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https://www.readbyqxmd.com/read/29141044/high-dimensional-linear-state-space-models-for-dynamic-microbial-interaction-networks
#1
Iris Chen, Yogeshwar D Kelkar, Yu Gu, Jie Zhou, Xing Qiu, Hulin Wu
Medical researchers are increasingly interested in knowing how the complex community of micro-organisms living on human body impacts human health. Key to this is to understand how the microbes interact with each other. Time-course studies on human microbiome indicate that the composition of microbiome changes over short time periods, primarily as a consequence of synergistic and antagonistic interactions of the members of the microbiome with each other and with the environment. Knowledge of the abundance of bacteria-which are the predominant members of the human microbiome-in such time-course studies along with appropriate mathematical models will allow us to identify key dynamic interaction networks within the microbiome...
2017: PloS One
https://www.readbyqxmd.com/read/29140991/a-bayesian-method-for-detecting-pairwise-associations-in-compositional-data
#2
Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower
Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix...
November 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29133803/microbial-diversity-of-genital-ulcers-of-hsv-2-seropositive-women
#3
Supriya D Mehta, Ashish K Pradhan, Stefan J Green, Ankur Naqib, Elijah Odoyo-June, Charlotte A Gaydos, Sheila Barry, Alan Landay, Robert C Bailey
We measured the microbial community structure of genital ulcers in women. Swabs from clinically detected ulcers were tested for HSV-2 and Treponema pallidum by polymerase chain reaction (PCR). HSV-2 and T. pallidum were detected by serum antibody testing. Microbial community structure was characterized by high-throughput 16 s rRNA gene amplicon sequencing. Multiple group testing and Elastic net and Lasso regressions identified taxa associated with differences in factors of interest. Among 49 ulcer specimens from 49 HSV-2 seropositive women, by PCR HSV-2 was recovered from 28 (57%) specimens and T...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29128344/validity-of-combining-history-elements-and-physical-examination-tests-to-diagnose-patellofemoral-pain
#4
Simon Décary, Pierre Frémont, Bruno Pelletier, Michel Fallaha, Belzile Sylvain, Johanne Martel-Pelletier, Pelletier Jean-Pierre, Debbie Feldman, Sylvestre Marie-Pierre, Pascal-André Vendittoli, François Desmeules
OBJECTIVE: to assess the validity of diagnostic clusters combining history elements and physical examination tests to diagnose or exclude patellofemoral pain (PFP). DESIGN: prospective diagnostic study. SETTINGS: orthopaedic outpatients clinics (n=2), family medicine clinics (n=2) and community-dwelling. PARTICIPANTS: consecutive patients (n=279) consulting one of the participating orthopaedic surgeons (n=3) or sport medicine physicians (n=2) for any knee complaint...
November 8, 2017: Archives of Physical Medicine and Rehabilitation
https://www.readbyqxmd.com/read/29126115/hominid-a-framework-for-identifying-associations-between-host-genetic-variation-and-microbiome-composition
#5
Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host SNPs that are correlated with microbial taxa abundances. Using simulated data we show that HOMINID has accuracy in identifying associated SNPs, and performs better compared to existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs...
November 8, 2017: GigaScience
https://www.readbyqxmd.com/read/29125989/prediction-of-mortality-risk-in-victims-of-violent-crimes
#6
Rolf Gedeborg, Bodil Svennblad, Liisa Byberg, Karl Michaëlsson, Ingemar Thiblin
BACKGROUND: To predict mortality risk in victims of violent crimes based on individual injury diagnoses and other information available in health care registries. METHODS: Data from the Swedish hospital discharge registry and the cause of death registry were combined to identify 15,000 hospitalisations or prehospital deaths related to violent crimes. The ability of patient characteristics, injury type and severity, and cause of injury to predict death was modelled using conventional, Lasso, or Bayesian logistic regression in a development dataset and evaluated in a validation dataset...
October 20, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29125957/a-network-perspective-on-comorbid-depression-in-adolescents-with-obsessive-compulsive-disorder
#7
Payton J Jones, Patrick Mair, Bradley C Riemann, Beth L Mugno, Richard J McNally
People with obsessive-compulsive disorder [OCD] frequently suffer from depression, a comorbidity associated with greater symptom severity and suicide risk. We examined the associations between OCD and depression symptoms in 87 adolescents with primary OCD. We computed an association network, a graphical LASSO, and a directed acyclic graph (DAG) to model symptom interactions. Models showed OCD and depression as separate syndromes linked by bridge symptoms. Bridges between the two disorders emerged between obsessional problems in the OCD syndrome, and guilt, concentration problems, and sadness in the depression syndrome...
