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big data analysis

Maya Cohn Adulamy, Varda Shalev
The use of big data is in its first years of entering the medical world. Big data research enables analysis of very large volumes of data, identifying patterns and findings which traditional statistical methods cannot handle. The diagnosis of colorectal cancer is often missed due to people's non-adherence to the occult fecal blood screening tool. We describe the case of a patient that led to the development of a novel big data algorithm to diagnose colorectal cancer. A 70 year old, previously healthy man, was diagnosed with metastatic colorectal cancer and succumbed to his illness...
October 2018: Harefuah
Suneetha Uppu, Aneesh Krishna
Identifying genetic variants associated with complex diseases is a central focus of genome-wide association studies. These studies extensively adopt univariate analysis by ignoring interaction effects. It is widely accepted that the etiology of most complex diseases depends on interactions between genetic variants and / or environmental factors. Several machine learning and data mining methods have been consistently successful in exposing these interaction effects. However, there has been no major breakthrough due to various biological complexities, and statistical computational challenges facing in the field of genetic epidemiology, despite of many efforts...
November 2018: International Journal of Medical Informatics
Carlos Sáez, Juan M García-Gómez
AIM: The increasing availability of Big Biomedical Data is leading to large research data samples collected over long periods of time. We propose the analysis of the kinematics of data probability distributions over time towards the characterization of data temporal variability. METHODS: First, we propose a kinematic model based on the estimation of a continuous data temporal trajectory, using Functional Data Analysis over the embedding of a non-parametric statistical manifold which points represent data temporal batches, the Information Geometric Temporal (IGT) plot...
November 2018: International Journal of Medical Informatics
Laurie Zawertailo, Tara Mansoursadeghi-Gilan, Helena Zhang, Sarwar Hussain, Bernard Le Foll, Peter Selby
BACKGROUND: Varenicline and bupropion are efficacious, prescription-only pharmacotherapies for smoking cessation; however, their real-world impact is limited by prescriber knowledge, affordability, and accessibility. OBJECTIVE: The primary objective of the MATCH (Medication Aids for Tobacco Cessation Health) study was to evaluate the real-world, long-term effectiveness of mailed bupropion and varenicline in a sample of interested smokers with the utilization of Web-based recruitment and follow-up...
October 18, 2018: JMIR Research Protocols
Keren Levinstein Hallak, Shay Tzur, Saharon Rosset
BACKGROUND: We study Phylotree, a comprehensive representation of the phylogeny of global human mitochondrial DNA (mtDNA) variations, to better understand the mtDNA substitution mechanism and its most influential factors. We consider a substitution model, where a set of genetic features may predict the rate at which mtDNA substitutions occur. To find an appropriate model, an exhaustive analysis on the effect of multiple factors on the substitution rate is performed through Negative Binomial and Poisson regressions...
October 19, 2018: BMC Genomics
Chamari Wijesooriya, Charles Nyamekye, Emily A Smith
Biological membranes serve as the fundamental unit of life, allowing the compartmentalization of cellular contents into subunits with specific functions. The bilayer structure, consisting of lipids, proteins, small molecules and sugars, also serves many other complex functions in addition to maintaining the relative stability of the inner compartments. Signal transduction, regulation of solute exchange, active transport, and energy transduction through ion gradients all take place at biological membranes, primarily with the assistance of membrane proteins...
October 19, 2018: Analytical Chemistry
Sorin Avram, Ramona Curpan, Alina Bora, Cristian Neanu, Liliana Halip
PURPOSE: The growing amount of heterogeneous bioactivity data requires effective strategies to assess the promiscuity/selectivity of small-molecules and aid drug discovery. In the current study, we aim to evaluate the potential of assay profiles (APs, i.e., unique combinations of assay-related features describing how activity determinations were performed and reported) in molecular promiscuity analysis. METHODS: Using PubChem bioactivity data, we computed for all Molecular Libraries Small Molecule Repository (MLSMR library) compounds the frequency of hits score (FoH, i...
