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Hierarchical clustering

Liang Wei, Qi Wang, Yanfei Zhang, Cheng Yang, Hongxin Guan, Jianxin Jiang, Zhiyang Sun
Intracranial aneurysm (IA) is a localized dilation of the blood vessel. The present study was designed to explore the mechanisms of rupture of IA. GSE13353 (including 11 ruptured and 8 unruptured IA samples) and GSE15629 (including 8 ruptured and 6 unruptured IA samples) were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) identified using limma and MetaDE packages were merged, and a protein-protein interaction (PPI) network analysis was performed using Cytoscape software...
April 2018: Oncology Letters
Minjung Park, Jennifer Hunter, Soonman Kwon
High demand for traditional Korean medicine led to a policy change in 2010 allowing hospitals to provide Integrative medicine care that combines Western medicine and Korean medicine. This study evaluated the effects of Integrative medicine compared to Western medicine-only for managing acute stroke in South Korean hospitals. A retrospective matched case-control observational study was conducted for acute stroke patients admitted nationwide in 2012 and 2013. Propensity score matching was used to adjust for the likelihood of selecting Integrative medicine...
March 6, 2018: Health Policy
Bo Zhuang, Zhi-Ming Bi, Zi-Yuan Wang, Li Duan, Chang-Jiang-Sheng Lai, E-Hu Liu
Platycladi Cacumen (PC) is a traditional Chinese medicine used for the treatment of hemorrhages, cough, asthma and hair loss. To get a better understanding of the chemical constituents in PC, ultra-high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS) and diagnostic ion filtering strategy were firstly employed for chemical profiling of PC. A total of 43 compounds including organic acids and derivatives, flavonoids as well as phenylpropanolds were unambiguously or reasonably identified...
March 9, 2018: Journal of Pharmaceutical and Biomedical Analysis
E Hanson, S Ingold, C Haas, J Ballantyne
The recovery of a DNA profile from the perpetrator or victim in criminal investigations can provide valuable 'source level' information for investigators. However, a DNA profile does not reveal the circumstances by which biological material was transferred. Some contextual information can be obtained by a determination of the tissue or fluid source of origin of the biological material as it is potentially indicative of some behavioral activity on behalf of the individual that resulted in its transfer from the body...
March 6, 2018: Forensic Science International. Genetics
Ji Ye, Yanxia Gao, Saisai Tian, Juan Su, Weidong Zhang
BACKGROUND: Panax ginseng (PG) is one of the most valuable and frequently used phytomedicine in Asia. In the current Chinese Pharmacopeia, only three ginsenosides, Rg1, Re and Rb1, were set as standard compounds for the quality evaluation of PG. However, only these three compounds could hardly reflect the quality and therapeutic efficacy of this traditional Chinese medicine (TCM). PURPOSE: Quantification analysis of quality markers (Q-markers) in PG is meaningful for determining the quality of this herbal medicine...
February 28, 2018: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
Jinny Robson, Parham Aram, Martyn P Nash, Chris P Bradley, Martin Hayward, David J Paterson, Peter Taggart, Richard H Clayton, Visakan Kadirkamanathan
In this paper, we present a novel approach to quantify the spatio-temporal organization of electrical activation during human ventricular fibrillation (VF). We propose three different methods based on correlation analysis, graph theoretical measures and hierarchical clustering. Using the proposed approach, we quantified the level of spatio-temporal organization during three episodes of VF in ten patients, recorded using multi-electrode epicardial recordings with 30 s coronary perfusion, 150 s global myocardial ischaemia and 30 s reflow...
March 15, 2018: Annals of Biomedical Engineering
M Hobbs, M J Duncan, P Collins, J Mckenna, S Schoeppe, A L Rebar, S Alley, C Short, C Vandelanotte
Background: The co-occurrence of unhealthy lifestyles, calls for interventions that target multiple health behaviours. This study investigates the clustering of health behaviours and examines demographic differences between each cluster. Methods: In total, 934 adults from Queensland, Australia completed a cross-sectional survey assessing multiple health behaviours. A two-step hierarchical cluster analysis using multiple iterations identified the optimal number of clusters and the subset of distinguishing health behaviour variables...
March 13, 2018: Journal of Public Health
Michael J R Martin, Stephen A Matthews, Barrett A Lee
Although increasing racial and ethnic diversity is a demographic trend with society-wide implications, it has advanced farther in some parts of the United States than others. Our research seeks to understand this unevenness at the local level. Drawing on 1980-2010 census data, we use an innovative spatial analytic approach to examine the spread or diffusion of diversity across counties in the 48 contiguous states. Three perspectives-locational persistence, spatial assimilation, and institutional hub-offer different expectations about the nature of the diffusion process...
