bluuebunny/crossref_metadata_2025_split huggingface dataset:
VNAR development through antigen immunization of Japanese topeshark (Hemitriakis japanica)
Authors: Takeda Hiroyuki , Ozawa Tatsuhiko , Zenke Hiroki , Ohnuki Yoh , Umeda Yuri , Zhou Wei , Tomoda Honoka , Takechi Akihiko , Narita Kimiyoshi , Shimizu Takaaki , Miyakawa Takuya , Ito Yuji , Sawasaki Tatsuya 
Published: September 2023

The VNAR (Variable New Antigen Receptor) is the smallest single-domain antibody derived from the variable domain of IgNAR of cartilaginous fishes. Despite its biomedical and diagnostic potential, research on VNAR has been limited due to the difficulties in obtaining and maintaining immune animals and the lack of research tools. In this study, we investigated the Japanese topeshark as a promising immune animal for the development of VNAR. This shark is an underutilized fishery resource readily available in East Asia coastal waters and can be safely handled without sharp teeth or venomous stingers. The administration of Venus fluorescent protein to Japanese topesharks markedly increased antigen-specific IgM and IgNAR antibodies in the blood. Both the phage-display library and the yeast-display library were constructed using RNA from immunized shark splenocytes. Each library was enriched by biopanning, and multiple antigen-specific VNARs were acquired. The obtained antibodies had affinities of 1 × 10−8 M order and showed high plasticity, retaining their binding activity even after high-temperature or reducing-agent treatment. The dissociation rate of a low-affinity VNAR was significantly improved via dimerization. These results demonstrate the potential utility of the Japanese topeshark for the development of VNAR. Furthermore, we conducted deep sequencing analysis to reveal the quantitative changes in the CDR3-coding sequences, revealing distinct enrichment bias between libraries. VNARs that were primarily enriched in the phage display had CDR3 coding sequences with fewer E. coli rare codons, suggesting translation machinery on the selection and enrichment process during biopanning.
Evidence supportive of a bacterial component in the etiology for Alzheimer’s disease and for a temporal-spatial development of a pathogenic microbiome in the brain
Authors: Moné Yves , Earl Joshua P. , Król Jarosław E. , Ahmed Azad , Sen Bhaswati , Ehrlich Garth D. , Lapides Jeffrey R. 
Published: September 2023

BackgroundOver the last few decades, a growing body of evidence has suggested a role for various infectious agents in Alzheimer’s disease (AD) pathogenesis. Despite diverse pathogens (virus, bacteria, fungi) being detected in AD subjects’ brains, research has focused on individual pathogens and only a few studies investigated the hypothesis of a bacterial brain microbiome. We profiled the bacterial communities present in non-demented controls and AD subjects’ brains.ResultsWe obtained postmortem samples from the brains of 32 individual subjects, comprising 16 AD and 16 control age-matched subjects with a total of 130 samples from the frontal and temporal lobes and the entorhinal cortex. We used full-length 16S rRNA gene amplification with Pacific Biosciences sequencing technology to identify bacteria. We detected bacteria in the brains of both cohorts with the principal bacteria comprising Cutibacterium acnes (formerly Propionibacterium acnes) and two species each of Acinetobacter and Comamonas genera. We used a hierarchical Bayesian method to detect differences in relative abundance among AD and control groups. Because of large abundance variances, we also employed a new analysis approach based on the Latent Dirichlet Allocation algorithm, used in computational linguistics. This allowed us to identify five sample classes, each revealing a different microbiota. Assuming that samples represented infections that began at different times, we ordered these classes in time, finding that the last class exclusively explained the existence or non-existence of AD.ConclusionsThe AD-related pathogenicity of the brain microbiome seems to be based on a complex polymicrobial dynamic. The time ordering revealed a rise and fall of the abundance of C. acnes with pathogenicity occurring for an off-peak abundance level in association with at least one other bacterium from a set of genera that included Methylobacterium, Bacillus, Caulobacter, Delftia, and Variovorax. C. acnes may also be involved with outcompeting the Comamonas species, which were strongly associated with non-demented brain microbiota, whose early destruction could be the first stage of disease. Our results are also consistent with a leaky blood–brain barrier or lymphatic network that allows bacteria, viruses, fungi, or other pathogens to enter the brain.
The gut microbiota from maintenance hemodialysis patients with sarcopenia influences muscle function in mice
Authors: Tang Jie , Zhang Hailin , Yin Lixia , Zhou Qifan , Zhang Huipin 
Published: September 2023

