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Hierarchical clustering

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https://www.readbyqxmd.com/read/28643439/a-simple-and-effective-physical-characteristic-profiling-method-for-methamphetamine-tablet-seized-in-china
#1
Tao Li, Zhendong Hua, Xin Meng, Cuimei Liu
Methamphetamine (MA) tablet production confers chemical and physical properties. This study developed a simple and effective physical characteristic profiling method for MA tablets with capital letter "WY" logos, which realized the discrimination between linked and unlinked seizures. Seventeen signature distances extracted from the "WY" logo were explored as factors for multivariate analysis and demonstrated to be effective to represent the features of tablets in the drug intelligence perspective. Receiver operating characteristic (ROC) curve was used to evaluate efficiency of different pretreatments and distance/correlation metrics, while "Standardization + Euclidean" and "Logarithm + Euclidean" algorithms outperformed the rest...
June 23, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28642738/distinct-bacterial-communities-associated-with-massive-and-branching-scleractinian-corals-and-potential-linkages-to-coral-susceptibility-to-thermal-or-cold-stress
#2
Jiayuan Liang, Kefu Yu, Yinghui Wang, Xueyong Huang, Wen Huang, Zhenjun Qin, Ziliang Pan, Qiucui Yao, Wenhuan Wang, Zhengchao Wu
It is well known that different coral species have different tolerances to thermal or cold stress, which is presumed to be related to the density of Symbiodinium. However, the intrinsic factors between stress-tolerant characteristics and coral-associated bacteria are rarely studied. In this study, 16 massive coral and 9 branching coral colonies from 6 families, 10 genera, and 18 species were collected at the same time and location (Xinyi Reef) in the South China Sea to investigate the bacterial communities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642031/clustering-of-ms-2-spectra-using-unsupervised-methods-to-aid-the-identification-of-secondary-metabolites-from-pseudomonas-aeruginosa
#3
Tobias Depke, Raimo Franke, Mark Brönstrup
Pseudomonas aeruginosa is an important opportunistic pathogen that produces a large arsenal of small molecule virulence factors and quorum sensing signal molecules. The annotation of these secondary metabolites in untargeted, mass spectrometry-based metabolomics is difficult, as many of them cannot be found in common metabolite databases, and as manual annotation is tedious. We therefore developed an algorithm named CluMSID that uses cosine similarities of product ion spectra and neutral loss patterns in combination with unsupervised clustering methods such as multidimensional scaling, density based clustering and hierarchical clustering to group structurally similar compounds and hence facilitate their annotation...
June 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28640232/why-do-children-engage-in-sedentary-behavior-child-and-parent-perceived-determinants
#4
Lisan M Hidding, Teatske M Altenburg, Evi van Ekris, Mai J M Chinapaw
Todays children spend a large amount of their time sedentary. There is limited evidence on the determinants of sedentary behavior in children, and qualitative studies are especially lacking. Therefore, this study aimed to explore determinants of children's sedentary behavior from the child- and parent perspective. Qualitative data were collected during concept mapping sessions with four groups of 11-13 years old children (n = 38) and two online sessions with parents (n = 21). Children and parents generated sedentary behavior motives, sorted related motives, and rated their importance in influencing children's sedentary time...
June 22, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28638001/comparison-between-glioblastoma-and-primary-central-nervous-system-lymphoma-using-mr-image-based-texture-analysis
#5
Akira Kunimatsu, Natsuko Kunimatsu, Kouhei Kamiya, Takeyuki Watadani, Harushi Mori, Osamu Abe
PURPOSE: To elucidate differences between glioblastoma (GBM) and primary central nervous system lymphoma (PCNSL) with magnetic resonance (MR) image-based texture features. METHODS: This was an Institutional Review Board (IRB)-approved retrospective study. Consecutive, pathologically proven, initially treated 44 patients with GBM and 16 patients with PCNSL were enrolled. We calculated a total of 67 image texture features on the largest contrast-enhancing lesion in each patient on post-contrast T1-weighted images...
