bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individualized survival prediction and surgery recommendation for patients with glioblastoma
Authors: Zhu Enzhao , Wang Jiayi , Jing Qi , Shi Weizhong , Xu Ziqin , Ai Pu , Chen Zhihao , Dai Zhihao , Shan Dan , Ai Zisheng 
Published: May 2024

BackgroundThere is a lack of individualized evidence on surgical choices for glioblastoma (GBM) patients.AimThis study aimed to make individualized treatment recommendations for patients with GBM and to determine the importance of demographic and tumor characteristic variables in the selection of extent of resection.MethodsWe proposed Balanced Decision Ensembles (BDE) to make survival predictions and individualized treatment recommendations. We developed several DL models to counterfactually predict the individual treatment effect (ITE) of patients with GBM. We divided the patients into the recommended (Rec.) and anti-recommended groups based on whether their actual treatment was consistent with the model recommendation.ResultsThe BDE achieved the best recommendation effects (difference in restricted mean survival time (dRMST): 5.90; 95% confidence interval (CI), 4.40–7.39; hazard ratio (HR): 0.71; 95% CI, 0.65–0.77), followed by BITES and DeepSurv. Inverse probability treatment weighting (IPTW)-adjusted HR, IPTW-adjusted OR, natural direct effect, and control direct effect demonstrated better survival outcomes of the Rec. group.ConclusionThe ITE calculation method is crucial, as it may result in better or worse recommendations. Furthermore, the significant protective effects of machine recommendations on survival time and mortality indicate the superiority of the model for application in patients with GBM. Overall, the model identifies patients with tumors located in the right and left frontal and middle temporal lobes, as well as those with larger tumor sizes, as optimal candidates for SpTR.
Identifying the risk factors of ICU-acquired fungal infections: clinical evidence from using machine learning
Authors: Zhao Yi-si , Lai Qing-pei , Tang Hong , Luo Ren-jie , He Zhi-wei , Huang Wei , Wang Liu-yang , Zhang Zheng-tao , Lin Shi-hui , Qin Wen-jian , Xu Fang 
Published: May 2024

BackgroundFungal infections are associated with high morbidity and mortality in the intensive care unit (ICU), but their diagnosis is difficult. In this study, machine learning was applied to design and define the predictive model of ICU-acquired fungi (ICU-AF) in the early stage of fungal infections using Random Forest.ObjectivesThis study aimed to provide evidence for the early warning and management of fungal infections.MethodsWe analyzed the data of patients with culture-positive fungi during their admission to seven ICUs of the First Affiliated Hospital of Chongqing Medical University from January 1, 2015, to December 31, 2019. Patients whose first culture was positive for fungi longer than 48 h after ICU admission were included in the ICU-AF cohort. A predictive model of ICU-AF was obtained using the Least Absolute Shrinkage and Selection Operator and machine learning, and the relationship between the features within the model and the disease severity and mortality of patients was analyzed. Finally, the relationships between the ICU-AF model, antifungal therapy and empirical antifungal therapy were analyzed.ResultsA total of 1,434 cases were included finally. We used lasso dimensionality reduction for all features and selected six features with importance ≥0.05 in the optimal model, namely, times of arterial catheter, enteral nutrition, corticosteroids, broadspectrum antibiotics, urinary catheter, and invasive mechanical ventilation. The area under the curve of the model for predicting ICU-AF was 0.981 in the test set, with a sensitivity of 0.960 and specificity of 0.990. The times of arterial catheter (p = 0.011, OR = 1.057, 95% CI = 1.053–1.104) and invasive mechanical ventilation (p = 0.007, OR = 1.056, 95%CI = 1.015–1.098) were independent risk factors for antifungal therapy in ICU-AF. The times of arterial catheter (p = 0.004, OR = 1.098, 95%CI = 0.855–0.970) were an independent risk factor for empirical antifungal therapy.ConclusionThe most important risk factors for ICU-AF are the six time-related features of clinical parameters (arterial catheter, enteral nutrition, corticosteroids, broadspectrum antibiotics, urinary catheter, and invasive mechanical ventilation), which provide early warning for the occurrence of fungal infection. Furthermore, this model can help ICU physicians to assess whether empiric antifungal therapy should be administered to ICU patients who are susceptible to fungal infections.
Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron
Authors: Yu Biao , Lu Zheng , Zhong Saiyi , Cheong Kit-Leong 
Published: May 2024

