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Computable phenotype

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https://www.readbyqxmd.com/read/28648836/cortical-and-trabecular-bone-analysis-of-patients-with-high-bone-mass-from-the-barcelona-osteoporosis-cohort-using-3-dimensional-dual-energy-x-ray-absorptiometry-a-case-control-study
#1
Guillermina Orduna, Ludovic Humbert, Roger Fonolla, Jordi Romera, M Lourdes Cos, Aboro Rial, Xavier Nogués, Adolfo Diez-Perez, Leonardo Mellibovsky
High bone mass (HBM), a rare phenotype, can be detected by dual-energy X-ray absorptiometry (DXA) scanning. Measurements with peripheral quantitative computed tomography at the tibia have found increased trabecular bone mineral density and changes in cortical bone density and structure, all of which lead to increased bone strength. However, no studies on cortical and trabecular bone have been performed at the femur. The recently developed 3-dimensional (3D)-DXA software algorithm quantifies the trabecular and cortical volumetric bone mineral density (vBMD) and the anatomical distribution of cortical thickness using routine hip DXA scans...
June 22, 2017: Journal of Clinical Densitometry
https://www.readbyqxmd.com/read/28647206/ct-at-onset-of-chronic-lung-allograft-dysfunction-in-lung-transplant-patients-predicts-development-of-the-restrictive-phenotype-and-survival
#2
Sabine Dettmer, Hoen-Oh Shin, Jens Vogel-Claussen, Max Westphal, Axel Haverich, Gregor Warnecke, Tobias Welte, Frank Wacker, Jens Gottlieb, Hendrik Suhling
PURPOSE: To describe early signs for restrictive subtype of chronic lung allograft dysfunction (CLAD) after lung transplantation in computed tomography (CT) and to evaluate the predictive value for disease progression and survival. MATERIAL AND METHODS: 52 CT examinations in lung transplant patients at CLAD onset were scored for CT features referring to airways disease, parenchymal or pleural abnormality. Patients with and without later development of restrictive CLAD (TLC≤80%) were compared...
June 15, 2017: European Journal of Radiology
https://www.readbyqxmd.com/read/28646471/decoding-early-myelopoiesis-from-dynamics-of-core-endogenous-network
#3
Hang Su, Gaowei Wang, Ruoshi Yuan, Junqiang Wang, Ying Tang, Ping Ao, Xiaomei Zhu
A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained...
May 29, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28645698/radiological-studies-of-fetal-alcohol-spectrum-disorders-in-humans-and-animal-models-an-updated-comprehensive-review
#4
Van T Nguyen, Suyinn Chong, Quang M Tieng, Karine Mardon, Graham J Galloway, Nyoman D Kurniawan
Fetal Alcohol Spectrum Disorders encompass a wide range of birth defects in children born to mothers who consumed alcohol during pregnancy. Typical mental impairments in FASD include difficulties in life adaptation and learning and memory, deficits in attention, visuospatial skills, language and speech disabilities, mood disorders and motor disabilities. Multimodal imaging methods have enabled in vivo studies of the teratogenic effects of alcohol on the central nervous system, giving more insight into the FASD phenotype...
June 20, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28645207/development-and-validation-of-an-electronic-medical-record-emr-based-computed-phenotype-of-hiv-1-infection
#5
Devon W Paul, Nigel B Neely, Meredith Clement, Isaretta Riley, Mashael Al-Hegelan, Matthew Phelan, Monica Kraft, David M Murdoch, Joseph Lucas, John Bartlett, Mehri McKellar, Loretta G Que
Background: Electronic medical record (EMR) computed algorithms allow investigators to screen thousands of patient records to identify specific disease cases. No computed algorithms have been developed to detect all cases of human immunodeficiency virus (HIV) infection using administrative, laboratory, and clinical documentation data outside of the Veterans Health Administration. We developed novel EMR-based algorithms for HIV detection and validated them in a cohort of subjects in the Duke University Health System (DUHS)...
