bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of novel parameters for pathogen identification in clinical metagenomic next-generation sequencing
Authors: Jiang Xiwen , Yan Jinghai , Huang Hao , Ai Lu , Yu Xuegao , Zhong Pengqiang , Chen Yili , Liang Zhikun , Qiu Wancen , Huang Huiying , Yan Wenyan , Liang Yan , Chen Peisong , Wang Ruizhi 
Published: November 2023

Introduction: Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for rapid pathogen identification in clinical practice. However, the parameters used to interpret mNGS data, such as read count, genus rank, and coverage, lack explicit performance evaluation. In this study, the developed indicators as well as novel parameters were assessed for their performance in bacterium detection.Methods: We developed several relevant parameters, including 10M normalized reads, double-discard reads, Genus Rank Ratio, King Genus Rank Ratio, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank. These parameters, together with frequently used read indicators including raw reads, reads per million mapped reads (RPM), transcript per kilobase per million mapped reads (TPM), Genus Rank, and coverage were analyzed for their diagnostic efficiency in bronchoalveolar lavage fluid (BALF), a common source for detecting eight bacterium pathogens: Acinetobacter baumannii, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Hemophilus influenzae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Aspergillus fumigatus.Results: The results demonstrated that these indicators exhibited good diagnostic efficacy for the eight pathogens. The AUC values of all indicators were almost greater than 0.9, and the corresponding sensitivity and specificity values were almost greater than 0.8, excepted coverage. The negative predictive value of all indicators was greater than 0.9. The results showed that the use of double-discarded reads, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank exhibited better diagnostic efficiency than that of raw reads, RPM, TPM, and in Genus Rank. These parameters can serve as a reference for interpreting mNGS data of BALF. Moreover, precision filters integrating our novel parameters were built to detect the eight bacterium pathogens in BALF samples through machine learning.Summary: In this study, we developed a set of novel parameters for pathogen identification in clinical mNGS based on reads and ranking. These parameters were found to be more effective in diagnosing pathogens than traditional approaches. The findings provide valuable insights for improving the interpretation of mNGS reports in clinical settings, specifically in BALF analysis.
The safety and efficacy of endoscopic ultrasound-guided portal pressure gradient measurement with concomitant endoscopic ultrasound-guided liver biopsy: a systematic review
Authors: Malik Alexander , Yousaf Muhammad Nadeem , Hammoud Ghassan M. 
Published: November 2023

IntroductionPortal hypertension (PH) is a complication of advanced liver disease. Traditionally, PH has been quantified using hepatic venous pressure gradient (HVPG) through an indirect transjugular approach requiring ionizing radiation exposure. Endoscopic ultrasound-guided porto-systemic pressure gradient (EUS-PPG) measurement is an emerging alternative, minimally invasive technique that provides direct portal pressure measurement. The aim of this systematic review is to evaluate the safety and efficacy of EUS-PPG measurement and concomitant EUS-guided liver biopsy (EUS-LB) in patients with chronic liver disease.MethodsThe preferred reporting items for systematic reviews and meta-analyses method was used. A PubMed, Medline, Web of Science, Google Scholar, and CINAHL search for terms “endoscopic ultrasound,” “EUS,” and “portal pressure gradient” was used to identify qualifying studies. Eligible studies included those which were published before 2022, reporting outcomes of EUS-PPG measurement, simultaneous EUS-LB if applicable, and adverse events rate. Risk of bias was assessed by Egger’s test. Results were synthesized using I2 to test heterogeneity.ResultsFour published studies including 147 patients met inclusion criteria, with mean age 59.6 years, 59% male. Indications for EUS-PPG measurement were history of chronic liver disease or suspected cirrhosis, viral hepatitis, alcohol associated liver disease, hepatic sinusoidal obstruction or Budd Chiari syndrome. The pooled technical success rate of EUS-PPG measurements was 98.61% with 95% confidence interval of 95.20% - 99.82%. A 25-gauge needle was used in 92% (135/147) of patients. EUS-PPG measurement was performed through a transgastric approach in all 147 (100%) patients using a compact manometer with pressure transducer and non-compressible tubing. The mean PPG was 10.07 (range 6.44 – 13.70) mmHg. Ninety-five patients underwent simultaneous EUS-LB using 19G needle with wet suction technique. Technical success rate of EUS-LB was 100% and specimen was adequate in 99% (94/95) patients to establish histological diagnosis. There were no major life-threatening complications of the EUS-PPG procedure. Predominant adverse events were abdominal pain 6.1% (9/147) and sore throat 5.4% (8/147).ConclusionEUS-PPG measurement is safe and useful in providing an assessment of portal pressure in patients with chronic liver disease. Future studies are needed to evaluate whether there is consistent correlation between EUS-PPG measurements and histologic fibrosis stage by liver biopsy.
Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance
Authors: Munjoma Privilege Tendai , Chandiwana Panashe , Wyss Jacqueline , Mazhandu Arthur John , Jordi Sebastian Bruno Ulrich , Gutsire Rutendo , Katsidzira Leolin , Yilmaz Bahtiyar , Misselwitz Benjamin , Duri Kerina 
Published: November 2023

