bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenome-wide association study identifies DNA methylation loci associated with handgrip strength in Chinese monozygotic twins
Authors: Luo Jia , Wang Weijing , Li Jingxian , Duan Haiping , Xu Chunsheng , Tian Xiaocao , Zhang Dongfeng 
Published: April 2024

Background: The decline in muscle strength and function with aging is well recognized, but remains poorly characterized at the molecular level. Here, we report the epigenetic relationship between genome-wide DNA methylation and handgrip strength (HGS) among Chinese monozygotic (MZ) twins.Methods: DNA methylation (DNAm) profiling was conducted in whole blood samples through Reduced Representation Bisulfite Sequencing method. Generalized estimating equation was applied to regress the DNAm of each CpG with HGS. The Genomic Regions Enrichment of Annotations Tool was used to perform enrichment analysis. Differentially methylated regions (DMRs) were detected using comb-p. Causal inference was performed using Inference about Causation through Examination of Familial Confounding method. Finally, we validated candidate CpGs in community residents.Results: We identified 25 CpGs reaching genome-wide significance level. These CpGs located in 9 genes, especially FBLN1, RXRA, and ABHD14B. Many enriched terms highlighted calcium channels, neuromuscular junctions, and skeletal muscle organ development. We identified 21 DMRs of HGS, with several DMRs within FBLN1, SLC30A8, CST3, and SOCS3. Causal inference indicated that the DNAm of 16 top CpGs within FBLN1, RXRA, ABHD14B, MFSD6, and TYW1B might influence HGS, while HGS influenced DNAm at two CpGs within FBLN1 and RXRA. In validation analysis, methylation levels of six CpGs mapped to FLBN1 and one CpG mapped to ABHD14B were negatively associated with HGS weakness in community population.Conclusion: Our study identified multiple DNAm variants potentially related to HGS, especially CpGs within FBLN1 and ABHD14B. These findings provide new clues to the epigenetic modification underlying muscle strength decline.
Luminescent Ln3+-based silsesquioxanes with a β-diketonate antenna ligand: toward the design of efficient temperature sensors
Authors: Félix Gautier , Kulakova Alena N. , Sene Saad , Khrustalev Victor N. , Hernández-Rodríguez Miguel A. , Shubina Elena S. , Pelluau Tristan , Carlos Luís D. , Guari Yannick , Carneiro Neto Albano N. , Bilyachenko Alexey N. , Larionova Joulia 
Published: April 2024

We report the synthesis and single-crystal X-ray diffraction, magnetic, and luminescence measurements of a novel family of luminescent cage-like tetranuclear silsesquioxanes (PhSiO1.5)8(LnO1.5)4(O)(C5H8O2)6(EtOH)2(CH3CN)2⋅2CH3CN (where Ln = Tb, 1; Tb/Eu, 2; and Gd, 3), featuring seven-coordinated lanthanide ions arranged in a one-capped trigonal prism geometry. Compounds 1 and 2 exhibit characteristic Tb3+ and Tb3+/Eu3+-related emissions, respectively, sensitized by the chelating antenna acetylacetonate (acac) ligands upon excitation in the UV and visible spectral regions. Compound 3 is used to assess the energies of the triplet states of the acac ligand. For compound 1, theoretical calculations on the intramolecular energy transfer and multiphonon rates indicate a thermal balance between the 5D4 Stark components, while the mixed Tb3+/Eu3+ analog 2, with a Tb:Eu ratio of 3:1, showcases intra-cluster Tb3+-to-Eu3+ energy transfer, calculated theoretically as a function of temperature. By utilizing the intensity ratio between the 5D4→7F5 (Tb3+) and 5D0→7F2 (Eu3+) transitions in the range 11–373 K, we demonstrate the realization of a ratiometric luminescent thermometer with compound 2, operating in the range 11–373 K with a maximum relative sensitivity of 2.0% K−1 at 373 K. These findings highlight the potential of cage-like silsesquioxanes as versatile materials for optical sensing-enabled applications.
Deciphering the epidemiological dynamics: Toxoplasma gondii seroprevalence in mainland China’s food animals, 2010-2023
Authors: Yang Zipeng , Yuan Hao , Nie Linchong , Wen Qingyuan , Li Haoxin , Yang Liulu , Song Yining , Luo Xun , Zhang Xiu-Xiang , Yuan Zi-Guo 
Published: April 2024

