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https://www.readbyqxmd.com/read/29145615/iptmnet-an-integrated-resource-for-protein-post-translational-modification-network-discovery
#1
Hongzhan Huang, Cecilia N Arighi, Karen E Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K Vijay-Shanker, Cathy H Wu
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145280/liver-stiffness-measurement-and-spleen-diameter-as-predictors-for-the-presence-of-esophageal-varices-in-chronic-hepatitis-c-patients
#2
Mohammed Tag-Adeen, Mohamed Alsenbesy, Ali Abdelrahman Ghweil, M Ali Hussein Abd Elrazek, Elsayed A Elgohary, Mohammad M Sallam, Ali Ismael, Abdallah Nawara
Although it is an invasive and unpleasant procedure, esophagogastroduodenoscopy (EGD) is still the gold standard for esophageal varices (EV) detection. The aim of this study was to investigate liver stiffness measurement (LSM) and spleen diameter as simple noninvasive tools for EV prediction in chronic hepatitis C patients (CHC).A total of 123 Egyptian patients with CHC have been included and were classified based on screening EGD result into 2 groups; group A (without EV) and group B (with EV). Group (B) was subclassified according to EV grade into 4 subgroups: (B1, grade I), (B2, grade II), (B3, grade III), and (B4, grade IV)...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29145129/high-contamination-in-the-areas-surrounding-abandoned-mines-and-mining-activities-an-impact-assessment-of-the-dilala-luilu-and-mpingiri-rivers-democratic-republic-of-the-congo
#3
Emmanuel K Atibu, Pierre Lacroix, Periyasamy Sivalingam, Nicolas Ray, Gregory Giuliani, Crispin K Mulaji, Jean-Paul Otamonga, Pius T Mpiana, Vera I Slaveykova, John Poté
Abandoned mines and mining activities constitute important sources of toxic metals and Rare Earth Elements (REEs) affecting surrounding environmental compartments and biota. This study investigates the contamination degree and distribution of toxic metals and REEs in contrasting sediment, soil and plant samples surrounding rivers in the African copperbelt area characterized by the presence of numerous abandoned mines, artisanal and industrial mining activities. ICP-MS results highlighted the highest concentration of Cu, Co and Pb in sediments reaching values of 146,801, 18,434 and 899 mg kg(-1), respectively...
October 21, 2017: Chemosphere
https://www.readbyqxmd.com/read/29143172/identification-of-key-genes-and-construction-of-microrna-mrna-regulatory-networks-in-bladder-smooth-muscle-cell-response-to-mechanical-stimuli-using-microarray-expression-profiles-and-bioinformatics-analysis
#4
Liao Peng, De-Yi Luo
PURPOSE: To identify keys genes and elucidate miRNA-mRNA regulatory networks in Bladder smooth muscle cell (BSMC) response to mechanical stimuli. METHODS: Human BSMCs, seeded on a silicone membrane, were subjected to mechanical stretch or without stretch. Microarray was used to analyze the differential expression of mRNAs and miRNAs between human BSMCs under mechanical stretch and control static control group. Differentially expressed genes(DEGs) and miRNAs (DEMs) in these two groups were identified...
November 15, 2017: World Journal of Urology
https://www.readbyqxmd.com/read/29142422/chemotaxonomic-diversity-of-three-ficus-species-their-discrimination-using-chemometric-analysis-and-their-role-in-combating-oxidative-stress
#5
Nawal Al-Musayeib, Sherif S Ebada, Haidy A Gad, Fadia S Youssef, Mohamed Lotfy Ashour
Background: Genus Ficus (Moraceae) constitutes more than 850 species and about 2000 varieties and it acts as a golden mine that could afford effective and safe remedies combating many health disorders. Objectives: Discrimination of Ficus cordata, Ficus ingens, and Ficus palmata using chemometric analysis and assessment of their role in combating oxidative stress. Materials and Methods: Phytochemical profiling of the methanol extracts of the three Ficus species and their successive fractions was performed using high-performance liquid chromatography/electrospray ionization mass spectrometry...
October 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/29141718/dengue-fever-surveillance-in-india-using-text-mining-in-public-media
#6
Andrea Villanes, Emily Griffiths, Michael Rappa, Christopher G Healey
Despite the improvement in health conditions across the world, communicable diseases remain among the leading mortality causes in many countries. Combating communicable diseases depends on surveillance, preventive measures, outbreak investigation, and the establishment of control mechanisms. Delays in obtaining country-level data of confirmed communicable disease cases, such as dengue fever, are prompting new efforts for short- to medium-term data. News articles highlight dengue infections, and they can reveal how public health messages, expert findings, and uncertainties are communicated to the public...
