bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural History of Type II Autosomal Dominant Osteopetrosis: A Single Center Retrospective Study
Authors: Wang Ziyuan , Li Xiang , Wang Ya , Fu Wenzhen , Liu Yujuan , Zhang Zhenlin , Wang Chun 
Published: March 2022

BackgroundAutosomal dominant osteopetrosis II (ADO II, MIM166600) is a sclerosing bone disorder caused by CLCN7 mutation. The main clinical characteristics include minor trauma-related fracture and hip osteoarthritis, whereas cranial nerve palsy and bone marrow failure rarely develop. Although it is generally believed that ADO II has a relatively benign course, the natural course of the disease in Chinese patients remains unclear.Materials and MethodsThirty-six patients diagnosed with ADO II in Shanghai Jiao Tong University Affiliated Sixth People’s Hospital from 2008 to 2021 were studied retrospectively. Among them, 15 patients were followed for an average of 6.3 years (1-14 years).ResultsIn this study, minor trauma-related fractures of the limb were the most typical clinical manifestations. Visual loss (1/36) and bone marrow failure (2/36), was rare in this study. The condition of ADO II seems to be stable in most patients. There were no correlations between markedly elevated bone mineral density (BMD) and minor trauma-related fractures. In total, 21 diseases causing mutations were detected. Among them, the mutation c.2299C&gt;T (p.Arg767Trp) was the most common (16.67%), and mutation c.937G&gt;A [p.(Glu313Lys)] was associated with severe fractures, haematological defects and cranial palsy.ConclusionsMinor trauma-related fracture is the most typical clinical manifestation of ADO II and always occurs in. The mutation c.2299C&gt;T (p.Arg767Trp) is in general a relatively common variant, while the mutation c.937G&gt;A [p.(Glu313Lys)] seems to be associated with severe phenotype. In our study, ADO II seems to remain stable over time.
A Model for Predicting Polycystic Ovary Syndrome Using Serum AMH, Menstrual Cycle Length, Body Mass Index and Serum Androstenedione in Chinese Reproductive Aged Population: A Retrospective Cohort Study
Authors: Xu Huiyu , Feng Guoshuang , Alpadi Kannan , Han Yong , Yang Rui , Chen Lixue , Li Rong , Qiao Jie 
Published: March 2022

BackgroundA clinical diagnosis of polycystic ovary syndrome (PCOS) can be tedious with many different required tests and examinations. Furthermore, women with PCOS have increased risks for several metabolic complications, which need long-term health management. Therefore, we attempted to establish an easily applicable model to identify such women at an early stage.ObjectiveTo develop an easy-to-use tool for screening PCOS based on medical records from a large assisted reproductive technology (ART) center in China.Materials and MethodsA retrospective observational cohort from Peking University Third Hospital was used in the study. Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression with 10-fold cross-validation was applied to construct the model. The area under the receiver operating characteristic curve (AUC), sensitivity, and specificity values were used to evaluate and compare the models.Design, Setting, and ParticipantsThis retrospective cohort study included 21,219 ovarian stimulation cycle records from January to December 2019 in Peking University Third Hospital.Main Outcomes and MeasuresThe main outcome was whether there was a clinical diagnosis of PCOS. The independent variables included were age, body mass index (BMI), upper limit of menstrual cycle length (UML), basal serum levels of anti-Müllerian hormone (AMH), testosterone androstenedione, antral follicle counts et al.ResultsWe have established a new mathematical model for diagnosing PCOS using serum AMH and androstenedione levels, UML, and BMI, with AUC values of 0.855 (0.838–0.870), 0.848 (0.791–0.891), 0.846 (0.812–0.875) in the training, validation, and testing sets, respectively. The contribution of each predictor to this model were: AMH 41.2%; UML 35.2%; BMI 4.3%; and androstenedione 3.7%. The top 10 groups of women most predicted to develop PCOS were demonstrated. An online tool (http://121.43.113.123:8888/) has been developed to assist Chinese ART clinics.ConclusionsThe models and online tool we established here might be helpful for screening and identifying women with undiagnosed PCOS in Asian populations and could assist in the long-term management of related metabolic disorders.
Genetic Predispositions Between COVID-19 and Three Cardio-Cerebrovascular Diseases
Authors: Tan Jiang-Shan , Liu Ningning , Guo Ting-Ting , Hu Song , Hua Lu , Qian Qiujin 
Published: March 2022

