bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-sampling to identify pathogens and inflammatory markers in patients with acute sore throat: Feasibility study
Authors: Lown Mark , Miles Elizabeth A. , Fisk Helena L. , Smith Kirsten A. , Muller Ingrid , Maund Emma , Rogers Kirsty , Becque Taeko , Hayward Gail , Moore Michael , Little Paul , Glogowska Margaret , Hay Alastair D. , Stuart Beth , Mantzourani Efi , Butler Chris , Bostock Jennifer , Davies Firoza , Dickerson Ian , Thompson Natalie , Francis Nick 
Published: October 2022

IntroductionSore throat is a common reason for overuse of antibiotics. The value of inflammatory or biomarkers in throat swab or saliva samples in predicting benefit from antibiotics is unknown.MethodsWe used the ‘person-based approach’ to develop an online tool to support self-swabbing and recruited adults and children with sore throats through participating general practices and social media. Participants took bacterial and viral swabs and a saliva sponge swab and passive drool sample. Bacterial swabs were cultured for streptococcus (Group A, B, C, F and G). The viral swab and saliva samples were tested using a routine respiratory panel PCR and Covid-19 PCR testing. We used remaining viral swab and saliva sample volume for biomarker analysis using a panel of 13 biomarkers.ResultsWe recruited 11 asymptomatic participants and 45 symptomatic participants. From 45 symptomatic participants, bacterial throat swab, viral throat swab, saliva sponge and saliva drool samples were returned by 41/45 (91.1%), 43/45 (95.6%), 43/45 (95.6%) and 43/45 (95.6%) participants respectively. Three saliva sponge and 6 saliva drool samples were of insufficient quantity. Two adult participants had positive bacterial swabs. Six participants had a virus detected from at least one sample (swab or saliva). All of the biomarkers assessed were detectable from all samples where there was sufficient volume for testing. For most biomarkers we found higher concentrations in the saliva samples. Due to low numbers, we were not able to compare biomarker concentrations in those who did and did not have a bacterial pathogen detected. We found no evidence of a difference between biomarker concentrations between the symptomatic and asymptomatic participants but the distributions were wide.ConclusionsWe have demonstrated that it is feasible for patients with sore throat to self-swab and provide saliva samples for pathogen and biomarker analysis. Typical bacterial and viral pathogens were detected but at low prevalence rates. Further work is needed to determine if measuring biomarkers using oropharyngeal samples can help to differentiate between viral and bacterial pathogens in patients classified as medium or high risk using clinical scores, in order to better guide antibiotic prescribing and reduce inappropriate prescriptions.
Histamine induced high mobility group box-1 release from vascular endothelial cells through H1 receptor
Authors: Gao Shangze , Liu Keyue , Ku Wenhan , Wang Dengli , Wake Hidenori , Qiao Handong , Teshigawara Kiyoshi , Nishibori Masahiro 
Published: October 2022

BackgroundSystemic allergic reaction is characterized by vasodilation and vascular leakage, which causes a rapid, precipitous and sustained decrease in arterial blood pressure with a concomitant decrease of cardiac output. Histamine is a major mediator released by mast cells in allergic inflammation and response. It causes a cascade of inflammation and strongly increases vascular permeability within minutes through its four G-protein-coupled receptors (GPCRs) on endothelial cells. High mobility group box-1 (HMGB1), a nonhistone chromatin-binding nuclear protein, can be actively secreted into the extracellular space by endothelial cells. HMGB1 has been reported to exert pro-inflammatory effects on endothelial cells and to increase vascular endothelial permeability. However, the relationship between histamine and HMGB1-mediated signaling in vascular endothelial cells and the role of HMGB1 in anaphylactic-induced hypotension have never been studied.Methods and resultsEA.hy 926 cells were treated with different concentrations of histamine for the indicated periods. The results showed that histamine induced HMGB1 translocation and release from the endothelial cells in a concentration- and time-dependent manner. These effects of histamine were concentration-dependently inhibited by d-chlorpheniramine, a specific H1 receptor antagonist, but not by H2 or H3/4 receptor antagonists. Moreover, an H1-specific agonist, 2-pyridylethylamine, mimicked the effects of histamine, whereas an H2-receptor agonist, 4-methylhistamine, did not. Adrenaline and noradrenaline, which are commonly used in the clinical treatment of anaphylactic shock, also inhibited the histamine-induced HMGB1 translocation in endothelial cells. We therefore established a rat model of allergic shock by i.v. injection of compound 48/80, a potent histamine-releasing agent. The plasma HMGB1 levels in compound 48/80-injected rats were higher than those in controls. Moreover, the treatment with anti-HMGB1 antibody successfully facilitated the recovery from compound 48/80-induced hypotension.ConclusionHistamine induces HMGB1 release from vascular endothelial cells solely through H1 receptor stimulation. Anti-HMGB1 therapy may provide a novel treatment for life-threatening systemic anaphylaxis.
Identifying a novel ferroptosis-related prognostic score for predicting prognosis in chronic lymphocytic leukemia
Authors: Pan Bihui , Li Yue , Xu Zhangdi , Miao Yi , Yin Hua , Kong Yilin , Zhang Xinyu , Liang Jinhua , Xia Yi , Wang Li , Li Jianyong , Wu Jiazhu , Xu Wei 
Published: October 2022

