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https://www.readbyqxmd.com/read/28712776/clonal-evolution-in-paired-endometrial-intraepithelial-neoplasia-atypical-hyperplasia-and-endometrioid-adenocarcinoma
#1
Mariano Russo, James Broach, Kathryn Sheldon, Kenneth R Houser, Dajiang J Liu, Joshua Kesterson, Rebecca Phaeton, Carrie Hossler, Nadine Hempel, Maria Baker, Jordan M Newell, Richard Zaino, Joshua I Warrick
Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically-defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma...
July 13, 2017: Human Pathology
https://www.readbyqxmd.com/read/28710315/shallow-whole-genome-sequencing-on-circulating-cell-free-dna-allows-reliable-non-invasive-copy-number-profiling-in-neuroblastoma-patients
#2
Nadine Van Roy, Malaika Van der Linden, Björn Menten, Annelies Dheedene, Charlotte Vandeputte, Jo Van Dorpe, Geneviève Laureys, Marleen Renard, Tom Sante, Tim Lammens, Bram De Wilde, Frank Speleman, Katleen De Preter
<p>Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of NB patients could offer a valuable alternative to primary tumor DNA for CNA profiling.</p> <br /><br />Experimental Design: <p>In 37 NB patients cfDNA analysis using shallow whole genome sequencing (sWGS) was compared to arrayCGH analysis of primary tumor tissue...
July 14, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28701032/bcl2-regulation-according-to-molecular-subtype-of-breast-cancer-by-analysis-of-the-cancer-genome-atlas-database
#3
Ki-Tae Hwang, Kwangsoo Kim, Ji Hyun Chang, Sohee Oh, Young A Kim, Jong Yoon Lee, Se Hee Jung, In Sil Choi
Purpose: We investigated BCL2 regulation across DNA, RNA, protein, and methylation status according to molecular subtype of breast cancer using The Cancer Genome Atlas (TCGA) database. Materials and Methods: We analyzed clinical and biological data on 1,096 breast cancers from the TCGA database. Biological data included reverse phase protein array (RPPA), mRNA sequencing (mRNA seq), mRNA microarray, methylation, copy number alteration linear, copy number alteration nonlinear, and mutation data...
July 4, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28683472/comprehensive-analysis-of-copy-number-aberrations-in-microsatellite-stable-colon-cancer-in-view-of-stromal-component
#4
M Henar Alonso, Susanna Aussó, Adriana Lopez-Doriga, David Cordero, Elisabet Guinó, Xavier Solé, Mercè Barenys, Javier de Oca, Gabriel Capella, Ramón Salazar, Rebeca Sanz-Pamplona, Victor Moreno
BACKGROUND: Somatic copy number aberrations (CNAs) are common acquired changes in cancer cells having an important role in the progression of colon cancer (colorectal cancer, CRC). This study aimed to perform a characterisation of CNA and their impact in gene expression. METHODS: Copy number aberrations were inferred from SNP array data in a series of 99 CRC. Copy number aberration events were calculated and used to assess the association between copy number dosage, clinical and molecular characteristics of the tumours, and gene expression changes...
July 6, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28665944/molecular-mechanics-of-staphylococcus-aureus-adhesin-cna-and-the-inhibition-of-bacterial-adhesion-by-stretching-collagen
#5
Ali Madani, Kiavash Garakani, Mohammad R K Mofrad
Bacterial adhesion to collagen, the most abundant protein in humans, is a critical step in the initiation and persistence of numerous bacterial infections. In this study, we explore the collagen binding mechanism of the multi-modular cell wall anchored collagen adhesin (CNA) in Staphylococcus aureus and examine how applied mechanical forces can modulate adhesion ability. The common structural-functional elements and domain organization of CNA are present across over 50 genera of bacteria. Through the use of molecular dynamics models and normal mode analysis, we shed light on the CNA's structural and conformational dynamics and its interactions with collagen that lead to collagen binding...
2017: PloS One
https://www.readbyqxmd.com/read/28636060/developing-mobile-clinical-decision-support-for-nursing-home-staff-assessment-of-urinary-tract-infection-using-goal-directed-design
#6
Wallace Jones, Cynthia Drake, David Mack, Blaine Reeder, Barbara Trautner, Heidi Wald
BACKGROUND: Unique characteristics of nursing homes (NHs) contribute to high rates of inappropriate antibiotic use for asymptomatic bacteriuria (ASB), a benign condition. A mobile clinical decision support system (CDSS) may support NH staff in differentiating urinary tract infections (UTI) from ASB and reducing antibiotic days. OBJECTIVES: We used Goal-Directed Design to: 1) Characterize information needs for UTI identification and management in NHs; 2) Develop UTI Decide, a mobile CDSS prototype informed by personas and scenarios of use constructed from Aim 1 findings; 3) Evaluate the UTI Decide prototype with NH staff...
