bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding the anomalies: a genome-based analysis of Bacillus cereus group strains closely related to Bacillus anthracis
Authors: Magome Thuto Gomolemo , Surleac Marius , Hassim Ayesha , Bezuidenhout Cornelius Carlos , van Heerden Henriette , Lekota Kgaugelo Edward 
Published: February 2025

IntroductionThe Bacillus cereus group encompasses a complex group of closely related pathogenic and non-pathogenic bacterial species. Key members include B. anthracis, B. cereus, and B. thuringiensis organisms that, despite genetic proximity, diverge significantly in morphology and pathogenic potential. Taxonomic challenges persist due to inconsistent classification methods, particularly for B. cereus isolates that resemble B. anthracis in genetic clustering.MethodsThis study investigated B. cereus group isolates from blood smears of animal carcasses in Kruger National Park, uncovering an unusual isolate with B. cereus features based on classical microbiological tests yet B. anthracis-like genomic similarities with an Average Nucleotide Identity (ANI) of ≥95%. Using comparative genomics, pan-genomics and whole genome Single Nucleotide Polymorphism (wgSNP) analysis, a total of 103 B. cereus group genomes were analyzed, including nine newly sequenced isolates from South Africa and a collection of isolates that showed some classification discrepancies, thus classified as “anomalous.”Results and discussionOf the 36 strains identified as B. anthracis in GenBank, 26 clustered phylogenetically with the four confirmed B. anthracis isolates from South Africa and shared 99% ANI. Isolates with less than 99% ANI alignment to B. anthracis exhibited characteristics consistent with B. cereus and/or B. thuringiensis, possessing diverse genetic profiles, insertion elements, resistance genes, and virulence genes features, contrasting with the genetic uniformity of typical B. anthracis. The findings underscore a recurrent acquisition of mobile genetic elements within B. cereus and B. thuringiensis, a process infrequent in B. anthracis.ConclusionThis study highlights the pressing need for standardized taxonomic criteria in B. cereus group classification, especially as anomalous isolates emerge. This study supports the existing nomenclature framework which offers an effective solution for classifying species into genomospecies groups. We recommend isolates with ANI ≥99% to standard reference B. anthracis be designated as typical B. anthracis in GenBank to maintain taxonomic clarity and precision.
Comparison of self-collected and healthcare worker-collected rectovaginal swabs for group B streptococcus detection in pregnancy using PCR with a commercial collection-enrichment device
Authors: Kukovica Iva , Omahen Neža , Klobučar Nika , Bučar Martina , Franko Rutar Anita , Perme Tina , Lučovnik Miha , Jeverica Samo 
Published: February 2025

IntroductionUniversal screening for the detection of group B streptococcus (GBS) colonization in pregnant women was recently introduced in Slovenia. The aim of our study was to determine whether self-collection of rectovaginal swabs is a valid alternative to collection by healthcare workers (HCWs).MethodsA prospective, multicenter study was conducted between June and November 2023. A total of 227 pregnant women (aged 20 to 44 years) from the University Medical Center Ljubljana (n = 136), the Novo mesto Community Health Center (n = 48) and the Trebnje Community Health Center (n = 43) were included. Two swabs were taken: swab A by the HCWs using standard semi-solid Amies transport medium (Meus; current standard) and swab B by the pregnant woman following visual instructions using a commercial LIM Broth (Copan). Swabs were inoculated onto ChromID Strepto B (STRB) agars directly and after overnight enrichment in LIM broth. The NeuMoDx GBS assay was performed from the enrichment broth. A self-assessment questionnaire was completed after sampling. Performance characteristics were calculated and compared between different diagnostics test algorithms using McNemar’s test for paired samples.ResultsOverall, GBS was detected in 18% (95% CI 13–23%; n = 40) of swabs A and 19% (95% CI 14–25%; n = 43) of swabs B. PCR was superior in both groups. In the group of swabs collected by HCWs, 4 (40 vs. 36; 11.1% difference; p = 0.046) and 3 (40 vs. 37; 8.1% difference; p = 0.083) additional positives were detected with PCR compared to direct and enrichment culture, respectively; in the group of self-collected swabs, 4 (43 vs. 39; 10.3% difference; p = 0.046) and 6 (43 vs. 36; 16.2% difference; p = 0.014) additional positives were detected with PCR compared to direct and enrichment culture, respectively. Self-collection showed a trend towards a higher diagnostic yield. PCR after enrichment from self-collected samples was found to be the most sensitive method overall. 58.5% (n = 124/212; 95% CI 52–65%) of women would prefer the swabs taken by HCWs.DiscussionSelf-collection of rectovaginal swabs during pregnancy is a good alternative to HCW-collected swabs. PCR from enrichment broth was better for the detection of GBS compared to enrichment culture. Majority of women preferred swabs taken by HCWs.
A systematic review of the efficacy of repetitive transcranial magnetic stimulation in treating dysarthria in patients with Parkinson's disease
Authors: Chen Kerong , Zhou Sitong , Lu Shiyu , Qin Yuliang , Li Xinyao , Li Yi , Liu Tianyun , Zhang Mei , Xu Kun , Shi Hongping , Lv Xiaoman , Yuan Kai , Shi Hongling , Qin Dongdong 
Published: February 2025

