bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Hybridization Risk Between ESA-Listed Native Bull Trout (Salvelinus confluentus) and Introduced Brook Trout (S. fontinalis) Using Habitat Modeling
Authors: Manning Michael A. , Arismendi Ivan , Olivos J. Andres , Giannico Guillermo 
Published: March 2022

The introduction of non-native species can negatively impact native species through reduced genetic fitness resulting from hybridization. The lack of spatiotemporal data on hybrid occurrences makes hybridization risk assessment difficult. Here, we developed a spatially-explicit Hybridization Risk Model (HRM) between native Oregon bull trout, an Endangered Species Act-listed Oregon species, and introduced brook trout by combining an intrinsic potential model (IPM) of brook trout spawning habitat and existing bull trout distribution and habitat use datasets in Oregon, United States. We created an expert-based brook trout IPM classification score (0–1) of streams based on the potential of geophysical attributes (i.e., temperature, discharge, gradient, and valley confinement) to sustain spawning habitats. The HRM included a risk matrix based on the presence/absence of both species as well as the type of habitat (spawning versus other) at 100-m stream segment resolution. We defined the hybridization risk as “extreme” when stream reaches contained bull trout spawning habitat and brook trout were present with IPM moderate or greater scores (IPM &gt;0.5). Conversely, “low” risk reaches contained historic or non-spawning bull trout habitat, brook trout were absent, and IPM scores were low (IPM &lt;0.25). Our HRM classified 34 km of streams with extreme risk of hybridization, 115 km with high risk, 178 km with moderate risk, and 6,023 km with low risk. Our HRM can identify a differential risk of hybridization at multiple spatial scales when either both species coexist in bull trout spawning habitat or are absent. The model can also identify stream reaches that would have higher risk of hybridization, but where brook trout are not currently present. Our modeling approach can be applied to other species, such as cutthroat trout and rainbow trout, Chinook and coho salmon, or similar species occurring elsewhere that potentially hybridize in freshwaters.
HSPB8 is a Potential Prognostic Biomarker that Correlates With Immune Cell Infiltration in Bladder Cancer
Authors: Tan Zhiyong , Fu Shi , Huang Yinglong , Duan Xianzhong , Zuo Yigang , Zhu Xiaorui , Wang Haifeng , Wang Jiansong 
Published: March 2022

Background: Heat shock protein B8 (HSPB8) is expressed in various cancers. However, the functional and clinicopathological significance of HSPB8 expression in bladder cancer (BC) remains unclear. The present study sought to elucidate the clinicopathological features and prognostic value of HSPB8 in BC.Methods: A BC RNA-seq data set was obtained from The Cancer Genome Atlas Urothelial Bladder Carcinoma (TCGA-BLCA) database, and the external validation dataset GSE130598 was downloaded from the GEO database. Samples in the TCGA-BLCA were categorized into two groups based on HSPB8 expression. Differentially expressed genes (DEGs) between the two groups were defined as HSPB8 co-expressed genes. Gene set enrichment analysis (GSEA), protein-protein interaction networks, and mRNA-microRNA (miRNA) interaction networks were generated to predict the function and interactions of genes that are co-expressed with HSPB8. Finally, we examined immune cell infiltration and constructed a survival prediction model for BC patients.Results: The expression level of HSBP8 has a significant difference between cancer samples and normal samples, and its diagnosis effect was validated by the ROC curve. 446 differential expressed genes between HSBP8 high-expression and HSBP8 low expression groups were identified. Gene enrichment analysis and GSEA analysis show that these differential gene functions are closely related to the occurrence and development of BC and the metabolic pathways of BC. The cancer-related pathways included Cytokine-cytokine receptor Interaction, Focal adhesion, and Proteoglycans in cancer. PPI and protein-coding gene-miRNA network visualized the landscape for these tightly bounded gene interactions. Immune cell infiltration shows that B cells, CD4+T cells, and CD8+T cells have strongly different infiltration levels between the HSBP8 high exp group and low exp group. The survival prediction model shows that HSBP8 has strong prognosis power in the BLCA cohort.Conclusion: Identifying DEGs may enhance understanding of BC development’s causes and molecular mechanisms. HSPB8 may play an essential role in BC progression and prognosis and serve as a potential biomarker for BC treatment.
Comprehensive Genetic Analysis of Tuberculosis and Identification of Candidate Biomarkers
Authors: Wen Zilu , Wu Liwei , Wang Lin , Ou Qinfang , Ma Hui , Wu Qihang , Zhang Shulin , Song Yanzheng 
Published: March 2022