IntroductionResearch on the mechanism of marine polysaccharide utilization by Bacteroides thetaiotaomicron has drawn substantial attention in recent years. Derived from marine algae, the marine algae polysaccharides could serve as prebiotics to facilitate intestinal microecological balance and alleviate colonic diseases. Bacteroides thetaiotaomicron, considered the most efficient degrader of polysaccharides, relates to its capacity to degrade an extensive spectrum of complex polysaccharides. Polysaccharide utilization loci (PULs), a specialized organization of a collection of genes-encoded enzymes engaged in the breakdown and utilization of polysaccharides, make it possible for Bacteroides thetaiotaomicron to metabolize various polysaccharides. However, there is still a paucity of comprehensive studies on the procedure of polysaccharide degradation by Bacteroides thetaiotaomicron.MethodsIn the current study, the degradation of four kinds of marine algae polysaccharides, including sodium alginate, fucoidan, laminarin, and Pyropia haitanensis polysaccharides, and the underlying mechanism by Bacteroides thetaiotaomicron G4 were investigated. Pure culture of Bacteroides thetaiotaomicron G4 in a substrate supplemented with these polysaccharides were performed. The change of OD600, total carbohydrate contents, and molecular weight during this fermentation were determined. Genomic sequencing and bioinformatic analysis were further performed to elucidate the mechanisms involved. Specifically, Gene Ontology (GO) annotation, Clusters of Orthologous Groups (COG) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were utilized to identify potential target genes and pathways.ResultsUnderlying target genes and pathways were recognized by employing bioinformatic analysis. Several PULs were found that are anticipated to participate in the breakdown of these four polysaccharides. These findings may help to understand the interactions between these marine seaweed polysaccharides and gut microorganisms.DiscussionThe elucidation of polysaccharide degradation mechanisms by Bacteroides thetaiotaomicron provides valuable insights into the utilization of marine polysaccharides as prebiotics and their potential impact on gut health. Further studies are warranted to explore the specific roles of individual PULs and their contributions to polysaccharide metabolism in the gut microbiota.
Metagenomic and metabolomic analyses reveal differences in rumen microbiota between grass- and grain-fed Sanhe heifers
Authors: Zhang Xinyu , Wang Wei , Wang Yajing , Cao Zhijun , Yang Hongjian , Li Shengli 
Published: May 2024

IntroductionThe aim of this study was to investigate the effects of diets on the composition and function of rumen microbiome and metabolites in Sanhe heifers.MethodsMetagenomic and metabolomic analyses were performed using rumen fluid samples collected from Sanhe heifers (n = 20) with similar body weights and ages from grass-fed and grain-fed systems.ResultsThe grain-fed group exhibited more intensive rumen fermentation than the grass-fed group. However, the grass-fed group exhibited carbohydrate metabolism and methane production higher than that of the grain-fed group; these increases were observed as a higher abundance of various bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Lentisphaerae, and Verrucomicrobia), families (Lachnospiraceae, Eubacteriaceae, and Eggerthellaceae), and the archaeal family Methanobacteriaceae. A comparison of genes encoding carbohydrate-active enzymes, using Kyoto Encyclopedia of Genes and Genome profiles, revealed noteworthy differences in the functions of rumen microbiota; these differences were largely dependent on the feeding system.ConclusionThese results could help manipulate and regulate feed efficiency in Sanhe cattle.
Persistence and risk factors of occult hepatitis B virus infections among antiretroviral therapy-naïve people living with HIV in Botswana
Authors: Anderson Motswedi , Phinius Bonolo B. , Phakedi Basetsana K. , Mudanga Mbatshi , Bhebhe Lynnette N. , Tlhabano Girlie N. , Motshosi Patience , Ratsoma Tsholofelo , Baruti Kabo , Mpebe Gorata , Choga Wonderful T. , Marlink Richard , Glebe Dieter , Blackard Jason T. , Moyo Sikhulile , Kramvis Anna , Gaseitsiwe Simani 
Published: May 2024

