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https://www.readbyqxmd.com/read/28812906/recent-advances-in-ct-imaging-in-chronic-obstructive-pulmonary-disease
#1
Sandeep Bodduluri, Joseph M Reinhardt, Eric A Hoffman, John D Newell, Surya P Bhatt
Lung imaging is increasingly being used to diagnose, quantify and phenotype chronic obstructive pulmonary disease (COPD). Although spirometry is the gold standard for the diagnosis of COPD and for severity staging, the role of computed tomography (CT) imaging has expanded in both clinical practice and research. COPD is a heterogeneous disease with considerable variability in clinical features, radiographic disease, progression and outcomes. Recent studies have examined the utility of CT imaging in enhancing diagnostic certainty, improving phenotyping, predicting disease progression and prognostication, patient selection for intervention, and also in furthering our understanding of the complex pathophysiology of this disease...
August 16, 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/28812537/leveraging-network-analytics-to-infer-patient-syndrome-and-identify-causal-genes-in-rare-disease-cases
#2
Andreas Krämer, Sohela Shah, Robert Anthony Rebres, Susan Tang, Daniel Rene Richards
BACKGROUND: Next-generation sequencing is widely used to identify disease-causing variants in patients with rare genetic disorders. Identifying those variants from whole-genome or exome data can be both scientifically challenging and time consuming. A significant amount of time is spent on variant annotation, and interpretation. Fully or partly automated solutions are therefore needed to streamline and scale this process. RESULTS: We describe Phenotype Driven Ranking (PDR), an algorithm integrated into Ingenuity Variant Analysis, that uses observed patient phenotypes to prioritize diseases and genes in order to expedite causal-variant discovery...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28812536/edgar-a-database-of-disease-gene-associations-with-annotated-relationships-among-genes
#3
Giulia Babbi, Pier Luigi Martelli, Giuseppe Profiti, Samuele Bovo, Castrense Savojardo, Rita Casadio
BACKGROUND: Genetic investigations, boosted by modern sequencing techniques, allow dissecting the genetic component of different phenotypic traits. These efforts result in the compilation of lists of genes related to diseases and show that an increasing number of diseases is associated with multiple genes. Investigating functional relations among genes associated with the same disease contributes to highlighting molecular mechanisms of the pathogenesis. RESULTS: We present eDGAR, a database collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28812535/associating-mutations-causing-cystinuria-with-disease-severity-with-the-aim-of-providing-precision-medicine
#4
Henry J Martell, Kathie A Wong, Juan F Martin, Ziyan Kassam, Kay Thomas, Mark N Wass
BACKGROUND: Cystinuria is an inherited disease that results in the formation of cystine stones in the kidney, which can have serious health complications. Two genes (SLC7A9 and SLC3A1) that form an amino acid transporter are known to be responsible for the disease. Variants that cause the disease disrupt amino acid transport across the cell membrane, leading to the build-up of relatively insoluble cystine, resulting in formation of stones. Assessing the effects of each mutation is critical in order to provide tailored treatment options for patients...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28808032/mechanical-constraint-from-growing-jaw-facilitates-mammalian-dental-diversity
#5
Elodie Renvoisé, Kathryn D Kavanagh, Vincent Lazzari, Teemu J Häkkinen, Ritva Rice, Sophie Pantalacci, Isaac Salazar-Ciudad, Jukka Jernvall
Much of the basic information about individual organ development comes from studies using model species. Whereas conservation of gene regulatory networks across higher taxa supports generalizations made from a limited number of species, generality of mechanistic inferences remains to be tested in tissue culture systems. Here, using mammalian tooth explants cultured in isolation, we investigate self-regulation of patterning by comparing developing molars of the mouse, the model species of mammalian research, and the bank vole...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807238/unravelling-the-complexity-of-signalling-networks-in-cancer-a-review-of-the-increasing-role-for-computational-modelling
#6
REVIEW
John Garland
Cancer induction is a highly complex process involving hundreds of different inducers but whose eventual outcome is the same. Clearly, it is essential to understand how signalling pathways and networks generated by these inducers interact to regulate cell behaviour and create the cancer phenotype. While enormous strides have been made in identifying key networking profiles, the amount of data generated far exceeds our ability to understand how it all "fits together". The number of potential interactions is astronomically large and requires novel approaches and extreme computation methods to dissect them out...
