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Computable phenotype

Mir B Alikhan, Garrison Pease, William Watkin, Raymon Grogan, Thomas Krausz, Tatjana Antic
Epithelioid sarcoma (ES) is a malignant mesenchymal neoplasm with some morphologic or immunophenotypic evidence of epithelial differentiation. The "classical" subtype occurs in younger patients, often in distal extremities as compared to the "proximal" type. Tumors of the proximal type primarily arising in solid organs are rare with only few case reports in the literature. We report two cases of primary ES in the kidney of a 27-year-old female and the adrenal gland of a 73-year-old male. Clinical exam and imaging, including computer tomography and positron emission tomography did not reveal tumor elsewhere in both cases...
October 18, 2016: Human Pathology
Torahiko Yamanouchi, Satoshi Kawanami, Takeshi Kamitani, Koji Sagiyama, Yuzo Yamasaki, Yuko Tanaka, Michinobu Nagao, Hidetake Yabuuchi, Naoki Hamada, Tatsuro Okamoto, Hidetaka Yamamoto, Hiroshi Honda
No abstract text is available yet for this article.
November 2016: Journal of Thoracic Imaging
Carolina Rodriguez-Tirado, Takanori Kitamura, Yu Kato, Jeffery W Pollard, John S Condeelis, David Entenberg
Metastasis to secondary sites such as the lung, liver and bone is a traumatic event with a mortality rate of approximately 90% (1). Of these sites, the lung is the most difficult to assess using intravital optical imaging due to its enclosed position within the body, delicate nature and vital role in sustaining proper physiology. While clinical modalities (positron emission tomography (PET), magnetic resonance imaging (MRI) and computed tomography (CT)) are capable of providing noninvasive images of this tissue, they lack the resolution necessary to visualize the earliest seeding events, with a single pixel consisting of nearly a thousand cells...
October 6, 2016: Journal of Visualized Experiments: JoVE
Yang Liu, Saad M Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, Joao V Maldonado Dos Santos, Babu Valliyodan, Prasad P Calyam, Nirav Merchant, Henry T Nguyen, Dong Xu, Trupti Joshi
BACKGROUND: With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS)...
October 6, 2016: BMC Bioinformatics
Brendan D Crawford, Christopher E Gillies, Catherine C Robertson, Matthias Kretzler, Edgar Otto, Virginia Vega-Wagner, Matthew G Sampson
BACKGROUND: More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation...
October 20, 2016: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
Ranjith Rajendran, Ali May, Leighann Sherry, Ryan Kean, Craig Williams, Brian L Jones, Karl V Burgess, Jaap Heringa, Sanne Abeln, Bernd W Brandt, Carol A Munro, Gordon Ramage
Candida albicans biofilm formation is an important virulence factor in the pathogenesis of disease, a characteristic which has been shown to be heterogeneous in clinical isolates. Using an unbiased computational approach we investigated the central metabolic pathways driving biofilm heterogeneity. Transcripts from high (HBF) and low (LBF) biofilm forming isolates were analysed by RNA sequencing, with 6312 genes identified to be expressed in these two phenotypes. With a dedicated computational approach we identified and validated a significantly differentially expressed subnetwork of genes associated with these biofilm phenotypes...
October 21, 2016: Scientific Reports
Mark A Applebaum, Aashish R Jha, Clara Kao, Kyle M Hernandez, Gillian DeWane, Helen R Salwen, Alexandre Chlenski, Marija Dobratic, Christopher J Mariani, Lucy A Godley, Nanduri Prabhakar, Kevin White, Barbara E Stranger, Susan L Cohn
Neuroblastoma is notable for its broad spectrum of clinical behavior ranging from spontaneous regression to rapidly progressive disease. Hypoxia is well known to confer a more aggressive phenotype in neuroblastoma. We analyzed transcriptome data from diagnostic neuroblastoma tumors and hypoxic neuroblastoma cell lines to identify genes whose expression levels correlate with poor patient outcome and are involved in the hypoxia response. By integrating a diverse set of transcriptome datasets, including those from neuroblastoma patients and neuroblastoma derived cell lines, we identified nine genes (SLCO4A1, ENO1, HK2, PGK1, MTFP1, HILPDA, VKORC1, TPI1, and HIST1H1C) that are up-regulated in hypoxia and whose expression levels are correlated with poor patient outcome in three independent neuroblastoma cohorts...
