bluuebunny/crossref_metadata_2025_split huggingface dataset:
NanoCoV19: An analytical pipeline for rapid detection of severe acute respiratory syndrome coronavirus 2
Authors: Lang Jidong 
Published: September 2022

Nanopore sequencing technology (NST) has become a rapid and cost-effective method for the diagnosis and epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic. Compared with short-read sequencing platforms (e.g., Illumina’s), nanopore long-read sequencing platforms effectively shorten the time required to complete the detection process. However, due to the principles and data characteristics of NST, the accuracy of sequencing data has been reduced, thereby limiting monitoring and lineage analysis of SARS-CoV-2. In this study, we developed an analytical pipeline for SARS-CoV-2 rapid detection and lineage identification that integrates phylogenetic-tree and hotspot mutation analysis, which we have named NanoCoV19. This method not only can distinguish and trace the lineages contained in the alpha, beta, delta, gamma, lambda, and omicron variants of SARS-CoV-2 but is also rapid and efficient, completing overall analysis within 1 h. We hope that NanoCoV19 can be used as an auxiliary tool for rapid subtyping and lineage analysis of SARS-CoV-2 and, more importantly, that it can promote further applications of NST in public-health and -safety plans similar to those formulated to address the COVID-19 outbreak.
STS-BN: An efficient Bayesian network method for detecting causal SNPs
Authors: Ma Yanran , Fa Botao , Yuan Xin , Zhang Yue , Yu Zhangsheng 
Published: September 2022

Background: The identification of the causal SNPs of complex diseases in large-scale genome-wide association analysis is beneficial to the studies of pathogenesis, prevention, diagnosis and treatment of these diseases. However, existing applicable methods for large-scale data suffer from low accuracy. Developing powerful and accurate methods for detecting SNPs associated with complex diseases is highly desired.Results: We propose a score-based two-stage Bayesian network method to identify causal SNPs of complex diseases for case-control designs. This method combines the ideas of constraint-based methods and score-and-search methods to learn the structure of the disease-centered local Bayesian network. Simulation experiments are conducted to compare this new algorithm with several common methods that can achieve the same function. The results show that our method improves the accuracy and stability compared to several common methods. Our method based on Bayesian network theory results in lower false-positive rates when all correct loci are detected. Besides, real-world data application suggests that our algorithm has good performance when handling genome-wide association data.Conclusion: The proposed method is designed to identify the SNPs related to complex diseases, and is more accurate than other methods which can also be adapted to large-scale genome-wide analysis studies data.
Case Report: Necrotizing fasciitis caused by Staphylococcus aureus positive for a new sequence variant of exfoliative toxin E
Authors: Sabat Artur J. , Wouthuyzen-Bakker Marjan , Rondags Angelique , Hughes Laura , Akkerboom Viktoria , Koutsopetra Olga , Friedrich Alexander W. , Bathoorn Erik 
Published: September 2022

Objectives: Necrotizing fasciitis (NF) caused by S. aureus is a rare, aggressive and rapidly progressing superficial fascia infection with a high mortality rate. The aim of this study was to identify virulence-related genes from a complete genome sequence of a methicillin-susceptible S. aureus (MSSA) isolate recovered from a monomicrobial case of NF.Materials and methods: The MSSA isolate UMCG579 was cultured from a pus collection from the subcutis of a patient with NF. The genome of isolate UMCG579 was sequenced using MinION (Oxford Nanopore) and MiSeq (illumina) platforms.Results: The genome of the UMCG579 isolate was composed of a 2,741,379 bp chromosome and did not harbor any plasmids. Virulence factor profiling identified multiple pore-forming toxin genes in the UMCG579 chromosome, including the Panton-Valentine leukocidin (PVL) genes, and none of the superantigen genes. The UMCG579 isolate harbored a new sequence variant of the recently described ete gene encoding exfoliative toxin (type E). A search in the GenBank database revealed that the new sequence variant (ete2) was exclusively found among isolates (n = 115) belonging to MLST CC152. While the majority of S. aureus ete-positive isolates were recovered from animal sources, S. aureus ete2-positive isolates originated from human carriers and human infections. Comparative genome analysis revealed that the ete2 gene was located on a 8777 bp genomic island.Conclusion: The combination of two heterogeneously distributed potent toxins, ETE2 and PVL, is likely to enhance the pathogenic ability of S. aureus isolates. Since anti-virulence therapies for the treatment of S. aureus infections continue to be explored, the understanding of specific pathogenetic mechanisms may have an important prophylactic and therapeutic value. Nevertheless, the exact contribution of ETE sequence variants to S. aureus virulence in NF infections must be determined.
Prognosis and immune infiltration analysis of endoplasmic reticulum stress-related genes in bladder urothelial carcinoma
Authors: Wang Yaxuan , Zhu Haixia , Wang Xiaolin 
Published: September 2022

