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Hierarchical clustering

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https://www.readbyqxmd.com/read/28551533/hydro-geochemical-paths-of-multi-layer-groundwater-system-in-coal-mining-regions-using-multivariate-statistics-and-geochemical-modeling-approaches
#1
Pu Liu, Nils Hoth, Carsten Drebenstedt, Yajun Sun, Zhimin Xu
Groundwater is an important drinking water resource that requires protection in North China. Coal mining industry in the area may influence the water quality evolution. To provide primary characterization of the hydrogeochemical processes and paths that control the water quality evolution, a complex multi-layer groundwater system in a coal mining area is investigated. Multivariate statistical methods involving hierarchical cluster analysis (HCA) and principal component analysis (PCA) are applied, 6 zones and 3 new principal components are classified as major reaction zones and reaction factors...
May 25, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28551361/sitting-too-much-a-hierarchy-of-socio-demographic-correlates
#2
Jeroen Lakerveld, Anne Loyen, Nina Schotman, Carel F W Peeters, Greet Cardon, Hidde P van der Ploeg, Nanna Lien, Sebastien Chastin, Johannes Brug
Too much sitting (extended sedentary time) is recognized as a public health concern in Europe and beyond. Time spent sedentary is influenced and conditioned by clusters of individual-level and contextual (upstream) factors. Identifying population subgroups that sit too much could help to develop targeted interventions to reduce sedentary time. We explored the relative importance of socio-demographic correlates of sedentary time in adults across Europe. We used data from 26,617 adults who participated in the 2013 Special Eurobarometer 412 "Sport and physical activity"...
May 24, 2017: Preventive Medicine
https://www.readbyqxmd.com/read/28551273/planning-a-mentorship-initiative-for-foster-parents-does-gender-matter
#3
J Jay Miller, Kalea Benner, Shawndaya Thrasher, Natalie Pope, Tamikia Dumas, Larry J Damron, Melissa Segress, Chunling Niu
Despite the use of mentoring programs in fields such as business, career training, and youth development, little is known about how mentoring can be used to train and support new foster parents. This paper describes how Concept Mapping was used with current foster parents to develop a conceptual framework suitable to plan a foster parent mentor program. A secondary aim of this study was to explore priority differences in the conceptualization by self-reported gender (foster mothers vs. foster fathers). Participant data was collected via three qualitative brainstorming sessions, and analyzed using non-metric multidimensional scaling and hierarchical cluster analysis...
May 8, 2017: Evaluation and Program Planning
https://www.readbyqxmd.com/read/28549077/clinical-criteria-for-subtyping-parkinson-s-disease-biomarkers-and-longitudinal-progression
#4
Seyed-Mohammad Fereshtehnejad, Yashar Zeighami, Alain Dagher, Ronald B Postuma
Parkinson's disease varies widely in clinical manifestations, course of progression and biomarker profiles from person to person. Identification of distinct Parkinson's disease subtypes is of great priority to illuminate underlying pathophysiology, predict progression and develop more efficient personalized care approaches. There is currently no clear way to define and divide subtypes in Parkinson's disease. Using data from the Parkinson's Progression Markers Initiative, we aimed to identify distinct subgroups via cluster analysis of a comprehensive dataset at baseline (i...
May 25, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28549048/disposable-versus-reusable-absorbent-underpads-for-prevention-of-hospital-acquired-incontinence-associated-dermatitis-and-pressure-injuries
#5
Kathleen Francis, Sau Man Pang, Brenda Cohen, Helene Salter, Peter Homel
PURPOSE: The primary purpose of our study was to determine if there is a difference in the occurrence of hospital-acquired pressure injuries (HAPIs) and incontinence-associated dermatitis (IAD) in incontinent adults using a disposable versus reusable absorptive underpads. We also compared hospital length of stay in the 2 groups. DESIGN: Randomized controlled trial using cluster randomization based on inpatient care unit. SUBJECTS AND SETTING: Four hundred sixty-two patients admitted to 4 medical-surgical study units participated in the study; 252 used reusable underpads (control group) and 210 subjects used disposable underpads (intervention group)...
