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Data Mining

Mikyung Lee, Zhichao Liu, Ruili Huang, Weida Tong
BACKGROUND: All biological processes are inherently dynamic. Biological systems evolve transiently or sustainably according to sequential time points after perturbation by environment insults, drugs and chemicals. Investigating the temporal behavior of molecular events has been an important subject to understand the underlying mechanisms governing the biological system in response to, such as, drug treatment. The intrinsic complexity of time series data requires appropriate computational algorithms for data interpretation...
October 6, 2016: BMC Bioinformatics
Ryan Eshleman, Rahul Singh
BACKGROUND: Adverse drug events (ADEs) constitute one of the leading causes of post-therapeutic death and their identification constitutes an important challenge of modern precision medicine. Unfortunately, the onset and effects of ADEs are often underreported complicating timely intervention. At over 500 million posts per day, Twitter is a commonly used social media platform. The ubiquity of day-to-day personal information exchange on Twitter makes it a promising target for data mining for ADE identification and intervention...
October 6, 2016: BMC Bioinformatics
Renata Havránková, Zuzana Freitinger Skalická, Jiří Havránek, Dana Novotná, Friedo Zölzer
Results are presented of a survey of almost 1000 dosimetric records of employees at the former uranium processing plant MAPE Mydlovary. Located ~20 km to the north-west of České Budějovice in South Bohemia, it was the place where most of the uranium ore mined in Czechoslovakia in the years from 1962 to 1991 was processed. The records refer to incorporation of short-lived radon progeny and long-lived radionuclides as well as external gamma exposure. The average annual doses calculated from the recorded data were 2...
October 7, 2016: Radiation Protection Dosimetry
Lydia Edjekouane, Samira Benhadjeba, Maïka Jangal, Hubert Fleury, Nicolas Gévry, Euridice Carmona, André Tremblay
Chromosomal and genome abnormalities at the 3p21.3 locus are frequent events linked to epithelial cancers, including ovarian and breast cancers. Genes encoded in the 3p21.3 cluster include HYAL1, HYAL2 and HYAL3 members of hyaluronidases involved in the breakdown of hyaluronan, an abundant component of the vertebrate extracellular matrix. However, the transcriptional regulation of HYAL genes is poorly defined. Here, we identified the estrogen receptor ERα as a negative regulator of HYAL1 expression in breast cancer cells...
October 13, 2016: Oncotarget
Fayyaz Ul Amir Afsar Minhas, Amina Asif, Muhammad Arif
: Feature selection and ranking is of great importance in the analysis of biomedical data. In addition to reducing the number of features used in classification or other machine learning tasks, it allows us to extract meaningful biological and medical information from a machine learning model. Most existing approaches in this domain do not directly model the fact that the relative importance of features can be different in different regions of the feature space. In this work, we present a context aware feature ranking algorithm called CAFÉ-Map...
October 11, 2016: Computers in Biology and Medicine
Nurkhalida Kamal, Christina V Viegelmann, Carol J Clements, RuAngelie Edrada-Ebel
Fungal endophytes offer diverse and unique secondary metabolites, making these organisms potential sources of promising drug leads. The application of high-resolution-liquid chromatography mass spectrometry and nuclear magnetic resonance-based metabolomics to fungal endophytes is practical in terms of dereplication studies and the mining of bioactive compounds. In this paper, we report the application of metabolomics in parallel with anti-trypanosomal assays to determine the ideal conditions for the medium-scale fermentation of the endophyte Lasiodiplodia theobromae...
October 19, 2016: Planta Medica
Andrew J Plumptre, Stuart Nixon, Deo K Kujirakwinja, Ghislain Vieilledent, Rob Critchlow, Elizabeth A Williamson, Radar Nishuli, Andrew E Kirkby, Jefferson S Hall
Grauer's gorilla (Gorilla beringei graueri), the World's largest primate, is confined to eastern Democratic Republic of Congo (DRC) and is threatened by civil war and insecurity. During the war, armed groups in mining camps relied on hunting bushmeat, including gorillas. Insecurity and the presence of several militia groups across Grauer's gorilla's range made it very difficult to assess their population size. Here we use a novel method that enables rigorous assessment of local community and ranger-collected data on gorilla occupancy to evaluate the impacts of civil war on Grauer's gorilla, which prior to the war was estimated to number 16,900 individuals...