Background: Abnormal activation of endoplasmic reticulum (ER) stress sensors and their downstream signalling pathways is a key regulator of tumour growth, tumour metastasis and the response to chemotherapy, targeted therapy and immunotherapy. However, the study of ER stress on the immune microenvironment of bladder urothelial carcinoma (BLCA) is still insufficient.Methods: Firstly, 23 ER stress genes were selected to analyse their expression differences and prognostic value in BLCA based on the existing BLCA genome atlas data. According to the expression level of ER stress-related genes in BLCA, two independent clusters were identified using consensus cluster analysis. Subsequently, the correlation between these two clusters in terms of the immune microenvironment and their prognostic value was analysed. Finally, we analysed the prognostic value of the key ER stress gene HSP90B1 in BLCA and its corresponding mechanism that affects the immune microenvironment.Results: Consensus clustering showed a worse prognosis and higher expression of immunoassay site-related genes (HAVCR2, PDCD1, CTLA4, CD274, LAG3, TIGIT and PDCD1LG2) in cluster 1 compared with cluster 2. Additionally, both TIMER and CIBERSORT algorithms showed that the expression of immune infiltrating cells in cluster 1 was significantly higher than that in cluster 2. Subsequently, HSP90B1 was identified as a key ER stress gene in BLCA, and its high expression indicated poor prognosis and was closely related to PD1. We also analysed the correlation between HSP90B1 expression and immune-infiltrating cell related biomarkers, which showed positive results. Finally, we verified the prognostic value of HSP90B1 in BLCA using an immunohistochemical assay in a tissue microarray of 100 patients with BLCA, validating the potential of HSP90B1 as a prognostic biomarker in patients with BLCA.Conclusion: Our work reveals that ER stress genes play a crucial role in the BLCA immunological milieu, and HSP90B1 is a potential prognostic biomarker and therapeutic target for cancer immunotherapy.
A comprehensive pancancer analysis reveals the potential value of RAR-related orphan receptor C (RORC) for cancer immunotherapy
Authors: He Shengfu , Yu Jiawen , Sun Weijie , Sun Yating , Tang Mingyang , Meng Bao , Liu Yanyan , Li Jiabin 
Published: September 2022

Background: RAR-related orphan receptor C (RORC) plays an important role in autoimmune responses and inflammation. However, its function in cancer immunity is still unclear. Its potential value in cancer immunotherapy (CIT) needs to be further studied.Methods: Expression and clinical data for 33 cancers were obtained from UCSC-Xena. The correlation between RORC expression and clinical parameters was analyzed using the limma software package to assess the prognostic value of RORC. Timer2.0 and DriverDBv3 were used to analyze the RORC mutation and methylation profiles. RORC-associated signaling pathways were identified by GSEA. The correlations of RORC expression with tumor microenvironment factors were further assessed, including immune cell infiltration (obtained by CIBERSORT) and immunomodulators (in pancancer datasets from the Tumor-Immune System Interactions and Drug Bank [TISIDB] database). In addition, the correlations of RORC with four CIT biomarkers (tumor mutational burden, microsatellite instability, programmed death ligand-1, and mismatch repair) were explored. Furthermore, three CIT cohorts (GSE67501, GSE168204, and IMvigor210) from the Gene Expression Omnibus database and a previously published study were used to determine the association between RORC expression and CIT response.Results: RORC was differentially expressed in many tumor tissues relative to normal tissues (20/33). In a small number of cancers, RORC expression was correlated with age (7/33), sex (4/33), and tumor stage (9/33). Furthermore, RORC expression showed prognostic value in many cancers, especially in kidney renal clear cell carcinoma (KIRC), brain lower grade glioma (LGG), and mesothelioma (MESO). The mutation rate of RORC in most cancer types was low, while RORC was hypermethylated or hypomethylated in multiple cancers. RORC was associated with a variety of biological processes and signal transduction pathways in various cancers. Furthermore, RORC was strongly correlated with immune cell infiltration, immunomodulators, and CIT biomarkers. However, no significant association was found between RORC and CIT response in the three CIT cohorts.Conclusion Our findings revealed the potential immunotherapeutic value of RORC for various cancers and provides preliminary evidence for the application of RORC in CIT.
Exploration of the underlying biological differences and targets in ovarian cancer patients with diverse immunotherapy response
Authors: Chen Jinjin , Chen Surong , Dai Xichao , Ma Liang , Chen Yu , Bian Weigang , Sun Yunhao 
Published: September 2022

