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Andrew J Tsung, Maheedhara R Guda, Swapna Asuthkar, Collin M Labak, Ian J Purvis, Yining Lu, Neha Jain, Sarah E Bach, Durbaka V R Prasad, Kiran K Velpula
Glioblastoma (GBM) remains one of the most lethal and difficult-to-treat cancers of the central nervous system. The poor prognosis in GBM patients is due in part to its resistance to available treatments, which calls for identifying novel molecular therapeutic targets. In this study, we identified a mediator of Notch signaling, HEY1, whose methylation status contributes to the pathogenesis of GBM. Datamining studies, immunohistochemistry and immunoblot analysis showed that HEY1 is highly expressed in GBM patient specimens...
May 16, 2017: Oncotarget
Marcel Hulst, Alfons Jansman, Ilonka Wijers, Arjan Hoekman, Stéphanie Vastenhouw, Marinus van Krimpen, Mari Smits, Dirkjan Schokker
BACKGROUND: Gene expression profiles of intestinal mucosa of chickens and pigs fed over long-term periods (days/weeks) with a diet rich in rye and a diet supplemented with zinc, respectively, or of chickens after a one-day amoxicillin treatment of chickens, were recorded recently. Such dietary interventions are frequently used to modulate animal performance or therapeutically for monogastric livestock. In this study, changes in gene expression induced by these three interventions in cultured "Intestinal Porcine Epithelial Cells" (IPEC-J2) recorded after a short-term period of 2 and 6 hours, were compared to the in vivo gene expression profiles in order to evaluate the capability of this in vitro bioassay in predicting in vivo responses...
2017: Genes & Nutrition
Márton Kolossváry, Miklós Kellermayer, Béla Merkely, Pál Maurovich-Horvat
Radiologic images are vast three-dimensional data sets in which each voxel of the underlying volume represents distinct physical measurements of a tissue-dependent characteristic. Advances in technology allow radiologists to image pathologies with unforeseen detail, thereby further increasing the amount of information to be processed. Even though the imaging modalities have advanced greatly, our interpretation of the images has remained essentially unchanged for decades. We have arrived in the era of precision medicine where even slight differences in disease manifestation are seen as potential target points for new intervention strategies...
March 24, 2017: Journal of Thoracic Imaging
Hardy Schweigel, Michael Wicht, Falk Schwendicke
We aimed to comprehensively compare two compartmented oral proteomes, the salivary and the dental pellicle proteome. Systematic review and datamining was used to obtain the physico-chemical, structural, functional and interactional properties of 1,515 salivary and 60 identified pellicle proteins. Salivary and pellicle proteins did not differ significantly in their aliphatic index, hydrophaty, instability index, or isoelectric point. Pellicle proteins were significantly more charged at low and high pH and were significantly smaller (10-20 kDa) than salivary proteins...
December 14, 2016: Scientific Reports
Olivier Tassy
Manteia is an integrative database available online at which provides a large array of OMICs data related to the development of the mouse, chicken, zebrafish and human. The system is designed to use different types of data together in order to perform advanced datamining, test hypotheses or provide candidate genes involved in biological processes or responsible for human diseases. In this new version of the database, Manteia has been enhanced with new expression data originating from microarray and next generation sequencing experiments...
January 4, 2017: Nucleic Acids Research
Gwo-Jen Liaw
Histone deacetylation plays an important role in transcriptional repression. Previous results showed that the genetic interaction between ttk and rpd3, which encodes a class I histone deacetylase, is required for tll repression. This study investigated the molecular mechanism by which Ttk69 recruits Rpd3. Using yeast two-hybrid screening and datamining, one novel protein was found that weakly interacts with Ttk69 and Sin3A, designated as Protein interacting with Ttk69 and Sin3A (Pits). Pits protein expressed in the early stages of embryos and bound to the region of the tor response element in vivo...