BackgroundChronic lymphocytic leukemia (CLL) is the most common leukemia in the western world. Although the treatment landscape for CLL is rapidly evolving, there are still some patients who develop drug resistance or disease refractory. Ferroptosis is a type of lipid peroxidation–induced cell death and has been suggested to have prognostic value in several cancers. Our research aims to build a prognostic model to improve risk stratification in CLL patients and facilitate more accurate assessment for clinical management.MethodsThe differentially expressed ferroptosis-related genes (FRGs) in CLL were filtered through univariate Cox regression analysis based on public databases. Least absolute shrinkage and selection operator (LASSO) Cox algorithms were performed to construct a prognostic risk model. CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) were performed to estimate the immune infiltration score and immune-related pathways. A total of 36 CLL patients in our center were enrolled in this study as a validation cohort. Moreover, a nomogram model was established to predict the prognosis.ResultsA total of 15 differentially expressed FRGs with prognostic significance were screened out. After minimizing the potential risk of overfitting, we constructed a novel ferroptosis-related prognostic score (FPS) model with nine FRGs (AKR1C3, BECN1, CAV1, CDKN2A, CXCL2, JDP2, SIRT1, SLC1A5, and SP1) and stratified patients into low- and high-risk groups. Kaplan–Meier analysis showed that patients with high FPS had worse overall survival (OS) (P&lt;0.0001) and treatment-free survival (TFS) (P&lt;0.0001). ROC curves evaluated the prognostic prediction ability of the FPS model. Additionally, the immune cell types and immune-related pathways were correlated with the risk scores in CLL patients. In the validation cohort, the results confirmed that the high-risk group was related to worse OS (P&lt;0.0001), progress-free survival (PFS) (P=0.0140), and TFS (P=0.0072). In the multivariate analysis, only FPS (P=0.011) and CLL-IPI (P=0.010) were independent risk indicators for OS. Furthermore, we established a nomogram including FPS and CLL-IPI that could strongly and reliably predict individual prognosis.ConclusionA novel FPS model can be used in CLL for prognostic prediction. The model index may also facilitate the development of new clinical ferroptosis-targeted therapies in patients with CLL.
Immunotherapy improves disease prognosis by affecting the tumor microenvironment: A bibliometric study
Authors: Wu Xin , Deng Zhen , Zhao Qiangqiang 
Published: October 2022

