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https://www.readbyqxmd.com/read/29784908/integration-of-multi-omics-data-and-deep-phenotyping-enables-prediction-of-cytokine-responses
#1
Olivier B Bakker, Raul Aguirre-Gamboa, Serena Sanna, Marije Oosting, Sanne P Smeekens, Martin Jaeger, Maria Zorro, Urmo Võsa, Sebo Withoff, Romana T Netea-Maier, Hans J P M Koenen, Irma Joosten, Ramnik J Xavier, Lude Franke, Leo A B Joosten, Vinod Kumar, Cisca Wijmenga, Mihai G Netea, Yang Li
The immune response to pathogens varies substantially among people. Whereas both genetic and nongenetic factors contribute to interperson variation, their relative contributions and potential predictive power have remained largely unknown. By systematically correlating host factors in 534 healthy volunteers, including baseline immunological parameters and molecular profiles (genome, metabolome and gut microbiome), with cytokine production after stimulation with 20 pathogens, we identified distinct patterns of co-regulation...
May 21, 2018: Nature Immunology
https://www.readbyqxmd.com/read/29780373/regulation-mechanism-mediated-by-trans-encoded-srna-nc117-in-short-chain-alcohols-tolerance-in-synechocystis-sp-pcc-6803
#2
Yanqi Bi, Guangsheng Pei, Tao Sun, Zixi Chen, Lei Chen, Weiwen Zhang
Microbial small RNAs (sRNAs) play essential roles against many stress conditions in cyanobacteria. However, little is known on their regulatory mechanisms on biofuels tolerance. In our previous sRNA analysis, a trans -encoded sRNA Nc117 was found involved in the tolerance to ethanol and 1-butanol in Synechocystis sp. PCC 6803. However, its functional mechanism is yet to be determined. In this study, functional characterization of sRNA Nc117 was performed. Briefly, the exact length of the trans -encoded sRNA Nc117 was determined to be 102 nucleotides using 3' RACE, and the positive regulation of Nc117 on short chain alcohols tolerance was further confirmed...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29779973/impact-of-device-host-interaction-on-paravalvular-aortic-regurgitation-with-different-transcatheter-heart-valves
#3
Ramón Rodríguez-Olivares, Nahid El Faquir, Zouhair Rahhab, Lennart van Gils, Ben Ren, Rafi Sakhi, Marcel L Geleijnse, Ron van Domburg, Peter P T de Jaegere, Jose L Zamorano Gómez, Nicolas M Van Mieghem
AIMS: We sought to evaluate the interaction of different aortic root phenotypes with self-expanding (SEV), balloon-expandable (BEV) and mechanically expanded (MEV) and the impact on significant aortic regurgitation. METHODS AND RESULTS: We included 392 patients with a SEV (N = 205), BEV (N = 107) or MEV (N = 80). Aortic annulus eccentricity index and calcification were measured by multi-slice CT scan. Paravalvular aortic regurgitation was assessed by contrast aortography (primary analysis) and transthoracic echocardiography (secondary analysis)...
May 6, 2018: Cardiovascular Revascularization Medicine: Including Molecular Interventions
https://www.readbyqxmd.com/read/29779949/disease-heritability-inferred-from-familial-relationships-reported-in-medical-records
#4
Fernanda C G Polubriaginof, Rami Vanguri, Kayla Quinnies, Gillian M Belbin, Alexandre Yahi, Hojjat Salmasian, Tal Lorberbaum, Victor Nwankwo, Li Li, Mark M Shervey, Patricia Glowe, Iuliana Ionita-Laza, Mary Simmerling, George Hripcsak, Suzanne Bakken, David Goldstein, Krzysztof Kiryluk, Eimear E Kenny, Joel Dudley, David K Vawdrey, Nicholas P Tatonetti
Heritability is essential for understanding the biological causes of disease but requires laborious patient recruitment and phenotype ascertainment. Electronic health records (EHRs) passively capture a wide range of clinically relevant data and provide a resource for studying the heritability of traits that are not typically accessible. EHRs contain next-of-kin information collected via patient emergency contact forms, but until now, these data have gone unused in research. We mined emergency contact data at three academic medical centers and identified 7...