AimThis study aimed to determine the kinetics of occult hepatitis B virus infections (OBI) among people with HIV (PWH).MethodsThe study used archived plasma samples from longitudinal HIV natural history studies. We identified new OBI cases and assessed risk factors for OBI using Cox proportional hazards regression analysis.ResultsAt baseline, 8 of 382 [(2.1%) (95% CI: 1.06–4.1)] samples tested positive for hepatitis B surface antigen (HBsAg+). Of the 374 HBsAg-negative samples, 76 had sufficient sample volume for HBV DNA screening. OBI positivity (OBI+) at baseline was reported in 11 of 76 [14.7 95% CI (8.3–24.1)] HBsAg-negative (HBsAg−) participants. Baseline HBsAg-negative samples with sufficient follow-up samples (n = 90) were used for analysis of newly identified OBI cases. Participants contributed 129.74 person-years to the study and were followed for a median of 1.02 years (IQR: 1.00–2.00). Cumulatively, there were 34 newly identified OBI cases from the 90 participants, at the rate of 26.2/100 person-years (95% CI: 18.7–36.7). Newly identified OBI cases were more common among men than women (61.1% vs. 31.9%) and among participants with CD4+ T-cell counts ≤450 cells/mL (p-value = 0.02). Most of the newly identified OBI cases [55.9% (19/34)] were possible reactivations as they were previously HBV core antibody positive.ConclusionThere was a high rate of newly identified OBI among young PWH in Botswana, especially in men and in participants with lower CD4+ T-cell counts. OBI screening in PWH should be considered because of the risk of transmission, possible reactivation, and risk factors for the development of chronic liver disease, including hepatocellular carcinoma.
The effect of Phyllanthus emblica (Amla) fruit supplementation on the rumen microbiota and its correlation with rumen fermentation in dairy cows
Authors: Tilahun Mekonnen , Ma Lu , Callaway Todd R. , Xu Jianchu , Bu Dengpan 
Published: May 2024

IntroductionMedicinal plants, rich in phytochemicals like phenolic acids, flavonoids, and tannins, offer potential benefits in enhancing productivity, quality, and animal health. Amla fruit (Phyllanthus emblica) is one such plant with promising attributes. This study aimed to investigate the impact of fresh Amla fruit (FAF) supplementation on ruminal microbial composition and its correlation with rumen fermentation in lactating dairy cows.MethodsThe study employed a repeated crossover design involving eight ruminally cannulated mid-lactation Holstein dairy cows. Animals received varying levels of fresh Amla fruit supplementation (0, 200, 400, and 600 g/d).ResultsWhen 400 g/d of FAF was added to the diet, there was a significant increase in the relative abundance of Firmicutes (p = 0.02). However, at 200 g/d, the relative abundance of ruminal Bacteroidota was higher than the 0 and 400 g/d FAF supplementation (p &lt; 0.01). LEfSe analysis identified distinct taxa, such as Clostridia vadinBB60 in the 200 g/d group, Oscillospiraceae in the 400 g/d group, and Elusimicrobium in the 600 g/d group. Notably, the random forest species abundance statistics identified Oscillospiraceae V9D2013 as a biomarker related to milk yield. Oscillospiraceae, Bacilli RF39, norank_f Prevotellaceae, and Bifidobacterium were positively correlated with ruminal total VFA and molar proportion of propionate, while Rikenellaceae RC9 gut group and Clostridia vadinBB60 were negatively correlated.DiscussionFAF supplementation affects the abundance of beneficial microbes in a dose-dependent manner, which can improve milk yield, efficiency, rumen health, desirable fatty acids, and animal health.
Anorexia nervosa and bulimia nervosa: a Mendelian randomization study of gut microbiota
Authors: Yu Zongliang , Guo Manping , Yu Binyang , Wang Yiming , Yan Zian , Gao Rui 
Published: May 2024

