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Hierarchical clustering

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https://www.readbyqxmd.com/read/28431359/reconstruction-of-microbial-community-structures-as-evidences-for-soil-redox-coupled-reductive-dechlorination-of-pcp-in-a-mangrove-soil
#1
Yan Xu, Yan He, Xianjin Tang, Philip C Brookes, Jianming Xu
The aim was to investigate the influence of pentachlorophenol (PCP) on the soil microbial communities and the coupled mechanism between PCP reductive dechlorination and soil redox under anaerobic condition. Accordingly, a slurry incubation experiment was carried out in which bacterial and archaeal communities were detected by MiSeq amplicon sequencing. The original microbial community balance was gradually disrupted and new microbial structure was reconstructed subsequently through self-regulation and acclimation during PCP transformation, coupling with the changes of soil biogeochemical redox dynamics...
April 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28430928/typology-and-dynamics-of-heavier-drinking-styles-in-great-britain-1978-2010
#2
Robin C Purshouse, Alan Brennan, Daniel Moyo, James Nicholls, Paul Norman
Aims: To identify a typology of heavier drinking styles in Great Britain and to identify socio-demographic trends in the typology over the period 1978-2010. Methods: We applied multiple correspondence analysis and agglomerative hierarchical clustering to beverage-specific quantity-frequency measures of alcohol consumption in the repeated cross-sectional General Lifestyle Survey of Great Britain, 1978-2010. The cluster analysis focuses on the 60,043 adult respondents over this period reporting average drinking levels above the UK Government guidelines...
May 1, 2017: Alcohol and Alcoholism: International Journal of the Medical Council on Alcoholism
https://www.readbyqxmd.com/read/28430808/quantification-of-hypoxia-related-gene-expression-as-a-potential-approach-for-clinical-outcome-prediction-in-breast-cancer
#3
Abderrahim El Guerrab, Anne Cayre, Fabrice Kwiatkowski, Maud Privat, Jean-Marc Rossignol, Fabrice Rossignol, Frédérique Penault-Llorca, Yves-Jean Bignon
Breast cancers are solid tumors frequently characterized by regions with low oxygen concentrations. Cellular adaptations to hypoxia are mainly determined by "hypoxia inducible factors" that mediate transcriptional modifications involved in drug resistance and tumor progression leading to metastasis and relapse occurrence. In this study, we investigated the prognostic value of hypoxia-related gene expression in breast cancer. A systematic review was conducted to select a set of 45 genes involved in hypoxia signaling pathways and breast tumor progression...
2017: PloS One
https://www.readbyqxmd.com/read/28429715/mapping-clinicopathological-entities-within-colorectal-mucinous-adenocarcinomas-a-hierarchical-clustering-approach
#4
Charly Liddell, Laure Droy-Dupré, Sylvie Métairie, Fabrice Airaud, Christelle Volteau, Stéphane Bezieau, Christian L Laboisse, Jean-François Mosnier
The aim of this study was to interrogate the heterogeneity of colorectal mucinous adenocarcinomas. This study is based on hierarchical clustering approach combining clinicopathological and molecular patterns known to be relevant to oncogenesis and therapeutic management of patients with colorectal carcinoma, ie, microsatellite instability, O6-methylguanine-DNA methyltransferase (MGMT) status, KRAS, and BRAF mutations and wnt signaling pathway activation. Comparison of the study group of 60 mucinous adenocarcinomas defined according to World Health Organization classification with control group of 136 colorectal adenocarcinomas successively removed shows higher frequency of BRAF and KRAS mutations and microsatellite instability-high status and lower frequency of wnt signaling pathway activation in mucinous adenocarcinomas...
April 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28428141/temporal-impact-of-the-vascular-wilt-pathogen-verticillium-dahliae-on-tomato-root-proteome
#5
Katja Witzel, Anja Buhtz, Rita Grosch
The soil-borne fungus Verticillium dahliae is the causal agent of wilting disease and affects a wide range of plant species worldwide. Here, we report on the time-resolved analysis of the tomato root proteome in response to fungal colonization. Tomato (Solanum lycopersicum cv. Hildares) was inoculated with V. dahliae at the two-leaf stage and roots were harvested at 7, 14 and 21 days post inoculation (dpi). In order to identify proteins related to the fungal spread at the different time points, a subsequent proteome analysis by two-dimensional differential gel electrophoresis (2D-DIGE) was conducted on samples from three independent experiments...
