keyword
MENU ▼
Read by QxMD icon Read
search

Signature

keyword
https://www.readbyqxmd.com/read/28340142/multigene-signature-for-predicting-prognosis-of-patients-with-1p19q-co-deletion-diffuse-glioma
#1
Xin Hu, Emmanuel Martinez-Ledesma, Siyuan Zheng, Hoon Kim, Floris Barthel, Tao Jiang, Kenneth R Hess, Roel G W Verhaak
Background.: Co-deletion of 1p and 19q marks a diffuse glioma subtype associated with relatively favorable overall survival; however, heterogeneous clinical outcomes are observed within this category. Methods.: We assembled gene expression profiles and sample annotation of 374 glioma patients carrying the 1p/19q co-deletion. We predicted 1p/19q status using gene expression when annotation was missing. A first cohort was randomly split into training (n = 170) and a validation dataset (n = 163)...
March 8, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28340056/neutrophil-derived-mitochondrial-dna-promotes-receptor-activator-of-nuclear-factor-%C3%AE%C2%BAb-and-its-ligand-signalling-in-rheumatoid-arthritis
#2
Anne Contis, Stéphane Mitrovic, Julie Lavie, Isabelle Douchet, Estibaliz Lazaro, Marie-Elise Truchetet, Cyril Goizet, Cécile Contin-Bordes, Thierry Schaeverbeke, Patrick Blanco, Rodrigue Rossignol, Benjamin Faustin, Christophe Richez, Pierre Duffau
Objectives.: Mitochondrial DNA (mtDNA) contains sequestered damage-associated molecular patterns that might be involved in osteoimmunological pathogenesis of RA. Here, we aimed to investigate the cellular source of mtDNA and its role in RANK ligand (RANKL) expression by RA SF neutrophils. Methods.: The gene expression signature of SF neutrophils was examined by proteomic quantitative analysis. Levels of mtDNA in circulating and SF neutrophils from RA patients and OA control subjects were assessed by real-time PCR...
March 13, 2017: Rheumatology
https://www.readbyqxmd.com/read/28339748/genotype-based-gene-signature-of-glioma-risk
#3
Yen-Tsung Huang, Yi Zhang, Zhijin Wu, Dominique S Michaud
Background.: Glioma accounts for 80% of malignant brain tumors, but its etiologic determinants remain elusive. Despite genetic susceptibility loci identified by genome-wide association study (GWAS), the agnostic approach leaves open the possibility that other susceptibility genes remain to be discovered. Here we conduct a gene-centric integrative GWAS (iGWAS) of glioma risk that combines transcriptomics and genetics. Methods.: We synthesized a brain transcriptomics dataset (n = 354), a GWAS dataset (n = 4203), and an advanced glioma tumor transcriptomic dataset (n = 483) to conduct an iGWAS...
February 22, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339517/omics-studies-their-use-in-diagnosis-and-reclassification-of-sle-and-other-systemic-autoimmune-diseases
#4
Maria Teruel, Chris Chamberlain, Marta E Alarcón-Riquelme
Omics studies of systemic autoimmune diseases (SADs) in general, and SLE in particular, have delivered isolated information from transcriptome, epigenome, genome, cytokine and metabolome analyses. Such analyses have resulted in the identification of disease susceptibility genes and the description of IFN expression signatures, allowing extensive insight into the mechanisms of disease and the development of new therapies. Access to such technologies allows the recognition of patterns of disease at a pathway level, thereby, to reclassify SLE and other SADs and to develop new therapeutics from a personalized perspective...
