bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of DNA repair-related genes predicting pathogenesis and prognosis for liver cancer
Authors: Zhu Wenjing , Zhang Qiliang , Liu Min , Yan Meixing , Chu Xiao , Li Yongchun 
Published: January 2021

AbstractBackgroundLiver cancer (LC) is one of the most fatal cancers throughout the world. More efficient and sensitive gene signatures that could accurately predict survival in LC patients are vitally needed to promote a better individualized and effective treatment.Material/methods422 LC and adjacent normal tissues with both RNA-Seq and clinical data in TCGA were embedded in our study. Gene set enrichment analysis (GSEA) was applied to identify genes and hallmark gene sets that are more valuable for liver cancer therapy. Cox regression analysis was used to identify genes related to overall survival (OS) and build the prediction model. cBioPortal database was used to examine the alterations of the panel mRNA signature. ROC curves and Kaplan–Meier curves were used to validate the prediction model. Besides, the expression of the genes in the model were validated using quantitative real-time PCR in clinical tissue specimens.ResultsThe panel of DNA repair-related mRNA signature consisted of seven mRNAs: RFC4 (replication factor C subunit 4), ZWINT (ZW10 interacting kinetochore protein), UPF3B (UPF3B regulator of nonsense mediated mRNA decay), NCBP2 (nuclear cap binding protein subunit 2), ADA (adenosine deaminase), SF3A3 (splicing factor 3a subunit 3) and GTF2H1 (general transcription factor IIH subunit 1). On-line analysis of cBioPortal database found that the expression of the panel mRNA has a wide variation ranging from 7 to 10%. All the mRNAs were significantly upregulated in LC tissues compared to normal tissues (P < 0.05). The risk model is closely related to the OS of LC patients. The hazard ratio (HR) is 2.184 [95% CI (confidence interval) 1.523–3.132] and log-rankP-value < 0.0001. For clinical specimen validation, we found that all of the genes in the model upregulated in liver cancer tissues versus normal liver tissues, which was consistent with the results predicted.ConclusionsOur study demonstrated a mRNA signature including seven mRNA for prognosis prediction of LC. This panel gene signature provides a new criterion for accurate diagnosis and therapeutic target of LC.
Treatment with therapeutic anticoagulation is not associated with immunotherapy response in advanced cancer patients
Authors: Johannet Paul , Sawyers Amelia , Gulati Nicholas , Donnelly Douglas , Kozloff Samuel , Qian Yingzhi , Floristan Alfredo , Hernando Eva , Zhong Judy , Osman Iman 
Published: January 2021

AbstractBackgroundRecent preclinical data suggest that there may be therapeutic synergy between immune checkpoint blockade and inhibition of the coagulation cascade. Here, we investigate whether patients who received immune checkpoint inhibitors (ICI) and were on concomitant anticoagulation (AC) experienced better treatment outcomes than individuals not on AC.Affiliation: Kindly confirm if corresponding authors affiliation is identified correctly.The corresponding author's affiliation is correct.MethodsWe studied a cohort of 728 advanced cancer patients who received 948 lines of ICI at NYU (2010–2020). Patients were classified based on whether they did (n = 120) or did not (n = 828) receive therapeutic AC at any point during their treatment with ICI. We investigated the relationship between AC status and multiple clinical endpoints including best overall response (BOR), objective response rate (ORR), disease control rate (DCR), progression free survival (PFS), overall survival (OS), and the incidence of bleeding complications.Affiliations: Journal instruction requires a country for affiliations; however, this is missing in affiliations 1 to 5. Please verify if the provided country is correct and amend if necessary.The country is correct for all affiliations (1 - 5).ResultsTreatment with AC was not associated with significantly different BOR (P = 0.80), ORR (P =0.60), DCR (P =0.77), PFS (P = 0.59), or OS (P =0.64). Patients who received AC were significantly more likely to suffer a major or clinically relevant minor bleed (P = 0.05).ConclusionAC does not appear to impact the activity or efficacy of ICI in advanced cancer patients. On the basis of our findings, we caution that there is insufficient evidence to support prospectively evaluating the combination of AC and immunotherapy.
Effectiveness of acupuncture on anxiety disorder: a systematic review and meta-analysis of randomised controlled trials
Authors: Yang Xiang-yun , Yang Ning-bo , Huang Fang-fang , Ren Shuai , Li Zhan-jiang 
Published: January 2021