April 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28427373/a-protocol-for-a-cluster-randomized-controlled-trial-of-a-self-help-psycho-education-programme-to-reduce-diagnosis-delay-in-women-with-breast-cancer-symptoms-in-indonesia
#6
Hari Setyowibowo, Marit Sijbrandij, Aulia Iskandarsyah, Joke A M Hunfeld, Sawitri S Sadarjoen, Dharmayanti F Badudu, Drajat R Suardi, Jan Passchier
BACKGROUND: Breast cancer (BC) is the most frequent cancer occurring in women across the world. Its mortality rate in low-middle income countries (LMICs) is higher than in high-income countries (HICs), and in Indonesia BC is the leading cause of cancer deaths among women. Delay in breast cancer diagnosis negatively impacts cancer prognosis. Only about 30% of patients who come to the hospital to check on their breast abnormalities, continue thorough examination to biopsy to get a diagnosis based on the results of anatomical pathology...
April 20, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28425934/evaluation-of-the-effects-of-airborne-particulate-matter-on-bone-marrow-mesenchymal-stem-cells-bm-mscs-cellular-molecular-and-systems-biological-approaches
#7
Muhammad Abu-Elmagd, Mansour A Alghamdi, Magdy Shamy, Mamdouh I Khoder, Max Costa, Mourad Assidi, Roaa Kadam, Haneen Alsehli, Mamdooh Gari, Peter Natesan Pushparaj, Gauthaman Kalamegam, Mohammed H Al-Qahtani
Particulate matter (PM) contains heavy metals that affect various cellular functions and gene expression associated with a range of acute and chronic diseases in humans. However, the specific effects they exert on the stem cells remain unclear. Here, we report the effects of PM collected from the city of Jeddah on proliferation, cell death, related gene expression and systems of biological analysis in bone marrow mesenchymal stem cells (BM-MSCs), with the aim of understanding the underlying mechanisms. PM2...
April 20, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28423217/in-vitro-discrimination-of-wound-associated-bacteria-by-volatile-compound-profiling-using-selected-ion-flow-tube-mass-spectrometry
#8
Elisabeth Alice Slade, Robin Michael Statham Thorn, Andrew M Lovering, Amber Young, Darren Michael Reynolds
AIMS: To determine if bacterial species responsible for clinically relevant wound infection produce specific volatile profiles that would allow their speciation. METHODS AND RESULTS: Selected-Ion Flow Tube-Mass Spectrometry in full mass scan mode was used to analyse headspace gases produced by wound-associated bacteria grown in vitro, so as to enable identification of bacterial volatile product ion profiles in the resulting mass spectra. Applying multivariate statistical analysis (hierarchical clustering and principal component analysis) to the resultant mass spectra enabled clear speciation...
April 19, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28421717/cognitive-profiles-in-euthymic-patients-with-bipolar-disorders-results-from-the-face-bd-cohort
#9
Paul Roux, Aurélie Raust, Anne Sophie Cannavo, Valérie Aubin, Bruno Aouizerate, Jean-Michel Azorin, Frank Bellivier, Raoul Belzeaux, Thierry Bougerol, Iréna Cussac, Philippe Courtet, Bruno Etain, Sébastien Gard, Sophie Job, Jean-Pierre Kahn, Marion Leboyer, Emilie Olié, Chantal Henry, Christine Passerieux
OBJECTIVES: Although cognitive deficits are a well-established feature of bipolar disorders (BD), even during periods of euthymia, little is known about cognitive phenotype heterogeneity among patients with BD. METHODS: We investigated neuropsychological performance in 258 euthymic patients with BD recruited via the French network of expert centers for BD. We used a test battery assessing six domains of cognition. Hierarchical cluster analysis of the cross-sectional data was used to determine the optimal number of subgroups and to assign each patient to a specific cognitive cluster...
