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https://www.readbyqxmd.com/read/29659838/comparative-methylome-analysis-of-icf-patients-identifies-heterochromatin-loci-that-require-zbtb24-cdca7-and-hells-for-their-methylated-state
#1
Guillaume Velasco, Giacomo Grillo, Nizar Touleimat, Laure Ferry, Ivana Ivkovic, Florence Ribierre, Jean-François Deleuze, Sophie Chantalat, Capucine Picard, Claire Francastel
Alterations of DNA methylation landscapes and machinery are a hallmark of many human diseases. A prominent case is the ICF syndrome, a rare autosomal recessive immunological/neurological disorder diagnosed by the loss of DNA methylation at (peri)centromeric repeats and its associated chromosomal instability. It is caused by mutations in the de novo DNA methyltransferase DNMT3B in about half of the patients (ICF1). In the remainder, the striking identification of mutations in factors devoid of DNA methyltransferase activity, ZBTB24 (ICF2), CDCA7 (ICF3) or HELLS (ICF4), raised key questions about common or distinguishing DNA methylation alterations downstream of these mutations and hence, about the functional link between the four factors...
April 12, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29656859/dual-molecular-effects-of-dominant-rora-mutations-cause-two-variants-of-syndromic-intellectual-disability-with-either-autism-or-cerebellar-ataxia
#2
Claire Guissart, Xenia Latypova, Paul Rollier, Tahir N Khan, Hannah Stamberger, Kirsty McWalter, Megan T Cho, Susanne Kjaergaard, Sarah Weckhuysen, Gaetan Lesca, Thomas Besnard, Katrin Õunap, Lynn Schema, Andreas G Chiocchetti, Marie McDonald, Julitta de Bellescize, Marie Vincent, Hilde Van Esch, Shannon Sattler, Irman Forghani, Isabelle Thiffault, Christine M Freitag, Deborah Sara Barbouth, Maxime Cadieux-Dion, Rebecca Willaert, Maria J Guillen Sacoto, Nicole P Safina, Christèle Dubourg, Lauren Grote, Wilfrid Carré, Carol Saunders, Sander Pajusalu, Emily Farrow, Anne Boland, Danielle Hays Karlowicz, Jean-François Deleuze, Monica H Wojcik, Rena Pressman, Bertrand Isidor, Annick Vogels, Wim Van Paesschen, Lihadh Al-Gazali, Aisha Mohamed Al Shamsi, Mireille Claustres, Aurora Pujol, Stephan J Sanders, François Rivier, Nicolas Leboucq, Benjamin Cogné, Souphatta Sasorith, Damien Sanlaville, Kyle Retterer, Sylvie Odent, Nicholas Katsanis, Stéphane Bézieau, Michel Koenig, Erica E Davis, Laurent Pasquier, Sébastien Küry
RORα, the RAR-related orphan nuclear receptor alpha, is essential for cerebellar development. The spontaneous mutant mouse staggerer, with an ataxic gait caused by neurodegeneration of cerebellar Purkinje cells, was discovered two decades ago to result from homozygous intragenic Rora deletions. However, RORA mutations were hitherto undocumented in humans. Through a multi-centric collaboration, we identified three copy-number variant deletions (two de novo and one dominantly inherited in three generations), one de novo disrupting duplication, and nine de novo point mutations (three truncating, one canonical splice site, and five missense mutations) involving RORA in 16 individuals from 13 families with variable neurodevelopmental delay and intellectual disability (ID)-associated autistic features, cerebellar ataxia, and epilepsy...
