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https://www.readbyqxmd.com/read/28214992/data-mining-in-hiv-aids-surveillance-system-application-to-portuguese-data
#1
Alexandra Oliveira, Brígida Mónica Faria, A Rita Gaio, Luís Paulo Reis
The Human Immunodeficiency Virus (HIV) is an infectious agent that attacks the immune system cells. Without a strong immune system, the body becomes very susceptible to serious life threatening opportunistic diseases. In spite of the great progresses on medication and prevention over the last years, HIV infection continues to be a major global public health issue, having claimed more than 36 million lives over the last 35 years since the recognition of the disease. Monitoring, through registries, of HIV-AIDS cases is vital to assess general health care needs and to support long-term health-policy control planning...
April 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28208453/nonparametric-bayesian-inference-of-the-microcanonical-stochastic-block-model
#2
Tiago P Peixoto
A principled approach to characterize the hidden structure of networks is to formulate generative models and then infer their parameters from data. When the desired structure is composed of modules or "communities," a suitable choice for this task is the stochastic block model (SBM), where nodes are divided into groups, and the placement of edges is conditioned on the group memberships. Here, we present a nonparametric Bayesian method to infer the modular structure of empirical networks, including the number of modules and their hierarchical organization...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28207523/pharmacological-and-psychotherapeutic-interventions-for-management-of-poststroke-depression-a-bayesian-network-meta-analysis-of-randomized-controlled-trials
#3
Xuejun Sun, Linghui Deng, Shi Qiu, Xiang Tu, Deren Wang, Ming Liu
INTRODUCTION: Poststroke depression (PSD) constitutes an important complication of stroke, leading to great disability as well as increased mortality. Since which treatment for PSD should be preferred are still matters of controversy, we are aiming to compare and rank these pharmacological and nonpharmacological interventions. METHODS AND ANALYSIS: We will employ a network meta-analysis to incorporate both direct and indirect evidence from relevant trials. We will search PubMed, the Cochrane Library Central Register of Controlled Trials, Embase, and the reference lists of relevant articles for randomized controlled trials (RCT) of different PSD treatment strategies...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28204986/validation-workflow-for-a-clinical-bayesian-network-model-in-multidisciplinary-decision-making-in-head-and-neck-oncology-treatment
#4
Mario A Cypko, Matthaeus Stoehr, Marcin Kozniewski, Marek J Druzdzel, Andreas Dietz, Leonard Berliner, Heinz U Lemke
PURPOSE: Oncological treatment is being increasingly complex, and therefore, decision making in multidisciplinary teams is becoming the key activity in the clinical pathways. The increased complexity is related to the number and variability of possible treatment decisions that may be relevant to a patient. In this paper, we describe validation of a multidisciplinary cancer treatment decision in the clinical domain of head and neck oncology. METHOD: Probabilistic graphical models and corresponding inference algorithms, in the form of Bayesian networks, can support complex decision-making processes by providing a mathematically reproducible and transparent advice...
February 15, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28192233/use-of-ontology-structure-and-bayesian-models-to-aid-the-crowdsourcing-of-icd-11-sanctioning-rules
#5
Yun Lou, Samson W Tu, Csongor Nyulas, Tania Tudorache, Robert J G Chalmers, Mark A Musen
The International Classification of Diseases (ICD) is the de facto standard international classification for mortality reporting and for many epidemiological, clinical, and financial use cases. The next version of ICD, ICD-11, will be submitted for approval by the World Health Assembly in 2018. Unlike previous versions of ICD, where coders mostly select single codes from pre-enumerated disease and disorder codes, ICD-11 coding will allow extensive use of multiple codes to give more detailed disease descriptions...
February 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28190902/constraining-the-kinematics-of-metropolitan-los-angeles-faults-with-a-slip-partitioning-model
#6
S Daout, S Barbot, G Peltzer, M-P Doin, Z Liu, R Jolivet
Due to the limited resolution at depth of geodetic and other geophysical data, the geometry and the loading rate of the ramp-décollement faults below the metropolitan Los Angeles are poorly understood. Here we complement these data by assuming conservation of motion across the Big Bend of the San Andreas Fault. Using a Bayesian approach, we constrain the geometry of the ramp-décollement system from the Mojave block to Los Angeles and propose a partitioning of the convergence with 25.5 ± 0.5 mm/yr and 3...