October 19, 2016: Rheumatology
https://www.readbyqxmd.com/read/28339273/search-for-electronic-recoil-event-rate-modulation-with-4-years-of-xenon100-data
#5
E Aprile, J Aalbers, F Agostini, M Alfonsi, F D Amaro, M Anthony, F Arneodo, P Barrow, L Baudis, B Bauermeister, M L Benabderrahmane, T Berger, P A Breur, A Brown, E Brown, S Bruenner, G Bruno, R Budnik, L Bütikofer, J Calvén, J M R Cardoso, M Cervantes, D Cichon, D Coderre, A P Colijn, J Conrad, J P Cussonneau, M P Decowski, P de Perio, P Di Gangi, A Di Giovanni, S Diglio, G Eurin, J Fei, A D Ferella, A Fieguth, D Franco, W Fulgione, A Gallo Rosso, M Galloway, F Gao, M Garbini, C Geis, L W Goetzke, Z Greene, C Grignon, C Hasterok, E Hogenbirk, R Itay, B Kaminsky, G Kessler, A Kish, H Landsman, R F Lang, D Lellouch, L Levinson, Q Lin, S Lindemann, M Lindner, J A M Lopes, A Manfredini, I Maris, T Marrodán Undagoitia, J Masbou, F V Massoli, D Masson, D Mayani, M Messina, K Micheneau, B Miguez, A Molinario, M Murra, J Naganoma, K Ni, U Oberlack, P Pakarha, B Pelssers, R Persiani, F Piastra, J Pienaar, V Pizzella, M-C Piro, G Plante, N Priel, L Rauch, S Reichard, C Reuter, A Rizzo, S Rosendahl, N Rupp, J M F Dos Santos, G Sartorelli, M Scheibelhut, S Schindler, J Schreiner, M Schumann, L Scotto Lavina, M Selvi, P Shagin, M Silva, H Simgen, M V Sivers, A Stein, D Thers, A Tiseni, G Trinchero, C Tunnell, H Wang, Y Wei, C Weinheimer, J Wulf, J Ye, Y Zhang
We report on a search for electronic recoil event rate modulation signatures in the XENON100 data accumulated over a period of 4 yr, from January 2010 to January 2014. A profile likelihood method, which incorporates the stability of the XENON100 detector and the known electronic recoil background model, is used to quantify the significance of periodicity in the time distribution of events. There is a weak modulation signature at a period of 431_{-14}^{+16} day in the low energy region of (2.0-5.8) keV in the single scatter event sample, with a global significance of 1...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28339253/distinct-evolutions-of-weyl-fermion-quasiparticles-and-fermi-arcs-with-bulk-band-topology-in-weyl-semimetals
#6
N Xu, G Autès, C E Matt, B Q Lv, M Y Yao, F Bisti, V N Strocov, D Gawryluk, E Pomjakushina, K Conder, N C Plumb, M Radovic, T Qian, O V Yazyev, J Mesot, H Ding, M Shi
The Weyl semimetal phase is a recently discovered topological quantum state of matter characterized by the presence of topologically protected degeneracies near the Fermi level. These degeneracies are the source of exotic phenomena, including the realization of chiral Weyl fermions as quasiparticles in the bulk and the formation of Fermi arc states on the surfaces. Here, we demonstrate that these two key signatures show distinct evolutions with the bulk band topology by performing angle-resolved photoemission spectroscopy, supported by first-principles calculations, on transition-metal monophosphides...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28339246/impact-of-atomic-scale-contact-geometry-on-andreev-reflection
#7
J Brand, P Ribeiro, N Néel, S Kirchner, J Kröger
Charge transport has been examined in junctions comprising the normal-metal tip of a low-temperature scanning tunneling microscope, the surface of a conventional superconductor, and adsorbed C_{60} molecules. The Bardeen-Cooper-Schrieffer energy gap gradually evolves into a zero-bias peak with decreasing electrode separation. The peak is assigned to the spectroscopic signature of Andreev reflection. The conductance due to Andreev reflection is determined by the atomic termination of the tip apex and the molecular adsorption orientation...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28335224/structural-changes-induced-in-grapevine-vitis-vinifera-l-dna-by-femtosecond-ir-laser-pulses-a-surface-enhanced-raman-spectroscopic-study
#8
Nicoleta E Dina, Cristina M Muntean, Nicolae Leopold, Alexandra Fălămaș, Adela Halmagyi, Ana Coste
In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300-1800 cm(-1). Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case...
May 25, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334937/dynamically-and-epigenetically-coordinated-gata-ets-sox-transcription-factor-expression-is-indispensable-for-endothelial-cell-differentiation
#9
Yasuharu Kanki, Ryo Nakaki, Teppei Shimamura, Taichi Matsunaga, Kohei Yamamizu, Shiori Katayama, Jun-Ichi Suehiro, Tsuyoshi Osawa, Hiroyuki Aburatani, Tatsuhiko Kodama, Youichiro Wada, Jun K Yamashita, Takashi Minami
Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analysed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334887/avoidance-of-apobec3b-induced-mutation-by-error-free-lesion-bypass
#10
James I Hoopes, Amber L Hughes, Lauren A Hobson, Luis M Cortez, Alexander J Brown, Steven A Roberts
APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR)...