May 15, 2018: Cell
https://www.readbyqxmd.com/read/29777750/post-a-framework-for-set-based-association-analysis-in-high-dimensional-data
#5
Xueyuan Cao, E Olusegun George, Mingjuan Wang, Dale B Armstrong, Cheng Cheng, Susana Raimondi, Jeffrey E Rubnitz, James R Downing, Mondira Kundu, Stanley B Pounds
Evaluating the differential expression of a set of genes belonging to a common biological process or ontology has proven to be a very useful tool for biological discovery. However, existing gene-set association methods are limited to applications that evaluate differential expression across k⩾2 treatment groups or biological categories. This limitation precludes researchers from most effectively evaluating the association with other phenotypes that may be more clinically meaningful, such as quantitative variables or censored survival time variables...
May 16, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29776990/effect-of-2-psoriasis-treatments-on-vascular-inflammation-and-novel-inflammatory-cardiovascular-biomarkers-a-randomized-placebo-controlled-trial
#6
Nehal N Mehta, Daniel B Shin, Aditya A Joshi, Amit K Dey, April W Armstrong, Kristina Callis Duffin, Zelma Chiesa Fuxench, Charlotte L Harrington, Rebecca A Hubbard, Robert E Kalb, Alan Menter, Daniel J Rader, Muredach P Reilly, Eric L Simpson, Junko Takeshita, Drew A Torigian, Thomas J Werner, Andrea B Troxel, Stephen K Tyring, Suzette Baez Vanderbeek, Abby S Van Voorhees, Martin P Playford, Mark A Ahlman, Abass Alavi, Joel M Gelfand
BACKGROUND: Psoriasis is a chronic inflammatory disease associated with dyslipidemia, cardiovascular events, and mortality. We aimed to assess and compare the effect of treatment of moderate-to-severe psoriasis with adalimumab or phototherapy on vascular inflammation and cardiovascular biomarkers. METHODS AND RESULTS: Randomized, double-blind, trial of adalimumab, phototherapy, and placebo (1:1:1) for 12 weeks, with crossover to adalimumab for 52 weeks total. Outcomes included vascular inflammation by 18 F-fluorodeoxyglucose positron emission tomography/computed tomography and biomarkers of inflammation, insulin resistance, and lipoproteins...
June 2018: Circulation. Cardiovascular Imaging
https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#7
Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto, Jan Baumbach
BACKGROUND: Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. RESULTS: We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29773872/computational-identification-of-specific-genes-for-glioblastoma-stem-like-cells-identity
#8
Giulia Fiscon, Federica Conte, Valerio Licursi, Sergio Nasi, Paola Paci
Glioblastoma, the most malignant brain cancer, contains self-renewing, stem-like cells that sustain tumor growth and therapeutic resistance. Identifying genes promoting stem-like cell differentiation might unveil targets for novel treatments. To detect them, here we apply SWIM - a software able to unveil genes (named switch genes) involved in drastic changes of cell phenotype - to public datasets of gene expression profiles from human glioblastoma cells. By analyzing matched pairs of stem-like and differentiated glioblastoma cells, SWIM identified 336 switch genes, potentially involved in the transition from stem-like to differentiated state...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29771274/identification-of-chronic-obstructive-pulmonary-disease-axes-that-predict-all-cause-mortality-the-copdgene-study
#9
Gregory L Kinney, Stephanie A Santorico, Kendra A Young, Michael H Cho, Peter J Castaldi, Raul San José Estépar, James C Ross, Jennifer G Dy, Barry J Make, Elizabeth A Regan, David A Lynch, Douglas C Everett, Sharon M Lutz, Edwin K Silverman, George R Washko, James D Crapo, John E Hokanson
Chronic Obstructive Pulmonary Disease (COPD) is a syndrome caused by damage to the lungs resulting in decreased pulmonary function and reduced structural integrity. Pulmonary function testing (PFT) is currently used to diagnose and stratify COPD into severity groups and chest computed tomography (CT) imaging is often used to assess structural changes in the lungs. We hypothesized that the combination of PFT and CT phenotypes would provide a more powerful tool for assessing underlying morphologic differences associated with pulmonary function in COPD than PFT alone...
