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Hierarchical clustering

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https://www.readbyqxmd.com/read/29160764/dna-methylation-profile-in-chronic-myelomonocytic-leukemia-associates-with-distinct-clinical-biological-and-genetic-features
#1
Laura Palomo, Roberto Malinverni, Marta Cabezón, Blanca Xicoy, Montserrat Arnan, Rosa Coll, Helena Pomares, Olga García, Francisco Fuster-Tormo, Javier Grau, Evarist Feliu, Francesc Solé, Marcus Buschbeck, Lurdes Zamora
Chromosomal abnormalities are detected in 20-30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. On the mutation level, disruptive alterations are particularly frequent in chromatin regulatory genes. However, little is known about the consequential alterations in the epigenetic marking of the genome. Here, we report the analysis of genomic DNA methylation patterns of 64 CMML patients and 10 healthy controls, using a DNA methylation microarray focused on promoter regions...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29158486/bl-hi-c-is-an-efficient-and-sensitive-approach-for-capturing-structural-and-regulatory-chromatin-interactions
#2
Zhengyu Liang, Guipeng Li, Zejun Wang, Mohamed Nadhir Djekidel, Yanjian Li, Min-Ping Qian, Michael Q Zhang, Yang Chen
In human cells, DNA is hierarchically organized and assembled with histones and DNA-binding proteins in three dimensions. Chromatin interactions play important roles in genome architecture and gene regulation, including robustness in the developmental stages and flexibility during the cell cycle. Here we propose in situ Hi-C method named Bridge Linker-Hi-C (BL-Hi-C) for capturing structural and regulatory chromatin interactions by restriction enzyme targeting and two-step proximity ligation. This method improves the sensitivity and specificity of active chromatin loop detection and can reveal the regulatory enhancer-promoter architecture better than conventional methods at a lower sequencing depth and with a simpler protocol...
November 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29156881/mesoscale-graphene-like-honeycomb-mono-and-multi-layers-constructed-via-self-assembly-of-co-clusters
#3
Xue-Sen Hou, Guo-Long Zhu, Li-Jun Ren, Zihan Huang, Rui-Bin Zhang, Goran Ungar, Li-Tang Yan, Wei Wang
Honeycomb structure endows graphene with extraordinary properties. But could a honeycomb monolayer superlattice also be gen-erated via self-assembly of colloids or nanoparticles? Here we report the construction of mono- and multilayer molecular films with honeycomb structure that can be regarded as self-assembled artificial graphene (SAAG). We construct fan-shaped molecular building blocks by covalently connecting two kinds of clusters, one polyoxometalate (POM) and four polyhedral oligomeric silsesquioxanes (POSS)...
November 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29156779/selecting-lncrnas-in-gastric-cancer-cells-for-directed-therapy-with-bioactive-peptides-and-chemotherapy-drugs
#4
Wenyan Han, Rui Xiao, Chuanling Zhang, Qimuge Suyila, Xian Li, Xiulan Su
Selecting lncRNAs for directed therapy with bioactive peptides and chemotherapy drugs may be an effective approach to treating gastric cancer (GC). We show genome-scale identification and characterization of differentially expressed lncRNAs in GC cells treated with a novel anti-cancer bioactive peptide (ACBP) and the chemotherapy drug oxaliplatin (ASLB). A total of 17,897 lncRNAs were identified through pairwise comparison, including 2,074 novel lncRNAs. Of those, 1,386 lncRNAs were differentially expressed (over 1...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155257/contrasting-the-microbiomes-from-forest-rhizosphere-and-deeper-bulk-soil-from-an-amazon-rainforest-reserve
#5
Jose Pedro Fonseca, Luisa Hoffmann, Bianca Catarina Azeredo Cabral, Victor Hugo Giordano Dias, Marcio Rodrigues Miranda, Allan Cezar de Azevedo Martins, Clarissa Boschiero, Wanderley Rodrigues Bastos, Rosane Silva
Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach...
November 15, 2017: Gene
https://www.readbyqxmd.com/read/29154167/genetic-clustering-of-depressed-patients-and-normal-controls-based-on-single-nucleotide-variant-proportion
#6
Chenglong Yu, Bernhard T Baune, Ke-Ang Fu, Ma-Li Wong, Julio Licinio
BACKGROUND: Genetic components play important roles in the susceptibility to major depressive disorder (MDD). The rapid development of sequencing technologies is allowing scientists to contribute new ideas for personalized medicine; thus, it is essential to design non-invasive genetic tests on sequencing data, which can help physicians diagnose and differentiate depressed patients and healthy individuals. METHODS: We have recently proposed a genetic concept involving single-nucleotide variant proportion (SNVP) in genes to study MDD...
