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Hierarchical clustering

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https://www.readbyqxmd.com/read/27921201/sensory-clusters-of-adults-with-and-without-autism-spectrum-conditions
#1
Marie Elwin, Agneta Schröder, Lena Ek, Tuula Wallsten, Lars Kjellin
We identified clusters of atypical sensory functioning adults with ASC by hierarchical cluster analysis. A new scale for commonly self-reported sensory reactivity was used as a measure. In a low frequency group (n = 37), all subscale scores were relatively low, in particular atypical sensory/motor reactivity. In the intermediate group (n = 17) hyperreactivity, sensory interests and sensory/motor issues were significantly elevated in relation to the first group, but not hyporeactivity. In a high frequency subgroup (n = 17) all subscale scores were significantly elevated and co-occurrence of hyper- and hyporeactivity was evident...
December 5, 2016: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/27919956/expression-patterns-of-growth-and-survival-genes-with-prognostic-implications-in-advanced-pancreatic-cancer
#2
Dimitrios Pectasides, Vasiliki Kotoula, George Papaxoinis, Zoi Alexopoulou, Christos Dervenis, Epaminontas Samantas, Kleo Papaparaskeva, Elpida Charalambous, Chrysoula Gkakou, Christos Agalianos, Konstantine T Kalogeras, George Pentheroudakis, George Fountzilas
AIM: The aim of this study was to evaluate the mRNA expression pattern of growth- and survival-related genes and assess their prognostic significance in patients with advanced pancreatic cancer. PATIENTS AND METHODS: In total, 98 patients were included in this retrospective translational research study and were evaluated for Kirsten rat sarcoma viral oncogene homolog (KRAS) mutational status, and v-akt murine thymoma viral oncogene homolog 1 (AKT1), AKT serine/threonine kinase 2 (AKT2), AKT serine/threonine kinase 3 (AKT3), cyclin D1 (CCND1), epidermal growth factor receptor (EGFR), mitogen-activated protein kinase 1 (MAPK1), hepatocellular growth factor receptor (MET), avian myelomatosis viral oncogene homolog (MYC), nuclear factor kappa B subunit 1 (NFKb1), phosphatase and tensin homolog (PTEN) and mechanistic target of rapamycin (FRAP1) genes mRNA expression...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27919923/clonality-increases-with-snow-depth-in-the-arctic-dwarf-shrub-empetrum-hermaphroditum
#3
Miriam J Bienau, R Lutz Eckstein, Annette Otte, Walter Durka
PREMISE OF THE STUDY: Vegetative reproduction and spread through clonal growth plays an important role in arctic-alpine ecosystems with short cool growing seasons. Local variation in winter snow accumulation leads to discrete habitat types that may provide divergent conditions for sexual and vegetative reproduction. Therefore, we studied variation in clonal structure of a dominant, evergreen, dwarf shrub (Empetrum nigrum s.l. with the two taxa E. nigrum L. s.s. and E. hermaphroditum Hagerup) along a snow cover gradient and compared clonal diversity and spatial genetic structure between habitats...
December 5, 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27919819/patterns-of-constitutively-phosphorylated-kinases-in-b-cells-are-associated-with-disease-severity-in-common-variable-immunodeficiency
#4
Eli Taraldsrud, Pål Aukrust, Silje Jørgensen, Ole Christian Lingjærde, Johanna Olweus, June H Myklebust, Børre Fevang
Patients with common variable immunodeficiency (CVID) constitute a clinically and immunologically heterogeneous group characterized by B-cell dysfunction with hypogammaglobulinemia and defective immunoglobulin class switch of unknown etiology. Current classification systems are insufficient to achieve precise disease management. Characterization of signaling pathways essential for B-cell differentiation and class switch could provide new means to stratify patients. We evaluated constitutive and induced signaling by phospho-specific flow cytometry in 26 CVID patients and 18 healthy blood donors...