November 16, 2016: Geophysical Research Letters
https://www.readbyqxmd.com/read/28189058/using-data-mining-techniques-to-predict-the-severity-of-bicycle-crashes
#7
Gabriele Prati, Luca Pietrantoni, Federico Fraboni
To investigate the factors predicting severity of bicycle crashes in Italy, we used an observational study of official statistics. We applied two of the most widely used data mining techniques, CHAID decision tree technique and Bayesian network analysis. We used data provided by the Italian National Institute of Statistics on road crashes that occurred on the Italian road network during the period ranging from 2011 to 2013. In the present study, the dataset contains information about road crashes occurred on the Italian road network during the period ranging from 2011 to 2013...
February 8, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28187713/novel-methods-to-optimize-gene-and-statistic-test-for-evaluation-an-application-for-escherichia-coli
#8
Tran Tuan-Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao
BACKGROUND: Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host's expression system, so the yields can fall down significantly...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28186942/use-of-combination-therapy-in-the-treatment-of-primary-osteoporosis-protocol-for-a-network-meta-analysis-of-randomised-trials
#9
Shenghan Lou, Houchen Lv, Yuxiang Chen, Licheng Zhang, Peifu Tang
INTRODUCTION: The existing medications approved for treatment of primary osteoporosis can be divided into antiresorptive drugs and anabolic drugs. According to the mechanisms of action, the combined therapy may produce a synergistic effect on bone mineral density (BMD) compared with monotherapy, and thus improves the efficacy of fracture resistance. This network meta-analysis aims to compare the efficacies of different combined methods for the treatment of primary osteoporosis. METHODS AND ANALYSIS: MEDLINE, EMBASE and Cochrane databases will be searched to identify all randomised controlled trials (RCTs) and quasi-RCTs that evaluate the effectiveness of combined therapy versus monotherapy for primary osteoporosis...
November 8, 2016: BMJ Open
https://www.readbyqxmd.com/read/28181298/prediction-model-for-cardiac-allograft-vasculopathy-comparison-of-three-multivariable-methods
#10
Evan P Kransdorf, Natasha A Loghmanpour, Manreet K Kanwar, M'hamed H Temkit, Josef Stehlik
BACKGROUND: Cardiac allograft vasculopathy (CAV) remains an important cause of graft failure after heart transplantation (HT). Although many risk factors for CAV have been identified, there are no clinical prediction models that enable clinicians to determine each recipient's risk of CAV. METHODS: We studied a cohort of 14,328 heart transplant recipients whose data were reported to the International Society for Heart and Lung Transplantation Registry between 2000 and 2010...
February 9, 2017: Clinical Transplantation
https://www.readbyqxmd.com/read/28180028/squish-near-optimal-compression-for-archival-of-relational-datasets
#11
Yihan Gao, Aditya Parameswaran
Relational datasets are being generated at an alarmingly rapid rate across organizations and industries. Compressing these datasets could significantly reduce storage and archival costs. Traditional compression algorithms, e.g., gzip, are suboptimal for compressing relational datasets since they ignore the table structure and relationships between attributes. We study compression algorithms that leverage the relational structure to compress datasets to a much greater extent. We develop Squish, a system that uses a combination of Bayesian Networks and Arithmetic Coding to capture multiple kinds of dependencies among attributes and achieve near-entropy compression rate...
August 2016: KDD: Proceedings
https://www.readbyqxmd.com/read/28179182/chloroplast-and-its-phylogenies-to-understand-the-evolutionary-history-of-southern-south-american-azorella-laretia-and-mulinum-azorelloideae-apiaceae
#12
Martina Fernández, Cecilia Ezcurra, Carolina I Calviño
Azorella, Laretia and Mulinum are taxonomically complex, and good candidates to study evolutionary radiations in the Andes and the importance of hybridizations. Previous phylogenetic studies of subfamily Azorelloideae agree that Azorella and Mulinum as currently conceived are not monophyletic, and hence a revision of their circumscription is necessary. However, these phylogenies were based only on chloroplast DNA sequence data. Here, phylogenetic relationships within Azorelloideae were inferred using sequence data from five chloroplast DNA (rps16 intron, trnQ-rps16, rps16-trnK(UUU) 5' -exon, trnG(GCC)-trnS(GCU) and rpL32-trnL(UAG)), and from nuclear rDNA ITS regions to assess the monophyly of Azorella and Mulinum and discuss generic re-circumscriptions, determine hybridization and radiation events, identify and characterize important lineages, and propose hypotheses on evolution of key morphological characters...
February 4, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28178269/correction-bayesian-inference-of-reticulate-phylogenies-under-the-multispecies-network-coalescent
#13
Dingqiao Wen, Yun Yu, Luay Nakhleh
[This corrects the article DOI: 10.1371/journal.pgen.1006006.].