BackgroundImmunotherapy has shown great potential for the treatment of multiple cancer and has been proven to be closely related to the tumor microenvironment. This article reveals collaborations and interactions among authors, nations, organizations, and periodicals assesses the knowledge base, and discovers hot tendencies and new topics associated with immunotherapy-tumor microenvironment (TME) research.MethodsThis article utilized bibliometrics and visual methods to provide a comprehensive overview of immunotherapy-TME research. Our team retrieved the WoSCC for research and reviews associated with immunotherapy and the tumor microenvironment. VOSviewer and Citespace were primarily used for literature measurement and knowledge graph analysis.ResultAll English articles and reviews on cancer immunotherapy effectiveness were collected, and 1,419 academic journals with 53,773 authors from 7,008 institutions in 92 countries/regions were found. Publications associated with immunotherapy-TME research were stably increasing. Frontiers of Immunology (n = 722) published the most papers on immunotherapy-TME, and Cancer Research (n = 6761) was the top co-cited journal. The published journals and co-cited journals focused on cancer and immunology fields. The League of European Research Universities (n = 978), Harvard University (n = 528), and the University of Texas system (n = 520) were the most productive institutions. Yang Liu (n = 34) and Topalian (n = 1978) ranked first among the top 10 scholars and co-cited scholars. Simultaneously, immunotherapy-TME researchers were involved in active collaborations. Elements of TME, the foundation of immunotherapy, and the application of immunotherapy in cancers represented the three principal aspects of immunotherapy-TME research. The latest hot spots are drug resistance, prognosis prediction, efficacy prediction, and m6A. Nanomedicine and m6A may be future hot topics. Future research in immunotherapy-TME may be directed at discovering how m6A modification affects tumor development by altering the tumor microenvironment and exploring how to enhance response or reduce drug resistance to immunotherapy by reversing or mediating the physicochemical properties of the TME.ConclusionsM6A and nanomedicine are also emerging hotspots in time zone diagrams with high centrality, and prognosis prediction using bioinformatics based on the development of prediction technology may be another future research hotspot.
A retrospective study of the correlation between herpes zoster neuralgia and the serum neuron-specific enolase level in the largest dermatological hospital in Zhejiang province, China
Authors: Zhong Changyang , Lin Ding , Liu Yuan , Wu Chunli 
Published: October 2022

We studied the changes and clinical significance of the serum neuron-specific enolase (NSE) level in peripheral blood of patients with post-herpetic neuralgia (PHN).Material and methodsPatients with PHN were divided into a mild PHN group and a severe PHN group according to their scores on a 100-point Likert scale representing the degree of neuralgia. NSE levels in neuralgia patients and healthy volunteers were then compared by t-test. Receiver operating characteristic curve analysis was performed to evaluate the diagnostic efficiency of NSE for PHN. The correlation between NSE level and Likert scale score after treatment was analyzed.ResultsNSE levels in PHN patients were higher than those in the healthy volunteers. Patients in the severe PHN group had higher NSE levels than those in the mild PHN group. NSE level at admission was associated with the Likert scale score recorded on the 14th day of treatment (136.1 ± 32.81 vs. 87.53 ± 16.23 pg/mL) (P &lt; 0.05). The ROC curve of NSE levels for PHN is shown that the area was 0.8713 (95% confidence interval, 0.7861–0.9564; p &lt; 0.0001).ConclusionsThere was a correlation between NSE and PHN, in that the NSE level positively correlated with the short-term prognosis of patients with PHN.
Tracing the depth-dependent changes in organic carbon and nutrient fluxes using high-resolution 228Ra profiles in the upper East Sea (Japan Sea)
Authors: Cho Hyung-Mi , Han Yongjin , Kim Young-Il , Baek Cheolmin , Kim Guebuem 
Published: October 2022

Vertical profiles of 228Ra (half-life: 5.75 years) in the ocean provide valuable information on water mixing and ages of the upper ocean. However, its application is hampered by extremely low levels of 228Ra in the deep ocean. In this study, we measured high-resolution 228Ra/226Ra ratio profiles (&gt;21 depths) in the East Sea (Japan Sea) by mooring Mn-fiber. Using the measured 228Ra profile from 228Ra/226Ra ratios and 226Ra activities, together with other previously published data, we estimated the vertical eddy diffusivity (8.7–9.6 cm2 s-1) in the permanent thermocline and water ages (10–15 years) in the upper 500–1000 m range. The estimated decomposition rate of organic carbon based on oxygen utilization rates using Ra-ages between 100 and 1000 m was 4.4 ± 0.8 mol C m-2 yr-1. Our results show that ~50% of the upward nutrients through 100 m support export production, and that dissolved organic carbon accounts for ~20% of carbon export. This 228Ra approach provides a holistic understanding of carbon and nutrient cycles in the ocean.
Biological variation and reference change value of the estimated glomerular filtration rate in humans: A systematic review and meta-analysis
Authors: Thöni Stefanie , Keller Felix , Denicolò Sara , Buchwinkler Lukas , Mayer Gert 
Published: October 2022