April 10, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29624713/clinical-and-imaging-hallmarks-of-the-myh7-related-myopathy-with-severe-axial-involvement
#3
Ivana Dabaj, Robert Y Carlier, David Gómez-Andrés, Osório Abath Neto, Enrico Bertini, Adele D'Amico, Fabiana Fattori, Yann Péréon, Claudia Castiglioni, Eliana Rodillo, Michela Catteruccia, Júlio Brandão Guimarães, Acary Souza Bulle Oliveira, Umbertina Conti Reed, Lilia Mesrob, Doris Lechner, Anne Boland, Jean-François Deleuze, Edoardo Malfatti, Carsten Bonnemann, Jocelyn Laporte, Norma Romero, Adrien Felter, Susana Quijano-Roy, Cristiane Araújo Martins Moreno, Edmar Zanoteli
INTRODUCTION: MYH7 gene mutations are related to a heterogeneous group of skeletal and cardiac myopathies. METHODS: We evaluated clinical and muscle magnetic resonance imaging changes in patients with mutations in the rod domain of MYH7 including one with mosaicism and three with novel missense mutations. RESULTS: Patients presented in childhood with a distal and axial phenotype. Biopsy findings were variable. Half of the cases displaying some type of core pathology, including minicores and eccentric cores...
April 6, 2018: Muscle & Nerve
https://www.readbyqxmd.com/read/29621323/performance-comparison-of-three-dna-extraction-kits-on-human-whole-exome-data-from-formalin-fixed-paraffin-embedded-normal-and-tumor-samples
#4
Eric Bonnet, Marie-Laure Moutet, Céline Baulard, Delphine Bacq-Daian, Florian Sandron, Lilia Mesrob, Bertrand Fin, Marc Delépine, Marie-Ange Palomares, Claire Jubin, Hélène Blanché, Vincent Meyer, Anne Boland, Robert Olaso, Jean-François Deleuze
Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling...
2018: PloS One
https://www.readbyqxmd.com/read/29614691/novel-speg-mutations-in-congenital-myopathy-without-centralized-nuclei
#5
Xavière Lornage, Pascal Sabouraud, Béatrice Lannes, Dominique Gaillard, Raphaël Schneider, Jean-François Deleuze, Anne Boland, Julie Thompson, Johann Böhm, Valérie Biancalana, Jocelyn Laporte
Congenital myopathies are clinically and genetically heterogeneous, and are classified based on typical structural abnormalities on muscle sections. Recessive mutations in the striated muscle preferentially expressed protein kinase (SPEG) were recently reported in patients with centronuclear myopathy (CNM) associated in most cases with dilated cardiomyopathy. Here we report the identification of novel biallelic truncating SPEG mutations in a patient with moderate congenital myopathy without clinical and histological hallmarks of CNM and without cardiomyopathy...
March 26, 2018: Journal of Neuromuscular Diseases
https://www.readbyqxmd.com/read/29529886/a-weak-scientific-basis-for-gaming-disorder-let-us-err-on-the-side-of-caution
#6
Antonius J van Rooij, Christopher J Ferguson, Michelle Colder Carras, Daniel Kardefelt-Winther, Jing Shi, Espen Aarseth, Anthony M Bean, Karin Helmersson Bergmark, Anne Brus, Mark Coulson, Jory Deleuze, Pravin Dullur, Elza Dunkels, Johan Edman, Malte Elson, Peter J Etchells, Anne Fiskaali, Isabela Granic, Jeroen Jansz, Faltin Karlsen, Linda K Kaye, Bonnie Kirsh, Andreas Lieberoth, Patrick Markey, Kathryn L Mills, Rune Kristian Lundedal Nielsen, Amy Orben, Arne Poulsen, Nicole Prause, Patrick Prax, Thorsten Quandt, Adriano Schimmenti, Vladan Starcevic, Gabrielle Stutman, Nigel E Turner, Jan van Looy, Andrew K Przybylski
We greatly appreciate the care and thought that is evident in the 10 commentaries that discuss our debate paper, the majority of which argued in favor of a formalized ICD-11 gaming disorder. We agree that there are some people whose play of video games is related to life problems. We believe that understanding this population and the nature and severity of the problems they experience should be a focus area for future research. However, moving from research construct to formal disorder requires a much stronger evidence base than we currently have...