December 2, 2016: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/27917180/role-of-the-gacs-sensor-kinase-in-the-regulation-of-volatile-production-by-plant-growth-promoting-pseudomonas-fluorescens-sbw25
#5
Xu Cheng, Viviane Cordovez, Desalegn W Etalo, Menno van der Voort, Jos M Raaijmakers
In plant-associated Pseudomonas species, the production of several secondary metabolites and exoenzymes is regulated by the GacS/GacA two-component regulatory system (the Gac-system). Here, we investigated if a mutation in the GacS sensor kinase affects the production of volatile organic compounds (VOCs) in P. fluorescens SBW25 (Pf.SBW25) and how this impacts on VOCs-mediated growth promotion and induced systemic resistance of Arabidopsis and tobacco. A total of 205 VOCs were detected by Gas Chromatography Mass Spectrometry for Pf...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27915188/combined-cluster-and-discriminant-analysis-an-efficient-chemometric-approach-in-diesel-fuel-characterization
#6
Márton Novák, Dóra Palya, Zsolt Bodai, Zoltán Nyiri, Norbert Magyar, József Kovács, Zsuzsanna Eke
Combined cluster and discriminant analysis (CCDA) as a chemometric tool in compound specific isotope analysis of diesel fuels was studied. The stable carbon isotope ratios (δ(13)C) of n-alkanes in diesel fuel can be used to characterize or differentiate diesels originating from different sources. We investigated 25 diesel fuel samples representing 20 different brands. The samples were collected from 25 different service stations in 11 European countries over a 2 year period. The n-alkane fraction of diesel fuels was separated using solid-state urea clathrate formation combined with silica gel fractionation...
November 23, 2016: Forensic Science International
https://www.readbyqxmd.com/read/27913798/generalizability-of-the-maximum-proportional-recovery-rule-to-visuospatial-neglect-early-poststroke
#7
Caroline Winters, Erwin E H van Wegen, Andreas Daffertshofer, Gert Kwakkel
Background and objective Proportional recovery of upper-extremity motor function and aphasia after stroke may suggest common mechanisms for spontaneous neurobiological recovery. This study aimed to investigate if the proportional recovery rule also applies to visuospatial neglect (VSN) in right-hemispheric first-ever ischemic stroke patients and explored the possible common underlying mechanisms. Methods Patients with upper-limb paresis and VSN were included. Recovery defined as the change in Letter Cancellation Test (LCT) score at ~8 days and 6 months poststroke...
December 2, 2016: Neurorehabilitation and Neural Repair
https://www.readbyqxmd.com/read/27913377/optimization-and-assessment-of-three-different-high-performance-liquid-chromatographic-systems-for-the-combinative-fingerprint-analysis-and-multi-ingredients-quantification-of-sangju-ganmao-tablet
#8
Meng-Zhe Guo, Jie Han, Dan-Dan He, Jia-Hui Zou, Zheng Li, Yan Du, Dao-Quan Tang
Chromatographic separation is still a critical subject for the quality control of traditional Chinese medicine. In this study, three different high performance liquid chromatographic (HPLC) systems employing commercially available columns packed with 1.8, 3.5 and 5.0 μm particles were respectively developed and optimized for the combinative fingerprint analysis and multi-ingredients quantification of Sangju Ganmao tablet (SGT). Chromatographic parameters including the repeatability of retention time and peak area, symmetry factor, resolution, number of theoretical plates and peak capacity were used to assess the chromatographic performance of different HPLC systems...
December 1, 2016: Journal of Chromatographic Science
https://www.readbyqxmd.com/read/27913304/effects-of-nongenetic-factors-on-immune-cell-dynamics-in-early-childhood-the-generation-r-study
#9
Diana van den Heuvel, Michelle A E Jansen, Kazem Nasserinejad, Willem A Dik, Ellen G van Lochem, Liesbeth E Bakker-Jonges, Halima Bouallouch-Charif, Vincent W V Jaddoe, Herbert Hooijkaas, Jacques J M van Dongen, Henriëtte A Moll, Menno C van Zelm
BACKGROUND: . Numbers of blood leukocyte subsets are highly dynamic in childhood and differ greatly between individuals. Inter-individual variation is only partly accounted for by genetic factors. OBJECTIVE: Determine which nongenetic factors affect the dynamics of innate leukocytes, and naive and memory lymphocyte subsets. METHODS: . We performed six-color flow cytometry and linear mixed effect modeling to define the dynamics of 62 leukocyte subsets from birth to 6 years of age in 1,182 children with one to five measurements per individual...
