needed assistance services are underutilized, is referred to as a \"service gap\". Understanding trends based on age and affected regions of the body is indispensable for developing strategies to address chronic musculoskeletal pain in workers. This study aimed to elucidate age-specific trends in the prevalence and number of pain sites in chronic musculoskeletal pain as well as the patterns of treatment during chronic musculoskeletal pain, categorized by age and affected site.</p><p><strong>Methods: </strong>This study was conducted in December 2022 in contract to Cross Marketing Inc. The survey began on December 12, 2022 and ended on December 15, 2022. An online survey was administered to 1,946 participants (973 women and 973 men), and responses were collected, ensuring a roughly equal distribution of samples among men and women across six age groups ranging from their 20 to 70 s. The survey inquired about the presence of chronic pain in each of the eight body parts and the adoption of five different treatments when experiencing pain. Statistical analysis was performed using the chi-square test, with the measurement data categorized by age group and body part.</p><p><strong>Results: </strong>The results indicated a significantly higher prevalence of chronic pain at three or more sites among individuals in their 30 s: the prevalence of pain at each of the eight body sites varied with age. Approximately half of the participants did not engage in specific treatments during episodes of chronic pain. The presence or absence of treatment showed no significant differences according to affected site or age group. This study revealed age- and body part-related relationships with chronic musculoskeletal pain in middle-aged patients and highlighted healthcare service gaps in its management in Japan.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seed priming enhances seed germination and plant growth in four neglected cultivars of <i>Capsicum annuum</i> L.","authors":"Angelo Granata, Fiore Capozzi, Anna Gaglione, Riccardo Riccardi, Patrizia Spigno, Simonetta Giordano, Maria Cristina Sorrentino, Valeria Spagnuolo","doi":"10.7717/peerj.18293","DOIUrl":"10.7717/peerj.18293","url":null,"abstract":"<p><p>Priming is basically a water-based technique inducing controlled seed rehydration to trigger the metabolic processes normally activated during the early phase of germination. It is regarded as an ecofriendly approach alternative to fertilizers in traditional agriculture, but also a method to synchronize off-field crops and resume stored seeds, improving vigor, and allowing for a rapid, uniform seedling emergence. In this work we tested several methods of seed priming (<i>i.e</i>., hydro-priming, halopriming by KNO₃, and acid priming with HCl) in four ancient and neglected cultivars of <i>Capsicum annuum</i> L., a crop species belonging to Solanaceae family cultivated worldwide. We followed germination performance, seedling growth and selected morphological traits, antioxidant production in the leaves, and protein content of the seeds. Apart from acid priming, which inhibited root emergence, both hydropriming and halopriming decreased the mean germination time in all cultivars. The best treatments were KNO₃ 6% for 96 h > KNO₃ 4% for 48 h > hydropriming for 24 h. In particular, KNO₃ 6% for 96 h in all four cultivars significantly increased plant growth, simple vigor index, development germination index, leaf antioxidant concentration and protein content in the seeds, in comparison to control and other priming treatments, indicating the prompt activation of pre-germinative processes.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An interpretable deep learning model for detecting <i>BRCA</i> pathogenic variants of breast cancer from hematoxylin and eosin-stained pathological images.","authors":"Yi Li, Xiaomin Xiong, Xiaohua Liu, Yihan Wu, Xiaoju Li, Bo Liu, Bo Lin, Yu Li, Bo Xu","doi":"10.7717/peerj.18098","DOIUrl":"10.7717/peerj.18098","url":null,"abstract":"<p><strong>Background: </strong>Determining the status of breast cancer susceptibility genes (<i>BRCA</i>) is crucial for guiding breast cancer treatment. Nevertheless, the need for <i>BRCA</i> genetic testing among breast cancer patients remains unmet due to high costs and limited resources. This study aimed to develop a Bi-directional Self-Attention Multiple Instance Learning (BiAMIL) algorithm to detect <i>BRCA</i> status from hematoxylin and eosin (H&E) pathological images.</p><p><strong>Methods: </strong>A total of 319 histopathological slides from 254 breast cancer patients were included, comprising two dependent cohorts. Following image pre-processing, 633,484 tumor tiles from the training dataset were employed to train the self-developed deep-learning model. The performance of the network was evaluated in the internal and external test sets.</p><p><strong>Results: </strong>BiAMIL achieved AUC values of 0.819 (95% CI [0.673-0.965]) in the internal test set, and 0.817 (95% CI [0.712-0.923]) in the external test set. To explore the relationship between <i>BRCA</i> status and interpretable morphological features in pathological images, we utilized Class Activation Mapping (CAM) technique and cluster analysis to investigate the connections between <i>BRCA</i> gene mutation status and tissue and cell features. Significantly, we observed that tumor-infiltrating lymphocytes and the morphological characteristics of tumor cells appeared to be potential features associated with <i>BRCA</i> status.</p><p><strong>Conclusions: </strong>An interpretable deep neural network model based on the attention mechanism was developed to predict the <i>BRCA</i> status in breast cancer. Keywords: Breast cancer, <i>BRCA</i>, deep learning, self-attention, interpretability.