bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.)
Authors: Bhat Javaid Akhter , Adeboye Kehinde Adewole , Ganie Showkat Ahmad , Barmukh Rutwik , Hu Dezhou , Varshney Rajeev K. , Yu Deyue 
Published: November 2022

Identifying the genetic components underlying yield-related traits in soybean is crucial for improving its production and productivity. Here, 211 soybean genotypes were evaluated across six environments for four yield-related traits, including seed yield per plant (SYP), number of pods per plant number of seeds per plant and 100-seed weight (HSW). Genome-wide association study (GWAS) and genomic prediction (GP) analyses were performed using 12,617 single nucleotide polymorphism markers from NJAU 355K SoySNP Array. A total of 57 SNPs were significantly associated with four traits across six environments and a combined environment using five Genome-wide association study models. Out of these, six significant SNPs were consistently identified in more than three environments using multiple GWAS models. The genomic regions (±670 kb) flanking these six consistent SNPs were considered stable QTL regions. Gene annotation and in silico expression analysis revealed 15 putative genes underlying the stable QTLs that might regulate soybean yield. Haplotype analysis using six significant SNPs revealed various allelic combinations regulating diverse phenotypes for the studied traits. Furthermore, the GP analysis revealed that accurate breeding values for the studied soybean traits is attainable at an earlier generation. Our study paved the way for increasing soybean yield performance within a short breeding cycle.
Unmet need for contraception among married adolescent girls and young women in Haramaya Health and demographic surveillance system, Eastern Ethiopia
Authors: Hailu Saba , Assefa Nega , Dingeta Tariku , Abdurahman Chaltu , Adem Mewardi 
Published: November 2022

BackgroundThe prevalence of unmet need for contraception is the highest in low- and middle-income countries (LMIC). Contraceptive use among young married or unmarried women is lower than that among older women in developing countries. Previous studies generalized the findings to all women of reproductive age and have not investigated psychosocial factors that influence contraceptive use. This study aimed to identify factors associated with unmet need for contraception among young married women in the Haramaya Health and Demographic Surveillance System (HDSS), eastern Ethiopia.MethodologyA cross-sectional, community-based study of young married women aged 15–24 years was conducted. A simple random sampling method was used to select 550 young married women. Data were collected using a pretested structured questionnaire. Using adjusted odds ratio (AOR) with a 95% confidence interval (CI), factors associated with unmet need for contraception were identified using multivariable logistic regression analysis.ResultsThe overall prevalence of unmet need for contraception was 154 (30.3%). Adolescents (15–19) (AOR = 2.05, 95% CI: 1.16–3.62), husbands' negative attitude toward contraception (AOR = 2.1, 95% CI: 1.05–4.46), and no previous use of contraception (AOR = 3.9, 95% CI: 2.29–6.71) were significantly and positively associated with unmet need for contraception. On the contrary, young women with secondary education or higher (AOR = 0.55, 95% CI: 0.28–1.084) were negatively and significantly associated with unmet need for contraception.ConclusionThe prevalence of unmet need for contraception among young women in Haramaya was high. Unmet need was affected by age, husbands' attitude toward contraceptives, the educational status of women, and previous use of contraception. This study underscored the need to improve girls' educational status to empower them in making contraceptive use decisions with their partners. Programs should also engage male partners who are perceived as key decision-makers when it comes to contraceptive use.
CD160 receptor in CLL: Current state and future avenues
Authors: Oumeslakht Loubna , Aziz Abdel-ilah , Bensussan Armand , Ben Mkaddem Sanae 
Published: November 2022

CD160 is a glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein expressed on cytotoxic natural killer (NK) cells and T-cell subsets. It plays a crucial role in the activation of NK-cell cytotoxicity and cytokine production. It also modulates the immune system and is involved in some pathologies, such as cancer. CD160 is abnormally expressed in B-cell chronic lymphocytic leukemia (CLL) but not expressed in normal B lymphocytes. Its expression in CLL enhances tumor cell proliferation and resistance to apoptosis. CD160 is also a potential prognostic marker for the detection of minimal residual disease (MRD) in CLL, which is important for the clinical management of CLL, the prevention of disease relapse, and the achievement of complete remission. In this review, we present an overview of CD160 and its involvement in the pathophysiology of CLL. We also discuss its use as a prognostic marker for the assessment of MRD in CLL.
Islands in the mud: The South Texas banks provide crucial mesophotic habitat for coral communities
Authors: Bollinger Maria , Macartney Keir J. , Easton Erin E. , Hicks David W. 
Published: November 2022