BackgroundKnowledge of the biological variation of serum or plasma creatinine (Cr) and the estimated glomerular filtration rate (eGFR) is important for understanding disease dynamics in Chronic Kidney Disease (CKD). The aim of our study was to determine the magnitude of random fluctuation of eGFR by determining its reference change value (RCV).MethodsWe performed a systematic review and meta-analysis of studies on biological variation of Cr. Relevant studies were identified by systematic literature search on PubMed. Additional studies were retrieved from the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Biological Variation Database. Random-effects meta-analysis was conducted to derive an overall estimate of intra-individual variation of creatinine (CVICr). Based on our estimate of CVICr and RCV for Cr, the RCV for the eGFR was determined.ResultsAmong identified studies, 37 met our inclusion criteria. Meta-analysis of all studies yielded a CVICr of 5.2% (95% confidence interval [CI] 4.6–5.8%), however high between-study heterogeneity (I2 = 82.3%) was found. Exclusion of outliers led to a significant reduction of heterogeneity while still including 85% of all studies and resulted in a slightly lower CVICr of 5.0% (95% CI 4.7–5.4%). Assuming an analytical variation of CVA 1.1%, we found an overall RCV for eGFR of ±16.5%. After exclusion of outlier studies, we found a minimum conservative RCV for eGFR of ±12.5%.ConclusionThe RCV of the eGFR represents a valuable tool for clinicians to discern true changes in kidney function from random fluctuation.
Diagnostic performance of the Qiaprep amp Viral RNA UM kit for the detection of COVID-19 compared to RT-PCR
Authors: Becerril Vargas Eduardo , Cojuc-Konigsberg Gabriel , Braverman-Poyastro Alan , Armendáriz Mendoza Erick , Mujica Sánchez Mario Alberto , García Colín María Del Carmen , Chávez Morales Hansel Hugo , Aguirre Pineda José Nicolás , Ibarra Cobas Luis Carlos 
Published: October 2022

BackgroundRT-PCR is the currently recommended laboratory method for diagnosing acute SARS-CoV-2 infection. Nevertheless, to carry out this assay, numerous manual steps are necessary, but they are long lasting and error-prone. A new sample preparation solution was launched, the Qiaprep &amp; amp Viral RNA UM kit, that combines a short, liquid-based sample preparation with one-step RT-PCR amplification and detection of SARS-CoV-2. Such alternative allows reducing the handling of samples and obtaining a result in a shorter period of time. The objective of the study was to compare the performance of the kit with RT-PCR.MethodsA prospective trial was carried out in the clinical microbiology laboratory of a tertiary care hospital. The pharyngeal and nasopharyngeal swabs included in the study were taken from patients who underwent medical consultation because compatible COVID-19 symptoms. Samples were processed simultaneously for the reference RT-PCR and by the QIA P&amp;A kit.Results190 samples were included in the clinical trial. The reference RT-PCR method indicated that 125 (66%) samples, out of the 190, were positive. The QIA P&amp;A kit showed 112 positive samples for SARS-CoV-2. The QIA P&amp;A kit has a sensitivity of 86% to detect SARS-CoV-2 and a 100% specificity, the positive predictive value was of 96%, the negative predictive value 78%, and the obtained Kappa value was 0,76. QIA P&amp;A kit showed a lower mean cycle threshold compared with the diagnostic standard, with a statistically significant difference (p &lt; 0.05).ConclusionThe QIA P&amp;A kit has an acceptable, yet not optimal performance for sample preparation and amplification of SARS-CoV-2 and further studying is required for it to be validated as a cost-effective, rapid diagnostic method for detecting infections.
A non-functional 5′ ALK fusion validated at the RNA level as a classical EML4-ALK that responds well to the novel ALK inhibitor ensartinib: A case report
Authors: Yang Hong , Li Haojing , Fang Yu , Li Zhijun , Zhu Jianhua , Liu Huan , Lu Chao , Zhang Xiaoyan , Ma Tonghui , Zhang Cuiying 
Published: October 2022