September 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28806730/a-systems-approach-reveals-distinct-metabolic-strategies-among-the-nci-60-cancer-cell-lines
#7
Maike K Aurich, Ronan M T Fleming, Ines Thiele
The metabolic phenotype of cancer cells is reflected by the metabolites they consume and by the byproducts they release. Here, we use quantitative, extracellular metabolomic data of the NCI-60 panel and a novel computational method to generate 120 condition-specific cancer cell line metabolic models. These condition-specific cancer models used distinct metabolic strategies to generate energy and cofactors. The analysis of the models' capability to deal with environmental perturbations revealed three oxotypes, differing in the range of allowable oxygen uptake rates...
August 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28805917/technical-note-impact-of-pedigree-depth-on-convergence-of-single-step-genomic-blup-in-a-purebred-swine-population
#8
I Pocrnic, D A L Lourenco, H L Bradford, C Y Chen, I Misztal
In genomic evaluations, it is desirable to have low computing cost while retaining high accuracy of evaluation for young animals. When the population is large but only few animals have phenotypes, especially for low heritability traits, the convergence rate of BLUP or single-step genomic BLUP (ssGBLUP) can be very slow. This study investigates the effect of pedigree truncation on convergence rate and solutions of ssGBLUP for data exhibiting slow convergence. The data consisted of 216,000, 221,000, 732,000, and 579,000 phenotypes on 4 traits...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28805044/nm%C3%AF-improved-re-implementation-of-nm-a-software-for-estimating-gene-dispersal-and-mating-patterns
#9
Igor J Chybicki
This paper introduces the NMπ computer program designed for estimation of plant mating system and seed and pollen dispersal kernels. NMπ is a re-implementation of the NM+ program and provides new features such as support for multi-core processors, explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighborhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system...
August 14, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28793223/constraint-and-contingency-pervade-the-emergence-of-novel-phenotypes-in-complex-metabolic-systems
#10
Sayed-Rzgar Hosseini, Andreas Wagner
An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. We know examples of such constraints, but we have no systematic understanding about their extent and causes for any one biological system. We here study metabolisms, genomically encoded complex networks of enzyme-catalyzed biochemical reactions, and the constraints they experience in bringing forth novel phenotypes that allow survival on novel carbon sources. Our computational approach does not limit us to analyzing constrained variation in any one organism, but allows us to quantify constraints experienced by any metabolism...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28792758/profiling-of-microbial-colonies-for-high-throughput-engineering-of-multi-step-enzymatic-reactions-via-optically-guided-maldi-ms
#11
Tong Si, Bin Li, Troy J Comi, Yuwei Wu, Pingfan Hu, Yuying Wu, Yuhao Min, Douglas A Mitchell, Huimin Zhao, Jonathan V Sweedler
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) imaging has been used for rapid phenotyping of enzymatic activities, but is mainly limited to single-step conversions. Herein we report a label-free method for high-throughput engineering of multi-step biochemical reactions based on optically guided MALDI-ToF MS analysis of bacterial colonies. The bacterial cells provide containment of multiple enzymes and access to substrates and cofactors via metabolism. Automated MALDI-ToF MS acquisition from randomly distributed colonies simplifies procedures to prepare strain libraries without liquid handling...
August 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28792442/complex-determinants-of-epithelial-mesenchymal-phenotypic-plasticity-in-ovarian-cancer
#12
REVIEW
Yuliya Klymenko, Oleg Kim, M Sharon Stack
Unlike most epithelial malignancies which metastasize hematogenously, metastasis of epithelial ovarian cancer (EOC) occurs primarily via transcoelomic dissemination, characterized by exfoliation of cells from the primary tumor, avoidance of detachment-induced cell death (anoikis), movement throughout the peritoneal cavity as individual cells and multi-cellular aggregates (MCAs), adhesion to and disruption of the mesothelial lining of the peritoneum, and submesothelial matrix anchoring and proliferation to generate widely disseminated metastases...
