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作者： Ziwen Wang Department of Biology's Program in Bioinformatics Northeastern University

Ischemic stroke is one of the two main forms of cerebrovascular accident that ranks the second highest leading killer *** attack of ischemic stroke would lead to rapid death of neurons accompanied with inflammatory events in the brain,causing acquired disabilities for the *** better drugs for ischemic stroke treatment are still in great *** this literature review,three major compounds are mentioned and concluded that 6-shogaol,6-paradol,and zingerone have neuroprotective potential and discussed the possibility to make them promising drugs for ischemic stroke treatment.

关键词： Ischemic stroke ginger ginger-derived compounds

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miRNA networks regulating gene expression in response to tension or compression forces in the cells of the periodontal ligament 4

miRNA networks regulating gene expression in response to ten...

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4th IEEE International Conference on BioInspired Processing, BIP 2022

作者： Valverde, Mariana Bonilla Rodriguez, Rodrigo Mora University of Costa Rica Postgraduate Program Sep Master Program on Bioinformatics and Systems Biology San José11501-2060 Costa Rica University of Costa Rica Faculty of Microbiology San José11501-2060 Costa Rica

ISBN: (纸本)9781665470483

In response to force application, biological reactions occur in the periodontal ligament that causes the orthodontic tooth movement. Differential expression of genes such as ALPL, FGF7, PDRM1, and NR4A2 are involved in the exposure to tension or compression forces by contributing to bone remodeling. In this study, a systems biology approach is used in order to identify a modulator of gene expression when mechanical loadings are applied in periodontal ligament cells. We developed a mathematical model of the interaction network of ALPL and FGF7 with several miRNAs and the transcription factor modulators in BioNetUCR, Cytoscape and COPASI software. We found that miR129-2 has a negative control in ALPL, FGF7, NR4A2 and PRDM1 genes, while miRNA192 has a negative control in ALPL and FGF7 genes in compression and tension side. Both miRNAs are proposed for future experimental validation. © 2022 IEEE.

关键词： RNA

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Microfluidic assembly blocks

Microfluidic assembly blocks

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12th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2008

作者： Rhee, Minsoung Burns, Mark A. Department of Chemical Engineering University of Michigan United States Bioinformatics Program University of Michigan United States Department of Biomedical Engineering University of Michigan United States

The use of microfluidic systems in the life sciences is still limited due to the high-level fabrication expertise required for construction. A novel assembly approach for microdevice construction is presented. This approach involves prefabrication of in-dividual "microfluidic assembly blocks" in PDMS that can be readily assembled on plain glass slides to form microfluidic systems in minutes by non-expert users. We describe the prefabrication of various blocks and the hermetic assembly of microflui-dic devices using the MAB methodology. Finally, we demonstrate common micro-fluidic applications including laminar flow development, valve control, and cell cul-ture. © 2008 CBMS.

关键词： Fabrication

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Genome-wide association analysis with matched samples discloses additional novel risk loci

Genome-wide association analysis with matched samples disclo...

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IEEE International Conference on bioinformatics and Biomedicine

作者： Jungsoo Gim Sungkyoung Choi Jongho Im Jae-Kwang Kim Taesung Park Interdisciplinary program for Bioinformatics and Department of Statistics Seoul National University Interdisciplinary program for Bioinformatics Seoul National University Department of Statistics Iowa State University