October 2017: Spatial Demography
Haiyan Gao, Mei Yang, Xiaolan Zhang
The present study aimed to investigate potential recurrence-risk biomarkers based on significant pathways for Luminal A breast cancer through gene expression profile analysis. Initially, the gene expression profiles of Luminal A breast cancer patients were downloaded from The Cancer Genome Atlas database. The differentially expressed genes (DEGs) were identified using a Limma package and the hierarchical clustering analysis was conducted for the DEGs. In addition, the functional pathways were screened using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and rank ratio calculation...
April 2018: Oncology Letters
Steven M Kornblau, Peter P Ruvolo, Rui-Yu Wang, V Lokesh Battula, Elisabeth J Shpall, Vivian R Ruvolo, Teresa McQueen, YiHua Qui, Zhihong Zeng, Sherry Pierce, Rodrigo Jacamo, Suk-Young Yoo, Phuong M Le, Jeffery Sun, Numsen Hail, Marina Konopleva, Michael Andreeff
Mesenchymal stromal cells support acute myeloid leukemia cell survival in the bone marrow microenvironment. Protein expression profiles of acute myeloid leukemia-derived mesenchymal stromal cells are unknown. Reverse phase protein array analysis was performed to compare expression of 151 proteins from acute myeloid leukemia mesenchymal stromal cells (n = 106) with mesenchymal stromal cells from healthy donors (n = 71). Protein expression differed significantly between the two groups with nineteen proteins overexpressed in leukemia stromal cells and nine overexpressed in normal stromal cells...
March 15, 2018: Haematologica
Zhengda Sun, Chih-Yang Wang, Devon A Lawson, Serena Kwek, Hugo Gonzalez Velozo, Mark Owyong, Ming-Derg Lai, Lawrence Fong, Mark Wilson, Hua Su, Zena Werb, Daniel L Cooke
Tumor endothelial cells (TEC) play an indispensible role in tumor growth and metastasis although much of the detailed mechanism still remains elusive. In this study we characterized and compared the global gene expression profiles of TECs and control ECs isolated from human breast cancerous tissues and reduction mammoplasty tissues respectively by single cell RNA sequencing (scRNA-seq). Based on the qualified scRNA-seq libraries that we made, we found that 1302 genes were differentially expressed between these two EC phenotypes...
February 16, 2018: Oncotarget
Zhishun He, Kai Wang, Shasha Zhu, Liang-Ai Huang, Miaomiao Chen, Jianfeng Guo, Shien Pei, Haibo Shao, Jianming Wang
Hierarchically nanostructured binary/multiple transition metal oxides with electrically conductive coatings are very attractive for lithium-ion batteries (LIBs) owing to their excellent electrochemical properties induced by their unique compositions and microstructures. Herein, hierarchical MnO doped Fe3O4@C composite nanospheres are prepared by a simple one-step annealing in Ar atmosphere, using Mn-doped Fe-based metal organic frameworks (Mn-doped MIL-53(Fe)) as precursor. The MnO doped Fe3O4@C composite particles have a uniform nanosphere structure with a diameter of ~100 nm, and each nanosphere is composed of clustered primary nanoparticles with an amorphous carbon shell, forming a unique hierarchical nanoarchitecture...
March 14, 2018: ACS Applied Materials & Interfaces
Sebastian T Tong, Camille J Hochheimer, Wendy B Barr, Matteo Leveroni-Calvi, Nicholas M Lefevre, Jordyn T Wallenborn, Lars E Peterson
BACKGROUND AND OBJECTIVES: Prior research found that 24% of graduating family medicine residents intend to provide obstetrical deliveries, but only 9% of family physicians 1 to 10 years into practice are doing so. Our study aims to describe the individual and residency program characteristics associated with intention to provide obstetrical deliveries and prenatal care. METHODS: Cross-sectional data on 2014-2016 graduating residents were obtained from the American Board of Family Medicine certification examination demographic questionnaire that asked about intended provision of specific clinical activities...
March 8, 2018: Family Medicine
Mona Dawood, Sami Hamdoun, Thomas Efferth
Arsenic trioxide is a traditional remedy in Chinese Medicine since ages. Nowadays, it is clinically used to treat acute promyelocytic leukemia (APL) by targeting PML/RARA. However, the drug's activity is broader and the mechanisms of action in other tumor types remain unclear. In this study, we investigated molecular modes of action by classical and network pharmacological approaches. CEM/ADR5000 resistance leukemic cells were similar sensitive to As2 O3 as their wild-type counterpart CCRF-CEM (resistance ratio: 1...
