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https://www.readbyqxmd.com/read/28922596/privileged-substructures-to-modulate-protein-protein-interactions
#1
Nicolas Bosc, Mélaine A Kuenemann, Jérome Bécot, Marek Vavrusa, Adrien H Cerdan, Olivier Sperandio
Given the difficulties to identify chemical probes that can modulate protein-protein interactions (PPIs), actors in the field start to agree on the necessity to use PPI-tailored screening chemical collections. However, which type of scaffolds may promote the binding of compounds to PPI targets remains unclear. In this big data analysis, we have identified a list of privileged chemical substructures that are most often observed within inhibitors of PPIs. Using molecular frameworks as a way to perceive chemical substructures with the combination of an experimental and a machine-learning based predicted dataset of iPPI compounds, we propose a list of privileged substructures in the form of scaffolds and chemical moieties that can be substantially chemically functionalized and do not present any toxicophore nor Pan-assay interference (PAINS) alerts...
September 18, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28922034/personality-traits-and-social-media-use-in-20-countries-how-personality-relates-to-frequency-of-social-media-use-social-media-news-use-and-social-media-use-for-social-interaction
#2
Homero Gil de Zúñiga, Trevor Diehl, Brigitte Huber, James Liu
This study examines the relationship between peoples' personality traits and social media uses with data from 20 societies (N = 21,314). A measure of the "Big Five" personality traits is tested on key social media dimensions: frequency of use, social interaction, and news consumption. Across diverse societies, findings suggest that while extraversion, agreeableness, and conscientiousness are all positive predictors of different types of social media use, emotional stability and openness are negatively related to them...
September 2017: Cyberpsychology, Behavior and Social Networking
https://www.readbyqxmd.com/read/28920910/online-density-estimation-of-nonstationary-sources-using-exponential-family-of-distributions
#3
Kaan Gokcesu, Suleyman S Kozat
We investigate online probability density estimation (or learning) of nonstationary (and memoryless) sources using exponential family of distributions. To this end, we introduce a truly sequential algorithm that achieves Hannan-consistent log-loss regret performance against true probability distribution without requiring any information about the observation sequence (e.g., the time horizon T and the drift of the underlying distribution C) to optimize its parameters. Our results are guaranteed to hold in an individual sequence manner...
September 13, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28919931/improving-hierarchical-models-using-historical-data-with-applications-in-high-throughput-genomics-data-analysis
#4
Ben Li, Yunxiao Li, Zhaohui S Qin
Modern high-throughput biotechnologies such as microarray and next generation sequencing produce a massive amount of information for each sample assayed. However, in a typical high-throughput experiment, only limited amount of data are observed for each individual feature, thus the classical 'large p, small n' problem. Bayesian hierarchical model, capable of borrowing strength across features within the same dataset, has been recognized as an effective tool in analyzing such data. However, the shrinkage effect, the most prominent feature of hierarchical features, can lead to undesirable over-correction for some features...
June 2017: Statistics in Biosciences
https://www.readbyqxmd.com/read/28918672/protein-complexes-big-data-machine-learning-and-integrative-proteomics-lessons-learned-over-a-decade-of-systematic-analysis-of-protein-interaction-networks
#5
Pierre C Havugimana, Pingzhao Hu, Andrew Emili
Elucidation of the networks of physical (functional) interactions present in cells and tissues is fundamental for understanding the molecular organization of biological systems, the mechanistic basis of essential and disease-related processes, and for functional annotation of previously uncharacterized proteins (via guilt-by-association or -correlation). After a decade in the field, we felt it timely to document our own experiences in the systematic analysis of protein interaction networks. Areas covered: Researchers worldwide have contributed innovative experimental and computational approaches that have driven the rapidly evolving field of 'functional proteomics'...
September 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28918390/a-glossary-for-big-data-in-population-and-public-health-discussion-and-commentary-on-terminology-and-research-methods
#6
Daniel Fuller, Richard Buote, Kevin Stanley
The volume and velocity of data are growing rapidly and big data analytics are being applied to these data in many fields. Population and public health researchers may be unfamiliar with the terminology and statistical methods used in big data. This creates a barrier to the application of big data analytics. The purpose of this glossary is to define terms used in big data and big data analytics and to contextualise these terms. We define the five Vs of big data and provide definitions and distinctions for data mining, machine learning and deep learning, among other terms...
