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Hierarchical clustering

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https://www.readbyqxmd.com/read/28092030/proteomic-clustering-analysis-of-sh2-domain-datasets
#1
Karl Jablonowski
Proteomic clustering analysis provides a means of identifying relationships and visualizing those relationships in an extremely complex field of study with many interacting parts. With recent high-throughput studies of Src Homology 2 (SH2) domains, many and varied datasets are being amassed. A strategy for analyzing patterns between these large datasets is required to transform the information into knowledge. The methods for creating neighbor-joining phylogenetic trees, pairs scatter plots, and two-dimensional hierarchical clustering heatmaps are just a few of the diverse methods available to a proteomic researcher...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091786/a-new-look-at-the-drug-resistance-investigation-of-uropathogenic-e-coli-strains
#2
Wioletta Adamus-Białek, Łukasz Lechowicz, Anna B Kubiak-Szeligowska, Monika Wawszczak, Ewelina Kamińska, Magdalena Chrapek
Bacterial drug resistance and uropathogenic tract infections are among the most important issues of current medicine. Uropathogenic Escherichia coli strains are the primary factor of this issue. This article is the continuation of the previous study, where we used Kohonen relations to predict the direction of drug resistance. The characterized collection of uropathogenic E. coli strains was used for microbiological (the disc diffusion method for antimicrobial susceptibility testing), chemical (ATR/FT-IR) and mathematical (artificial neural networks, Ward's hierarchical clustering method, the analysis of distributions of inhibition zone diameters for antibiotics, Cohen's kappa measure of agreement) analysis...
January 13, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28089736/antibacterial-activity-of-limonium-brasiliense-baicuru-against-multidrug-resistant-bacteria-using-a-statistical-mixture-design
#3
Andressa Blainski, Barbara Gionco, Admilton G Oliveira, Galdino Andrade, Ieda S Scarminio, Denise B Silva, Norberto P Lopes, João C P Mello
ETHNOPHARMACOLOGICAL RELEVANCE: Limonium brasiliense (Boiss.) Kuntze (Plumbaginaceae) is commonly known as "baicuru" or "guaicuru" and preparations of its dried rhizomes have been populary used in the treatment of premenstrual syndrome and menstrual disorder, and as an antiseptic in genito-urinary infections. This study evaluated the potential antibacterial activity of rhizome extracts against multidrug-resistant bacterial strains using statistical mixture design. MATERIALS AND METHODS: The statistical design of four components (water, methanol, acetone and ethanol) produced 15 different extracts and also a confirmatory experiment, which was performed using water:acetone (3:7, v/v)...
January 13, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28088709/characterization-of-smokeless-powders-using-multiplexed-collision-induced-dissociation-mass-spectrometry-and-chemometric-procedures
#4
Kristen L Reese, A Daniel Jones, Ruth Waddell Smith
This work demonstrates a non-targeted mass spectrometry approach for identification of organic compounds in smokeless powders. Unburned powders were removed from various commercial ammunitions of different brand, primer composition, caliber, and age. The unburned powders and corresponding fired residues were analyzed by liquid chromatography-atmospheric pressure chemical ionization-time-of-flight mass spectrometry (LC-APCI-TOFMS). Multiplexed collision-induced dissociation was performed at increasing collision potentials resulting in successive fragmentation that provided structural information for compound identification in a non-targeted manner...
December 21, 2016: Forensic Science International
https://www.readbyqxmd.com/read/28086754/making-the-most-of-mealtimes-m3-protocol-of-a-multi-centre-cross-sectional-study-of-food-intake-and-its-determinants-in-older-adults-living-in-long-term-care-homes
#5
Heather H Keller, Natalie Carrier, Susan Slaughter, Christina Lengyel, Catriona M Steele, Lisa Duizer, K Steve Brown, Habib Chaudhury, Minn N Yoon, Alison M Duncan, Veronique M Boscart, George Heckman, Lita Villalon
BACKGROUND: Older adults living in long term care (LTC) homes are nutritionally vulnerable, often consuming insufficient energy, macro- and micronutrients to sustain their health and function. Multiple factors are proposed to influence food intake, yet our understanding of these diverse factors and their interactions are limited. The purpose of this paper is to fully describe the protocol used to examine determinants of food and fluid intake among older adults participating in the Making the Most of Mealtimes (M3) study...
January 13, 2017: BMC Geriatrics
https://www.readbyqxmd.com/read/28079015/chemometrics-expertise-in-the-links-between-ecotoxicity-and-physicochemical-features-of-silver-nanoparticles-environmental-aspects
#6
Miroslava A Nedyalkova, Borjana V Donkova, Vasil D Simeonov
Studies of the ecotoxicological aspects of nanomaterials in aquatic environments are scarce. Given the growing varietyof nanoparticles (NPs), along with the diversity of aquatic species and environments, the key to promoting sound risk assessment in nanoecotoxicology is understanding the mechanisms that govern the fate of NPs in aquatic environments and their behavior at the NP-biota interface. In this paper, data collected from the literature on ecotoxicological effects observed in aquatic species is discussed and analyzed using multivariate statistics techniques...