IntroductionCombination antiretroviral therapy (cART) effectively controls HIV; however, chronic low-level viremia and gut microbiota dysbiosis remain significant drivers of gut and systemic inflammation. In this study, we explored the relationship between gut microbiota composition, intestinal inflammation, microbial translocation, and systemic inflammation in women on cART in Sub-Saharan Africa.MethodsWe conducted a study in HIV-infected and HIV-uninfected lactating women followed up at 6 weeks and 6 months postpartum in Harare, Zimbabwe. We used 16S ribosomal Ribonucleic Acid (rRNA) sequencing and MesoScale Discovery V-Plex assays to examine the gut microbiome and to quantify plasma inflammatory biomarkers, respectively. In addition, we measured fecal calprotectin, plasma lipopolysaccharide-binding protein (LBP), and soluble cluster of differentiation 14 (sCD14) by enzyme-linked immunosorbent assay to assess gut inflammation, microbial translocation, and monocyte/macrophage activation.ResultsA group of 77 lactating women were studied, of which 35% were HIV-infected. Fecal calprotectin levels were similar by HIV status at both follow-up time points. In the HIV-infected group at 6 weeks postpartum, fecal calprotectin was elevated: median (interquartile range) [158.1 µg/g (75.3–230.2)] in women who had CD4+ T-lymphocyte counts &lt;350 cells/µL compared with those with ≥350 cells/µL [21.1 µg/g (0–58.4)], p = 0.032. Plasma sCD14 levels were significantly higher in the HIV-infected group at both 6 weeks and 6 months postpartum, p &lt; 0.001. Plasma LBP levels were similar, but higher levels were observed in HIV-infected women with elevated fecal calprotectin. We found significant correlations between fecal calprotectin, LBP, and sCD14 with proinflammatory cytokines. Gut microbial alpha diversity was not affected by HIV status and was not affected by use of antibiotic prophylaxis. HIV significantly affected microbial beta diversity, and significant differences in microbial composition were noted. The genera Slackia and Collinsella were relatively more abundant in the HIV-infected group, whereas a lower relative abundance of Clostriduim sensu_stricto_1 was observed. Our study also found correlations between gut microbial taxa abundance and systemic inflammatory biomarkers.Discussion and conclusionHIV-infected lactating women had increased immune activation and increased microbial translocation associated with increased gut inflammation. We identified correlations between the gut inflammation and microbial composition, microbial translocation, and systemic inflammation. The interplay of these parameters might affect the health of this vulnerable population.
Impact of SARS-CoV-2 vaccination on FcγRIIIA/CD16 dynamics in Natural Killer cells: relevance for antibody-dependent functions
Authors: Capuano Cristina , De Federicis Davide , Ciuti Daniel , Turriziani Ombretta , Angeloni Antonio , Anastasi Emanuela , Giannini Giuseppe , Belardinilli Francesca , Molfetta Rosa , Alvaro Domenico , Palmieri Gabriella , Galandrini Ricciarda 
Published: November 2023

