bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does scale or method matter for conservation? Application of directional and omnidirectional connectivity models in spatial prioritizations
Authors: Dertien Jeremy S. , Baldwin Robert F. 
Published: March 2023

IntroductionThe maintenance of habitat connections between fragmented habitat patches is vital for the conservation of wildlife populations and ecosystem functioning. The awareness of connectivity issues for species conservation has resulted in a growth of connectivity modeling and the application of these results in conservation planning. Such connectivity modeling efforts can include several decisions or data limitations, which could influence the connectivity results and ultimately a systematic conservation plan (SCP). However, there has been little investigation of how these different decisions on species, scale, and extent influence the ultimate conservation planning outcomes.MethodsWe modeled the connectivity of northern bobwhite (Colinus virginianus), North American river otter (Lontra canadensis), and black bear (Ursus americanus), three species with varying ecological requirements, through the Congaree Biosphere Region, South Carolina, USA. We modeled habitat suitability for each species using boosted regression trees and converted these results into resistance layers for the connectivity analyses. We compared models for each species at multistate regional and local extents using directional and omnidirectional circuit theory approaches. We then used the results from each modeling combination as conservation goals for three different SCPs to determine how connectivity modeling decisions may influence geographic conservation decisions.ResultsThere was substantial positive spatial correlation between the three connectivity models of each species, and there appeared to be general agreement among mammals as to most important primary corridors. Across all species, the greatest agreement was between the omnidirectional and local directional models as compared with the regional directional plan, which highlighted a unique corridor. The omnidirectional conservation plan required the least amount of planning units to achieve its conservation goals, followed by the local and then regional directional plans that required over 200 km2more land area to be conserved.DiscussionOur results indicate that overall variations in connectivity modeling decisions may have only a moderate impact on the identification of important movement corridors for conservation at the local scale. Practitioners should base modeling decisions on the ecology of the study region, conservation question, and available computing resource.
Coronary artery disease-associated immune gene RBP1 and its pan-cancer analysis
Authors: Wang Yumian , Zhang Li , Chen Han , Yang Juan , Cui Yun , Wang Hong 
Published: March 2023

PurposeTo identify immune-related biomarkers in coronary artery disease (CAD), investigate their possible function in the immunological milieu of tumors, and initially investigate the mechanisms and therapeutic targets shared by CAD and cancer.MethodsDownload the CAD-related dataset GSE60681 from the GEO database. GSVA and WGCNA analyses were performed based on the GSE60681 dataset to identify the modules most pertinent to CAD, identify candidate hub genes and finally intersect the genes associated with immunity downloaded from the import database to find the hub genes. The GTEx, CCLE, and TCGA database were used to examine the expression of the hub gene in normal tissues, tumor cell lines, tumor tissues, and different tumor STAGES. One-factor cox and Kaplan-Meier analyses were performed to explore the prognosis of hub genes. Hub gene methylation levels in CAD and cancer were analyzed in the diseaseMeth 3.0 and ualcan databases, respectively. R package CiberSort processed the GSE60681 dataset to assess immune infiltration in CAD. TIMER2.0 evaluated hub genes with pan-cancer immune infiltration. The hub genes were analyzed for drug sensitivity and correlation with TMB, MSI, MMR, cancer-related functional status, and immune checkpoints in different tumors. Finally, GSEA was carried out on the crucial genes.ResultsWGCNA were used to pinpoint the green modules that were most closely related to CAD and intersections with immune-related genes were taken to remember the pivotal gene RBP1. RBP1 is hypermethylated in CAD and multiple cancers. Its expression levels in different cancers were associated with poor prognosis of cancer, with significant expression levels at higher stages of cancer staging. The immune infiltration results showed that RBP1 was closely associated with CAD and tumor-associated immune infiltration. The results indicated that RBP1 was strongly correlated with TMB, MSI, MMR, cancer-associated functional status, and immune checkpoints in various cancers. RBP1 was related to the sensitivity of six anticancer drugs. GSEA showed RBP1 was associated with immune cell activation, immune response, and cancer development.ConclusionRBP1 is a pivotal gene associated with immunity in CAD and pan-cancer and may mediate the development of CAD and cancer through immunity, making it a common therapeutic target for both.
Adipokines as predictive factor of cardiac function in pediatric patients with chronic kidney disease
Authors: Villasis-Keever Miguel Angel , Zurita-Cruz Jessie Nallely , Zepeda-Martinez Claudia , Alegria-Torres Gabriela , Serret-Montoya Juana , Estrada-Loza Maria de Jesus , Hernández-Hernández Beatriz Carolina , Alonso-Flores Sara , Zavala-Serret Monica 
Published: March 2023

