bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic insights into microbial community, functional annotation, and antibiotic resistance genes in Himalayan Brahmaputra River sediment, India
Authors: Sharma Niti , Das Basanta Kumar , Bhattacharjya Birendra Kumar , Chaudhari Aparna , Behera Bijay Kumar , Kumar Annam Pavan , Chakraborty Hirak Jyoti 
Published: November 2024

IntroductionThe Brahmaputra, a major transboundary river of the Himalayas flowing predominantly through Northeast India, particularly Assam, is increasingly endangered by contamination due to rapid urbanization and anthropogenic pressures. These environmental changes pose significant risks at the microbial level, affecting nutrient cycling and productivity, and thereby impacting river ecosystem health. The next-generation sequencing technology using a metagenomics approach has revolutionized our understanding of the microbiome and its critical role in various aquatic environments.MethodsThe present study aimed to investigate the structure of the bacterial community and its functional potentials within the sediments of the Brahmaputra River, India, using high-throughput shotgun metagenomics. Additionally, this study sought to explore the presence of antimicrobial resistance genes in the river’s sediment.Results and discussionShotgun metagenomics revealed a diverse bacterial community comprising 31 phyla, 52 classes, 291 families, 1,016 genera, and 3,630 species. Dominant phyla included Pseudomonadota (62.47–83.48%), Actinobacteria (11.10–24.89%), Bacteroidetes (0.97–3.82%), Firmicutes (0.54–3.94%), Cyanobacteria (0.14–1.70%), and Planctomycetes (0.30–0.78%). Functional profiling highlighted significant involvement in energy metabolism, amino acid and central carbon metabolism, stress response, and degradation pathways, emphasizing the microbial community’s role in ecosystem functioning and resilience. Notably, 50 types of antibiotic resistance genes (ARGs) were detected, with resistance profiles spanning multidrug, aminoglycoside, β-lactam, fluoroquinolone, rifampicin, sulfonamide, and tetracycline classes. Network analysis underscored the intricate relationships among ARG subtypes, suggesting potential mechanisms of resistance propagation. Furthermore, plasmid-related genes and 185 virulence factor genes (VFGs) were identified, indicating additional layers of microbial adaptation and potential pathogenicity within the river sediments. This comprehensive microbial and functional profiling of the Brahmaputra’s sediment metagenome provides crucial insights into microbial diversity, resistance potential, and ecological functions, offering a foundation for informed management and mitigation strategies to preserve river health and mitigate pollution impacts.
Patterns of antibiotic resistance genes and virulence factor genes in the gut microbiome of patients with osteoarthritis and rheumatoid arthritis
Authors: Guo Yaqi , Feng Hang , Du Lin , Yu Zhenghong 
Published: November 2024

BackgroundThe gut microbiome compositions of osteoarthritis (OA) and rheumatoid arthritis (RA) patients have been revealed; however, the functional genomics, particularly antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), have not yet been explored.MethodsWe used gut metagenomic data to elucidate the distribution of ARGs and VFGs. Building on these differences in gut microbiome, we developed a diagnostic model using a random forest classifier based on ARG and VFG abundances.ResultsOur results indicated that both OA and RA patients exhibit significantly higher alpha diversity in ARGs, as measured by observed genes, the Shannon index, and the Simpson index, compared to healthy controls. However, this increased diversity is not significantly different between OA and RA patients. In contrast, VFGs showed higher diversity in RA patients than in healthy individuals, which was not as pronounced in OA patients. An analysis of the top 20 ARGs and VFGs revealed a largely similar composition between the three groups, with notable exceptions of certain genes that were uniquely enriched in either OA or RA patients. This suggests unique microbial patterns associated with each condition. Our beta diversity analysis further demonstrated distinct distributions of ARG and VFG profiles across the three groups, with several genes significantly enriched in both OA and RA patients, indicating potential markers for these diseases. The model achieved high accuracy (74.7–83.6%) when distinguishing both OA and RA from healthy controls using ARG profiles and substantial accuracy using VFG profiles.ConclusionThese results support the potential of ARGs and VFGs as reliable biomarkers for diagnosing OA and RA.
Body roundness index and cognitive function in older adults: a nationwide perspective
Authors: Zhang Feng , Ning Zhongxing , Wang Can 
Published: November 2024