November 10, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29152120/hierarchical-clustering-analysis-identifies-metastatic-colorectal-cancers-patients-with-more-aggressive-phenotype
#7
Giuseppina Opinto, Nicola Silvestris, Matteo Centonze, Giusi Graziano, Rosamaria Pinto, Livia Fucci, Giovanni Simone, Anita Mangia
A large percentage of metastatic colorectal cancer (mCRC) patients presents metastasis at the time of diagnosis. In the last years, great efforts have been made in the treatment of these patients with the identification of different phenotypes playing a key role in the definition of new systemic therapies. Unsupervised hierarchical clustering analysis (HCA) was performed considering the clinicopathological characteristics of 51 mCRCs. Using immunohistochemistry on tissue microarrays, we assessed the expression of β-catenin, NHERF1, RASSF1A, TWIST1, HIF-1α proteins in tumors and paired liver metastases...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29151832/relationship-between-agricultural-biodiversity-and-dietary-diversity-of-children-aged-6-36-months-in-rural-areas-of-northern-ghana
#8
Mahama Saaka, Shaibu Mohammed Osman, Irmgard Hoeschle-Zeledon
In this study, we investigated the relationship between agricultural biodiversity and dietary diversity of children and whether factors such as economic access may affect this relationship. This paper is based on data collected in a baseline cross-sectional survey in November 2013.The study population comprising 1200 mother-child pairs was selected using a two-stage cluster sampling. Dietary diversity was defined as the number of food groups consumed 24 h prior to the assessment. The number of crop and livestock species produced on a farm was used as the measure of production diversity...
2017: Food & Nutrition Research
https://www.readbyqxmd.com/read/29151691/parallel-mrna-proteomics-and-mirna-expression-analysis-in-cell-line-models-of-the-intestine
#9
Finbarr O'Sullivan, Joanne Keenan, Sinead Aherne, Fiona O'Neill, Colin Clarke, Michael Henry, Paula Meleady, Laura Breen, Niall Barron, Martin Clynes, Karina Horgan, Padraig Doolan, Richard Murphy
AIM: To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. METHODS: Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array...
November 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29148410/th17-gene-expression-in-psoriatic-arthritis-synovial-fluid-and-peripheral-blood-compared-to-osteoarthritis-and-cutaneous-psoriasis
#10
Fatima Abji, Remy A Pollock, Kun Liang, Vinod Chandran, Dafna D Gladman
OBJECTIVES: The IL-23/IL-17 axis is central to the pathogenesis of psoriatic arthritis (PsA). We aimed to identify Th17 signalling genes that are dysregulated in synovial fluid of PsA compared to osteoarthritis (OA) patients and to determine if differences in peripheral blood can distinguish PsA from psoriasis patients and controls. METHODS: Synovial fluid cells (SFCs) from 14 PsA and 9 OA patients were obtained and stored in TRIzol reagent. RNA was isolated by phenol-chloroform extraction and purified with RNeasy miniprep kits...
November 9, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/29146759/visual-field-indices-and-patterns-of-visual-field-deficits-in-mesopic-and-dark-adapted-two-colour-fundus-controlled-perimetry-in-macular-diseases
#11
Maximilian Pfau, Moritz Lindner, Julia S Steinberg, Sarah Thiele, Christian K Brinkmann, Monika Fleckenstein, Frank G Holz, Steffen Schmitz-Valckenberg
BACKGROUND/AIMS: To analyse the retest reliability of visual field indices and to describe patterns of visual field deficits in mesopic and dark-adapted two-colour fundus-controlled perimetry (FCP) in macular diseases. METHODS: Seventy-seven eyes (30 eyes with macular diseases and 47 normal eyes) underwent duplicate mesopic and dark-adapted two-colour FCP (Scotopic Macular Integrity Assessment, CenterVue). Non-weighted (mean defect, loss variance), variability-weighted (mean deviation, pattern standard deviation (PSD)) and graphical (cumulative defect (Bebie) curves) indices were computed...
November 16, 2017: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/29146350/emerging-approach-for-analytical-characterization-and-geographical-classification-of-moroccan-and-french-honeys-by-means-of-a-voltammetric-electronic-tongue
#12
Nadia El Alami El Hassani, Khalid Tahri, Eduard Llobet, Benachir Bouchikhi, Abdelhamid Errachid, Nadia Zine, Nezha El Bari
Moroccan and French honeys from different geographical areas were classified and characterized by applying a voltammetric electronic tongue (VE-tongue) coupled to analytical methods. The studied parameters include color intensity, free lactonic and total acidity, proteins, phenols, hydroxymethylfurfural content (HMF), sucrose, reducing and total sugars. The geographical classification of different honeys was developed through three-pattern recognition techniques: principal component analysis (PCA), support vector machines (SVMs) and hierarchical cluster analysis (HCA)...
March 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29145392/conservation-of-a-microrna-cluster-in-parasitic-nematodes-and-profiling-of-mirnas-in-excretory-secretory-products-and-microvesicles-of-haemonchus-contortus
#13
Henry Y Gu, Neil D Marks, Alan D Winter, William Weir, Thomas Tzelos, Tom N McNeilly, Collette Britton, Eileen Devaney
microRNAs are small non-coding RNAs that are important regulators of gene expression in a range of animals, including nematodes. We have analysed a cluster of four miRNAs from the pathogenic nematode species Haemonchus contortus that are closely linked in the genome. We find that the cluster is conserved only in clade V parasitic nematodes and in some ascarids, but not in other clade III species nor in clade V free-living nematodes. Members of the cluster are present in parasite excretory-secretory products and can be detected in the abomasum and draining lymph nodes of infected sheep, indicating their release in vitro and in vivo...