Purpose: The purpose of this study is to use the data in the GEO database to analyze, screen biomarkers that can diagnose tuberculosis, and verification of candidate biomarkers.Materials and methods: GSE158767 dataset were used to process WGCNA analysis, differential gene analysis, Gene ontology and KEGG analysis, protein-protein network analysis and hub genes analysis. Based on our previous study, the intersect between WGCNA and differential gene analysis could be used as candidate biomarkers. Then, the enzyme-linked immunosorbent assay was used to validate candidate biomarkers, and receiver operating characteristic was used to assess diagnose ability of candidate biomarkers.Results: A total of 412 differential genes were screened. And we obtained 105 overlapping genes between DEGs and WGCNA. GO and KEGG analysis showed that most of the differential genes were significantly enriched in innate immunity. A total of 15 hub genes were screened, and four of them were verified by Enzyme-linked immunosorbent assay. CCL5 performed well in distinguishing the healthy group from the TB group (AUC = 0.723). And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811).Conclusion: CCL19, C1Qb, CCL5 and HLA-DMB may play important role in tuberculosis, which indicated four genes may become effective biomarkers and could be conveniently used to facilitate the individual tuberculosis diagnosis in Chinese people.
A Resampling Method to Improve the Prognostic Model of End-Stage Kidney Disease: A Better Strategy for Imbalanced Data
Authors: Shi Xi , Qu Tingyu , Van Pottelbergh Gijs , van den Akker Marjan , De Moor Bart 
Published: March 2022

BackgroundPrognostic models can help to identify patients at risk for end-stage kidney disease (ESKD) at an earlier stage to provide preventive medical interventions. Previous studies mostly applied the Cox proportional hazards model. The aim of this study is to present a resampling method, which can deal with imbalanced data structure for the prognostic model and help to improve predictive performance.MethodsThe electronic health records of patients with chronic kidney disease (CKD) older than 50 years during 2005–2015 collected from primary care in Belgium were used (n = 11,645). Both the Cox proportional hazards model and the logistic regression analysis were applied as reference model. Then, the resampling method, the Synthetic Minority Over-Sampling Technique-Edited Nearest Neighbor (SMOTE-ENN), was applied as a preprocessing procedure followed by the logistic regression analysis. The performance was evaluated by accuracy, the area under the curve (AUC), confusion matrix, and F3 score.ResultsThe C statistics for the Cox proportional hazards model was 0.807, while the AUC for the logistic regression analysis was 0.700, both on a comparable level to previous studies. With the model trained on the resampled set, 86.3% of patients with ESKD were correctly identified, although it was at the cost of the high misclassification rate of negative cases. The F3 score was 0.245, much higher than 0.043 for the logistic regression analysis and 0.022 for the Cox proportional hazards model.ConclusionThis study pointed out the imbalanced data structure and its effects on prediction accuracy, which were not thoroughly discussed in previous studies. We were able to identify patients with high risk for ESKD better from a clinical perspective by using the resampling method. But, it has the limitation of the high misclassification of negative cases. The technique can be widely used in other clinical topics when imbalanced data structure should be considered.
The Clinical Phenotype of Chinese Patients With Autoimmune Pancreatitis Differs Significantly From Western Patients
Authors: Jin Qiwen , Ge Yongpeng , Chen Xixia , Tan Chang , Huang Zhenguo , Wang Bei , Zhang Bo , Peng Qinglin , Wang Xiaodi , Wang Guochun 
Published: March 2022