BackgroundAnorexia nervosa (AN) and bulimia nervosa (BN) poses a significant challenge to global public health. Despite extensive research, conclusive evidence regarding the association between gut microbes and the risk of AN and BN remains elusive. Mendelian randomization (MR) methods offer a promising avenue for elucidating potential causal relationships.Materials and methodsGenome-wide association studies (GWAS) datasets of AN and BN were retrieved from the OpenGWAS database for analysis. Independent single nucleotide polymorphisms closely associated with 196 gut bacterial taxa from the MiBioGen consortium were identified as instrumental variables. MR analysis was conducted utilizing R software, with outlier exclusion performed using the MR-PRESSO method. Causal effect estimation was undertaken employing four methods, including Inverse variance weighted. Sensitivity analysis, heterogeneity analysis, horizontal multivariate analysis, and assessment of causal directionality were carried out to assess the robustness of the findings.ResultsA total of 196 bacterial taxa spanning six taxonomic levels were subjected to analysis. Nine taxa demonstrating potential causal relationships with AN were identified. Among these, five taxa, including Peptostreptococcaceae, were implicated as exerting a causal effect on AN risk, while four taxa, including Gammaproteobacteria, were associated with a reduced risk of AN. Similarly, nine taxa exhibiting potential causal relationships with BN were identified. Of these, six taxa, including Clostridiales, were identified as risk factors for increased BN risk, while three taxa, including Oxalobacteraceae, were deemed protective factors. Lachnospiraceae emerged as a common influence on both AN and BN, albeit with opposing effects. No evidence of heterogeneity or horizontal pleiotropy was detected for significant estimates.ConclusionThrough MR analysis, we revealed the potential causal role of 18 intestinal bacterial taxa in AN and BN, including Lachnospiraceae. It provides new insights into the mechanistic basis and intervention targets of gut microbiota-mediated AN and BN.
Efficacy and safety of transcranial pulse stimulation in young adolescents with attention-deficit/hyperactivity disorder: a pilot, randomized, double-blind, sham-controlled trial
Authors: Cheung Teris , Yee Benjamin K. , Chau Bolton , Lam Joyce Yuen Ting , Fong Kwan Hin , Lo Herman , Li Tim Man Ho , Li Albert Martin , Sun Lei , Beisteiner Roland , Cheng Calvin Pak Wing 
Published: May 2024

BackgroundThis is the first study to evaluate the efficacy and safety of transcranial pulse stimulation (TPS) for the treatment of attention-deficit/hyperactivity disorder (ADHD) among young adolescents in Hong Kong.MethodsThis double-blind, randomized, sham-controlled trial included a TPS group and a sham TPS group, encompassing a total of 30 subjects aged 12–17 years who were diagnosed with ADHD. Baseline measurements SNAP-IV, ADHD RS-IV, CGI and executive functions (Stroop tests, Digit Span) and post-TPS evaluation were collected. Both groups were assessed at baseline, immediately after intervention, and at 1-month and 3-month follow-ups. Repeated-measures ANOVAs were used to analyze data.ResultsThe TPS group exhibited a 30% reduction in the mean SNAP-IV score at postintervention that was maintained at 1- and 3-month follow-ups.ConclusionTPS is an effective and safe adjunct treatment for the clinical management of ADHD.Clinical trial registrationClinicalTrials.Gov, identifier NCT05422274.
Aberrant individual structure covariance network in patients with mesial temporal lobe epilepsy
Authors: Huang Yuda , Wang Ningrui , Li Wei , Feng Tao , Zhang Huaqiang , Fan Xiaotong , Chen Sichang , Wang Yihe , Shan Yongzhi , Wei Penghu , Zhao Guoguang 
Published: May 2024

ObjectiveMesial temporal lobe epilepsy (mTLE) is a complex neurological disorder that has been recognized as a widespread global network disorder. The group-level structural covariance network (SCN) could reveal the structural connectivity disruption of the mTLE but could not reflect the heterogeneity at the individual level.MethodsThis study adopted a recently proposed individual structural covariance network (IDSCN) method to clarify the alternated structural covariance connection mode in mTLE and to associate IDSCN features with the clinical manifestations and regional brain atrophy.ResultsWe found significant IDSCN abnormalities in the ipsilesional hippocampus, ipsilesional precentral gyrus, bilateral caudate, and putamen in mTLE patients than in healthy controls. Moreover, the IDSCNs of these areas were positively correlated with the gray matter atrophy rate. Finally, we identified several connectivities with weak associations with disease duration, frequency, and surgery outcome.SignificanceOur research highlights the role of hippo-thalamic-basal-cortical circuits in the pathophysiologic process of disrupted whole-brain morphological covariance networks in mTLE, and builds a bridge between brain-wide covariance network changes and regional brain atrophy.
Differentiation of hemispheric white matter lesions in migraine and multiple sclerosis with similar radiological features using advanced MRI
Authors: John Flóra , Kis-Jakab Gréta , Komáromy Hedvig , Perlaki Gábor , Orsi Gergely , Bosnyák Edit , Rozgonyi Renáta , Trauninger Anita , Eklics Kata , Kamson David Olayinka , Pfund Zoltán 
Published: May 2024