BackgroundSarcopenia is a common complication in patients undergoing maintenance hemodialysis (MHD). Growing evidence suggests a close relationship between the gut microbiota and skeletal muscle. However, research on gut microbiota in patients with sarcopenia undergoing MHD (MS) remains scarce. To bridge this knowledge gap, we aimed to evaluate the pathogenic influence of gut microbiota in the skeletal muscle of patients with MS, to clarify the causal association between gut microbiota and skeletal muscle symptoms in patients with MS and identify the potential mechanisms underlying this causal association.MethodsFecal samples were collected from 10 patients with MS and 10 patients without MS (MNS). Bacteria were extracted from these samples for transplantation. Mice (n=42) were randomly divided into three groups and, after antibiotic treatment, fecal microbiota transplantation (FMT) was performed once a day for 3 weeks. Skeletal muscle and fecal samples from the mice were collected for 16S rRNA gene sequencing and for histological, real-time PCR, and metabolomic analyses.ResultsMice colonized with gut microbiota from MS patients exhibited notable decreases in muscle function and muscle mass, compared with FMT from patients with MNS. Moreover, 16S rRNA sequencing revealed that the colonization of MS gut microbiota reduced the abundance of Akkermansia in the mouse intestines. Metabolome analysis revealed that seven metabolic pathways were notably disrupted in mice transplanted with MS microbiota.ConclusionThis study established a connection between skeletal muscle and the gut microbiota of patients with MS, implying that disruption of the gut microbiota may be a driving factor in the development of skeletal muscle disorders in patients undergoing MHD. This finding lays the foundation for understanding the pathogenesis and potential treatment methods for sarcopenia in patients undergoing MHD.
The incidence of hepatocellular carcinoma and clearance of hepatitis B surface for CHB patients in the indeterminate phase: a systematic review and meta-analysis
Authors: Liu Min , Zhao Taixue , Zhang Yuting , Zhang A-Mei , Geng Jiawei , Xia Xueshan 
Published: September 2023

BackgroundNearly 30%–40% of patients with chronic hepatitis B do not fall into any of the traditional natural history classification and thus are classified as indeterminate. However, it is unclear whether patients in the indeterminate phase (IP) are at a higher risk for hepatocellular carcinoma (HCC) than those in the defined phases (DP) and would benefit from antiviral therapy. We performed a systematic review and meta-analysis of HCC incidence and HBsAg clearance among patients in the IP versus DP.MethodsWe defined the clinical phases as per the AASLD 2018 hepatitis B guidance. We searched PubMed, Embase, Medline, and Web of Science for relevant studies that reported HCC incidence or HBsAg clearance in IP versus DP patients published between January 2007 and March 2023. Annual HCC incidence and HBsAg clearance rates were pooled using a random/common-effects model.ResultsWe analyzed data from 14 studies, comprising 7798 IP patients (222 patients developed HCC and 239 achieved HBsAg clearance) and 10,725 DP patients. The pooled annual HCC incidence was 2.54 cases per 1,000 person-years (95% CI, 1.14–4.39) and HBsAg clearance rate was 12.36 cases per 1,000 person-years (95% CI, 10.70–14.13) for the IP patients. IP patients were associated with significantly higher HCC incidence risk (RR = 1.64, 95% CI, 1.34–2.00) and slightly lower annual HBsAg clearance rate (RR = 0.83, 95% CI, 0.70–0.99) than the DP patients. In addition, HBeAg-negative IP patients (2.31%; 95% CI, 0.87–4.45) showed a significantly higher HCC incidence than those who were HBeAg positive (0.00%; 95% CI, 0.00–0.99) (p&lt; 0.001). The Asia-Pacific region IP patients (4.30%; 95% CI, 2.07–7.27) were also associated with a higher HCC incidence versus Europe (0.05%; 95% CI, 0.00–1.39) (p&lt; 0.001). However, there were no significant differences between different strategies (treated vs. untreated: 2.56%; 95% CI, 1.01–4.63 vs. 1.61%; 95% CI, 0.00–5.81, p = 0.09), and heterogeneity was substantial across the studies (I2 = 89%).ConclusionThe systematic review and meta-analysis showed a high HCC incidence and low HBsAg clearance among patients in the IP, especially for HBeAg-negative patients and the Asian population. We emphasize that future multicenter prospective cohort studies or randomized trials are needed to verify if expanding antiviral therapy for patients in the IP is associated with reduced HCC risk or good treatment outcomes.
Diagnostic efficiency of metagenomic next-generation sequencing for suspected infection in allogeneic hematopoietic stem cell transplantation recipients
Authors: Huang Jiayu , Zhao Yeqian , Jiang Chuanhe , Han Dongsheng , Pan Zengkai , Zhang Zilu , Wang Luxiang , Chen Wei , Li Su , Zhao Yanmin , Hu Xiaoxia 
Published: September 2023

