bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vitamin D supplementation is beneficial in improving the prognosis of patients with acute respiratory failure in the intensive care unit: a retrospective study based on the MIMIC-IV database
Authors: Hu Song , He Qian , Xie Jun , Liu Hui , Zhou Rong , Li Chong 
Published: November 2023

BackgroundVitamin D plays a critical role in the regulation of multiple physiological pathways. Vitamin D deficiency may be a risk factor for life-threatening clinical conditions. Several studies have found that vitamin D supplementation in critically ill patients improves prognosis. The purpose of this study was to determine the association between vitamin D and the prognosis of patients with acute respiratory failure (ARF).MethodsIn this retrospective cohort study, we collected clinical information of ARF patients from the Medical Information Mart for Intensive Care IV (MIMIC-IV) version 2.0 database. The outcome of this study was in-hospital mortality, intensive care unit (ICU) mortality. Patients were divided into the no-vitamin D and vitamin D groups according to whether they received supplementation or not. The correlation between vitamin D and outcome was examined using Kaplan–Meier (KM) survival curves, Cox proportional risk regression models and subgroup analyses. Propensity-score matching (PSM) was used to ensure the robustness of our findings.ResultsThe study finally included 7,994 patients with ARF, comprising 6,926 and 1,068 in the no-vitamin D and vitamin D groups, respectively. The Kaplan–Meier survival curve indicated a significant difference in survival probability between the two groups. After adjustment for a series of confounders, the multivariate Cox proportional hazards models showed that the hazard ratio (95% confidence interval) values for in-hospital and ICU mortality in the no-vitamin D group were 1.67 (1.45, 1.93) and 1.64 (1.36, 1.98), respectively. The results of propensity score-matched (PSM) analysis were consistent with the original population. In the subgroup analysis, Vitamin D supplementation was associated with lower in-hospital mortality in patients with higher clinical scores (SOFA score ≥ 8, OASIS ≥ 38).ConclusionOur study concluded that Vitamin D supplementation may reduce in-hospital and ICU mortality in patients with ARF in the ICU. There may be a beneficial effect on in-hospital mortality in patients with higher clinical scores. Additional randomized controlled trials are needed to follow up to confirm the relationship between vitamin D supplementation and ARF.
Distribution, characterization, and evolution of heavy metal resistance genes and Tn7-like associated heavy metal resistance Gene Island of Burkholderia
Authors: Lan Yanhong , Liu Meijia , Song Yao , Cao Yu , Li Fosheng , Luo Dening , Qiao Dairong 
Published: November 2023

IntroductionBurkholderia is a rod-shaped aerobic Gram-negative bacteria with considerable genetic and metabolic diversity, which can beused for bioremediation and production applications, and has great biotechnology potential. However, there are few studies on the heavy metal resistance of the Burkholderia genus.MethodsIn this paper, the distribution, characteristics and evolution of heavy metal resistance genes in Burkholderia and the gene island of Tn7-like transposable element associated with heavy metal resistance genes in Burkholderia were studied by comparative genomic method based on the characteristics of heavy metal resistance.Results and discussionThe classification status of some species of the Burkholderia genus was improved, and it was found that Burkholderia dabaoshanensis and Burkholderia novacaledonica do not belong to the Burkholderia genus.Secondly, comparative genomics studies and pan-genome analysis found that the core genome of Burkholderia has alarger proportion of heavy metal resistance genes and a greater variety of heavy metalresistance genes than the subsidiary genome and strain specific genes. Heavy metal resistance genes are mostly distributed in the genome in the form of various gene clusters (for example, mer clusters, ars clusters, czc/cusABC clusters). At the same time, transposase, recombinase, integrase and other genes were foundupstream and downstream of heavy metal gene clusters, indicating that heavy metal resistance genes may beobtained through horizontal transfer. The analysis of natural selection pressure of heavy metal resistance genes showed that heavy metal resistance genes experienced strong purification selection under purification selection pressure in the genome.The Tn7 like transposable element of Burkholderia was associated with the heavy metal resistance gene island, and there were a large number of Tn7 transposable element insertion events in genomes. At the same time, BGI metal gene islands related to heavy metal resistance genes of Tn7 like transposable element were found, and these gene islands were only distributed in Burkholderia cepacia, Burkholderia polyvora, and Burkholderia contaminant.
Gut microbiota and risk of lower respiratory tract infections: a bidirectional two-sample Mendelian randomization study
Authors: Liu Wei , Wang Xinyan , Feng Ruizhi , Zhao Chen , Luo Jian , Zhang Xiawei , Liu Xuemei , Yang Mei , Min Jie , Mao Bing , Jiang Hongli 
Published: November 2023