AbstractBackgroundA number of studies have shown the positive effects of acupuncture on state anxiety. However, the efficacy of acupuncture in treating anxiety disorder remains unclear. This review and meta-analysis aimed to explore whether acupuncture has a positive effect on anxiety disorder.MethodsRandomised controlled trials (RCTs) published in English and Chinese were found through various electronic databases, including PubMed, Scopus, the Cochrane Central Register of Controlled Trials, Embase, and the Chinese databases WanFang data, VIP Chinese Sci tech periodical database, and China National Knowledge Infrastructure. The primary outcome variable was extent of anxiety symptoms. The secondary outcomes included side effects and dropout rate. Effect sizes were pooled by random-effects modelling using Rev Man 5.3.ResultsTwenty RCTs were included in this systematic review and meta-analysis. All included studies were designed for patients with generalised anxiety disorder (GAD), and 18 studies were published in Chinese. Egger’s test showed that the asymmetry of the funnel plot in all studies was not significant (t = − 0.34,p = 0.74). The meta-analysis of anxiety symptoms showed that acupuncture was more effective than the control condition, with a standard mean effect size of − 0.41 (95% CI − 0.50 to − 0.31;p < 0.001), and that acupuncture intervention showed good tolerance and safety in the treatment of anxiety disorder.ConclusionOur findings suggest that acupuncture therapy aimed at reducing anxiety in patients with GAD has certain beneficial effects compared to controls. More RCTs with high quality should be conducted to fully understand the role of acupuncture in the treatment of various types of anxiety disorder. The protocol of this review was registered at the Prospero International Prospective Register of Systematic Reviews (Registration ID: PROSPERO 2020CRD42020148536).
Polysaccharide from Angelica sinensis attenuates SNP-induced apoptosis in osteoarthritis chondrocytes by inducing autophagy via the ERK1/2 pathway
Authors: Xu Chao , Ni Su , Zhuang Chao , Li Chenkai , Zhao Gongyin , Jiang Shijie , Wang Liangliang , Zhu Ruixia , van Wijnen Andre J. , Wang Yuji 
Published: January 2021

Abstract
Objective
Chondrocyte apoptosis plays a vital role in osteoarthritis (OA) progression. Angelica sinensis polysaccharide (ASP), a traditional Chinese medicine, possesses anti-inflammatory and anti-apoptotic properties in chondrocytes. This study aimed to determine the protective role of ASP on sodium nitroprusside (SNP)-induced chondrocyte apoptosis, and explore the underlying mechanism.

Method
Human primary chondrocytes isolated from the articular cartilage of OA patients were treated with SNP alone or in combination with different doses of ASP. Cell viability and apoptosis were assessed, and apoptosis-related proteins including Bcl-2 and Bax were detected. Autophagy levels were evaluated by light chain 3 (LC3) II immunofluorescence staining, mRFP-GFP-LC3 fluorescence localization, and western blot (LC3II, p62, Beclin-1, Atg5). Meanwhile, activation of the ERK 1/2 pathway was determined by western blot. The autophagy inhibitors, 3-methyladenine (3-MA), chloroquine (CQ), and a specific inhibitor of ERK1/2, SCH772984, were used to confirm the autophagic effect of ASP.

Results
The results showed that SNP-induced chondrocyte apoptosis was significantly rescued by ASP, whereas ASP alone promoted chondrocyte proliferation. The anti-apoptotic effect of ASP was related to the enhanced autophagy and depended on the activation of the ERK1/2 pathway.

Conclusion
ASP markedly rescued SNP-induced apoptosis by activating ERK1/2-dependent autophagy in chondrocytes, and it made ASP as a potential therapeutic supplementation for OA treatment.
Age-dependent changes of gender disparities in nasopharyngeal carcinoma survival
Authors: Li Wang-Zhong , Lv Shu-Hui , Liu Guo-Ying , Liang Hu , Xia Wei-Xiong , Xiang Yan-Qun 
Published: January 2021

Abstract
Background
The mortality of nasopharyngeal carcinoma (NPC) is usually lower in females than in males, but the underlying mechanism remains largely unknown. We sought to describe the age-dependent patterns of gender disparities in NPC survival and explore the extent to which the confounder or mediation effects could explain these differences.