2018: Frontiers in Pharmacology
Mohamed E M Saeed, Nuha Mahmoud, Yoshikazu Sugimoto, Thomas Efferth, Heba Abdel-Aziz
For decades, natural products represented a significant source of diverse and unique bioactive lead compounds in drug discovery field. In Clinical oncology, complete tumors remission is hampered by the development of drug-resistance. Therefore, development of cytotoxic agents that may overcome drug resistance is urgently needed. Here, the natural benzophenanthridine alkaloid sanguinarine has been studied for its cytotoxic activity against multidrug resistance (MDR) cancer cells. We investigated the role of the ATP-binding cassette (ABC) transporters BCRP/ABCG2, P-glycoprotein/ABCB1 and its close relative ABCB5 in drug resistance...
2018: Frontiers in Pharmacology
Xiaoying Wang, Jiefu Peng, Jing Wang, Miao Li, Di Wu, Songyan Wu, Jipei Liao, Jun Dou
Background: Despite the breadth of understanding the noncoding RNAs' function in molecular biology, their functional roles in hepatocellular carcinoma (HCC) is poorly understood. In this study, we investigated the effect of hepatitis C virus (HCV) core upon the expression of noncoding RNAs. Methods: The lncRNAs, mRNAs, and circRNAs were employed for identification of HCV core protein gene expression in human Huh7 hepatoma (Huh7) cell line. In data analysis, we applied a threshold that eliminated all genes that were not increased or decreased by at least a 2-fold change in a comparison between transfected and control cells...
2018: OncoTargets and Therapy
Nicole Varble, Vincent M Tutino, Jihnhee Yu, Ashish Sonig, Adnan H Siddiqui, Jason M Davies, Hui Meng
BACKGROUND AND PURPOSE: Many ruptured intracranial aneurysms (IAs) are small. Clinical presentations suggest that small and large IAs could have different phenotypes. It is unknown if small and large IAs have different characteristics that discriminate rupture. METHODS: We analyzed morphological, hemodynamic, and clinical parameters of 413 retrospectively collected IAs (training cohort; 102 ruptured IAs). Hierarchal cluster analysis was performed to determine a size cutoff to dichotomize the IA population into small and large IAs...
March 13, 2018: Stroke; a Journal of Cerebral Circulation
Ellen McCreedy, Lacey Loomer, Jennifer A Palmer, Susan L Mitchell, Angelo Volandes, Vincent Mor
OBJECTIVES: Federally mandated assessments of nursing home (NH) residents drive individualized care planning. Residents with cognitive impairment may not be able to meaningfully communicate their care needs and preferences during this process-a gap that may be partially addressed by involving surrogates. We describe the prevalence of family participation in the care planning process for long-stay NH residents with varying degrees of cognitive impairment. DESIGN: Retrospective study using administrative data made available as part of an ongoing pragmatic cluster randomized controlled trial...
March 10, 2018: Journal of the American Medical Directors Association
Fajin Chen, Jing Lin, Bihua Qian, Zhai Wu, Peng Huang, Kai Chen, Tianyao Li, Minggang Cai
The Beibu Gulf (also named the Gulf of Tonkin), located in the northwest of the South China Sea, is representative of a bay suffering from turbulence and contamination associated with rapid industrialization and urbanization. In this study, we aim to provide the novel baseline levels of heavy metals for the research area. Concentrations of five heavy metals (i.e., Cu, Pb, Zn, Cd and Cr) were determined in surface sediments from 35 sites in the eastern Beibu Gulf. The heavy metal content varied from 6.72 to 25...
March 12, 2018: International Journal of Environmental Research and Public Health
Hans G Drexler, Claudia Pommerenke, Sonja Eberth, Stefan Nagel
A characteristic component of the Hodgkin lymphoma (HL) tissue are the mono- or multinucleated Hodgkin-Reed-Sternberg (HRS) cells. Given the challenges of isolating these rare malignant cells and the difficulty in culturing cells from patients, many investigators have tried to establish cell lines in efforts to develop cellular tools for in vitro studies. A limited number of HL cell lines exist and have provided valuable insights into HL pathobiology. A literature survey indicated that 35 cell lines derived from HL patients have been published...
December 20, 2017: Biological Chemistry
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