ObjectiveTo analyze the literature on the efficacy of repetitive transcranial magnetic stimulation (rTMS) in treating dysarthria in patients with Parkinson's disease (PD) and provide a reference for targeted clinical treatment of dysarthria in PD patients.MethodsA systematic search was conducted in English and Chinese databases, including Embase, Cochrane, Medline, PubMed, CNKI, Wanfang, Chinese Biomedical Literature Database, and VIP Database, for relevant literature on rTMS treatment for dysarthria in PD patients. The search timeframe was from the inception of each database to October 2023. Literature was screened according to inclusion and exclusion criteria. Two researchers extracted information on study subjects, age, intervention methods, intervention duration, intervention frequency, evaluation indicators, and intervention results from the included literature. The modified Jadad scale was used to evaluate the quality of the literature.ResultsA total of seven studies were included, mainly focusing on the frequency, duration, and stimulation site of rTMS for dysarthria in PD patients. Six studies indicated that rTMS treatment improved dysarthria in PD patients.ConclusionRepetitive transcranial magnetic stimulation has a positive effect on improving dysarthria in PD patients, but further research is needed to determine its efficacy.
Role of visual function and performance of activities of daily living in cognitive function in patients with mild cognitive impairment: a cross-sectional study
Authors: Zhou Chunhui , Yang Ganfeng , Theeboom Marc , Yang Hua , Zhu Ruiting , Zhou Zijian , Zhu Dong 
Published: February 2025

BackgroundMild cognitive impairment (MCI) is a precursor to dementia, with many patients showing early decline in activities of daily living (ADLs). However, the role of visual impairment in this process is underexplored despite evidence suggesting it may accelerate cognitive decline. Current research does not understand how visual dysfunction affects cognitive abilities and how ADLs might moderate this relationship. This gap is crucial because early interventions targeting visual impairments could potentially delay progression to dementia, offering new avenues for supporting MCI patients.ObjectiveThis study investigates the relationship between visual function and cognitive abilities in patients with MCI. Specifically, it seeks to determine how different aspects of visual function, such as visual field indices and visual acuity, correlate with various cognitive domains measured by standardized assessments. Additionally, the study aims to examine the role of ADLs as a potential moderating factor in this relationship. By analyzing how ADL performance influences the strength and direction of the association between visual impairments and cognitive function, this research intends to identify key areas where visual deficits may contribute to cognitive decline in MCI.MethodsThis is a cross-sectional study. Two hundred and seventy four elderly patients were diagnosed with MCI from various communities in Taicang City, Jiangsu Province, China. Most participants were women (68.6%), and the average age was 69 years. Notable comorbidities included hypertension (41.6%) and diabetes (33.2%), indicating a higher burden of health conditions than typical older adult populations. Visual function, Montreal Cognitive Assessment (MoCA), and the ADLs were measured. Pearson's correlation coefficients were used to examine the unadjusted associations between visual function measures and cognitive performance. Multivariable linear regression models were employed to further explore these relationships and to assess the moderating role of ADLs.ResultsSignificant positive correlations were found between visual function and cognitive performance, particularly with Visual Function Index (VFI) showing a strong initial correlation with the total MoCA score (r = 0.61, p &lt; 0.001), which was attenuated after adjusting for ADL (β = 0.06, p = 0.23). Maximum Visual Field (Max VF) was positively correlated with language skills (r = 0.13, p &lt; 0.05). The negative correlation of Minimum Visual Field (Min VF) with cognitive performance became positive after ADL adjustment (β = 0.12, p = 0.04).ConclusionsThese findings suggest that visual function plays a crucial role in the cognitive and functional abilities of patients with MCI. Early interventions targeting visual impairments may help mitigate cognitive decline and improve the quality of life for these patients.
Inflammation and endothelial gene polymorphism are associated with ischemic stroke
Authors: Chen Wanli , Li Jie , Zhou Jintao , Yi Xingyang , Chen Hong 
Published: February 2025

