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Detection and analysis of CpG sites with multimodal DNA methylation level distributions and their relationships with SNPs

DNA methylation levels at cytosine-phosphate-guanine (CpG) sites with multimodal distributions among different samples have been reported recently. One possible explanation for such variability is that genetic variants might affect epigenetic variation. One obvious case is that mutations such as single-nucleotide polymorphisms (SNPs) interrupt CpG sites, resulting in different...

An integrative framework for the identification of double minute chromosomes using next generation sequencing data

Background Double minute chromosomes are circular fragments of DNA whose presence is associated with the onset of certain cancers. Double minutes are lethal, as they are highly amplified and typically contain oncogenes. Locating double minutes can supplement the process of cancer diagnosis, and it can help to identify therapeutic targets. However, there is currently a dearth of...

BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data

Background Bisulfite sequencing is one of the most widely used technologies in analyzing DNA methylation patterns, which are important in understanding and characterizing the mechanism of DNA methylation and its functions in disease development. Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. However...

Cetuximab ameliorates suppressive phenotypes of myeloid antigen presenting cells in head and neck cancer patients

Cytometry Facility that is supported in part by award P30CA047904. Jing Li is supported by the China Scholarship Council. Financial Support: Funded by NIH grant R01 DE019727 and P50 CA097190. 1. Vermorken JB

Comparison of predictive modeling approaches for 30-day all-cause non-elective readmission risk

Background This paper explores the importance of electronic medical records (EMR) for predicting 30-day all-cause non-elective readmission risk of patients and presents a comparison of prediction performance of commonly used methods. Methods The data are extracted from eight Advocate Health Care hospitals. Index admissions are excluded from the cohort if they are observation...

PD-1/SHP-2 negatively regulate Tc1/Th1 phenotypic responses and activation of T cells in the tumor microenvironment

Jing Li 0 Robert L Ferris 1 From Society for Immunotherapy of Cancer th Annual Meeting National Harbor USA. November 0 Department of Pharmacy, School of Medicine, Tsinghua University , Beijing, China

Differential expression of PD-1 and Tim-3 marks activation versus exhaustion status of T cells in the tumor microenvironment

Jing Li 1 Robert L Ferris 0 From Society for Immunotherapy of Cancer th Annual Meeting National Harbor USA. November 0 University of Pittsburgh Cancer Institute , Pittsburgh, PA , USA 1 Department of

Project ACHIEVE – using implementation research to guide the evaluation of transitional care effectiveness

Kentucky - Mark V. Williams, MD; Jing Li, MD, MS; Glen Mays, PhD, MPH; Arnold Stromberg, PhD; Heather Bush, PhD; Allison Scott, PhD; Robert Duff; Emily Clear, MPH; Hannah Keeler, MPH Boston Medical Center

Organizational culture in cardiovascular care in Chinese hospitals: a descriptive cross-sectional study

Background Organizational learning, the process by which a group changes its behavior in response to newly acquired knowledge, is critical to outstanding organizational performance. In hospitals, strong organizational learning culture is linked with improved health outcomes for patients. This study characterizes the organizational learning culture of hospitals in China from the...

Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data

Matthew Hayes 0 Jing Li 0 0 Department of Electrical Engineering and Computer Science, Case Western Reserve University , 10900 Euclid Ave., Cleveland, OH , USA Background: Somatically-acquired

Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference

We developed a general framework for family-based imputation using single-nucleotide polymorphism data and sequence data distributed by Genetic Analysis Workshop 18. By using PedIBD, we first inferred haplotypes and inheritance patterns of each family from SNP data. Then new variants in unsequenced family members can be obtained from sequenced relatives through their shared...

A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study

Background Combining information from different studies is an important and useful practice in bioinformatics, including genome-wide association study, rare variant data analysis and other set-based analyses. Many statistical methods have been proposed to combine p-values from independent studies. However, it is known that there is no uniformly most powerful test under all...

Maternal tea consumption and the risk of preterm delivery in urban China: a birth cohort study

Background Studies investigating the relationship between maternal tea drinking and risk of preterm birth have reached inconsistent results. Methods The present study analyzed data from a birth cohort study including 10,179 women who delivered a singleton live birth were conducted in Lanzhou, China between 2010 and 2012. Results Drinking tea (OR = 1.36, 95 % CI: 1.09–1.69), and...

Safety and tolerability of an anti-CD19 monoclonal antibody, MEDI-551, in subjects with systemic sclerosis: a phase I, randomized, placebo-controlled, escalating single-dose study

, escalating single-dose study Elena Schiopu 0 Soumya Chatterjee 2 Vivien Hsu 1 Armando Flor 6 Daniel Cimbora 6 Kaushik Patra 6 Wenliang Yao 6 Jing Li 5 Katie Streicher 6 Kathleen McKeever 4 6 Barbara White 3

Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa

the late Ivane Nasidze for valuable contributions to this work. This research was funded by the Max Planck Society and the National Science Foundation (OPP-0732857). Jing Li was supported by the

Partial eNOS deficiency causes spontaneous thrombotic cerebral infarction, amyloid angiopathy and cognitive impairment

Background Cerebral infarction due to thrombosis leads to the most common type of stroke and a likely cause of age-related cognitive decline and dementia. Endothelial nitric oxide synthase (eNOS) generates NO, which plays a crucial role in maintaining vascular function and exerting an antithrombotic action. Reduced eNOS expression and eNOS polymorphisms have been associated with...

Natural killer cells are crucial for the efficacy of Icon (factor VII/human IgG1 Fc) immunotherapy in human tongue cancer

Background Icon is a novel, dual neovascular- and cancer cell-targeting immunotherapeutic agent and has shown efficacy in the treatment of cancer, wet form macular degeneration and endometriosis. However, its underlying mechanism remains to be investigated. The objective of this study is to elucidate the mechanism of Icon immunotherapy in cancer using a squamous carcinoma human...