October 23, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29139572/exposing-ecological-and-economic-costs-of-the-research-implementation-gap-and-compromises-in-decision-making
#7
Santtu Kareksela, Atte Moilanen, Olli Ristaniemi, Reima Välivaara, Janne S Kotiaho
The frequently discussed gap between conservation science and practice is manifest in the gap between spatial conservation prioritization plans and their implementation. We analyzed the research-implementation gap of 1 zoning case by comparing results of a spatial prioritization analysis aimed at avoiding ecological impact of peat mining in a regional zoning process with the final zoning plan. We examined the relatively complex planning process to determine the gaps among research, zoning, and decision making...
November 15, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/29138317/reviewer-bias-in-single-versus-double-blind-peer-review
#8
Andrew Tomkins, Min Zhang, William D Heavlin
Peer review may be "single-blind," in which reviewers are aware of the names and affiliations of paper authors, or "double-blind," in which this information is hidden. Noting that computer science research often appears first or exclusively in peer-reviewed conferences rather than journals, we study these two reviewing models in the context of the 10th Association for Computing Machinery International Conference on Web Search and Data Mining, a highly selective venue (15.6% acceptance rate) in which expert committee members review full-length submissions for acceptance...
November 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29137404/the-role-of-tfpi2-hypermethylation-in-the-detection-of-gastric-and-colorectal-cancer
#9
Haochang Hu, Xiaoying Chen, Cheng Wang, Yuting Jiang, Jingjing Li, Xiuru Ying, Yong Yang, Bin Li, Cong Zhou, Jie Zhong, Dongping Wu, Jieer Ying, Shiwei Duan
Gastrointestinal cancer is a prevalent disease with high morbidity and mortality. Tissue factor pathway inhibitor 2 (TFPI2) gene could protect the extracellular matrix of cancer cells from degradation and tumor invasion. The goal of our study was to estimate the diagnostic value of TFPI2 hypermethylation in gastric cancer (GC) and colorectal cancer (CRC). TFPI2 methylation was measured by quantitative methylation-specific polymerase chain reaction (qMSP) method in 114 GC and 80 CRC tissues and their paired non-tumor tissues...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137373/ceacam6-is-a-prognostic-biomarker-and-potential-therapeutic-target-for-gastric-carcinoma
#10
Guo-Qing Ru, Yong Han, Wei Wang, Yuan Chen, Hui-Ju Wang, Wen-Juan Xu, Jie Ma, Meihua Ye, Xi Chen, Xiang-Lei He, Balázs Győrffy, Zhong-Sheng Zhao, Dongsheng Huang
This study aims to investigate the prognostic power of carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) in gastric cancer (GC) and its potential role in cancer development and progression. Data mining results show that CEACAM6 is overexpressed in gastric cancer and is correlated with lymph node metastasis. Subsequently, immunohistochemical staining was performed to determine CEACAM6 protein levels in paraffin gastric tumor specimens. Real-time reverse-transcription-polymerase chain reaction (RT-PCR) was conducted to detect CEACAM6 mRNA levels in fresh GC samples...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137211/community-mining-of-open-clinical-trial-data
#11
EDITORIAL
Teemu D Laajala, Justin Guinney, James C Costello
No abstract text is available yet for this article.
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136180/bcntb-bioinformatics-the-next-evolutionary-step-in-the-bioinformatics-of-breast-cancer-tissue-banking
#12
Emanuela Gadaleta, Stefano Pirrò, Abu Zafer Dayem Ullah, Jacek Marzec, Claude Chelala
Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to query findings from publicly available, in-house and experimental data generated using samples supplied from the Breast Cancer Now Tissue Bank. This in silico environment aims to help researchers use breast cancer data to their full potential, irrespective of any bioinformatics barriers...
October 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29133591/chemokine-signaling-facilitates-early-stage-breast-cancer-survival-and-invasion-through-fibroblast-dependent-mechanisms
#13
Gage Brummer, Diana S Acevedo, Qingting Hu, Mike Portsche, Wei Fang, Min Yao, Brandon Zinda, Megan Myers, Nehemiah S Alvarez, Patrick Fields, Yan Hong, Fariba Behbod, Nikki Cheng
Ductal carcinoma in situ (DCIS) is the most common form of breast cancer, with 50,000 cases diagnosed every year in the United States. Over-treatment and under-treatment remain significant clinical challenges in patient care. Identifying key mechanisms associated with DCIS progression could uncover new biomarkers to better predict patient prognosis and improve guided treatment. Chemokines are small soluble molecules that regulate cellular homing through molecular gradients. CCL2-mediated recruitment of CCR2+ macrophages are a well-established mechanism for metastatic progression...