2016: Scientific Reports
Fernanda Khouri Barreto, Ricardo Khouri, Filipe Ferreira de Almeida Rego, Luciane Amorim Santos, Maria Fernanda de Castro-Amarante, Izabela Bialuk, Cynthia A Pise-Masison, Bernardo Galvão-Castro, Antoine Gessain, Steven Jacobson, Genoveffa Franchini, Luiz Carlos Alcantara
The region known as pX in the 3' end of the human T-cell lymphotropic virus type 1 (HTLV-1) genome contains four overlapping open reading frames (ORF) that encode regulatory proteins. HTLV-1 ORF-I produces the protein p12 and its cleavage product p8. The functions of these proteins have been linked to immune evasion and viral infectivity and persistence. It is known that the HTLV-1 infection does not necessarily imply the development of pathological processes and here we evaluated whether natural mutations in HTLV-1 ORF-I can influence the proviral load and clinical manifestation of HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP)...
November 2016: Infection, Genetics and Evolution
Blair Ney, F Hafna Ahmed, Carlo R Carere, Ambarish Biswas, Andrew C Warden, Sergio E Morales, Gunjan Pandey, Stephen J Watt, John G Oakeshott, Matthew C Taylor, Matthew B Stott, Colin J Jackson, Chris Greening
F420 is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds. Considered one of the rarest cofactors in biology, F420 is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria. In this work, we show that this cofactor is more widely distributed than previously reported. We detected the genes encoding all five known F420 biosynthesis enzymes (cofC, cofD, cofE, cofG and cofH) in at least 653 bacterial and 173 archaeal species, including members of the dominant soil phyla Proteobacteria, Chloroflexi and Firmicutes...
January 2017: ISME Journal
Quan Zou, Jiasheng Guo, Ying Ju, Meihong Wu, Xiangxiang Zeng, Zhiling Hong
tRNAScan-SE is a tRNA detection program that is widely used for tRNA annotation; however, the false positive rate of tRNAScan-SE is unacceptable for large sequences. Here, we used a machine learning method to try to improve the tRNAScan-SE results. A new predictor, tRNA-Predict, was designed. We obtained real and pseudo-tRNA sequences as training data sets using tRNAScan-SE and constructed three different tRNA feature sets. We then set up an ensemble classifier, LibMutil, to predict tRNAs from the training data...
November 2015: Molecular Informatics
Kaija Saranto, Virginia Saba, Patricia Dykes, Ulla-Mari Kinnunen, Minna Mykkänen
The purpose of this panel is to discuss milestones and experiences of a standardized nursing terminology for the documentation of nursing practice using Clinical Care Classification as an example. The aim is to describe the value of using the CCC as the standardized nursing terminology and framework for the multidisciplinary care plans and how its interoperability with SNOMED CT, LOINC, and other required terminologies can be used for the electronic health record systems. Further the aim is to discuss the advantages a multidisciplinary documentation system and how it impacts on nursing practice, management, and research as well as highlight the monitoring of nursing documentation...
2016: Studies in Health Technology and Informatics
Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu
MOTIVATION: Identifying drug-target interactions is an important task in drug discovery. To reduce heavy time and financial cost in experimental way, many computational approaches have been proposed. Although these approaches have used many different principles, their performance is far from satisfactory, especially in predicting drug-target interactions of new candidate drugs or targets. METHODS: Approaches based on machine learning for this problem can be divided into two types: feature-based and similarity-based methods...
June 15, 2016: Bioinformatics
Robert Hoehndorf, Georgios V Gkoutos, Paul N Schofield
The use of ontologies has increased rapidly over the past decade and they now provide a key component of most major databases in biology and biomedicine. Consequently, datamining over these databases benefits from considering the specific structure and content of ontologies, and several methods have been developed to use ontologies in datamining applications. Here, we discuss the principles of ontology structure, and datamining methods that rely on ontologies. The impact of these methods in the biological and biomedical sciences has been profound and is likely to increase as more datasets are becoming available using common, shared ontologies...