AimEvaluate the correlation between ischemic stroke and genetic variations related to inflammation and endothelial function.MethodsThis was a multicenter cross-sectional research conducted in southwestern China. Residents aged ≥40 years voluntarily join in the face-to-face survey in 8 communities. 2,377 participants were at high risk of stroke, of which 429 had a previous history of ischemic stroke. We selected the 429 ischemic stroke patients as the research subjects, and adopted a 1:1 matching method to select 429 healthy people with a 2-year age difference and the same gender and hypertension as the control group. We detected genotypes of 19 variants in 10 genes related to inflammation and endothelial function. Analyze gene–gene interaction through generalized multifactor dimensionality reduction (GMDR).ResultsAnalysis found no statistically significant differences in age, gender, hypertension, BMI, and smoking history between ischemic stroke patients and healthy control group. Compared with the healthy group, ischemic stroke group has a higher proportion of diabetes, heart disease, dyslipidemia, stroke family history, and a higher proportion of lack of exercise. HABP2 rs7923349, NOS2A rs8081248, HABP2 rs932650 were related to stroke in univariate analysis. GMDR analysis showed significant gene–gene interactions between HABP2 rs7923349, HABP2 rs932650. After adjusting for covariates, high-risk interaction genotypes between these two variants were independently associated with higher stroke risk (OR, 3.578, 95% CI: 2.618–4.890, p &lt; 0.001).ConclusionThis study found that specific variations in genes related to inflammation and endothelial function are associated with ischemic stroke. The high-risk interactive genotypes among HABP2 rs7923349, HABP2 rs932650 distinctly increased the risk of ischemic stroke.
Analyzing the correlation between acute ischemic stroke and triglyceride-glucose index based on ordered logistic regression
Authors: He Liu , Li Rong , Wang Lei , Zhu Xi , Zhou Qiang , Yang Zhiyong , Liu Hua 
Published: February 2025

ObjectiveTo investigate the association between insulin resistance, measured by the triglyceride-glucose (TyG) index, and clinical outcomes in patients with acute ischemic stroke who underwent intravenous thrombolysis with alteplase.MethodsThis retrospective study included 165 patients with acute ischemic stroke treated with intravenous alteplase. Insulin resistance was evaluated using the TyG index, and its relationship with the modified Rankin Scale (mRS) scores was analyzed. The analysis was conducted using R software (version R 4.1.3) to evaluate the correlation between the TyG index and functional outcomes at 14, 30, and 90 days post-stroke.ResultsThe study found that each unit increase in the TyG index significantly raised the risk of poor functional outcomes at 14 days (OR 9.86; 95% CI: 3.32–32.21; P &lt; 0.001), 30 days (OR 5.82; 95% CI: 2.08–17.45; P = 0.001), and 90 days (OR 9.79; 95% CI: 3.33–31.66; P &lt; 0.001) following a stroke. Higher TyG index values were associated with worse neurological outcomes. Although male gender, older age, and smoking were also linked to poorer outcomes, these associations did not reach statistical significance.ConclusionThe findings suggest that a higher TyG index, indicating greater insulin resistance, is associated with worse neurological outcomes in stroke patients. Early intervention targeting insulin resistance may improve clinical outcomes in ischemic stroke patients, and further research is needed to explore additional factors affecting neurological recovery.
A pooled analysis of the side effects of non-invasive Transcutaneous Auricular Vagus Nerve Stimulation (taVNS)
Authors: Giraudier Manon , Ventura-Bort Carlos , Szeska Christoph , Weymar Mathias 
Published: February 2025