May 25, 2017: Journal of Wound, Ostomy, and Continence Nursing
https://www.readbyqxmd.com/read/28548961/identification-and-validation-of-a-prognostic-9-genes-expression-signature-for-gastric-cancer
#6
Zhiqiang Wang, Gongxing Chen, Qilong Wang, Wei Lu, Meidong Xu
Gastric cancer (GC) is a common malignant tumor with high incidence and mortality. Reasonable assessment of prognosis is essential to improve the outcomes of patients. In this study, we constructed and validated a prognostic gene model to evaluate the risks of GC patients. To identify the differentially expressed genes between GC patients and controls, we extracted Gene expression profiles of GC patients (N=432) from Gene Expression Omnibus database and then stable signature genes by using Robust likelihood-based modeling with 1000 iterations...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28546534/classification-of-paediatric-inflammatory-bowel-disease-using-machine-learning
#7
E Mossotto, J J Ashton, T Coelho, R M Beattie, B D MacArthur, S Ennis
Paediatric inflammatory bowel disease (PIBD), comprising Crohn's disease (CD), ulcerative colitis (UC) and inflammatory bowel disease unclassified (IBDU) is a complex and multifactorial condition with increasing incidence. An accurate diagnosis of PIBD is necessary for a prompt and effective treatment. This study utilises machine learning (ML) to classify disease using endoscopic and histological data for 287 children diagnosed with PIBD. Data were used to develop, train, test and validate a ML model to classify disease subtype...
May 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28545423/determinants-of-tuberculosis-transmission-and-treatment-abandonment-in-fortaleza-brazil
#8
Guy Harling, Antonio S Lima Neto, Geziel S Sousa, Marcia M T Machado, Marcia C Castro
BACKGROUND: Tuberculosis (TB) remains a public health problem, despite recent achievements in reducing incidence and mortality rates. In Brazil, these achievements were above the worldwide average, but marked by large regional heterogeneities. In Fortaleza (5th largest city in Brazil), the tuberculosis cure rate has been declining and treatment abandonment has been increasing in the past decade, despite a reduction in incidence and an increase in directly observed therapy (DOT). These trends put efforts to eliminate tuberculosis at risk...
May 25, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28545042/hierarchical-ordering-with-partial-pairwise-hierarchical-relationships-on-the-macaque-brain-data-sets
#9
Woosang Lim, Jungsoo Lee, Yongsub Lim, Doo-Hwan Bae, Haesun Park, Dae-Shik Kim, Kyomin Jung
Hierarchical organizations of information processing in the brain networks have been known to exist and widely studied. To find proper hierarchical structures in the macaque brain, the traditional methods need the entire pairwise hierarchical relationships between cortical areas. In this paper, we present a new method that discovers hierarchical structures of macaque brain networks by using partial information of pairwise hierarchical relationships. Our method uses a graph-based manifold learning to exploit inherent relationship, and computes pseudo distances of hierarchical levels for every pair of cortical areas...
2017: PloS One
https://www.readbyqxmd.com/read/28544375/proteomic-analysis-of-hair-shafts-from-monozygotic-twins-expression-profiles-and-genetically-variant-peptides
#10
Pei-Wen Wu, Katelyn E Mason, Blythe P Durbin-Johnson, Michelle Salemi, Brett S Phinney, David M Rocke, Glendon J Parker, Robert H Rice
Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from 10 pairs of monozygotic twins...
May 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28544181/the-k-2-conundrum
#11
Jasmine K Janes, Joshua M Miller, Julian R Dupuis, René M Malenfant, Jamieson C Gorrell, Catherine I Cullingham, Rose L Andrew
Assessments of population genetic structure have become an increasing focus as they can provide valuable insight into patterns of migration and gene flow. STRUCTURE, the most highly cited of several clustering-based methods, was developed to provide robust estimates without the need for populations to be determined a priori. STRUCTURE introduces the problem of selecting the optimal number of clusters and as a result the ΔK method was proposed to assist in the identification of the 'true' number of clusters...
