bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the quality of electronic medical records in academic hospitals: A multi-center study in Iran
Authors: Zabolinezhad Hedieh , Eslami Saeid , Hassibian Mohammad Reza , Dorri Sara 
Published: November 2022

ObjectiveThe present study aimed to assess the quality of electronic medical records (EMR) retrieved from hospital information systems (HIS) of three educational hospitals in Mashhad, Iran.MethodsIn this multi-center, cross-sectional study, inpatient electronic records collected from three academic hospitals were categorized into five data groups, namely demographics (D); care handler (CH), indicating the doers of the medical actions; diagnosis and treatment (DT); administrative and financial (AF); and laboratory and Para clinic (LP). Next, we asked 25 physicians from the three academic hospitals to determine data elements of medical research and education value (called research and educational data) in every group. Flowingly, the quality of the five data groups (completeness * accuracy) was reported for entire sampled data and those specified as research and educational data, based on the exact concordance between electronic medical records and corresponding paper records. HISRA, standing for HIS recording ability, was also assessed compared to data elements of standard paper forms.ResultsFor entire data, HISRA was 58.5%. In all hospitals, the highest data quality (more than 90%) belongs to D and AF data groups, and the lowest quality goes to CH and DT groups (less than 50%, and 60%, respectively). For research and educational data, HISRA was 47%, and the quality of D and AF data groups were the highest (nearly 100%), while CH and DT stood around 50% and 60% in order. The quality of the LP data group was almost 85% in all hospitals but hospital C (well over 30%). Total data quality for the hospitals was almost less than 70%.ConclusionsThe low quality of electronic medical records was mostly a result of incompleteness, while the accuracy was relatively good. Results showed that the HIS application development mainly focused on administrative and financial aspects rather than academic and clinical goals.
Oncologic outcomes of calcitonin-negative medullary thyroid carcinoma
Authors: Yue Wenliang , Zhang Yong 
Published: November 2022

ObjectiveCalcitonin (Ct)-negative medullary thyroid carcinoma (MTC) is a rare neuroendocrine tumor. This study aimed to clarify its incidence, clinicopathologic characteristics, management, and treatment outcome.MethodsWe retrospectively analyzed data of patients with primary MTC. Patients were divided into two groups according to the preoperative serum Ct level (Ct-negative and Ct-positive). The demographic, pathologic, and molecular characteristics, and treatment outcomes were compared between the two groups. In the Ct-negative group, we analyzed the association between the operation type and treatment outcome.ResultsOf the total 312 patients, 24 were diagnosed with Ct-negative MTC. The rate of lymph node metastasis was significantly higher in the Ct-positive than in the Ct-negative group (47.9% vs. 0%, p&lt;0.001). The proportion of patients with Ki-67 ≤10% was significantly higher in the Ct-negative than in the Ct-positive group (87.5% vs. 38.2%, p&lt;0.001). Excellent response was achieved by 91.7% and 34.7% of patients in the Ct-negative and Ct-positive groups, respectively (p&lt;0.001). In the Ct-negative group, excellent response was achieved by all female patients, but only 50% of male patients.ConclusionsCt-negative MTC is rare and unlikely to develop lymph node metastasis. Unilateral lobectomy tends to provide a satisfactory chance of excellent response; however, this requires further validation.
Characterization of immune microenvironment infiltration and m6A regulator-mediated RNA methylation modification patterns in osteoarthritis
Authors: Ouyang Yulong , Tu Yuanqing , Chen Shuilin , Min Huan , Wen Zhexu , Zheng Guihao , Wan Ting , Fan Hao , Yang Wenzhao , Sun Guicai 
Published: November 2022

