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27 papers found.
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Establishment of an innovative staging system for extramedullary plasmacytoma

Background Extramedullary plasmacytoma (EMP) is a rare malignant disease that lacks a unique clinical staging system to predict the survival of EMP patients and to design individualized treatment. Instead, clinicians have chosen to use the multiple myeloma (MM) staging system. Methods Forty-eight EMP patients treated between 1996 and 2014 were included in this study. The new ...

EHR based Genetic Testing Knowledge Base (iGTKB) Development

Background The gap between a large growing number of genetic tests and a suboptimal clinical workflow of incorporating these tests into regular clinical practice poses barriers to effective reliance on advanced genetic technologies to improve quality of healthcare. A promising solution to fill this gap is to develop an intelligent genetic test recommendation system that not only ...

Overexpression of acylglycerol kinase is associated with poorer prognosis and lymph node metastasis in nasopharyngeal carcinoma

Cancer Center for her critical reviewing this article. Qian Zhu performed the Western blotting and drafted the manuscript. Su-Mei Cao collected the tissue specimens and patient information as well as

Organelle-Specific Nitric Oxide Detection in Living Cells via HaloTag Protein Labeling

Nitric oxide (NO) is a membrane-permeable signaling molecule that is constantly produced, transferred, and consumed in vivo. NO participates and plays important roles in multiple biological processes. However, spatiotemporal imaging of NO in living cells is challenging. To fill the gap in currently used techniques, we exploited the versatility of HaloTag technology and synthesized ...

Qualitative and quantitative uncertainties in regional rainfall frequency analysis

Uncertainty exists widely in hydrological analysis, and this makes the process of uncertainty assessment very important for making robust decisions. In this study, uncertainty sources in regional rainfall frequency analysis are identified for the first time. The numeral unite spread assessment pedigree (NUSAP) method is introduced and is first employed to quantify qualitative ...

Risk factors for ectopic pregnancy: a multi-center case-control study

Background Ectopic pregnancy (EP) is the leading cause of maternal death during the first trimester of pregnancy. A better understanding of EP risk can help prevent its occurrence. We carried out a multi-center, large-sample, case-control study to evaluate the risk factors for EP in Shanghai, China. Methods Women who were diagnosed with EP (n = 2411) and women with intrauterine ...

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

Motivation: Leveraging gene expression data through large-scale integrative analyses for multicellular organisms is challenging because most samples are not fully annotated to their tissue/cell-type of origin. A computational method to classify samples using their entire gene expression profiles is needed. Such a method must be applicable across thousands of independent studies, ...

Correlation between deletion of the CDKN2 gene and tyrosine kinase inhibitor resistance in adult Philadelphia chromosome-positive acute lymphoblastic leukemia

Background Frequency relapses are common in Philadelphia chromosome-positive (Ph-positive) acute lymphoblastic leukemia (ALL) following tyrosine kinase inhibitors (TKIs). CDKN2A/B is believed to contribute to this chemotherapy resistance. Methods To further investigate the association between CDKN2 status and TKI resistance, the prevalence of CDKN2 deletions and its correlation ...

Analysis of Social and Genetic Factors Influencing Heterosexual Transmission of HIV within Serodiscordant Couples in the Henan Cohort

There is considerable variability between individuals in susceptibility to infection by human immunodeficiency virus (HIV). Many social, clinical and genetic factors are known to contribute to the likelihood of HIV transmission, but there is little consensus on the relative importance and potential interaction of these factors. Additionally, recent studies of several variants in ...

Contraceptive Use and the Risk of Ectopic Pregnancy: A Multi-Center Case-Control Study

Xiaowei Xi 5 6 Qian Zhu 0 6 Xiao-Cui Li 0 6 Jian Zhang * 0 6 0 Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong

TTG2-regulated development is related to expression of putative AUXIN RESPONSE FACTOR genes in tobacco

Background The phytohormone auxin mediates a stunning array of plant development through the functions of AUXIN RESPONSE FACTORs (ARFs), which belong to transcription factors and are present as a protein family comprising 10–43 members so far identified in different plant species. Plant development is also subject to regulation by TRANSPARENT TESTA GLABRA (TTG) proteins, such as ...

The collapse of gene complement following whole genome duplication

Background Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial. Reduction after whole genome duplication (WGD) represents an ...

WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications

Background In recent years, there has been a huge increase in the amount of publicly-available and proprietary information pertinent to drug discovery. However, there is a distinct lack of data mining tools available to harness this information, and in particular for knowledge discovery across multiple information sources. At Indiana University we have an ongoing project with Eli ...

Semantic inference using chemogenomics data for drug discovery

Background Semantic Web Technology (SWT) makes it possible to integrate and search the large volume of life science datasets in the public domain, as demonstrated by well-known linked data projects such as LODD, Bio2RDF, and Chem2Bio2RDF. Integration of these sets creates large networks of information. We have previously described a tool called WENDI for aggregating information ...

ABCB1 Variation and Treatment Response in AIDS Patients: Initial Results of the Henan Cohort

HIV/AIDS has the highest mortality among infectious diseases in China. In ongoing efforts to alleviate this crisis, the national government has placed great emphasis on efforts in Henan province where HIV-infected former plasma donors in the 1990s contributed to AIDS becoming a public health crisis. Concomitant with a national initiative focusing the use of phamacogenetics for the ...

Polyploids, genome halving and phylogeny

Motivation: Autopolyploidization and allopolyploidization events multiply the number of chromosomes and genomic content. Genome rearrangement phylogenetics requires that all genomes analyzed have the same set of orthologs, so that it is not possible to include diploid and polyploid genomes in the same phylogeny. Results: We propose a framework for solving this difficulty by ...

Gene Clusters Located on Two Large Plasmids Determine Spore Crystal Association (SCA) in Bacillus thuringiensis Subsp. finitimus Strain YBT-020

Crystals in Bacillus thuringiensis are usually formed in the mother cell compartment during sporulation and are separated from the spores after mother cell lysis. In a few strains, crystals are produced inside the exosporium and are associated with the spores after sporulation. This special phenotype, named ‘spore crystal association’ (SCA), typically occurs in B. thuringiensis ...

Scaffold filling, contig fusion and comparative gene order inference

Background There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use ...

Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes

Motivation: Some present day species have incurred a whole genome doubling event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to ‘halve’ the genome, i.e. to reconstruct the ancestral genome at the moment of doubling, but the solution is often highly ...

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

Background Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as Bio2RDF and LODD have tackled the problem of linking biological data and drug data respectively ...