March 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334820/high-resolution-time-course-mapping-of-early-transcriptomic-molecular-and-cellular-phenotypes-in-huntington-s-disease-cag-knock-in-mice-across-multiple-genetic-backgrounds
#11
Seth A Ament, Jocelynn R Pearl, Andrea Grindeland, Jason St Claire, John C Earls, Marina Kovalenko, Tammy Gillis, Jayalakshmi Mysore, James F Gusella, Jong-Min Lee, Seung Kwak, David Howland, Min Young Lee, David Baxter, Kelsey Scherler, Kai Wang, Donald Geman, Jeffrey B Carroll, Marcy E MacDonald, George Carlson, Vanessa C Wheeler, Nathan D Price, Leroy E Hood
Huntington's disease is a dominantly inherited neurodegenerative disease caused by the expansion of a CAG repeat in the HTT gene. In addition to the length of the CAG expansion, factors such as genetic background have been shown to contribute to the age at onset of neurological symptoms. A central challenge in understanding the disease progression that leads from the HD mutation to massive cell death in the striatum is the ability to characterize the subtle and early functional consequences of the CAG expansion longitudinally...
February 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334819/comparative-analyses-of-the-thermodynamic-rna-binding-signatures-of-different-types-of-rna-recognition-motifs
#12
Brighton Samatanga, Antoine Cléry, Pierre Barraud, Frédéric H-T Allain, Ilian Jelesarov
RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334816/dynamic-changes-in-chromatin-states-during-specification-and-differentiation-of-adult-intestinal-stem-cells
#13
Juri Kazakevych, Sergi Sayols, Berith Messner, Christina Krienke, Natalia Soshnikova
Epigenetic mechanisms, including chromatin structure, chromatin dynamics and histone modifications play an important role for maintenance and differentiation of pluripotent embryonic stem cells. However, little is known about the molecular mechanisms of adult stem cell specification and differentiation. Here, we used intestinal stem cells (ISCs) as a model system to reveal the epigenetic changes coordinating gene expression programs during these processes. We found that two distinct epigenetic mechanisms participate in establishing the transcriptional program promoting ISC specification from embryonic progenitors...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334209/comparative-study-of-chemosensory-organs-of-shrimp-from-hydrothermal-vent-and-coastal-environments
#14
Magali Zbinden, Camille Berthod, Nicolas Montagné, Julia Machon, Nelly Léger, Thomas Chertemps, Nicolas Rabet, Bruce Shillito, Juliette Ravaux
The detection of chemical signals is involved in a variety of crustacean behaviors, such as social interactions, search and evaluation of food and navigation in the environment. At hydrothermal vents, endemic shrimp may use the chemical signature of vent fluids to locate active edifices, however little is known on their sensory perception in these remote deep-sea habitats. Here, we present the first comparative description of the sensilla on the antennules and antennae of 4 hydrothermal vent shrimp (Rimicaris exoculata, Mirocaris fortunata, Chorocaris chacei, and Alvinocaris markensis) and of a closely related coastal shrimp (Palaemon elegans)...
February 22, 2017: Chemical Senses
https://www.readbyqxmd.com/read/28334208/morphologically-constrained-spectral-unmixing-by-dictionary-learning-for-multiplex-fluorescence-microscopy
#15
Murad Megjhani, Pedro Correa de Sampaio, Julienne Leigh Carstens, Raghu Kalluri, Badrinath Roysam
Motivation: Current spectral unmixing methods for multiplex fluorescence microscopy have a limited ability to cope with high spectral overlap as they only analyze spectral information over individual pixels. Here, we present adaptive Morphologically Constrained Spectral Unmixing (MCSU) algorithms that overcome this limitation by exploiting morphological differences between sub-cellular structures, and their local spatial context. Results: The proposed method was effective at improving spectral unmixing performance by exploiting: (i) a set of dictionary-based models for object morphologies learned from the image data; and (ii) models of spatial context learned from the image data using a total variation algorithm...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334074/genome-wide-analysis-reveals-that-exon-methylation-facilitates-its-selective-usage-in-the-human-transcriptome
#16
Shengli Li, Jiwei Zhang, Shenglin Huang, Xianghuo He
DNA methylation, especially in promoter regions, is a well-characterized epigenetic marker related to gene expression regulation in eukaryotes. However, the role of intragenic DNA methylation in the usage of corresponding exons still remains elusive. In this study, we described the DNA methylome across 10 human tissues. The human genome showed both conserved and varied methylation levels among these tissues. We found that the methylation densities in promoters and first exons were negatively correlated with the corresponding gene expression level...
