bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nomogram based on a circular RNA biomarker for predicting the likelihood of successful sperm retrieval via microdissection testicular sperm extraction in patients with idiopathic non-obstructive azoospermia
Authors: Shi Shengjia , Wang Tianwei , Wang Lei , Wang Mingjuan 
Published: January 2023

BackgroundMany circular RNAs (circRNAs) are specifically expressed in the testes and seminal plasma of patients with non-obstructive azoospermia (NOA), highlighting them as potential predictors of microdissection testicular sperm extraction (micro-TESE) outcomes. Although research has indicated that circular RNA monoglyceride lipase (circ_MGLL) is highly expressed in the testicular tissues of patients with NOA, the association between circ_MGLL expression and sperm retrieval outcomes (SROs) in patients with idiopathic non-obstructive azoospermia (iNOA) receiving micro-TESE remains unclear.MethodsThis single-center, retrospective cohort study enrolled 114 patients with iNOA who underwent micro-TESE at Northwest Women’s and Children’s Hospital from January 2017 to November 2021. A logistic regression model was used to examine associations between SRO and circ_MGLL expression in testicular tissues, the results of which were used in conjunction with previous findings to establish a nomogram. The predictive performance of the circ_MGLL-based nomogram was evaluated via calibration curves, receiver operating characteristic curves, and decision curve analysis (DCA) using an internal validation method.ResultsThe generalized additive model indicated that the probability of successful SRO for micro-TESE decreased as circ_MGLL expression increased in testicular tissues. Across the entire cohort, univariate logistic regression analysis revealed that circ_MGLL expression was inversely associated with SRO in patients with NOA. This trend did not change after stratification according to age, body mass index, testicular volume, follicle-stimulating hormone (FSH) level, luteinizing hormone (LH) level, testosterone (T) level, or pathological type (or after adjusting for these confounders) (odds ratio &lt;1, P &lt; 0.001). A nomogram was then generated by integrating circ_MGLL, pathological types, and FSH, LH, and T levels. The circ_MGLL-based predictive model achieved satisfactory discrimination, with an area under the curve of 0.857, and the calibration curves demonstrated impressive agreement. The DCA indicated that the net clinical benefit of the circ_MGLL-based predictive model was greater than that of circ_MGLL alone.Conclusioncirc_MGLL is significantly associated with the SRO of micro-TESE in patients with iNOA. The circ_MGLL-based nomogram developed in the current study can predict successful SRO with high accuracy.
Co-benefits of the National Key Ecological Function Areas in China for carbon sequestration and environmental quality
Authors: Chen Hanyu , Hou Mengyang , Xi Zenglei , Zhang Xiao , Yao Shunbo 
Published: January 2023

IntroductionThe National Key Ecological Functional Areas (NKEFAs) are location-oriented ecological engineering of China, which rely on the main functional area planning. The co-benefits of ecological product supply and ecological environment improvement of NKEFAs has not been fully assessed in the literature.MethodsNKEFAs is considered a quasi-natural experiment, and the time-varying difference-in-differences (DID) model is used to assess the impact of NKEFAs on carbon sequestration (CS) and environmental quality (EQ) based on the panel data of 330 cities in China from 2001 to 2019. Then, we explore whether the co-benefits of ecological product supply and eco-environment protection can be achieved.Results and discussionNKEFAs can enhance CS and EQ and thus achieve co-benefits for both. NKEFAs can achieve the co-benefits of CS and EQ through territory spatial allocation and labor force aggregation, but industrial structure upgrading only positively mediates the impact of NKEFAs on CS. The co-benefits of CS and EQ are heterogeneous across functional area types, geospatial locations, and quantiles, while only CS at windbreak-sand fixation area, northwestern region, and low quantile regions is enhanced. This study makes a theoretical and methodological contribution to the existing literature on the policy effect assessment of ecological engineering. It also provides a comprehensive framework for evaluating the ecological effects of relevant policies in other countries by integrating the co-benefits of ecological products and eco-environment, analyzing regional heterogeneity, and exploring the underlying mechanisms.
Identification of m6a-related signature genes in esophageal squamous cell carcinoma by machine learning method
Authors: Shang Qi-Xin , Kong Wei-Li , Huang Wen-Hua , Xiao Xin , Hu Wei-Peng , Yang Yu-Shang , Zhang Hanlu , Yang Lin , Yuan Yong , Chen Long-Qi 
Published: January 2023