On the continental shelf off the coast of South Texas lie a series of natural hard-bottom structures (rocky outcrops and relic coral-algal reefs) known as the South Texas Banks (STB), which provide critical habitat for benthic organisms and pelagic fish. The depth of the banks, a persistent nepheloid layer, and strong currents have resulted in few studies that provide quantitative biodiversity data on the STB. Using a remotely operated vehicle (ROV), video surveys were conducted to quantitatively describe the mesophotic coral communities and assess habitat suitability of five STB: North Hospital, Hospital, Southern, Big Adam, and Mysterious Banks. Each of these STB have significantly different benthic communites, with coral communities composed primarily of antipatharians and octocorals. Big Adam Bank had the lowest biodiversity and the least coral cover. Mysterious Bank had abundant antipatharians, specifically Stichopathes spp., but low biodiversity overall. Hospital Bank had low coral diversity that was offset by high diversity in sponges and other invertebrate species. North Hospital and Southern Banks had abundant and diverse populations of coral species, including scleractinians, and other benthic invertebrates. These data indicate that the STB are crucial islands of biodiversity in an area with few suitable areas for coral reef species. In addition, predictive modelling of habitat suitability provided valuable estimates on the potential distribution of key benthic community members, such as scleractinians and antipatharians, throughout the entire areas of the five banks assessed.
Venous thromboembolism in in-hospital cirrhotic patients: A systematic review
Authors: da Cruz Renó Leonardo , Tustumi Francisco , Waisberg Daniel Reis , Rocha-Santos Vinicius , Pinheiro Rafael Soares , Macedo Rubens Arantes , Nacif Lucas Souto , Ducatti Liliana , De Martino Rodrigo Bronze , Trevisan Alexandre Maximiliano , Carneiro-D’Albuquerque Luiz , Andraus Wellington 
Published: November 2022

IntroductionPatients with liver cirrhosis are at a higher risk of hospitalization. The present review aimed to assess the risk of thromboembolism and its burden on hospitalized cirrhotic patients.Materials and methodsA systematic review (PROSPERO: CRD42021256869) was conducted in PubMed, Embase, Cochrane, Lilacs, and a manual search of references. It evaluated studies that compare cirrhotic patients with venous thromboembolism (VTE) with cirrhotic patients without VTE or studies that compare cirrhotic patients with non-cirrhotic patients. No restrictions were set for the date of publication or language. The last search was conducted in June 2021.ResultsAfter selection, 17 studies were included from an initial search of 5,323 articles. The chronic liver disease etiologies comprise viral, alcohol, autoimmune, NASH (non-alcoholic steatohepatitis), cryptogenic, hemochromatosis, cholestasis, and drug-related. The included studies were conflicted regarding the outcomes of VTE, pulmonary embolism, or bleeding. Patients with cirrhosis associated with VTE had prolonged length of hospital stay, and patients with cirrhosis were at higher risk of portal thrombosis.ConclusionIn-hospital cirrhotic patients are a heterogeneous group of patients that may present both thrombosis and bleeding risk. Clinicians should take extra caution to apply both prophylactic and therapeutic anticoagulation strategies.Systematic review registration[https://www.crd.york.ac.uk/PROSPERO/], identifier [CRD42021256869].
MicroRNA panels as diagnostic biomarkers for colorectal cancer: A systematic review and meta-analysis
Authors: Sur Daniel , Advani Shailesh , Braithwaite Dejana 
Published: November 2022