BackgroundPreclinical trials of immunotherapy in ovarian cancer (OC) have shown promising results. This makes it meaningful to prospectively examine the biological mechanisms explaining the differences in response performances to immunotherapy among OC patients.MethodsOpen-accessed data was obtained from the Cancer Genome Atlas and Gene Expression Omnibus database. All the analysis was conducted using the R software.ResultsWe firstly performed the TIDE analysis to evaluate the immunotherapy response rate of OC patients. The machine learning algorithm LASSO logistic regression and SVM-RFE were used to identify the characteristic genes. The genes DPT, RUNX1T1, PTPRN, LSAMP, FDCSP and COL6A6 were selected for molecular typing. Our result showed that the patients in Cluster1 might have a better prognosis and might be more sensitive to immunotherapy, including PD-1 and CTLA4 therapy options. Pathway enrichment analysis showed that in Cluster2, the pathway of EMT, TNFα/NF-kB signaling, IL2/STAT5 signaling, inflammatory response, KRAS signaling, apical junction, complement, interferon-gamma response and allograft rejection were significantly activated. Also, genomic instability analysis was performed to identify the underlying genomic difference between the different Cluster patients. Single-cell analysis showed that the DPT, COL6A6, LSAMP and RUNX1T1 were mainly expressed in the fibroblasts. We then quantified the CAFs infiltration in the OC samples. The result showed that patients with low CAFs infiltration might have a lower TIDE score and a higher proportion of immunotherapy responders. Also, we found all the characteristic genes DPT, RUNX1T1, PTPRN, LSAMP, FDCSP and COL6A6 were upregulated in the patients with high CAFs infiltration. Immune infiltration analysis showed that the patients in Cluster2 might have a higher infiltration of naive B cells, activated NK cells and resting Dendritic cells.ConclusionsIn summary, our study provides new insights into ovarian cancer immunotherapy. Meanwhile, specific targets DPT, RUNX1T1, PTPRN, LSAMP, FDCSP, COL6A6 and CAFs were identified for OC immunotherapy.
The corrosion behavior and tensile strength of the 2060 Al-Li alloy with different heat treatments
Authors: Zheng Xingwei , Yin Haohao , Shu Yan , Chu Zhenhua , Liu Zhiwei 
Published: September 2022

The structural safety and service life of civil aircraft can be decreased by corrosion damage to their aluminum components caused by long-term service in corrosive conditions. In this work, the effect of heat treatment on corrosion behavior and tensile strength was systematically analyzed for 2060 Al-Li alloy immersed in 3.5 wt% NaCl solution for different corrosion times. The results show that the corrosion depths of the 2060-T4 and 2060-T6 Al-Li alloys immersed for 720 h are 85 and 93 μm, respectively. The ultimate tensile strengths of 2060-T4 and 2060-T6 Al-Li alloys immersed for 720 h were reduced by 5.8 and 6.4%, respectively. Linear relationships between tensile strength and the corrosion depths of 2060-T4 and 2060-T6 Al-Li alloys were established as σres=486−0.33h and σres=547−0.35h respectively.
Mucoid Acinetobacter baumannii enhances anti-phagocytosis through reducing C3b deposition
Authors: Gong Xiaoxia , Zhao Qian , Wu Yifan , Zhou Hongwei , Ding Shuangyang , Zhu Kui 
Published: September 2022