ISBN: (纸本)9781479956708

Genome-wide association studies have identified many candidate causal variants associated with common complex diseases and traits, but most of them have been drawn from nonrandomized case/control designs. In nonrandomized experiments, the results drawn from two different groups can be misleading because the units exposed to one group generally differ systematically from the units exposed to the other group. Propensity score is widely used to group case and control units for a more direct and significant comparison even with nonrandomized experiments. This propensity score matching can help with prioritizing additional uncovered variants on disease risk via sub-group analysis in genome-wide association studies. The aim of this work is to propose a post-hoc association test based on the subsets of samples. For that purpose, this paper presents a new paradigm for a post-hoc genome-wide association test when the sample size of controls are larger than that of cases: selecting control samples by equating the distribution of covariates in the case and control groups and re-performing association analysis upon these matched samples. We demonstrated the feasibility of this approach by applying it to 2752 type II diabetes patients in 8842 Korean population. Genome-wide association approach with matched samples is able to disclose 9 additional novel variants and 7 out of 9 have not identified from the association test of whole control samples. The process described here can successfully be combined with other types of case/control studies with large covariate information. This indicates that there a possibility of obtaining additional candidate causal variants responsible for common diseases through genome-wide association analysis with matched samples.

关键词： Propensity score Matching Genome-wide association study

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Paralog-divergent Features May Help Reduce Off-target Effects of Drugs:Hints from Glucagon Subfamily Analysis

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Genomics, Proteomics & bioinformatics 2017年第4期15卷 246-254页

作者： Zhining Sa Jingqi Zhou Yangyun Zou Zhixi Su Xun Gu State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology School of LifeSciencesFudan UniversityShanghai 200433China Department of Genetics Development and Cell BiologyProgram of Bioinformatics and Computational BiologyIowa State UniversityAmesIA 50011USA

Side effects from targeted drugs remain a serious conccrn. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which arc highly homologous in sequences and have similar structures and drug-binding pockets. To identify targctablc differences between paralogs, we analyzed two types （type-I and type-ll） of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors （GPCRs） at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor （GCGR） and glucagon-like peptide-I receptor （GLP-I R）, exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-ll alnino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR. which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-IR. The divergent features between GCGR and GLP-I R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.

关键词： Paralog Functional divergence Functional site Drug specificity Evolutionary conservation

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iSNP: An integrated, automatically updated SNP database

iSNP: An integrated, automatically updated SNP database

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2012 7th International Symposium on Health Informatics and bioinformatics, HIBIT 2012

作者： Çarkacioǧlu, Levent Gedikoǧlu, Ceyhun Son, Yeşim Aydin Bioinformatics Graduate Program Middle East Technical University 06800 Ankara Turkey Health Informatics Department Middle East Technical University 06800 Ankara Turkey

ISBN: (纸本)9781467308786

Single Nucleotide Polymorphisms (SNP) is a DNA sequence variation that occurs when a single nucleotide differs between members of a biological species or paired chromosomes in an individual. Studies on SNP data are important for scientists to shed light on identifying genetic variations underlying complex diseases. While recent advances in high-throughput genotyping technologies are resulting in data accumulation at large scales, the need for collection and service of this data under a standard format and globally normalized and structured metadata that houses the structured SNP data is becoming essential. Here, we present iSNP that is a regularly updated, machine curated database that holds SNP and its associated metadata from publicly available databases under a structured standard format that can be efficiently utilized within different applications. © 2012 IEEE.

关键词： Metadata

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Commentary on whole-grain intake and pancreatic cancer risk-the danish,diet,cancer and health cohort by Schacht et al.

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Hepatobiliary Surgery and Nutrition 2021年第5期10卷 702-704页

作者： Rick J.Jansen Department of Public Health GenomicsPhenomicsand Bioinformatics ProgramCenter for Immunization Research and Education(CIRE)Center for Diagnostic and Therapeutic Strategies in Pancreatic CancerNorth Dakota State UniversityFargoNDUSA

In their manuscript,“Whole-Grain Intake and Pancreatic Cancer Risk-The Danish,Diet,Cancer and Health Cohort”,Schacht et al.(1)report that total whole-grain product(per 50 g/d serving)intake was significantly associated with lower incidence of pancreatic cancer(HR:0.93;95%CI:0.86,1.00).A sex-specific analysis revealed that this association only held among ***,neither total whole-grain(per 16-g serving)or specific individual whole-grain products and cereals were significantly associated with lower pancreatic cancer *** this commentary,I will describe some of the assumptions and biases associated with assessing dietary intake and attempting to find associations with disease.