BackgroundToxoplasma gondii (T. gondii) is a significant protozoan pathogen among food animals. Despite the threat to public health by T. gondii infections, there’s limited understanding of its seroprevalence and trends in food animals across mainland China. This study aimed to estimate the seroprevalence of T. gondii infections among swine, sheep, goats, chickens, and cattle in mainland China from 2010 to 2023.MethodsWe searched cross-sectional studies published between 2010 and 2023 that reported the prevalence of T. gondii in food animals from databases including PubMed, Embase, Web of Science, China Biology Medicine Disc (CBM), China National Knowledge Infrastructure (CNKI), Wanfang data, and the China Science and Technology Journal Database (CQVIP). We performed subgroup analyses to explore the impact of different factors on the seroprevalence of T. gondii. Pooled estimates of T. gondii seroprevalence were calculated with a random-effects model.ResultsAn analysis of 184 studies involving 211985 animals revealed a T. gondii overall seroprevalence of 15.3% (95% CI: 13.1-17.8). Although the seroprevalence of food animals across mainland China was relatively stable from 2010 to 2023, notable variations were observed across different animal types and regions (P &lt; 0.01), along with changes in geographical distribution. Sample type, detection method, animal age, and history of abortion were identified as key risk factors for T. gondii seroprevalence.ConclusionThe study conducted a meta-analysis on the seroprevalence of T. gondii in mainland China’s Food Animals from 2010 to 2023, and identified key risk factors. These findings advance our understanding of T. gondii infection dynamics, offering critical insights for developing control strategies and guiding public health policies.
Applying machine-learning models to differentiate benign and malignant thyroid nodules classified as C-TIRADS 4 based on 2D-ultrasound combined with five contrast-enhanced ultrasound key frames
Authors: Chen Jia-hui , Zhang Yu-Qing , Zhu Tian-tong , Zhang Qian , Zhao Ao-xue , Huang Ying 
Published: April 2024

ObjectivesTo apply machine learning to extract radiomics features from thyroid two-dimensional ultrasound (2D-US) combined with contrast-enhanced ultrasound (CEUS) images to classify and predict benign and malignant thyroid nodules, classified according to the Chinese version of the thyroid imaging reporting and data system (C-TIRADS) as category 4.Materials and methodsThis retrospective study included 313 pathologically diagnosed thyroid nodules (203 malignant and 110 benign). Two 2D-US images and five CEUS key frames (“2nd second after the arrival time” frame, “time to peak” frame, “2nd second after peak” frame, “first-flash” frame, and “second-flash” frame) were selected to manually label the region of interest using the “Labelme” tool. A total of 7 images of each nodule and their annotates were imported into the Darwin Research Platform for radiomics analysis. The datasets were randomly split into training and test cohorts in a 9:1 ratio. Six classifiers, namely, support vector machine, logistic regression, decision tree, random forest (RF), gradient boosting decision tree and extreme gradient boosting, were used to construct and test the models. Performance was evaluated using a receiver operating characteristic curve analysis. The area under the curve (AUC), sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy (ACC), and F1-score were calculated. One junior radiologist and one senior radiologist reviewed the 2D-US image and CEUS videos of each nodule and made a diagnosis. We then compared their AUC and ACC with those of our best model.ResultsThe AUC of the diagnosis of US, CEUS and US combined CEUS by junior radiologist and senior radiologist were 0.755, 0.750, 0.784, 0.800, 0.873, 0.890, respectively. The RF classifier performed better than the other five, with an AUC of 1 for the training cohort and 0.94 (95% confidence interval 0.88–1) for the test cohort. The sensitivity, specificity, accuracy, PPV, NPV, and F1-score of the RF model in the test cohort were 0.82, 0.93, 0.90, 0.85, 0.92, and 0.84, respectively. The RF model with 2D-US combined with CEUS key frames achieved equivalent performance as the senior radiologist (AUC: 0.94 vs. 0.92, P = 0.798; ACC: 0.90 vs. 0.92) and outperformed the junior radiologist (AUC: 0.94 vs. 0.80, P = 0.039, ACC: 0.90 vs. 0.81) in the test cohort.ConclusionsOur model, based on 2D-US and CEUS key frames radiomics features, had good diagnostic efficacy for thyroid nodules, which are classified as C-TIRADS 4. It shows promising potential in assisting less experienced junior radiologists.
Service life estimation of electric vehicle lithium-ion battery pack using arrhenius mathematical model
Authors: Rammohan A. , Wang Yong , Kannappan S Subbu , Kumar P Suresh , Ashok Bragadeshwaran , Kotb Hossam , AboRas Kareem M. , Yousef Amr 
Published: April 2024