BackgroundCirculating microRNAs (miRNA) have emerged as promising diagnostic biomarkers for several diseases, including cancer. However, the diagnostic accuracy of miRNA panels in colorectal cancer (CRC) remains inconsistent and there is still lack of meta-analyses to determine whether miRNA panels can serve as robust biomarkers for CRC diagnosis.MethodsThis study performed a systematic review and meta-analysis to evaluate the clinical utility of miRNA panels as potential biomarkers for the diagnosis of CRC. The investigation systematically searched PubMed, Medline, Web of Science, Cochrane Library, and Google Scholar (21-year span, between 2000 and 2021) to retrieve articles reporting the diagnostic role of miRNA panels in detecting CRC. Diagnostic meta-analysis of miRNA panels used diverse evaluation indicators, including sensitivity, specificity, Positive Likelihood Ratio (PLR), Negative Likelihood Ratio (NLR), Diagnostic Odds Ratio (DOR), and the area under the curve (AUC) values.ResultsAmong the 313 articles identified, 20 studies met the inclusion criteria. The pooled estimates of miRNA panels for the diagnosis of CRC were 0.85 (95% CI: 0.84–0.86), 0.79 (95% CI: 0.78–0.80), 4.06 (95% CI: 3.89–4.23), 0.20 (95% CI: 0.19–0.20), 22.50 (95% CI: 20.81–24.32) for sensitivity, specificity, PLR, NLR, and DOR, respectively. Moreover, the summary receiver operating characteristics (SROC) curve revealed an AUC value of 0.915 (95% CI: 0.914–0.916), suggesting an outstanding diagnostic accuracy for overall miRNA panels. Subgroup and meta-regression analyses demonstrated that miRNA panels have the highest diagnostic accuracy within serum samples, rather than in other sample-types – with a sensitivity, specificity, PLR, NLR, DOR, and AUC of 0.87, 0.86, 7.33, 0.13, 55.29, and 0.943, respectively. Sensitivity analysis revealed that DOR values did not differ markedly, which indicates that the meta-analysis had strong reliability. Furthermore, this study demonstrated no proof of publication bias for DOR values analyzed using Egger’s regression test (P &gt; 0.05) and funnel plot. Interestingly, miR-15b, miR-21 and miR-31 presented the best diagnostic accuracy values for CRC with sensitivity, specificity, PLR, NLR, DOR, and AUC values of 0.95, 0.94, 17.19, 0.05, 324.81, and 0.948, respectively.ConclusionThis study’s findings indicated that miRNA panels, particularly serum-derived miRNA panels, can serve as powerful and promising biomarkers for early CRC screening.Systematic review registration[www.crd.york.ac.uk/prospero], identifier [CRD42021268172].
PET/CT-based radiomics analysis may help to predict neoadjuvant chemotherapy outcomes in breast cancer
Authors: Yang Liping , Chang Jianfei , He Xitao , Peng Mengye , Zhang Ying , Wu Tingting , Xu Panpan , Chu Wenjie , Gao Chao , Cao Shaodong , Kang Shi 
Published: November 2022

BackgroundThe aim of this study was to evaluate the clinical usefulness of radiomics signature-derived 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography–computed tomography (PET-CT) for the early prediction of neoadjuvant chemotherapy (NAC) outcomes in patients with (BC).MethodsA total of 124 patients with BC who underwent pretreatment PET-CT scanning and received NAC between December 2016 and August 2019 were studied. The dataset was randomly assigned in a 7:3 ratio to either the training or validation cohort. Primary tumor segmentation was performed, and radiomics signatures were extracted from each PET-derived volume of interest (VOI) and CT-derived VOI. Radiomics signatures associated with pathological treatment response were selected from within a training cohort (n = 85), which were then applied to generate different classifiers to predict the probability of pathological complete response (pCR). Different models were then independently tested in the validation cohort (n = 39) regarding their accuracy, sensitivity, specificity, and area under the curve (AUC).ResultsThirty-five patients (28.2%) had pCR to NAC. Twelve features consisting of five PET-derived signatures, four CT-derived signatures, and three clinicopathological variables were candidates for the model’s development. The random forest (RF), k-nearest neighbors (KNN), and decision tree (DT) classifiers were established, which could be utilized to predict pCR to NAC with AUC ranging from 0.819 to 0.849 in the validation cohort.ConclusionsThe PET/CT-based radiomics analysis might provide efficient predictors of pCR in patients with BC, which could potentially be applied in clinical practice for individualized treatment strategy formulation.
Prognostic and diagnostic value of circRNA expression in prostate cancer: A systematic review and meta-analysis
Authors: Xie Jingling , Jiang Hui , Zhao Yuanqing , Jin Xin rui , Li Baolin , Zhu Zixin , Zhang Limei , Liu Jinbo 
Published: November 2022