BackgroundMultidrug resistant (MDR) Acinetobacter baumannii causes serious infections in intensive care units and is hard to be eradicated by antibiotics. Many A. baumannii isolates are identified as the mucoid type recently, but the biological characteristics of mucoid A. baumannii and their interactions with host cells remains unclear.MethodsThe mucoid phenotype, antimicrobial susceptibility, biofilm-forming ability, acid resistance ability, peroxide tolerance, and in vivo toxicity of clinical ICUs derived A. baumannii isolates were first investigated. Secondly, the phagocytic resistance and invasive capacity of A. baumannii isolates to macrophages (MH-S, RAW264.7) and epithelial cells (A549) were analyzed. Furthermore, the abundance of C3b (complement factor C3 degradation product) deposition on the surface of A. baumannii was investigated. Last, the relationship between C3b deposition and the abundance of capsule in A. baumannii isolates were analyzed.ResultsThese A. baumannii strains showed different mucoid phenotypes including hyper mucoid (HM), medium mucoid (MM), and low mucoid (LM). All tested strains were MDR with high tolerance to either acid or hydrogen peroxide exposure. Notably, these mucoid strains showed the increase of mortality in the Galleria mellonella infection models. Besides, the HM strain exhibited less biofilm abundance, higher molecular weight (MW) of capsule, and greater anti-phagocytic activity to macrophages than the LM strain. Together with the increased abundance of capsule, high expression of tuf gene (associated with the hydrolysis of C3b), the HM strain effectively inhibits C3b deposition on bacterial surface, resulting in the low-opsonization phenotype.ConclusionCapsular characteristics facilitate the anti-phagocytic activity in hyper mucoid A. baumannii through the reduction of C3b deposition. Mucoid A. baumannii exhibits high phagocytosis resistance to both macrophages and epithelial cells.
Is high intensity laser therapy more effective than other physical therapy modalities for treating knee osteoarthritis? A systematic review and network meta-analysis
Authors: Wu Menglai , Luan Lijiang , Pranata Adrian , Witchalls Jeremy , Adams Roger , Bousie Jaquelin , Han Jia 
Published: September 2022

BackgroundThe use of physical therapy modalities, especially high intensity laser therapy (HILT), for individuals with knee osteoarthritis (KOA) is still controversial.ObjectiveTo compare the effects of HILT to other physical therapy modalities on symptoms and function in individuals with KOA.MethodsSix databases (PubMed, Embase, Cochrane Library, Web of Science, EBSCO, and PEDro) were searched in March 2022. Included studies were randomized controlled trials involving HILT conducted on individuals with KOA. The end-trial weighted mean difference (WMD) and standard deviations (SD) with 95% confidence intervals (CI) were analyzed.ResultsTen studies with 580 participants were obtained, of which nine were included in the final network meta-analysis. In terms of relieving pain, HILT demonstrated the highest probability of being among the most effective treatments, with surface under the cumulative ranking (SUCRA) = 100%, and compared to a control (placebo laser or exercise or a combination of both) on the visual analog scale (VAS) for pain it demonstrated significant benefits (WMD 1.66, 95% CI 1.48–1.84). For improving self-reported function, as measured by the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) total scores, the HILT SUCRA value led with 98.9%. When individuals with KOA were treated by HILT, the improvement in stiffness was statistically significant (WMD 0.78, 95% CI 0.52–1.04) but the amount of improvement was smaller than the minimal clinically important difference (MCID).ConclusionThe current evidence suggests that HILT may be more effective than other physical therapy modalities for improving pain and function in individuals with KOA. For improving stiffness, however, it may not be clinically effective.Systematic review registration[https://www.researchregistry.com], identifier [1148].
A nomogram incorporating red blood cell indices to predict post-stroke cognitive impairment in the intracerebral hemorrhage population
Authors: Gu Yongzhe , Wang Fang , Gong Li , Fang Min , Liu Xueyuan 
Published: September 2022

BackgroundPost-stroke cognitive impairment (PSCI) plagues 20–80% of stroke survivors worldwide. There is a lack of an easy and effective scoring tool to predict the risk of PSCI in intracerebral hemorrhage (ICH) patients. We aimed to develop a risk prediction model incorporating red blood cell (RBC) indices to identify ICH populations at risk of PSCI.MethodsPatients diagnosed with ICH at the stroke center were consecutively enrolled in the study as part of the development cohort from July 2017 to December 2018, and of the validation cohort from July 2019 to February 2020. Univariable and multivariable analyses were applied in the development cohort to screen the patients for PSCI risk factors. Then, a nomogram based on RBC indices and other risk factors was developed and validated to evaluate its performance in predicting PSCI occurrence.ResultsA total of 123 patients were enrolled in the development cohort, of which 69 (56.1%) were identified as PSCI, while 38 (63.3%) of 60 patients in the validation cohort were identified as PSCI. According to the multivariate analysis, seven independent risk factors, including three RBC indices (hemoglobin, mean corpuscular volume, RBC distribution width), as well as age, education level, hematoma volume, and dominant-hemisphere hemorrhage were incorporated into the model. The nomogram incorporating RBC indices displayed good discrimination and calibration. The area under the receiver operating characteristic curve was 0.940 for the development cohort and 0.914 for the validation cohort. Decision curve analysis and clinical impact curve showed that the nomogram was clinically useful.ConclusionRBC indices are independent and important predictors of PSCI. A nomogram incorporating RBC indices can be used as a reasonable and reliable graphic tool to help clinicians identify high cognition impairment-risk patients and adjust individualized therapy.
A bibliometric of research trends in acupuncture for spinal cord injury: Quantitative and qualitative analyses
Authors: Huang Yi , He Kelin , Fang Dandan , Ni Fengjia , Qiu Bei , Liang Kang , Ma Ruijie 
Published: September 2022