AimTo characterize the clinical features of autoimmune pancreatitis (AIP) in China and compare differences between our Chinese cohort and Western cohorts.MethodsThis was a retrospective study of patients with AIP that was carried out in the China-Japan Friendship Hospital between January 2010 and April 2021. We included a total of 50 patients (46 males and 4 females) aged between 27 and 86 years who fulfilled the international Consensus Diagnostic (ICD) Criteria. For comparative purposes, we included data from seven representative Western cohorts.ResultWhen comparing Chinese and Western patients, we found that obstructive jaundice was the most frequent initial symptom (68 vs. 43%, P &lt; 0.001). Extra-pancreatic organ involvement was more common in Chinese patients (68 vs. 30%, P &lt; 0.001). Sclerosing cholangitis was the most frequent extrapancreatic lesion (48 vs. 24%, P = 0.001). The elevation of serum IgG4 was more obvious in our cohort (86 vs. 49%, P &lt; 0.001). Conversely, the rates of ANA-positivity were significantly higher in Western populations (17 vs. 50%, P = 0.006). With regards to imaging, diffuse swelling was significantly more common in China (44 vs. 27%, P = 0.021). Steroid therapy was used more frequently in our Chinese patients (84 vs. 59%, P = 0.001). The steroid-response rate was also significantly higher in our Chinese patients (85 vs. 54%, P = 0.001); However, the rate of resection was higher in Western cohorts (2 vs. 31%, P &lt; 0.001). There was no significant difference between the two populations with regards to recurrence rate (33 vs. 33%, P = 1.000).ConclusionThis study identified significant differences between Chinese and Western populations of patients with AIP. Within the Chinese population, AIP was more likely to have jaundice and extra-pancreatic organ involvement, and elevated serum IgG4 levels. Chinese patients were also showed favorable responses to treatment with glucocorticoids.
Development and Validation of Prognostic Nomogram for Postpartum Hemorrhage After Vaginal Delivery: A Retrospective Cohort Study in China
Authors: Song Zixuan , Wang Xiaoxue , Zhou Yangzi , Wang Yuting , Zhang Dandan 
Published: March 2022

BackgroundPostpartum hemorrhage (PPH) is a common complication following vaginal delivery and in severe cases can lead to maternal death. A straightforward predictive model is required to enable prenatal evaluations by obstetricians to prevent PPH complications.MethodsData of patients who delivered vaginally after 37 weeks of gestation were retrospectively collected from the medical database at Shengjing Hospital of China Medical University for the period 2016 to 2020. PPH was defined as blood loss of 500 mL or more within 24 h of delivery, and important independent prognostic factors were determined using univariate and multivariate logistic regression analyses to construct nomograms regarding PPH.ResultsA total of 24,833 patients who delivered vaginally were included in this study. The training cohort included 22,302 patients who delivered between 2016 and 2019 and the external validation cohort included 2,531 patients who delivered during 2020. Nomogram was created using data such as age, race, occupation, parity, gestational weeks, labor time, neonatal weight, analgesic delivery, gestational diabetes mellitus, premature rupture of membranes, anemia, hypertension, adenomyosis, and placental adhesion. The nomogram has good predictive power and clinical practicality through the analysis of the area under the curve and decision curve analysis. Internal verification was performed on the nomogram for PPH, demonstrating consistency between the nomogram's predicted probability and actual probability.ConclusionsThe developed and validatable nomogram is a good predictor of PPH in vaginal delivery and can be used in clinical practice to guide obstetricians to administer preventive therapies before delivery.
Cyclosporine Monotherapy in Pediatric Patients With Non-severe Aplastic Anemia: A Retrospective Analysis
Authors: Li Hongmin , Fu Lingling , Yang Bixi , Chen Hui , Ma Jie , Wu Runhui 
Published: March 2022