BackgroundObesity negatively impacts cognitive function. However, the correlation between the body roundness index (BRI) and cognitive performance remains inadequately explored.MethodsThis study used data from the National Health and Nutrition Examination Survey (NHANES) collected from 2011 to 2014 to examine the correlation between BRI and cognitive function in individuals aged 65 and older. Models of multiple linear regression were used to investigate the relationship between BRI and cognitive performance. Additionally, smoothed curve fittings explored potential non-linear associations. Interaction tests and subgroup analyses were also performed.ResultsOne thousand eight hundred seventy participants were taken into account, revealing an important negative relationship between BRI levels and cognitive performance. In the fully adjusted model, elevated BRI was substantially correlated with lower Digit Symbol Substitution Test (DSST) scores (β = −0.34, 95% CI = −0.64 to −0.05, p = 0.023), indicating that the higher BRI values are linked to worse cognitive performance. Sex differences were observed, with males showing a stronger negative association (p for interaction = 0.040).ConclusionElevated BRI is related to worse cognitive function in the elderly population.
Skeletal muscle proteome differs between young APOE3 and APOE4 targeted replacement mice in a sex-dependent manner
Authors: Johnson Chelsea N. , Lysaker Colton R. , McCoin Colin S. , Evans Mara R. , Thyfault John P. , Wilkins Heather M. , Morris Jill K. , Geiger Paige C. 
Published: November 2024

IntroductionApolipoprotein E4 (APOE4) is the strongest genetic risk factor for Alzheimer's disease (AD), yet it's unclear how this allele mediates risk. APOE4 carriers experience reduced mobility and faster decline in muscle strength, suggesting skeletal muscle involvement. Mitochondria are critical for muscle function and although we have reported defects in muscle mitochondrial respiration during early cognitive decline, APOE4-mediated effects on muscle mitochondria are unknown.MethodsHere, we sought to determine the impact of APOE4 on skeletal muscle bioenergetics using young, male and female APOE3 (control) and APOE4 targeted replacement mice (n = 8 per genotype/sex combination). We examined the proteome, mitochondrial respiration, fiber size, and fiber-type distribution in skeletal muscle.ResultsWe found that APOE4 alters mitochondrial pathway expression in young mouse muscle in a sex-dependent manner without affecting respiration and fiber size or composition relative to APOE3. In both sexes, the expression of mitochondrial pathways involved in electron transport, ATP synthesis, and heat production by uncoupling proteins and mitochondrial dysfunction significantly differed between APOE4 and APOE3 muscle. For pathways with predicted direction of activation, electron transport and oxidative phosphorylation were upregulated while mitochondrial dysfunction and sirtuin signaling were downregulated in female APOE4 vs. APOE3 muscle. In males, sulfur amino acid metabolism was upregulated in APOE4 vs. APOE3 muscle.DiscussionThis work highlights early involvement of skeletal muscle in a mouse model of APOE4-linked AD, which may contribute to AD pathogenesis or serve as a biomarker for brain health.
Brain function assessment of acupuncture for chronic insomnia disorder with mild cognitive dysfunction based on fNIRS: protocol for a randomized controlled trial
Authors: Wang Tianyu , Li Zhi , Ma Tingting , Zhu Fengya , Yang Bin , Kim Sieun , Miao Runqing , Wu Jie 
Published: November 2024