Background: We aimed to construct and validate the esophageal squamous cell carcinoma (ESCC)-related m6A regulators by means of machine leaning.Methods: We used ESCC RNA-seq data of 66 pairs of ESCC from West China Hospital of Sichuan University and the transcriptome data extracted from The Cancer Genome Atlas (TCGA)-ESCA database to find out the ESCC-related m6A regulators, during which, two machine learning approaches: RF (Random Forest) and SVM (Support Vector Machine) were employed to construct the model of ESCC-related m6A regulators. Calibration curves, clinical decision curves, and clinical impact curves (CIC) were used to evaluate the predictive ability and best-effort ability of the model. Finally, western blot and immunohistochemistry staining were used to assess the expression of prognostic ESCC-related m6A regulators.Results: 2 m6A regulators (YTHDF1 and HNRNPC) were found to be significantly increased in ESCC tissues after screening out through RF machine learning methods from our RNA-seq data and TCGA-ESCA database, respectively, and overlapping the results of the two clusters. A prognostic signature, consisting of YTHDF1 and HNRNPC, was constructed based on our RNA-seq data and validated on TCGA-ESCA database, which can serve as an independent prognostic predictor. Experimental validation including the western and immunohistochemistry staining were further successfully confirmed the results of bioinformatics analysis.Conclusion: We constructed prognostic ESCC-related m6A regulators and validated the model in clinical ESCC cohort as well as in ESCC tissues, which provides reasonable evidence and valuable resources for prognostic stratification and the study of potential targets for ESCC.
Efficacy of chimeric antigen receptor T cell therapy and autologous stem cell transplant in relapsed or refractory diffuse large B-cell lymphoma: A systematic review
Authors: Tian Linyan , Li Cheng , Sun Juan , Zhai Yixin , Wang Jinhuan , Liu Su , Jiang Yanan , Wu Wenqi , Xing Donghui , Lv Yangyang , Guo Jing , Xu Hong , Sun Huimeng , Li Yuhang , Li Lanfang , Zhao Zhigang 
Published: January 2023

BackgroundWe aimed to compare the efficacy of chimeric antigen receptor T (CAR-T) cell therapy with that of autologous stem cell transplantation (auto-HSCT) in relapsed/refractory diffuse large B cell lymphoma (R/R DLBCL).Research design and methodsWe searched eligible publications up to January 31st, 2022, in PubMed, Cochrane Library, Springer, and Scopus. A total of 16 publications with 3484 patients were independently evaluated and analyzed using STATA SE software.ResultsPatients who underwent CAR-T cell therapy showed a better overall response rate (ORR) and partial response (PR) than those treated with auto-HSCT (CAR-T vs. auto-HSCT, ORR: 80% vs. 73%, HR:0.90,95%CI:0.76-1.07,P = 0.001; PR: 20% vs. 14%, HR:0.65,95%CI:0.62-0.68,P = 0.034). No significant difference was observed in 6-month overall survival (OS) (CAR-T vs. auto-HSCT, six-month OS: 81% vs. 84%, HR:1.23,95%CI:0.63-2.38, P = 0.299), while auto-HSCT showed a favorable 1 and 2-year OS (CAR-T vs. auto-HSCT, one-year OS: 64% vs. 73%, HR:2.42,95%CI:2.27-2.79, P &lt; 0.001; two-year OS: 54% vs. 68%, HR:1.81,95%CI:1.78-1.97, P &lt; 0.001). Auto-HSCT also had advantages in progression-free survival (PFS) (CAR-T vs. auto-HSCT, six-month PFS: 53% vs. 76%, HR:2.81,95%CI:2.53-3.11,P &lt; 0.001; one-year PFS: 46% vs. 61%, HR:1.84,95%CI:1.72-1.97,P &lt; 0.001; two-year PFS: 42% vs. 54%, HR:1.62,95%CI:1.53-1.71, P &lt; 0.001). Subgroup analysis by age, prior lines of therapy, and ECOG scores was performed to compare the efficacy of both treatment modalities.ConclusionAlthough CAR-T cell therapy showed a beneficial ORR, auto-HSCT exhibited a better long-term treatment superiority in R/R DLBCL patients. Survival outcomes were consistent across different subgroups.
Transcriptomic analysis of asthma and allergic rhinitis reveals CST1 as a biomarker of unified airways
Authors: Wang Mingming , Gong Li , Luo Yang , He Shaojuan , Zhang Xianxing , Xie Xinyu , Li Xuezhong , Feng Xin 
Published: January 2023