IntroductionImmunosuppression predisposes allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients to infection. Prompt and accurate identification of pathogens is crucial to optimize treatment strategies. This multi-center retrospective study aimed to assess the ability of metagenomic next-generation sequencing (mNGS) to detect causative pathogens in febrile allo-HSCT recipients and examined its concordance with conventional microbiological tests (CMT).MethodsWe performed mNGS and CMT on samples obtained from 153 patients with suspected infection during allo-HSCT. Patients were grouped based on their neutropenic status at the time of sampling.ResultsThe mNGS test was more sensitive than CMT (81.1% vs. 53.6%, P&lt;0.001) for diagnosing clinically suspected infection, especially in the non-neutropenia cohort. mNGS could detect fungi and viruses better than bacteria, with a higher sensitivity than CMT. Immune events were diagnosed in 57.4% (35/61) of the febrile events with negative mNGS results, and 33.5% (48/143) with negative CMT results (P=0.002). The treatment success rate of the targeted anti-infection strategy was significantly higher when based on mNGS than on empirical antibiotics (85% vs. 56.5%, P=0.004).ConclusionThe mNGS test is superior to CMT for identifying clinically relevant pathogens, and provides valuable information for anti-infection strategies in allo-HSCT recipients. Additionally, attention should be paid to immune events in patients with negative mNGS results.
Modifying Escherichia coli to mimic Shigella for medical microbiology laboratory teaching: a new strategy to improve biosafety in class
Authors: Zhang Guangyuan , Liu Jia , He Yonglin , Du Yuheng , Xu Lei , Chen Tingting , Guo Yanan , Fu Huichao , Li Anlong , Tian Yunbo , Hu Yan , Yang Chun , Lu Mingqi , Deng Xichuan , Wang Jingsong , Lu Nan 
Published: September 2023