October 17, 2016: Oncotarget
Siroon Bekkering, Inge van den Munckhof, Tim Nielen, Evert Lamfers, Charles Dinarello, Joost Rutten, Jacqueline de Graaf, Leo A B Joosten, Mihai G Netea, Marc E R Gomes, Niels P Riksen
BACKGROUND AND AIMS: We have recently reported that monocytes can undergo functional and transcriptional reprogramming towards a long-term pro-inflammatory phenotype after brief in vitro exposure to atherogenic stimuli such as oxidized LDL. This process is termed 'trained immunity', and is mediated by epigenetic remodeling and a metabolic switch towards increased aerobic glycolysis. We hypothesize that trained immunity contributes to atherogenesis. Therefore, we investigated the inflammatory phenotype and epigenetic remodeling of monocytes from patients with and without established atherosclerosis...
October 12, 2016: Atherosclerosis
Elisabeth Wiig, Janne E Reseland, Kjartan Østbye, Håvard J Haugen, Leif A Vøllestad
INTRODUCTION: It is important to understand the drivers leading to adaptive phenotypic diversity within and among species. The threespine stickleback (Gasterosteus aculeatus) has become a model system for investigating the genetic and phenotypic responses during repeated colonization of fresh waters from the original marine habitat. During the freshwater colonization process there has been a recurrent and parallel reduction in the number of lateral bone plates, making it a suitable system for studying adaptability and parallel evolution...
2016: PloS One
Rafael O Alvim, Andréa R V R Horimoto, Camila M Oliveira, Luiz A Bortolotto, José E Krieger, Alexandre C Pereira
BACKGROUND: Increased arterial stiffness is an important determinant of cardiovascular disease risk. In addition, it has been recognized that arterial stiffness has familial aggregation; however, there are no studies involving Brazilian families. Thus, the aim of this study was to evaluate the heritability of arterial stiffness in a Brazilian population. METHODS: In this study, 1675 eligible individuals (both sexes and aged 18-102 years) were distributed in 125 families resident in the municipality of Baependi, a city located in the southeast of Brazil...
October 19, 2016: Journal of Hypertension
Pallavi Surase, Gita Nataraj, Sunil Kuyare, Preeti Mehta
OBJECTIVES: The study was carried out to determine the extent and type of contamination of the hands and accessories of staff from different settings and also to determine the phenotypic similarity between the isolates recovered from the same staff. DESIGN: Prospective cross-sectional study. SETTING: Tertiary care center. PARTICIPANTS: Health care workers (HCWs') and administrative staff. METHODS: Samples were collected and processed for bacteriology from the dominant hand, mobiles, aprons, stethoscopes and computer keyboards of 280 staff working in different settings after consent...
August 2016: Journal of the Association of Physicians of India
Songjia Lu, Chunhui Cai, Gonghong Yan, Zhuan Zhou, Yong Wan, Vicky Chen, Lujia Chen, Gregory F Cooper, Lina M Obeid, Yusuf A Hannun, Adrian V Lee, Xinghua Lu
Defining processes that are synthetic lethal with p53 mutations in cancer cells may reveal possible therapeutic strategies. In this study, we report the development of a signal-oriented computational framework for cancer pathway discovery in this context. We applied our bipartite-graph-based functional module discovery algorithm to identify transcriptomic modules abnormally expressed in multiple tumors, such that the genes in a module were likely regulated by a common, perturbed signal. For each transcriptomic module, we applied our weighted k-path merge algorithm to search for a set of somatic genome alterations (SGA) that likely perturbed the signal, i...
October 10, 2016: Cancer Research
S Di Mauro, M Ragusa, F Urbano, A Filippello, A Di Pino, A Scamporrino, A Pulvirenti, A Ferro, A M Rabuazzo, M Purrello, F Purrello, S Piro
BACKGROUND & AIMS: Nonalcoholic fatty liver disease (NAFLD) represents the most common chronic liver disease in industrialized countries. NAFLD has the potential to progress through the inflammatory phase of nonalcoholic steatohepatitis (NASH) to fibrosis, cirrhosis, and hepatocellular carcinoma. Identifying patients at risk for this transition is a relevant clinical challenge. The complexity of these phenotypes in vivo made necessary the development of in vitro models in order to dissect the molecular signalling affected in NAFLD and NASH, but also to identify potential circulating biomarkers...