BackgroundFew studies have been reported the potential role of N6-methyladenosine (m6A) modification in osteoarthritis (OA). We investigated the patterns of m6A modification in the immune microenvironment of OA.MethodsWe evaluated the m6A modification patterns based on 22 m6A regulators in 139 OA samples and systematically associated these modification patterns with immune cell infiltration characteristics. The function of m6A phenotype-related differentially expressed genes (DEGs) was investigated using gene enrichment analysis. An m6A score model was constructed using principal component analysis (PCA), and an OA prediction model was established based on the key m6A regulators. We used real-time PCR analysis to detect the changes of gene expression in the cell model of OA.ResultsHealthy and OA samples showed significant differences in the expression of m6A regulators. Nine key m6A regulators, two m6A modification patterns, m6A-related genes and two gene clusters were identified. Some m6A regulators had a strong correlation with each other. Gene clusters and m6A clusters have high similarity, and cluster A corresponds to a high m6A score. Immunocytes infiltration differed significantly between the two clusters, with the m6A cluster B and gene cluster B having more types of infiltrating immunocytes than cluster A. The predictive model can also predict the progression of OA through m6A regulators expression. The results of real-time PCR analysis showed that the gene expression in the cell model of OA is similar to that of the m6A cluster B.ConclusionsOur study reveals for the first time the potential regulatory mechanism of m6A modification in the immune microenvironment of OA. This study also sheds new light on the pathogenesis of OA.
An EGFR L858R mutation identified in 1862 Chinese NSCLC patients can be a promising neoantigen vaccine therapeutic strategy
Authors: Lin Jing , Liu Jun , Hao Shi-guang , Lan Bin , Zheng Xiao-bin , Xiong Jia-ni , Zhang Ying-qian , Gao Xuan , Chen Chuan-ben , Chen Ling , Huang Yu-fang , Luo Hong , Yi Yu-ting , Yi Xin , Lu Jian-ping , Zheng Xiong-wei , Chen Gang , Wang Xue-feng , Chen Yu 
Published: November 2022

BackgroundThis study aimed to develop a vaccine that targets mutation-derived neoantigen in Chinese non-small-cell lung cancer (NSCLC).MethodsA cohort of 1862 Chinese NSCLC patients who underwent targeted sequencing with a 1021-gene panel was investigated. HLA typing was done using OptiType v1.0 and neoantigens were predicted by netMHCpan v4.0. HLA LOH was inferred using the lohhla algorithm and TMB were quantified by counting the total number of non-synonymous ones based on our panel data. CIBERSORT was utilized to estimate the TME in different EGFR mutant subtype by using TCGA data.ResultsHLA-A*11:01(42.59%) was the top one allele and HLA-A*33:03(12.94%) ranked 12th. EGFR L858R (22.61%) was the most prevalent gene variant. The binding affinity (IC50 MT = 22.9 nM) and shared frequency (2.93%) of EGFR L858R in combination with HLA-A*33:03 were optimal. In a subsequent further analysis on immunological features of EGFR mutant subtypes, 63.1% HLA loss of heterozygosity LOH (HLA LOH) and 0.37% (7 of 1862) B2M aberrations were found in our population, both had no significant association with EGFR mutant subtypes suggesting that the process of antigen presentation involved HLA LOH and B2M mechanisms in EGFR L858R is working. Tumor mutation burden (TMB) was investigated by utilizing our panel and showed that EGFR L858R had the lowest TMB compared with other EGFR mutant subtypes. In addition, analysis of 22 immune cell types from The Cancer Genome Atlas (TCGA) data showed EGFR L858R was correlated with low level of CD8 T cells, activated CD4 memory T cells and elevated level of macrophage M2 suggesting an inhibited tumor microenvironment (TME).ConclusionOur study identified that EGFR L858R neoantigen had the potential to generate cancer vaccines in NSCLC patients with HLA A*33:03. The neoantigen-based vaccines may become an effective salvage regimen for EGFR L858R subgroup after targeted therapy or immune checkpoint inhibitors (ICIs) failure.
Tolerogenic dendritic cells pulsed with islet antigen induce long-term reduction in T-cell autoreactivity in type 1 diabetes patients
Authors: Nikolic Tatjana , Suwandi Jessica S. , Wesselius Joris , Laban Sandra , Joosten Antoinette M. , Sonneveld Petra , Mul Dick , Aanstoot Henk-Jan , Kaddis John S. , Zwaginga Jaap Jan , Roep Bart O. 
Published: November 2022

IntroductionRestoration of immune tolerance may halt progression of autoimmune diseases. Tolerogenic dendritic cells (tolDC) inhibit antigen-specific proinflammatory T-cells, generate antigen-specific regulatory T-cells and promote IL-10 production in-vitro, providing an appealing immunotherapy to intervene in autoimmune disease progression.MethodsA placebo-controlled, dose escalation phase 1 clinical trial in nine adult patients with long-standing type 1 diabetes (T1D) demonstrated the safety and feasibility of two (prime-boost) vaccinations with tolDC pulsed with a proinsulin peptide. Immunoregulatory effects were monitored by antigen-specific T-cell assays and flow and mass cytometry.ResultsThe tolDC vaccine induced a profound and durable decline in pre-existing autoimmune responses to the vaccine peptide up to 3 years after therapy and temporary decline in CD4 and CD8+ T-cell responses to other islet autoantigens. While major leukocyte subsets remained stable, ICOS+CCR4+TIGIT+ Tregs and CD103+ tissue-resident and CCR6+ effector memory CD4+ T-cells increased in response to the first tolDC injection, the latter declining thereafter below baseline levels.DiscussionOur data identify immune correlates of mechanistic efficacy of intradermally injected tolDC reducing proinsulin autoimmunity in T1D.
Standardization of neutrophil CD64 and monocyte HLA-DR measurement and its application in immune monitoring in kidney transplantation
Authors: Peng Bo , Yang Min , Zhuang Quan , Li Junhui , Zhang Pengpeng , Liu Hong , Cheng Ke , Ming Yingzi 
Published: November 2022