June 22, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28642364/the-accuracy-and-bias-of-single-step-genomic-prediction-for-populations-under-selection
#6
Wan-Ling Hsu, Dorian J Garrick, Rohan Luigi Fernando
In single-step analyses, missing genotypes are explicitly or implicitly imputed, and this requires centering the observed genotypes, using the means of the unselected founders. If genotypes are only available on selected individuals, centering on the unselected founder mean is not straightforward. Here, computer simulation is used to study an alternative analysis that does not require centering genotypes but fits the mean μg of unselected individuals as a fixed effect. Centering the entire matrix of observed and imputed genotypes using their sample means can be done to improve numerical properties of the analysis, in addition to fitting μg...
June 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28642271/powerful-genetic-association-analysis-for-common-or-rare-variants-with-high-dimensional-structured-traits
#7
Xiang Zhan, Ni Zhao, Anna Plantinga, Timothy A Thornton, Karen N Conneely, Michael P Epstein, Michael C Wu
Many genetic association studies collect a wide range of complex traits. As these traits may be correlated and share a common genetic mechanism, joint analysis can be statistically more powerful and biologically more meaningful. However, most existing tests for multiple traits cannot be used for high-dimensional and possibly structured traits, such as network-structured transcriptomic pathway expressions. To overcome potential limitations, in this paper we propose the dual kernel-based association test (DKAT) for testing the association between multiple traits and multiple genetic variants, both common and rare...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28637421/a-novel-pathway-based-distance-score-enhances-assessment-of-disease-heterogeneity-in-gene-expression
#8
Xiting Yan, Anqi Liang, Jose Gomez, Lauren Cohn, Hongyu Zhao, Geoffrey L Chupp
BACKGROUND: Distance based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and relatively high correlation between genes are often encountered, so traditional distances such as Euclidean distance may not be effective at discriminating the biological differences between samples. An alternative method to examine disease phenotypes is to use pre-defined biological pathways. These pathways have been shown to be perturbed in different ways in different subjects who have similar clinical features...
June 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28635495/analysis-of-audiometric-notch-as-a-noise-induced-hearing-loss-phenotype-in-us-youth-data-from-the-national-health-and-nutrition-examination-survey-2005-2010
#9
Ishan S Bhatt, O'neil Guthrie
OBJECTIVE: Bilateral audiometric notch (BN) at 4000-6000 Hz was identified as a noise-induced hearing loss (NIHL) phenotype for genetic association analysis in college-aged musicians. This study analysed BN in a sample of US youth. DESIGN: Prevalence of the BN within the study sample was determined and logistic-regression analyses were performed to identify audiologic and other demographic factors associated with BN. Computer-simulated "flat" audiograms were used to estimate potential influence of false-positive rates in estimating the prevalence of the BN...
February 8, 2017: International Journal of Audiology
https://www.readbyqxmd.com/read/28633344/pheno4j-a-gene-to-phenotype-graph-database
#10
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
Summary: Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632201/advantageous-developmental-outcomes-of-advancing-paternal-age
#11
M Janecka, F Rijsdijk, D Rai, A Modabbernia, A Reichenberg
Advanced paternal age (APA) at conception has been associated with negative outcomes in offspring, raising concerns about increasing age at fatherhood. Evidence from evolutionary and psychological research, however, suggests possible link between APA and a phenotypic advantage. We defined such advantage as educational success, which is positively associated with future socioeconomic status. We hypothesised that high IQ, strong focus on the subject of interest and little concern about 'fitting in' will be associated with such success...