November 2, 2017: Journal of Anxiety Disorders
https://www.readbyqxmd.com/read/29111463/diagnostic-validity-of-combining-history-elements-and-physical-examination-tests-for-traumatic-and-degenerative-symptomatic-meniscal-tears
#8
Simon Décary, Michel Fallaha, Pierre Frémont, Johanne Martel-Pelletier, Jean-Pierre Pelletier, Debbie Feldman, Marie-Pierre Sylvestre, Pascal-André Vendittoli, François Desmeules
BACKGROUND: Current approach to the clinical diagnosis of traumatic and degenerative symptomatic meniscal tears (SMT) propose combining history elements and physical examination tests without systematic prescription of imaging investigations, yet the evidence to support this diagnostic approach is scarce. OBJECTIVE: To assess the validity of diagnostic clusters combining history elements and physical examination tests to diagnose or exclude traumatic and degenerative SMT compared to other knee disorders...
October 27, 2017: PM & R: the Journal of Injury, Function, and Rehabilitation
https://www.readbyqxmd.com/read/29109667/health-system-reform-plan-and-performance-of-hospitals-an-iranian-case-study
#9
Yusefzadeh Hasan, Salem Safi Parviz, Nabilou Bahram
Background: Health system reform is essential to make desired Changes. In Iran, first phase of Health Reform Plan (HRP) was implemented in hospitals affiliated with Ministry of Health and Medical Education (MHME) in 2014. Aim: The present study was carried out to evaluate the performance of hospitals affiliated with Urmia University of Medical Sciences at the time of the implementation of HRP. Methods: This cross-sectional study carried out in two stages, before (2012- 2013) and during (2014- 2015) implementation of the HRP in district and teaching hospitals...
September 2017: Materia Socio-medica
https://www.readbyqxmd.com/read/29107999/association-between-biomarkers-and-clinical-characteristics-in-chronic-subdural-hematoma-patients-assessed-with-lasso-regression
#10
Are Hugo Pripp, Milo Stanišić
Chronic subdural hematoma (CSDH) is characterized by an "old" encapsulated collection of blood and blood breakdown products between the brain and its outermost covering (the dura). Recognized risk factors for development of CSDH are head injury, old age and using anticoagulation medication, but its underlying pathophysiological processes are still unclear. It is assumed that a complex local process of interrelated mechanisms including inflammation, neomembrane formation, angiogenesis and fibrinolysis could be related to its development and propagation...
2017: PloS One
https://www.readbyqxmd.com/read/29104964/a-machine-learning-algorithm-for-identifying-atopic-dermatitis-in-adults-from-electronic-health-records
#11
Erin Gustafson, Jennifer Pacheco, Firas Wehbe, Jonathan Silverberg, William Thompson
The current work aims to identify patients with atopic dermatitis for inclusion in genome-wide association studies (GWAS). Here we describe a machine learning-based phenotype algorithm. Using the electronic health record (EHR), we combined coded information with information extracted from encounter notes as features in a lasso logistic regression. Our algorithm achieves high positive predictive value (PPV) and sensitivity, improving on previous algorithms with low sensitivity. These results demonstrate the utility of natural language processing (NLP) and machine learning for EHR-based phenotyping...
August 2017: IEEE International Conference on Healthcare Informatics IEEE International Conference on Healthcare Informatics
https://www.readbyqxmd.com/read/29100117/csp-tsm-optimizing-the-performance-of-riemannian-tangent-space-mapping-using-common-spatial-pattern-for-mi-bci
#12
Shiu Kumar, Kabir Mamun, Alok Sharma
BACKGROUND: Classification of electroencephalography (EEG) signals for motor imagery based brain computer interface (MI-BCI) is an exigent task and common spatial pattern (CSP) has been extensively explored for this purpose. In this work, we focused on developing a new framework for classification of EEG signals for MI-BCI. METHOD: We propose a single band CSP framework for MI-BCI that utilizes the concept of tangent space mapping (TSM) in the manifold of covariance matrices...
October 24, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29098645/neurocognitive-graphs-of-first-episode-schizophrenia-and-major-depression-based-on-cognitive-features
#13
Sugai Liang, Roberto Vega, Xiangzhen Kong, Wei Deng, Qiang Wang, Xiaohong Ma, Mingli Li, Xun Hu, Andrew J Greenshaw, Russell Greiner, Tao Li
Neurocognitive deficits are frequently observed in patients with schizophrenia and major depressive disorder (MDD). The relations between cognitive features may be represented by neurocognitive graphs based on cognitive features, modeled as Gaussian Markov random fields. However, it is unclear whether it is possible to differentiate between phenotypic patterns associated with the differential diagnosis of schizophrenia and depression using this neurocognitive graph approach. In this study, we enrolled 215 first-episode patients with schizophrenia (FES), 125 with MDD, and 237 demographically-matched healthy controls (HCs)...