IntroductionTranscutaneous auricular vagus nerve stimulation (taVNS) is a promising technique for modulating vagal afferent fibers non-invasively and has shown therapeutic potential in neurological, cognitive, and affective disorders. While previous research highlights its efficacy, the safety profile of taVNS has been less extensively examined.MethodsThis study therefore aimed to systematically investigate side effects of taVNS in a large pooled dataset consisting of n = 488 participants, utilizing a standardized questionnaire to assess ten reported side effects. Analyses included effects of stimulation type (interval vs. continuous), stimulation duration, stimulation intensity and participant characteristics (age and gender) as potential modulators.ResultsThe findings support the safety of taVNS, with minimal and mild side effects reported across participants (M = 1.86, SD = 1.36). Although participants receiving sham stimulation were 32.4% less likely to report unpleasant feelings compared to participants receiving taVNS, this effect was driven primarily by low-end ratings (specifically, a rating of 1, indicating not at all when experiencing the corresponding side effect), thus suggesting limited clinical relevance. Interval stimulation notably reduced the likelihood of some side effects, particularly for neck pain, dizziness and unpleasant feelings, suggesting potential for optimizing taVNS protocols. Stimulation intensity and duration showed few statistically significant, but clinically minimal (i.e., very small) effects.ConclusionOverall, these findings demonstrate a favorable safety profile of taVNS, with mostly mild and transient effects, supporting its use as a suitable non-invasive tool in both research and clinical applications.
Multiple patterns of EEG parameters and their role in the prediction of patients with prolonged disorders of consciousness
Authors: Li Hui , Dong Linghui , Su Wenlong , Liu Ying , Tang Zhiqing , Liao Xingxing , Long Junzi , Zhang Xiaonian , Sun Xinting , Zhang Hao 
Published: February 2025

IntroductionPrognostication in patients with prolonged disorders of consciousness (pDoC) remains a challenging task. Electroencephalography (EEG) is a neurophysiological method that provides objective information for evaluating overall brain function. In this study, we aim to investigate the multiple features of pDoC using EEG and evaluate the prognostic values of these indicators.MethodsWe analyzed the EEG features: (i) spectral power; (ii) microstates; and (iii) mismatch negativity (MMN) and P3a of healthy controls, patients in minimally conscious state (MCS), and unresponsive wakefulness syndrome (UWS). Patients were followed up for 6 months. A combination of machine learning and SHapley Additive exPlanations (SHAP) were used to develop predictive model and interpret the results.ResultsThe results indicated significant abnormalities in low-frequency spectral power, microstate parameters, and amplitudes of MMN and P3a in MCS and UWS. A predictive model constructed using support vector machine achieved an area under the curve (AUC) of 0.95, with the top 10 SHAP values being associated with transition probability (TP) from state C to F, time coverage of state E, TP from state D to F and D to F, mean duration of state A, TP from state F to C, amplitude of MMN, time coverage of state F, TP from state C to D, and mean duration of state E. Predictive models constructed for each component using support vector machine revealed that microstates had the highest AUC (0.95), followed by MMN and P3a (0.65), and finally spectral power (0.05).DiscussionThis study provides preliminary evidence for the application of microstate-based multiple EEG features for prognosis prediction in pDoC.Clinical trial registrationchictr.org.cn, identifier ChiCTR2200064099.
Uncovering proteome variations and concomitant quality changes of different drying methods Cordyceps sinensis by 4D-DIA structural proteomics
Authors: Xiao Mengjun , Tang Chuyu , Wang Tao , He Min , Li Yuling , Li Xiuzhang 
Published: February 2025

IntroductionCordyceps sinensis is a fungus, serves dual purposes as both a medicinal herb and a food source. Due to its high water content, fresh Cordyceps sinensis is difficult to preserve, necessitating the drying necessary to process Cordyceps sinensis.MethodsUsing 4D-DIA proteomics, researchers analyzed the proteome profiles of fresh Cordyceps sinensis (CK) under three different drying conditions: vacuum freeze-drying (FD), oven-drying (OD), and air-drying (AD). In addition, it was found that the protein and free sulfhydryl content of Cordyceps sinensis decreased significantly and the disulfide bond content increased after different drying methods.Results and discussionA total of 3762 proteins were identified, showing variations between groups and high protein content. In the control groups consisting of fresh Cordyceps sinensis samples and the three drying methods, FD. vs CK exhibited the fewest differentially abundant proteins, with the majority being upregulated. On the other hand, CK vs OD displayed the greatest amount of distinct proteins, with a significant rise in both up-regulated and down-regulated proteins. Analysis of KEGG indicated that the distinct proteins were predominantly concentrated in pathways like the ribosome, synthesis of coenzymes, and metabolism of amino sugar and nucleotide sugar. Notably, there was a significant overlap between ribosome and ribosome biogenesis in eukaryotes pathways. The process of drying Cordyceps sinensis resulted in a significant upregulation of the expression of proteins linked to various metabolic pathways. This observation suggests that the drying treatment might activate or enhance certain biochemical processes within the organism, potentially influencing its overall metabolic activity. This finding highlights the importance of post-harvest dry methods on the biochemical properties of Cordyceps sinensis, which could have implications for its nutritional and medicinal value.This study provides a theoretical basis for the realization of Cordyceps sinensis resource utilization and storage methods, and provides theoretical support for guaranteeing the sustainable development of Cordyceps sinensis resources.
Clinical calculator based on clinicopathological characteristics predicts local recurrence and overall survival following radical resection of stage II-III colorectal cancer
Authors: Huang Fei , Wei Ran , Mei Shiwen , Xiao Tixian , Zhao Wei , Zheng Zhaoxu , Liu Qian 
Published: February 2025