BackgroundChronic Insomnia Disorder (CID) is highly prevalent among older adults and impairs cognitive function. Insomnia accelerates the progression of mild cognitive impairment (MCI) and increases the risk of developing dementia. Acupuncture has been demonstrated in improving sleep quality and cognitive function. This study aims to explore the functional brain characteristics of CID with MCI patients and to assess the effects of acupuncture therapy using functional near-infrared spectroscopy (fNIRS).Methods and designThis study is a single-center randomized controlled trial. Participants will be randomly assigned to the manual acupuncture group or the placebo acupuncture group for an 8-week intervention period. fNIRS data will be collected during resting test and working memory test at baseline and at end of the intervention. The primary outcome is the change of the Montreal Cognitive Assessment (MoCA) score, secondary outcomes include the change of Mini-Mental State Examination (MMSE), Insomnia Severity Index (ISI), Patient Health Questionnaire-9 (PHQ-9), Generalized Anxiety Disorder Scale (GAD-7), and Apathy Evaluation Scale-Informant (AES-I).DiscussionThe results of the study will provide insights into the effects of acupuncture on sleep quality and cognitive performance in CID with MCI patients. By utilizing fNIRS technology, we will elucidate the neural functional characteristic underlying the therapeutic benefits of acupuncture.Clinical trial registrationhttps://ClinicalTrials.gov, identifier ChiCTR2300076182.
Study protocol for a randomized trial comparing two electroacupuncture waveforms for different severity groups of Bell palsy
Authors: Bian Zhiyuan , Wang Jiawei , Fang Fei , Yu Binyan , Shi Yan , Wan Yijia , Hong Mei , Ji Conghua , Shao Xiaomei , Liang Yi , Fang Jianqiao , Sun Jing 
Published: November 2024

BackgroundBell palsy (BP) is the most common cause of acute peripheral facial palsy which leads to functional and esthetic disturbances in patients and has a negative influence on daily living. Electroacupuncture (EA) has been considered an alternative treatment for improving facial function in patients with BP. However, there is no agreement on the preferred waveform type of the EA for treating BP.MethodsThis is a study protocol for a pilot randomized, two-arm, three-center, clinical trial at the Third Affiliated hospital of Zhejiang Chinese Medical University, the First Affiliated hospital of Zhejiang Chinese Medical University, and the Hangzhou First People’s Hospital. The trial began in November 2023 and is expected to end in December 2025. Sixty patients with BP whose electroneurography (ENoG) value is at least 20% and 60 patients with BP whose ENoG value is less than 20% will be randomly assigned to the low frequency continuous waveform group or the intermittent waveform group in a 1:1 ratio. Participants will receive 4 weeks of EA treatment and clinical assessments. The primary outcome is the change from baseline score of the Facial Nerve Grading System 2.0. The secondary outcomes include the change from baseline score of the Sunnybrook grading scale and the change from baseline amplitude of the compound muscle action potential of the affected side in the ENoG tests.DiscussionThis is the first study protocol to compare the treatment effect and safety of EA with low frequency continuous waveform and intermittent waveform for different severity groups of BP. This study will contribute to subsequent studies for exploring optimal EA parameters for BP treatment.Clinical trial registrationClinicalTrials.gov, NCT06063954.
Embodied echoes: navigating the familiarity in continued intention to play VR game
Authors: Yang Ling , Xiao Daibo 
Published: November 2024

IntroductionVirtual reality (VR) games, propelled by advancements in VR and artificial intelligence technologies, offer a level of realism and interactivity that traditional games cannot match. However, despite their immersive potential, VR games have not yet reached the widespread popularity of their conventional counterparts. While VR can craft the illusion of a parallel reality, users often remain cognizant of the delineation between the virtual and the real.MethodsIn this paper, we employ a blend of qualitative and quantitative research methods to explore the impact of familiarity with virtual environments and interactive elements on users sense of embodiment, flow experience, and their intention to continue playing VR games. Additionally, we examine the moderating influence of perceived cost within this framework.Results and discussionsOur analysis of 307 collected responses, facilitated by PLS-SEM, reveals that familiarity with interactivity is positively associated with both sense of embodiment and flow experience, whereas familiarity with the virtual scene primarily influences sense of embodiment. Interestingly, perceived cost exerts a positive moderating effect on the relationship between flow experience and the intention to persist with VR gaming, while it negatively moderates the impact of sense of embodiment on this intention. This study offers theoretical insights that can guide future research in the domain of VR gaming, as well as practical takeaways for companies in the VR game industry, shedding light on how to enhance user engagement and sustain long-term interest in VR gaming experiences.
Experimental test of neutron intensity monitor with isomer production reaction for p-Li neutron source for boron neutron capture therapy
Authors: Tamaki Shingo , Ohtani Yuuki , Kusaka Sachie , Sato Fuminobu , Murata Isao 
Published: November 2024