ObjectiveThe management of children with non-severe aplastic anemia (NSAA) is undefined and the efficacies and benefits of immunosuppressive therapy remain inconsistent. The study aimed to investigate the efficacy of Cyclosporine (CsA) monotherapy for pediatric NSAA.MethodsClinical data of children with NSAA who had been treated with CsA monotherapy at the outpatient department of Beijing Children's Hospital, Capital Medical University, National Children's Medical Center from January 2017 to March 2021 was collected retrospectively. Patients who had been treated &lt;1 years until the end of follow-up were excluded. Transfusion-independent NSAA was further divided into moderate NSAA and mild NSAA according to the degree of cytopenia. Progression was defined as the development of transfusion-dependent AA or SAA and relapse was considered when treatment failed after initial response.ResultsA total of 95 pediatric patients with NSAA were enrolled in this study with 49 (51.6%) patients confirmed as mild NSAA, 38 (40%) as moderate NSAA and 8 (8.4%) as transfusion-dependent NSAA. The median treatment time of CsA was 22 (12–44) months. The overall response rate (ORR) was 57.9%, with 30.5% CR and 27.4% PR. Unexpectedly, patients with mild NSAA acquired lowest ORR (46.9%), then patients with moderate NSAA (63.2%), while 8 patients who were transfusion-dependent all had an active response to CsA. The granulocyte and megakaryocyte response was 46.9 and 55.8% respectively, while the erythrocyte response rate was as low as 22.5%. Univariate analyses revealed that patients with lower platelet count and higher interleukin 10 level predict an active response to CsA while higher level of fetal hemoglobin (HbF) tended to be a negative factor. Data of Treg cells before and after 1 year's treatment was available in a total number of 40 patients. Paired comparison found that the percentage of Treg cells in CD4+ T cells was decreased after 1 year's treatment of CsA (6.78 ± 2.72 vs. 5.23 ± 2.06, P = 0.001),both in responders and non-responders. The degree of decline in Treg cells between two distinctive response groups had no significant difference (P&gt;0.05). With a median follow-up time of 22 months, 10.9% of responders relapsed and maintained NSAA while 27.5% of non-responders progressed to SAA or became transfusion-dependent. The overall progression rate was 11.6%.ConclusionCsA monotherapy had heterogeneous effects in the treatment of children NSAA Treatment approaches should be hierarchical and individual in clinical. Patients with lower platelet count and higher interleukin 10 level predicted an active response to CsA. While higher level of fetal hemoglobin (HbF) tended to be a negative factor. The percentage of Treg cells in CD4+ T cells was decreased broadly after treatment.
Anterior Segment Optical Coherence Tomography Angiography Following Trabecular Bypass Minimally Invasive Glaucoma Surgery
Authors: Gan Jinyuan , Sng Chelvin C. A. , Ke Mengyuan , Chieh Chew Shi , Tan Bingyao , Schmetterer Leopold , Ang Marcus 
Published: March 2022

ObjectiveTo assess anterior segment optical coherence tomography angiography (AS-OCTA) imaging of the episcleral vessels before and after trabecular bypass minimally invasive glaucoma surgery (MIGS).DesignA prospective, clinical, single-centre, single-arm pilot feasibility study conducted at National University Hospital, Singapore.SubjectsPatients with primary glaucomatous optic neuropathy undergoing Hydrus Microstent (Ivantis Inc., Irvine, CA, USA) implantation, who require at least one intra-ocular pressure-lowering medication. One or two eyes per patient may be enrolled.MethodsWe performed AS-OCTA (Nidek RS-3000 Advance 2, Gamagori, Japan) pre- and up to 6 months post-MIGS implantation using a standard protocol in all cornealimbal quadrants, to derive episcleral vessel densities (VD) using a previously described technique.Main Outcome MeasuresEpiscleral VD pre- and post-surgery, in sectors with and without the implant.ResultsWe obtained serial AS-OCTA images in 25 eyes undergoing MIGS implantation (23 subjects, mean age 70.3 ± 1.5, 61% female) with mean preoperative intraocular pressure (IOP) of 15.5 mmHg ± 4.0. We observed reductions in postoperative episcleral VD compared to preoperative VD at month 1 (mean difference −3.2, p = 0.001), month 3 (mean difference −2.94, p = 0.004) and month 6 (mean difference −2.19, p = 0.039) in sectors with implants (overall 6 month follow-up, p = 0.011). No significant changes were detected in episcleral VD in the sectors without implants (p = 0.910).ConclusionIn our pilot study, AS-OCTA was able to detect changes in the episcleral VD following trabecular bypass MIGS, which may be a useful modality to evaluate surgical outcomes if validated in future studies.
The Value of Neutrophil-To-Lymphocyte Ratio for Evaluating Blood Stream Infection Caused by Carbapenem-Resistant Klebsiella pneumoniae: A Retrospective Cohort Study
Authors: Wu Heng , Mao Yihan , Du Xiaoxing , Zhao Feng , Jiang Yan , Yu Yunsong 
Published: March 2022