2016: PloS One
Jyothi Padiadpu, Priyanka Baloni, Kushi Anand, MohamedHusen Munshi, Chandrani Thakur, Abhilash Mohan, Amit Singh, Nagasuma Chandra
The global mechanisms and associated molecular alterations that occur in drug-resistant mycobacteria are poorly understood. To address this, we obtain genomics data and then construct a genome-scale response network in isoniazid-resistant Mycobacterium smegmatis and apply a network-mining algorithm. Through this, we decipher global alterations in an unbiased manner and identify emergent vulnerabilities in resistant bacilli, of which redox response was prominent. Using phenotypic profiling, we find that resistant bacilli exhibit collateral sensitivity to several compounds that block antioxidant responses...
September 9, 2016: ACS Infectious Diseases
Noah Edward Jemison, Thomas M Johnson, Alyssa Shiel, Craig Lundstrom
Uranium groundwater contamination due to U mining and processing affects numerous sites globally. Bioreduction of soluble, mobile U(VI) to U(IV)-bearing solids is potentially a very effective remediation strategy. Uranium isotopes (238U/235U) have been utilized to track the progress of microbial reduction, with laboratory and field studies finding a ~1‰ isotopic fractionation, with the U(IV) product enriched in 238U. However, the isotopic fractionation produced by adsorption may complicate the use of 238U/235U to trace microbial reduction...
October 19, 2016: Environmental Science & Technology
Ashfaq Khokhar, Muhammad Kamran Lodhi, Yingwei Yao, Rashid Ansari, Gail Keenan, Diana J Wilkie
Despite an unprecedented amount of health-related data being amassed from various technological innovations, our ability to process this data and extract hidden knowledge has yet to catch up with this explosive growth. Although nursing care plans can be an effective tool to support the achievement of desired patient outcomes, their online collection, storage, and processing is lagging far behind. As a result, the impact of nursing care is not well understood from qualitative as well as quantitative perspectives...
October 18, 2016: Western Journal of Nursing Research
Jiefang Guo, Jun Hao, Hongxue Jiang, Jing Jin, Hongyu Wu, Zhendong Jin, Zhaoshen Li
Pancreatic cancer has the worst prognosis among all cancers and novel markers and therapeutic targets are desperately needed for this terribly deadly disease. Proteasome activator subunit 3 (PSME3) is highly involved in the initiation and progression of many human cancers. However, the potential effect of PSME3 on pancreatic cancer remains largely unknown. In the present study, we first found that PSME3 was significantly upregulated in pancreatic cancer cells and tissues at both mRNA and protein levels using qRT-PCR, western blot analysis, Oncomine data mining and immunohistochemical analysis...
October 15, 2016: Cancer Letters
Jacqueline M Cole, Xie Cheng, Michael C Payne
The use of principal component analysis (PCA) to statistically infer features of local structure from experimental pair distribution function (PDF) data is assessed on a case study of rare-earth phosphate glasses (REPGs). Such glasses, codoped with two rare-earth ions (R and R') of different sizes and optical properties, are of interest to the laser industry. The determination of structure-property relationships in these materials is an important aspect of their technological development. Yet, realizing the local structure of codoped REPGs presents significant challenges relative to their singly doped counterparts; specifically, R and R' are difficult to distinguish in terms of establishing relative material compositions, identifying atomic pairwise correlation profiles in a PDF that are associated with each ion, and resolving peak overlap of such profiles in PDFs...
October 18, 2016: Inorganic Chemistry
Jeganathan Manivannan, Manjunath Prashanth, Venkatesan Saravana Kumar, Manickaraj Shairam, Jayachandran Subburaj
Since there is no precise therapy for treating vascular calcification by directly targeting the vascular wall, we aim to unveil novel drug targets through mining the molecular effect of a high phosphate environment on vascular cells through computational methods. Here, we hypothesize that manipulation of the vascular pathogenic network by small molecule therapeutics predicted from prior knowledge might offer great promise. With this, we intend to understand the publicly available transcriptomic data of vascular smooth muscle cells and endothelial cells exposed to the high phosphate induced vascular calcification milieu and to re-examine the above published experiments for reasons different from those examined in the previous studies through multilevel systems biological understanding...