August 9, 2017: Cancers
https://www.readbyqxmd.com/read/28783155/histocat-analysis-of-cell-phenotypes-and-interactions-in-multiplex-image-cytometry-data
#13
Denis Schapiro, Hartland W Jackson, Swetha Raghuraman, Jana R Fischer, Vito R T Zanotelli, Daniel Schulz, Charlotte Giesen, Raúl Catena, Zsuzsanna Varga, Bernd Bodenmiller
Single-cell, spatially resolved omics analysis of tissues is poised to transform biomedical research and clinical practice. We have developed an open-source, computational histology topography cytometry analysis toolbox (histoCAT) to enable interactive, quantitative, and comprehensive exploration of individual cell phenotypes, cell-cell interactions, microenvironments, and morphological structures within intact tissues. We highlight the unique abilities of histoCAT through analysis of highly multiplexed mass cytometry images of human breast cancer tissues...
August 7, 2017: Nature Methods
https://www.readbyqxmd.com/read/28777478/a-simplified-method-of-calculating-cpra-for-kidney-allocation-application-in-hong-kong
#14
Yuen Piu Chan, Monica Wing Kan Wong, Lydia Wing Mui Tang, Mengbiao Guo, Wanling Yang, Patrick Ip, Philip Kam Tao Li, Chi Bon Leung, Ka Foon Chau, Johnny Chi Kwong Lam, Nicholas Ka Ming Yeung, Janette Siu Yin Kwok
Calculated panel reactive antibody (cPRA) represents possibility of encountering an incompatible donor for organ transplant candidates, and has gradually replaced traditional PRA as a measurement of sensitization level. We tested two cPRA calculation methods on a cohort of renal candidate (n=613). HLA typing of 563 Chinese deceased renal donors were used to estimate allele and haplotype frequencies of Hong Kong donor pool. The OPTN formula was adopted to generate cPRA (cPRA(freq)). We also incorporated a computer script to compare unacceptable antigens of patients against HLA phenotype of donors...
August 4, 2017: Transplant International: Official Journal of the European Society for Organ Transplantation
https://www.readbyqxmd.com/read/28775673/the-image-data-resource-a-bioimage-data-integration-and-publication-platform
#15
Eleanor Williams, Josh Moore, Simon W Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Bálint Antal, Richard K Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E Carazo Salas, Jason R Swedlow
Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links data from several imaging modalities, including high-content screening, super-resolution and time-lapse microscopy, digital pathology, public genetic or chemical databases, and cell and tissue phenotypes expressed using controlled ontologies...
August 2017: Nature Methods
https://www.readbyqxmd.com/read/28774469/thalamic-neurometabolic-alterations-in-tremulous-parkinson-s-disease-a-preliminary-proton-mr-spectroscopy-study
#16
Gaetano Barbagallo, Gennarina Arabia, Maurizio Morelli, Rita Nisticò, Fabiana Novellino, Maria Salsone, Federico Rocca, Andrea Quattrone, Manuela Caracciolo, Umberto Sabatini, Andrea Cherubini, Aldo Quattrone
INTRODUCTION: The objective of this study was to investigate the thalamic biochemical changes in tremor-dominant Parkinson's disease (tPD) patients in comparison with essential tremor with resting tremor (rET) patients, by using proton MR spectroscopy ((1)H-MRS). METHODS: Fourteen tPD patients, 12 rET patients and 10 controls participated in this study. All patients underwent dopamine transporter single-photon emission computed tomography (DAT-SPECT) with (123)I-ioflupane, and a short-echo single-voxel (1)H-MRS on a 3T scanner...
