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https://www.readbyqxmd.com/read/28211093/gsskat-rapid-gene-set-analysis-and-multiple-testing-correction-for-rare-variant-association-studies-using-weighted-linear-kernels
#1
Nicholas B Larson, Shannon McDonnell, Lisa Cannon Albright, Craig Teerlink, Janet Stanford, Elaine A Ostrander, William B Isaacs, Jianfeng Xu, Kathleen A Cooney, Ethan Lange, Johanna Schleutker, John D Carpten, Isaac Powell, Joan E Bailey-Wilson, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Alice S Whittemore, Chih-Lin Hsieh, Fredrik Wiklund, William J Catolona, William Foulkes, Diptasri Mandal, Rosalind Eeles, Zsofia Kote-Jarai, Michael J Ackerman, Timothy M Olson, Christopher J Klein, Stephen N Thibodeau, Daniel J Schaid
Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data...
February 16, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28202670/mechanisms-of-lrrk2-dependent-neurodegeneration-role-of-enzymatic-activity-and-protein-aggregation
#2
REVIEW
Md Shariful Islam, Darren J Moore
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most common cause of familial Parkinson's disease (PD) with autosomal dominant inheritance. Accordingly, LRRK2 has emerged as a promising therapeutic target for disease modification in PD. Since the first discovery of LRRK2 mutations some 12 years ago, LRRK2 has been the subject of intense investigation. It has been established that LRRK2 can function as a protein kinase, with many putative substrates identified, and can also function as a GTPase that may serve in part to regulate kinase activity...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28202141/non-intact-families-and-diverging-educational-destinies-a-decomposition-analysis-for-germany-italy-the-united-kingdom-and-the-united-states
#3
Fabrizio Bernardi, Diederik Boertien
We examine whether the presence of non-intact families in society is related to increased inequality in educational attainment according to social background, as suggested by the 'diverging destinies' thesis. We analyze four countries, Germany, Italy, the United Kingdom, and the United States, that differ in the prevalence of non-intact families and in the strength of the negative association between growing up in a non-intact family and children's educational attainment. We use a Blinder-Oaxaca decomposition approach to calculate a 'counterfactual' estimate of differences in educational attainment between socioeconomically advantaged and disadvantaged children in the hypothetical absence of non-intact families...
March 2017: Social Science Research
https://www.readbyqxmd.com/read/28199923/assistance-at-mealtimes-in-hospital-settings-and-rehabilitation-units-for-patients-65years-from-the-perspective-of-patients-families-and-healthcare-professionals-a-mixed-methods-systematic-review
#4
REVIEW
Deborah Edwards, Judith Carrier, Jane Hopkinson
BACKGROUND: Malnutrition is one of the key issues affecting the health of older people (>65years). With an aging population the problem is expected to increase further since the prevalence of malnutrition increases with age. Studies worldwide have identified that some older patients with good appetites do not receive sufficient nourishment because of inadequate feeding assistance. Mealtime assistance can enhance nutritional intake, clinical outcomes and patient experience. OBJECTIVES/AIM: To determine the effectiveness of meal time assistance initiatives for improving nutritional intake and nutritional status for older adult patients (>65years) in hospital settings and rehabilitation units...
January 30, 2017: International Journal of Nursing Studies
https://www.readbyqxmd.com/read/28196272/deep-sequencing-of-71-candidate-genes-to-characterize-variation-associated-with-alcohol-dependence
#5
Shaunna L Clark, Daniel E Adkins, Gaurav Kumar, Karolina A Aberg, Sri Nerella, Linying Xie, Ann L Collins, James J Crowley, Corey R Quackenbush, Christopher E Hilliard, Andrey A Shabalin, Scott I Vrieze, Roseann E Peterson, William E Copeland, Judy L Silberg, Matt McGue, Hermine Maes, William G Iacono, Patrick F Sullivan, Elizabeth J Costello, Edwin J van den Oord
BACKGROUND: Previous genome-wide association studies (GWASs) have identified a number of putative risk loci for alcohol dependence (AD). However, only a few loci have replicated and these replicated variants only explain a small proportion of AD risk. Using an innovative approach, the goal of this study was to generate hypotheses about potentially causal variants for AD that can be explored further through functional studies. METHODS: We employed targeted capture of 71 candidate loci and flanking regions followed by next-generation deep sequencing (mean coverage 78X) in 806 European Americans...
