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https://www.readbyqxmd.com/read/29865805/the-nature-of-the-pt-111-%C3%AE-fe-2-o-3-0001-interfaces-revealed-by-dft-calculations
#1
Agnes Mahmoud, Pierre-Marie Deleuze, Céline Dupont
Density functional theory calculations are performed to give a thorough description of structural, energetic, and electronic properties of Pt(111)/α-Fe2 O3 (0001) systems by spin-polarized calculations, accounting for the on-site Coulomb interaction. Toward the better understanding of Pt(111)/α-Fe2 O3 (0001) interfaces, two terminations of α-Fe2 O3 (0001) surface, namely, the single Fe- and the O3 -termination, are considered and coupled with the four possible (top, hcp, fcc, and bridge) sites on Pt(111)...
May 28, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29726922/macaron-a-python-framework-to-identify-and-re-annotate-multi-base-affected-codons-in-whole-genome-exome-sequence-data
#2
Waqasuddin Khan, Ganapathi Varma- Saripella, Thomas Ludwig, Tania Cuppens, Florian Thibord, Emmanuelle Génin, Jean-Francois Deleuze, David-Alexandre Trégouët
Summary: Predicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon...
May 3, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29708508/second-hit-mosaic-mutation-in-mtorc1-repressor-depdc5-causes-focal-cortical-dysplasia-associated-epilepsy
#3
Théo Ribierre, Charlotte Deleuze, Alexandre Bacq, Sara Baldassari, Elise Marsan, Mathilde Chipaux, Giuseppe Muraca, Delphine Roussel, Vincent Navarro, Eric Leguern, Richard Miles, Stéphanie Baulac
DEP domain-containing 5 protein (DEPDC5) is a repressor of the recently recognized amino acid-sensing branch of the mTORC1 pathway. So far, its function in the brain remains largely unknown. Germline loss-of-function mutations in DEPDC5 have emerged as a major cause of familial refractory focal epilepsies, with case reports of sudden unexpected death in epilepsy (SUDEP). Remarkably, a fraction of patients also develop focal cortical dysplasia (FCD), a neurodevelopmental cortical malformation. We therefore hypothesized that a somatic second-hit mutation arising during brain development may support the focal nature of the dysplasia...
June 1, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29697281/enrichment-of-methylated-molecules-using-enhanced-ice-co-amplification-at-lower-denaturation-temperature-pcr-e-ice-cold-pcr-for-the-sensitive-detection-of-disease-related-hypermethylation
#4
Florence Mauger, Magali Kernaleguen, Céline Lallemand, Vessela N Kristensen, Jean-François Deleuze, Jörg Tost
AIM: The detection of specific DNA methylation patterns bears great promise as biomarker for personalized management of cancer patients. Co-amplification at lower denaturation temperature-PCR (COLD-PCR) assays are sensitive methods, but have previously only been able to analyze loss of DNA methylation. MATERIALS & METHODS: Enhanced (E)-ice-COLD-PCR reactions starting from 2 ng of bisulfite-converted DNA were developed to analyze methylation patterns in two promoters with locked nucleic acid (LNA) probes blocking amplification of unmethylated CpGs...
April 26, 2018: Epigenomics
https://www.readbyqxmd.com/read/29695756/disease-causing-variants-in-tcf4-are-a-frequent-cause-of-intellectual-disability-lessons-from-large-scale-sequencing-approaches-in-diagnosis
#5
Laura Mary, Amélie Piton, Elise Schaefer, Francesca Mattioli, Elsa Nourisson, Claire Feger, Claire Redin, Magali Barth, Salima El Chehadeh, Estelle Colin, Christine Coubes, Laurence Faivre, Elisabeth Flori, David Geneviève, Yline Capri, Laurence Perrin, Jennifer Fabre-Teste, Dana Timbolschi, Alain Verloes, Robert Olaso, Anne Boland, Jean-François Deleuze, Jean-Louis Mandel, Bénédicte Gerard, Irina Giurgea
High-throughput sequencing (HTS) of human genome coding regions allows the simultaneous screen of a large number of genes, significantly improving the diagnosis of non-syndromic intellectual disabilities (ID). HTS studies permit the redefinition of the phenotypical spectrum of known disease-causing genes, escaping the clinical inclusion bias of gene-by-gene Sanger sequencing. We studied a cohort of 903 patients with ID not reminiscent of a well-known syndrome, using an ID-targeted HTS of several hundred genes and found de novo heterozygous variants in TCF4 (transcription factor 4) in eight novel patients...
April 26, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29692974/lipid-nanocapsules-formulation-and-cellular-activities-evaluation-of-a-promising-anticancer-agent-eapb0503
#6
Adrien Chouchou, Anne Aubert-Pouëssel, Christophe Dorandeu, Zahraa Zghaib, Pierre Cuq, Jean-Marie Devoisselle, Pierre-Antoine Bonnet, Sylvie Bégu, Carine Deleuze-Masquefa
Objective: EAPB0503, lead compound of imiqualines, presented high antitumor activities but also a very low water solubility which was critical for further preclinical studies. To apply to EAPB0503, a robust and safe lipid formulation already used for poor soluble anticancer agents for injectable administration at a concentration higher than 1 mg/mL. Materials and Methods: Physicochemical properties of EAPB0503 were determined to consider an adapted formulation. In a second time, lipid nanocapsules (LNC) formulations based on the phase-inversion process were developed for EAPB0503 encapsulation...
October 2017: International Journal of Pharmaceutical Investigation
https://www.readbyqxmd.com/read/29688594/whole-genome-sequencing-in-patients-with-ciliopathies-uncovers-a-novel-recurrent-tandem-duplication-in-ift140
#7
Véronique Geoffroy, Corinne Stoetzel, Sophie Scheidecker, Elise Schaefer, Isabelle Perrault, Séverine Bär, Ariane Kröll, Marion Delbarre, Manuela Antin, Anne-Sophie Leuvrey, Charline Henry, Hélène Blanché, Eva Decker, Katja Kloth, Günter Klaus, Christoph Mache, Dominique Martin-Coignard, Steven McGinn, Anne Boland, Jean-François Deleuze, Sylvie Friant, Sophie Saunier, Jean-Michel Rozet, Carsten Bergmann, Hélène Dollfus, Jean Muller
Ciliopathies represent a wide spectrum of rare diseases with overlapping phenotypes and a high genetic heterogeneity. Among those, IFT140 is implicated in a variety of phenotypes ranging from isolated retinis pigmentosa to more syndromic cases. Using whole-genome sequencing in patients with uncharacterized ciliopathies, we identified a novel recurrent tandem duplication of exon 27-30 (6.7 kb) in IFT140, c.3454-488_4182+2588dup p.(Tyr1152_Thr1394dup), missed by whole-exome sequencing. Pathogenicity of the mutation was assessed on the patients' skin fibroblasts...
July 2018: Human Mutation
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
#8
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
#9
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...
May 3, 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
#10
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 MRI changes in patients with mutations in the rod domain of MYH7, including 1 with mosaicism and 3 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
#11
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
#12
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
#13
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 1, 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
#14
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
#15
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)...
July 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
#16
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
#17
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
#18
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
#19
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
#20
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)...
February 15, 2018: Nature Communications
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