May 16, 2018: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29769129/a-powerful-nonparametric-method-for-detecting-differentially-co-expressed-genes-distance-correlation-screening-and-edge-count-test
#10
Qingyang Zhang
BACKGROUND: Differential co-expression analysis, as a complement of differential expression analysis, offers significant insights into the changes in molecular mechanism of different phenotypes. A prevailing approach to detecting differentially co-expressed genes is to compare Pearson's correlation coefficients in two phenotypes. However, due to the limitations of Pearson's correlation measure, this approach lacks the power to detect nonlinear changes in gene co-expression which is common in gene regulatory networks...
May 16, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29768460/a-guide-to-automated-apoptosis-detection-how-to-make-sense-of-imaging-flow-cytometry-data
#11
Dennis Pischel, Jörn H Buchbinder, Kai Sundmacher, Inna N Lavrik, Robert J Flassig
Imaging flow cytometry is a powerful experimental technique combining the strength of microscopy and flow cytometry to enable high-throughput characterization of cell populations on a detailed microscopic scale. This approach has an increasing importance for distinguishing between different cellular phenotypes such as proliferation, cell division and cell death. In the course of undergoing these different pathways, each cell is characterized by a high amount of properties. This makes it hard to filter the most relevant information for cell state discrimination...
2018: PloS One
https://www.readbyqxmd.com/read/29768320/monocyte-chemoattractant-protein-1-as-a-predictor-of-coronary-atherosclerosis-in-patients-receiving-coronary-angiography
#12
Simon A Mahler, Thomas C Register, Robert F Riley, Ralph B D'Agostino, Jason P Stopyra, Chadwick D Miller
BACKGROUND: Animal studies suggest that monocyte chemoattractant protein-1 (MCP-1) is a promising biomarker for coronary artery atherosclerosis (CAA), but human studies have been inconclusive. OBJECTIVE: To determine potential relationships between plasma MCP-1 and CAA in patients with acute chest pain. METHODS: A secondary analysis of 150 patients enrolled in emergency department chest pain risk stratification clinical investigations was conducted...
June 2018: Critical Pathways in Cardiology
https://www.readbyqxmd.com/read/29767469/cd109-deficiency-induces-osteopenia-with-an-osteoporosis-like-phenotype-in-vivo
#13
Shinji Mii, Akiyoshi Hoshino, Atsushi Enomoto, Yoshiki Murakumo, Masako Ito, Akira Yamaguchi, Masahide Takahashi
Osteoporosis is a global public health problem that is increasing along with an aging population. A major determinant of osteoporosis is high bone turnover, which results from osteoclast activation. CD109 is a glycosylphosphatidylinositol-anchored glycoprotein, a deficiency that leads to a psoriasis-like skin inflammation in mice. Although the expression of CD109 has been reported in mouse pre-osteoclast cells, its function in osteoclasts in vivo remains largely unknown. To investigate the physiological role of CD109 in bone metabolism, we analyzed bones from wild-type and CD109-deficient adult mice...
May 16, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/29766384/increased-functional-meg-connectivity-as-a-hallmark-of-mri-negative-focal-and-generalized-epilepsy
#14
Yiwen Li Hegner, Justus Marquetand, Adham Elshahabi, Silke Klamer, Holger Lerche, Christoph Braun, Niels K Focke
Epilepsy is one of the most prevalent neurological diseases with a high morbidity. Accumulating evidence has shown that epilepsy is an archetypical neural network disorder. Here we developed a non-invasive cortical functional connectivity analysis based on magnetoencephalography (MEG) to assess commonalities and differences in the network phenotype in different epilepsy syndromes (non-lesional/cryptogenic focal and idiopathic/genetic generalized epilepsy). Thirty-seven epilepsy patients with normal structural brain anatomy underwent a 30-min resting state MEG measurement with eyes closed...
May 15, 2018: Brain Topography
https://www.readbyqxmd.com/read/29764690/inter-ray-variation-in-metatarsal-strength-properties-in-humans-and-african-apes-implications-for-inferring-bipedal-biomechanics-in-the-olduvai-hominid-8-foot
#15
Biren A Patel, Tea Jashashvili, Stephanie H Bui, Kristian J Carlson, Nicole L Griffin, Ian J Wallace, Caley M Orr, Randall L Susman
When measured as a ratio of mean midshaft diameter to bone length, the OH 8 fossil hominin foot exhibits a metatarsal (Mt) robusticity pattern of 1 > 5 > 3 > 4 > 2, which differs from the widely perceived "common" modern human pattern (1 > 5 > 4 > 3 > 2); African apes generally exhibit a third pattern (1 > 2 > 3 > 4 > 5). Largely because of the relative ranking of Mt2 and Mt5, OH 8 metatarsals structurally resemble the pattern exhibited by bipedal humans more than the pattern of quadrupedal and climbing African apes...
