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https://www.readbyqxmd.com/read/29353280/microstructure-of-strategic-white-matter-tracts-and-cognition-in-memory-clinic-patients-with-vascular-brain-injury
#1
J Matthijs Biesbroek, Alexander Leemans, Hanna den Bakker, Marco Duering, Benno Gesierich, Huiberdina L Koek, Esther van den Berg, Albert Postma, Geert Jan Biessels
BACKGROUND: White matter injury is an important factor for cognitive impairment in memory clinic patients. We determined the added value of diffusion tensor imaging (DTI) of strategic white matter tracts in explaining variance in cognition in memory clinic patients with vascular brain injury. METHODS: We included 159 patients. Conventional MRI markers (white matter hyperintensity volume, lacunes, nonlacunar infarcts, brain atrophy, and microbleeds), and fractional anisotropy and mean diffusivity (MD) of the whole brain white matter and of 18 white matter tracts were related to cognition using linear regression and Bayesian network analysis...
January 19, 2018: Dementia and Geriatric Cognitive Disorders
https://www.readbyqxmd.com/read/29347355/inverse-ising-problem-in-continuous-time-a-latent-variable-approach
#2
Christian Donner, Manfred Opper
We consider the inverse Ising problem: the inference of network couplings from observed spin trajectories for a model with continuous time Glauber dynamics. By introducing two sets of auxiliary latent random variables we render the likelihood into a form which allows for simple iterative inference algorithms with analytical updates. The variables are (1) Poisson variables to linearize an exponential term which is typical for point process likelihoods and (2) Pólya-Gamma variables, which make the likelihood quadratic in the coupling parameters...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346915/efficient-method-for-estimating-the-number-of-communities-in-a-network
#3
Maria A Riolo, George T Cantwell, Gesine Reinert, M E J Newman
While there exist a wide range of effective methods for community detection in networks, most of them require one to know in advance how many communities one is looking for. Here we present a method for estimating the number of communities in a network using a combination of Bayesian inference with a novel prior and an efficient Monte Carlo sampling scheme. We test the method extensively on both real and computer-generated networks, showing that it performs accurately and consistently, even in cases where groups are widely varying in size or structure...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29344193/identification-of-differentially-expressed-molecular-functions-associated-with-breast-cancer-using-gibbs-sampling
#4
Gang Zhou, Ming-Qian Lu, Dao-Jun Li, Bao-An Gao, Rong Guo
The aim of the present study was to identify differentially expressed molecular functions (DEMFs) for breast cancer using the Gibbs sampling approach. Molecular functions (MFs) were obtained on the basis of the Bayesian Approach for Geneset Selection package. Subsequently, MFs were converted into Markov chains (MCs) prior to calculating their probabilities, utilizing the MC Monte Carlo algorithm. DEMFs were identified with probabilities ≥0.8 and the gene compositions were studied. Finally, a co-expression network was constructed via the empirical Bayes method and a pathway enrichment analysis of genes in DEMFs was performed...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29338862/new-generation-stents-compared-with-coronary-bypass-surgery-for-unprotected-left-main-disease-a-word-of-caution
#5
Umberto Benedetto, David P Taggart, Miguel Sousa-Uva, Giuseppe Biondi-Zoccai, Antonino Di Franco, Lucas B Ohmes, Mohamed Rahouma, Mohamed Kamel, Massimo Caputo, Leonard N Girardi, Gianni D Angelini, Mario Gaudino
BACKGROUND: With the advent of bare metal stents and drug-eluting stents, percutaneous coronary intervention has emerged as an alternative to coronary artery bypass grafting surgery for unprotected left main disease. However, whether the evolution of stents technology has translated into better results after percutaneous coronary intervention remains unclear. We aimed to compare coronary artery bypass grafting with stents of different generations for left main disease by performing a Bayesian network meta-analysis of available randomized controlled trials...