March 13, 2018: Journal of Behavioral Addictions
https://www.readbyqxmd.com/read/29524144/whole-genome-bisulfite-sequencing-for-the-analysis-of-genome-wide-dna-methylation-and-hydroxymethylation-patterns-at-single-nucleotide-resolution
#7
Magali Kernaleguen, Christian Daviaud, Yimin Shen, Eric Bonnet, Victor Renault, Jean-François Deleuze, Florence Mauger, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29522932/passion-or-addiction-correlates-of-healthy-versus-problematic-use-of-videogames-in-a-sample-of-french-speaking-regular-players
#8
Jory Deleuze, Jiang Long, Tie-Qiao Liu, Pierre Maurage, Joël Billieux
A criticism of current diagnostic approaches to gaming disorder is that they fail to take into account that high and repeated engagement is not problematic per se, nor is it necessarily associated with adverse consequences. To tackle this controversy, we used Confirmatory Factor Analysis (CFA) to test, in regular gamers (N = 268), whether high (but healthy) engagement can be distinguished from problematic engagement by using the Addiction-Engagement Questionnaire (Charlton & Danforth, 2007). We then tested whether differential relationships exist between the engagement and addiction constructs, DSM-5 criteria for Internet gaming disorder (IGD), and psychological factors linked to gaming use and misuse (self-reported impulsivity, motives to play, and depression)...
February 27, 2018: Addictive Behaviors
https://www.readbyqxmd.com/read/29506156/the-il-4-stat6-ppar%C3%AE-signaling-axis-is-driving-the-expansion-of-the-rxr-heterodimer-cistrome-providing-complex-ligand-responsiveness-in-macrophages
#9
Bence Daniel, Gergely Nagy, Attila Horvath, Zsolt Czimmerer, Ixchelt Cuaranta-Monroy, Szilard Poliska, Tristan T Hays, Sascha Sauer, Jean Francois-Deleuze, Laszlo Nagy
Retinoid X receptor (RXR) is an obligate heterodimeric partner of several nuclear receptors (NRs), and as such a central component of NR signaling regulating the immune and metabolic phenotype of macrophages. Importantly, the binding motifs of RXR heterodimers are enriched in the tissue-selective open chromatin regions of resident macrophages, suggesting roles in subtype specification. Recent genome-wide studies revealed that RXR binds to thousands of sites in the genome, but the mechanistic details how the cistrome is established and serves ligand-induced transcriptional activity remained elusive...
February 28, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29500350/strong-selection-during-the-last-millennium-for-african-ancestry-in-the-admixed-population-of-madagascar
#10
Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Veronica Pereda-Loth, Jazmin Sanchez, Omar Alva, Amal Arachiche, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Francois-Xavier Ricaut, Jean-Aimé Rakotoarisoa, Chantal Radimilahy, Mark Stoneking, Thierry Letellier
While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2...
March 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29485293/a-time-to-live-and-a-time-to-die-heterotopian-spatialities-and-temporalities-in-a-pediatric-palliative-care-team
#11
Christine S Davis, Meghan J Snider, Lynná King, Allison Shukraft, James D Sonda, Laurie Hicks, Lauren Irvin
The death of a child creates especially poignant feelings and extreme stress, distress, and devastation for family members and healthcare providers. In addition, serious or long-term illness forces a reconstruction of our experiences with time and space. In this paper, we report on a long-term ethnographic study of a Pediatric Palliative Care Team (PPCT). Using the concepts of spatiality and temporality; Deleuze's concepts of smooth and striated spaces; Innis's concepts of space and time biases; Foucault's concept of heterotopian space-places with multiple layers of meaning; and a related concept of heterokairoi-moments in time with multiple possibilities-we consider how the PPCT constructs and reconstructs meaning in the midst of chaos, ethical dilemmas, and heartbreaking choices...
February 27, 2018: Health Communication
https://www.readbyqxmd.com/read/29480197/biallelic-loss-of-function-of-sorl1-in-an-early-onset-alzheimer-s-disease-patient
#12
Kilan Le Guennec, Hélène Tubeuf, Didier Hannequin, David Wallon, Olivier Quenez, Stéphane Rousseau, Anne-Claire Richard, Jean-François Deleuze, Anne Boland, Thierry Frebourg, Pascaline Gaildrat, Dominique Campion, Alexandra Martins, Gaël Nicolas
Heterozygous SORL1 protein truncating variants (PTV) are a strong risk factor for early-onset Alzheimer's disease (EOAD). In case control studies performed at the genome-wide level, PTV definition is usually straightforward. Regarding splice site variants, only those affecting canonical sites are typically included. Some other variants, not annotated as PTV, could, however, affect splicing and hence result in a loss of SORL1 function. We took advantage of the whole exome sequencing data from the 9/484 patients with a previously reported SORL1 PTV in the French EOAD series and searched for a second variant which may affect splicing and eventually result in more than 50% loss of function overall...