IntroductionNatural Killer (NK) cells contribute to the protective effects of vaccine-induced antibodies thanks to the low affinity receptor for IgG, FcγRIIIA/CD16, whose aggregation leads to the killing of infected cells and IFNγ release, through which they potentiate adaptive immune responses.MethodsForty-seven healthy young individuals undergoing either homologous (ChAdOx1-S/ChAdOx1-S) or heterologous (ChAdOx1-S/BNT162B2) SARS-CoV-2 vaccination settings were recruited. Peripheral blood samples were collected immediately prior to vaccination and 8 weeks after the booster dose. The phenotypic and functional profile of NK cells was evaluated by flow cytometry at both time points. Serum samples were tested to evaluate circulating anti-Spike IgG levels and cytomegalovirus serostatus. CD16 F158V polymorphism was assessed by sequencing analysis.ResultsThe downregulation of CD16 and the selective impairment of antibody-dependent cytotoxicity and IFNγ production in CD56dim NK population, persisting 8 weeks after boosting, were observed in heterologous, but not in homologous SARS-CoV-2 vaccination scheme. While the magnitude of CD16-dependent functions of the global CD56dim pool correlated with receptor levels before and after vaccination, the responsivity of NKG2C+ subset, that displays amplified size and functionality in HCMV+ individuals, resulted intrinsically insensitive to CD16 levels. Individual CD16 responsiveness was also affected by CD16F158V polymorphism; F/F low affinity individuals, characterized by reduced CD16 levels and functions independently of vaccination, did not show post-vaccinal functional impairment with respect to intermediate and high affinity ones, despite a comparable CD16 downregulation. Further, CD16 high affinity ligation conditions by means of afucosylated mAb overcame vaccine-induced and genotype-dependent functional defects. Finally, the preservation of CD16 expression directly correlated with anti-Spike IgG titer, hinting that the individual magnitude of receptor-dependent functions may contribute to the amplification of the vaccinal response.ConclusionThis study demonstrates a durable downmodulation of CD16 levels and Ab-dependent NK functions after SARS-CoV-2 heterologous vaccination, and highlights the impact of genetic and environmental host-related factors in modulating NK cell susceptibility to post-vaccinal Fc-dependent functional impairment.
Mechanical analysis of helmeted headforms under ballistic impact with implications in performance evaluation of ballistic helmets
Authors: Harmukh Atul , Singh Abhilash , Kumar Praveen , Verma Sanjeev K. , Kumar Pal Dinesh , Ganpule S. G. 
Published: November 2023

Behind helmet blunt trauma is a significant health concern in modern warfare. The ballistic response of the human head under ballistic impact is highly sought. Towards this end, we conducted ballistic experiments on three different headforms. The following headforms were considered: a) National Institute of Justice based rigid headform, b) Hybrid-III based flexible headform, and c) head model based headform. Headforms b, c were assembled with the Hybrid-III neck. An advanced combat helmet was fitted to the headforms. Helmet-head assembly was subjected to a 9 mm × 19 mm full metal jacket projectile having velocities of 430 ± 15 m/s. The response of the head surrogate in the front, back, side, and crown orientations was studied. Back face deformation (BFD), head kinematics, and intracranial pressures in headforms were measured. In addition, equivalent stress and maximum principal strain in the brain were obtained using concurrent finite element simulations. Results suggest that both local (i.e., due to the localized crushing of the helmet) and global (i.e., due to the bulk motion of the helmet-head parenchyma) responses were dominant under investigated ballistic impacts. Further, the type of the headform affected the biomechanical response. As compared to the rigid headform, a statistically significant increase in head kinematics was observed with the flexible headforms; changes in BFD were statistically insignificant. The orientation dependent responses have been observed. Overall, these results provide novel insights regarding the ballistic response of the headforms with the combat helmet and underscore critical considerations during the ballistic evaluation of helmets.
Identification of immunological characterization and Anoikis-related molecular clusters in rheumatoid arthritis
Authors: Zhao Jianan , Wei Kai , Shi Yiming , Jiang Ping , Xu Lingxia , Chang Cen , Xu Linshuai , Zheng Yixin , Shan Yu , Liu Jia , Li Li , Guo Shicheng , Schrodi Steven J. , Wang Rongsheng , He Dongyi 
Published: November 2023