October 18, 2016: Molecular BioSystems
Li-Ming Ma, Zi-Rui Liang, Ke-Ren Zhou, Hui Zhou, Liang-Hu Qu
27-hydroxycholesterol (27-HC), the most abundant metabolite of cholesterol, is a risk factor for breast cancer. It can increase the proliferation of breast cancer cells and promote the metastasis of breast tumours in mouse models. Myc is a critical oncoprotein overexpressed in breast cancer. However, whether 27-HC affects Myc expression has not been reported. In the current study, we aimed to investigate the effects of 27-HC on Myc and the underlying mechanisms in MCF-7 breast cancer cells. Our data demonstrated that 27-HC activated Myc via increasing its protein stability...
October 14, 2016: Biochemical and Biophysical Research Communications
Antonio López-Orenes, María C Bueso, Héctor M Conesa, Antonio A Calderón, María A Ferrer
Soil pollution by heavy metals/metalloids (HMMs) is a problem worldwide. To prevent dispersion of contaminated particles by erosion, the maintenance of a vegetative cover is needed. Successful plant establishment in multi-polluted soils can be hampered not only by HMM toxicities, but also by soil nutrient deficiencies and the co-occurrence of abiotic stresses. Some plant species are able to thrive under these multi-stress scenarios often linked to marked fluctuations in environmental factors. This study aimed to investigate the metabolic adjustments involved in Zygophyllum fabago acclimative responses to conditions prevailing in HMM-enriched mine-tailings piles, during Mediterranean spring and summer...
October 14, 2016: Science of the Total Environment
Jiangan Xie, Christopher Codd, Kevin Mo, Yongqun He
M. bovis strain Bacillus Calmette-Guérin (BCG) has been the only licensed live attenuated vaccine against tuberculosis (TB) for nearly one century and has also been approved as a therapeutic vaccine for bladder cancer treatment since 1990. During its long time usage, different adverse events (AEs) have been reported. However, the AEs associated with the BCG preventive TB vaccine and therapeutic cancer vaccine have not been systematically compared. In this study, we systematically collected various BCG AE data mined from the US VAERS database and PubMed literature reports, identified statistically significant BCG-associated AEs, and ontologically classified and compared these AEs related to these two types of BCG vaccine...
2016: PloS One
(no author information available yet)
No abstract text is available yet for this article.
October 2016: Computers, Informatics, Nursing: CIN
Bo Gao, Wang Sun, Xianzhi Meng, Dongbo Xue, Weihui Zhang
Hematological abnormalities are frequently observed in patients with liver cirrhosis (LC). A previous study demonstrated that the apoptosis and damage of endothelial cells could cause the hematological abnormalities in LC. Protein kinases are one of the most important factors that regulate cell behavior, and are potential therapeutic targets for the treatment of a number of diseases. In a previous study, whole genome profiling was used to identify differentially expressed genes in human bone marrow endothelial cells treated with serum from 26 patients with LC...
October 12, 2016: Molecular Medicine Reports
D J Hamilton, D W Wheeler, C M White, C L Rees, A O Komendantov, M Bergamino, G A Ascoli
Widely spread naming inconsistencies in neuroscience pose a vexing obstacle to effective communication within and across areas of expertise. This problem is particularly acute when identifying neuron types and their properties. is a web-accessible neuroinformatics resource that organizes existing data about essential properties of all known neuron types in the rodent hippocampal formation. links evidence supporting the assignment of a property to a type with direct pointers to quotes and figures...
June 9, 2016: Brain Informatics
Xiaohui Yao, Jingwen Yan, Sungeun Kim, Kwangsik Nho, Shannon L Risacher, Mark Inlow, Jason H Moore, Andrew J Saykin, Li Shen
Enrichment analysis has been widely applied in the genome-wide association studies, where gene sets corresponding to biological pathways are examined for significant associations with a phenotype to help increase statistical power and improve biological interpretation. In this work, we expand the scope of enrichment analysis into brain imaging genetics, an emerging field that studies how genetic variation influences brain structure and function measured by neuroimaging quantitative traits (QT). Given the high dimensionality of both imaging and genetic data, we propose to study Imaging Genetic Enrichment Analysis (IGEA), a new enrichment analysis paradigm that jointly considers meaningful gene sets (GS) and brain circuits (BC) and examines whether any given GS-BC pair is enriched in a list of gene-QT findings...
May 13, 2016: Brain Informatics
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