关键词： intake cancer

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Pre-Treatment Higher Eosinophil Count Is Associated with Improved Survival after Autologous CAR-T Therapy for Hematologic Malignancies

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Transplantation and Cellular Therapy 2025年第2期31卷 S334-S334页

作者： Kagalwalla, Sana, MD Sumransub, Nuttavut, MD Cao, Qing, MS Hu, Marie, MD Tracy, Sean, MD, PhD O'Leary, Daniel, MD Maakaron, Joseph E., MD Juckett, Mark Bachanova, Veronika Department of Medicine University of Minnesota Minneapolis MN Division of Hematology Oncology and Transplantation University of Minnesota Minneapolis MN Biostatistics and Bioinformatics Masonic Cancer Center University of Minnesota Minneapolis MN Bone and Marrow Transplant Program University of Minnesota Medical Center Minneapolis MN Division of Hematology Oncology and Transplantation University of Minnesota Minneapolis MN

IntroductionEosinophils (Eo) play an important role in recruiting T-cells to tumors, and recently were associated with an improved response to immune checkpoint inhibitor therapy. Preclinical studies showed that combining stem cell-derived eosinophil therapy with CAR-T leads to improved treatment efficacy. Limited clinical observations reported that patients greater eosinophil counts after CAR-T had superior CR rate and survival. We therefore examined associations between eosinophil count and immunologic recovery pre and post CAR-T cell therapy and treatment outcomes. MethodsWe included consecutive patients (>18 yrs) with leukemia, lymphoma or myeloma treated between January 2018 and June 2023 on the observational phase 2 study using commercial CAR-T products targeting CD19 and BCMA (NCT03642626). We collected CAR-T related toxicities, history of autoimmune diseases, peak absolute and percentage eosinophil counts and lymphocyte subset before aphaeresis, CAR-T cell therapy and at ∼30, 60, and 100 days after CAR-T infusion. Analysis of categorical variables was performed by Chi-square and of continuous variables by Wilcoxon rank-sum tests. Recursive partitioning methods were used to find the optimal eosinophil count cutoff based on two-year overall survival (OS) and progression-free survival (PFS). ResultsWe included 106 patients with a median age of 62.3 years (range 19-86), 61% were male, 66% had DLBCL. Peak eosinophil count varied widely among patients at baseline (0-2400 cells/μl), median was 200 cells/μl. Using recursive partitioning, pre-apheresis Eo count 150 determined the high eosinophil group (n=56, 53%; median eo count of 300 (range 100-2400) and low eo group (n=50, 47%, median 100; range 0 - 100 cells/μl). Baseline characteristics of the two groups were similar except in the low eo group, more patients had pre-existing autoimmune condition (34% vs 11%; P<0.01), and high ferritin levels. Eo levels (hi vs low) were not associated with CR rate (76% vs 66%) no

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Physiologically based serum ferritin thresholds for iron deficiency among women and children from Africa, Asia, Europe, and central America: a multinational comparative study

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The Lancet Global Health 2025年第5期13卷 e831-e842页

作者： Addo, O Yaw Mei, Zuguo Jefferds, Maria Elena D Jenkins, Mica Flores-Ayala, Rafael Williams, Anne M Young, Melissa Fox Luo, Hanqi Ko, Yi-An Papassotiriou, Ioannis Palmieri, Mireya Mesarina, Karla Bhutta, Zulfiqar Suchdev, Parminder S Brittenham, Gary M Nutrition Branch International Micronutrient Malnutrition Prevention and Control Program (IMMPaCt) Team National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) US Centers for Disease Control and Prevention Atlanta GA United States National Health and Nutrition Examination Survey Analysis Branch National Center for Health Statistics US Centers for Disease Control and Prevention Hyattsville MD United States Hubert Department of Global Health Emory University Rollins School of Public Health Atlanta GA United States Department of Biostatistics and Bioinformatics Emory University Rollins School of Public Health Atlanta GA United States Department of Paediatrics Emory University School of Medicine Atlanta GA United States First Department of Paediatrics National and Kapodistrian University of Athens School of Medicine Athens Greece Instituto de Nutrición de Centro América y Panamá – INCAP Guatemala City Guatemala Secretariat of Food and Nutrition Security (SESAN) Guatemala City Guatemala Institute for Global Health & Development The Aga Khan University Karachi Pakistan Division of Global Health Protection US Centers for Disease Control and Prevention Central America Regional Office Guatemala City Guatemala Department of Paediatrics College of Physicians and Surgeons Columbia University New York NY United States