2016: Methods in Molecular Biology
Shyama Pal, Prayag J Amin, K B Sainis, Bhavani S Shankar
Apo2L/tumor necrosis factor (TNF)-α-related apoptosis-inducing ligand (TRAIL, TNFSF10) is an important cytokine in the tumor microenvironment and plays a major role in the balance of cell survival/death pathways. Bioinformatic analyses of 839 adenocarcinoma (AC) and 356 squamous cell lung carcinoma patient data (SCC) by cBioPortal (genomic analyses) shows that TRAIL expression leads to differential outcomes of disease free survival in AC and SCC. Oncomine datamining (transcript analyses) reveal that TRAIL is upregulated in 167 SCC as compared to 350 AC patients from six data sets...
December 2016: Cancer Microenvironment: Official Journal of the International Cancer Microenvironment Society
Yichang Xu, Cheng Luo, Hiroshi Mamitsuka, Shanfeng Zhu
Recent computational approaches in bioinformatics can achieve high performance, by which they can be a powerful support for performing real biological experiments, making biologists pay more attention to bioinformatics than before. In immunology, predicting peptides which can bind to MHC alleles is an important task, being tackled by many computational approaches. However, this situation causes a serious problem for immunologists to select the appropriate method to be used in bioinformatics. To overcome this problem, we develop an ensemble prediction-based Web server, which we call MetaMHCpan, consisting of two parts: MetaMHCIpan and MetaMHCIIpan, for predicting peptides which can bind MHC-I and MHC-II, respectively...
2016: Methods in Molecular Biology
Xiangxiang Zeng, Yuanlu Liao, Yuansheng Liu, Quan Zou
Deciphering the gene disease association is an important goal in biomedical research. In this paper, we use a novel relevance measure, called HeteSim, to prioritize candidate disease genes. Two methods based on heterogeneous networks constructed using protein-protein interaction, gene-phenotype associations, and phenotype-phenotype similarity, are presented. In HeteSim MultiPath (HSMP), HeteSim scores of different paths are combined with a constant that dampens the contributions of longer paths. In HeteSim SVM (HSSVM), HeteSim scores are combined with a machine learning method...
February 12, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
C Daniel, R Choquet
OBJECTIVES: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. METHOD: We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section...
August 13, 2015: Yearbook of Medical Informatics
L F Soualmia, T Lecroq
OBJECTIVES: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. METHOD: We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section...
August 13, 2015: Yearbook of Medical Informatics
D Thwaites, L Holloway, M Bailey, S Barakat, M Carolan, G Delaney, M Field, A Dekker, T Lustberg, A Miller, J van Soest, S Vinod, S Walsh
PURPOSE: Large amounts of routine radiotherapy (RT) data are available, which can potentially add clinical evidence to support better decisions. A developing collaborative Australian network, with a leading European partner, aims to validate, implement and extend European predictive models (PMs) for Australian practice and assess their impact on future patient decisions. Wider objectives include: developing multi-institutional rapid learning, using distributed learning approaches; and assessing and incorporating radiomics information into PMs...
June 2015: Medical Physics
H Zhong, J Wang, L Shen, W Hu, J Wan, Z Zhou, Z Zhang
PURPOSE: The purpose of this study is to investigate the relationship between computed tomographic (CT) texture features of primary lesions and metastasis-free survival for rectal cancer patients; and to develop a datamining prediction model using texture features. METHODS: A total of 220 rectal cancer patients treated with neoadjuvant chemo-radiotherapy (CRT) were enrolled in this study. All patients underwent CT scans before CRT. The primary lesions on the CT images were delineated by two experienced oncologists...
June 2015: Medical Physics
D Thwaites
PURPOSE: A national Australian inter-university medical physics (MP) group was formed in 2011/12, supported by Department of Health Better Access to Radiation Oncology BARO) seed funding. Core membership includes the six universities providing postgraduate MP courses. Objectives include increasing capacity, development and efficiency of national academic MP structures/systems and hence supporting education, clinical training and research, for the MP workforce support. Although the BARO scheme focuses on Radiation Oncology, the group has wider MP interests...
June 2015: Medical Physics
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