May 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28543517/intermediate-and-advanced-topics-in-multilevel-logistic-regression-analysis
#12
Peter C Austin, Juan Merlo
Multilevel data occur frequently in health services, population and public health, and epidemiologic research. In such research, binary outcomes are common. Multilevel logistic regression models allow one to account for the clustering of subjects within clusters of higher-level units when estimating the effect of subject and cluster characteristics on subject outcomes. A search of the PubMed database demonstrated that the use of multilevel or hierarchical regression models is increasing rapidly. However, our impression is that many analysts simply use multilevel regression models to account for the nuisance of within-cluster homogeneity that is induced by clustering...
May 23, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28542379/disease-related-gene-module-detection-based-on-a-multi-label-propagation-clustering-algorithm
#13
Xue Jiang, Han Zhang, Xiongwen Quan, Zhandong Liu, Yanbin Yin
Detecting disease-related gene modules by analyzing gene expression data is of great significance. It is helpful for exploratory analysis of the interaction mechanisms of genes under complex disease phenotypes. The multi-label propagation algorithm (MLPA) has been widely used in module detection for its fast and easy implementation. The accuracy of MLPA greatly depends on the connections between nodes, and most existing research focuses on measuring the similarity between nodes. However, MLPA does not perform well with loose connections between disease-related genes...
2017: PloS One
https://www.readbyqxmd.com/read/28541078/ensembles-in-medial-and-lateral-orbitofrontal-cortex-construct-cognitive-maps-emphasizing-different-features-of-the-behavioral-landscape
#14
Nina Lopatina, Brian F Sadacca, Michael A McDannald, Clay V Styer, Jacob F Peterson, Joseph F Cheer, Geoffrey Schoenbaum
The orbitofrontal cortex (OFC) has long been implicated in the ability to use the current value of expected outcomes to guide behavior. More recently, this specific role has been conceptualized as a special case of a more general function that OFC plays in constructing a "cognitive map" of the behavioral task space by labeling the current task state and learning relationships among task states. Here, we have used single unit recording data from 2 prior studies to examine whether and how information relating different states within and across trials is represented in medial versus lateral OFC in rats...
June 2017: Behavioral Neuroscience
https://www.readbyqxmd.com/read/28537888/high-expression-of-mir-493-5p-positively-correlates-with-clinical-prognosis-of-non-small-cell-lung-cancer-by-targeting-oncogene-itgb1
#15
Zhu Liang, Rui Kong, Zhan He, Li-Yao Lin, Shan-Shan Qin, Chun-Yuan Chen, Zhan-Qiang Xie, Fei Yu, Guo-Qian Sun, Chun-Guang Li, Da Fu, Geng-Xi Jiang, Jie Chen, Yu-Shui Ma
Increasing evidence supports that microRNA (miRNA)-mediated gene regulation plays a significant functional role in cancer progression. To investigate the expression and clinical significance of ITGB1 in non small cell lung cancer (NSCLC), the expression levels of ITGB1 in NSCLC tissues and human normal lung tissues were analyzed in silico using genes microarray, KEGG pathway and hierarchical clustering analysis followed by validation with quantitative RT-PCR. Our results showed that ITGB1 was upregulated in NSCLC tissues when compared with normal lung tissues...
May 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28537313/control-of-the-hierarchical-assembly-of-%C3%AF-conjugated-optoelectronic-peptides-by-ph-and-flow
#16
Rachael A Mansbach, Andrew L Ferguson
Self-assembled nanoaggregates of π-conjugated peptides possess optoelectronic properties due to electron delocalization over the conjugated peptide groups that make them attractive candidates for the fabrication of bioelectronic materials. We present a computational and theoretical study to resolve the microscopic effects of pH and flow on the non-equilibrium morphology and kinetics of early-stage assembly of an experimentally-realizable optoelectronic peptide that displays pH triggerable assembly. Employing coarse-grained molecular dynamics simulations, we probe the effects of pH on growth kinetics and aggregate morphology to show that control of the peptide protonation state by pH can be used to modulate the assembly rates, degree of molecular alignment, and resulting morphologies within the self-assembling nanoaggregates...