April 19, 2017: Bipolar Disorders
https://www.readbyqxmd.com/read/28420888/global-gene-expression-profiling-of-healthy-human-brain-and-its-application-in-studying-neurological-disorders
#10
Simarjeet K Negi, Chittibabu Guda
Brain function is governed by precise regulation of gene expression across its anatomically distinct structures; however, the expression patterns of genes across hundreds of brain structures are not clearly understood. Here, we describe a gene expression model, which is representative of the healthy human brain transcriptome by using data from the Allen Brain Atlas. Our in-depth gene expression profiling revealed that 84% of genes are expressed in at least one of the 190 brain structures studied. Hierarchical clustering based on gene expression profiles delineated brain regions into structurally tiered spatial groups and we observed striking enrichment for region-specific processes...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420804/contemporary-trends-and-outcomes-associated-with-the-preprocedural-use-of-oral-p2y12-inhibitors-in-patients-undergoing-percutaneous-coronary-intervention-insights-from-the-blue-cross-blue-shield-of-michigan-cardiovascular-consortium-bmc2
#11
Devraj Sukul, Milan Seth, Simon R Dixon, Akshay Khandelwal, Thomas A LaLonde, Hitinder S Gurm
OBJECTIVES: We sought to describe trends in the use of preprocedural P2Y12 inhibitors and their clinical impact in patients undergoing percutaneous coronary intervention (PCI). BACKGROUND: Oral P2Y12 inhibitors are ubiquitously used medications; however, the specific timing of initial P2Y12 inhibitor administration remains intensely debated. METHODS: Our study population comprised 74,053 consecutive patients undergoing PCI at 47 hospitals in Michigan from January 2013 through June 2015...
April 15, 2017: Journal of Invasive Cardiology
https://www.readbyqxmd.com/read/28419182/molecular-classification-of-pulmonary-sarcomatoid-carcinomas-suggests-new-therapeutic-opportunities
#12
N Pécuchet, T Vieira, N Rabbe, M Antoine, H Blons, J Cadranel, P Laurent-Puig, M Wislez
Background: Pulmonary sarcomatoid carcinoma (SC) is a rare disease with poor prognosis and with strong inter- and intratumor heterogeneity. However, molecular classification is currently focused on activating MET mutations. We sought to better characterize the molecular diversity of SC using mutational signatures that reflect different mutational processes, such as tobacco-associated adducts (signature 4), BRCA1/BRCA2 deficiency (signature 3) or APOBEC enzyme deamination (signatures 2&13)...
April 13, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28418682/mesoscale-simulation-and-machine-learning-of-asphaltene-aggregation-phase-behavior-and-molecular-assembly-landscapes
#13
Jiang Wang, Mohit Gayatri, Andrew L Ferguson
Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood...
April 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28418253/species-level-discrimination-of-psychrotrophic-pathogenic-and-spoilage-gram-negative-raw-milk-isolates-using-a-combined-maldi-tof-ms-proteomics-bioinformatics-based-approach
#14
Nuwan R Vithanage, Thomas Richard Yeager, Jeevana Bhongir, Snehal R Jadhav, Chaminda Senaka Ranadheera, Enzo A Palombo, Nivedita Datta
Identification of psychrotrophic pathogenic and spoilage Gram-negative bacteria using rapid and reliable techniques is important in commercial milk processing, as these bacteria can produce heat-resistant proteases and act as post-processing contaminants in pasteurised milk. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a proven technology for identification of bacteria in food, however may require optimisation for identification of pathogenic and spoilage bacteria in milk and dairy products...