BackgroundInfections cause high mortality in kidney transplant recipients (KTRs). The expressions of neutrophil CD64 (nCD64) and monocyte HLA-DR (mHLA-DR) provide direct evidence of immune status and can be used to evaluate the severity of infection. However, the intensities of nCD64 and mHLA-DR detected by flow cytometry (FCM) are commonly measured by mean fluorescence intensities (MFIs), which are relative values, thus limiting their application. We aimed to standardize nCD64 and mHLA-DR expression using molecules of equivalent soluble fluorochrome (MESF) and to explore their role in immune monitoring for KTRs with infection.MethodsThe study included 50 KTRs diagnosed with infection, 65 immunologically stable KTRs and 26 healthy controls. The blood samples were collected and measured simultaneously by four FCM protocols at different flow cytometers. The MFIs of nCD64 and mHLA-DR were converted into MESF by Phycoerythrin (PE) Fluorescence Quantitation Kit. The intraclass correlation coefficients (ICCs) and the Bland-Altman plots were used to evaluate the reliability between the four FCM protocols. MESFs of nCD64 and mHLA-DR, nCD64 index and sepsis index (SI) with the TBNK panel were used to evaluate the immune status. Comparisons among multiple groups were performed with ANOVA one-way analysis. Receiver operating characteristics (ROC) curve analysis was performed to diagnose infection or sepsis. Univariate and multivariate logistic analysis examined associations of the immune status with infection.ResultsMESFs of nCD64 and mHLA-DR measured by four protocols had excellent reliability (ICCs 0.993 and 0.957, respectively). The nCD64, CD64 index and SI in infection group were significantly higher than those of stable KTRs group. Patients with sepsis had lower mHLA-DR but higher SI than non-sepsis patients. ROC analysis indicated that nCD64 had the highest area under the curve (AUC) for infection, and that mHLA-DR had the highest AUC for sepsis. Logistic analysis indicated that nCD64 &gt; 3089 and B cells counts were independent risk factors for infection.ConclusionThe standardization of nCD64 and mHLA-DR made it available for widespread application. MESFs of nCD64 and mHLA-DR had good diagnostic performance on infection and sepsis, respectively, which could be promising indicators for immune status of KTRs and contributed to individualized treatment.
Health self-perception is associated with life-styles and comorbidities and its effect on mortality is confounded by age. A population based study
Authors: Rañó-Santamaría Oscar , Fernandez-Merino Carmen , Castaño-Carou Ana Isabel , Lado-Baleato Óscar , Fernández-Domínguez María José , Sanchez-Castro Juan Jose , Gude Francisco 
Published: November 2022

BackgroundHealth self-perception (HSP) is the individual and subjective concept that a person has of their state of health. Despite its simplicity, HSP is considered a valid and relevant indicator employed in epidemiological research and in professional practice as an overall measure of health.Objectives(1) To describe and analyze the associations between HSP and demographic variables, lifestyle and diseases prevalent in a population and (2) to investigate the relationship between HSP and mortality.Materials and methodsIn a primary care setting, we conducted a longitudinal study of a random populational sample of a Galician municipality, stratified by decade of life. A total of 1,516 adults older than 18 years, recruited by the 2013–2015 AEGIS study, were followed-up for more than 5 years. During the clinical interview, data were collected on lifestyle and prevalent diseases. The HSP was grouped into 2 categories (good/poor). The statistical analysis consisted of a logistic regression, Kaplan–Meier curves and Cox regression.ResultsA total of 540 (35.6%) participants reported poor HSP. At the end of the follow-up, 78 participants had died (5.1%). The participants with increased age and body mass index and chronic diseases (anxiety, depression, ischemic heart disease, diabetes, and cancer) presented a poorer subjective health. A high level of physical activity and moderate alcohol consumption were associated with better HSP. A poorer HSP was associated with increased mortality, an association that disappeared after adjusting for the rest of the covariates (HR, 0.82; 95% CI 0.50–1.33).Conclusion(1) Health self-perception is associated with age, lifestyle, and certain prevalent diseases. (2) A poorer HSP is associated with increased mortality, but this predictive capacity disappeared after adjusting for potential confounders such as age, lifestyle, and prevalent diseases.
Trends in Helicobacter pylori-related gastric ulcer research from 2012 to 2022: A bibliometric and visual analysis
Authors: Yu Chang , Qiu Jingyue , Xiong Meng , Ou Chen , Zeng Meiyan , Song Houpan 
Published: November 2022