BackgroundAdipokines are associated with cardiovascular disease; in chronic kidney disease (CKD) patients adipokines could be useful prognostic factors.ObjectivesTo explore whether leptin and adiponectin in kidney replacement therapy (KRT) children could have a role on their cardiac function, in the long-term.DesignProspective cohort study was performed with pediatric KRT patients, aged 8 to 17 years who were undergoing hemodialysis or peritoneal dialysis. At enrollment, lipid profile, adipokines (leptin, leptin receptor, free leptin, and adiponectin), anthropometric measurements and cardiological evaluation were determined. At two-year follow-up, a new cardiological evaluation was performed. Statistical analysis: Quantitative data are presented as median and interquartile range (IQR). Mann-Whitney U test and Chi-squared were used for the between-group comparison. Multivariate analyzes were performed to determine the association of adipokines levels with ventricular ejection fraction (LEVF).ResultsWe included 56 patients, with a median age of 12.5 years. In the first cardiological evaluation, median LVEF was 70.0% (IQR 61%, 76%), 20 patients (35.7%) had some cardiovascular condition, and 10 (17.8%) altered LVEF. At 24-month follow-up, the median LVEF was 70.5% (IQR 65.1%, 77%), while the delta-LVEF values was 3% (IQR -6.5%, 7%). Delta-LVEF were correlated with baseline adipokines serum levels, and the only positive correlation found was with free leptin (r=0.303, p=0.025). In multivariate analysis, levels of free leptin (Coef. 0.12, p&lt;0.036) and leptin (coef. 1.72, p=0.049), as well as baseline LVEF (Coef. -0.65, p&lt;0.001) were associated with delta-LVEF.ConclusionsFree leptin, leptin and LVEF at the beginning of follow-up were associated with the LVEF decrease at the 24-month follow-up in KRT children.
Comparative efficacy of second-generation androgen receptor inhibitors for treating prostate cancer: A systematic review and network meta-analysis
Authors: Chen Xiangyu , Wang Qihua , Pan Yang , Wang Shangren , Li Yuezheng , Zhang Hao , Xu Mingming , Zhou Hang , Liu Xiaoqiang 
Published: March 2023

IntroductionSecond-generation androgen receptor inhibitors (SGARIs), namely enzalutamide, apalutamide, and darolutamide, are good for improving survival outcomes in prostate cancer patients, but some researchers have shown that using SGARIs increases side effects, which complicates clinicians’ choice of. Therefore, we performed this network meta-analysis to assess the efficacy and toxicity of several SGARIs in the treatment of patients with metastatic hormone-sensitive prostate cancer (mHSPC), non-metastatic castration-resistant prostate cancer (nmCRPC), and metastatic castration-resistant prostate cancer (mCRPC).MethodsWe searched PubMed, EMBASE and Cochrane Library databases from January 2000 to December 2022 to identify randomized controlled studies associated with SGARIs. We use Stata 16.0 and R 4.4.2 for data analysis, hazard ratio (HR) with 95% confidence intervals (CI) were used to assess the results.ResultsThis meta-analysis included 7 studies with a total of 9488 patients. In mHSPC, enzalutamide and darolutamide had a positive effect on overall survival (OS) (HR, 0.70; 95% CI, 0.59-0.82), but we did not find a difference in their efficacy to improve OS (HR, 1.19; 95% CI, 0.75-1.89). Also in nmCRPC, enzalutamide, apalutamide and darolutamide were beneficial for metastasis-free survival (MFS) (HR, 0.32; 95% CI, 0.25-0.41). Compared to darolutamide, enzalutamide (HR, 0.71; 95% CI, 0.54-0.93) and apalutamide (HR, 0.68; 95% CI, 0.51-0.91) prolonged MFS, but there was no difference in efficacy between enzalutamide and apalutamide (HR, 0.97; 95% CI, 0.73-1.28). Finally in mCRPC, there was no significant difference in indirect effects on OS between pre- and post-chemotherapy enzalutamide (HR, 0.89; 95% CI, 0.70-1.13). However, using enzalutamide before chemotherapy to improve radiographic progression-free survival (rPFS) was a better option (HR, 2.11; 95% CI, 1.62-2.73).ConclusionThe SGARIs used in each trial were beneficial for the primary endpoint in the study. Firstly there was no significant difference in the effect of enzalutamide and darolutamide in improving OS in patients with mHSPC. Secondly improving MFS in patients with nmCRPC was best achieved with enzalutamide and apalutamide. In addition both pre- and post-chemotherapy use of enzalutamide was beneficial for OS in mCRPC patients, but for improving rPFS pre-chemotherapy use of enzalutamide should be preferred.The INPLASY registration number of this systematic review is INPLASY202310084.
Estimation of hazardous and noxious substance (toluene) thickness using hyperspectral remote sensing
Authors: Park Jae-Jin , Park Kyung-Ae , Foucher Pierre-Yves , Kim Tae-Sung , Lee Moonjin 
Published: March 2023