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a welfare assessment tool for tourist camp elephants in Asia.","authors":"Raman Ghimire, Janine L Brown, Chatchote Thitaram, Sharon S Glaeser, Kannika Na-Lampang, Pawinee Kulnanan, Pakkanut Bansiddhi","doi":"10.7717/peerj.18370","DOIUrl":"10.7717/peerj.18370","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Approximately one-third of Asian elephants are managed under human care, participating in educational, cultural, religious, and tourist activities. Management conditions vary considerably among venues, raising questions about whether welfare needs are consistently being met, particularly for Asian tourist camp elephants. To evaluate the well-being of elephants engaged in tourist activities, an evidence-based tool is needed for routine assessments to identify potential welfare risks, aid in the development of better camp standards, and enable caretakers to address specific concerns. While many animal welfare tools exist, none have been designed to consider specific environments and management practices faced by elephants living and working in tourist camps.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Using direct observations and interviews, the Elephant Welfare Assessment Tool (EWAT) was developed for tourist camp elephants using the Five Domains Model as a framework. Measures were selected based on peer-reviewed literature, existing standards and guidelines, and opinions from animal welfare experts working with zoo and tourist camp elephants. The EWAT differs from existing tools by including criteria on work activities and restraint methods (&lt;i&gt;e.g&lt;/i&gt;., chaining and ankus use), factors common in Asia but not often encountered by western zoo elephants. Measures were scored using a 0-2 Likert Scale. The tool was tested in Thailand and determined by calculating a content validity index (CVI) and conducting inter-rater and test-retest reliability tests.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;The initial tool included 18 animal-based and 21 resource-based measures across four domains: Nutrition (&lt;i&gt;n&lt;/i&gt; = 5), Environment (&lt;i&gt;n&lt;/i&gt; = 14), Health (&lt;i&gt;n&lt;/i&gt; = 10), and Behavior and Mental State (&lt;i&gt;n&lt;/i&gt; = 10). Index scores of content validity (CVI) (Item CVI (0.83), Scale CVI/Average (0.98), and Scale CVI/Universal (0.89)) were high. Measures scoring less than 0.83 were removed: the opportunity to mate, the mahout-elephant relationship, and mahout job satisfaction. The final tool consisted of 42 questions related to 36 measures, including 18 animal-based and 18 resource-based measures within the Nutrition (&lt;i&gt;n&lt;/i&gt; = 5), Environment (&lt;i&gt;n&lt;/i&gt; = 11), Health (&lt;i&gt;n&lt;/i&gt; = 10), and Behavior and Mental State (&lt;i&gt;n&lt;/i&gt; = 10) domains. Intraclass correlation coefficients (ICC) for inter-rater reliability (0.78-0.90, &lt;i&gt;p&lt;/i&gt; &lt; 0.05) and test-retest (0.77-0.91, &lt;i&gt;p&lt;/i&gt; &lt; 0.05) analyses conducted at two camps showed good agreement.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;This new assessment tool (EWAT) is a context-specific, holistic method designed to offer a practical means of conducting individual and institutional-level assessments of elephant welfare in tourist camps. It is based on the Five Domains Model using reliable and validated animal- and resource-based measures, data collection through direct observation and interviews, and a numerical sco","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index.","authors":"Congcang Tang, Qiao Li, Hongfei Tao, Mahemujiang Aihemaiti, Zhenxia Mu, Youwei Jiang","doi":"10.7717/peerj.18368","DOIUrl":"10.7717/peerj.18368","url":null,"abstract":"<p><p>Changes in the ecological environment quality (EEQ) in the main inland Tarim River Basin in China substantially impact the regional development. Indeed, comprehensive ecological environment measures have been implemented in the Tarim River Basin since 2000. In this context, the main objective of the present study was to investigate the spatiotemporal evolution of the EEQ and monitor the effectiveness of ecological restoration measures in the Tarim River Basin over the 2000-2020 period using remote sensing data. First, a Remote Sensing Ecological Index (RSEI) was constructed based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Second, the spatial distributions and factors of the RSEI were analyzed by using Moran's Index and Geodetector. The results indicated that the overall RSEI values for the Tarim River Basin increased from 0.22 in 2000 to 0.25 in 2020. Moreover, the values for areas with poor EEQ decreased from 50.7% to 44.73%, while those with moderate EEQ increased from 11.45% to 16.91%. Therefore, the results demonstrated a slight overall improvement in the EEQ of the study area over the 2000-2020 period. On the other hand, the EEQ in the Tarim River Basin exhibited a significant spatial autocorrelation in the 2000-2020 period, with a relatively stable overall spatial distribution. Areas with high-high aggregation were distributed in the high-elevation mountainous areas in the western, northern, and southern parts of the study area. In contrast, areas with low-low aggregation were observed in the central and eastern low-elevation desert areas. The EEQ in the Tarim River Basin was driven by the interactions of several factors, including the normalized difference vegetation index, land surface moisture, land surface temperature, normalized differential build-up and bare soil index, and elevation. In particular, heat was the main driving factor that severely impacted the EEQ in the study area. Indeed, increase in the heat values could directly enhance meltwater runoff from glaciers in the basin, thereby resulting in short-term improvement in the basin EEQ. Furthermore, rapid urbanization from 2015 to 2020 resulted in a decrease in the average RSEI value of the Tarim River Basin by 0.1 over this period, consequently, the EEQ level decreased slightly. Briefly, the EEQ in the Tarim River Basin showed an overall increasing trend from 2000 to 2020, further demonstrating the effectiveness of a series of implemented ecological restoration measures in the Tarim River Basin over this period.