May 12, 2018: Journal of Human Evolution
https://www.readbyqxmd.com/read/29763435/personality-differentially-affects-individual-mate-choice-decisions-in-female-and-male-western-mosquitofish-gambusia-affinis
#16
Bo-Jian Chen, Kai Liu, Lin-Jun Zhou, Guilherme Gomes-Silva, Carolin Sommer-Trembo, Martin Plath
Consistent individual differences in behavioral tendencies (animal personality) can affect individual mate choice decisions. We asked whether personality traits affect male and female mate choice decisions similarly and whether potential personality effects are consistent across different mate choice situations. Using western mosquitofish (Gambusia affinis) as our study organism, we characterized focal individuals (males and females) twice for boldness, activity, and sociability/shoaling and found high and significant behavioral repeatability...
2018: PloS One
https://www.readbyqxmd.com/read/29761492/c7-vertebra-homeotic-transformation-in-domestic-dogs-are-pug-dogs-breaking-mammalian-evolutionary-constraints
#17
J Brocal, S De Decker, R José-López, E G Manzanilla, J Penderis, C Stalin, S Bertram, J J Schoenebeck, C Rusbridge, N Fitzpatrick, R Gutierrez-Quintana
The number of cervical vertebrae in mammals is almost constant at seven, regardless of their neck length, implying that there is selection against variation in this number. Homebox (Hox) genes are involved in this evolutionary mammalian conservation, and homeotic transformation of cervical into thoracic vertebrae (cervical ribs) is a common phenotypic abnormality when Hox gene expression is altered. This relatively benign phenotypic change can be associated with fatal traits in humans. Mutations in genes upstream of Hox, inbreeding and stressors during organogenesis can also cause cervical ribs...
May 14, 2018: Journal of Anatomy
https://www.readbyqxmd.com/read/29760766/holistic-and-component-plant-phenotyping-using-temporal-image-sequence
#18
Sruti Das Choudhury, Srinidhi Bashyam, Yumou Qiu, Ashok Samal, Tala Awada
Background: Image-based plant phenotyping facilitates the extraction of traits noninvasively by analyzing large number of plants in a relatively short period of time. It has the potential to compute advanced phenotypes by considering the whole plant as a single object (holistic phenotypes) or as individual components, i.e., leaves and the stem (component phenotypes), to investigate the biophysical characteristics of the plants. The emergence timing, total number of leaves present at any point of time and the growth of individual leaves during vegetative stage life cycle of the maize plants are significant phenotypic expressions that best contribute to assess the plant vigor...
2018: Plant Methods
https://www.readbyqxmd.com/read/29760052/spatial-mutation-patterns-as-markers-of-early-colorectal-tumor-cell-mobility
#19
Marc D Ryser, Byung-Hoon Min, Kimberly D Siegmund, Darryl Shibata
A growing body of evidence suggests that a subset of human cancers grows as single clonal expansions. In such a nearly neutral evolution scenario, it is possible to infer the early ancestral tree of a full-grown tumor. We hypothesized that early tree reconstruction can provide insights into the mobility phenotypes of tumor cells during their first few cell divisions. We explored this hypothesis by means of a computational multiscale model of tumor expansion incorporating the glandular structure of colorectal tumors...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29758261/annotating-diseases-using-human-phenotype-ontology-improves-prediction-of-disease-associated-long-non-coding-rnas
#20
Duc-Hau Le, Lan T M Dao
Recently, many long non-coding RNAs (lncRNAs) have been identified and their biological function has been characterized; however, our understanding of their underlying molecular mechanisms related to disease is still limited. To overcome the limitation in experimentally identifying disease-lncRNA associations, computational methods have been proposed as a powerful tool to predict such associations. These methods are usually based on the similarities between diseases or lncRNAs since it was reported that similar diseases are associated with functionally similar lncRNAs...
May 11, 2018: Journal of Molecular Biology
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