October 18, 2018: Pharmaceutical Research
Sam Duffy, Marcus Pearce
Clapping Music is a minimalist work by Steve Reich based on twelve phased variations of a rhythmic pattern. It has been reimagined as a game-based mobile application, designed with a dual purpose. First, to introduce new audiences to the Minimalist genre through interaction with the piece presented as an engaging game. Second, to use large-scale data collection within the app to address research questions about the factors determining rhythm production performance. The twelve patterns can be differentiated using existing theories of rhythmic complexity...
2018: PloS One
Matteo Lambertini, Samuel Martel, Christine Campbell, Sébastien Guillaume, Florentine S Hilbers, Uwe Schuehly, Larissa Korde, Hatem A Azim, Serena Di Cosimo, Richard C Tenglin, Jens Huober, José Baselga, Alvaro Moreno-Aspitia, Martine Piccart-Gebhart, Richard D Gelber, Evandro de Azambuja, Michail Ignatiadis
BACKGROUND: Limited data exist on the safety of using anti-human epidermal growth factor receptor 2 (HER2) targeted agents during pregnancy. To date, only retrospective studies have assessed the prognosis of patients with a pregnancy after prior early breast cancer, with no data in HER2-positive patients. METHODS: The Neoadjuvant Lapatinib and/or Trastuzumab Treatment Optimization (NeoALTTO) trial and the Adjuvant Lapatinib and/or Trastuzumab Treatment Optimization (ALTTO) trial were randomized phase 3 trials for patients with HER2-positive early breast cancer...
October 18, 2018: Cancer
Yongbing Zhao, Jinyue Wang, Fang Liang, Yanxia Liu, Qi Wang, Hao Zhang, Meiye Jiang, Zhewen Zhang, Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W Asmann, Rujiao Li, Jingfa Xiao
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, NucMap includes 798 experimental data from 477 samples across 15 species...
October 18, 2018: Nucleic Acids Research
Daniel Reker, J B Brown
High-throughput and high-content screening campaigns have resulted in the creation of large chemogenomic matrices. These matrices form the training data which is used to build ligand-target interaction models for pharmacological and chemical biology research. While academic, government, and industrial efforts continuously add to the ligand-target data pairs available for modeling, major research efforts are devoted to improving machine learning techniques to cope with the sparseness, heterogeneity, and size of available datasets as well as inherent noise and bias...
2018: Methods in Molecular Biology
Brian M Schmidt, Crystal M Holmes, Wen Ye, Rodica Pop-Busui
AIMS/HYPOTHESIS: Diabetes foot complications remain very prevalent in US and worldwide, and a major risk for devastating amputations. We evaluated the impact of establishing a fully integrated and specialized Podiatry service into a large tertiary academic health system to implement structured and targeted preventative foot care on limb salvage rates. METHODS: Cross-sectional cohorts' data mining analysis of all encounters for diabetes and any foot complications between 2000-2005 and 2010-2015, preceding and after full implementation of podiatry service, respectively...
October 16, 2018: Current Diabetes Reviews
Lorraine Johnson, Mira Shapiro, Jennifer Mankoff
Lyme disease is caused by the bacteria borrelia burgdorferi and is spread primarily through the bite of a tick. There is considerable uncertainty in the medical community regarding the best approach to treating patients with Lyme disease who do not respond fully to short-term antibiotic therapy. These patients have persistent Lyme disease symptoms resulting from lack of treatment, under-treatment, or lack of response to their antibiotic treatment protocol. In the past, treatment trials have used small restrictive samples and relied on average treatment effects as their measure of success and produced conflicting results...
October 12, 2018: Healthcare (Basel, Switzerland)
A Vinciguerra, C Réveillère, C Potard, B Lyant, L Cornu, R Courtois
INTRODUCTION: Preventing students from dropping out of higher education, and particularly university, requires understanding the different factors that can lead to individuals failing to complete their studies. The role of personality in academic success or failure remains poorly understood. Block's personality profile model (Resilients, Overcontrollers, Undercontrollers) has been used to link personality traits to academic performance. The objective of this study is to apply this model to the risk factors of dropping out of higher education courses, including psychological vulnerability, level of autonomy, and the feeling of not being able to keep up...