BackgroundAllergic rhinitis (AR) is an important risk factor for the development of asthma. The “unified airway” theory considers the upper and lower airways as a morphological and functional whole. However, studies exploring biomarkers linking the upper and lower airways in allergic disease are lacking, which may provide insight into the mechanisms underlying AR comorbid asthma.PurposeTo integrate bioinformatics techniques to explore biomarkers in airway allergic diseases, and to provide a molecular etiology profile for preventing the development of asthma in AR patients.MethodsBiomarkers were screened by identifying key genes common between AR and asthma through WGCNA and differential gene analysis. GO and KEGG analyses were performed using DAVID. Immuno-infiltration analysis was performed by CIBERSORTx. The predictive value of CST1 to distinguish Th2-high asthma was determined by ROC curves. GSEA was used to analyze the signaling pathways involved in CST1. TargetScan and miRNet were combined with GSE142237 to construct ceRNA network. CMap was used to explore potential therapeutic drugs.ResultsValidation of datasets showed that CST1 was the only gene that was up-regulated in both upper and lower airways in patients with AR and asthma, and correlation heatmaps showed that CST1 was the gene with the highest sum of correlation coefficients. GO and KEGG analysis demonstrated that the lower airways of AR patients were mainly involved in inflammatory and immune responses, similar to asthma. Immune infiltration showed that CST1 was mainly positively correlated with activated CD4 memory T cells. According to the ROC curve, CST1 showed excellent diagnostic efficiency for Th2-high asthma. GSEA indicated that CST1 was involved in the FcϵRI signaling pathway and O-glycan biosynthesis. A ceRNA network including the lncRNAs KCNQ1OT1 and NEAT1 was constructed. Four drugs, including verrucarin-A, had the potential to prevent the development of asthma in AR patients. In addition, corticosteroids were found to downregulate CST1 expression.ConclusionCST1 plays a key role in the development of AR comorbid asthma and may be a biomarker for airway allergic diseases. Targeted treatment of CST1 has the potential to prevent the development of asthma in AR patients and deserves further study.
Silent peripheral neuropathy determined by high-resolution ultrasound among contacts of patients with Hansen's disease
Authors: Voltan Glauber , Marques-Júnior Wilson , Santana Jaci Maria , Lincoln Silva Claudia Maria , Leite Marcel Nani , De Paula Natália Aparecida , Bernardes Filho Fred , Barreto Josafá Gonçalves , Da Silva Moises Batista , Conde Guilherme , Salgado Claudio Guedes , Frade Marco Andrey Cipriani 
Published: January 2023