BackgroundCircular RNAs (circRNAs) are receiving increasing attention as novel biomarkers. Our goal was to investigate the diagnostic, clinicopathological, and prognostic utility of circRNAs in prostate cancer (PCa).MethodsRelevant literature was searched in PubMed, Web of Science, and EMBASE. Sensitivity, specificity, diagnostic odds ratio (DOR), negative likelihood ratio (NLR), positive likelihood ratio (PLR), and the area under the curve (AUC) were calculated to evaluate the diagnostic accuracy of circRNA expression. circRNAs’ clinical, pathological, and prognostic value was examined using pooled odds ratios (ORs) and hazard ratios (HRs).ResultsThis meta-analysis included 23 studies, with 5 for diagnosis, 16 for clinicopathological parameters, and 10 for prognosis. For diagnostic value, the pooled sensitivity, pooled specificity, PLR, NLR, DOR, and AUC were 0.82, 0.62, 2.17, 0.29, 7.37, and 0.81, respectively. Upregulation of carcinogenic circRNAs was associated with poor clinical parameters (Gleason score: OR = 0.222, 95% CI: 0.145–0.340; T classification: OR = 0.274, 95% CI: 0.175–0.430; lymph node metastasis: OR = 0.353, 95% CI: 0.175–0.716; tumor size: OR = 0.226, 95% CI: 0.099–0.518) and could predict poor survival outcomes (HR = 2.408, 95% CI: 1.559–3.720, p &lt; 0.001). Conversely, downregulation of tumor-suppressor circRNAs was also associated with poor clinical parameters (Gleason score: OR = 1.689, 95% CI: 1.144–2.493; T classification: OR = 2.586, 95% CI: 1.779–3.762) and worse prognosis (HR = 1.739, 95% CI: 1.147–2.576, p = 0.006).ConclusionOur results showed that circRNAs might be useful biomarkers for the diagnosis and prognosis of PCa.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier CRD42021284785.
Clinical features and prognostic factors of children with profound sudden sensorineural hearing loss
Authors: Xiao Ling , Su Shuping , Liang Jia , Jiang Ying , Shu Yan , Yao Hongbing , Ding Ling 
Published: November 2022

ObjectiveTo investigate the clinical features and factors affecting the prognosis of children with profound sudden sensorineural hearing loss (SSNHL).MethodsWe retrospectively analyzed the clinical data of 147 children with profound SSNHL who received inpatient treatment at our department from January 2016 to January 2021. All children were administered with systemic steroid therapy and/or intratympanic steroid (ITS) treatment for 2 weeks. Statistical analyses were performed for the clinical features, treatment effectiveness, and factors affecting the prognosis using SPSS 23.0.ResultsThe median age of the study population was 8 (6–10) years. The median treatment onset time was 8 (4–20) days. The most common concomitant symptom was tinnitus (45.58%). Laboratory findings showed that the percentages of children with abnormal leukocytes was 25.85%, abnormal platelet counts was 17.01%, abnormal cytomegalovirus IgG antibodies was 36.73% and abnormal Epstein–Barr (EB) virus IgG antibodies was 41.50%. The overall recovery rate of the treatment was 20.04%. The univariate analysis showed that age, treatment onset time, tinnitus, and ITS treatment were associated with the prognosis (p &lt; 0.05). Regarding laboratory findings, the neutrophil count, lymphocyte count, and neutrophil-to-lymphocyte ratio differed significantly between the effective and invalid treatment effect groups (p &lt; 0.05). The multivariable logistic regression analysis showed that treatment onset time [odds ratio (OR) = 0.936, 95% confidence interval (CI): 0.881–0.994] and ITS treatment (OR = 0.174, 95% CI: 0.044–0.0687) correlated with hearing recovery (p &lt; 0.05).ConclusionIn this study, the earlier the treatment start time of children with profound SSNHL, the better was the prognosis. Further, ITS could be an effective treatment option.
Correlation of systemic immune-inflammation Index with surgical necrotizing enterocolitis
Authors: Feng Wei , Hou Jinping , Xiang Chenzhu , Die Xiaohong , Sun Jing , Guo Zhenhua , Liu Wei , Wang Yi 
Published: November 2022

BackgroundSystemic Immune-Inflammation Index (SII), known as an easy, economical and useful marker, correlates with the severity of inflammatory response. However, the usefulness of SII in necrotizing enterocolitis (NEC) remains unclear. Therefore, we evaluated the correlation of SII at NEC diagnosis and subsequent surgery.MethodsRetrospective review of 131 neonates with NEC in a tertiary-level pediatric referral hospital was conducted with assessments of demographic data, general blood examination results at NEC diagnosis, treatment strategies and clinical outcomes. The receiver operating characteristic (ROC) curve determined the optimal cut-off values of SII, platelet-to-lymphocyte ratio (PLR), and neutrophil-to-lymphocyte ratio. Univariate/multivariate logistic regression analysis and ROC curve were conducted to evaluate the predictive significance of SII in identifying the patients who eventually received surgery. Additionally, NEC-related deaths were assessed.ResultsOverall, 49 (37.4%) cases received surgical intervention and mortality was 12.3% (14/131). The area under ROC curve of SII at NEC diagnosis to predict subsequent surgery was 0.833 (optimal cut-off value: 235.85). The SII value in surgical intervention group was significantly higher than that in medical treatment group (332.92 ± 158.52 vs. 158.84 ± 106.82, P &lt; 0.001). Independent influencing factors for surgical NEC were SII (95% confidence interval [CI]: 4.568∼36.449, odds ratio [OR]:12.904, P &lt; 0.001) and PLR (95% CI: 1.071∼7.356, OR:2.807, P = 0.036). SII ≤ 235.85 could identify patients at high risk for surgery, with 87.76% sensitivity, 73.17% specificity, outperformed PLR. Furthermore, mortality was significantly higher in patients with SII ≤ 235.85 than those with SII &gt; 235.85 (20.0% vs. 1.5%, P &lt; 0.001).ConclusionSII and PLR at NEC diagnosis were independent influencing factors for subsequent surgery. SII ≤ 235.85 may be a useful predictive marker for the identification of surgical NEC and mortality.
Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
Authors: Yu Xuefei , Liu Ziyun , Pan Yuqing , Cui Xuewei , Zhao Xinyi , Li Danni , Xue Xindong , Fu Jianhua 
Published: November 2022