February 14, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28195742/enhanced-davydov-splitting-in-crystals-of-a-perylene-diimide-derivative
#6
Ashli Austin, Nicholas J Hestand, Ian G McKendry, Chuwei Zhong, Xuanyu Zhu, Michael J Zdilla, Frank C Spano, Jodi M Szarko
We report the polarized absorption spectra of high quality, thin crystals of a perylene diimide (PDI) species with branched side chains (B2). The absorption spectrum shows exemplary polarization-dependent H-like and J-like aggregate behavior upon orthogonal excitation, with a sizable Davydov splitting (DS) of 1230 cm-1 and peak to peak splitting of 3040 cm-1. The experimental results are compared to theoretical calculations with remarkable agreement. The theoretical analysis of the polarized absorption spectra shows evidence of a high degree of intermolecular charge transfer, which, along with Coulombic coupling, conspire to create the unprecedented DS for this family of dye molecules...
February 14, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28192290/site-specific-structural-dynamics-of-%C3%AE-synuclein-revealed-by-time-resolved-fluorescence-spectroscopy-a-review
#7
Shruti Sahay, G Krishnamoorthy, Samir K Maji
Aggregation of α-Synuclein (α-Syn) into amyloid fibrils is known to be associated with the pathogenesis of Parkinson's disease (PD). Several missense mutations of the α-Syn gene have been associated with rare, early onset familial forms of PD. Despite several studies done so far, the local/residue-level structure and dynamics of α-Syn in its soluble and aggregated fibril form and how these are affected by the familial PD associated mutations are still not clearly understood. Here, we review studies performed by our group as well as other research groups, where time-resolved fluorescence spectroscopy has been used to understand the site-specific structure and dynamics of α-Syn under physiological conditions as well as under conditions that alter the aggregation properties of the protein such as low pH, high temperature, presence of membrane mimics and familial PD associated mutations...
October 11, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28192200/the-binding-capacity-of-%C3%AE-1%C3%AE-1-%C3%AE-2%C3%AE-1-and-%C3%AE-10%C3%AE-1-integrins-depends-on-non-collagenous-surface-macromolecules-rather-than-the-collagens-in-cartilage-fibrils
#8
Christian Woltersdorf, Melanie Bonk, Birgit Leitinger, Mikko Huhtala, Jarmo Käpylä, Jyrki Heino, Christian Gil Girol, Stephan Niland, Johannes A Eble, Peter Bruckner, Rita Dreier, Uwe Hansen
Interactions of cells with supramolecular aggregates of the extracellular matrix (ECM) are mediated, in part, by cell surface receptors of the integrin family. These are important molecular components of cell surface-suprastructures regulating cellular activities in general. A subfamily of β1-integrins with von Willebrand-factorA-like domains (I-domains) in their α-chains can bind to collagen molecules and, therefore, are considered as important cellular mechano-receptors. Here we show that chondrocytes strongly bind to cartilage collagens in the form of individual triple helical molecules but very weakly to fibrils formed by the same molecules...
February 10, 2017: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/28192145/population-based-familial-aggregation-of-eosinophilic-esophagitis-suggests-a-genetic-contribution
#9
Kristina Allen-Brady, Rafael Firszt, John C Fang, Jathine Wong, Ken R Smith, Kathryn A Peterson
BACKGROUND: Prior familial clustering studies have observed an increased risk of eosinophilic esophagitis (EoE) mostly among first-degree relatives suggesting a genetic contribution to EoE, and twin studies have suggested a powerful contribution from environmental factors. OBJECTIVE: Clarify the contribution of genetic factors to EoE through estimation of familial aggregation and risk of EoE in extended relatives. METHODS: The Utah Population Database, a population-based genealogy resource linked to electronic medical records for healthcare systems across the state of Utah, was used to identify EoE cases and age, sex and birthplace-matched controls at a 5:1 ratio...
February 10, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28191890/refining-the-role-of-de-novo-protein-truncating-variants-in-neurodevelopmental-disorders-by-using-population-reference-samples
#10
Jack A Kosmicki, Kaitlin E Samocha, Daniel P Howrigan, Stephan J Sanders, Kamil Slowikowski, Monkol Lek, Konrad J Karczewski, David J Cutler, Bernie Devlin, Kathryn Roeder, Joseph D Buxbaum, Benjamin M Neale, Daniel G MacArthur, Dennis P Wall, Elise B Robinson, Mark J Daly
Recent research has uncovered an important role for de novo variation in neurodevelopmental disorders. Using aggregated data from 9,246 families with autism spectrum disorder, intellectual disability, or developmental delay, we found that ∼1/3 of de novo variants are independently present as standing variation in the Exome Aggregation Consortium's cohort of 60,706 adults, and these de novo variants do not contribute to neurodevelopmental risk. We further used a loss-of-function (LoF)-intolerance metric, pLI, to identify a subset of LoF-intolerant genes containing the observed signal of associated de novo protein-truncating variants (PTVs) in neurodevelopmental disorders...