October 9, 2018: L'Encéphale
Teresa Schreckenbach, Falk Ochsendorf, Jasmina Sterz, Miriam Rüsseler, Wolf Otto Bechstein, Bernd Bender, Myriam N Bechtoldt
BACKGROUND: This study assessed the impact of medical students' emotion recognition ability and extraversion on their empathic communication, as perceived by simulated patients in a training context. METHODS: This study used a crossed-effect data structure and examined 245 students in their fourth year of medical school. The students' personality traits were assessed based on a self-assessment questionnaire of the short form of the Big Five Inventory; their emotion recognition ability was measured using a performance test (Diagnostic Analysis of Nonverbal Accuracy-2, Adult Facial Expressions)...
October 11, 2018: BMC Medical Education
Andrey Kim, Yongsoo Song, Miran Kim, Keewoo Lee, Jung Hee Cheon
BACKGROUND: Security concerns have been raised since big data became a prominent tool in data analysis. For instance, many machine learning algorithms aim to generate prediction models using training data which contain sensitive information about individuals. Cryptography community is considering secure computation as a solution for privacy protection. In particular, practical requirements have triggered research on the efficiency of cryptographic primitives. METHODS: This paper presents a method to train a logistic regression model without information leakage...
October 11, 2018: BMC Medical Genomics
Lu-Lu Zhang, Guo-Hong Li, Yi-Yang Li, Zhen-Yu Qi, Ai-Hua Lin, Ying Sun
Purpose: The incidence, risk factors and survival impact of secondary primary malignancies (SPMs) among survivors of nasopharyngeal carcinoma (NPC) treated with definitive intensity-modulated radiation therapy (IMRT) with or without chemotherapy are poorly characterized. Methods and Materials: Consecutive patients (n=6,377) from the big-data intelligence platform at Sun Yat-Sen University Cancer Center, China (in a high-incidence area) with newly diagnosed non-metastatic pathologically proven non-keratinizing undifferentiated NPC treated with IMRT±chemotherapy between January 2003 and June 2013 were retrospectively analyzed...
October 11, 2018: Cancer Research and Treatment: Official Journal of Korean Cancer Association
Marcello Ienca, Agata Ferretti, Samia Hurst, Milo Puhan, Christian Lovis, Effy Vayena
Big data trends in biomedical and health research enable large-scale and multi-dimensional aggregation and analysis of heterogeneous data sources, which could ultimately result in preventive, diagnostic and therapeutic benefit. The methodological novelty and computational complexity of big data health research raises novel challenges for ethics review. In this study, we conducted a scoping review of the literature using five databases to identify and map the major challenges of health-related big data for Ethics Review Committees (ERCs) or analogous institutional review boards...
2018: PloS One
Harshana Liyanage, Siaw-Teng Liaw, Jitendra Jonnagaddala, William Hinton, Simon de Lusignan
Common data models (CDM) have enabled the simultaneous analysis of disparate and large data sources. A literature review identified three relevant CDMs: The Observational Medical Outcomes Partnership (OMOP) was the most cited; next the Sentinel; and then the Patient Centered Outcomes Research Institute (PCORI). We tested these three CDMs with fifteen pre-defined criteria for a diabetes cohort study use case, assessing the benefit (good diabetes control), risk (hypoglycaemia) and cost effectiveness of recently licenced medications...
2018: Studies in Health Technology and Informatics
Yang Fei, Xiao-Qiang Liu, Kun Gao, Cheng-Bin Xue, Liang Tang, Jian-Feng Tu, Wei Wang, Wei-Qin Li
OBJECTIVES: To evaluate the epidemiological characteristics of acute pancreatitis (AP) and explore potential relationships between these factors and severity. METHODOLOGY: Data-sets of 5,659 patients with AP from health statistics and the Information Center of Jiangsu province, between 2014 and 2016, were analyzed. A self-organizing map (SOM) neural network was used for data clustering. RESULTS: Biliary acute pancreatitis (BAP) (86.7%) was the most frequent etiological factor...
May 2018: Revista da Associação Médica Brasileira
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