IntroductionObservational studies have reported the association between gut microbiota and the risk of lower respiratory tract infections (LRTIs). However, whether the association reflects a causal relationship remains obscure.MethodsA bidirectional twosample Mendelian randomization (MR) analysis was conducted by assessing genome-wide association study (GWAS) summary statistics for gut microbiota taxa and five common LRTIs. MR methods including inverse-variance-weighted (IVW), MR-Egger, weighted median, simple mode, and weighted mode were used to analyze the causality. Gene pleiotropy was tested using MR-Egger regression and MR-PRESSO methods. Cochran’s Q test was used to check for heterogeneity. Leave-one-out analysis was used to assess the stability of effect sizes. Detected significant associations were validated by using an independent LRTI GWAS summary statistics dataset. An optional MR method of causal analysis using summary effect estimates (CAUSE) was further performed as a validation to avoid potential false-positive results.ResultsAccording to the MR-Egger estimates in forward MR analysis, a causal effect of gut Blautia on increased odds of bronchiectasis and pneumonia was suggested. MR-Egger regression pleiotropy intercept methods detected no significant horizontal pleiotropy between the instrumental variables of these associations. MR-PRESSO global test examined no potential horizontal pleiotropy. Cochran’s Q test showed that no heterogeneity biased the results. The leave-one-out sensitivity analyses suggested robust causality results. These associations with consistent effect direction were successfully replicated in IVW analysis by using the validation GWAS dataset. However, these evidence of causality did not survive after applying strict Bonferroni correction or CAUSE analysis. The reverse MR analysis failed to achieve consistent results in the effect of LRTIs on gut microbiota through comprehensive discovery and validation processes.DiscussionThis study established no strong causality between genetically predicted gut microbiome and the risk of lower respiratory tract infections. However, specific subtypes of microbial genera, such as Blautia, were identified as potential influencers and require further investigation, particularly at the species or strain levels.
Efficacy and safety of fecal microbiota transplantation for chronic insomnia in adults: a real world study
Authors: Fang Haiming , Yao Tingting , Li Wanli , Pan Na , Xu Hang , Zhao Qian , Su Yuan , Xiong Kangwei , Wang Jiajia 
Published: November 2023

ObjectiveTo assess the efficacy and safety of fecal microbiota transplantation (FMT) for adult chronic insomnia.MethodsPatients treated with FMT for chronic diseases were divided into chronic insomnia and non-insomnia group. The primary endpoint was the efficacy of FMT for insomnia 4 weeks after treatment, the secondary endpoints included the impacts of FMT on anxiety, depression, health-related quality of life, gut microbiota, and adverse events associated with FMT. Insomnia Severity Index (ISI) and Pittsburgh Sleep Quality Index (PSQI) were utilized to assess the efficacy of FMT on insomnia, self-rating anxiety/depression scale [Zung Self-Rating Anxiety Scale (SAS), Zung Self-Rating Depression Scale (SDS)] was employed to evaluate anxiety and depression. Quality of life was evaluated by SF-36. 16S rRNA sequencing was employed to analyze the gut microbiota and correlation analysis was performed.ResultsForty patients met the inclusion criteria and seven were excluded. 33 patients were enrolled and stratified into chronic insomnia group (N = 17) and non-insomnia group (N = 16). Compared to baseline, FMT significantly ameliorated the ISI (17.31 ± 5.12 vs. 5.38 ± 5.99), PSQI (14.56 ± 2.13 vs. 6.63 ± 4.67), SAS (54.25 ± 8.90 vs. 43.68 ± 10.64) and SDS (57.43 ± 10.96 vs. 50.68 ± 15.27) score and quality of life of chronic insomnia patients. 76.47% (13/17) of insomnia patients achieved the primary endpoints. In chronic insomnia patients, the relative abundance of Eggerthella marked enhanced at baseline, while the relative abundance of Lactobacillus, Bifidobacterium, Turicibacter, Anaerostipes, and Eisenbergiella significantly increased after FMT treatment, the latter positive correlated with the efficacy of FMT. Encouragingly, FMT also improved the sleep quality of non-insomnia patients.ConclusionEggerthella may potentially serve as a distinctive genus associated with chronic insomnia. FMT maybe a novel treatment option for adults with chronic insomnia and provide an alternative to traditional treatments for insomnia. The effects were positive correlated with the augmentation of probiotics, such as Bifidobacterium, Lactobacillus, Turicibacter, and Fusobacterium.
National Danish surveillance of invasive clinical Haemophilus influenzae isolates and their resistance profile
Authors: Slotved Hans-Christian , Johannesen Thor Bech , Stegger Marc , Dalby Tine , Fuursted Kurt 
Published: November 2023