November 13, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29133402/assigning-chemoreceptors-to-chemosensory-pathways-in-pseudomonas-aeruginosa
#14
Davi R Ortega, Aaron D Fleetwood, Tino Krell, Caroline S Harwood, Grant J Jensen, Igor B Zhulin
In contrast to Escherichia coli, a model organism for chemotaxis that has 5 chemoreceptors and a single chemosensory pathway, Pseudomonas aeruginosa PAO1 has a much more complex chemosensory network, which consists of 26 chemoreceptors feeding into four chemosensory pathways. While several chemoreceptors were rigorously linked to specific pathways in a series of experimental studies, for most of them this information is not available. Thus, we addressed the problem computationally. Protein-protein interaction network prediction, coexpression data mining, and phylogenetic profiling all produced incomplete and uncertain assignments of chemoreceptors to pathways...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29132626/early-hospital-mortality-prediction-of-intensive-care-unit-patients-using-an-ensemble-learning-approach
#15
Aya Awad, Mohamed Bader-El-Den, James McNicholas, Jim Briggs
BACKGROUND: Mortality prediction of hospitalized patients is an important problem. Over the past few decades, several severity scoring systems and machine learning mortality prediction models have been developed for predicting hospital mortality. By contrast, early mortality prediction for intensive care unit patients remains an open challenge. Most research has focused on severity of illness scoring systems or data mining (DM) models designed for risk estimation at least 24 or 48h after ICU admission...
December 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29131975/identification-of-urinary-biomarkers-of-exposure-to-di-2-propylheptyl-phthalate-using-high-resolution-mass-spectrometry-and-two-data-screening-approaches
#16
Chia-Lung Shih, Pao-Mei Liao, Jen-Yi Hsu, Yi-Ning Chung, Victor G Zgoda, Pao-Chi Liao
Di-(2-propylheptyl) phthalate (DPHP) is a plasticizer used in polyvinyl chloride and vinyl chloride copolymer that has been suggested to be a toxicant in rats and may affect human health. Because the use of DPHP is increasing, the general German population is being exposed to DPHP. Toxicant metabolism is important for human toxicant exposure assessments. To date, the knowledge regarding DPHP metabolism has been limited, and only four metabolites have been identified in human urine. Ultra-performance liquid chromatography was coupled with Orbitrap high-resolution mass spectrometry (MS) and two data-screening approaches-the signal mining algorithm with isotope tracing (SMAIT) and the mass defect filter (MDF)-for DPHP metabolite candidate discovery...
October 30, 2017: Chemosphere
https://www.readbyqxmd.com/read/29131829/a-non-linear-data-mining-parameter-selection-algorithm-for-continuous-variables
#17
Peyman Tavallali, Marianne Razavi, Sean Brady
In this article, we propose a new data mining algorithm, by which one can both capture the non-linearity in data and also find the best subset model. To produce an enhanced subset of the original variables, a preferred selection method should have the potential of adding a supplementary level of regression analysis that would capture complex relationships in the data via mathematical transformation of the predictors and exploration of synergistic effects of combined variables. The method that we present here has the potential to produce an optimal subset of variables, rendering the overall process of model selection more efficient...
2017: PloS One
https://www.readbyqxmd.com/read/29129128/convergent-time-varying-regression-models-for-data-streams-tracking-concept-drift-by-the-recursive-parzen-based-generalized-regression-neural-networks
#18
Piotr Duda, Maciej Jaworski, Leszek Rutkowski
One of the greatest challenges in data mining is related to processing and analysis of massive data streams. Contrary to traditional static data mining problems, data streams require that each element is processed only once, the amount of allocated memory is constant and the models incorporate changes of investigated streams. A vast majority of available methods have been developed for data stream classification and only a few of them attempted to solve regression problems, using various heuristic approaches...
October 12, 2017: International Journal of Neural Systems
https://www.readbyqxmd.com/read/29127788/rapid-prediction-of-total-petroleum-hydrocarbons-concentration-in-contaminated-soil-using-vis-nir-spectroscopy-and-regression-techniques
#19
R K Douglas, S Nawar, M C Alamar, A M Mouazen, F Coulon
Visible and near infrared spectrometry (vis-NIRS) coupled with data mining techniques can offer fast and cost-effective quantitative measurement of total petroleum hydrocarbons (TPH) in contaminated soils. Literature showed however significant differences in the performance on the vis-NIRS between linear and non-linear calibration methods. This study compared the performance of linear partial least squares regression (PLSR) with a nonlinear random forest (RF) regression for the calibration of vis-NIRS when analysing TPH in soils...
November 8, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29126716/antitumor-and-antimetastatic-effects-of-walnut-oil-in-esophageal-adenocarcinoma-cells
#20
Saime Batirel, Ayse Mine Yilmaz, Ali Sahin, Nikolaos Perakakis, Nesrin Kartal Ozer, Christos S Mantzoros
BACKGROUND: Walnuts contain many components including specific fatty acids, which could be active against cancer. Even though the anticarcinogenic effect of some of the individual fatty acids in walnut oil has been described, the effect of walnut oil itself on esophageal cancer cells hasn't yet been investigated. OBJECTIVE: We aimed to investigate whether walnut oil affects tumor growth and metastatic potential in esophageal cancer cells. METHODS: The human esophageal adenocarcinoma cell line, OE19, was treated with different doses of walnut oil and cell viability, apoptosis/necrosis and cell cycle analyses were performed using WST-1 assay and flow cytometry respectively...
November 1, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
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