July 28, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28770004/discovery-and-replication-of-snp-snp-interactions-for-quantitative-lipid-traits-in-over-60-000-individuals
#17
Emily R Holzinger, Shefali S Verma, Carrie B Moore, Molly Hall, Rishika De, Diane Gilbert-Diamond, Matthew B Lanktree, Nathan Pankratz, Antoinette Amuzu, Amber Burt, Caroline Dale, Scott Dudek, Clement E Furlong, Tom R Gaunt, Daniel Seung Kim, Helene Riess, Suthesh Sivapalaratnam, Vinicius Tragante, Erik P A van Iperen, Ariel Brautbar, David S Carrell, David R Crosslin, Gail P Jarvik, Helena Kuivaniemi, Iftikhar J Kullo, Eric B Larson, Laura J Rasmussen-Torvik, Gerard Tromp, Jens Baumert, Karen J Cruickshanks, Martin Farrall, Aroon D Hingorani, G K Hovingh, Marcus E Kleber, Barbara E Klein, Ronald Klein, Wolfgang Koenig, Leslie A Lange, Winfried Mӓrz, Kari E North, N Charlotte Onland-Moret, Alex P Reiner, Philippa J Talmud, Yvonne T van der Schouw, James G Wilson, Mika Kivimaki, Meena Kumari, Jason H Moore, Fotios Drenos, Folkert W Asselbergs, Brendan J Keating, Marylyn D Ritchie
BACKGROUND: The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits: low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC), and triglycerides (TG). RESULTS: Our analysis consisted of a discovery phase using a merged dataset of five different cohorts (n = 12,853 to n = 16,849 depending on lipid phenotype) and a replication phase with ten independent cohorts totaling up to 36,938 additional samples...
2017: BioData Mining
https://www.readbyqxmd.com/read/28769780/automated-functional-analysis-of-astrocytes-from-chronic-time-lapse-calcium-imaging-data
#18
Yinxue Wang, Guilai Shi, David J Miller, Yizhi Wang, Congchao Wang, Gerard Broussard, Yue Wang, Lin Tian, Guoqiang Yu
Recent discoveries that astrocytes exert proactive regulatory effects on neural information processing and that they are deeply involved in normal brain development and disease pathology have stimulated broad interest in understanding astrocyte functional roles in brain circuit. Measuring astrocyte functional status is now technically feasible, due to recent advances in modern microscopy and ultrasensitive cell-type specific genetically encoded Ca(2+) indicators for chronic imaging. However, there is a big gap between the capability of generating large dataset via calcium imaging and the availability of sophisticated analytical tools for decoding the astrocyte function...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28768758/low-endothelial-shear-stress-predicts-evolution-to-high-risk-coronary-plaque-phenotype-in-the-future-a-serial-optical-coherence-tomography-and-computational-fluid-dynamics-study
#19
Erika Yamamoto, Gerasimos Siasos, Marina Zaromytidou, Ahmet U Coskun, Lei Xing, Krzysztof Bryniarski, Thomas Zanchin, Tomoyo Sugiyama, Hang Lee, Peter H Stone, Ik-Kyung Jang
BACKGROUND: Low endothelial shear stress (ESS) is associated with plaque progression and vulnerability. To date, changes in plaque phenotype over time in relation to ESS have not been studied in humans. The aim of this study was to investigate whether local ESS can predict subsequent changes to plaque phenotype using optical coherence tomography. METHODS AND RESULTS: A total of 25 coronary arteries from 20 patients who underwent baseline and 6-month follow-up optical coherence tomography were included...
August 2017: Circulation. Cardiovascular Interventions
https://www.readbyqxmd.com/read/28768687/hit-ndrive-patient-specific-multidriver-gene-prioritization-for-precision-oncology
#20
Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C Collins, S Cenk Sahinalp
Prioritizing molecular alterations that act as drivers of cancer remains a crucial bottleneck in therapeutic development. Here we introduce HIT'nDRIVE, a computational method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence over dysregulated transcripts. HIT'nDRIVE aims to solve the "random walk facility location" (RWFL) problem in a gene (or protein) interaction network, which differs from the standard facility location problem by its use of an alternative distance measure: "multihitting time," the expected length of the shortest random walk from any one of the set of sequence-altered genes to an expression-altered target gene...
July 18, 2017: Genome Research
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