IntroductionBoron Neutron Capture Therapy (BNCT) is a promising cancer therapy. At present, development of accelerator based neutron source (ABNS) is underway to be utilized as a neutron source instead of nuclear reactor. However, it is known that the neutron field formed with accelerators have different characteristics depending on kinds of accelerators. We thus have to characterize the field before practical use.MethodIn the authors’ group, various neutronics characterization devices have been developed for our p-Li based BNCT machine named CSePT. In this paper, three neutron intensity monitor foils with an isomer production reaction for several tens to 800 keV of the p-Li neutrons were proposed, i.e., 107Ag, 115In and 189Os.Result and DiscussionFrom the experimental test results, two activation foils of 107Ag and 115In were confirmed to be a possible candidate as the monitor. However, the isomer production cross sections of them should be examined for practical use.
Association between branched-chain amino acid levels and gastric cancer risk: large-scale prospective cohort study
Authors: Yu Liang , Bao Shiming , Zhu Feng , Xu Yanyan , Liu Yanwei , Jiang Runben , Yang Chuang , Cao Feng , Chen Wei , Li Pengtao 
Published: November 2024

BackgroundGastric cancer (GC) remains a malignancy with high incidence and mortality rates worldwide. Although branched-chain amino acids (BCAAs) play a crucial role in various physiological and pathological processes, their specific relationship with risk of GC remains unclear.MethodsWe conducted a large-scale prospective cohort from UK Biobank database. We evaluated the relationship between BCAA levels and risk of GC using Cox regression, Kaplan–Meier survival curves, the accelerated failure time (AFT) model, and restricted cubic spline (RCS) analysis.ResultsDuring the follow-up of 12 years, 247,753 participants were included in the study. And the Cox regression analysis revealed that higher levels of isoleucine (HR = 0.65, 95% CI 0.48–0.89; p = 0.007), leucine (HR = 0.57, 95% CI 0.42–0.79; p &lt; 0.001), valine (HR = 0.53, 95% CI 0.39–0.73; p &lt; 0.001), and total BCAAs were associated with a reduced risk of GC (HR = 0.51, 95% CI 0.37–0.70; p &lt; 0.001). Kaplan–Meier curves and the AFT model confirmed that elevated BCAA levels significantly delayed the onset of GC. Additionally, RCS analysis identified nonlinear dose–response relationships between BCAAs and risk of GC. Stratified analyses indicated that the protective effect of BCAAs was consistent across various subgroups, with a more pronounced impact in older individuals without chronic diseases.ConclusionElevated BCAA levels are significantly associated with a reduced risk of GC, particularly in older adults. This finding highlights the potential of BCAAs in GC prevention and suggests that future research and clinical practice should emphasize regulating BCAA levels.
Case report: Spindle cell sarcoma and pituitary adenoma in the sella region—a rare collision tumor
Authors: Ding Peng-fei , Zhu Ting , Cui Yue , Yan Hui-ying , Wang Yun-feng , Hang Chun-hua , Li Wei 
Published: November 2024

BackgroundCollision tumors are defined as two or more distinctly bordered, mutually invasive tumors in the same anatomical region. Characterized by low incidence and lack of specificity, they often pose a significant challenge to disease diagnosis. Among these, collision tumors in the sella region are incredibly rare.Case descriptionOn 13 June 2023, the Department of Neurosurgery at Drum Tower Hospital admitted a patient with a pituitary adenoma in the sella region complicated by spindle cell sarcoma. After reviewing the literature, no related cases were reported. A patient presenting with complex clinical symptoms and preoperative imaging showing occupancy in the sella region is considered to have a recurrence of pituitary adenoma. After thorough preoperative evaluation and discussion, a trans-sphenoidal approach (with the aid of an endoscope) was performed to resect the pituitary lesions. Combined with postoperative pathological tissue and imaging, the patient was diagnosed with a pituitary adenoma (postoperative recurrence) in the sella region complicated by spindle cell sarcoma. The patient made a fair recovery and was discharged on the 8th postoperative day.ConclusionThis case report aims to elucidate and discuss the diagnosis and screening of rare collision tumors in the sella region to reduce the misdiagnosis rate and provide accurate treatment.
The survival and safety of metastatic hepatocellular carcinoma treated with lenalidomide as second-line therapy: a case report and review of the literature
Authors: Li Tao , Zhao Ying , Li Keren , Li Gong , Li Guangxin 
Published: November 2024