BackgroundHelicobacter pylori-related gastric ulcer (H. pylori-related GU) is one of the most common digestive system diseases that have received widespread attention from researchers. The purpose of this article was to analyze the research status and hotspots of H. pylori-related GU and to predict its future research directions.MethodsThe article and review papers associated with H. pylori-related GU published from 2012 to 2022 were retrieved from the Web of Science Core Collection (WoSCC). The analysis of knowledge maps and bibliometrics was done with CiteSpace 6.1.R2 Basic and VOSviewer 1.6.18.ResultsA total of 2,971 articles were included in the study. Between 2012 and 2022, the number of papers published showed an increasing trend. China was the most prolific country, and the United States was the most influential country. Baylor College of Medicine had the largest number of publications and citations among publishing agencies. World Journal of Gastroenterology published the most articles on the H. pylori-related GU field, and GUT was the journal with the most cited articles. Yamaoka Y from Japan was the most productive author, and Graham DY from the USA was the most influential author. A keyword and reference analysis showed that the hot topics of research were the mechanism of H. pylori and the treatment of H. pylori-related GU. The keywords that emerged in the recent 5 years were oxidative stress, probiotics, competitive acid blocker, vonoprazan, gut microbiota, and neutrophil-activating protein.ConclusionOver the recent 10 years, research on H. pylori-related GU has generally shown an increasing trend. The treatment and pathogenesis of H. pylori-related GU remain a hot topic of research. The treatment of H. pylori by oxidative stress and competitive acid inhibitor mechanisms, the influence of gastrointestinal flora on H. pylori, probiotic adjuvant therapy of H. pylori-related GU, and the immunoprotective effect of neutrophil activator protein could be popular research directions and trends in the future.
Predicting COVID-19 progression in hospitalized patients in Belgium from a multi-state model
Authors: Mertens Elly , Serrien Ben , Vandromme Mathil , Peñalvo José L. 
Published: November 2022

ObjectivesTo adopt a multi-state risk prediction model for critical disease/mortality outcomes among hospitalised COVID-19 patients using nationwide COVID-19 hospital surveillance data in Belgium.Materials and methodsInformation on 44,659 COVID-19 patients hospitalised between March 2020 and June 2021 with complete data on disease outcomes and candidate predictors was used to adopt a multi-state, multivariate Cox model to predict patients’ probability of recovery, critical [transfer to intensive care units (ICU)] or fatal outcomes during hospital stay.ResultsMedian length of hospital stay was 9 days (interquartile range: 5–14). After admission, approximately 82% of the COVID-19 patients were discharged alive, 15% of patients were admitted to ICU, and 15% died in the hospital. The main predictors of an increased probability for recovery were younger age, and to a lesser extent, a lower number of prevalent comorbidities. A patient’s transition to ICU or in-hospital death had in common the following predictors: high levels of c-reactive protein (CRP) and lactate dehydrogenase (LDH), reporting lower respiratory complaints and male sex. Additionally predictors for a transfer to ICU included middle-age, obesity and reporting loss of appetite and staying at a university hospital, while advanced age and a higher number of prevalent comorbidities for in-hospital death. After ICU, younger age and low levels of CRP and LDH were the main predictors for recovery, while in-hospital death was predicted by advanced age and concurrent comorbidities.ConclusionAs one of the very few, a multi-state model was adopted to identify key factors predicting COVID-19 progression to critical disease, and recovery or death.
Characterization and identification of a novel chromosomal class C β-lactamase, LAQ-1, and comparative genomic analysis of a multidrug resistance plasmid in Lelliottia amnigena P13
Authors: Li Anqi , Yan Chunxia , Zhang Lei , Liu Shuang , Feng Chunlin , Zhang Linhua , Dong Fubo , Sheng Xiusheng , Wang Lan , Zhang Yanfang , Lu Junwan , Xu Jiefeng , Zheng Lin , Bao Qiyu , Cheng Cong , Huang Dawei 
Published: November 2022