IntroductionThis study aimed to investigate the epidemiology, serotype distribution, phenotypical antibiogram, and molecular resistance gene characteristics of invasive Haemophilus influenzae infections in Denmark from 2014 to 2022. Additionally, the potential impact of outdoor temperature and COVID-19 restrictions on the epidemiology of H. influenzae was assessed.Materials and methodsInvasive H. influenzae isolates were received from patients with positive culture results from cerebrospinal fluid, blood, or other sterile sites. Sample data were obtained from the Danish laboratory surveillance system/MiBa database, and whole-genome sequencing (WGS) was performed on the isolates. The incidence rates and distribution of H. influenzae cases were analyzed, and antibiotic susceptibility were assessed.ResultsA total of 1,007 invasive H. influenzae cases were identified, with serotyping conducted for 752 (74.7%) isolates. The median incidence per year of H. influenzae was 2.0 cases per 100,000, with the highest incidence in 2014 and the lowest in 2020. The majority of H. influenzae isolates were non-typeable H. influenzae (NTHi), while the most prominent serotypes were serotype f followed by serotype b. Bacteremia cases accounted for the majority (88.6%) of occurrences, although meningitis cases showed an increasing trend during the time period. The age group 85+ exhibited the highest incidence. The implementation of COVID-19 preventive interventions in 2020 resulted in a significant reduction in H. influenzae incidence, which returned to pre-COVID levels in 2021. A negative correlation was observed between monthly H. influenzae cases and outdoor temperature. An overall level of genetic beta-lactamase resistance of 26.3% was observed divided into 10.6% beta-lactamase-positive ampicillin-resistant (gBLPAR), 13.6% beta-lactamase-negative ampicillin-resistant (gBLNAR) and 2.1% beta-lactamase-positive amoxicillin clavulanate-resistant (gBLPACR). Other non-beta-lactam resistance traits were detected in 7.6% of isolates (primarily aminoglycoside-modifying enzymes).ConclusionThe overall incidence of H. influenzae in Denmark returned to stable levels after the COVID-19 epidemic, with NTHi strains dominating. The COVID-19 preventive interventions led to a major reduction in incidence. A significant negative correlation between the incidence of H. influenzae and temperature was observed. The study revealed an overall genetic beta-lactam resistance rate of 26.3%, and the concordance between genotypic and phenotypic beta-lactam resistance was high (98.2%).
Chronic interleukin-6 mediated neuroinflammation decreases anxiety, and impaires spatial memory in aged female mice
Authors: Wagnon Ingrid Marguerite , Jabur Lillian Jocelyn , Niedermayer Garry , Münch Gerald , Karl Tim , Chesworth Rose , Gyengesi Erika 
Published: November 2023