IntroductionLaboratory teaching of medical microbiology involves highly pathogenic microorganisms, thus posing potential biosafety risks to the students and the teacher. To address these risks, non/low-pathogenic microorganisms were modified to mimic highly pathogenic ones or highly pathogenic microorganisms were attenuated directly using the CRISPR/Cas9 technology. This study describes the modification of Escherichia coli DH5α to mimic Shigella and its evaluation as a safe alternative for medical laboratory teaching.MethodsTo generate E. coli DH5α△FliC△tnaA2a, the tnaA and FliC genes in E. coli DH5α were knocked out using CRISPR/Cas9 technology; a plasmid bearing the O-antigen determinant of S. flexneri 2a was then constructed and transformed. Acid tolerance assays and guinea pig eye tests were used to assess the viability and pathogenicity, respectively. Questionnaires were used to analyze teaching effectiveness and the opinions of teachers and students.ResultsThe survey revealed that most teachers and students were inclined towards real-time laboratory classes than virtual classes or observation of plastic specimens. However, many students did not abide by the safety regulations, and most encountered potential biosafety hazards in the laboratory. E. coli DH5α△FliC△tnaA2a was biochemically and antigenically analogous to S. flexneri 2a and had lower resistance to acid than E. coli. There was no toxicity observed in guinea pigs. Most of teachers and students were unable to distinguish E. coli DH5α△FliC△tnaA2a from pure S. flexneri 2a in class. Students who used E. coli DH5α△FliC△tnaA2a in their practice had similar performance in simulated examinations compared to students who used real S. flexneri 2a, but significantly higher than the virtual experimental group.DiscussionThis approach can be applied to other high-risk pathogenic microorganisms to reduce the potential biosafety risks in medical laboratory-based teaching and provide a new strategy for the development of experimental materials.
Metagenomic characterization of the microbiomes in five different body habitats of otherwise healthy individuals with periodontal disease
Authors: Oh Sujin , Lee Hyo-Jung , Park Kyoung Un 
Published: September 2023

IntroductionRecent studies have proposed several plausible mechanisms supporting the association between periodontal disease and systemic disease. However, characterizing the microbial communities in individuals with periodontal disease before onset of other diseases is an important first step in determining how the altered microbial state contributes to disease progression. This study established microbiome profiles for five body habitats of carefully selected, otherwise healthy individuals with periodontal disease.MethodsBlood, oral (buccal mucosa, dental plaque, and saliva), and stool samples were collected from ten healthy subjects with periodontal disease. Using 16S rRNA metagenomics, the taxonomic and functional compositions of microbiomes were investigated.ResultsThe most predominant phylum in blood and stool was Bacillota. Pseudomonadota accounted for the largest proportion of microbes in the buccal mucosa and saliva, whereas Bacteroidota were the most prevalent in dental plaque. Differential abundance analysis revealed that 12 phyla and 139 genera were differentially abundant between body habitats. Comparison of alpha diversity showed that the blood microbiome has the most diverse community close to neither oral nor stool microbiomes. We also predicted the functional configurations of the microbiome in otherwise healthy subjects with periodontal disease. Principal coordinate analysis based on functional abundance revealed distinct clustering of the microbial communities between different body habitats, as also observed for taxonomic abundance. In addition, 13 functional pathways, including lipopolysaccharide biosynthesis, glutathione metabolism, and proteasome, showed differential expression between habitats.DiscussionOur results offer insight into the effects of the microbiome on systemic health and disease in people with periodontal disease.
Predictors of diastolic deceleration time of coronary flow velocity of infarct related and reference coronary artery assessed by transthoracic Doppler echocardiography in the chronic phase of successfully reperfused anterior myocardial infarction: relation to infarct size
Authors: Giga Vojislav , Tesic Milorad , Beleslin Branko , Boskovic Nikola , Sobic-Saranovic Dragana , Jovanovic Ivana , Nedeljkovic Ivana , Paunovic Ivana , Dedic Srdjan , Djordjevic-Dikic Ana 
Published: September 2023

