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https://www.readbyqxmd.com/read/28487279/single-cell-sequencing-deciphers-a-convergent-evolution-of-copy-number-alterations-from-primary-to-circulating-tumour-cells
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/28424921/evolution-of-psychological-condition-in-caregivers-of-patients-with-disorders-of-consciousness-a-longitudinal-study
#7
Francesco Corallo, Lilla Bonanno, Viviana Lo Buono, Simona De Salvo, Cettina Allone, Rosanna Palmeri, Elena La Gattuta, Carmela Rifici, Antonella Alagna, Antonino Todaro, Placido Bramanti, Silvia Marino
The aim of this study is to evaluate mood disorders and needs in caregivers of disorders of consciousness (DOC) patients during the admission to Neurorehabilitation Unit. A total of 80 caregivers was enrolled and divided in two groups (caregivers of vegetative state-VS patients and caregivers of minimally conscious state-MCS patients). Paired sample t tests were carried out to test differences between baseline observation (T0) and after 6 months (T1). Caregivers of VS patients showed an improvement between T0 and T1 especially, in vitality, mean health, Beck Depression Inventory (BDI-II), Spielberger State-Trait Anxiety Inventory-Y (STAI-Y), Prolonged Grief Disorder (PG 12) and Caregiver Needs Assessment (CNA)...
April 19, 2017: Neurological Sciences
https://www.readbyqxmd.com/read/28415968/how-to-explore-the-needs-of-informal-caregivers-of-individuals-with-cognitive-impairment-in-alzheimer-s-disease-or-related-diseases-a-systematic-review-of-quantitative-and-qualitative-studies
#8
REVIEW
T Novais, V Dauphinot, P Krolak-Salmon, C Mouchoux
BACKGROUND: This study aims to review the methodologies used to identify the needs, the existing needs assessment instruments and the main topics of needs explored among caregivers of patients with mild cognitive impairment to dementia. METHODS: MEDLINE, PsycINFO, The Cochrane Library and Web of science were searched from January 1980 to January 2017. Research studies in English or French were eligible for inclusion if they fulfilled the following criteria: quantitative, qualitative and mixed method studies that used instrument, focus group or semi-structured interviews to assess the informal caregiver's needs in terms of information, coping skills, support and service...
April 17, 2017: BMC Geriatrics
https://www.readbyqxmd.com/read/28415743/survival-differences-of-cimp-subtypes-integrated-with-cna-information-in-human-breast-cancer
#9
Huihan Wang, Weili Yan, Shumei Zhang, Yue Gu, Yihan Wang, Yanjun Wei, Hongbo Liu, Fang Wang, Qiong Wu, Yan Zhang
CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation...
March 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28411282/genomic-architecture-and-treatment-outcome-in-pediatric-acute-myeloid-leukemia-a-children-s-oncology-group-report
#10
Marijana Vujkovic, Edward F Attiyeh, Rhonda E Ries, Elizabeth K Goodman, Yang Ding, Marko Kavcic, Todd A Alonzo, Yi-Cheng Wang, Robert B Gerbing, Lillian Sung, Betsy Hirsch, Susana Raimondi, Alan S Gamis, Soheil Meshinchi, Richard Aplenc
Childhood acute myeloid leukemia (AML) is frequently characterized by chromosomal instability. Approximately 50% of patients have disease relapse, and novel prognostic markers are needed to improve risk stratification. We performed genome-wide genotyping in 446 pediatric patients with de novo AML enrolled on Children's Oncology Group (COG) studies, AAML0531 (NCT01407757), AAML03P1 (NCT00070174), and CCG2961 (NCT00003790). Affymetrix and Illumina Omni 2.5 platforms were used to evaluate copy number alterations (CNAs) and determine their associations with treatment outcome...
April 14, 2017: Blood
https://www.readbyqxmd.com/read/28409485/cohesion-network-analysis-of-cscl-participation
#11
Mihai Dascalu, Danielle S McNamara, Stefan Trausan-Matu, Laura K Allen
The broad use of computer-supported collaborative-learning (CSCL) environments (e.g., instant messenger-chats, forums, blogs in online communities, and massive open online courses) calls for automated tools to support tutors in the time-consuming process of analyzing collaborative conversations. In this article, the authors propose and validate the cohesion network analysis (CNA) model, housed within the ReaderBench platform. CNA, grounded in theories of cohesion, dialogism, and polyphony, is similar to social network analysis (SNA), but it also considers text content and discourse structure and, uniquely, uses automated cohesion indices to generate the underlying discourse representation...
April 13, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28401483/molecular-profiling-of-gene-copy-number-abnormalities-in-key-regulatory-genes-in-high-risk-b-lineage-acute-lymphoblastic-leukemia-frequency-and-their-association-with-clinicopathological-findings-in-indian-patients
#12
Prerana Bhandari, Firoz Ahmad, Bibhu Ranjan Das
Genes related to key cellular pathways are frequently altered in B cell ALL and are associated with poor survival especially in high-risk (HR) subgroups. We examined gene copy number abnormalities (CNA) in 101 Indian HR B cell ALL patients and their correlation with clinicopathological features by multiplex ligation-dependent probe amplification. Overall, CNA were detected in 59 (59%) cases, with 26, 10 and 23% of cases harboring 1, 2 or +3 CNA. CNA were more prevalent in BCR-ABL1 (60%), pediatric (64%) and high WCC (WBC count) (63%) patients...