June 22, 2017: Magnetic Resonance in Medical Sciences: MRMS
https://www.readbyqxmd.com/read/28637835/do-copd-subtypes-really-exist-copd-heterogeneity-and-clustering-in-10-independent-cohorts
#6
Peter J Castaldi, Marta Benet, Hans Petersen, Nicholas Rafaels, James Finigan, Matteo Paoletti, H Marike Boezen, Judith M Vonk, Russell Bowler, Massimo Pistolesi, Milo A Puhan, Josep Anto, Els Wauters, Diether Lambrechts, Wim Janssens, Francesca Bigazzi, Gianna Camiciottoli, Michael H Cho, Craig P Hersh, Kathleen Barnes, Stephen Rennard, Meher Preethi Boorgula, Jennifer Dy, Nadia N Hansel, James D Crapo, Yohannes Tesfaigzi, Alvar Agusti, Edwin K Silverman, Judith Garcia-Aymerich
BACKGROUND: COPD is a heterogeneous disease, but there is little consensus on specific definitions for COPD subtypes. Unsupervised clustering offers the promise of 'unbiased' data-driven assessment of COPD heterogeneity. Multiple groups have identified COPD subtypes using cluster analysis, but there has been no systematic assessment of the reproducibility of these subtypes. OBJECTIVE: We performed clustering analyses across 10 cohorts in North America and Europe in order to assess the reproducibility of (1) correlation patterns of key COPD-related clinical characteristics and (2) clustering results...
June 21, 2017: Thorax
https://www.readbyqxmd.com/read/28637148/pure-tone-hearing-profiles-in-children-with-otitis-media-with-effusion
#7
Ting Cai, Bradley McPherson, Caiwei Li, Feng Yang
INTRODUCTION: Otitis media with effusion (OME) is a common middle ear disease in children. The associated conductive hearing loss is a major concern for hearing health professionals. The aim of the present study was to describe the configuration of pure tone audiograms of children with OME and to design a statistical stratification algorithm to facilitate hearing loss profiling in children with OME. METHODS: School age children with OME were recruited. Bone and air conduction thresholds were obtained using standard procedures...
February 25, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28636340/three-dimensional-modeling-of-quasicrystal-structures-from-x-ray-diffraction-an-icosahedral-al-cu-fe-alloy
#8
Seung-Tae Hong
Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al0.63Cu0.25Fe0.12. Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2(5) = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis...
June 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28635441/the-extension-of-a-set-of-needs-led-mental-health-clusters-to-accommodate-people-accessing-uk-intellectual-disability-health-services
#9
Jon Painter, Liam Trevithick, Richard Hastings, Barry Ingham, Ashok Roy
BACKGROUND: A development of a needs-led mental health classification system based on the Health of the National Outcome Scales (HoNOS) has previously been developed. AIMS: To extend the needs-based mental health (MH) clusters to accommodate the additional needs of people accessing UK intellectual disabilities health services. METHOD: Hierarchical cluster analysis was performed on assessment data from 18 National Health Service (NHS) provider organisations...
March 2, 2017: Journal of Mental Health
https://www.readbyqxmd.com/read/28634007/gene-expression-differences-between-ductal-carcinoma-in-situ-with-and-without-progression-to-invasive-breast-cancer
#10
Shusma C Doebar, Anieta M Sieuwerts, Vanja de Weerd, Hans Stoop, John W M Martens, Carolien H M van Deurzen
To understand the molecular alterations driving the progression of ductal carcinoma in situ (DCIS), we compared patients with pure DCIS and patients with DCIS and synchronous invasive breast cancer (IBC). Twelve patients with extensive pure DCIS were included as a representation of indolent lesions with limited invasive capacity. These cases were matched with 12 patients with a limited DCIS component and IBC, representing lesions with a high invasive potential. Matching included age and surrogate DCIS subtypes...