January 12, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28078662/low-immunoglobulin-e-flags-two-distinct-types-of-immune-dysregulation
#7
M Elkuch, V Greiff, C T Berger, M Bouchenaki, T Daikeler, A Bircher, A A Navarini, I Heijnen, M Recher
During the last two decades, hyper-immunoglobulin (Ig)E syndromes have been characterized clinically and molecularly in patients with genetically determined primary immunodeficiencies. However, the detection of low IgE levels, defined here as below detection limit in the routine clinical immunology laboratory, has received little attention. We analysed the association of serum IgA, IgM and IgG levels (including IgG subclasses) with low, normal or high serum IgE levels in patients evaluated in a single-centre out-patient immunodeficiency and allergy clinic...
January 11, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28078265/classification-of-31-korean-wheat-triticum-aestivum-l-cultivars-based-on-the-chemical-compositions
#8
Induck Choi, Chon-Sik Kang, Choon-Kee Lee, Sun-Lim Kim
Whole grain wheat flour (WGWF) is the entire grain (bran, endosperm, and germ) milled to make flour. The WGWF of 31 Korean wheat (Triticum aestivum L.) cultivars were analyzed for the chemical compositions, and classified into groups by hierarchical cluster analysis (HCL). The average composition values showed a substantial variation among wheat varieties due to different wheat varieties. Wheat cv. Shinmichal1 (waxy wheat) had the highest ash, lipid, and total dietary fiber contents of 1.76, 3.14, and 15.49 g/100 g, respectively...
December 2016: Preventive Nutrition and Food Science
https://www.readbyqxmd.com/read/28077965/distinct-profiles-of-reactive-and-proactive-aggression-in-adolescents-associations-with-cognitive-and-affective-empathy
#9
Felix Euler, Célia Steinlin, Christina Stadler
BACKGROUND: Aggression comprises a heterogeneous set of behavioral patterns that aim to harm and hurt others. Empathy represents a potential mechanism that inhibits aggressive conduct and enhances prosocial behavior. Nevertheless, research results on the relationship between empathy and aggression are mixed. Subtypes of aggressive behavior, such as reactive and proactive aggression might be differently related to empathy. The aim of the present study was to investigate the interrelations of cognitive and affective empathy with reactive and proactive aggression...
2017: Child and Adolescent Psychiatry and Mental Health
https://www.readbyqxmd.com/read/28075549/solvent-morphology-property-relationship-of-ptb7-pc71bm-polymer-solar-cells
#10
Shuai Guo, Weijia Wang, Eva M Herzig, Anna Naumann, Gregory Tainter, Jan Perlich, Peter Muller-Buschbaum
The influence of three different solvents and a solvent additive on the morphology and photovoltaic performance of bulk heterojunction films made of the copolymer based on thieno[3,4-b]thiophene-alt-benzodithiophene unit PTB7-F40 blended with [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) is investigated. Optical microscopy and atomic force microscopy (AFM) are combined with X-ray reflectivity (XRR) and grazing incidence small and wide angle X-ray scattering (GISAXS and GIWAXS) enabling the characterization of the morphology of the whole photoactive film...
January 11, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28073363/swept-away-ocean-currents-and-seascape-features-influence-genetic-structure-across-the-18-000-km-indo-pacific-distribution-of-a-marine-invertebrate-the-black-lip-pearl-oyster-pinctada-margaritifera
#11
Monal M Lal, Paul C Southgate, Dean R Jerry, Cyprien Bosserelle, Kyall R Zenger
BACKGROUND: Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28071864/simultaneous-determination-of-four-triterpenoid-saponins-in-aralia-elata-leaves-by-hplc-elsd-combined-with-hierarchical-clustering-analysis
#12
Yichun Sun, Baimei Li, Xiaoting Lin, Juan Xue, Zhibin Wang, Hongwei Zhang, Hai Jiang, Qiuhong Wang, Haixue Kuang
INTRODUCTION: Aralia elata leaves are known to have several biological activities, including anti-arrythmia, antitumor, anti-inflammatory, anti-fatigue, antimicrobial and antiviral effects. Our previous study found that triterpenoid saponins from the leaves of A. elata had antitumor effects. Quantification of the triterpenoids is important for the quality control of A. elata leaves. OBJECTIVE: To establish high-performance liquid chromatography coupled with evaporative light scattering detection (HPLC-ELSD) for the simultaneous determination of four major triterpenoid saponins, including Aralia-saponin IV, Aralia-saponin VI, 3-O-β-d- glucopyranosyl-(1 → 3)-β-d-glucopyranosyl-(1 → 3)-β-d-glucopyranosyl oleanolic acid 28-O-β-d-glucopyranoside (Aralia-saponin TTP)and Aralia-saponin V...
January 10, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28071788/chromosome-inversions-and-ecological-plasticity-in-the-main-african-malaria-mosquitoes
#13
Diego Ayala, Pelayo Acevedo, Marco Pombi, Ibrahima Dia, Daniela Boccolini, Carlo Costantini, Frédéric Simard, Didier Fontenille
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range...