Aims: This study was aimed to apply a Mendelian randomization design to explore the causal association between coronavirus disease 2019 (COVID-19) and three cardio-cerebrovascular diseases, including atrial fibrillation, ischemic stroke, and coronary artery disease.Methods: Two-sample Mendelian randomization was used to determine the following: 1) the causal effect of COVID-19 on atrial fibrillation (55,114 case participants vs 482,295 control participants), coronary artery disease (34,541 case participants vs 261,984 control participants), and ischemic stroke (34,217 case participants vs 40,611 control participants), which were obtained from the European Bioinformatics Institute, and 2) the causal effect of three cardio-cerebrovascular diseases on COVID-19. The single-nucleotide polymorphisms (SNPs) of COVID-19 were selected from the summary-level genome-wide association study data of COVID-19-hg genome-wide association study (GWAS) meta-analyses (round 5) based on the COVID-19 Host Genetics Initiative for participants with European ancestry. The random-effects inverse-variance weighted method was conducted for the main analyses, with a complementary analysis of the weighted median and Mendelian randomization (MR)-Egger approaches.Results: Genetically predicted hospitalized COVID-19 was suggestively associated with ischemic stroke, with an odds ratio (OR) of 1.049 [95% confidence interval (CI) 1.003–1.098; p = 0.037] in the COVID-19 Host Genetics Initiative GWAS. When excluding the UK Biobank (UKBB) data, our analysis revealed a similar odds ratio of 1.041 (95% CI 1.001–1.082; p = 0.044). Genetically predicted coronary artery disease was associated with critical COVID-19, with an OR of 0.860 (95% CI 0.760–0.973; p = 0.017) in the GWAS meta-analysis and an OR of 0.820 (95% CI 0.722–0.931; p = 0.002) when excluding the UKBB data, separately. Limited evidence of causal associations was observed between critical or hospitalized COVID-19 and other cardio-cerebrovascular diseases included in our study.Conclusion: Our findings provide suggestive evidence about the causal association between hospitalized COVID-19 and an increased risk of ischemic stroke. Besides, other factors potentially contribute to the risk of coronary artery disease in patients with COVID-19, but not genetics.
An Effective Hypoxia-Related Long Non-Coding RNA Assessment Model for Prognosis of Lung Adenocarcinoma
Authors: Li Yuanshuai , Sun Xiaofang 
Published: March 2022

Background: Lung adenocarcinoma (LUAD) represents one of the highest incidence rates worldwide. Hypoxia is a significant biomarker associated with poor prognosis of LUAD. However, there are no definitive markers of hypoxia-related long non-coding RNAs (lncRNAs) in LUAD.Methods: From The Cancer Genome Atlas (TCGA) and the Molecular Signatures Database (MSigDB), we acquired the expression of hypoxia-related lncRNAs and corresponding clinical information of LUAD patients. The hypoxia-related prognostic model was constructed by univariable COX regression analysis, least absolute shrinkage and selection operator (LASSO), and multivariable Cox regression analysis. To assess the performance of the model, the Kaplan–Meier (KM) survival and receiver operating characteristic (ROC) curve analyses were performed.Results: We found seven lncRNAs, AC022613.1, AC026355.1, GSEC, LINC00941, NKILA, HSPC324, and MYO16-AS1, as biomarkers of the potential hypoxia-related prognostic signature. In the low-risk group, patients had a better overall survival (OS). In addition, the results of ROC analysis indicated that the risk score predicted LUAD prognosis exactly. Furthermore, combining the expression of lncRNAs with clinical features, two predictive nomograms were constructed, which could accurately predict OS and had high clinical application value.Conclusion: In summary, the seven-lncRNA prognostic signature related to hypoxia might be useful in predicting clinical outcomes and provided new molecular targets for the research of LUAD patients.
Hybrid RNA Sequencing Strategy for the Dynamic Transcriptomes of Winter Dormancy in an Evergreen Herbaceous Perennial, Iris japonica
Authors: Li Danqing , Shao Lingmei , Xu Tong , Wang Xiaobin , Zhang Runlong , Zhang Kaijing , Xia Yiping , Zhang Jiaping 
Published: March 2022