July 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28632777/immunohistochemiocal-subtyping-using-ck20-and-ck5-can-identify-urothelial-carcinomas-of-the-upper-urinary-tract-with-a-poor-prognosis
#11
Danijel Sikic, Bastian Keck, Sven Wach, Helge Taubert, Bernd Wullich, Peter J Goebell, Andreas Kahlmeyer, Peter Olbert, Philipp Isfort, Wilhelm Nimphius, Arndt Hartmann, Johannes Giedl
PURPOSE: Genome-wide analyses revealed basal and luminal subtypes of urothelial carcinomas of the bladder. It is unknown if this subtyping can also be applied to upper tract urothelial carcinomas. MATERIALS AND METHODS: Tumor samples from 222 patients with upper tract urothelial carcinomas who were treated with radical nephroureterectomy were analyzed for the expression of seven basal/luminal immunohistochemical markers (CK5, EGFR, CD44, CK20, p63, GATA3, FOXA1)...
2017: PloS One
https://www.readbyqxmd.com/read/28631275/a-typology-of-interprofessional-teamwork-in-acute-geriatric-care-a-study-in-55-units-in-belgium
#12
Ruth D Piers, Karen J J Versluys, Johan Devoghel, Sophie Lambrecht, André Vyt, Nele J Van Den Noortgate
OBJECTIVES: To explore the quality of interprofessional teamwork in acute geriatric care and to build a model of team types. DESIGN: Cross-sectional multicenter study. SETTING: Acute geriatric units in Belgium. PARTICIPANTS: Team members of different professional backgrounds. MEASUREMENTS: Perceptions of interprofessional teamwork among team members of 55 acute geriatric units in Belgium were measured using a survey covering collaborative practice and experience, managerial coaching and open team culture, shared reflection and decision-making, patient files facilitating teamwork, members' belief in the power of teamwork, and members' comfort in reporting incidents...
June 20, 2017: Journal of the American Geriatrics Society
https://www.readbyqxmd.com/read/28631213/the-constitutive-protease-release-by-primary-human-acute-myeloid-leukemia-cells
#13
Maria Honnemyr, Øystein Bruserud, Annette K Brenner
INTRODUCTION: Acute myeloid leukemia (AML) cells show constitutive release of matrix metalloproteases and their inhibitors. We now investigated this constitutive release of protease/protease regulators associated with carcinogenesis (ADAM12, uPA, cystatin B), angiogenesis (serpin E1, uPA, CD147), cancer cell migration (uPA, cystatin C), coagulation (ADAM TS13, serpin C1), inflammation (fetuin A, caspase 1, cystatin C), monocytic differentiation (CFD) or regulation of hematopoiesis (neutrophil elastase)...
June 19, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28630951/phenotyping-hypotensive-patients-in-critical-care-using-hospital-discharge-summaries
#14
Yang Dai, Sharukh Lokhandwala, William Long, Roger Mark, Li-Wei H Lehman
Among critically-ill patients, hypotension represents a failure in compensatory mechanisms and may lead to organ hypoperfusion and failure. In this work, we adopt a data-driven approach for phenotype discovery and visualization of patient similarity and cohort structure in the intensive care unit (ICU). We used Hierarchical Dirichlet Process (HDP) as a nonparametric topic modeling technique to automatically learn a d-dimensional feature representation of patients that captures the latent "topic" structure of diseases, symptoms, medications, and findings documented in hospital discharge summaries...
February 2017: IEEE-EMBS International Conference on Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28630804/diversity-analysis-of-gut-microbiota-in-osteoporosis-and-osteopenia-patients
#15
Jihan Wang, Yangyang Wang, Wenjie Gao, Biao Wang, Heping Zhao, Yuhong Zeng, Yanhong Ji, Dingjun Hao
Some evidence suggests that bone health can be regulated by gut microbiota. To better understand this, we performed 16S ribosomal RNA sequencing to analyze the intestinal microbial diversity in primary osteoporosis (OP) patients, osteopenia (ON) patients and normal controls (NC). We observed an inverse correlation between the number of bacterial taxa and the value of bone mineral density. The diversity estimators in the OP and ON groups were increased compared with those in the NC group. Beta diversity analyses based on hierarchical clustering and principal coordinate analysis (PCoA) could discriminate the NC samples from OP and ON samples...