February 13, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28191591/plasmacytoid-dendritic-cell-proliferations-and-neoplasms-involving-the-bone-marrow-summary-of-the-workshop-cases-submitted-to-the-18th-meeting-of-the-european-association-for-haematopathology-eahp-organized-by-the-european-bone-marrow-working-group-basel-2016
#11
Alexandar Tzankov, Konnie Hebeda, Markus Kremer, Roos Leguit, Attilio Orazi, Jon van der Walt, Umberto Gianelli
Two distinct forms of neoplasms derived from plasmacytoid dendritic cells (PDC) exist: mature PDC proliferations associated with myeloid neoplasms and blastic PDC neoplasms (BPDCN). Ten cases of PDC proliferations and neoplasms in the bone marrow have been submitted to the bone marrow workshop held at the 18th EAHP meeting. Based on observations from the submitted cases, scattered PDC (≤1% of cells) and PDC aggregates (≤10 PDC/HPF) reflect the normal bone marrow composition, while in myelodysplastic syndromes (MDS), there is a propensity for larger/more PDC aggregates (1-5% and 35 PDC/HPF)...
February 12, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28190458/detection-of-imprinted-genes-by-single-cell-allele-specific-gene-expression
#12
Federico A Santoni, Georgios Stamoulis, Marco Garieri, Emilie Falconnet, Pascale Ribaux, Christelle Borel, Stylianos E Antonarakis
Genomic imprinting results in parental-specific gene expression. Imprinted genes are involved in the etiology of rare syndromes and have been associated with common diseases such as diabetes and cancer. Standard RNA bulk cell sequencing applied to whole-tissue samples has been used to detect imprinted genes in human and mouse models. However, lowly expressed genes cannot be detected by using RNA bulk approaches. Here, we report an original and robust method that combines single-cell RNA-seq and whole-genome sequencing into an optimized statistical framework to analyze genomic imprinting in specific cell types and in different individuals...
February 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28188264/immortalized-human-myotonic-dystrophy-muscle-cell-lines-to-assess-therapeutic-compounds
#13
Arandel Ludovic, Polay-Espinosa Micaela, Matloka Magdalena, Bazinet Audrey, De Dea Diniz Damily, Naouar Naïra, Rau Frédérique, Jollet Arnaud, Edom-Vovard Frédérique, Mamchaoui Kamel, Tarnopolsky Mark, Puymirat Jack, Battail Christophe, Boland Anne, Deleuze Jean-Francois, Mouly Vincent, Klein F Arnaud, Furling Denis
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant neuromuscular diseases caused by microsatellite expansions and belong to the family of RNA dominant disorders. Availability of cellular models in which the DM mutation is expressed within its natural context is essential to facilitate efforts to identify new therapeutic compounds. Here we generated immortalized DM1 and DM2 human muscle cell lines that display nuclear RNA-aggregates of expanded repeats, a hallmark of myotonic dystrophy. Selected clones of DM1 and DM2 immortalized myoblasts behave as parental primary myoblasts with a reduced fusion capacity of immortalized DM1 myoblasts when compared to control and DM2 cells...
February 10, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28185980/a-new-quantitative-measure-of-disc-degeneration
#14
Tapio Videman, Michele C Battié, Laura E Gibbons, Kevin Gill
BACKGROUND CONTEXT: The ability to adequately measure a phenomenon is critical to studying and understanding it. Since 1957, a variety of subjective visual grading methods have been used to assess disc degeneration, but have been limited by gross ordinal scales and imprecision, as well as suboptimal reliability. Conceptually sound, objective, precise measurements are needed to advance knowledge of disc degeneration and its causes, progression and consequences. PURPOSE: To investigate the reliability and validity of a new system ('SpIn' for Spine Insight) to quantitatively measure lumbar disc degeneration or pathology...