Durability is a desired characteristic for all battery packs in Electric Vehicles. In this study, the service life of the EV battery pack under real-world operating conditions is projected using an Arrhenius mathematical simulation model. The model comprises a 39.2 kWh EV Lithium-Ion battery pack integrated with a three-phase inverter to convert the battery pack’s Direct Current output to Alternating Current. In addition, the Alternating Current output is coupled to a 100 kW permanent magnet synchronous motor, which is regarded as the load. A field-oriented controller provides pulse width-modulated output signals that are supplied back to the inverter to generate the correct driving current. Variable conditions of charge rate (C-rate: 1.25C − 4C), discharge rate (C-rate: 0.5C − 4C), temperature (25°C–60°C), and depth of discharge (30%–90%) are evaluated to determine the battery pack’s service life. Under a 4C charge rate/0.5C discharge rate and 50% depth of discharge, the modeling results indicate the battery pack has a service life of approximately 6,000 h at low temperatures (25°C) and roughly 3,000 h at high temperatures (60°C). The model has been validated by comparing the results with experimental data from the literature.
CD8+ T cells are necessary for improved sepsis survival induced by CD28 agonism in immunologically experienced mice
Authors: Anyalebechi Jerome C. , Sun Yini , Davis Carolyn , Wagener Maylene E. , Liang Zhe , Burd Eileen M. , Coopersmith Craig M. , Ford Mandy L. 
Published: April 2024

IntroductionA hallmark of T cell dysregulation during sepsis is the downregulation of costimulatory molecules. CD28 is one of T cell costimulatory molecules significantly altered on memory T cells during sepsis. We recently showed that treatment with a αCD28 agonist in septic immunologically experienced mice led to improved survival. Therefore, here we aimed to identify the cell subset(s) necessary for the survival benefit observed in the context of CD28 agonism, and to further investigate the mechanism by which CD28 agonism improves sepsis survival in immunologically experienced mice. Methods: Mice received specific pathogen inoculation to generate memory T cell populations similar in frequency to that of adult humans. Once these infections were cleared and the T cell response had transitioned to the memory phase, animals were rendered septic via cecal ligation and puncture in the presence or absence of an agonistic anti-CD28 mAb.ResultsResults demonstrated that CD8+ T cells, and not bulk CD4+ T cells or CD25+ regulatory T cells, were necessary for the survival benefit observed in CD28 agonist-treated septic immunologically experienced mice. Upon examination of these CD8+ T cells, we found that CD28 agonism in septic immunologically experienced mice was associated with an increase in Foxp3+ CD8+ T cells as compared to vehicle-treated controls. When CD8+ T cells were depleted in septic immunologically experienced mice in the setting of CD28 agonism, a significant increase in levels of inflammatory cytokines in the blood was observed.DiscussionTaken together, these results indicate that CD28 agonism in immunologically experienced mice effectively suppresses inflammation via a CD8+-dependent mechanism to decrease mortality during sepsis.
Coupled scRNA-seq and Bulk-seq reveal the role of HMMR in hepatocellular carcinoma
Authors: Su Zhixiong , He Yufang , You Lijie , Zhang Guifeng , Chen Jingbo , Liu Zhenhua 
Published: April 2024