A hazardous noxious substance (HNS) spill accident is one of the most devastating maritime disasters as it is accompanied by toxicity, fire, and explosions in the ocean. To monitor an HNS spill, it is necessary to develop a remote sensing–based HNS monitoring technique that can observe a wide area with high resolution. We designed and performed a ground HNS spill experiment using a hyperspectral sensor to detect HNS spill areas and estimate the spill volume. HNS images were obtained by pouring 1 L of toluene into an outdoor marine pool and observing it with a hyperspectral sensor capable of measuring the shortwave infrared channel installed at a height of approximately 12 m. The pure endmember spectra of toluene and seawater were extracted using principal component analysis and N-FINDR, and a Gaussian mixture model was applied to the toluene abundance fraction. Consequently, a toluene spill area of approximately 2.4317 m2 was detected according to the 36% criteria suitable for HNS detection. The HNS thickness estimation was based on a three-layer two-beam interference theory model. Because toluene has a maximum extinction coefficient of 1.3055 mm at a wavelength of 1,678 nm, the closest 1,676.5 nm toluene reflectance image was used for thickness estimation. Considering the detection area and ground resolution, the amount of leaked toluene was estimated to be 0.9336 L. As the amount of toluene used in the actual ground experiment was 1 L, the accuracy of our estimation is approximately 93.36%. Previous studies on HNS monitoring based on remote sensing are lacking in comparison to those on oil spills. This study is expected to contribute to the establishment of maritime HNS spill response strategies in the near future based on the novel hyperspectral HNS experiment.
Identification of immune-related genes in diagnosing atherosclerosis with rheumatoid arthritis through bioinformatics analysis and machine learning
Authors: Liu Fuze , Huang Yue , Liu Fuhui , Wang Hai 
Published: March 2023

BackgroundIncreasing evidence has proven that rheumatoid arthritis (RA) can aggravate atherosclerosis (AS), and we aimed to explore potential diagnostic genes for patients with AS and RA.MethodsWe obtained the data from public databases, including Gene Expression Omnibus (GEO) and STRING, and obtained the differentially expressed genes (DEGs) and module genes with Limma and weighted gene co-expression network analysis (WGCNA). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis, the protein–protein interaction (PPI) network, and machine learning algorithms [least absolute shrinkage and selection operator (LASSO) regression and random forest] were performed to explore the immune-related hub genes. We used a nomogram and receiver operating characteristic (ROC) curve to assess the diagnostic efficacy, which has been validated with GSE55235 and GSE57691. Finally, immune infiltration was developed in AS.ResultsThe AS dataset included 5,322 DEGs, while there were 1,439 DEGs and 206 module genes in RA. The intersection of DEGs for AS and crucial genes for RA was 53, which were involved in immunity. After the PPI network and machine learning construction, six hub genes were used for the construction of a nomogram and for diagnostic efficacy assessment, which showed great diagnostic value (area under the curve from 0.723 to 1). Immune infiltration also revealed the disorder of immunocytes.ConclusionSix immune-related hub genes (NFIL3, EED, GRK2, MAP3K11, RMI1, and TPST1) were recognized, and the nomogram was developed for AS with RA diagnosis.
Which are the most frequently involved peripheral joints in calcium pyrophosphate crystal deposition at imaging? A systematic literature review and meta-analysis by the OMERACT ultrasound – CPPD subgroup
Authors: Adinolfi Antonella , Sirotti Silvia , Sakellariou Garifallia , Cipolletta Edoardo , Filippucci Emilio , Porta Francesco , Zanetti Anna , Ughi Nicola , Sarzi-Puttini Piercarlo , Scirè Carlo Alberto , Keen Helen , Pineda Carlos , Terslev Lene , D’Agostino Maria Antonietta , Filippou Georgios 
Published: March 2023