February 6, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28181366/molecular-phenotype-and-bleeding-risks-of-an-inherited-platelet-disorder-in-a-family-with-a-runx1-frameshift-mutation
#15
M S Badin, J K Iyer, M Chong, L Graf, G E Rivard, J S Waye, A D Paterson, G Pare, C P M Hayward
INTRODUCTION: Inherited defects in RUNX1 are important causes of platelet function disorders. AIM: Our goals were to evaluate RUNX1-related platelet disorders among individuals evaluated for uncharacterized, inherited platelet function disorders and test a proof of concept that bleeding risks could be quantitatively estimated for typical families with an inherited platelet function disorder. METHODS: Index cases with an uncharacterized inherited platelet function disorder were subjected to exome sequencing with confirmation of RUNX1 mutations by Sanger sequencing...
February 8, 2017: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/28179006/revised-computational-metagenomic-processing-uncovers-hidden-and-biologically-meaningful-functional-variation-in-the-human-microbiome
#16
Ohad Manor, Elhanan Borenstein
BACKGROUND: Recent metagenomic analyses of the human gut microbiome identified striking variability in its taxonomic composition across individuals. Notably, however, these studies often reported marked functional uniformity, with relatively little variation in the microbiome's gene composition or in its overall metabolic capacity. RESULTS: Here, we address this surprising discrepancy between taxonomic and functional variations and set out to track its origins. Specifically, we demonstrate that the functional uniformity observed in microbiome studies can be attributed, at least partly, to common computational metagenomic processing procedures that mask true functional variation across microbiome samples...
February 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28178571/genome-wide-identification-and-analysis-of-biotic-and-abiotic-stress-regulation-of-small-heat-shock-protein-hsp20-family-genes-in-bread-wheat
#17
Senthilkumar K Muthusamy, Monika Dalal, Viswanathan Chinnusamy, Kailash C Bansal
Small Heat Shock Proteins (sHSPs)/HSP20 are molecular chaperones that protect plants by preventing protein aggregation during abiotic stress conditions, especially heat stress. Due to global climate change, high temperature is emerging as a major threat to wheat productivity. Thus, the identification of HSP20 and analysis of HSP transcriptional regulation under different abiotic stresses in wheat would help in understanding the role of these proteins in abiotic stress tolerance. We used sequences of known rice and Arabidopsis HSP20 HMM profiles as queries against publicly available wheat genome and wheat full length cDNA databases (TriFLDB) to identify the respective orthologues from wheat...
January 22, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28178331/large-scale-bioactivity-analysis-of-the-small-molecule-assayed-proteome
#18
Tyler William H Backman, Daniel S Evans, Thomas Girke
This study presents an analysis of the small molecule bioactivity profiles across large quantities of diverse protein families represented in PubChem BioAssay. We compared the bioactivity profiles of FDA approved drugs to non-FDA approved compounds, and report several distinct patterns characteristic of the approved drugs. We found that a large fraction of the previously reported higher target promiscuity among FDA approved compounds, compared to non-FDA approved bioactives, was frequently due to cross-reactivity within rather than across protein families...
2017: PloS One
https://www.readbyqxmd.com/read/28178021/the-meanings-young-people-assign-to-living-with-mental-illness-and-their-experiences-in-managing-their-health-and-lives-a-systematic-review-of-qualitative-evidence
#19
Roberta L Woodgate, Corey Sigurdson, Lisa Demczuk, Pauline Tennent, Bernadine Wallis, Pamela Wener
BACKGROUND: It is estimated that less than 25% of young people in need of treatment for mental illness receive specialized services, and even fewer receive a diagnosis by their doctor. These findings are troubling given that living with a mental illness can have a significant impact on a young person's life, the lives of his/her family members, the young person's community and society generally. OBJECTIVE: The objective of this systematic review was to synthesize the best available qualitative evidence on the meanings young people assign to living with mental illness and their experiences in managing their health and lives...
February 2017: JBI Database of Systematic Reviews and Implementation Reports
https://www.readbyqxmd.com/read/28176975/familial-aggregation-of-the-cerebellar-signs-in-familial-essential-tremor
#20
Elan D Louis, Nora Hernandez, Karen P Chen, Kelly V Naranjo, Jemin Park, Lorraine N Clark, Ruth Ottman
BACKGROUND: Although the hallmark feature of essential tremor (ET) is kinetic tremor, patients may exhibit additional motor features (e.g., intention tremor and mild gait ataxia) that are markers of an underlying abnormality of cerebellar function. ET is also a highly familial disorder, but we do not know whether the presence and expression of cerebellar signs are similar across family members. There are simply no published data. The alternative possibility is that these features are not heritable...
2017: Tremor and Other Hyperkinetic Movements
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