IntroductionHigh-frequency transthoracic Doppler echocardiography (TDE) enables the assessment of flow velocity and velocity pattern in different coronary arteries, including the assessment of diastolic deceleration time (DDT) of coronary flow velocity. Short DDT of infarct related artery (IRA) (&lt;600 msec) in the acute phase of anterior myocardial infarction (MI) is the predictor of adverse left ventricular (LV) remodeling and prognosis. The significance of DDT of coronary flow velocity assessment in the chronic phase of anterior MI is not well established. Our study aimed to establish the predictors of DDT of the coronary flow velocity of infarct related (left anterior descendent-DDT of LAD) and reference coronary artery, evaluated by TDE, and to assess their relation to infarct size in the chronic phase of successfully reperfused first anterior MI.MethodsOur study included 40 consecutive patients (34 men, mean age 52 ± 12 years) one month after the first anterior STEMI and single vessel disease successfully treated with primary PCI. All patients underwent SPECT MPI for the assessment of LV volumes, ejection fraction, and percentage of the myocardium with fixed perfusion abnormalities and echocardiographic examination including the evaluation of DDT of IRA and reference coronary artery TDE.ResultsDDT of LAD correlated significantly to the WMSI (r = −0.467, p = 0.002), LV end-systolic volume (r = −0.412, p = 0.008), LV ejection fraction (r = 0.427, p = 0.006), while the strongest correlation was observed between DDT of LAD and the extent of fixed perfusion abnormality (r = −0.627, p &lt; 0.0001), Multivariate analysis revealed percentage of fixed perfusion abnormalities along with DDT of reference coronary artery as the independent predictors of DDT of IRA. DDT of IRA shorter than 886 msec predicts large fixed perfusion abnormalities (&gt;20%) with a sensitivity of 89% and specificity of 62% (AUC 0.842).ConclusionDDT of LAD assessed by TDE in the chronic phase of successfully reperfused first anterior MI is a usefull variable for the assessment of microcirculatory function that exclusively reflects the extent of microvascular damage and relates to infarct size.
Associations among risk perception, health efficacy, and health behaviors for cardiovascular disease: an application of risk perception attitude framework
Authors: Guo Zhiting , Chen Yun , Zhang Yuping , Ding Chuanqi , Li Mei , Xu Linyan , Jin Jingfen 
Published: September 2023

BackgroundThere is currently a pervasive prevalence of cardiovascular disease (CVD) risk worldwide and an inadequate amount of action is being taken to promote healthy lifestyle habits. The risk perception attitude (RPA) framework, which classifies individuals based on their risk perception and efficacy belief, enables us to predict their preventive behaviors. We applied the RPA framework to analyze CVD prevention behaviors among Chinese adults and extended its application to CVD objective risk.MethodsA cross-sectional survey was performed in two sites in Zhejiang Province, from March to August 2022, which contained self-reported CVD risk perception, objective CVD risk, efficacy belief, physical activity, healthy diet, and covariates. We used the RPA framework to categorize participants into four groups, then analysis was conducted to estimate inter-group differences in healthy behaviors. We further conducted a hierarchical logistic regression analysis with individuals' health behaviors as the dependent variable, using three blocks of independent variables.ResultsAmong 739 participants, healthy physical activity and healthy diet had significant differences among four RPA groups, post hoc tests clarified that the proportion of respondents with healthy PA in the responsive group (61.6%) was significantly higher than that in the other three groups. Risk perception and efficacy belief significantly predicted health behavior against CVD; the relationship between absolute CVD risk and health behavior was moderated by efficacy belief.ConclusionsEarly CVD risk screening is crucial, but tailored support and a proper understanding of personal risk are essential to promote healthy behaviors. Developing communication and behavioral counseling intervention strategies on the basis of the RPA framework has the potential to promote healthy behaviors for CVD prevention.
A stratospheric mission – design of a conceptual framework to bring weather balloons and STEM into the classroom
Authors: Connolly Cornelia , Johnson Patrick , Johnson Kevin , Fitzpatrick Mary , O’Keeffe Derek T. 
Published: September 2023

IntroductionIntegrated STEM education makes learning relevant and applicable, blending the mindset, skillset, and toolset necessary in developing a depth of understanding for science, technology, engineering and mathematics.MethodsBased on the theoretical framework of Kelley and Knowles the ‘Spaceship Earth’ project was designed to engage primary school children in 4th class (ages 9 and 10 years old) in real-world project-based experiments in the classroom that are used to develop collaborative problem-solving skills and a framework for asking and answering scientific questions. This project involved researchers from two Universities and the Irish National Meteorological Service working collaboratively on a high-altitude balloon mission.ResultsHigh-altitude balloons have an established track record of safe and effective use in weather forecasting, astronomy, and STEM outreach. During the project lifecycle the children devised experiments that they launched to the stratosphere using the high-altitude balloons. Once the experiments returned to Earth, the children engaged in analysis and discussion about their experiments that extended and deepened their learning.DiscussionThis celestial project framework represents a new dawn of innovation for STEM education and public engagement.