IntroductionSpinal cord injury (SCI) is a severe disease of the central nervous system with a very high disability rate that seriously affects the daily life of patients. Acupuncture is one of the rehabilitation therapies that has shown significant efficacy in treating post-SCI complications such as motor disorders, neuropathic pain, and neurogenic bladder. Current studies have focused on the effectiveness and mechanisms of acupuncture for SCI, but no studies are available to analyze the bibliometrics of publications related to this area.MethodsPublications related to acupuncture for SCI were retrieved from the Web of Science Core Collection for quantitative and qualitative analyses. The quantitative analysis was unfolded in the following six main areas: annual publications, countries, institutions, authors, sources, and keywords. The qualitative analysis section screened out publications with high annual citation rates and categorized them according to the study content.ResultsThere were 213 relevant publications, more than half of which were journal articles. The number of publications showed a fluctuating upward trend. China and the United States were hub countries for related publications and had extensive cooperation with other countries. The most relevant author was Yuanshan Zeng from Sun Yat-sen University, China. The efficacy and mechanism of acupuncture for neuropathic pain after SCI was the first research hotspot in this field, and electroacupuncture was the most widely used technique. In the past 5 years, the mechanism of acupuncture to improve the local microenvironment of SCI and promote nerve regeneration had become a new research trend. At the same time, acupuncture had been gradually applied to various complications after SCI and in veterinary medicine.ConclusionThe findings suggest that research on acupuncture for SCI is still flourishing, and more research on electroacupuncture for promoting nerve repair and regeneration after SCI will be available in the future.
Predictors of futile recanalization in patients with acute ischemic stroke undergoing mechanical thrombectomy in late time windows
Authors: Ni Heng , Liu Xinglong , Hang Yu , Jia Zhenyu , Cao Yuezhou , Shi Haibin , Liu Sheng , Zhao Linbo 
Published: September 2022

Background and purposeFutile recanalization (FR), defined as functional dependence despite successful reperfusion, is common in patients who experience an acute stroke after thrombectomy. We aimed to determine the predictors of FR in patients who underwent thrombectomy in late time windows (6 h or more after symptom onset).MethodsThis retrospective review included patients who underwent thrombectomy for acute anterior circulation large vessel occlusion from October 2019 to June 2021. Successful reperfusion was defined as a modified Thrombolysis in Cerebral Infarction (mTICI) score of 2b/3. Functional dependence at 90 days was defined as a modified Rankin scale score of 3–6. Multivariate analysis and a receiver operating characteristic (ROC) curve were used to identify the predictors of FR in patients treated in delayed time windows.ResultsOf the 99 patients included, FR was observed in 51 (51.5%). In the multivariate analysis, older age (OR, 1.12; 95% CI, 1.04–1.22; P = 0.005), female sex (OR, 3.79; 95% CI, 1.08–13.40; P = 0.038), a higher National Institutes of Health Stroke Score (NIHSS) score upon admission (OR, 1.11; 95% CI, 1.02–1.22; P = 0.023), and an increased number of passes per procedure (OR, 2.07; 95% CI, 1.11–3.86; P = 0.023) were independently associated with FR after thrombectomy. The ROC curve indicated that the model that combined age, female sex, baseline NIHSS score, and the number of passes per procedure (area under the curve, 0.84; 95% CI, 0.75–0.90, P &lt; 0.001) was able to predict FR accurately.ConclusionsOlder age, female sex, higher NIHSS score upon admission, and an increased number of passes per procedure were independent predictors of FR in patients who experienced acute ischemic strokes after thrombectomy in late time windows.