ObjectivesTo identify the prevalence of calcium pyrophosphate crystal deposition (CPPD) using ultrasound and conventional radiology at peripheral joints in patients with suspected or definite CPPD.MethodsA systematic literature search was performed in PubMed and Embase using pre-defined search strategies from inception to April 2021 to identify studies that evaluated conventional radiology and ultrasound in detecting CPPD at peripheral joints, including definite or suspected CPPD [Research question 1 (RQ1) and Research Question 2 (RQ2), respectively]. For the meta-analysis, the first, second, and third sub-analysis included studies with the knee, and knee or wrist as the index joint for CPPD (without restrictions on the reference standard) and synovial fluid analysis or histology as a reference standard (without restrictions on the index joint), respectively.ResultsOne-thousand eight hundred and twenty-seven manuscripts were identified, of which 94 articles were finally included. Twenty-two and seventy-two papers were included in RQ1 and RQ2, respectively. The knee had the highest prevalence for RQ1 and RQ2 by both conventional radiology and ultrasound, followed by the wrist with the highest prevalence for RQ1. The hand had the lowest CPPD prevalence. The third sub-analysis showed a higher CPPD prevalence on ultrasound than conventional radiology at the knee (only data available).ConclusionAmong all peripheral joints, the knees and wrists could be regarded as the target joints for CPPD detection by imaging. Furthermore, ultrasound seems to detect a higher number of calcium pyrophosphate deposits than conventional radiology, even when using a more restrictive reference standard.
Telomere-related genes as potential biomarkers to predict endometriosis and immune response: Development of a machine learning-based risk model
Authors: Zhang He , Kong Weimin , Xie Yunkai , Zhao Xiaoling , Luo Dan , Chen Shuning , Pan Zhendong 
Published: March 2023

IntroductionEndometriosis (EM) is an aggressive, pleomorphic, and common gynecological disease. Its clinical presentation includes abnormal menstruation, dysmenorrhea, and infertility, which seriously affect the patient's quality of life. However, the pathogenesis underlying EM and associated regulatory genes are unknown.MethodsTelomere-related genes (TRGs) were uploaded from TelNet. RNA-sequencing (RNA-seq) data of EM patients were obtained from three datasets (GSE5108, GSE23339, and GSE25628) in the GEO database, and a random forest approach was used to identify telomere signature genes and build nomogram prediction models. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis were used to identify the pathways involved in the action of the signature genes. Finally, the CAMP database was used to screen drugs for potential use in EM treatment.ResultsFifteen total genes were screened as EM–telomere differentially expressed genes. Further screening by machine learning obtained six genes as characteristic predictive of EM. Immuno-infiltration analysis of the telomeric genes showed that expressions including macrophages and natural killer cells were significantly higher in cluster A. Further enrichment analysis showed that the differential genes were mainly enriched in biological pathways like cell cycle and extracellular matrix. Finally, the Connective Map database was used to screen 11 potential drugs for EM treatment.DiscussionTRGs play a crucial role in EM development, and are associated with immune infiltration and act on multiple pathways, including the cell cycle. Telomere signature genes can be valuable predictive markers for EM.
Effects of resistance and balance exercises for athletic ability and quality of life in people with osteoporotic vertebral fracture: Systematic review and meta-analysis of randomized control trials
Authors: Li Xuefei , Chen Wenhua , Chen Qian , Li Fangfang , Chen Chen , Li Pan , Li Fangyu , Guo Suxia , Chen Pinghua , Yuan Weina , Liu Dan , Wang Shiyun , Hu Zhijun 
Published: March 2023