IntroductionLelliottia amnigena, a bacterium usually isolated from natural environments, may cause human infections and has been suggested to be naturally resistant to second- and third-generation cephalosporins.MethodsIn this study, we determined the whole-genome sequence of an isolate, L. Amnigena P13, isolated from animal farm sewage. On the basis of genome sequence analysis, susceptibility testing, molecular cloning, and enzyme kinetic parameter analysis, we identified a novel chromosome-encoded AmpC β-lactamase, LAQ-1.Results and DiscussionblaLAQ-1 is resistant to penicillin G, ampicillin, and several first- to fourth-generation cephalosporins, such as cefazolin, cefoxitin and cefepime. The MIC levels of some β-lactams, such as cefoxitin, cefepime, aztreonam and cefazolin, for the recombinant clone (pUCP24-blaLAQ-1/DH5α) increased by approximately 4- to 64-fold compared with those of the control strain (pUCP24/DH5α). The kinetic properties of LAQ-1, with the highest catalytic activity observed toward piperacillin, were basically the same as those of typical class C β-lactamases, and avibactam had a strong inhibitory effect on its hydrolytic activity. The genetic background of blaLAQ-1 was relatively conserved, and no mobile genetic element (MGE) was found around it. The plasmid pP13-67 of L. amnigena P13 harbored 12 resistance genes [qnrS1, aph(6)-Id, aadA2, sul1, sul2,blaTEM-1, qacEΔ1, dfrA12, tetA and floR] related to different mobile genetic elements within an ~22 kb multidrug resistance region. The multidrug resistance region shared the highest nucleotide sequence similarities with those of the chromosomes or plasmids of different bacterial species, indicating the possibility of horizontal transfer of these resistance genes among different bacterial species.
Dysphagia assessment in ischemic stroke after mechanical thrombectomy: When and how?
Authors: Lapa Sriramya , Neuhaus Elisabeth , Harborth Elena , Neef Vanessa , Steinmetz Helmuth , Foerch Christian , Reitz Sarah Christina 
Published: November 2022

BackgroundDysphagia is a frequent symptom in acute ischemic stroke (AIS). Endovascular treatment (EVT) has become the standard of care for acute stroke secondary to large vessel occlusion. Although standardized guidelines for poststroke dysphagia (PSD) management exist, they do not account for this setting in which patients receive EVT under general anesthesia. Therefore, the aim of this study was to evaluate PSD prevalence and severity, as well as an appropriate time point for the PSD evaluation, in patients undergoing EVT under general anesthesia (GA).MethodsWe prospectively included 54 AIS patients undergoing EVT under GA. Fiberoptic Endoscopic Evaluation of Swallowing (FEES) was performed within 24 h post-extubation in all patients. Patients presenting significant PSD received a second FEES-assessment to determine the course of dysphagia deficits over time. Dysphagia severity was rated according the Fiberoptic Dysphagia Severity Scale (FEDSS).ResultsAt first FEES (FEES 1) assessment, performed in the median 13 h (IQR 5–17) post-extubation, 49/54 patients (90.7%) with dysphagia were observed with a median FEDSS of 4 (IQR 3–6). Severe dysphagia requiring tube feeding was identified in 28/54 (51.9%) subjects, whereas in 21 (38.9%) patients early oral diet with certain food restrictions could be initiated. In the follow up FEES examination conducted in the median 72 h (IQR 70–97 h) after initial FEES 34/49 (69.4%) patients still presented PSD. Age (p = 0.030) and ventilation time (p = 0.035) were significantly associated with the presence of PSD at the second FEES evaluation. Significant improvement of dysphagia frequency (p = 0.006) and dysphagia severity (p = 0.001) could be detected between the first and second dysphagia assessment.ConclusionsPSD is a frequent finding both immediately within 24 h after extubation, as well as in the short-term course. In contrast to common clinical practice, to delay evaluation of swallowing for at least 24 h post-extubation, we recommend a timely assessment of swallowing function after extubation, as 50% of patients were safe to begin oral intake. Given the high amount of severe dysphagic symptoms, we strongly recommend application of instrumental swallowing diagnostics due to its higher sensitivity, when compared to clinical swallowing examination. Furthermore, advanced age, as well as prolonged intubation, were identified as significant predictors for delayed recovery of swallowing function.