January 10, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28071765/neural-codes-of-seeing-architectural-styles
#14
Heeyoung Choo, Jack L Nasar, Bardia Nikrahei, Dirk B Walther
Images of iconic buildings, such as the CN Tower, instantly transport us to specific places, such as Toronto. Despite the substantial impact of architectural design on people's visual experience of built environments, we know little about its neural representation in the human brain. In the present study, we have found patterns of neural activity associated with specific architectural styles in several high-level visual brain regions, but not in primary visual cortex (V1). This finding suggests that the neural correlates of the visual perception of architectural styles stem from style-specific complex visual structure beyond the simple features computed in V1...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070610/automated-tetraploid-genotype-calling-by-hierarchical-clustering
#15
Cari A Schmitz Carley, Joseph J Coombs, David S Douches, Paul C Bethke, Jiwan P Palta, Richard G Novy, Jeffrey B Endelman
New software to make tetraploid genotype calls from SNP array data was developed, which uses hierarchical clustering and multiple F1 populations to calibrate the relationship between signal intensity and allele dosage. SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, the relationship between signal intensity and allele dosage must be calibrated for each marker. We developed an improved computational method to automate this process, which is provided as the R package ClusterCall...
January 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28069345/patients-perspectives-on-quality-of-life-after-burn
#16
Marianne B Kool, Rinie Geenen, Marthe R Egberts, Hendriët Wanders, Nancy E Van Loey
BACKGROUND: The concept quality of life (QOL) refers to both health-related outcomes and one's skills to reach these outcomes, which is not yet incorporated in the burn-related QOL conceptualisation. The aim of this study was to obtain a comprehensive overview of relevant burn-specific domains of QOL from the patient's perspective and to determine its hierarchical structure. METHODS: Concept mapping was used comprising a focus group (n=6), interviews (n=25), and a card-sorting task (n=24) in burn survivors...
January 6, 2017: Burns: Journal of the International Society for Burn Injuries
https://www.readbyqxmd.com/read/28069026/multimorbidity-and-health-related-quality-of-life-hrqol-in-a-nationally-representative-population-sample-implications-of-count-versus-cluster-method-for-defining-multimorbidity-on-hrqol
#17
Lili Wang, Andrew J Palmer, Fiona Cocker, Kristy Sanderson
BACKGROUND: No universally accepted definition of multimorbidity (MM) exists, and implications of different definitions have not been explored. This study examined the performance of the count and cluster definitions of multimorbidity on the sociodemographic profile and health-related quality of life (HRQoL) in a general population. METHODS: Data were derived from the nationally representative 2007 Australian National Survey of Mental Health and Wellbeing (n = 8841)...
January 9, 2017: Health and Quality of Life Outcomes
https://www.readbyqxmd.com/read/28068969/factors-associated-with-infant-mortality-in-nepal-a-comparative-analysis-of-nepal-demographic-and-health-surveys-ndhs-2006-and-2011
#18
Reeta Lamichhane, Yun Zhao, Susan Paudel, Emmanuel O Adewuyi
BACKGROUND: Infant mortality is one of the priority public health issues in developing countries like Nepal. The infant mortality rate (IMR) was 48 and 46 per 1000 live births for the year 2006 and 2011, respectively, a slight reduction during the 5 years' period. A comprehensive analysis that has identified and compared key factors associated with infant mortality is limited in Nepal, and, therefore, this study aims to fill the gap. METHODS: Datasets from Nepal Demographic and Health Surveys (NDHS) 2006 and 2011 were used to identify and compare the major factors associated with infant mortality...
January 10, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28068911/genotyping-by-sequencing-of-a-melon-cucumis-melo-l-germplasm-collection-from-a-secondary-center-of-diversity-highlights-patterns-of-genetic-variation-and-genomic-features-of-different-gene-pools
#19
Stefano Pavan, Angelo Raffaele Marcotrigiano, Elena Ciani, Rosa Mazzeo, Vito Zonno, Valentino Ruggieri, Concetta Lotti, Luigi Ricciardi
BACKGROUND: Melon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics. RESULTS: We report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068844/hierarchical-cluster-analysis-and-chemical-characterisation-of-myrtus-communis-l-essential-oil-from-yemen-region-and-its-antimicrobial-antioxidant-and-anti-colorectal-adenocarcinoma-properties
#20
Sirajudheen Anwar, Rebecca A Crouch, Nasser A Awadh Ali, Mohamed A Al-Fatimi, William N Setzer, Ludger Wessjohann
The hydrodistilled essential oil obtained from the dried leaves of Myrtus communis, collected in Yemen, was analysed by GC-MS. Forty-one compounds were identified, representing 96.3% of the total oil. The major constituents of essential oil were oxygenated monoterpenoids (87.1%), linalool (29.1%), 1,8-cineole (18.4%), α-terpineol (10.8%), geraniol (7.3%) and linalyl acetate (7.4%). The essential oil was assessed for its antimicrobial activity using a disc diffusion assay and resulted in moderate to potent antibacterial and antifungal activities targeting mainly Bacillus subtilis, Staphylococcus aureus and Candida albicans...
January 9, 2017: Natural Product Research
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