January 12, 2018: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/29337235/frequency-specific-effective-connectivity-in-subjects-with-cerebral-infarction-as-revealed-by-nirs-method
#6
Qianying Liu, Bitian Wang, Ying Liu, Zeping Lv, Wenhao Li, Zengyong Li, Yubo Fan
A connectivity-based approach can highlight the network reorganization in the chronic phases after stroke and contributes to the development of therapeutic interventions. Using dynamic Bayesian inference, this study aimed to assess the effective connectivity(EC)in various frequency bands through the near-infrared spectroscopy(NIRS) method in subjects with cerebral infarction(CI). A phase-coupling model was established based on phase information extracted using the wavelet transform of NIRS signals. Coupling strength and the main coupling direction were estimated using dynamic Bayesian inference...
January 11, 2018: Neuroscience
https://www.readbyqxmd.com/read/29335598/gene-and-microrna-perturbations-of-cellular-response-to-pemetrexed-implicate-biological-networks-and-enable-imputation-of-response-in-lung-adenocarcinoma
#7
Eric R Gamazon, Matthew R Trendowski, Yujia Wen, Claudia Wing, Shannon M Delaney, Won Huh, Shan Wong, Nancy J Cox, M Eileen Dolan
Pemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335342/comparative-efficacy-of-tumor-necrosis-factor-%C3%AE-inhibitors-in-ankylosing-spondylitis-a-systematic-review-and-bayesian-network-metaanalysis
#8
Runsheng Wang, Abhijit Dasgupta, Michael M Ward
OBJECTIVE: To compare the efficacy of 6 tumor necrosis factor-α inhibitors (TNFi) in treatment of ankylosing spondylitis (AS) at 12 weeks and 24 weeks. METHODS: We performed a systematic literature review of randomized controlled trials of TNFi in patients with active AS. We included trials that reported efficacy at 10 to 14 weeks (12-week analysis) and at 24 to 30 weeks (24-week analysis). We used Bayesian network metaanalysis (NMA) to compare their relative efficacy to improve the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), and C-reactive protein (CRP) level...
January 15, 2018: Journal of Rheumatology
https://www.readbyqxmd.com/read/29334136/a-bayesian-network-meta-analysis-efficacy-of-air-insufflation-co2-insufflation-water-exchange-and-water-immersion-in-colonoscopy
#9
REVIEW
Zhen Zhang, Yifeng Wu, Guangge Sun, Jing Zhang, Jiaxin Li, Chongyang Qiu, Xin Zheng, Botao Wang, Lei Yang, Ximo Wang
BACKGROUND: Colonoscopy is one of the excellent tools for screening colorectal cancer. There were four colonoscopy techniques containing air insufflation, CO2 insufflation, water exchange, and water immersion. Some studies reported that these methods are better than the criterion standard (air insufflation), while some studies showed not. In order to evaluate the efficacy of four colonoscopy techniques, a network meta-analysis was performed in present study. METHODS: We searched randomized controlled trials (RCTs) published up to September 2017 from PubMed, Embase, Cochrane library, and Web of Science...
January 15, 2018: Digestive Endoscopy: Official Journal of the Japan Gastroenterological Endoscopy Society
https://www.readbyqxmd.com/read/29332315/comparison-of-treatment-strategies-for-femoro-popliteal-disease-a-network-meta-analysis
#10
Edward Koifman, Michael J Lipinski, Kyle Buchanan, Won Yu Kang, Ricardo O Escarcega, Ron Waksman, Nelson L Bernardo
OBJECTIVES: We sought to compare treatment strategies in a Bayesian network meta-analysis of randomized controlled trials. BACKGROUND: Peripheral artery disease (PAD) is a prevalent morbidity that is treated with various strategies. METHODS: We performed a MEDLINE search for randomized studies comparing at least 2 treatment strategies, including bypass surgery, percutaneous transluminal angioplasty (PTA) balloons, stents, covered stents, drug-eluting stents (DES), and drug-coated balloons (DCB), in patients with native femoro-popliteal disease...