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma.","authors":"Jesadakorn Worasilchai, Piyapat Thongchaichayakon, Kittipat Chansri, Supichaya Leelahavanichkul, Vathin Chiewvit, Peerapat Visitchanakun, Poorichaya Somparn, Pratsanee Hiengrach","doi":"10.7717/peerj.18421","DOIUrl":"10.7717/peerj.18421","url":null,"abstract":"<p><p>Innate immunity in asthma may be influenced by alterations in lung microbiota, potentially affecting disease severity. This study investigates the differences in lung inflammation and microbiome between asthma-ovalbumin (OVA) administered with and without fluconazole treatment in C57BL/6 mice. Additionally, the role of inflammation was examined in an <i>in vitro</i> study using a pulmonary cell line. At 30 days post-OVA administration, allergic asthma mice exhibited increased levels of IgE and IL-4 in serum and lung tissue, higher pathological scores, and elevated eosinophils in bronchoalveolar lavage fluid (BALF) compared to control mice. Asthma inflammation was characterized by elevated serum IL-6, increased lung cytokines (TNF-α, IL-6, IL-10), and higher fungal abundance confirmed by polymerase chain reaction (PCR). Fluconazole-treated asthma mice displayed higher levels of cytokines in serum and lung tissue (TNF-α and IL-6), increased pathological scores, and a higher number of mononuclear cells in BALF, with undetectable fungal levels compared to untreated mice. Lung microbiome analysis revealed similarities between control and asthma mice; however, fluconazole-treated asthma mice exhibited higher Bacteroidota levels, lower Firmicutes, and reduced bacterial abundance. Pro-inflammatory cytokine production was increased in supernatants of the pulmonary cell line (NCI-H292) after co-stimulation with LPS and beta-glucan (BG) compared to LPS alone. Fluconazole treatment in OVA-induced asthma mice exacerbated inflammation, partially due to fungi and Gram-negative bacteria, as demonstrated by LPS+BG-activated pulmonary cells. Therefore, fluconazole should be reserved for treating fungal asthma rather than asthma caused by other etiologies.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of thyroid hormones with the severity of chronic kidney disease: a cross-sectional observational study at Tabuk, Saudi Arabia.","authors":"Basmah Awwaadh, Amal Hussain Mohammed, Basmah F Alharbi, Abdulmohsen Alruwetei, Tarique Sarwar, Hajed Obaid Alharbi, Fahad Alhumaydhi","doi":"10.7717/peerj.18338","DOIUrl":"10.7717/peerj.18338","url":null,"abstract":"<p><strong>Background: </strong>The interplay between chronic kidney disease (CKD) and thyroid dysfunction is becoming more evident in the biomedical community. However, the intricacies of their relationship warrant deeper investigation to understand the clinical implications fully.</p><p><strong>Objective: </strong>This study aims to systematically evaluate the correlation between thyroid hormone levels, including thyroid-stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4), and markers of renal disease severity. These markers include serum creatinine, urea, and parathyroid hormone (PTH) levels in individuals diagnosed with CK).</p><p><strong>Methods: </strong>We conducted a cross-sectional observational study involving a cohort of 86 participants with CKD recruited from the renal clinic at King Fahad Hospital in Tabuk. Biochemical parameters, encompassing plasma electrolytes and thyroid hormone concentrations, were quantitatively assessed. These measurements were performed with the aid of a Roche Cobas E411 analyzer. The Pearson correlation coefficient was employed to delineate the strength and direction of the associations between the thyroid function markers and renal disease indicators.</p><p><strong>Results: </strong>The statistical analysis highlighted a generally weak correlation between the concentrations of thyroid hormones and the indicators of renal disease severity, with Pearson correlation coefficients between -0.319 and 0.815. Critically, no significant correlation was found between creatinine and thyroid hormones (TSH, T3, T4), nor was any substantial correlation between urea and thyroid hormones. Conversely, a robust positive correlation was noted between the levels of parathyroid hormone and serum creatinine (<i>r</i> = 0.718, <i>p</i> < 0.001).</p><p><strong>Conclusion: </strong>The data suggests that thyroid hormone levels have a minimal correlation with the severity of renal disease markers. In contrast, the pronounced correlation between PTH and creatinine underscores the importance of considering PTH as a significant factor in managing and therapeutic intervention of CKD complications. These initial findings catalyze further research to thoroughly investigate the pathophysiological relationships and potential therapeutic targets concerning thyroid dysfunction in patients with renal impairment.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}