BackgroundBronchopulmonary dysplasia (BPD) is the most common neonatal chronic lung disease. However, its exact molecular pathogenesis is not understood. We aimed to identify relevant gene modules that may play crucial roles in the occurrence and development of BPD by weighted gene co-expression network analysis (WGCNA).MethodsWe used RNA-Seq data of BPD and healthy control rats from our previous studies, wherein data from 30 samples was collected at days 1, 3, 7, 10, and 14. Data for preprocessing analysis included 17,613 differentially expressed genes (DEGs) with false discovery rate &lt;0.05.ResultsWe grouped the highly correlated genes into 13 modules, and constructed a network of mRNA gene associations, including the 150 most associated mRNA genes in each module. Lgals8, Srpra, Prtfdc1, and Thap11 were identified as the key hub genes. Enrichment analyses revealed Golgi vesicle transport, coated vesicle, actin-dependent ATPase activity and endoplasmic reticulum pathways associated with these genes involved in the pathological process of BPD in module.ConclusionsThis is a study to analyze data obtained from BPD animal model at different time-points using WGCNA, to elucidate BPD-related susceptibility modules and disease-related genes.
Myocardial extracellular volume is a non-invasive tissue marker of heart failure in patients with transposition of the great arteries and systemic right ventricle
Authors: Al-Wakeel-Marquard Nadya , Ferreira da Silva Tiago , Berger Felix , Kuehne Titus , Messroghli Daniel R. 
Published: November 2022

BackgroundFocal myocardial fibrosis in the systemic right ventricle (RV) is related to ventricular dysfunction and adverse outcome in patients with d-transposition of the great arteries (dTGA) post atrial redirection and those with congenitally corrected TGA (ccTGA). The role of diffuse fibrotic lesions in these conditions remains poorly understood. Our study aimed to investigate diffuse myocardial fibrosis by measuring extracellular volume (ECV) with cardiovascular magnetic resonance (CMR) and to explore correlations between ECV and clinical as well as functional markers of heart failure in patients with TGA and systemic RV.MethodsWe prospectively included dTGA and ccTGA patients aged ≥14 years and compared them to healthy controls. Standardized CMR included modified Look-Locker Inversion recovery T1 mapping to quantify diffuse myocardial fibrosis in the systemic RV and the subpulmonary left ventricle (LV). The centerline of RV and LV myocardium was marked with a line of interest tool to determine native and post-contrast T1 for quantification of ECV.ResultsIn total, 13 patients (dTGA: n  =  8, ccTGA: n = 5) with a median age of 30.3 years were enrolled. LV ECV was higher in patients than in controls [34% (30%–41%) vs. 26% (23%–27%), p &lt; 0.001], with values increased above the upper limit of normal in 10/13 patients (77%). RV ECV tended to be higher in patients than in controls, albeit without statistical significance [29% (27%–32%) vs. 28% (26%–29%), p = 0.316]. Patients with elevated LV ECV had lower LV ejection fraction than those with normal ECV (52 ± 5% vs. 65 ± 4%, p = 0.007). Correlations with clinical parameters were not observed. LV ECV was significantly higher than RV ECV (p = 0.016) in the patient group.ConclusionsIn this study, LV ECV was significantly increased in TGA patients compared to controls, and was associated with LV dysfunction. Our data suggest that ECV may serve as a non-invasive tissue marker of heart failure in TGA with systemic RV. Further research is necessary to evaluate the prognostic implications and the potential role of ECV in monitoring disease progression and guiding therapy, aiming to maintain LV function or train the LV for subaortic location in TGA patients from infancy to adulthood.