PurposeThis study aimed to use meta-analysis to determine the impact of resistance and balance training on athletic ability and quality of life for patients with osteoporotic vertebral fracture (OVF).MethodsThis study followed the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) criteria for systematic reviews and meta-analyzes. The PubMed, Web of science, Cochrane, Embase, and CNKI databases were searched for randomized controlled trials (RCTs) up to September 2022. The search strategy was related to the intervention measures, population, and results, and was structured around the search terms: “Exercise,” “Osteoporotic vertebral fracture,” and “activities of function.” Two reviewers strictly implemented the inclusion and exclusion criteria. Subgroup analyzes of age and training duration were performed for the main outcomes.ResultsWe included 12 RCTs (n = 1,289) of resistance and balance training in patients with OVF. Compared with controls, the intervention group showed improvements on the Quality of Life Questionnaire issued by the European Foundation for Osteoporosis, visual analog pain scale, Timed Up and Go, falls efficacy scale international (FES-I), kyphosis, and functional reach. On subgroup analysis, the effect was more significant when training continued &gt;10 weeks.ConclusionResistance and balance exercise training improved function and balance, and reduced fall risk in patients with OVF. We recommend resistance and balance training for at least 10 weeks. Future multicenter, large sample trials are needed for more reliable conclusions.
The role of periodontitis in the link between alpha-tocopherol intake and cognitive performance: A mediation analysis in older adults
Authors: Zhang Heming , Sun Li , Zhang Lin , Li Jiangjing , Liu Yongfei , Chen Zhiyang , Wang Shuang , Gao Changjun , Sun Xude 
Published: March 2023

BackgroundEpidemiological evidence on alpha (α)-tocopherol intake and cognitive performance in older individuals is controversial and the effect of periodontitis in this chain is sparse and limited. The goal of this study was to characterize the association between α-tocopherol intake and cognitive performance and the mediating role of periodontitis in a nationally representative sample of older adults.MethodsData from the National Health and Nutrition Examination Survey (NHANES), 2011–2014, were used. Multivariate logistic regression analysis was performed to explore the association of α-tocopherol intake, periodontal measures (mean attachment loss [AL] and mean probing depth [PD]), and clinical periodontitis defined by the European Workshop in Periodontology with poor cognitive performance evaluated by Consortium to Establish a Registry for Alzheimer’s disease (CERAD); the animal fluency test (AFT); and the Digit Symbol Substitution test (DSST) and the correlation between α-tocopherol intake and clinical periodontitis. Multiple linear regression analysis was used to explore the relationship between α-tocopherol intake and periodontal measures. Mediation analysis was used to test the effects of periodontal measures on the association between α-tocopherol intake and cognitive measures.ResultsA total of 1,749 older participants (≥60 years of age) with complete periodontal diagnosis, dietary retrospective survey, and cognitive tests were included. In the fully adjusted model, the odds ratio (OR) with 95% confidence interval (CI) of CERAD score, AFT score and DSST score were 0.214 (0.137–0.327), 0.378 (0.241–0.585) and 0.298 (0.169–0.512) for the highest versus lowest tertile of α-tocopherol intake, respectively. And participants with clinical periodontitis were more likely to exhibit lower DSST score (OR = 1.689; 95 CI%: 1.018–2.771) than those without periodontitis. Mean AL (OR = 1.296; 95 CI%: 1.102–1.524) and PD (OR = 1.667; 95 CI%: 1.18–2.363) were negatively correlated with DSST, and were estimated to mediate 9.1 and 8.2% of the total association between α-tocopherol intake and cognitive performance, respectively.ConclusionFinding of the present study suggested that participants with low α-tocopherol intake were at higher risk for developing cognitive decline. Moreover, periodontitis mediated the association between α-tocopherol intake and cognitive performance.