BackgroundCurrently, many targeted drugs are approved for treatment of ALK fusion non-small cell lung cancer. However, it has been previously assumed that patients with 5′ non-oncogenic kinase (5′ NOK) fusion detected by DNA next-generation sequencing (NGS) would not benefit from ALK inhibitors because of lack of an intact kinase domain.Case descriptionA novel 5′ NOK fusion form, ALK-CYP27C1 (A19:C5), was detected by DNA NGS in surgical tissue specimens of a patient with recurrent lung adenosquamous carcinoma. The patient achieved 29 months of progression-free survival with ensartinib treatment. The results of RNA NGS from the same operative tissue identified EML4-ALK (E13:A20) fusion variant type I.ConclusionThis is the first case to provide real-world evidence of effective treatment of a patient with the 5′ NOK fusion form at the DNA level but functional EML4-ALK at the RNA level, illustrating the need for RNA testing in 5′ NOK patients.
Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories
Authors: Matharu Dollwin , Ponsero Alise J. , Dikareva Evgenia , Korpela Katri , Kolho Kaija-Leena , de Vos Willem M. , Salonen Anne 
Published: October 2022

Background and aimsBirth mode and other early life factors affect a newborn's microbial colonization with potential long-term health effects. Individual variations in early life gut microbiota development, especially their effects on the functional repertoire of microbiota, are still poorly characterized. This study aims to provide new insights into the gut microbiome developmental trajectories during the first year of life.MethodsOur study comprised 78 term infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 280 total samples), and their mothers were sampled in late pregnancy (n = 50). Fecal DNA was subjected to shotgun metagenomic sequencing. Infant samples were studied for taxonomic and functional maturation, and maternal microbiota was used as a reference. Hierarchical clustering on taxonomic profiles was used to identify the main microbiota developmental trajectories in the infants, and their associations with perinatal and postnatal factors were assessed.ResultsIn line with previous studies, infant microbiota composition showed increased alpha diversity and decreased beta diversity by age, converging toward an adult-like profile. However, we did not observe an increase in functional alpha diversity, which was stable and comparable with the mother samples throughout all the sampling points. Using a de novo clustering approach, two main infant microbiota clusters driven by Bacteroidaceae and Clostridiaceae emerged at each time point. The clusters were associated with birth mode and their functions differed mainly in terms of biosynthetic and carbohydrate degradation pathways, some of which consistently differed between the clusters for all the time points. The longitudinal analysis indicated three main microbiota developmental trajectories, with the majority of the infants retaining their characteristic cluster until 1 year. As many as 40% of vaginally delivered infants were grouped with infants delivered by C-section due to their clear and persistent depletion in Bacteroides. Intrapartum antibiotics, any perinatal or postnatal factors, maternal microbiota composition, or other maternal factors did not explain the depletion in Bacteroides in the subset of vaginally born infants.ConclusionOur study provides an enhanced understanding of the compositional and functional early life gut microbiota trajectories, opening avenues for investigating elusive causes that influence non-typical microbiota development.
The prevalence and associated factors of dysphagia in Parkinson's disease: A systematic review and meta-analysis
Authors: Gong Siyuan , Gao Yan , Liu Jihong , Li Jia , Tang Xueqin , Ran Qian , Tang Rongzhu , Liao Chunlian 
Published: October 2022

BackgroundThe prevalence and associated factors of dysphagia in Parkinson's disease (PD) are different in studies conducted in different countries. The purpose of our systematic review and meta-analysis was to evaluate the prevalence of dysphagia in PD and to clarify its associated factors.MethodsTwo researchers systematically searched PubMed, Embase, Web of Science, Cochrane Library, CNKI, Wanfang Database, SinoMed and VIP databases and manually searched references in the retrieved articles to identify potential research subjects. The last search was conducted on June 28, 2022. Finally, a total of 58 studies including 60 observations with 20,530 PD patients were included in our meta-analysis.ResultsThe meta-analysis estimated that the pooled prevalence rate of dysphagia in PD was 36.9% (95% CI: 30.7–43.6%) and instrumental examination showed a higher prevalence (57.3%, 95% CI: 44.3–69.1%). Oceania showed the highest prevalence of dysphagia in PD (56.3%) compared to Africa (39.5%), Asia (38.6%), Europe (36.1%) and America (28.9%). Dysphagia in PD was associated with older age, lower body mass index, longer disease duration, higher Hoehn and Yahr stage and levodopa equivalent daily dose, PIGD subtype, severe motor symptoms, drooling and higher levels of depression, and lower quality of life.ConclusionsIn conclusion, our meta-analysis showed that dysphagia occurs in more than one-third of PD patients and was associated with several demographic characteristics and PD-related characteristics, motor symptoms, non-motor symptoms, as well as decreased quality of life. It deserves early screening, diagnosis, and treatment in clinical practice to prevent serious complications from dysphagia.