Japanese iris (Iris japonica) is a popular perennial ornamental that originated in China; it has a long display period and remains green outdoors throughout the year. winter dormancy characteristics contribute greatly to the evergreenness of herbaceous perennials. Thus, it is crucial to explore the mechanism of winter dormancy in this evergreen herbaceous perennial. Here, we used the hybrid RNA-seq strategy including single-molecule real-time (SMRT) and next-generation sequencing (NGS) technologies to generate large-scale Full-length transcripts to examine the shoot apical meristems of Japanese iris. A total of 10.57 Gb clean data for SMRT and over 142 Gb clean data for NGS were generated. Using hybrid error correction, 58,654 full-length transcripts were acquired and comprehensively analysed, and their expression levels were validated by real-time qPCR. This is the first full-length RNA-seq study in the Iris genus; our results provide a valuable resource and improve understanding of RNA processing in this genus, for which little genomic information is available as yet. In addition, our data will facilitate in-depth analyses of winter dormancy mechanisms in herbaceous perennials, especially evergreen monocotyledons.
Identification of Four Novel COL4A5 Variants and Detection of Splicing Abnormalities in Three Chinese X-Linked Alport Syndrome Families
Authors: Wang Sai , Shao Yingfei , Wang Yixiu , Lu Jingru , Shao Leping 
Published: March 2022

Chronic renal disease associated with X-linked Alport syndrome (XLAS) is relatively rare. However, due to the lack of specificity in the pathologic and clinical manifestations of the disease, it is easy to be misdiagnosed. In this study, we included three Chinese families with XLAS and used targeted NGS to find gene variants. In family X1, the 36-year-old male proband had hematuria, massive proteinuria, sensorineural deafness and ESRD at 33. In silico prediction showed the novel c.1424-4C &gt; G variant reduced the score of the normal 3’ splice site from 0.47 to 0.00 (according to BDGP). Transcriptional analysis from his peripheral blood cells indicated that it caused the insertion of an amino acid [p.(Lys474_Gly475insVal)]. In family X2, the proband was a 32-year-old male, who had hematuria, proteinuria, hypertension, hearing loss and progressed into ESRD at 30 years. He carried a novel missense variant c.2777G &gt; T p.(Gly926Val). In family X3, the proband, a 16-year-old male, had hematuria, massive proteinuria, sensorineural deafness and ESRD; the results of renal pathological findings were consistent with AS. He carried a novel variant c.4529-2A &gt; T, so did his mother with ESRD and probable XLAS. Bioinformatic analysis with BDGP showed that it abolished the acceptor site from 0.83 to 0.00. RT-PCR analysis from his kidney tissue indicated that it caused exon 50 skipping and exon 50 skipping along with inserting a cryptic exon derived from intron 49 p.[Gly1510Aspfs*11, Gly1510Alafs*35]. Another novel missense variant c.1552G &gt; A p.(Gly518Arg) was identified in his mother and his aunt. No skewed X-chromosome inactivation was involved in these two female patients. In conclusion, four novel variants in COL4A5 were identified and transcriptional analysis is essential to investigate the pathogenicity of intronic variants. Thus we found a rare event in a female patient with XLAS caused by two COL4A5 variants in trans.
Tenascin-C can Serve as an Indicator for the Immunosuppressive Microenvironment of Diffuse Low-Grade Gliomas
Authors: Zhang Po , Liu Guohao , Hu Jinyang , Chen Sui , Wang Baofeng , Peng Peng , Yu Xingjiang , Guo Dongsheng 
Published: March 2022