Methods
A total of 11,980 patients with NPC were reviewed. The effect of gender on cancer-specific survival (CSS) was assessed using Cox regression analyses. Two propensity score methods were conducted to control the confounding bias between genders. Restricted cubic spline regression was used to model the association of gender and age with mortality flexibly. Multiple mediation analysis was applied to estimate the direct or indirect effect of gender on CSS.

Results
Overall, 7026 males and 2320 females were analyzed. The crude CSS was significantly higher for females than males (10-year CSS 78.4% vs 70.3%; P < 0.001). Similar results were observed after adjusting for confounding bias. Gender disparities in NPC-specific mortality were age-dependent, where they would increase with age until peaking at age 55–60 years and decline rapidly afterward. Subgroup analyses revealed that females’ survival advantage was observed in the 18–45 age group and was more prominent in the 46–55 age group, but vanished in the > 55 age group. Either confounder or mediation effects only accounted for approximately 20% of the gender differences.

Conclusions
Gender disparities in cancer-specific mortality for patients with NPC were age-dependent. The differences mostly cannot be explained by confounder or mediation effects.
A mapping of facilitators and barriers to evidence-based management in health systems: a scoping review study
Authors: Shafaghat Tahereh , Imani Nasab Mohammad Hasan , Bahrami Mohammad Amin , Kavosi Zahra , Roozrokh Arshadi Montazer Mahsa , Rahimi Zarchi Mohammad Kazem , Bastani Peivand 
Published: January 2021

Abstract
Background
Healthcare settings are complex, and the decision-making process is usually complicated, too. Precise use of best evidence from different sources for increasing the desired outcomes is the result of EBM. Therefore, this study aimed to map the potential facilitators and barriers to EBM in health systems to help the healthcare managers to better implement EBM in their organizations.

Methods
The present study was a scoping review (SR) conducted in 2020 based on the integration of the frameworks presented by Arksey and O’Malley (2005) and Levac et al. (2010) considering the Joanna Briggs Institute guideline (2015). These frameworks consist of 6 steps. After finalizing the search strategy, 7 databases were searched, and the PRISMA-ScR was used to manage the retrieval and inclusion of the evidence. Microsoft Excel 2013 was used to extract the data, and the graphic description was presented. The summative analysis approach was used applying MAXQDA10.

Results
According to the systematic search, 4815 studies were retrieved after eliminating duplicates and unrelated articles, 49 articles remained to extract EBM facilitators and barriers. Six main aspects attitude toward EBM, external factors, contextual factors, resources, policies and procedures, and research capacity and data availability were summarized as EBM facilitators. The barriers to EBM were similarly summarized as attitude toward EBM, external factors, contextual factors, policies and procedures, limited resources, and research capacity and data availability. The streamgraphs describe that the international attention to the sub-aspects of facilitators and barriers of EBM has been increased since 2011.

Conclusions
The importance of decision-making regarding complex health systems, especially in terms of resource constraints and uncertainty conditions, requires EBM in the health system as much as possible. Identifying the factors that facilitate the use of evidence, as well as its barriers to management and decision-making in the organization, can play an important role in making systematic and reliable decisions that can be defended by the officials and ultimately lead to greater savings in organization resources and prevent them from being wasted.
Note on a discrete initial value problem from a competition
Authors: Stević Stevo 
Published: January 2021

AbstractThe following discrete initial value problem$$ x_{n+1}=x_{n}\bigl(x_{n-1}^{2}-2 \bigr)-x_{1},\quad n\in {\mathbb{N}}, $$xn+1=xn(xn−12−2)−x1,n∈N,$x_{0}=2$x0=2and$x_{1}=5/2$x1=5/2, appeared at an international competition. It is known that the problem can be solved in closed form. Here we discuss the solvability of a more general initial value problem which includes the former one. We show that, in a sense, there are not so many solvable discrete initial value problems related to this one, showing its specificity, which is a bit surprising result.
Emergency ward ultrasound: clinical audit on disinfection practices during routine and sterile examinations
Authors: Andolfo A. , Maatoug R. , Peiffer-Smadja N. , Fayolle C. , Blanckaert K. 
Published: January 2021

Abstract
Context
In the emergency ward, where the use of ultrasound is common (including for sterile procedures), ward equipment is constantly exposed to high risks of microbiological contamination. There are no clear guidelines for disinfection control practices in emergency departments, and it is not known how emergency ward doctors follow good hygiene practices.