BackgroundThe neutrophil-to-lymphocyte ratio (NLR) is a useful marker of inflammation. However, the prognostic function of the NLR in patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) blood stream infection (BSI) remains largely unknown. The aim of this study was to explore the potential relationship between the NLR and mortality in these patients.MethodsWe performed a retrospective cohort study based on data retrieved from the computerized patient record system in a tertiary hospital from 1 January 2017 to 31 October, 2020. A total of 134 inpatients with CRKP BSI were enrolled in this study, including 54 fatal cases and 80 survival cases, 28 days after the onset of CRKP BSI. A logistic analysis was performed to assess the association between the NLR on the 4th day and 28-day mortality. Multivariate analyses were used to control for the confounders.ResultsThe overall 28-day mortality rate of patients with a CRKP BSI episode was 40.3% (54/134). We conducted a multivariate analysis of the data of 134 patients and found that the NLR on the 4th day [odds ratio (OR) 1.148, 95% confidence interval (CI) 1.076–1.225, p &lt; 0.001] and antibiotic exposure before BSI onset (OR 3.847, 95% CI 1.322–11.196, p = 0.013) were independent risk factors for 28-day mortality of patients with CRKP BSI, while appropriate initial therapy (AIT, OR 0.073, 95% CI 0.017–0.307, p &lt; 0.001) was an independent protective factor. Among patients treated with AITs, the Cox proportional hazards regression analysis revealed a significant difference in prognosis (p = 0.006) between the ceftazidime/avibactam contained (CAZ) group and non CAZ-AVI groups. After dividing the non CAZ-AVI group into the tigecycline (TGC), colistin (COL), and TGC + COL groups, there were no differences between the CAZ-AVI group and the TGC group (p = 0.093), but CAZ-AVI group showed lower 28-day mortality than COL (p = 0.002) and TGC + COL (p = 0.002) groups. Meanwhile, there was no difference in NLR on the 1st day (p = 0.958) of patients in different groups but significant difference in NLR on the 4th day (p = 0.047).ConclusionsThe NLR on the 4th day is a readily available and independent prognostic biomarker for patients with CRKP BSI. This marker may have the potential for use in evaluating the efficacy of different anti-infection therapy strategies at an early stage.
Correlation Analysis Among Genotype Resistance, Phenotype Resistance, and Eradication Effect After Resistance-Guided Quadruple Therapies in Refractory Helicobacter pylori Infections
Authors: Guo Zijun , Tian Shuxin , Wang Weijun , Zhang Yanbin , Li Jing , Lin Rong 
Published: March 2022

ObjectivesThe antimicrobial resistance of Helicobacter pylori (H. pylori) in most countries and regions has increased significantly. It has not been fully confirmed whether the detection of H. pylori resistance gene mutation can replace antibiotic drug sensitivity test to guide the clinical personalized treatment. The objective of this study was to assess and compare the efficacy of different antimicrobial resistance-guided quadruple therapies in refractory H. pylori-infected individuals who had undergone unsuccessful prior eradication treatments.MethodsFrom January 2019 to February 2020, genotypic and phenotypic resistances were determined by polymerase chain reaction (PCR), whole genome sequencing (WGS) and broth microdilution test, respectively, in 39 H. pylori-infected patients who have failed eradication for at least twice. The patients were retreated with bismuth quadruple therapy for 14 days according to individual antibiotic resistance results. Eradication status was determined by the 13C-urea breath test.ResultsThe overall eradication rate was 79.5% (31/39, 95% CI 64.2–89.5%) in the intention-to-treat (ITT) analysis and 88.6% (31/35, 95% CI 73.5–96.1%) in the per- protocol analysis (PP) analysis. The presence of amoxicillin resistance (OR, 15.60; 95% CI, 1.34–182.09; p = 0.028), female sex (OR, 12.50; 95% CI, 1.10–142.31; p = 0.042) and no less than 3 prior eradication treatments (OR, 20.25; 95% CI, 1.67–245.44; p = 0.018), but not the methods for guiding therapy (p &gt; 0.05) were associated with treatment failure. Resistance-guided therapy achieved eradication rates of more than 80% in these patients. The eradication rate of H. pylori in the phenotypic resistance-guided group was correlated well with genotype resistance-guided groups, including PCR and WGS.ConclusionCulture or molecular method guiding therapy can enable personalized, promise salvage treatments, and achieve comparably high eradication rates in patients with refractory H. pylori infection. The detection of H. pylori resistance mutations has a good clinical application prospect.Protocol Study Register[clinicaltrials.gov], identifier [ChiCTR1800020009].