2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29449551/mutations-in-cfap43-and-cfap44-cause-male-infertility-and-flagellum-defects-in-trypanosoma-and-human
#13
Charles Coutton, Alexandra S Vargas, Amir Amiri-Yekta, Zine-Eddine Kherraf, Selima Fourati Ben Mustapha, Pauline Le Tanno, Clémentine Wambergue-Legrand, Thomas Karaouzène, Guillaume Martinez, Serge Crouzy, Abbas Daneshipour, Seyedeh Hanieh Hosseini, Valérie Mitchell, Lazhar Halouani, Ouafi Marrakchi, Mounir Makni, Habib Latrous, Mahmoud Kharouf, Jean-François Deleuze, Anne Boland, Sylviane Hennebicq, Véronique Satre, Pierre-Simon Jouk, Nicolas Thierry-Mieg, Beatrice Conne, Denis Dacheux, Nicolas Landrein, Alain Schmitt, Laurence Stouvenel, Patrick Lorès, Elma El Khouri, Serge P Bottari, Julien Fauré, Jean-Philippe Wolf, Karin Pernet-Gallay, Jessica Escoffier, Hamid Gourabi, Derrick R Robinson, Serge Nef, Emmanuel Dulioust, Raoudha Zouari, Mélanie Bonhivers, Aminata Touré, Christophe Arnoult, Pierre F Ray
Spermatogenesis defects concern millions of men worldwide, yet the vast majority remains undiagnosed. Here we report men with primary infertility due to multiple morphological abnormalities of the sperm flagella with severe disorganization of the sperm axoneme, a microtubule-based structure highly conserved throughout evolution. Whole-exome sequencing was performed on 78 patients allowing the identification of 22 men with bi-allelic mutations in DNAH1 (n = 6), CFAP43 (n = 10), and CFAP44 (n = 6). CRISPR/Cas9 created homozygous CFAP43/44 male mice that were infertile and presented severe flagellar defects confirming the human genetic results...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29437287/novel-mutations-in-dnajb6-cause-lgmd1d-and-distal-myopathy-in-french-families
#14
Per H Jonson, Johanna Palmio, Mridul Johari, Sini Penttilä, Anni Evilä, Isabelle Nelson, Gisèle Bonne, Nicolas Wiart, Vincent Meyer, Anne Boland, Jean-François Deleuze, Cécile Masson, Tanya Stojkovic, Françoise Chapon, Norma B Romero, Guilhem Solé, Xavier Ferrer, Ana Ferreiro, Peter Hackman, Isabelle Richard, Bjarne Udd
BACKGROUND AND PURPOSE: To determine the genetic background of unknown muscular dystrophy in five French families. METHODS: Twelve patients with limb girdle muscular dystrophy or distal myopathy were clinically evaluated. Gene mutations were identified using targeted exon sequencing and mutated DNAJB6 was tested in vitro. RESULTS: Five patients presented with distal lower limb weakness while others had proximal presentation with variable rate of progression starting at the median age of 34...
February 13, 2018: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/29402293/genetic-variants-of-rnase3-ecp-and-susceptibility-to-severe-malaria-in-senegalese-population
#15
Gora Diop, Céline Derbois, Cheikh Loucoubar, Babacar Mbengue, Bineta Niakhana Ndao, Fatou Thiam, Alassane Thiam, Rokhaya Ndiaye, Yakhya Dieye, Robert Olaso, Jean-Francois Deleuze, Alioune Dieye
BACKGROUND: Severe forms of malaria (SM) are an outcome of Plasmodium falciparum infection and can cause death especially in children under 4 years of age. RNASE3 (ECP) has been identified as an inhibitor of Plasmodium parasites growth in vitro, and genetic analysis in hospitalized Ghanaian subjects has revealed the RNASE3 +371G/C (rs2073342) polymorphism as a susceptibility factor for cerebral malaria. The +371 C allele results in an Arg/Thr mutation that abolishes the cytotoxic activity of the ECP protein...