January 14, 2018: Catheterization and Cardiovascular Interventions
https://www.readbyqxmd.com/read/29330211/olanzapine-based-triple-regimens-versus-neurokinin-1-receptor-antagonist-based-triple-regimens-in-preventing-chemotherapy-induced-nausea-and-vomiting-associated-with-highly-emetogenic-chemotherapy-a-network-meta-analysis
#11
Zhonghan Zhang, Yaxiong Zhang, Gang Chen, Shaodong Hong, Yunpeng Yang, Wenfeng Fang, Fan Luo, Xi Chen, Yuxiang Ma, Yuanyuan Zhao, Jianhua Zhan, Cong Xue, Xue Hou, Ting Zhou, Shuxiang Ma, Fangfang Gao, Yan Huang, Likun Chen, Ningning Zhou, Hongyun Zhao, Li Zhang
BACKGROUND: The current antiemetic prophylaxis for patients treated with highly emetogenic chemotherapy (HEC) included the olanzapine-based triplet and neurokinin-1 receptor antagonists (NK-1RAs)-based triplet. However, which one shows better antiemetic effect remained unclear. MATERIALS AND METHODS: We systematically reviewed 43 trials, involving 16,609 patients with HEC, which compared the following antiemetics at therapeutic dose range for the treatment of chemotherapy-induced nausea and vomiting: olanzapine, aprepitant, casopitant, fosaprepitant, netupitant, and rolapitant...
January 12, 2018: Oncologist
https://www.readbyqxmd.com/read/29325013/effects-of-task-demands-on-olfactory-auditory-and-visual-event-related-potentials-suggest-similar-top-down-modulation-across-senses
#12
Linus Andersson, Petra Sandberg, Jonas Olofsson, Steven Nordin
A widely held view is that top-down modulation of sensory information relies on an amodal control network that acts through the thalamus to regulate incoming signals. Olfaction lacks a direct thalamic projection, which suggests that it may differ from other modalities in this regard. We investigated the late positive complex (LPC) amplitudes of event-related potentials (ERP) from 28 participants, elicited by intensity-matched olfactory, auditory and visual stimuli, during a condition of focused attention, a neutral condition, and a condition in which stimuli were to be actively ignored...
January 8, 2018: Chemical Senses
https://www.readbyqxmd.com/read/29324886/changes-in-network-connectivity-during-motor-imagery-and-execution
#13
Yun Kwan Kim, Eunhee Park, Ahee Lee, Chang-Hwan Im, Yun-Hee Kim
BACKGROUND: Recent studies of functional or effective connectivity in the brain have reported that motor-related brain regions were activated during motor execution and motor imagery, but the relationship between motor and cognitive areas has not yet been completely understood. The objectives of our study were to analyze the effective connectivity between motor and cognitive networks in order to define network dynamics during motor execution and motor imagery in healthy individuals. Second, we analyzed the differences in effective connectivity between correct and incorrect responses during motor execution and imagery using dynamic causal modeling (DCM) of electroencephalography (EEG) data...
2018: PloS One
https://www.readbyqxmd.com/read/29324649/machine-learning-methods-for-analysis-of-metabolic-data-and-metabolic-pathway-modeling
#14
REVIEW
Miroslava Cuperlovic-Culf
Machine learning uses experimental data to optimize clustering or classification of samples or features, or to develop, augment or verify models that can be used to predict behavior or properties of systems. It is expected that machine learning will help provide actionable knowledge from a variety of big data including metabolomics data, as well as results of metabolism models. A variety of machine learning methods has been applied in bioinformatics and metabolism analyses including self-organizing maps, support vector machines, the kernel machine, Bayesian networks or fuzzy logic...
January 11, 2018: Metabolites
https://www.readbyqxmd.com/read/29323542/the-comparative-efficacy-of-brodalumab-in-patients-with-moderate-to-severe-psoriasis-a-systematic-literature-review-and-network-meta-analysis
#15
Laura Sawyer, Iain Fotheringham, Emily Wright, Najeeda Yasmeen, Carl Gibbons, Anders Holmen Møller
PURPOSE: To evaluate the relative efficacy of brodalumab compared with approved biologic therapies and apremilast for moderate-to-severe psoriasis. METHODS: We searched MEDLINE, Embase and Cochrane for randomized controlled trials reporting induction phase responses. The primary analysis examined the proportion of patients achieving Psoriasis Area Severity Index (PASI) 50, 75, 90 or 100 responses using a random-effects Bayesian multinomial likelihood model with probit link, with and without adjustment for variation in study-level placebo responses...