November 29, 2016: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/27912172/brain-heart-communication-evidence-for-central-pacemaker-oscillations-with-a-dominant-frequency-at-0-1hz-in-the-cingulum
#10
Gert Pfurtscheller, Andreas R Schwerdtfeger, Annemarie Seither-Preisler, Clemens Brunner, Christoph Stefan Aigner, Joana Brito, Marciano P Carmo, Alexandre Andrade
OBJECTIVES: In the brain and heart, oscillations at about 0.1Hz are conspicuous. It is therefore worthwhile to study the interaction between intrinsic BOLD oscillations (0.1Hz) and slow oscillations in heart rate interval (RRI) signals and differentiate between their neural and vascular origin. METHODS: We studied the phase-coupling with a 3T scanner with high scanning rate between BOLD signals in 22 regions and simultaneously recorded RRI oscillations in 23 individuals in two resting states...
November 10, 2016: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/27910790/exploring-geographical-differentiation-of-the-hoelen-medicinal-mushroom-wolfiporia-extensa-agaricomycetes-using-fourier-transform-infrared-spectroscopy-combined-with-multivariate-analysis
#11
Yan Li, Ji Zhang, Yanli Zhao, Honggao Liu, Yuanzhong Wang, Hang Jin
In this study the geographical differentiation of dried sclerotia of the medicinal mushroom Wolfiporia extensa, obtained from different regions in Yunnan Province, China, was explored using Fourier-transform infrared (FT-IR) spectroscopy coupled with multivariate data analysis. The FT-IR spectra of 97 samples were obtained for wave numbers ranging from 4000 to 400 cm-1. Then, the fingerprint region of 1800-600 cm-1 of the FT-IR spectrum, rather than the full spectrum, was analyzed. Different pretreatments were applied on the spectra, and a discriminant analysis model based on the Mahalanobis distance was developed to select an optimal pretreatment combination...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27907142/ibisa_tools-a-computational-toolkit-for-ion-binding-state-analysis-in-molecular-dynamics-trajectories-of-ion-channels
#12
Kota Kasahara, Kengo Kinoshita
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering...
2016: PloS One
https://www.readbyqxmd.com/read/27901127/gap-shape-classification-using-landscape-indices-and-multivariate-statistics
#13
Chih-Da Wu, Chi-Chuan Cheng, Che-Chang Chang, Chinsu Lin, Kun-Cheng Chang, Yung-Chung Chuang
This study proposed a novel methodology to classify the shape of gaps using landscape indices and multivariate statistics. Patch-level indices were used to collect the qualified shape and spatial configuration characteristics for canopy gaps in the Lienhuachih Experimental Forest in Taiwan in 1998 and 2002. Non-hierarchical cluster analysis was used to assess the optimal number of gap clusters and canonical discriminant analysis was used to generate the discriminant functions for canopy gap classification. The gaps for the two periods were optimally classified into three categories...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27898719/myocardial-gene-expression-profiling-to-predict-and-identify-cardiac-allograft-acute-cellular-rejection-the-get-study
#14
Diane Bodez, Hakim Hocini, Nicolas Tchitchek, Pascaline Tisserand, Nicole Benhaiem, Caroline Barau, Mounira Kharoubi, Aziz Guellich, Soulef Guendouz, Costin Radu, Jean-Paul Couetil, Bijan Ghaleh, Jean-Luc Dubois-Randé, Emmanuel Teiger, Luc Hittinger, Yves Levy, Thibaud Damy
AIMS: Serial invasive endomyocardial biopsies (EMB) remain the gold standard for acute cellular rejection (ACR) diagnosis. However histological grading has several limitations. We aimed to explore the value of myocardial Gene Expression Profiling (GEP) for diagnosing and identifying predictive biomarkers of ACR. METHODS: A case-control study nested within a retrospective heart transplant patients cohort included 126 patients with median (IQR) age 50 (41-57) years and 111 (88%) males...