2017: PeerJ
https://www.readbyqxmd.com/read/28627571/the-fractal-correlation-between-relaxation-dynamics-and-atomic-level-structures-observed-in-metallic-glasses-by-computer-simulation
#16
M H Yang, J H Li, B X Liu
In the present study, atomistic simulation reveals that the microscopic mechanism of the relaxation dynamics in amorphous materials is governed by the activating atoms that jump more than half of the average nearest neighbor distance within a given time. Based on the unsupervised machine-learning algorithm, hierarchical clustering analysis shows that the activating atoms are excited in a cooperative and avalanche-like model to form activating units. Correlation analysis suggests that large free volumes facilitate the formation of activating atoms...
June 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28626349/identifying-mixtures-of-mixtures-using-bayesian-estimation
#17
Gertraud Malsiner-Walli, Sylvia Frühwirth-Schnatter, Bettina Grün
The use of a finite mixture of normal distributions in model-based clustering allows us to capture non-Gaussian data clusters. However, identifying the clusters from the normal components is challenging and in general either achieved by imposing constraints on the model or by using post-processing procedures. Within the Bayesian framework, we propose a different approach based on sparse finite mixtures to achieve identifiability. We specify a hierarchical prior, where the hyperparameters are carefully selected such that they are reflective of the cluster structure aimed at...
April 3, 2017: Journal of Computational and Graphical Statistics
https://www.readbyqxmd.com/read/28623815/colorimetric-sensor-array-for-protein-discrimination-based-on-different-dna-chain-length-dependent-gold-nanoparticles-aggregation
#18
Xiangcong Wei, Yuxian Wang, Yingxin Zhao, Zhengbo Chen
A facile colorimetric sensor array for detection of proteins was demonstrated using DNA as nonspecific receptors. We found that different proteins could trigger the DNA-protected gold nanoparticles (AuNPs) to show different aggregation behaviors in the presence of salt with high concentrations along with various color changes. As a proof-of-concept application, a multi-protein discrimination array was fabricated with two ssDNA strands (15A and 30A bases) as a receptor array. The combinatorial colorimetric response of this sensor array can be analyzed by linear discriminant analysis (LDA) and hierarchical cluster analysis (HCA)...
June 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28622790/early-life-risk-factors-identified-for-owner-reported-feline-overweight-and-obesity-at-around-two-years-of-age
#19
E C Rowe, W J Browne, R A Casey, T J Gruffydd-Jones, J K Murray
Obesity is considered the second most common health problem in pet cats in developed countries. This study used prospective data from a longitudinal study of pet cats ('C.L.A.W.S.', www.bristol.ac.uk/vetscience/claws) to identify early-life risk factors for feline overweight/obesity occurring at around two years of age. Data were collected via five owner-completed questionnaires (for cats aged two-six months, six months, 12 months, 18 months and two years respectively) completed between May 2011 and April 2015...
August 1, 2017: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/28622634/type-of-gonadotropin-used-during-controlled-ovarian-stimulation-induces-differential-gene-expression-in-human-cumulus-cells-a-randomized-study
#20
María Cruz, Antonio Requena, David Agudo, Juan Antonio García-Velasco
BACKGROUND: The cumulus-oocyte complex plays a central role in the regulation of folliculogenesis where it is important for the maturation, reprogramming, and fertilization of oocytes. Consequently, cumulus cell gene expression profiling is being explored as a promising method for assessing oocyte competence in the near future. Through DNA microarray technology, we analyzed the potential differences in the gene expression profiles of cumulus cells from preovulatory follicles after controlled ovarian stimulation using different types of gonadotropins...
June 8, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
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