PurposeThe development and progression of glioma are associated with the tumor immune microenvironment. Diffuse low-grade gliomas (LGGs) with higher immunosuppressive microenvironment tend to have a poorer prognosis. The study aimed to find a biological marker that can reflect the tumor immune microenvironment status and predict prognosis of LGGs.MethodsThe target gene tenascin-C (TNC) was obtained by screening the Chinese Glioma Genome Atlas (CGGA) and the Cancer Genome Atlas (TCGA) databases. Then samples of LGGs were collected for experimental verification with immunohistochemistry, immunofluorescence, immunoblotting, quantitative real-time PCR. ELISA was employed to determine the content of TNC in serum and examine its relationship with the tumor immune microenvironment. Eventually, the sensitivity of immunotherapy was predicted on the basis of the content of TNC in LGGs.ResultsIn the high-TNC subgroup, the infiltration of immunosuppressive cells was increased (MDSC: r=0.4721, Treg: r=0.3154, etc.), and immune effector cells were decreased [NKT, γδT, etc. (p&lt;0.05)], immunosuppressive factors were elevated [TGF-β, IL10, etc. (p&lt;0.05)], immunostimulatory factors, such as NKG2D, dropped (p&lt;0.05), hypoxia scores increased (p&lt;0.001), and less benefit from immunotherapy (p&lt;0.05). Serum TNC level could be used to assess the status of tumor immune microenvironment in patients with grade II (AUC=0.8571; 95% CI: 0.6541-1.06) and grade III (AUC=0.8333; 95% CI: 0.6334-1.033) glioma.ConclusionsOur data suggested that TNC could serve as an indicator for the immunosuppressive microenvironment status and the prognosis of LGGs. Moreover, it could also act as a predictor for the effect of immunotherapy on LGG patients.
CD56-Negative Extranodal Natural Killer/T-Cell Lymphoma: A Retrospective Study in 443 Patients Treated by Chemotherapy With or Without Asparaginase
Authors: Yang Jing , Li Pengfei , Piao Yingshi , Liu Xindi , Wei Liqiang , Sang Wei , Zhang Luo , Wang Liang 
Published: March 2022