June 20, 2017: Applied Clinical Informatics
https://www.readbyqxmd.com/read/28631967/reasons-for-referral-and-findings-of-clinical-neuropsychological-assessment-in-youth-with-mental-illness-a-clinical-file-audit
#7
Tina-Marie Proffitt, Warrick J Brewer, Emma M Parrish, Patrick D McGorry, Kelly A Allott
Study aims were to 1) determine the characteristics and reasons for referral for Clinical Neuropsychological Assessment (CNA) and 2) characterize the findings and recommendations contained in the CNA reports, of clients attending a youth mental health service. File audit of all CNA reports (N = 140) of youth attending a mental health service. Cognitive performances on neuropsychological tests that were administered to >50% of clients were examined. Referral reasons, findings, and recommendations for future treatment were coded and described from neuropsychological files...
February 22, 2017: Applied Neuropsychology. Child
https://www.readbyqxmd.com/read/28631637/an-integrated-genomic-profile-that-includes-copy-number-alterations-is-highly-predictive-of-minimal-residual-disease-status-in-childhood-precursor-b-lineage-acute-lymphoblastic-leukemia
#8
Nikhil Patkar, P G Subramanian, Prashant Tembhare, Sneha Mandalia, Gaurav Chaterjee, Nikhil Rabade, Rohan Kodgule, Karishma Chopra, Asma Bibi, Swapnali Joshi, Shruti Chaudhary, Russel Mascerhenas, Pratibha Kadam-Amare, Gaurav Narula, Brijesh Arora, Shripad Banavali, Sumeet Gujral
INTRODUCTION: Copy number alterations (CNA) have been described in childhood precursor B-lineage acute lymphoblastic leukemia (B-ALL) which in conjunction with chromosomal abnormalities drive leukemogenesis. There is no consensus on the clinical incorporation of CNA in B-ALL. An integrated genomic classification (IGC) has been proposed which includes CNA and cytogenetics. METHODS: We correlated this IGC with immunophenotypic minimal residual disease (MRD) as well as other standard criteria for 245 patients of B-ALL such as National Cancer Institute (NCI) risk, D+8 prednisolone response, cytogenetics, and ploidy status...
April 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/28584253/prediction-of-outcome-in-newly-diagnosed-myeloma-a-meta-analysis-of-the-molecular-profiles-of-1-905-trial-patients
#9
V Shah, A L Sherborne, B A Walker, D C Johnson, E M Boyle, S Ellis, D B Begum, P Z Proszek, J R Jones, C Pawlyn, S Savola, M W Jenner, M T Drayson, R G Owen, R S Houlston, D A Cairns, W M Gregory, G Cook, F E Davies, G H Jackson, G J Morgan, M F Kaiser
Robust establishment of survival in multiple myeloma (MM) and its relationship to recurrent genetic aberrations is required as outcomes are variable despite apparent similar staging. We assayed copy number alterations (CNA) and translocations in 1036 patients from the NCRI Myeloma XI trial and linked these to overall survival (OS) and progression-free survival. Through a meta-anlysis of these data with data from MRC Myeloma IX trial, totalling 1905 newly diagnosed MM patients (NDMM), we confirm the association of t(4;14), t(14;16), t(14;20), del(17p) and gain(1q21) with poor prognosis with hazard ratios (HRs) for OS of 1...
June 6, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28573936/exploring-variation-in-certified-nursing-assistant-assignments-from-the-perspective-of-nursing-home-residents-a-comparison-of-adopters-and-nonadopters-of-consistent-assignment
#10
Tonya J Roberts, Kimberly Nolet, Barbara Bowers
OBJECTIVE: To describe and compare certified nursing assistant (CNA) staffing between adopter and nonadopters of consistent assignment. DATA SOURCES: One month of preexisting CNA assignment and scheduling sheets from a purposive sample of 30 homes. STUDY DESIGN: A descriptive comparative study was conducted to calculate and compare numbers of CNAs assigned per resident across homes. DATA EXTRACTION: Resident names and CNA assignments were abstracted from assignment records and entered into the Advancing Excellence consistent assignment tool to calculate numbers of CNAs assigned per resident...