February 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333954/distance-in-cancer-gene-expression-from-stem-cells-predicts-patient-survival
#17
Markus Riester, Hua-Jun Wu, Ahmet Zehir, Mithat Gönen, Andre L Moreira, Robert J Downey, Franziska Michor
The degree of histologic cellular differentiation of a cancer has been associated with prognosis but is subjectively assessed. We hypothesized that information about tumor differentiation of individual cancers could be derived objectively from cancer gene expression data, and would allow creation of a cancer phylogenetic framework that would correlate with clinical, histologic and molecular characteristics of the cancers, as well as predict prognosis. Here we utilized mRNA expression data from 4,413 patient samples with 7 diverse cancer histologies to explore the utility of ordering samples by their distance in gene expression from that of stem cells...
2017: PloS One
https://www.readbyqxmd.com/read/28333933/geometry-dependent-functional-changes-in-ipsc-derived-cardiomyocytes-probed-by-functional-imaging-and-rna-sequencing
#18
Christopher A Werley, Miao-Ping Chien, Jellert Gaublomme, Karthik Shekhar, Vincent Butty, B Alexander Yi, Joel M Kralj, William Bloxham, Laurie A Boyer, Aviv Regev, Adam E Cohen
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are a promising platform for cardiac studies in vitro, and possibly for tissue repair in humans. However, hiPSC-CM cells tend to retain morphology, metabolism, patterns of gene expression, and electrophysiology similar to that of embryonic cardiomyocytes. We grew hiPSC-CM in patterned islands of different sizes and shapes, and measured the effect of island geometry on action potential waveform and calcium dynamics using optical recordings of voltage and calcium from 970 islands of different sizes...
2017: PloS One
https://www.readbyqxmd.com/read/28333931/differential-gene-expression-in-patients-with-subsyndromal-symptomatic-depression-and-major-depressive-disorder
#19
Chengqing Yang, Guoqin Hu, Zezhi Li, Qingzhong Wang, Xuemei Wang, Chengmei Yuan, Zuowei Wang, Wu Hong, Weihong Lu, Lan Cao, Jun Chen, Yong Wang, Shunying Yu, Yimin Zhou, Zhenghui Yi, Yiru Fang
BACKGROUND: Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and can lead to significant psychosocial functional impairment. Although the pathogenesis of major depressive disorder (MDD) and SSD still remains poorly understood, a set of studies have found that many same genetic factors play important roles in the etiology of these two disorders. Nowadays, the differential gene expression between MDD and SSD is still unknown. In our previous study, we compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD and matched healthy controls (8 subjects in each group), and finally determined 48 gene expression signatures...
2017: PloS One
https://www.readbyqxmd.com/read/28333845/changes-in-the-extracellular-matrix-are-associated-with-the-development-of-serous-tubal-intraepithelial-carcinoma-into-high-grade-serous-carcinoma
#20
Sophieke C H A van der Steen, Johan Bulten, Koen K Van de Vijver, Toin H van Kuppevelt, Leon F A G Massuger
OBJECTIVE: The identification of a marker for early progression of preinvasive lesions into invasive pelvic high-grade serous carcinoma (HGSC) may provide novel handles for innovative screening and prevention strategies. The interplay between cancer cells and the extracellular matrix (ECM) is one of the main principles in cancer development and growth, but has been largely neglected in preinvasive lesions. This is the first study addressing the involvement of the ECM in the "step-by-step" transition of normal fallopian tube epithelium into preinvasive lesions, and eventually the progression of preinvasive lesions into invasive HGSC...
March 23, 2017: International Journal of Gynecological Cancer
keyword
keyword
3543
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"