Method
A multi-centre audit was conducted in 16 emergency services from Northern France regional hospitals, in form of a questionnaire. It was proposed to all emergency ward physicians. We excluded questionnaires when physicians mentioned that they did not use ultrasound on a daily basis. The questionnaire was designed using existing hygiene and ultrasound disinfection practices guidelines from varying French medical societies. It included three different clinical scenarios: (a) ultrasound on healthy skin, (b) on injured skin, and (c) ultrasound-guided punctures. All questions were closed-ended, with only one answer corresponding to the guidelines. We then calculated compliance rates for each question, each clinical situation, and an overall compliance rate for all the questions.

Results
104 questionnaires were collected, and 19 were excluded. For the 85 analysed questionnaires, the compliance rates were 60.4% 95% CI [56.4–64.7] for ultrasound on healthy skin, 70.9% 95% CI [66.3–76.1] on injured skin and 69.4% 95% CI [65.1–73.6] for ultrasound-guided punctures. The overall compliance rate for the compliance questions was 66.1% 95% CI [62.8–69.1]. Analysis of the questionnaires revealed severe asepsis errors, misuse of gel, ignorance of infection control practices to be applied in the context of ultrasound-guided puncture and exposure of the probe to body fluids.

Conclusion
This study details areas for quality improvement in the disinfection of emergency ultrasound scanner use. Consequently, we propose a standardized protocol based upon the recommendations used for the questionnaire drafting, with a visual focus on the low compliance points that have been revealed in this audit. This protocol has been distributed to all the medical emergency services audited and included in the emergency resident’s ultrasound learning program.
Accurate identification and quantification of commensal microbiota bound by host immunoglobulins
Authors: Jackson Matthew A. , Pearson Claire , Ilott Nicholas E. , Huus Kelsey E. , Hegazy Ahmed N. , Webber Jonathan , Finlay B. Brett , Macpherson Andrew J. , Powrie Fiona , Lam Lilian H. 
Published: January 2021

Abstract
Background
Identifying which taxa are targeted by immunoglobulins can uncover important host-microbe interactions. Immunoglobulin binding of commensal taxa can be assayed by sorting bound bacteria from samples and using amplicon sequencing to determine their taxonomy, a technique most widely applied to study Immunoglobulin A (IgA-Seq). Previous experiments have scored taxon binding in IgA-Seq datasets by comparing abundances in the IgA bound and unbound sorted fractions. However, as these are relative abundances, such scores are influenced by the levels of the other taxa present and represent an abstract combination of these effects. Diversity in the practical approaches of prior studies also warrants benchmarking of the individual stages involved. Here, we provide a detailed description of the design strategy for an optimised IgA-Seq protocol. Combined with a novel scoring method for IgA-Seq datasets that accounts for the aforementioned effects, this platform enables accurate identification and quantification of commensal gut microbiota targeted by host immunoglobulins.

Results
Using germ-free and Rag1−/− mice as negative controls, and a strain-specific IgA antibody as a positive control, we determine optimal reagents and fluorescence-activated cell sorting (FACS) parameters for IgA-Seq. Using simulated IgA-Seq data, we show that existing IgA-Seq scoring methods are influenced by pre-sort relative abundances. This has consequences for the interpretation of case-control studies where there are inherent differences in microbiota composition between groups. We show that these effects can be addressed using a novel scoring approach based on posterior probabilities. Finally, we demonstrate the utility of both the IgA-Seq protocol and probability-based scores by examining both novel and published data from in vivo disease models.

Conclusions
We provide a detailed IgA-Seq protocol to accurately isolate IgA-bound taxa from intestinal samples. Using simulated and experimental data, we demonstrate novel probability-based scores that adjust for the compositional nature of relative abundance data to accurately quantify taxon-level IgA binding. All scoring approaches are made available in the IgAScores R package. These methods should improve the generation and interpretation of IgA-Seq datasets and could be applied to study other immunoglobulins and sample types.
Convergent lines of evidence support BIN1 as a risk gene of Alzheimer’s disease
Authors: Zhu Jin , Liu Xia , Yin Hongtao , Gao Yan , Yu Hao 
Published: January 2021