Background: Diagnosis of iron deficiency commonly relies on measurement of serum ferritin concentrations. WHO guidelines identify serum ferritin thresholds for iron deficiency among healthy individuals of less than 15 μg/L for women and less than 12 μg/L for children under 5 years, based on expert opinion. We report thresholds for iron deficiency for apparently healthy non-pregnant women and young children based on physiological indicators. Methods: We performed secondary analyses of cross-sectional data from women (aged 15–49 years) and children (aged 6–59 months) from 12 countries in Africa, Asia, Europe, and central America from available surveys (2007–19). Using haemoglobin and soluble transferrin receptor concentrations as individual-level indicators of iron deficiency, we identified country-specific serum ferritin thresholds. We conducted multivariate meta-analysis using individual participant data to assess multinational heterogeneity and intercountry consistency. Findings: Data were collected from July, 2007 to March, 2019. 18 251 individuals (13 864 women and 4387 children) were included in the final analysis. The thresholds of pooled serum ferritin levels corresponding to the starting point of decline in circulating haemoglobin concentrations were 24·8 μg/L (95% CI 24·4–25·2) for women and 22·1 μg/L (20·8–23·4) for children based on the national survey data from 12 countries. The thresholds were consistent among countries (p_{heterogeneity}: women=0·73, children=0·43) but median serum ferritin concentrations and lower 5% reference ranges differed. In all countries, the prevalence of iron deficiency was higher using physiologically based thresholds than that using WHO current guidelines for women (36·0% [95% CI 25·3–46·8] vs 20·1% [11·5–28·7], p<0·0001) and for children (34·2% [24·3–44·1] vs 16·6% [11·2–22·0], p<0·0001). Interpretation: These results provide evidence that the prevalence of iron deficiency as indicated by physiological measures is su

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Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures

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细胞研究（英文版） 2021年第5期31卷 495-516页

作者： Lei Sun Kui Xu Wenze Huang Yucheng T.Yang Pan Li Lei Tang Tuanlin Xiong Qiangfeng Cliff Zhang MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China Program in Computational Biology and Bioinformatics Yale UniversityNew HavenCT 06520USA Department of Molecular Biophysics and Biochemistry Yale UniversityNew HavenCT 06520USA

Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular regulation,and dynamically reflect specific cellular ***,presently available tools for predicting RBP-RNA interactions employ RNA sequence and/or predicted RNA structures,and therefore do not capture their condition-dependent ***,after profiling transcriptome-wide in vivo RNA secondary structures in seven cell types,we developed PrismNet,a deep learning tool that integrates experimental in vivo RNA structure data and RBP binding data for matched cells to accurately predict dynamic RBP binding in various cellular *** results for 168 RBPs support its utility for both understanding CUP-seq results and largely extending such interaction data to accurately analyze additional cell ***,PrismNet employs an 'attention' strategy to computationally identify exact RBP-binding nucleotides,and we discovered enrichment among dynamic RBP-binding sites for structure-changing variants(riboSNitches),which can link genetic diseases with dysregulated RBP *** rich profiling data and deep learning-based prediction tool provide access to a previously inaccessible layer of cell-type-specific RBP-RNA interactions,with clear utility for understanding and treating human diseases.

关键词： bioinformatics Mechanisms of disease Molecular biology

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