June 20, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28631404/structural-connectivity-differences-in-motor-network-between-tremor-dominant-and-nontremor-parkinson-s-disease
#12
Gaetano Barbagallo, Maria Eugenia Caligiuri, Gennarina Arabia, Andrea Cherubini, Angela Lupo, Rita Nisticò, Maria Salsone, Fabiana Novellino, Maurizio Morelli, Giuseppe Lucio Cascini, Domenico Galea, Aldo Quattrone
Motor phenotypes of Parkinson's disease (PD) are recognized to have different prognosis and therapeutic response, but the neural basis for this clinical heterogeneity remains largely unknown. The main aim of this study was to compare differences in structural connectivity metrics of the main motor network between tremor-dominant and nontremor PD phenotypes (TD-PD and NT-PD, respectively) using probabilistic tractography-based network analysis. A total of 63 PD patients (35 TD-PD patients and 28 NT-PD patients) and 30 healthy controls underwent a 3 T MRI...
June 20, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28631251/regulation-of-cardiac-myocyte-cell-death-and-differentiation-by-myocardin
#13
REVIEW
Joseph W Gordon
Myocardin is a cardiac- and smooth muscle-enriched transcriptional co-activator that was originally described as an interacting partner of the serum response factor. Shortly after myocardin's discovery, a wealth of published literature described the role of myocardin as a regulator of smooth muscle differentiation and phenotype modulation, while gene-targeting studies confirmed the essential role of myocardin in vascular development. More recently, myocardin has been implicated as an important regulator of cardiac myocyte differentiation in studies demonstrating direct programming of fibroblasts towards the cardiac lineage...
June 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28628708/brain-calcifications-in-adult-onset-genetic-leukoencephalopathies-a-review
#14
Xavier Ayrignac, Gaël Nicolas, Clarisse Carra-Dallière, Didier Hannequin, Pierre Labauge
Importance: Adult-onset genetic leukoencephalopathies and leukodystrophies are increasingly recognized as a heterogeneous group of disorders with new diagnostic approaches and potential treatments. In the new era of genomics, the challenging interpretation of individual genetic variations requires an accurate phenotypic description and classification. Clinical and magnetic resonance imaging (MRI)-based approaches have been proposed to improve the diagnostic process of adult-onset leukoencephalopathies...
June 19, 2017: JAMA Neurology
https://www.readbyqxmd.com/read/28628421/high-grade-serous-ovarian-cancer-associations-between-brca-mutation-status-ct-imaging-phenotypes-and-clinical-outcomes
#15
Stephanie Nougaret, Yulia Lakhman, Mithat Gönen, Debra A Goldman, Maura Miccò, Melvin D'Anastasi, Sarah A Johnson, Krishna Juluru, Angela G Arnold, Ramon E Sosa, Robert A Soslow, Hebert Alberto Vargas, Hedvig Hricak, Noah D Kauff, Evis Sala
Purpose To investigate the associations between BRCA mutation status and computed tomography (CT) phenotypes of high-grade serous ovarian cancer (HGSOC) and to evaluate CT indicators of cytoreductive outcome and survival in patients with BRCA-mutant HGSOC and those with BRCA wild-type HGSOC. Materials and Methods This HIPAA-compliant, institutional review board-approved retrospective study included 108 patients (33 with BRCA mutant and 75 with BRCA wild-type HGSOC) who underwent CT before primary debulking...
June 16, 2017: Radiology
https://www.readbyqxmd.com/read/28625502/a-computable-phenotype-improves-cohort-ascertainment-in-a-pediatric-pulmonary-hypertension-registry
#16
Alon Geva, Jessica L Gronsbell, Tianxi Cai, Tianrun Cai, Shawn N Murphy, Jessica C Lyons, Michelle M Heinz, Marc D Natter, Nandan Patibandla, Jonathan Bickel, Mary P Mullen, Kenneth D Mandl
OBJECTIVES: To compare registry and electronic health record (EHR) data mining approaches for cohort ascertainment in patients with pediatric pulmonary hypertension (PH) in an effort to overcome some of the limitations of registry enrollment alone in identifying patients with particular disease phenotypes. STUDY DESIGN: This study was a single-center retrospective analysis of EHR and registry data at Boston Children's Hospital. The local Informatics for Integrating Biology and the Bedside (i2b2) data warehouse was queried for billing codes, prescriptions, and narrative data related to pediatric PH...