IntroductionNeuroinflammation is a common feature of many psychiatric disorders as well as a common underlying mechanism of neurodegenerative diseases. Sex has been shown to strongly influence the development as well as the clinical expression of these pathologies. However, there is still a neglect regarding the consideration of sex effects in rodent experiments, and a substantial underrepresentation of females in studies. This work set out to expand our knowledge of neuroinflammatory mechanisms in female mice, at both a behavioral and molecular level.MethodsThis study used GFAP-IL6 mice, a model of chronic neuroinflammation, in which interleukin-6 (IL6) is overexpressed in the central nervous system under the control of the glial fibrillary acidic protein (GFAP) promoter. We evaluated aged (11-15-month-old) wild type-like (WT) and GFAP-IL6 female mice in behavioral tests assessing anxiety (elevated plus-maze, EPM, Light/dark box), and spatial learning and memory (Y-maze, YM and Barnes Maze, BM) and associative learning (fear conditioning, FC). We also examined gene expression of markers linked to neuroinflammation, neurodegeneration and neurotransmission via RT-qPCR in brain regions involved in motor control, anxiety, learning and memory.ResultsFemale GFAP-IL6 mice exhibited reduced anxiety-like behavior in the EPM, and hypolocomotion in the light-dark test and EPM. Short-term memory impairment was evident in the YM but associative learning in FC was intact in GFAP-IL6 mice, suggesting domain-specific cognitive deficits in female GFAP-IL6 mice. In the BM, all mice showed intact learning and memory, but GFAP-IL6 mice exhibited higher latencies to enter the escape hole than WT mice. We analyzed the search strategy and found differences in the way GFAP-IL6 mice searched for the escape hole compared to WTs. RT-qPCR showed increased mRNA levels for molecules involved in pro-inflammatory pathways in the cerebellum, motor cortex, hippocampus, and amygdala in GFAP-IL6 mice. Of the regions examined, the cerebellum and the hippocampus showed upregulation of neuroinflammatory makers as well as dysregulation of glutamatergic and GABAergic neurotransmission gene expression in GFAP-IL6 mice compared to WTs.ConclusionIn conclusion, we showed that chronic neuroinflammation via IL6 overexpression in aged female mice led to a less anxious-like phenotype, hypolocomotion and impaired intermediate-term spatial learning and memory in the YM.
A quantization algorithm of visual fatigue based on underdamped second order stochastic resonance for steady state visual evoked potentials
Authors: Tian Peiyuan , Xu Guanghua , Han Chengcheng , Zhang Xun , Zheng Xiaowei , Wei Fan , Zhang Sicong , Zhao Zhe 
Published: November 2023

IntroductionIn recent years, more and more attention has been paid to the visual fatigue caused by steady state visual evoked potential (SSVEP) paradigm. It is well known that the large-scale application of brain-computer interface is closely related to SSVEP, and the fatigue caused by SSVEP paradigm leads to the reduction of application effect. At present, the mainstream method of objectively quantifying visual fatigue in SSVEP paradigm is based on traditional canonical correlation analysis (CCA).MethodsIn this paper, we propose a new SSVEP paradigm visual fatigue quantification algorithm based on underdamped second-order stochastic resonance (USSR) to accurately quantify visual fatigue caused by SSVEP paradigm in different working modes using single-channel electroencephalogram (EEG) signals. This scheme uses the fixed-step energy parameter optimization algorithm we designed, combined with the USSR model, to significantly improve the signal-to-noise ratio of the processed signal at the target characteristic frequency. We not only compared the new algorithm with CCA, but also with the traditional subjective quantitative visual fatigue gold standard Likert fatigue scale.ResultsThere was no significant difference (p = 0.090) between the quantitative value of paradigm fatigue obtained by the single channel SSVEP processed by the new algorithm and the gold standard of subjective fatigue quantification, while there was a significant difference (p &lt; 0.001***) between the quantitative value of paradigm fatigue obtained by the traditional multi-channel CCA algorithm and the gold standard of subjective fatigue quantification.DiscussionThe conclusion shows that the quantization value obtained by the new algorithm can better match the subjective gold standard score, which also shows that the new algorithm is more reliable, which reflects the superiority of the new algorithm.
Efficacy and safety of tyrosine kinase inhibitors plus PD-1 inhibitor in patients with transarterial chemoembolization- refractory hepatocellular carcinoma: a two-center retrospective study
Authors: Gao Ya , Lu Haohao , Xiong Zhifan 
Published: November 2023

ObjectTo investigate the efficacy and safety of tyrosine kinase inhibitors (TKIs: sorafenib and lenvatinib) plus PD-1 inhibitor (camrelizumab) versus TKIs alone in transarterial chemoembolization-refractory (TACE-refractory) hepatocellular carcinoma (HCC).Materials and methodsData of TACE-refractory HCC patients treated with TACE+TKIs+PD-1 inhibitor (TACE+TKIs+PD-1group) (n=57) or TACE+TKIs (TACE+TKIs group) (n=50) from January 2019 to January 2022 were retrospectively collected and analyzed. The differences in overall survival (OS), progression-free survival (PFS), tumor responses (based on modified Response Evaluation Criteria in Solid Tumors) and adverse events (AEs) were compared between the two groups. Potential factors affecting OS and PFS were evaluated by univariate and multivariate analyses.ResultsCompared with the TKIs group, both PFS and OS were prolonged in the TACE+TKIs+PD-1 group (median PFS: 7 months vs. 5 months, P=0.007; median OS: 17 months vs. 11 months, P=0.002). In multivariate analysis, tumor size and treatment were independent prognostic factors for PFS and OS. The incidence and severity of AEs related to the treatment between the two groups showed no significant difference.ConclusionThe treatment of TACE combined with TKIs plus camrelizumab demonstrated promising efficacy and safety in TACE-refractory HCC.
The effect of an exopolysaccharide probiotic molecule from Bacillus subtilis on breast cancer cells
Authors: Nguyen Mai R. , Ma Emily , Wyatt Debra , Knight Katherine L. , Osipo Clodia 
Published: November 2023