AbstractGenome-wide association studies (GWAS) have identified several susceptibility loci of Alzheimer’s disease (AD), which were mainly located in noncoding regions of the genome. Meanwhile, the putative biological mechanisms underlying AD susceptibility loci were still unclear. At present, identifying the functional variants of AD pathogenesis remains a major challenge. Herein, we first used summary data-based Mendelian randomization (SMR) with AD GWAS summary and expression quantitative trait loci (eQTL) data to identify variants who affects expression levels of nearby genes and contributed to the risk of AD. Using the SMR integrative analysis, we totally identified 14 SNPs significantly affected the expression level of 16 nearby genes in blood or brain tissues and contributed to the AD risk. Then, to confirm the results, we replicated the GWAS and eQTL results across multiple samples. Totally, four risk SNP (rs11682128, rs601945, rs3935067, and rs679515) were validated to be associated with AD and affected the expression level of nearby genes (BIN1, HLA-DRA, EPHA1-AS1, and CR1). Besides, our differential expression analysis showed that the BIN1 gene was significantly downregulated in the hippocampus (P = 2.0 × 10−3) and survived after multiple comparisons. These convergent lines of evidence suggest that the BIN1 gene identified by SMR has potential roles in the pathogenesis of AD. Further investigation of the roles of the BIN1 gene in the pathogenesis of AD is warranted.
Outgrowth of a CSF3R-mutant clone drives a second myeloproliferative neoplasm in a chronic myeloid leukemia patient: a case report
Authors: Carratt Sarah A. , Brewer Diana , Maxson Julia E. , Druker Brian J. , Braun Theodore P. 
Published: January 2021

Abstract
Background
Chronic myeloid leukemia (CML) and chronic neutrophilic leukemia (CNL) are two myeloproliferative neoplasms with mutually exclusive diagnostic criteria. A hallmark of CML is the Philadelphia chromosome (Ph), which results in a BCR-ABL1 fusion gene and constitutive tyrosine kinase activity. CNL is a Ph-negative neoplasm and is defined in part by the presence of CSF3R mutations, which drive constative JAK/STAT signaling.

Case presentation
Here, we report the exceedingly rare co-occurrence of two granulocytic myeloproliferative neoplasms in a 69-year old male patient. After an initial diagnosis of chronic myeloid leukemia, the patient’s clinical course was shaped by hematologic toxicity, the emergence of treatment-resistant BCR-ABL1 clones, and the expansion of a CSF3R-mutant clone without ABL1 mutations under selective pressure from tyrosine kinase inhibitors. The emergence of the CSF3R-mutant, neutrophilic clone led to the diagnosis of CNL as a second myeloproliferative neoplasm in the same patient.

Conclusions
This is the first reported case of CNL arising subsequent to CML, which occurred under selective pressure from targeted therapy in a patient with complex clonal architecture. Patients with such molecularly complex disease may ultimately benefit from combination therapy that targets multiple oncogenic pathways.
Cotton stalk-derived hydrothermal carbon for methylene blue dye removal: investigation of the raw material plant tissues
Authors: Zhang Libo , Tan Junyan , Xing Gangying , Dou Xintong , Guo Xuqiang 
Published: January 2021

AbstractConversion of the abundant agricultural residual cotton stalk (CS) into useful chemicals or functional materials could alleviate the fossil fuels caused energy shortages and environmental crises. Although some advances have been achieved, less attention has been paid to the plant tissues effect. In this study, the plant tissue of CS was changed by part degradation of some components (hemicelluloses and lignin, for example) with the aid of acid/base (or both). The pretreated CS was transformed into hydrochar by hydrothermal carbonization (HTC) method. Morphological and chemical compositions of CS hydrochar were analyzed by various techniques, including elemental analysis, Fourier transform infrared (FTIR), BET analysis, X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD). Methylene blue (MB) removal of prepared CS hydrochar was used to evaluate CS hydrochar pollutions adsorption capacity. Results reveal acid/base (or both) pretreatment is beneficial for CS raw material to prepare high-quality CS hydrochar. The effects of some parameters, such as initial MB concentration, temperature, pH value and recyclability on the adsorption of MB onto both acid and base-pretreated CS hydrochar (CS-H2SO4 + NaOH-HTC) were studied. The present work exhibits the importance of agricultural waste biomass material plant tissues on its derived materials, which will have a positive effect on the direct utilization of waste biomass.