January 11, 2018: Journal of Dermatological Treatment
https://www.readbyqxmd.com/read/29321854/phylogenetic-relationships-and-phylogeography-of-relevant-lineages-within-the-complex-campanulaceae-family-in-macaronesia
#16
Tiago Menezes, Maria M Romeiras, Miguel M de Sequeira, Mónica Moura
Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29321258/functional-variants-in-the-lrrk2-gene-confer-shared-effects-on-risk-for-crohn-s-disease-and-parkinson-s-disease
#17
Ken Y Hui, Heriberto Fernandez-Hernandez, Jianzhong Hu, Adam Schaffner, Nathan Pankratz, Nai-Yun Hsu, Ling-Shiang Chuang, Shai Carmi, Nicole Villaverde, Xianting Li, Manual Rivas, Adam P Levine, Xiuliang Bao, Philippe R Labrias, Talin Haritunians, Darren Ruane, Kyle Gettler, Ernie Chen, Dalin Li, Elena R Schiff, Nikolas Pontikos, Nir Barzilai, Steven R Brant, Susan Bressman, Adam S Cheifetz, Lorraine N Clark, Mark J Daly, Robert J Desnick, Richard H Duerr, Seymour Katz, Todd Lencz, Richard H Myers, Harry Ostrer, Laurie Ozelius, Haydeh Payami, Yakov Peter, John D Rioux, Anthony W Segal, William K Scott, Mark S Silverberg, Jeffery M Vance, Iban Ubarretxena-Belandia, Tatiana Foroud, Gil Atzmon, Itsik Pe'er, Yiannis Ioannou, Dermot P B McGovern, Zhenyu Yue, Eric E Schadt, Judy H Cho, Inga Peter
Crohn's disease (CD), a form of inflammatory bowel disease, has a higher prevalence in Ashkenazi Jewish than in non-Jewish European populations. To define the role of nonsynonymous mutations, we performed exome sequencing of Ashkenazi Jewish patients with CD, followed by array-based genotyping and association analysis in 2066 CD cases and 3633 healthy controls. We detected association signals in the LRRK2 gene that conferred risk for CD (N2081D variant, P = 9.5 × 10-10) or protection from CD (N551K variant, tagging R1398H-associated haplotype, P = 3...
January 10, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29320496/bayesian-inference-of-phylogenetic-networks-from-bi-allelic-genetic-markers
#18
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M Meudt, Luay Nakhleh
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a powerful source of genome-wide data. In a recent paper, a method called SNAPP was introduced for statistical inference of species trees from unlinked bi-allelic markers...
January 10, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29312831/translating-genomics-into-practice-for-real-time-surveillance-and-response-to-carbapenemase-producing-enterobacteriaceae-evidence-from-a-complex-multi-institutional-kpc-outbreak
#19
Jason C Kwong, Courtney R Lane, Finn Romanes, Anders Gonçalves da Silva, Marion Easton, Katie Cronin, Mary Jo Waters, Takehiro Tomita, Kerrie Stevens, Mark B Schultz, Sarah L Baines, Norelle L Sherry, Glen P Carter, Andre Mu, Michelle Sait, Susan A Ballard, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
Background: Until recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks...
2018: PeerJ
https://www.readbyqxmd.com/read/29311603/attentional-gain-is-modulated-by-probabilistic-feature-expectations-in-a-spatial-cueing-task-erp-evidence
#20
Anna Marzecová, Antonio Schettino, Andreas Widmann, Iria SanMiguel, Sonja A Kotz, Erich Schröger
Several theoretical and empirical studies suggest that attention and perceptual expectations influence perception in an interactive manner, whereby attentional gain is enhanced for predicted stimuli. The current study assessed whether attention and perceptual expectations interface when they are fully orthogonal, i.e., each of them relates to different stimulus features. We used a spatial cueing task with block-wise spatial attention cues that directed attention to either left or right visual field, in which Gabor gratings of either predicted (more likely) or unpredicted (less likely) orientation were presented...
January 8, 2018: Scientific Reports
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