BackgroundHyaluronan-mediated motility receptor (HMMR) is overexpressed in multiple carcinomas and influences the development and treatment of several cancers. However, its role in hepatocellular carcinoma (HCC) remains unclear.MethodsThe “limma” and “GSVA” packages in R were used to perform differential expression analysis and to assess the activity of signalling pathways, respectively. InferCNV was used to infer copy number variation (CNV) for each hepatocyte and “CellChat” was used to analyse intercellular communication networks. Recursive partitioning analysis (RPA) was used to re-stage HCC patients. The IC50 values of various drugs were evaluated using the “pRRophetic” package. In addition, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm HMMR expression in an HCC tissue microarray. Flow cytometry (FCM) and cloning, Edu and wound healing assays were used to explore the capacity of HMMR to regulate HCC tumour.ResultsMultiple cohort studies and qRT-PCR demonstrated that HMMR was overexpressed in HCC tissue compared with normal tissue. In addition, HMMR had excellent diagnostic performance. HMMR knockdown inhibited the proliferation and migration of HCC cells in vitro. Moreover, high HMMR expression was associated with “G2M checkpoint” and “E2F targets” in bulk RNA and scRNA-seq, and FCM confirmed that HMMR could regulate the cell cycle. In addition, HMMR was involved in the regulation of the tumour immune microenvironment via immune cell infiltration and intercellular interactions. Furthermore, HMMR was positively associated with genomic heterogeneity with patients with high HMMR expression potentially benefitting more from immunotherapy. Moreover, HMMR was associated with poor prognosis in patients with HCC and the re-staging by recursive partitioning analysis (RPA) gave a good prognosis prediction value and could guide chemotherapy and targeted therapy.ConclusionThe results of the present study show that HMMR could play a role in the diagnosis, prognosis, and treatments of patients with HCC based on bulk RNA-seq and scRAN-seq analyses and is a promising molecular marker for HCC.
Antimalarial drug resistance profiling of Plasmodium falciparum infections in India using Ion Torrent deep sequencing
Authors: Kale Sonal , Uplekar Swapna M. , Bandyopadhyay Nabamita , Rao Pavitra N. , Ali Syed Z. , Sharma Surya Kant , Tandel Nikunj , Patel Ankita , Singh Ranvir , Dank Aaron , Ravishankaran Sangamithra , Priya G. Sri Lakshmi , Asokan Aswin , Eapen Alex , Singh Om. P. , Carlton Jane M. , Mallick Prashant K. 
Published: April 2024

IntroductionTracking the emergence and spread of antimalarial drug resistance is critical for supporting progress towards the control and eventual elimination of malaria in South Asia, especially India. Plasmodium falciparum has evolved resistance to virtually every antimalarial drug, and significant progress has been made to identify the molecular genetic mechanisms involved in the most common types of resistance.MethodsAn amplicon sequencing protocol was used for molecular surveillance of antimalarial drug resistance in a total of 158 patient isolates collected from December 2012 to September 2015 from three sites in south, west and east India: Tamil Nadu, Gujarat, and Odisha respectively. Five full length Plasmodium falciparum genes whose mutant proteins are implicated in antimalarial drug resistance were investigated: Pfcrt for chloroquine, Pfdhfr for pyrimethamine, Pfdhps for sulfadoxine, Pfk13 for artemisinin and Pfmdr1 for resistance to multiple antimalarial drugs.ResultsWe observed a high proportion of wild-type Pfcrt and Pfdhfr haplotypes from the P. falciparum-dominant site Rourkela, while mutant Pfcrt and Pfdhfr haplotypes were fixed at the P. vivax dominant sites Chennai and Nadiad. The wild-type Pfdhps haplotype was predominant across all study sites. We identified mutations in the propeller domain of Pfk13, although they are not associated with resistance to artemisinin. Finally, using samples taken from the same patient on day 2, day 7, and day 14 after artemisinin combination treatment, we were able to observe changes in allele frequency of drug resistance genes during the course of an infection.DiscussionThis is the first high-throughput deep sequencing study of five full-length P. falciparum genes in clinical isolates from three different study sites in India with varying transmission ecologies. Amplicon sequencing based on ion-torrent has the potential to track changes in the frequency of drug resistant alleles as a patient is undergoing drug therapy, and to identify new resistance mutations as they increase in frequency in the patient. This study showed possibility of whole gene sequencing, leads to in-depth molecular surveillance of multiple antimalarial resistant candidates and furthermore suggests investigations on reversal of resistant genotypes due to usage of artemisinin combination therapy in P. falciparum prevalent areas of the country.
A meta-analysis on first-trimester blood count parameters—is the neutrophil-to-lymphocyte ratio a potentially novel method for first-trimester preeclampsia screening?
Authors: Mészáros Balázs , Veres Dániel S. , Nagyistók Luca , Kovács Bence G. , Kukor Zoltán , Valent Sándor 
Published: April 2024