April 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28416947/dna-methylation-profiles-of-blood-cells-are-distinct-between-early-onset-obese-and-control-individuals
#15
Je-Keun Rhee, Jin-Hee Lee, Hae Kyung Yang, Tae-Min Kim, Kun-Ho Yoon
Obesity is a highly prevalent, chronic disorder that has been increasing in incidence in young patients. Both epigenetic and genetic aberrations may play a role in the pathogenesis of obesity. Therefore, in-depth epigenomic and genomic analyses will advance our understanding of the detailed molecular mechanisms underlying obesity and aid in the selection of potential biomarkers for obesity in youth. Here, we performed microarray-based DNA methylation and gene expression profiling of peripheral white blood cells obtained from six young, obese individuals and six healthy controls...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416643/can-serum-cytokine-profile-discriminate-irritant-induced-and-allergen-induced-symptoms-a-cross-sectional-study-in-workers-mostly-exposed-to-laboratory-animals
#16
Muriel Lemaire, Anne Oppliger, Philipp Hotz, Jean-Christophe Renauld, Julia Braun, Marion Maggi, Fabio Barresi, Peter Schmid-Grendelmeier, François Huaux, Holger Dressel
BACKGROUND: In workers exposed mostly to laboratory animals (LA), symptoms may be due to irritants or allergens. Correct aetiological diagnosis is important for health surveillance. OBJECTIVES: This study aims to test whether work-related (WR) allergen-induced symptoms are associated with a cytokine profile distinct from that due to irritants. METHODS: In a cross-sectional study (n=114), WR respiratory and/or skin symptoms were assessed through a standardised clinical examination and sensitisation to rat and/or mouse allergen determined by serum immunoglobulin E...
April 17, 2017: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28415032/comparative-metabolome-analysis-of-wheat-embryo-and-endosperm-reveals-the-dynamic-changes-of-metabolites-during-seed-germination
#17
Caixia Han, Shoumin Zhen, Gengrui Zhu, Yanwei Bian, Yueming Yan
In this study, we performed the first comparative metabolomic analysis of the wheat embryo and endosperm during seed germination using GC-MS/MS. In total, 82 metabolites were identified in the embryo and endosperm. Principal component analysis (PCA), metabolite-metabolite correlation and hierarchical cluster analysis (HCA) revealed distinct dynamic changes in metabolites between the embryo and endosperm during seed germination. Generally, the metabolite changes in the embryo were much greater than those in the endosperm, suggesting that the embryo is more active than the endosperm during seed germination...
April 10, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28414611/population-genetic-structure-of-venturia-effusa-cause-of-pecan-scab-in-the-southeastern-united-states
#18
Clive H Bock, Michael W Hotchkiss, Carolyn A Young, Nikki D Charlton, Mattupalli Chakradhar, Katherine L Stevenson, Bruce W Wood
Venturia effusa is the most important pathogen of pecan in the southeastern United States. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of 784 isolates from 63 trees in 11 pecan orchards in the southeastern United States were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (n = 2), Florida (n = 1), Alabama (n = 2), Mississippi (n = 1), Louisiana (n = 1), Illinois (n = 1), Oklahoma (n = 1), Texas (n = 1), and Kansas (n = 1)...
May 2017: Phytopathology
https://www.readbyqxmd.com/read/28412487/occurrence-homologue-patterns-and-source-apportionment-of-short-%C3%A2-and-medium-chain-chlorinated-paraffins-in-suburban-soils-of-shanghai-china
#19
Xue-Tong Wang, Si-Yue Xu, Xi-Kui Wang, Bao-Ping Hu, Hao-Hao Jia
In order to systematically investigate the spatial distribution, homologue profiles, and sources of short- and medium-chain chlorinated paraffins (SCCPs and MCCPs) in suburban soils in Shanghai, SCCPs and MCCPs in soils were analyzed using gas chromatography coupled with low resolution mass spectrometry in electron capture negative ion (ECNI) mode (GC-ECNI-MS). The CP concentrations in soils were between not detected (ND) - 697 ng g(-1) with a median value of 3.52 ng g(-1) for SCCPs, and ND - 666 ng g(-1) with a median value of 15...
April 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28410538/synthesis-of-co3o4-nanoclusters-via-an-edtana4-assisted-route-for-enhanced-electrochemical-application
#20
Zhifang Huang, Yan Zhao, Yuehong Song, Jingzhe Zhao
Three-dimensional (3D) Co3O4 nanoclusters were fabricated with the assistance of tetrasodium ethylene diamine tetraacetic acid (EDTANa4) through a one-pot wet-chemical reaction, featuring self-limiting assembly of building blocks and controlled regrowth process. The molar ratio of Co(2+) and EDTANa4 plays a key role in building initial clusters as blocks, and the amount of NaOH effects the regrowth process. A possible formation mechanism for the Co3O4 nanoclusters was proposed based on the characterization results of X-ray diffraction (XRD), Fourier-transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM)...
April 5, 2017: Journal of Colloid and Interface Science
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