BackgroundHepatocellular carcinoma (HCC) is a highly lethal and invasive cancer. Targeted and immunotherapies are the primary treatment options for unresectable advanced HCC. There are no recognized and consistent systemic follow-up treatments for patients with HCC who experience disease progression after first-line targeted therapies and immune checkpoint inhibitors (ICIs). According to a few studies, lenalidomide is an immunomodulatory drug that has the potential to be an effective treatment for patients who have progressed after treatment with targeted drugs and ICIs.Case summaryThis article focuses on a patient with HCC whose disease progressed after first-line targeted therapy and ICI therapy combined with lenalidomide as second-line therapy on the basis of the original targeted and ICI regimens, resulting in a favorable oncologic outcome with acceptable toxicity. The progression-free survival (PFS) of the patients in this study reached 3 years, which is much longer than that previously reported, and no progression has occurred thus far.ConclusionsThis case implies that in patients with hepatocellular carcinoma who have failed first-line targeted therapy and ICIs, targeted therapy and ICIs can be restarted with the addition of lenalidomide, with surprising results.
Health-related quality of life in patients treated with en bloc resection for primary tumors of the spine
Authors: Noli Luigi Emanuele , Alcherigi Chiara , Griffoni Cristiana , Pesce Eleonora , Rosa Simona , Evangelisti Gisberto , Pipola Valerio , Davassi Paolo Francesco , Monetta Annalisa , Barbanti Brodano Giovanni , Terzi Silvia , Ghermandi Riccardo , Tedesco Giuseppe , Girolami Marco , Bandiera Stefano , Gasbarrini Alessandro 
Published: November 2024

Study designRetrospective analysisObjectiveThe aim of this study is to evaluate the functional outcomes and the health-related quality of life (HRQOL) in patients undergoing en bloc resection of spinal tumor.Summary of background dataEn bloc resection in the spine is a surgical procedure designed to completely remove a tumor in one piece, with wide margins preserved, in order to reduce the risk of local recurrences. This demanding procedure has been shown to improve local control and survival rate, besides a relatively high morbidity.MethodsBetween 2016 and 2021, 70 patients underwent en bloc resection surgery for a primary spine tumor and 38 came out to be eligible for this analysis. Eligibility criteria include at least one follow-up visit within a two-year period from surgery and Patient Reported Outcomes evaluation collected prospectively at baseline and at least one follow- up in the range 4-24 months. The outcome variables (EQ5D Numeric Scale and Index, SF36 scores and NRS score) were analyzed with multilevel linear mixed-effects regression. Baseline- (age, gender, localization, histotype, number of levels of resection, previous surgery) and time-dependent covariates (adverse events, spinal cord damage) were included.ResultsBeside a slight improvement of all the scores, no significant differences were found between baseline and follow up times for EQ-5D-3L Numeric Scale and Index and for SF-36 Standardized Physical component. SF-36 Standardized Mental component appeared to be significantly better at 12-month FU compared to baseline. Ultimately, age over 50 years old and the occurrence of adverse events emerged to be as the two main factor determining worsening in several HRQOL scores. Pain came out to be significantly reduce at 24-month compared to baseline.ConclusionsThe aim of en bloc resection in the treatment of primary spinal tumors is to improve survival rates and reduce local recurrences. Despite its radicality, our preliminary results suggest that patients experience a slight to moderate improvement postoperatively compared to their preoperative perceived health status.