2016: PloS One
https://www.readbyqxmd.com/read/27896962/adaptive-testing-of-snp-brain-functional-connectivity-association-via-a-modular-network-analysis
#15
Chen Gao, Junghi Kim, Wei Pan
Due to its high dimensionality and high noise levels, analysis of a large brain functional network may not be powerful and easy to interpret; instead, decomposition of a large network into smaller subcomponents called modules may be more promising as suggested by some empirical evidence. For example, alteration of brain modularity is observed in patients suffering from various types of brain malfunctions. Although several methods exist for estimating brain functional networks, such as the sample correlation matrix or graphical lasso for a sparse precision matrix, it is still difficult to extract modules from such network estimates...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896751/clustering
#16
G J McLachlan, R W Bean, S K Ng
Clustering techniques are used to arrange genes in some natural way, that is, to organize genes into groups or clusters with similar behavior across relevant tissue samples (or cell lines). These techniques can also be applied to tissues rather than genes. Methods such as hierarchical agglomerative clustering, k-means clustering, the self-organizing map, and model-based methods have been used. Here we focus on mixtures of normals to provide a model-based clustering of tissue samples (gene signatures) and of gene profiles, including time-course gene expression data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27891101/spatio-temporal-structure-path-characteristics-and-perceptual-grouping-in-immediate-serial-spatial-recall
#17
Carlo De Lillo, Melissa Kirby, Daniel Poole
Immediate serial spatial recall measures the ability to retain sequences of locations in short-term memory and is considered the spatial equivalent of digit span. It is tested by requiring participants to reproduce sequences of movements performed by an experimenter or displayed on a monitor. Different organizational factors dramatically affect serial spatial recall but they are often confounded or underspecified. Untangling them is crucial for the characterization of working-memory models and for establishing the contribution of structure and memory capacity to spatial span...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27890118/3d-digital-headform-models-of-australian-cyclists
#18
Thierry Ellena, Sebastian Skals, Aleksandar Subic, Helmy Mustafa, Toh Yen Pang
Traditional 1D anthropometric data have been the primary source of information used by ergonomists for the dimensioning of head and facial gear. Although these data are simple to use and understand, they only provide univariate measures of key dimensions. 3D anthropometric data, however, describe the complete shape characteristics of the head surface, but are complicated to interpret due to the abundance of information they contain. Consequently, current headform standards based on 1D measurements may not adequately represent the actual head shape variations of the intended user groups...
March 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/27890116/forms-of-work-organization-and-associations-with-shoulder-disorders-results-from-a-french-working-population
#19
Julie Bodin, Ronan Garlantézec, Nathalie Costet, Alexis Descatha, Natacha Fouquet, Sandrine Caroly, Yves Roquelaure
The aim of this study was to identify forms of work organization in a French region and to study associations with the occurrence of symptomatic and clinically diagnosed shoulder disorders in workers. Workers were randomly included in this cross-sectional study from 2002 to 2005. Sixteen organizational variables were assessed by a self-administered questionnaire: i.e. shift work, job rotation, repetitiveness of tasks, paced work/automatic rate, work pace dependent on quantified targets, permanent controls or surveillance, colleagues' work and customer demand, and eight variables measuring decision latitude...
March 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/27889515/quality-assessment-of-traditional-chinese-medicine-using-hplc-pad-combined-with-tchebichef-image-moments
#20
Xue Wang, Bao Qiong Li, Min Li Xu, Jin Jin Liu, Hong Lin Zhai
Traditional Chinese medicines have gotten growing attention and the product quality also became uneven. In this paper, Tchebichef image moments coupled with high performance liquid chromatography with photodiode array detector were proposed to the similarity analysis of the fourteen batches of Pudilan Xiaoyan tablets (Chinese medicine complex), which were based on the grayscale images of three dimensional (3D) fingerprint spectra. Hierarchical cluster analysis was used for displaying the classification results...
November 18, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
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