IntroductionMany well-known risk factors for breast cancer are associated with dysbiosis (an aberrant microbiome). However, how bacterial products modulate cancer are poorly understood. In this study, we investigated the effect of an exopolysaccharide (EPS) produced by the commensal bacterium Bacillus subtilis on breast cancer phenotypes. Although B. subtilis is commonly included in probiotic preparations and its EPS protects against inflammatory diseases, it was virtually unknown whether B. subtilis-derived EPS affects cancer.MethodsThis work investigated effects of EPS on phenotypes of breast cancer cells as a cancer model. The phenotypes included proliferation, mammosphere formation, cell migration, and tumor growth in two immune compromised mouse models. RNA sequencing was performed on RNA from four breast cancer cells treated with PBS or EPS. IKKβ or STAT1 signaling was assessed using pharmacologic or RNAi-mediated knock down approaches. ResultsShort-term treatment with EPS inhibited proliferation of certain breast cancer cells (T47D, MDA-MB-468, HCC1428, MDA-MB-453) while having little effect on others (MCF-7, MDA-MB-231, BT549, ZR-75-30). EPS induced G1/G0 cell cycle arrest of T47D cells while increasing apoptosis of MDA-MB-468 cells. EPS also enhanced aggressive phenotypes in T47D cells including cell migration and cancer stem cell survival. Long-term treatment with EPS (months) led to resistance in vitro and promoted tumor growth in immunocompromised mice. RNA-sequence analysis showed that EPS increased expression of pro-inflammatory pathways including STAT1 and NF-κB. IKKβ and/or STAT1 signaling was necessary for EPS to modulate phenotypes of EPS sensitive breast cancer cells. DiscussionThese results demonstrate a multifaceted role for an EPS molecule secreted by the probiotic bacterium B. subtilis on breast cancer cell phenotypes. These results warrant future studies in immune competent mice and different cancer models to fully understand potential benefits and/or side effects of long-term use of probiotics.
Long-term follow-up after retrosternal ileocolic esophagoplasty in two cases of long-gap esophageal atresia: why it is still a valid option as a rescue strategy
Authors: Léonard Matthieu , Deswysen Yannick , Scheers Isabelle , Thoma Maximilien , de Magnée Catherine , Stephenne Xavier , Dumitriu Dana , Menten Renaud , Reding Raymond , Tambucci Roberto 
Published: November 2023

IntroductionEsophageal replacement surgery in children is sometimes necessary for long-gap esophageal atresia. Ileocolic esophagoplasty in the retrosternal space can serve as a good alternative technique in case of hostile posterior mediastinum. We present two cases of successful ileocolic transposition performed at 6 months of age.MethodsEsophageal replacement was performed through a midline laparotomy incision associated with a left cervical approach. The ileocolic transplant was pediculized on the right superior colic artery after ligating the right colic and ileocolic vessels. A retrosternal tunnel was created, and the ileocolic transplant pulled through it to reach the cervical region. Proximally, esophageal-ileal anastomosis and, distally, colonic–gastric anastomosis were performed. Ileocolic continuity was repaired.ResultsThere were no early postoperative complications. In both cases, the patients presented oral feeding difficulties during the first 6 postoperative months. Thereafter, full oral feeding was achieved, and both patients were clinically asymptomatic during the following 18 and 20 years, respectively, with satisfactory oral radiological assessments, showing no redundancy or inappropriate growth of the graft and no anastomotic stricture. Currently, these patients do not complain of dysphagia, pathological reflux, or respiratory symptoms.ConclusionWhen native esophagus preservation in long-gap esophageal atresia is estimated unfeasible, ileocolic transposition in the retrosternal space might be considered a good and safe option, particularly in those difficult cases after multiple previous surgical attempts and mediastinitis. This technique is putatively associated with a beneficial anti-reflux effect, thanks to the presence of the ileocecal valve, in preventing cervical peptic esophagitis. Long-term follow-up confirms that the transposed colon in the retrosternal space did not suffer any abnormal modification in size and growth.