June 1, 2017: Journal of Applied Gerontology: the Official Journal of the Southern Gerontological Society
https://www.readbyqxmd.com/read/28561911/biofilm-formation-and-virulence-factor-analysis-of-staphylococcus-aureus-isolates-collected-from-ovine-mastitis
#11
E Azara, C Longheu, G Sanna, S Tola
AIMS: To perform a phenotypic and genotypic characterization of 258 Staphylococcus aureus isolates from clinical ovine mastitis and used for the preparation of inactivated autogenous vaccines. METHODS AND RESULTS: The potential for biofilm production was determined by phenotypic test of Congo Red Agar (CRA) and by PCR for the detection of icaA/D genes. Isolates were also screened by PCR for the presence of enterotoxins (sea, seb, sec, sed and see), toxic shock syndrome toxin (tsst), leukotoxins (lukD-E, lukM and lukPV83), haemolysins (hly-β and hly-γ), autolysin (atlA) genes and encoding microbial surface components recognizing adhesive matrix molecules (MSCRAMMs: clfA, clfB, fnbA, fnbB, bbp, cna, eno, fib, epbs, sdrC, sdrD and SdrE)...
May 31, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28559012/establishment-and-characterization-of-an-oral-tongue-squamous-cell-carcinoma-cell-line-from-a-never-smoking-patient
#12
Steven J Wang, Saurabh Asthana, Annemieke van Zante, Chase M Heaton, Janyaporn Phuchareon, Leighton Stein, Saito Higuchi, Tomoya Kishimoto, Charles Y Chiu, Adam B Olshen, Frank McCormick, Osamu Tetsu
OBJECTIVE: The rising incidence of oral tongue squamous cell carcinoma (OTSCC) in patients who have never smoked and the paucity of knowledge of its biological behavior prompted us to develop a new cell line originating from a never-smoker. MATERIALS AND METHODS: Fresh tumor tissue of keratinizing OTSCC was collected from a 44-year-old woman who had never smoked. Serum-free media with a low calcium concentration were used in cell culture, and a multifaceted approach was taken to verify and characterize the cell line, designated UCSF-OT-1109...
June 2017: Oral Oncology
https://www.readbyqxmd.com/read/28555401/emerging-multidrug-resistant-bengal-bay-clone-st772-mrsa-v-in-norway-molecular-epidemiology-2004-2014
#13
A Blomfeldt, K W Larssen, A Moghen, C Gabrielsen, P Elstrøm, H V Aamot, S B Jørgensen
A multidrug-resistant, methicillin-resistant Staphylococcus aureus (MRSA) clone, PVL-positive ST772-MRSA-V, named the Bengal Bay clone, is emerging worldwide. In Norway, where MRSA prevalence is low, a sudden increase in ST772-MRSA-V initiated a nationwide molecular epidemiological study. Clinical data were obtained from the Norwegian Surveillance System for Communicable Diseases (MSIS). S. aureus isolates were characterised by antibiotic susceptibility profiles and comprehensive genotyping (spa typing, MLVA, DNA microarray)...
May 29, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28548965/inhibition-of-colorectal-cancer-genomic-copy-number-alterations-and-chromosomal-fragile-site-tumor-suppressor-fhit-and-wwox-deletions-by-dna-mismatch-repair
#14
Sohail Jahid, Jian Sun, Ozkan Gelincik, Pedro Blecua, Winfried Edelmann, Raju Kucherlapati, Kathy Zhou, Maria Jasin, Zeynep H Gümüş, Steven M Lipkin
Homologous recombination (HR) enables precise DNA repair after DNA double strand breaks (DSBs) using identical sequence templates, whereas homeologous recombination (HeR) uses only partially homologous sequences. Homeologous recombination introduces mutations through gene conversion and genomic deletions through single-strand annealing (SSA). DNA mismatch repair (MMR) inhibits HeR, but the roles of mammalian MMR MutL homologues (MLH1, PMS2 and MLH3) proteins in HeR suppression are poorly characterized. Here, we demonstrate that mouse embryonic fibroblasts (MEFs) carrying Mlh1, Pms2, and Mlh3 mutations have higher HeR rates, by using 7,863 uniquely mapping paired direct repeat sequences (DRs) in the mouse genome as endogenous gene conversion and SSA reporters...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28487279/single-cell-sequencing-deciphers-a-convergent-evolution-of-copy-number-alterations-from-primary-to-circulating-tumour-cells
#15
Yan Gao, Xiaohui Ni, Hua Guo, Zhe Su, Yi Ba, Zhongsheng Tong, Zhi Guo, Xin Yao, Xixi Chen, Jian Yin, Zhao Yan, Lin Guo, Ying Liu, Fan Bai, Xiaoliang Sunney Xie, Ning Zhang
Copy number alteration (CNA) is a major contributor to genome instability, a hallmark of cancer. Here we studied genomic alterations in single primary tumour cells and circulating tumour cells (CTCs) from the same patient. Single-nucleotide variations (SNVs) in single cells from both samples occurred sporadically, whereas CNAs among primary tumour cells emerged accumulatively rather than abruptly, converging toward that of CTCs. Focal CNAs affecting MYC gene and PTEN gene were observed only in a minor portion of primary tumour cells but were present in all CTCs, suggesting a strong selection toward metastasis...