June 15, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28616054/an-investigation-on-non-invasive-fungal-sinusitis-molecular-identification-of-etiologic-agents
#17
Abdolrasoul Mohammadi, Seyed Mostafa Hashemi, Sayed Hamidreza Abtahi, Seyed Mohammad Lajevardi, Sahar Kianipour, Rasoul Mohammadi
BACKGROUND: Fungal sinusitis is increasing worldwide in the past two decades. It is divided into two types including invasive and noninvasive. Noninvasive types contain allergic fungal sinusitis (AFS) and fungus ball. AFS is a hypersensitivity reaction to fungal allergens in the mucosa of the sinonasal tract in atopic individuals. The fungus ball is a different type of noninvasive fungal rhinosinusitis which is delineated as an accumulation of debris and fungal elements inside a paranasal sinus...
2017: Journal of Research in Medical Sciences: the Official Journal of Isfahan University of Medical Sciences
https://www.readbyqxmd.com/read/28615899/clinical-and-imaging-study-of-isolated-and-mixed-rest-and-action-tremor-essential-tremor-versus-parkinson-s-disease
#18
Sandro Zambito Marsala, Michele Pistacchi, Manuela Gioulis, Franco Ferracci, Livio Capus
BACKGROUND: Some patients present an unusual association of both action tremor (AT) and rest tremor (RT) making the differential diagnosis between essential tremor (ET) and Parkinson's disease (PD) difficult. AIM: To investigate this particular clinical picture trying to focus on possible peculiar clinical inferences. PATIENTS AND METHODS: Twenty-three patients with atypical tremor syndrome were selected for the study. They underwent neurological examination, neuroimaging study, and brain DaTSCAN single-photon emission computed tomography...
April 2017: Annals of Indian Academy of Neurology
https://www.readbyqxmd.com/read/28615677/associations-between-radiologist-defined-semantic-and-automatically-computed-radiomic-features-in-non-small-cell-lung-cancer
#19
Stephen S F Yip, Ying Liu, Chintan Parmar, Qian Li, Shichang Liu, Fangyuan Qu, Zhaoxiang Ye, Robert J Gillies, Hugo J W L Aerts
Tumor phenotypes captured in computed tomography (CT) images can be described qualitatively and quantitatively using radiologist-defined "semantic" and computer-derived "radiomic" features, respectively. While both types of features have shown to be promising predictors of prognosis, the association between these groups of features remains unclear. We investigated the associations between semantic and radiomic features in CT images of 258 non-small cell lung adenocarcinomas. The tumor imaging phenotypes were described using 9 qualitative semantic features that were scored by radiologists, and 57 quantitative radiomic features that were automatically calculated using mathematical algorithms...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611425/pancreatic-adenocarcinoma-response-to-chemotherapy-enhanced-with-non-invasive-radio-frequency-evaluated-via-an-integrated-experimental-computational-approach
#20
Matthew J Ware, Louis T Curtis, Min Wu, Jason C Ho, Stuart J Corr, Steven A Curley, Biana Godin, Hermann B Frieboes
Although chemotherapy combined with radiofrequency exposure has shown promise in cancer treatment by coupling drug cytotoxicity with thermal ablation or thermally-induced cytotoxicity, limited access of the drug to tumor loci in hypo-vascularized lesions has hampered clinical application. We recently showed that high-intensity short-wave capacitively coupled radiofrequency (RF) electric-fields may reach inaccessible targets in vivo. This non-invasive RF combined with gemcitabine (Gem) chemotherapy enhanced drug uptake and effect in pancreatic adenocarcinoma (PDAC), notorious for having poor response and limited therapeutic options, but without inducing thermal injury...
June 13, 2017: Scientific Reports
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