IntroductionHansen's disease (HD) primarily infects peripheral nerves, with patients without HD being free of peripheral nerve damage. Household contacts (HHCs) of patients with HD are at a 5–10 times higher risk of HD than the general population. Neural thickening is one of the three cardinal signs that define a case of HD according to WHO guidelines, exclusively considering palpation examination that is subjective and may not detect the condition in the earliest cases even when performed by well-trained professionals. High-resolution ultrasound (HRUS) can evaluate most peripheral nerves, a validated technique with good reproducibility allowing detailed and accurate examination.ObjectiveThis study aimed to use the peripheral nerve HRUS test according to the HD protocol as a diagnostic method for neuropathy comparing HHCs with healthy volunteers (HVs) and patients with HD.MethodsIn municipalities from 14 different areas of Brazil we selected at random 83 HHC of MB-patients to be submitted to peripheral nerve ultrasound and compared to 49 HVs and 176 HD-patients.ResultsHousehold contacts assessed by HRUS showed higher median and mean absolute peripheral nerve cross-sectional area (CSA) values and greater asymmetries (ΔCSA) compared to HVs at the same points. Median and mean absolute peripheral nerve CSA values were higher in patients with HD compared to HCCs at almost all points, while ΔCSA values were equal at all points. Mean ± SD focality (ΔTpT) values for HHCs and patients with HD, respectively, were 2.7 ± 2.2/2.6 ± 2.2 for the median nerve, 2.9 ± 2.7/3.3 ± 2.9 for the common fibular nerve (p&gt; 0.05), and 1.3 ± 1.3/2.2 ± 3.9 for the ulnar nerve (p&lt; 0.0001).DiscussionConsidering HRUS findings for HHCs, asymmetric multiple mononeuropathy signs (thickening or asymmetry) in at least 20% of the nerves evaluated could already indicates evidence of HD neuropathy. Thus, if more nerve points are assessed in HHCs (14 instead of 10), the contacts become more like patients with HD according to nerve thickening determined by HRUS, which should be a cutting-edge tool for an early diagnosis of leprosy cases.
Case report: Brucellosis with rare multiple pulmonary nodules in a depressed patient
Authors: Zhou Mingjing , Wang Ke , Liu Haoyuan , Ran Ran , Wang Xuan , Yang Yuqian , Han Qunying , Zhou Yi , Liu Xiaojing 
Published: January 2023

BackgroundBrucellosis is a zoonotic disease that threatens public health and creates an economic burden. Unfortunately, it is often overlooked in developing countries, with misdiagnosis causing negative impacts on those with low income. Although the symptoms of brucellosis are commonly reported as fever and fatigue, rare pulmonary, and psychiatric involvements should also be considered. We present the first brucellosis patient in China with multiple pulmonary nodules and depression. Furthermore, this report highlights the importance of collecting patient history in epidemic areas of brucellosis.Case presentationWe report the case of a 40-year-old woman with intermittent fever for 2 months and gradually accompanied by chills, dry cough, arthralgia, and fatigue. The patient was also diagnosed with depression after fever. She received symptomatic treatment at a regional hospital; however, there was no significant symptom relief. She suddenly developed hemoptysis 1 day prior to arrival at our hospital, where we discovered that her liver, spleen, neck, and axillary lymph nodes were enlarged, and there were multiple nodules in both lungs. The patient was eventually diagnosed with brucellosis after the serum agglutination test and received antibiotic therapy, which provided symptom relief.ConclusionThis report describes a case of brucellosis with uncommon multipulmonary nodules and depression in China. This study has widened the evidence of respiratory involvement due to brucellosis. Second, it demonstrates the importance of collecting a comprehensive medical history, especially in epidemic areas. In conclusion, for febrile patients with pulmonary nodules and depression, especially in endemic areas, brucellosis should be considered.
Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms
Authors: Willemin Mathilde Stéphanie , Hamelin Romain , Armand Florence , Holliger Christof , Maillard Julien 
Published: January 2023

IntroductionDesulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use different electron donors and acceptors and to grow fermentatively. Desulfitobacterium genomes display numerous and apparently redundant members of redox enzyme families which confirm their metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified.MethodsIn the present work, we conducted an extended proteomic study by comparing the proteomes of Desulfitobacterium hafniense strain DCB-2 cultivated in combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. Tandem Mass Tag labelling proteomics allowed us to identify and quantify almost 60% of the predicted proteome of strain DCB-2 (2,796 proteins) in all six growth conditions. Raw data are available via ProteomeXchange with identifier PXD030393.Results and discussionThis dataset was analyzed in order to highlight the proteins that were significantly up-regulated in one or a subset of growth conditions and to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium – a very widespread practice in the cultivation of strictly anaerobic bacteria – triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favorable conditions such as fermentative growth on pyruvate, respiration with H2 as electron donor and OHR conditions. The presence of H2, CO2 and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters, as well as four new proteins related to corrinoid metabolism. We believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing future research questions.
Trends in the diagnostic delay and pathway for amyotrophic lateral sclerosis patients across different countries
Authors: Falcão de Campos Catarina , Gromicho Marta , Uysal Hilmi , Grosskreutz Julian , Kuzma-Kozakiewicz Magdalena , Oliveira Santos Miguel , Pinto Susana , Petri Susanne , Swash Michael , de Carvalho Mamede 
Published: January 2023

BackgroundAmyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disease with a median survival of 2–5 years. An early diagnosis is essential for providing ALS patients the finest management possible. Studies from different countries report a similar median diagnostic delay of around 12 months, which is still far from desirable. We analyzed the diagnostic pathway in different countries in order to identify the major challenges.MethodsWe studied a cohort of 1,405 ALS patients from five different centers, in four different countries (Turkey, Germany, Poland, and Portugal), which collaborated in a common database. Demographic, disease and sociocultural factors were collected. Time from first symptom onset to first medical evaluation and to diagnosis, the specialist assessment and investigations requested were analyzed. Factors contributing to diagnostic delay were evaluated by multivariate linear regression.ResultsThe median diagnostic delay from first symptom onset was 11 months and was similar between centers. Major differences were seen in the time from symptom onset to first medical evaluation. An earlier first medical evaluation was associated with a longer time to diagnosis, highlighting that ALS diagnosis is not straightforward in the early stages of the disease. The odds for ALS diagnosis were superior when evaluated by a neurologist and increased over time. Electromyography was decisive in establishing the diagnosis.ConclusionsWe suggest that a specific diagnostic test for ALS—a specific biomarker—will be needed to achieve early diagnosis. Early referral to a neurologist and to electromyography is important for early ALS diagnosis.
A radiomics-based study of deep medullary veins in infants: Evaluation of neonatal brain injury with hypoxic-ischemic encephalopathy via susceptibility-weighted imaging
Authors: Zhuang Xiamei , Jin Ke , Li Junwei , Yin Yan , Dong Xiao , Lin Huashan 
Published: January 2023

ObjectiveThe deep medullary veins (DMVs) can be evaluated using susceptibility-weighted imaging (SWI). This study aimed to apply radiomic analysis of the DMVs to evaluate brain injury in neonatal patients with hypoxic-ischemic encephalopathy (HIE) using SWI.MethodsThis study included brain magnetic resonance imaging of 190 infants with HIE and 89 controls. All neonates were born at full-term (37+ weeks gestation). To include the DMVs in the regions of interest, manual drawings were performed. A Rad-score was constructed using least absolute shrinkage and selection operator (LASSO) regression to identify the optimal radiomic features. Nomograms were constructed by combining the Rad-score with a clinically independent factor. Receiver operating characteristic curve analysis was applied to evaluate the performance of the different models. Clinical utility was evaluated using a decision curve analysis.ResultsThe combined nomogram model incorporating the Rad-score and clinical independent predictors, was better in predicting HIE (in the training cohort, the area under the curve was 0.97, and in the validation cohort, it was 0.95) and the neurologic outcomes after hypoxic-ischemic (in the training cohort, the area under the curve was 0.91, and in the validation cohort, it was 0.88).ConclusionBased on radiomic signatures and clinical indicators, we developed a combined nomogram model for evaluating neonatal brain injury associated with perinatal asphyxia.