May 9, 2017: Genome Research
https://www.readbyqxmd.com/read/28486536/stratification-of-clear-cell-renal-cell-carcinoma-ccrcc-genomes-by-gene-directed-copy-number-alteration-cna-analysis
#16
H-J Thiesen, F Steinbeck, M Maruschke, D Koczan, B Ziems, O W Hakenberg
Tumorigenic processes are understood to be driven by epi-/genetic and genomic alterations from single point mutations to chromosomal alterations such as insertions and deletions of nucleotides up to gains and losses of large chromosomal fragments including products of chromosomal rearrangements e.g. fusion genes and proteins. Overall comparisons of copy number alterations (CNAs) presented in 48 clear cell renal cell carcinoma (ccRCC) genomes resulted in ratios of gene losses versus gene gains between 26 ccRCC Fuhrman malignancy grades G1 (ratio 1...
2017: PloS One
https://www.readbyqxmd.com/read/28477236/pathogen-related-factors-affecting-outcome-of-catheter-related-bacteremia-due-to-methicillin-susceptible-staphylococcus-aureus-in-a-spanish-multicenter-study
#17
R San-Juan, D Pérez-Montarelo, E Viedma, A Lalueza, J Fortún, E Loza, M Pujol, C Ardanuy, I Morales, M de Cueto, E Resino-Foz, M A Morales-Cartagena, M Fernández-Ruiz, A Rico, M P Romero, M Fernández de Mera, F López-Medrano, M Á Orellana, J M Aguado, F Chaves
Even with appropriate clinical management, complicated methicillin-susceptible Staphylococcus aureus (MSSA) catheter-related bacteremia (CRB) is frequent. We investigated the influence of molecular characteristics of MSSA strains on the risk of complicated bacteremia (CB) in MSSA-CRB. A multicenter prospective study was conducted in Spain between 2011 and 2014 on MSSA-CRB. Optimized protocol-guided clinical management was required. CB included endocarditis, septic thrombophlebitis, persistent bacteremia and/or end-organ hematogenous spread...
May 5, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28468230/developing-a-water-quality-index-wqi-for-an-irrigation-dam
#18
Celia De La Mora-Orozco, Hugo Flores-Lopez, Hector Rubio-Arias, Alvaro Chavez-Duran, Jesus Ochoa-Rivero
Pollution levels have been increasing in water ecosystems worldwide. A water quality index (WQI) is an available tool to approximate the quality of water and facilitate the work of decision-makers by grouping and analyzing numerous parameters with a single numerical classification system. The objective of this study was to develop a WQI for a dam used for irrigation of about 5000 ha of agricultural land. The dam, La Vega, is located in Teuchitlan, Jalisco, Mexico. Seven sites were selected for water sampling and samples were collected in March, June, July, September, and December 2014 in an initial effort to develop a WQI for the dam...
April 29, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28464328/inferring-gene-regulatory-relationships-with-a-high-dimensional-robust-approach
#19
Yangguang Zang, Qing Zhao, Qingzhao Zhang, Yang Li, Sanguo Zhang, Shuangge Ma
Gene expression (GE) levels have important biological and clinical implications. They are regulated by copy number alterations (CNAs). Modeling the regulatory relationships between GEs and CNAs facilitates understanding disease biology and can also have values in translational medicine. The expression level of a gene can be regulated by its cis-acting as well as trans-acting CNAs, and the set of trans-acting CNAs is usually not known, which poses a high-dimensional selection and estimation problem. Most of the existing studies share a common limitation in that they cannot accommodate long-tailed distributions or contamination of GE data...
May 2, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28460482/gene-based-comparative-analysis-of-tools-for-estimating-copy-number-alterations-using-whole-exome-sequencing-data
#20
Hyung-Yong Kim, Jin-Woo Choi, Jeong-Yeon Lee, Gu Kong
Accurate detection of copy number alterations (CNAs) using next-generation sequencing technology is essential for the development and application of more precise medical treatments for human cancer. Here, we evaluated seven CNA estimation tools (ExomeCNV, CoNIFER, VarScan2, CODEX, ngCGH, saasCNV, and falcon) using whole-exome sequencing data from 419 breast cancer tumor-normal sample pairs from The Cancer Genome Atlas. Estimations generated using each tool were converted into gene-based copy numbers; concordance for gains and losses and the sensitivity and specificity of each tool were compared to validated copy numbers from a single nucleotide polymorphism reference array...
April 18, 2017: Oncotarget
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