ObjectiveMeta-analysis focusing on the role of first-trimester neutrophil-to-lymphocyte ratio (NLR) in the prediction of preeclampsia.Data sourcesPubMed, Scopus, Web of Science, Cochrane Library, and Embase databases were queried from inception up to December 31, 2022.Study eligibility criteriaThe study included all types of original research that was conducted in humans and values of NLR were measured during the first trimester, among patients who later developed preeclampsia, compared to the values of control groups.Study appraisal and synthesis methodsTwo reviewers independently performed data abstraction and quality appraisal, and disagreements were resolved by consensus and, if necessary, by the opinion of a third reviewer. During the analysis, PRISMA and MOOSE guidelines were followed. All statistical analyses were made with R.ResultsFor the research on the predictive role of NLR values in the first trimester for preeclampsia, a total of 6 studies were selected for analysis, covering 2,469 patients. The meta-analysis revealed a 95% confidence interval (CI) for the effect size of 0.641 to 1.523, with a prediction interval of 0.027 to 2.137.ConclusionBased on the analysis, NLR is a promising biochemical marker for future pieces of research that try to find new screening methods for first-trimester preeclampsia. We encourage other researchers to examine NLR’s predictive value combined with other markers in preeclampsia screening, this way being able to find new and affordable protocols for first-trimester preeclampsia screening.Systematic review registrationidentifier CRD42023392663.
Assessing multidisciplinary follow-up pattern efficiency and cost in follow-up care for patients in cervical spondylosis surgery: a non-randomized controlled study
Authors: Fu Zhongmin , Xie Yan , Li Peifang , Gao Menghui , Chen Jiali , Ning Ning 
Published: April 2024

BackgroundThe use of multidisciplinary treatment programs in out-of-hospital healthcare is a new area of research. Little is known about the benefits of this method in the management of discharged patients undergoing cervical spondylosis surgery.ObjectiveThis study aimed to explore the effect of a contracted-based, multidisciplinary follow-up plan in patients after cervical spondylosis surgery.MethodsThis non-blinded non-randomized controlled study was conducted with 88 patients (44 in the intervention group, 44 in the control group). The clinical outcomes, including Neck Disability Index (NDI), pain score (VAS), Self-Efficacy for Managing Chronic Disease 6-item Scale (SECD-6), and 12-Item Short-Form Health Survey (SF-12) score were assessed at the time of discharge, 24–72 h, 1 month, and 3 months post-discharge. The complications, patient satisfaction, and economic indicators were assessed at the final follow-up (3 months).ResultsPatients who received contracted follow-up showed greater improvement in neck dysfunction at 24–72 h, 1 month, and 3 months after discharge compared to those who received routine follow-up (p &lt; 0.001). At 1 month after discharge, the intervention group exhibited better self-efficacy (p = 0.001) and quality of life (p &lt; 0.001) than the control group, and these improvements lasted for 3 months. The intervention group reported lower pain scores at 24–72 h and 1 month (p = 0.008; p = 0.026) compared to the control group. The incidence of complications was significantly lower in the intervention group (11.4%) compared to the control group (40.9%). The total satisfaction score was significant difference between the two groups (p &lt; 0.001). Additionally, the intervention group had lower direct medical costs (p &lt; 0.001), direct non-medical costs (p = 0.035), and total costs (p = 0.04) compared to the control group. However, there was no statistically significant difference in indirect costs between the two groups (p = 0.59).ConclusionA multidisciplinary contract follow-up plan has significant advantages regarding neck disability, self-efficacy, quality of life, postoperative complications, patient satisfaction, and direct costs compared with routine follow-up.
Transcriptomic analysis of the response of Avena sativa to Bacillus amyloliquefaciens DGL1
Authors: Yang Xue , Xie Yongli , Wang Tian , Qiao Youming , Li Junxi , Wu Lingling , Gao Ying 
Published: April 2024

IntroductionBacillus amyloliquefaciens DGL1, isolated from the arid sandy areas in Dagler, Qinghai Province, China, promotes the growth of Avena sativa variety “Qing Yan 1”.MethodsTo elucidate the transcriptomic changes in the oat root system following interaction with DGL1 and to reveal the molecular mechanism by which DGL1 promotes oat growth, treatment and control groups of oat roots at 2, 4, 8, and 12 h after inoculation with a suspension of strain DGL1 were analyzed using Illumina high-throughput transcriptome sequencing technology. The differentially expressed genes were determined through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and the metabolic pathways and key genes were analyzed.ResultsThe results showed that 7874, 13,392, 13,169, and 19,026 differentially expressed genes were significantly enriched in the glycolysis/gluconeogenesis pathway, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction, and other related metabolic pathways in the oat roots at 2, 4, 8, and 12 h after inoculation with a DGL1 suspension. The GO and KEGG enrichment analyses revealed that the genes encoding plasma membrane ATPase, phosphoglycerate kinase gene PGK, ammonium transporter protein gene AMT, cellulose synthase gene CSLF6, and growth hormone response family gene IAA18 were significantly upregulated.DiscussionIt is hypothesized that the pro-growth mechanism of strain DGL1 in oats is the result of the coordination of multiple pathways through the promotion of oat energy metabolism, phytohormone signaling, secondary metabolite synthesis, and amino acid metabolism.