ObjectiveExtranodal natural killer/T cell lymphoma (NKTCL) is an aggressive EBV-related lymphoma, originating from NK cells or T cells. Previous study demonstrated that CD56 negative NKTCL should be recognized as a distinct subtype. In this study, the value of CD56 in NKTCL is validated in the era of asparaginase, and genomic analysis was done to dissect the differences between CD56-negative and positive NKTCL.Methods443 patients with newly diagnosed NKTCL were enrolled in this retrospective study, and correlation between CD56 positivity and survival outcomes was analyzed. The gene sequencing data was downloaded (http://www.biosino.org/node/project/detail/OEP000498), and bioinformatics analysis was done to delineate the tumor microenvironment and differentially expressed genes.ResultsCD56 was expressed in 337 patients (76.1%). Within a median follow-up time of 51 months, the 5-year overall survival (OS) and progression free survival (PFS) rates were 63.8% and 51.9%, respectively. For the whole cohort, patients who were CD56-positive had superior OS (5-year OS, 86.2% vs. 51.9%, p=0.019) and PFS (5-year PFS, 55.9% vs. 40.1%, p=0.016). For patients in early stage disease, CD56 positivity was associated with superior OS and PFS (p=0.008 and 0.005, respectively). In patients who received non-asparaginase-based chemotherapy, CD56-negative was associated with shorter OS and PFS (p&lt;0.001), and in patients who received asparaginase-based chemotherapy, CD56-negative was not related to inferior OS and PFS (p=0.093 and p=0.829, respectively). The genomic analysis demonstrated that CD56 positive NKTCL probably originated from NK cells and CD56 negative NKTCL originated from T cells. CD56 positive NKTCL had significantly higher proportion of resting NK cells, activated NK cells, and activated CD8+ and CD4+ T cells in the tumor microenvironment.ConclusionsCD56 negative NKTCL differs from CD56 positive NKTCL in both the tumor microenvironment and survival outcomes, and asparaginase-based treatment may overcome the poor prognosis brought by CD56 negativity.
Plasma Markers of Neutrophil Extracellular Trap Are Linked to Survival but Not to Pulmonary Embolism in COVID-19-Related ARDS Patients
Authors: Prével Renaud , Dupont Annabelle , Labrouche-Colomer Sylvie , Garcia Geoffrey , Dewitte Antoine , Rauch Antoine , Goutay Julien , Caplan Morgan , Jozefowicz Elsa , Lanoix Jean-Philippe , Poissy Julien , Rivière Etienne , Orieux Arthur , Malvy Denis , Gruson Didier , Garçon Loic , Susen Sophie , James Chloé 
Published: March 2022

IntroductionCoronavirus disease 2019 (COVID-19) can cause life-threatening acute respiratory distress syndrome (ARDS). Recent data suggest a role for neutrophil extracellular traps (NETs) in COVID-19-related lung damage partly due to microthrombus formation. Besides, pulmonary embolism (PE) is frequent in severe COVID-19 patients, suggesting that immunothrombosis could also be responsible for increased PE occurrence in these patients. Here, we evaluate whether plasma levels of NET markers measured shorty after admission of hospitalized COVID-19 patients are associated with clinical outcomes in terms of clinical worsening, survival, and PE occurrence.Patients and MethodsNinety-six hospitalized COVID-19 patients were included, 50 with ARDS (severe disease) and 46 with moderate disease. We collected plasma early after admission and measured 3 NET markers: total DNA, myeloperoxidase (MPO)–DNA complexes, and citrullinated histone H3. Comparisons between survivors and non-survivors and patients developing PE and those not developing PE were assessed by Mann–Whitney test.ResultsAnalysis in the whole population of hospitalized COVID-19 patients revealed increased circulating biomarkers of NETs in patients who will die from COVID-19 and in patients who will subsequently develop PE. Restriction of our analysis in the most severe patients, i.e., the ones who enter the hospital for COVID-19-related ARDS, confirmed the link between NET biomarker levels and survival but not PE occurrence.ConclusionOur results strongly reinforce the hypothesis that NETosis is an attractive therapeutic target to prevent COVID-19 progression but that it does not seem to be linked to PE occurrence in patients hospitalized with COVID-19.
Relationship Between Endothelial and Angiogenesis Biomarkers Envisage Mortality in a Prospective Cohort of COVID-19 Patients Requiring Respiratory Support
Authors: Maldonado Felipe , Morales Diego , Díaz-Papapietro Catalina , Valdés Catalina , Fernandez Christian , Valls Nicolas , Lazo Marioli , Espinoza Carolina , González Roberto , Gutiérrez Rodrigo , Jara Álvaro , Romero Carlos , Cerda Oscar , Cáceres Mónica 
Published: March 2022