Objective: To investigate the potential association between Anoikis-related genes, which are responsible for preventing abnormal cellular proliferation, and rheumatoid arthritis (RA).Methods: Datasets GSE89408, GSE198520, and GSE97165 were obtained from the GEO with 282 RA patients and 28 healthy controls. We performed differential analysis of all genes and HLA genes. We performed a protein-protein interaction network analysis and identified hub genes based on STRING and cytoscape. Consistent clustering was performed with subgrouping of the disease. SsGSEA were used to calculate immune cell infiltration. Spearman’s correlation analysis was employed to identify correlations. Enrichment scores of the GO and KEGG were calculated with the ssGSEA algorithm. The WGCNA and the DGIdb database were used to mine hub genes’ interactions with drugs.Results: There were 26 differentially expressed Anoikis-related genes (FDR = 0.05, log2FC = 1) and HLA genes exhibited differential expression (P &lt; 0.05) between the disease and control groups. Protein-protein interaction was observed among differentially expressed genes, and the correlation between PIM2 and RAC2 was found to be the highest; There were significant differences in the degree of immune cell infiltration between most of the immune cell types in the disease group and normal controls (P &lt; 0.05). Anoikis-related genes were highly correlated with HLA genes. Based on the expression of Anoikis-related genes, RA patients were divided into two disease subtypes (cluster1 and cluster2). There were 59 differentially expressed Anoikis-related genes found, which exhibited significant differences in functional enrichment, immune cell infiltration degree, and HLA gene expression (P &lt; 0.05). Cluster2 had significantly higher levels in all aspects than cluster1 did. The co-expression network analysis showed that cluster1 had 51 hub differentially expressed genes and cluster2 had 72 hub differentially expressed genes. Among them, three hub genes of cluster1 were interconnected with 187 drugs, and five hub genes of cluster2 were interconnected with 57 drugs.Conclusion: Our study identified a link between Anoikis-related genes and RA, and two distinct subtypes of RA were determined based on Anoikis-related gene expression. Notably, cluster2 may represent a more severe state of RA.
A non-expensive bidimensional kinematic balance assessment can detect early postural instability in people with Parkinson’s disease
Authors: Santos Gabriel Venas , d'Alencar Matheus Silva , Helene Andre Frazão , Roque Antonio C. , Miranda José Garcia Vivas , Piemonte Maria Elisa Pimentel 
Published: November 2023

BackgroundPostural instability is a debilitating cardinal symptom of Parkinson’s disease (PD). Its onset marks a pivotal milestone in PD when balance impairment results in disability in many activities of daily living. Early detection of postural instability by non-expensive tools that can be widely used in clinical practice is a key factor in the prevention of falls in widespread population and their negative consequences.ObjectiveThis study aimed to investigate the effectiveness of a two-dimensional balance assessment to identify the decline in postural control associated with PD progression.MethodsThis study recruited 55 people with PD, of which 37 were men. Eleven participants were in stage I, twenty-three in stage II, and twenty-one in stage III. According to the Hoehn and Yahr (H&amp;Y) rating scale, three clinical balance tests (Timed Up and Go test, Balance Evaluation Systems Test, and Push and Release test) were carried out in addition to a static stance test recorded by a two-dimensional movement analysis software. Based on kinematic variables generated by the software, a Postural Instability Index (PII) was created, allowing a comparison between its results and those obtained by clinical tests.ResultsThere were differences between sociodemographic variables directly related to PD evolution. Although all tests were correlated with H&amp;Y stages, only the PII was able to differentiate the first three stages of disease evolution (H&amp;Y I and II: p = 0.03; H&amp;Y I and III: p = 0.00001; H&amp;Y II and III: p = 0.02). Other clinical tests were able to differentiate only people in the moderate PD stage (H&amp;Y III).ConclusionBased on the PII index, it was possible to differentiate the postural control decline among the first three stages of PD evolution. This study offers a promising possibility of a low-cost, early identification of subtle changes in postural control in people with PD in clinical practice.
Psychometric evaluation and reference values for the German Postconcussion Symptom Inventory (PCSI-SR8) in children aged 8–12 years
Authors: Zeldovich Marina , Krol Leonie , Timmermann Dagmar , Krenz Ugne , Arango-Lasprilla Juan Carlos , Gioia Gerard , Brockmann Knut , Koerte Inga K. , Buchheim Anna , Roediger Maike , Kieslich Matthias , von Steinbuechel Nicole , Cunitz Katrin 
Published: November 2023