September 16, 2017: Journal of Epidemiology and Community Health
https://www.readbyqxmd.com/read/28918048/mir-133a-promotes-trail-resistance-in-glioblastoma-via-suppressing-death-receptor-5-and-activating-nf-%C3%AE%C2%BAb-signaling
#7
Shan-Shan Wang, Lu Feng, Bao-Guang Hu, Ying-Fei Lu, Wei-Mao Wang, Wei Guo, Chun-Wai Suen, Bao-Hua Jiao, Jian-Xin Pang, Wei-Ming Fu, Jin-Fang Zhang
Recombinant tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), as a novel cancer therapeutic, is being tested in phase II and III clinical trials; however, TRAIL resistance remains a big obstacle preventing its clinical application. Considering that TRAIL-induced apoptosis through death receptors DR4 and DR5, their activation may be an alternative pathway to suppress TRAIL resistance. In this study, a negative correlation between DR5 expression and TRAIL resistance was observed, and miR-133a was predicted to be the most promising candidate to suppress DR5 expression...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28915865/informed-consent-and-registry-based-research-the-case-of-the-danish-circumcision-registry
#8
Thomas Ploug, Søren Holm
BACKGROUND: Research into personal health data holds great potential not only for improved treatment but also for economic growth. In these years many countries are developing policies aimed at facilitating such research often under the banner of 'big data'. A central point of debate is whether the secondary use of health data requires informed consent if the data is anonymised. In 2013 the Danish Minister of Health established a new register collecting data about all ritual male childhood circumcisions in Denmark...
September 15, 2017: BMC Medical Ethics
https://www.readbyqxmd.com/read/28914775/new-methods-to-address-old-challenges-the-use-of-administrative-data-for-longitudinal-replication-studies-of-child-maltreatment
#9
Emily Hurren, Anna Stewart, Susan Dennison
Administrative data are crucial to the "big data" revolution of social science and have played an important role in the development of child maltreatment research. These data are also of value to administrators, policy makers, and clinicians. The focus of this paper is the use of administrative data to produce and replicate longitudinal studies of child maltreatment. Child protection administrative data have several advantages. They are often population-based, and allow longitudinal examination of child maltreatment and complex multi-level analyses...
September 15, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28913771/criminal-prohibition-of-wrongful-re%C3%A2-identification-legal-solution-or-minefield-for-big-data
#10
Mark Phillips, Edward S Dove, Bartha M Knoppers
The collapse of confidence in anonymization (sometimes also known as de-identification) as a robust approach for preserving the privacy of personal data has incited an outpouring of new approaches that aim to fill the resulting trifecta of technical, organizational, and regulatory privacy gaps left in its wake. In the latter category, and in large part due to the growth of Big Data-driven biomedical research, falls a growing chorus of calls for criminal and penal offences to sanction wrongful re-identification of "anonymized" data...
September 14, 2017: Journal of Bioethical Inquiry
https://www.readbyqxmd.com/read/28913177/big-data-in-designing-clinical-trials-opportunities-and-challenges
#11
Charles S Mayo, Martha M Matuszak, Matthew J Schipper, Shruti Jolly, James A Hayman, Randall K Ten Haken
Emergence of big data analytics resource systems (BDARSs) as a part of routine practice in Radiation Oncology is on the horizon. Gradually, individual researchers, vendors, and professional societies are leading initiatives to create and demonstrate use of automated systems. What are the implications for design of clinical trials, as these systems emerge? Gold standard, randomized controlled trials (RCTs) have high internal validity for the patients and settings fitting constraints of the trial, but also have limitations including: reproducibility, generalizability to routine practice, infrequent external validation, selection bias, characterization of confounding factors, ethics, and use for rare events...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28912831/genome-sequencing-and-transcriptome-analysis-of-trichoderma-reesei-qm9978-strain-reveals-a-distal-chromosome-translocation-to-be-responsible-for-loss-of-vib1-expression-and-loss-of-cellulase-induction
#12
Christa Ivanova, Jonas Ramoni, Thiziri Aouam, Alexa Frischmann, Bernhard Seiboth, Scott E Baker, Stéphane Le Crom, Sophie Lemoine, Antoine Margeot, Frédérique Bidard
BACKGROUND: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28906244/hearing-aid-use-and-mild-hearing-impairment-learnings-from-big-data
#13
Barbra H B Timmer, Louise Hickson, Stefan Launer
BACKGROUND: Previous research, mostly reliant on self-reports, has indicated that hearing aid (HA) use is related to the degree of hearing impairment (HI). No large-scale investigation of the relationship between data-logged HA use and HI has been conducted to date. PURPOSE: This study aimed to investigate if objective measures of overall daily HA use and HA use in various listening environments are different for adults with mild HI compared to adults with moderate HI...