PurposeEndothelial damage and angiogenesis are fundamental elements of neovascularisation and fibrosis observed in patients with coronavirus disease 2019 (COVID-19). Here, we aimed to evaluate whether early endothelial and angiogenic biomarkers detection predicts mortality and major cardiovascular events in patients with COVID-19 requiring respiratory support.MethodsChanges in serum syndecan-1, thrombomodulin, and angiogenic factor concentrations were analysed during the first 24 h and 10 days after COVID-19 hospitalisation in patients with high-flow nasal oxygen or mechanical ventilation. Also, we performed an exploratory evaluation of the endothelial migration process induced by COVID-19 in the patients' serum using an endothelial cell culture model.ResultsIn 43 patients, mean syndecan-1 concentration was 40.96 ± 106.9 ng/mL with a 33.9% increase (49.96 ± 58.1 ng/mL) at day 10. Both increases were significant compared to healthy controls (Kruskal–Wallis p &lt; 0.0001). We observed an increase in thrombomodulin, Angiopoietin-2, human vascular endothelial growth factor (VEGF), and human hepatocyte growth factor (HGF) concentrations during the first 24 h, with a decrease in human tissue inhibitor of metalloproteinases-2 (TIMP-2) that remained after 10 days. An increase in human Interleukin-8 (IL-8) on the 10th day accompanied by high HGF was also noted. The incidence of myocardial injury and pulmonary thromboembolism was 55.8 and 20%, respectively. The incidence of in-hospital deaths was 16.3%. Biomarkers showed differences in severity of COVID-19. Syndecan-1, human platelet-derived growth factor (PDGF), VEGF, and Ang-2 predicted mortality. A multiple logistic regression model with TIMP-2 and PDGF had positive and negative predictive powers of 80.9 and 70%, respectively, for mortality. None of the biomarkers predicted myocardial injury or pulmonary thromboembolism. A proteome profiler array found changes in concentration in a large number of biomarkers of angiogenesis and chemoattractants. Finally, the serum samples from COVID-19 patients increased cell migration compared to that from healthy individuals.ConclusionWe observed that early endothelial and angiogenic biomarkers predicted mortality in patients with COVID-19. Chemoattractants from patients with COVID-19 increase the migration of endothelial cells. Trials are needed for confirmation, as this poses a therapeutic target for SARS-CoV-2.
Modified Intraperitoneal Chemotherapy Without Bevacizumab as a First-Line Therapy for Newly Diagnosed Advanced Epithelial Ovarian Cancer-Two Centers Experiences
Authors: Shen Yuanming , Tang Sangsang , Xu Junfen , Xie Xing , Chen Zhongbo 
Published: March 2022

ObjectivesTo evaluate whether the modified intraperitoneal plus intravenous chemotherapy regimen as a first-line therapy for advanced epithelial ovarian cancer (EOC) in China can be well-tolerated or confer any potential benefit on survival.MethodsWe evaluated the outcomes of women with newly diagnosed advanced-stage III-IV EOC treated with optimal cytoreductive surgery (&lt;1 cm) and subsequent intraperitoneal plus intravenous chemotherapy or intravenous chemotherapy from January 2005 to December 2017 at two Gynecologic Oncology Centers in China. Kaplan-Meier survival analysis and Cox regression multivariate analysis models were performed to determine the toxicities and survival outcomes.ResultsA total of 463 patients with stage III-IV EOC were enrolled. According to the propensity scores (1:2), 85 patients who received intraperitoneal plus intravenous chemotherapy (group A) were matched to 170 patients who received intravenous chemotherapy (group B). The median follow-up time was 41 months (range 6–155 months). However, there was no statistically significant difference in the median progression-free survival (PFS) (20 vs. 22 months, P = 0.351) or 3-year overall survival (OS) rate (80 vs. 78%, P = 0.749) between the two groups. R0 primary cytoreductive surgery was the only factor related to PFS (P = 0.028) and OS (P = 0.005) by Cox regression analysis. The incidence of grade 3/4 adverse events did not significantly differ between the two groups.ConclusionThe efficacy of intraperitoneal chemotherapy mainly comes from the intraperitoneal drug dose intensity and cumulative dose. High-efficiency and low-toxicity intraperitoneal chemotherapy regimens still need to be found and validated.