August 20, 2016: Nutrition, Metabolism, and Cardiovascular Diseases: NMCD
Sung Eun Song, Min Sun Bae, Jung Min Chang, Nariya Cho, Han Suk Ryu, Woo Kyung Moon
BACKGROUND: Human epidermal growth factor receptor 2-positive (HER2+) breast cancer has two distinct subtypes according to hormone receptor (HR) status. Survival, pattern of recurrence, and treatment response differ between HR-/HER2+ and HR+/HER2+ cancers. PURPOSE: To investigate imaging and clinicopathologic features of HER2+ cancers and their correlation with HR expression. MATERIAL AND METHODS: Between 2011 and 2013, 252 consecutive patients with 252 surgically confirmed HER2+ cancers (125 HR- and 127 HR+) were included...
October 17, 2016: Acta Radiologica
Steven Steinhubl
Despite having the basic tools necessary to appropriately identify and manage individuals with hypertension for over half a century it remains the single greatest contributing risk factor to morbidity and mortality worldwide today. Since diagnosis and effective treatment availability are not issues, this major failing in care can be attributed to inadequate systems of care: systems that have led to only <20% of hypertensive individuals globally having their blood pressure adequately controlled. Even in the US, where it is one of the most common reasons for a primary care visit, and with over $42...
September 2016: Journal of Hypertension
Alberto Avolio
Blood vessels function as conduits for distribution of blood throughout the circulatory system. Large arteries, in addition to the essential conduit function, also serve to dampen the effect of pulsatile ventricular ejection that generates pulsatile pressure with each cardiac cycle; that is, they exhibit a 'cushion' function. The conduit function can be compromised by intimal effects that cause obstruction to flow, generally attributed to plaque formation due to intimal changes affected by atherosclerotic processes...
September 2016: Journal of Hypertension
Qian Wang, Renato Polimanti, Henry R Kranzler, Lindsay A Farrer, Hongyu Zhao, Joel Gelernter
Schizophrenia (SZ) and HIV infection are serious disorders with a complex phenotypic relationship. Observational studies have described their comorbidity; their genetic correlation is not well studied. We performed extensive analysis in search of common genetic factors for SZ and HIV, and their relationship with risky sexual behavior (RSB). Summary statistics from genome-wide association studies of HIV infection and schizophrenia were obtained and 2379 European Americans were genotyped and assessed for RSB score...
October 17, 2016: Human Genetics
Wolfgang Kuchinke, Christian Krauth, René Bergmann, Töresin Karakoyun, Astrid Woollard, Irene Schluender, Benjamin Braasch, Martin Eckert, Christian Ohmann
BACKGROUND: In an unprecedented rate data in the life sciences is generated and stored in many different databases. An ever increasing part of this data is human health data and therefore falls under data protected by legal regulations. As part of the BioMedBridges project, which created infrastructures that connect more than 10 ESFRI research infrastructures (RI), the legal and ethical prerequisites of data sharing were examined employing a novel and pragmatic approach. METHODS: We employed concepts from computer science to create legal requirement clusters that enable legal interoperability between databases for the areas of data protection, data security, Intellectual Property (IP) and security of biosample data...
July 7, 2016: BMC Medical Informatics and Decision Making
Jenny M Pedersen, Yoo-Sik Shim, Vaibhav Hans, Martin B Phillips, Jeffrey M Macdonald, Glenn Walker, Melvin E Andersen, Harvey J Clewell, Miyoung Yoon
Accurate prediction of metabolism is a significant outstanding challenge in toxicology. The best predictions are based on experimental data from in vitro systems using primary hepatocytes. The predictivity of the primary hepatocyte-based culture systems, however, is still limited due to well-known phenotypic instability and rapid decline of metabolic competence within a few hours. Dynamic flow bioreactors for three-dimensional cell cultures are thought to be better at recapitulating tissue microenvironments and show potential to improve in vivo extrapolations of chemical or drug toxicity based on in vitro test results...
2016: Frontiers in Bioengineering and Biotechnology
Eitan Halper-Stromberg, Michael H Cho, Carla Wilson, Dipti Nevrekar, James D Crapo, George Washko, Raúl San José Estépar, David A Lynch, Edwin K Silverman, Sonia Leach, Peter J Castaldi
RATIONALE: Automated analysis of computed tomographic (CT) lung images for epidemiologic nand genetic association studies is increasingly common, but little is known about the utility of visual versus semi-automated emphysema and airway assessments for genetic association studies. OBJECTIVES: Assess the relative utility of visual versus semi-automated emphysema and airway assessments for genetic association studies. METHODS: A standardized inspection protocol was used to visually assess chest CTs for 1540 non-Hispanic white subjects within the COPDGene Study for the presence and severity of radiographic features representing airway wall thickness and emphysema...
October 14, 2016: Annals of the American Thoracic Society
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