May 2017: Medical Oncology
https://www.readbyqxmd.com/read/28397966/synthesis-and-assembly-of-click-nucleic-acid-containing-peg-plga-nanoparticles-for-dna-delivery
#13
Albert Harguindey, Dylan W Domaille, Benjamin D Fairbanks, Justine Wagner, Christopher N Bowman, Jennifer N Cha
Co-delivery of both chemotherapy drugs and siRNA from a single delivery vehicle can have a significant impact on cancer therapy due to the potential for overcoming issues such as drug resistance. However, the inherent chemical differences between charged nucleic acids and hydrophobic drugs have hindered entrapment of both components within a single carrier. While poly(ethylene glycol)-block-poly(lactic-co-glycolic acid) (PEG-PLGA) copolymers have been used successfully for targeted delivery of chemotherapy drugs, loading of DNA or RNA has been poor...
April 11, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28390427/synthex-a-synthetic-normal-based-dna-sequencing-tool-for-copy-number-alteration-detection-and-tumor-heterogeneity-profiling
#14
Grace O Silva, Marni B Siegel, Lisle E Mose, Joel S Parker, Wei Sun, Charles M Perou, Mengjie Chen
Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues limit current CNA calling based upon DNA sequencing. We present SynthEx, a novel tool for detecting CNAs from whole exome and genome sequencing. SynthEx utilizes a "synthetic-normal" strategy to overcome technical and financial issues. In terms of accuracy and precision, SynthEx is highly comparable to array-based methods and outperforms sequencing-based CNA detection tools...
April 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28380716/dietary-service-staffing-impact-nutritional-quality-in-nursing-homes
#15
Kelly M Smith, Kali S Thomas, Shanthi Johnson, Hongdao Meng, Kathryn Hyer
OBJECTIVE: To examine the relationship between dietary service staff and dietary deficiency citations in nursing homes (NHs). METHOD: 2007-2011 Online Survey and Certification and Reporting data for 14,881 freestanding NHs were used to examine the relationship between dietary service staff and the probability of receiving a dietary service-related deficiency citation. An unconditional logit model with random effects was employed. RESULTS: Findings suggest that higher staffing levels for dietitians (odds ratio [OR] = ...
January 1, 2017: Journal of Applied Gerontology: the Official Journal of the Southern Gerontological Society
https://www.readbyqxmd.com/read/28369518/misregulation-of-calcium-handling-proteins-promotes-hyperactivation-of-calcineurin-nfat-signaling-in-skeletal-muscle-of-dm1-mice
#16
Aymeric Ravel-Chapuis, Guy Bélanger, Jocelyn Côté, Robin N Michel, Bernard J Jasmin
Myotonic Dystrophy type 1 (DM1) is caused by an expansion of CUG repeats in DMPK mRNAs. This mutation affects alternative splicing through misregulation of RNA-binding proteins. Amongst pre-mRNAs that are misspliced, several code for proteins involved in calcium homeostasis suggesting that calcium-handling and signaling are perturbed in DM1. Here, we analyzed expression of such proteins in DM1 mouse muscle. We found that the levels of several sarcoplasmic reticulum proteins (SERCA1, sarcolipin and calsequestrin) are altered, likely contributing to an imbalance in calcium homeostasis...
March 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28356086/characterization-of-calcineurin-from-cryptococcus-humicola-and-the-application-of-calcineurin-in-aluminum-tolerance
#17
Lei Zhang, Jing-Jing Zhang, Shuai Liu, Hong-Juan Nian, Li-Mei Chen
BACKGROUND: Calcineurin (CaN) is a Ca(2+)- and calmodulin (CaM)-dependent serine/threonine phosphatase. Previous studies have found that CaN is involved in the regulation of the stress responses. RESULTS: In this study, the growth of Cryptococcus humicola was inhibited by the CaN inhibitor tacrolimus (FK506) under aluminum (Al) stress. The expression of CNA encoding a catalytic subunit A (CNA) and its interaction with CaM were upregulated when the concentration of Al was increased...
March 29, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28349590/benzalkonium-chloride-a-bronchoconstricting-preservative-in-continuous-albuterol-nebulizer-solutions
#18
Sreekala Prabhakaran, Mutasim Abu-Hasan, Leslie Hendeles
For convenience, many pediatric hospitals are preparing solutions for continuous nebulized albuterol using the 0.5% 20-ml multidose albuterol dropper bottle. This product contains benzalkonium chloride (BAC) that, by itself, produces bronchospasm that is dose dependent and cumulative. The bronchoconstrictive effects of BAC are greater in patients with more severe airway obstruction and increased airway responsiveness. Use of BAC-containing albuterol during severe acute asthma exacerbations may antagonize the bronchodilator response to albuterol, prolong treatment, and increase the risk of albuterol-related systemic adverse effects...
March 28, 2017: Pharmacotherapy
https://www.readbyqxmd.com/read/28344372/radicals-and-molecular-products-from-the-gas-phase-pyrolysis-of-lignin-model-compounds-cinnamyl-alcohol
#19
Lavrent Khachatryan, Meng-Xia Xu, Ang-Jian Wu, Mikhail Pechagin, Rubik Asatryan
The experimental results on detection and identification of intermediate radicals and molecular products from gas-phase pyrolysis of cinnamyl alcohol (CnA), the simplest non-phenolic lignin model compound, over the temperature range of 400-800 °C are reported. The low temperature matrix isolation - electron paramagnetic resonance (LTMI-EPR) experiments along with the theoretical calculations, provided evidences on the generation of the intermediate carbon and oxygen centered as well as oxygen-linked, conjugated radicals...
September 2016: Journal of Analytical and Applied Pyrolysis
https://www.readbyqxmd.com/read/28298214/climat-het-detecting-subclonal-copy-number-alterations-and-loss-of-heterozygosity-in-heterogeneous-tumor-samples-from-whole-genome-sequencing-data
#20
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
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