November 2, 2017: Neuroscience Bulletin
https://www.readbyqxmd.com/read/29096792/targeted-metabolomic-profiling-of-plasma-and-survival-in-heart-failure-patients
#14
David E Lanfear, Joseph J Gibbs, Jia Li, Ruicong She, Christopher Petucci, Jeffrey A Culver, W H Wilson Tang, Yigal M Pinto, L Keoki Williams, Hani N Sabbah, Stephen J Gardell
OBJECTIVES: This study sought to derive and validate plasma metabolite associations with survival in heart failure (HF) patients. BACKGROUND: Profiling of plasma metabolites to predict the course of HF appears promising, but validation and incremental value of these profiles are less established. METHODS: Patients (n = 1,032) who met Framingham HF criteria with a history of reduced ejection fraction were randomly divided into derivation and validation cohorts (n = 516 each)...
November 2017: JACC. Heart Failure
https://www.readbyqxmd.com/read/29096036/data-driven-confounder-selection-via-markov-and-bayesian-networks
#15
Jenny Häggström
To unbiasedly estimate a causal effect on an outcome unconfoundedness is often assumed. If there is sufficient knowledge on the underlying causal structure then existing confounder selection criteria can be used to select subsets of the observed pretreatment covariates, X, sufficient for unconfoundedness, if such subsets exist. Here, estimation of these target subsets is considered when the underlying causal structure is unknown. The proposed method is to model the causal structure by a probabilistic graphical model, for example, a Markov or Bayesian network, estimate this graph from observed data and select the target subsets given the estimated graph...
November 2, 2017: Biometrics
https://www.readbyqxmd.com/read/29095651/factors-associated-with-vitamin-d-testing-deficiency-intake-and-supplementation-in-patients-with-chronic-pain
#16
Manasi Gaikwad, Simon Vanlint, G Lorimer Moseley, Murthy N Mittinty, Nigel Stocks
Vitamin D deficiency is a public health issue, with reports of six- to twenty-five-fold rise in vitamin D testing. Vitamin D deficiency has been linked to many chronic diseases such as diabetes mellitus, cardiovascular disease, depression, and chronic pain. Identifying factors associated with risk of deficiency in individuals with chronic pain will help minimize time and cost. This study aims to examine the factors associated with vitamin D testing, intake, and physician-advised supplementation in individuals with chronic pain...
November 2, 2017: Journal of Dietary Supplements
https://www.readbyqxmd.com/read/29095620/resolving-transition-metal-chemical-space-feature-selection-for-machine-learning-and-structure-property-relationships
#17
Jon Paul Janet, Heather J Kulik
Machine learning (ML) of quantum mechanical properties shows promise for accelerating chemical discovery. For transition metal chemistry where accurate calculations are computationally costly and available training data sets are small, the molecular representation becomes a critical ingredient in ML model predictive accuracy. We introduce a series of revised autocorrelation functions (RACs) that encode relationships between the heuristic atomic properties (e.g., size, connectivity, and electronegativity) on a molecular graph...
November 2, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29094006/neuropathic-pain-like-symptoms-and-pre-surgery-radiographic-severity-contribute-to-patient-satisfaction-4-8-years-post-total-joint-replacement
#18
Sophie C Warner, Helen Richardson, Wendy Jenkins, Thomas Kurien, Michael Doherty, Ana M Valdes
AIM: To investigate a comprehensive range of factors that contribute to long-term patient satisfaction post-total joint replacement (TJR) in people who had undergone knee or hip replacement for osteoarthritis. METHODS: Participants (n = 1151) were recruited from Nottinghamshire post-total hip or knee replacement. Questionnaire assessment included medication use, the pain-DETECT questionnaire (PDQ) to assess neuropathic pain-like symptoms (NP) and TJR satisfaction measured on average 4...
October 18, 2017: World Journal of Orthopedics
https://www.readbyqxmd.com/read/29092948/dcmqi-an-open-source-library-for-standardized-communication-of-quantitative-image-analysis-results-using-dicom
#19
Christian Herz, Jean-Christophe Fillion-Robin, Michael Onken, Jörg Riesmeier, Andras Lasso, Csaba Pinter, Gabor Fichtinger, Steve Pieper, David Clunie, Ron Kikinis, Andriy Fedorov
Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29091799/molecular-classification-substitutes-for-the-prognostic-variables-stage-age-and-mycn-status-in-neuroblastoma-risk-assessment
#20
Carolina Rosswog, Rene Schmidt, André Oberthuer, Dilafruz Juraeva, Benedikt Brors, Anne Engesser, Yvonne Kahlert, Ruth Volland, Christoph Bartenhagen, Thorsten Simon, Frank Berthold, Barbara Hero, Andreas Faldum, Matthias Fischer
BACKGROUND: Current risk stratification systems for neuroblastoma patients consider clinical, histopathological, and genetic variables, and additional prognostic markers have been proposed in recent years. We here sought to select highly informative covariates in a multistep strategy based on consecutive Cox regression models, resulting in a risk score that integrates hazard ratios of prognostic variables. METHODS: A cohort of 695 neuroblastoma patients was divided into a discovery set (n=75) for multigene predictor generation, a training set (n=411) for risk score development, and a validation set (n=209)...
October 26, 2017: Neoplasia: An International Journal for Oncology Research
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