February 5, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29343442/the-transcription-factor-stat6-mediates-direct-repression-of-inflammatory-enhancers-and-limits-activation-of-alternatively-polarized-macrophages
#16
Zsolt Czimmerer, Bence Daniel, Attila Horvath, Dominik Rückerl, Gergely Nagy, Mate Kiss, Matthew Peloquin, Marietta M Budai, Ixchelt Cuaranta-Monroy, Zoltan Simandi, Laszlo Steiner, Bela Nagy, Szilard Poliska, Csaba Banko, Zsolt Bacso, Ira G Schulman, Sascha Sauer, Jean-Francois Deleuze, Judith E Allen, Szilvia Benko, Laszlo Nagy
The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, but our understanding remains limited regarding the molecular determinants of repression. Here we show that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during in vitro and in vivo alternative macrophage polarization. Repression results in decreased lineage-determining transcription factor, p300, and RNA polymerase II binding followed by reduced enhancer RNA expression, H3K27 acetylation, and chromatin accessibility...
January 16, 2018: Immunity
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#17
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29339726/publisher-correction-identification-and-characterization-of-two-functional-variants-in-the-human-longevity-gene-foxo3
#18
Friederike Flachsbart, Janina Dose, Liljana Gentschew, Claudia Geismann, Amke Caliebe, Carolin Knecht, Marianne Nygaard, Nandini Badarinarayan, Abdou ElSharawy, Sandra May, Anne Luzius, Guillermo G Torres, Marlene Jentzsch, Michael Forster, Robert Häsler, Kathrin Pallauf, Wolfgang Lieb, Céline Derbois, Pilar Galan, Dmitriy Drichel, Alexander Arlt, Andreas Till, Ben Krause-Kyora, Gerald Rimbach, Hélène Blanché, Jean-François Deleuze, Lene Christiansen, Kaare Christensen, Michael Nothnagel, Philip Rosenstiel, Stefan Schreiber, Andre Franke, Susanne Sebens, Almut Nebel
The original version of this Article contained an error in the spelling of the author Robert Häsler, which was incorrectly given as Robert Häesler. This has now been corrected in both the PDF and HTML versions of the Article.
January 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29305762/the-dance-of-attention-toward-an-aesthetic-dimension-of-attention-deficit
#19
Kasper Levin
What role does the aesthetics of bodily movement play in the understanding of attention among children diagnosed with attention-deficit/hyperactivity disorder (ADHD)? This article animates a phenomenological approach to attention and embodiment with a special focus on the relation between aesthetic or expressive bodily movement and behavioral awareness in children diagnosed with ADHD. However, beyond this it is argued that the aesthetic aspect of movement calls for an expansion of the phenomenological perspective...
March 2018: Integrative Psychological & Behavioral Science
https://www.readbyqxmd.com/read/29304377/the-comoros-show-the-earliest-austronesian-gene-flow-into-the-swahili-corridor
#20
Nicolas Brucato, Veronica Fernandes, Stéphane Mazières, Pradiptajati Kusuma, Murray P Cox, Joseph Wainaina Ng'ang'a, Mohammed Omar, Marie-Claude Simeone-Senelle, Coralie Frassati, Farida Alshamali, Bertrand Fin, Anne Boland, Jean-Francois Deleuze, Mark Stoneking, Alexander Adelaar, Alison Crowther, Nicole Boivin, Luisa Pereira, Pascal Bailly, Jacques Chiaroni, François-Xavier Ricaut
At the dawn of the second millennium, the expansion of the Indian Ocean trading network aligned with the emergence of an outward-oriented community along the East African coast to create a cosmopolitan cultural and trading zone known as the Swahili Corridor. On the basis of analyses of new genome-wide genotyping data and uniparental data in 276 individuals from coastal Kenya and the Comoros islands, along with large-scale genetic datasets from the Indian Ocean rim, we reconstruct historical population dynamics to show that the Swahili Corridor is largely an eastern Bantu genetic continuum...
January 4, 2018: American Journal of Human Genetics
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