September 2017: Journal of the American Academy of Audiology
https://www.readbyqxmd.com/read/28905886/time-series-oligonucleotide-count-to-assign-antiviral-sirnas-with-long-utility-fit-in-the-big-data-era
#14
K Wada, Y Wada, Y Iwasaki, T Ikemura
Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes...
September 14, 2017: Gene Therapy
https://www.readbyqxmd.com/read/28905472/design-paper-japan-endoscopy-database-jed-a-prospective-big-database-project-related-to-gastroenterological-endoscopy-in-japan
#15
K Matsuda, K Tanaka, M Fujishiro, Y Saito, K Ohtsuka, I Oda, C Katada, M Kato, M Kida, K Kobayashi, S Hoteya, T Horimatsu, S Kodashima, T Matsuda, M Muto, H Yamamoto, S Ryozawa, R Iwakiri, H Kutsumi, H Miyata, M Kato, K Haruma, K Fujimoto, N Uemura, M Kaminishi, H Tajiri
The advent of electrical medical records brought image filing systems to many hospitals, as well as electrical endoscopic medical records. However, data integration among multiple different venders has not yet been accomplished. We start the Japan Endoscopic Database (JED) Project endorsed by Japan Gastroenterological Endoscopy Society (JGES) from January 2015. The purposes of this project are as follows: 1) developing the world's largest endoscopic database generated from daily use of the reporting system 2) capturing the actual performance of endoscopic practice in Japan; and 3) standardizing the terminology and fundamental items for the registry of clinical studies...
September 14, 2017: Digestive Endoscopy: Official Journal of the Japan Gastroenterological Endoscopy Society
https://www.readbyqxmd.com/read/28903886/patient-privacy-in-the-era-of-big-data
#16
Mehmet Kayaalp
Privacy was defined as a fundamental human right in the Universal Declaration of Human Rights at the 1948 United Nations General Assembly. However, there is still no consensus on what constitutes privacy. In this review, we look at the evolution of privacy as a concept from the era of Hippocrates to the era of social media and big data. To appreciate the modern measures of patient privacy protection and correctly interpret the current regulatory framework in the United States, we need to analyze and understand the concepts of individually identifiable information, individually identifiable health information, protected health information (PHI), and de-identification...
September 13, 2017: Balkan Medical Journal
https://www.readbyqxmd.com/read/28901885/teaching-and-researching-the-history-of-medicine-in-the-era-of-big-data-reflections
#17
Frederick W Gibbs, Jeffrey S Reznick
No abstract text is available yet for this article.
October 2017: Medical History
https://www.readbyqxmd.com/read/28899706/big-data-and-machine-learning-a-resident-s-perspective-of-the-2016-intersociety-conference
#18
David C Gimarc, Alexander S Misono
No abstract text is available yet for this article.
September 9, 2017: Journal of the American College of Radiology: JACR
https://www.readbyqxmd.com/read/28893854/will-big-data-close-the-missing-heritability-gap
#19
Hwasoon Kim, Alexander Grueneberg, Ana I Vazquez, Stephen Hsu, Gustavo de Los Campos
Despite the important discoveries reported by Genome-Wide Association studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of Big Data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28889809/leukocyte-telomere-length-and-personality-associations-with-the-big-five-and-type-d-personality-traits
#20
D Schoormans, J E Verhoeven, J Denollet, L van de Poll-Franse, B W J H Penninx
Backgrounds Accelerated cellular ageing, which can be examined by telomere length (TL), may be an overarching mechanism underlying the association between personality and adverse health outcomes. This 6-year longitudinal study examined the relation between personality and leukocyte telomere length (LTL) across time among adults with a wide age-range. METHODS: Data from the Netherlands Study of Depression and Anxiety were used and included patients with a depression and/or anxiety disorder and healthy controls...
September 11, 2017: Psychological Medicine
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