BackgroundPost-concussion symptoms (PCS) are a common consequence of pediatric traumatic brain injury (pTBI). They include cognitive, emotional, and physical disturbances. To address the lack of age-adapted instruments assessing PCS after pTBI, this study examines the psychometric properties of the German 17-item post-TBI version of the Postconcussion Symptom Inventory (PCSI-SR8) in children aged 8–12 years. The study also aims to establish reference values based on data from a pediatric general population sample to better estimate the prevalence and clinical relevance of PCS after pTBI in clinical and research settings.MethodsA total of 132 children aged 8–12 years from a post-acute TBI sample and 1,047 from a general population sample were included in the analyses. The questionnaire was translated from English into German and linguistically validated using forward and backward translation and cognitive debriefing to ensure comprehensibility of the developed version. Reliability and validity were examined; descriptive comparisons were made with the results of the English study. Measurement invariance (MI) analyses between TBI and general population samples were conducted prior to establishing reference values. Factors contributing to the total and scale scores of the PCSI-SR8 were identified using regression analyses. Reference values were calculated using percentiles.ResultsMost children (TBI: 83%; general population: 79%) rated at least one symptom as “a little” bothersome. The German PCSI-SR8 met the psychometric assumptions in both samples and was comparable to the English version. The four-factor structure comprising physical, emotional, cognitive, and fatigue symptoms could be replicated. The MI assumption was retained. Therefore, reference values could be provided to determine the symptom burden of patients in relation to a comparable general population. Clinical relevance of reported symptoms is indicated by a score of 8, which is one standard deviation above the mean of the general population sample.ConclusionThe German version of the PCSI-SR8 is suitable for assessment of PCS after pTBI. The reference values allow for a more comprehensive evaluation of PCS following pTBI. Future research should focus on validation of the PCSI-SR8 in more acute phases of TBI, psychometric examination of the pre-post version, and child-proxy comparisons.
A model for predicting return of spontaneous circulation and neurological outcomes in adults after in-hospital cardiac arrest: development and evaluation
Authors: Li Zheng , Xing Jihong 
Published: November 2023

IntroductionIn-hospital CA (IHCA) is associated with rates of high incidence, low return of spontaneous circulation (ROSC), low survival to discharge, and poor neurological outcomes. We aimed to construct and evaluate prediction models for non-return of spontaneous circulation (non-ROSC) and poor neurological outcomes 12 months after ROSC (PNO-12).MethodsWe retrospectively analyzed baseline and clinical data from patients experiencing cardiac arrest (CA) in a big academic hospital of Jilin University in China. Patients experiencing CA between September 1, 2019 and December 31, 2020 were categorized into the ROSC and non-ROSC groups. Patients maintaining ROSC &gt;20 min were divided into the good and PNO-12 subgroups.ResultsUnivariate and multivariate logistic regression identified independent factors associated with non-ROSC and PNO-12. Two nomogram prediction models were constructed and evaluated. Of 2,129 patients with IHCA, 851 were included in the study. Multivariate logistic regression analysis revealed that male sex, age &gt;80 years, CPR duration &gt;23 min, and total dose of adrenaline &gt;3 mg were significant risk factors for non-ROSC. Before CA, combined arrhythmia, initial defibrillation rhythm, and advanced airway management (mainly as endotracheal intubation) also influenced outcomes. The area under the receiver operating characteristic curve in the prediction model was 0.904 (C-index: 0.901). Respiratory failure, shock, CA in the monitoring area, advanced airway management, and noradrenaline administration were independent risk factors for PNO-12. The AUC was 0.912 (C-index: 0.918).ConclusionsPrediction models based on IHCA data could be helpful to reduce mortality rates and improve prognosis.