PurposeThis study aimed to analyze the risk factors and survival prognosis of local recurrence in stage II-III colorectal cancer (CRC) and develop a clinical risk calculator and nomograms to predict local recurrence and survival in treated patients.MethodsPatients who underwent radical surgery between January 2009 and December 2019 at the China National Cancer Center were included. Multivariate nomograms and a clinical risk calculator based on Cox regression were developed. Discrimination was measured with an area under curve (AUC) and variability in individual predictions was assessed with calibration curves. We stratified patients into different risk groups according to the established model to predict their prognosis and guide clinical practice.ResultsThe clinical risk calculator incorporated six variables: tumor thrombus, perineural invasion, tumor grade, pathology T-stage, pathology N-stage, and whether more than 12 lymph nodes were harvested. Our clinical risk calculator provided good discrimination, with AUC values of local recurrence-free survival (LRFS) (0.764) and overall survival (OS) (0.815) in the training cohort and LRFS (0.740) and OS (0.730) in the test cohort. Calibration plots illustrated excellent agreement between the clinical risk calculator predictions and actual observations for 3- and 5-year LRFS and OS. Recurrence risk-stratified analysis showed that low-risk patients were more likely to undergo salvage radical surgery when recurrent disease existed.ConclusionThe clinical calculator can better account for tumor and patient heterogeneity, providing a more individualized outcome prognostication. The model is expected to aid in treatment planning, such as resectability evaluation, and it can be used in postoperative surveillance (https://oldcoloncancer.shinyapps.io/dynnomapp/).
Efficacy and safety of immune checkpoint inhibitors in patients with advanced intrahepatic cholangiocarcinoma
Authors: Peng Ziting , Dong Jianhui , Tang Shuyao , Shi Jiaxu , Shi Tongdong 
Published: February 2025

BackgroundTo assess the efficacy and safety of PD-1 and PD-L1 immune checkpoint inhibitors (ICIs) in managing advanced intrahepatic cholangiocarcinoma (ICC).MethodsA retrospective analysis of treatment data for patients with advanced ICC who received ICIs at the Second Affiliated Hospital of Chongqing Medical University from the inception of the inpatient medical record database until 30 April 2024. The analysis concentrated on the safety and efficacy of the treatment. The primary endpoint was progression-free survival (PFS), while the secondary endpoints included overall survival (OS) and safety. The Kaplan-Meier method was employed to plot survival curves, and differences between groups were assessed using log-rank tests.Results96 patients diagnosed with ICC were included, comprising 60 males (62.50%) and 36 females (37.50%). 85 patients exhibited disease progression, 22 patients succumbed, and 38 patients were lost to follow-up finally. Those who initiated immunotherapy promptly following first-line antitumor treatment exhibited a notably prolonged PFS compared to those experiencing tumor progression (5.63 months (95%CI: 3.12~8.14) vs 2.50 months (95%CI: 1.83~3.17), P=0.002). However, no significant disparity in the PFS with immunotherapy in different lines therapy(P=0.406) and the OS was observed between the two groups(P=0.360). 18 patients (18.75%) experienced treatment-emergent adverse events (AEs), with 3 patients encountering AEs of grade ≥3. All patients returned to normal after symptomatic treatment.ConclusionsIn patients with advanced ICC, the timely initiation of ICIs as adjuvant therapy following first-line antitumor treatment can result in favorable efficacy and a good safety profile.