May 24, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28536884/an-update-in-symptom-clusters-using-the-edmonton-symptom-assessment-system-in-a-palliative-radiotherapy-clinic
#17
Vithusha Ganesh, Liying Zhang, Stephanie Chan, Bo Angela Wan, Leah Drost, May Tsao, Cyril Danjoux, Elizabeth Barnes, Rachel McDonald, Leigha Rowbottom, Pearl Zaki, Ronald Chow, Matthew K Hwang, Carlo DeAngelis, Nicholas Lao, Edward Chow
PURPOSE: To identify symptom clusters in advanced cancer patients attending a palliative radiotherapy clinic using the Edmonton Symptom Assessment System (ESAS). METHODS: Principal component analysis (PCA), exploratory factor analysis (EFA), and hierarchical cluster analysis (HCA) were used to identify symptom clusters among the nine ESAS items using scores from each patient's first visit. RESULTS: ESAS scores from 182 patients were analyzed...
May 23, 2017: Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer
https://www.readbyqxmd.com/read/28536307/gene-expression-profiling-in-braf-mutated-melanoma-reveals-patient-subgroups-with-poor-outcomes-to-vemurafenib-that-may-be-overcome-by-cobimetinib-plus-vemurafenib
#18
Matthew J Wongchenko, Grant A McArthur, Brigitte Dréno, James Larkin, Paolo A Ascierto, Jeffrey Sosman, Luc Andries, Mark Kockx, Stephen D Hurst, Ivor Caro, Isabelle Rooney, Priti S Hegde, Luciana Molinero, Huibin Yue, Ilsung Chang, Lukas C Amler, Yibing Yan, Antoni Ribas
The association of tumor gene expression profiles with progression-free survival (PFS) outcomes in patients with BRAF(V600)-mutated melanoma treated with vemurafenib or cobimetinib combined with vemurafenib was evaluated. <br /><br />Experimental Design: Gene expression of archival tumor samples from patients in four trials (BRIM-2, BRIM-3, BRIM-7, and coBRIM) was evaluated. Genes significantly associated with PFS (P<0 .05) were identified by univariate Cox proportional hazards modeling, then subjected to unsupervised hierarchical clustering, principal component analysis, and recursive partitioning to develop optimized gene signatures...
May 23, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28532454/proteomic-profiling-of-peripheral-blood-neutrophils-identifies-two-inflammatory-phenotypes-in-stable-copd-patients
#19
Adèle Lo Tam Loi, Susan Hoonhorst, Corneli van Aalst, Jeroen Langereis, Vera Kamp, Simone Sluis-Eising, Nick Ten Hacken, Jan-Willem Lammers, Leo Koenderman
BACKGROUND: COPD is a heterogeneous chronic inflammatory disease of the airways and it is well accepted that the GOLD classification does not fully represent the complex clinical manifestations of COPD and this classification therefore is not well suited for phenotyping of individual patients with COPD. Besides the chronic inflammation in the lung compartment, there is also a systemic inflammation present in COPD patients. This systemic inflammation is associated with elevated levels of cytokines in the peripheral blood, but the precise composition is unknown...
May 22, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28532446/dual-burden-of-malnutrition-in-us-affiliated-pacific-jurisdictions-in-the-children-s-healthy-living-program
#20
Rachel Novotny, Fenfang Li, Rachael Leon Guerrero, Patricia Coleman, Aifili J Tufa, Andrea Bersamin, Jonathan Deenik, Lynne R Wilkens
BACKGROUND: Few data are available on dual burden of under and over nutrition of children in the Pacific region. The objective was to examine prevalence of stunting at birth and current stunting and their relationship to obesity in US Affiliated Pacific (USAP) jurisdictions. METHODS: Cross sectional survey with cluster sampling by community. 5558, 2-8 years olds were measured in 51 communities in 11 USAP jurisdictions. The main outcome measures were stunting at birth, current stunting and obesity by body mass index...
May 22, 2017: BMC Public Health
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