Background and aimWhite matter hyperintensities (WMHs), presented on T2-weighted or fluid-attenuated inversion recovery magnetic resonance imaging (MRI) sequences, are lesions in the human brain that can be observed in both migraine and multiple sclerosis (MS).MethodsSeventeen migraine patients and 15 patients with relapsing–remitting multiple sclerosis with WMHs, and 17 healthy subjects age-and sex-matched to the migraine group were prospectively enrolled and underwent conventional and advanced MRI studies with diffusion-and perfusion-weighted imaging and single voxel proton magnetic resonance spectroscopy.ResultsIn both disease groups, elevated T2 relaxation time, apparent diffusion coefficient (ADC) values, and decreased N-acetyl-aspartate levels were found in the intralesional white matter compared to the contralateral normal-appearing white matter (NAWM), while there was no difference between the hemispheres of the control subjects. Migraine patients had the lowest intralesional creatine + phosphocreatine and myo-inositol (mI) values among the three groups, while patients with MS showed the highest intralesional T1 and T2 relaxation times, ADC, and mI values. In the contralateral NAWM, the same trend with mI changes was observed in migraineurs and MS patients. No differences in perfusion variables were observed in any groups.ConclusionOur multimodal study showed that tissue damage is detectable in both diseases. Despite the differences in various advanced MRI measures, with more severe injury detected in MS lesions, we could not clearly differentiate the two white matter lesion types.
Exercise attenuates high-fat diet-induced PVAT dysfunction through improved inflammatory response and BMP4-regulated adipose tissue browning
Authors: Liu Xiaojie , Jiang Xi , Hu Jing , Ding Mingxing , Lee Sang Ki , Korivi Mallikarjuna , Qian Yongdong , Li Ting , Wang Lifeng , Li Wei 
Published: May 2024

BackgroundPerivascular adipose tissue (PVAT) dysfunction impairs vascular homeostasis. Impaired inflammation and bone morphogenetic protein-4 (BMP4) signaling are involved in thoracic PVAT dysfunction by regulating adipokine secretion and adipocyte phenotype transformation. We investigated whether aerobic exercise training could ameliorate high-fat diet (HFD)-induced PVAT dysfunction via improved inflammatory response and BMP4-mediated signaling pathways.MethodsSprague-Dawley rats (n = 24) were divided into three groups, namely control, high-fat diet (HFD), and HFD plus exercise (HEx). After a 6-week intervention, PVAT functional efficiency and changes in inflammatory biomarkers (circulating concentrations in blood and mRNA expressions in thoracic PVAT) were assessed.ResultsChronic HFD feeding caused obesity and dyslipidemia in rats. HFD decreased the relaxation response of PVAT-containing vascular rings and impaired PVAT-regulated vasodilatation. However, exercise training effectively reversed these diet-induced pathological changes to PVAT. This was accompanied by significantly (p &lt; 0.05) restoring the morphological structure and the decreased lipid droplet size in PVAT. Furthermore, HFD-induced impaired inflammatory response (both in circulation and PVAT) was notably ameliorated by exercise training (p &lt; 0.05). Specifically, exercise training substantially reversed HFD-induced WAT-like characteristics to BAT-like characteristics as evidenced by increased UCP1 and decreased FABP4 protein levels in PVAT against HFD. Exercise training promoted transcriptional activation of BMP4 and associated signaling molecules (p38/MAPK, ATF2, PGC1α, and Smad5) that are involved in browning of adipose tissue. In conjunction with gene expressions, exercise training increased BMP4 protein content and activated downstream cascades, represented by upregulated p38/MAPK and PGC1α proteins in PVAT.ConclusionRegular exercise training can reverse HFD-induced obesity, dyslipidemia, and thoracic PVAT dysfunction in rats. The browning of adipose tissue through exercise appears to be modulated through improved inflammatory response and/or BMP4-mediated signaling cascades in obese rats.