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28178135/durability-of-cervical-disc-arthroplasties-and-its-influence-factors-a-systematic-review-and-a-network-meta-analysis
#14
Chao Chen, Xiaolin Zhang, Xinlong Ma
BACKGROUND: The durability of cervical disc arthroplasties (CDA) may vary significantly because of different designs and implanting techniques of the devices. Nevertheless, the comparative durability remains unknown. OBJECTIVES: We aimed to assess the durability of CDAs in at least 2-year follow-up. We analyzed the classifications and causes of secondary surgical procedures, as well as the structural designs of the devices that might influence the durability. METHODS: PubMed, Medline, Embase, and Cochrane Central Register of Controlled Trials were searched from the inception of each database to September 2015 using the following Keywords: "cervical disc replacement" OR "cervical disc arthroplasty" AND "randomized controlled trial (RCT)...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28176892/comparative-efficacy-of-long-acting-%C3%AE-2-agonists-as-monotherapy-for-chronic-obstructive-pulmonary-disease-a-network-meta-analysis
#15
James F Donohue, Keith A Betts, Ella Xiaoyan Du, Pablo Altman, Pankaj Goyal, Dorothy L Keininger, Jean-Bernard Gruenberger, James E Signorovitch
PURPOSE: Long-acting β2-agonists (LABAs) have demonstrated efficacy in patients with COPD in clinical trials. The purpose of this study was to assess the comparative efficacy of all available dosages of all LABA monotherapies using a network meta-analysis. METHODS: A systematic literature review identified 33 randomized controlled trials of LABA monotherapies (salmeterol 50 μg twice daily [BID]; formoterol 12 μg BID; indacaterol 75, 150, and 300 μg once daily [OD]; olodaterol 5 and 10 μg OD, and vilanterol 25 μg OD)...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28176850/application-of-machine-learning-models-to-predict-tacrolimus-stable-dose-in-renal-transplant-recipients
#16
Jie Tang, Rong Liu, Yue-Li Zhang, Mou-Ze Liu, Yong-Fang Hu, Ming-Jie Shao, Li-Jun Zhu, Hua-Wen Xin, Gui-Wen Feng, Wen-Jun Shang, Xiang-Guang Meng, Li-Rong Zhang, Ying-Zi Ming, Wei Zhang
Tacrolimus has a narrow therapeutic window and considerable variability in clinical use. Our goal was to compare the performance of multiple linear regression (MLR) and eight machine learning techniques in pharmacogenetic algorithm-based prediction of tacrolimus stable dose (TSD) in a large Chinese cohort. A total of 1,045 renal transplant patients were recruited, 80% of which were randomly selected as the "derivation cohort" to develop dose-prediction algorithm, while the remaining 20% constituted the "validation cohort" to test the final selected algorithm...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28166542/expectation-propagation-for-large-scale-bayesian-inference-of-non-linear-molecular-networks-from-perturbation-data
#17
Zahra Narimani, Hamid Beigy, Ashar Ahmad, Ali Masoudi-Nejad, Holger Fröhlich
Inferring the structure of molecular networks from time series protein or gene expression data provides valuable information about the complex biological processes of the cell. Causal network structure inference has been approached using different methods in the past. Most causal network inference techniques, such as Dynamic Bayesian Networks and ordinary differential equations, are limited by their computational complexity and thus make large scale inference infeasible. This is specifically true if a Bayesian framework is applied in order to deal with the unavoidable uncertainty about the correct model...
2017: PloS One
https://www.readbyqxmd.com/read/28165112/bayesian-network-response-regression
#18
Lu Wang, Daniele Durante, Rex E Jung, David B Dunson
No abstract text is available yet for this article.
February 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28159843/both-intrinsic-substrate-preference-and-network-context-contribute-to-substrate-selection-of-classical-tyrosine-phosphatases
#19
Anita Palma, Michele Tinti, Serena Paoluzi, Elena Santonico, Bernd Willem Brandt, Rob Hooft van Huijsduijnen, Antonia Masch, Jaap Heringa, Mike Schutkowski, Luisa Castagnoli, Gianni Cesareni
Reversible tyrosine phosphorylation is a widespread post-translational modification mechanism underlying cell physiology. Thus, understanding the mechanisms responsible for substrate selection by kinases and phosphatases is central to our ability to model signal transduction at a system level. Classical protein tyrosine phosphatases (PTP) can exhibit substrate specificity, in vivo, by combining intrinsic enzymatic specificity with the network of protein-protein interactions, which positions the enzymes in close proximity to their substrates...
February 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28150241/functional-interaction-network-construction-and-analysis-for-disease-discovery
#20
Guanming Wu, Robin Haw
Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform...
2017: Methods in Molecular Biology
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