November 16, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29143706/potential-sensitivity-of-pork-production-situations-aiming-at-high-quality-products-to-the-use-of-entire-male-pigs-as-an-alternative-to-surgical-castrates
#14
M Bonneau, M Čandek-Potokar, M Škrlep, M Font-I-Furnols, M Aluwé, L Fontanesi
The perspective of a possible ban on surgical castration of male pigs in the EU is a real challenge for pork production systems aiming at (very) high-quality products. Information was collected from a total of 272 situations in 16 European countries, including 170 situations related to EU protected designations (Database of Origin & Registration (DOOR) database) and 102 other situations related to high-quality products or differentiated production systems, in order to evaluate their potential sensitivity to the use of entire male pigs along four dimensions: BT_Inc, likelihood of increased levels of boar taint compounds compared with conventional production of entire males; BT_Per, extent to which (some of) the associated pork product(s) are susceptible to perception of boar taint by consumers; FatQQ, likelihood that the quality of (some of) the related products is decreased due to the lower fat quantity and quality in entire males; Manag, increased likelihood of animal management and welfare problems compared with conventional production of entire males...
November 16, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29142741/statistical-sleep-pattern-modelling-for-sleep-quality-assessment-based-on-sound-events
#15
Hongle Wu, Takafumi Kato, Masayuki Numao, Ken-Ichi Fukui
A good sleep is important for a healthy life. Recently, several consumer sleep devices have emerged on the market claiming that they can provide personal sleep monitoring; however, many of them require additional hardware or there is a lack of scientific evidence regarding their reliability. In this paper we proposed a novel method to assess the sleep quality through sound events recorded in the bedroom. We used subjective sleep quality as training label, combined several machine learning approaches including kernelized self organizing map, hierarchical clustering and hidden Markov model, obtained the models to indicate the sleep pattern of specific quality level...
December 2017: Health Information Science and Systems
https://www.readbyqxmd.com/read/29142422/chemotaxonomic-diversity-of-three-ficus-species-their-discrimination-using-chemometric-analysis-and-their-role-in-combating-oxidative-stress
#16
Nawal Al-Musayeib, Sherif S Ebada, Haidy A Gad, Fadia S Youssef, Mohamed Lotfy Ashour
Background: Genus Ficus (Moraceae) constitutes more than 850 species and about 2000 varieties and it acts as a golden mine that could afford effective and safe remedies combating many health disorders. Objectives: Discrimination of Ficus cordata, Ficus ingens, and Ficus palmata using chemometric analysis and assessment of their role in combating oxidative stress. Materials and Methods: Phytochemical profiling of the methanol extracts of the three Ficus species and their successive fractions was performed using high-performance liquid chromatography/electrospray ionization mass spectrometry...
October 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/29142266/hyperspectral-raman-imaging-of-neuritic-plaques-and-neurofibrillary-tangles-in-brain-tissue-from-alzheimer-s-disease-patients
#17
Ralph Michael, Aufried Lenferink, Gijs F J M Vrensen, Ellen Gelpi, Rafael I Barraquer, Cees Otto
Neuritic plaques and neurofibrillary tangles are crucial morphological criteria for the definite diagnosis of Alzheimer's disease. We evaluated 12 unstained frontal cortex and hippocampus samples from 3 brain donors with Alzheimer's disease and 1 control with hyperspectral Raman microscopy on samples of 30 × 30 µm. Data matrices of 64 × 64 pixels were used to quantify different tissue components including proteins, lipids, water and beta-sheets for imaging at 0.47 µm spatial resolution. Hierarchical cluster analysis was performed to visualize regions with high Raman spectral similarities...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142224/health-and-disease-phenotyping-in-old-age-using-a-cluster-network-analysis
#18
Jesus Felix Valenzuela, Christopher Monterola, Victor Joo Chuan Tong, Tze Pin Ng, Anis Larbi
Human ageing is a complex trait that involves the synergistic action of numerous biological processes that interact to form a complex network. Here we performed a network analysis to examine the interrelationships between physiological and psychological functions, disease, disability, quality of life, lifestyle and behavioural risk factors for ageing in a cohort of 3,270 subjects aged ≥55 years. We considered associations between numerical and categorical descriptors using effect-size measures for each variable pair and identified clusters of variables from the resulting pairwise effect-size network and minimum spanning tree...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142207/phosphorylation-dynamics-dominate-the-regulated-proteome-during-early-xenopus-development
#19
Elizabeth H Peuchen, Olivia F Cox, Liangliang Sun, Alex S Hebert, Joshua J Coon, Matthew M Champion, Norman J Dovichi, Paul W Huber
The earliest stages of animal development are largely controlled by changes in protein phosphorylation mediated by signaling pathways and cyclin-dependent kinases. In order to decipher these complex networks and to discover new aspects of regulation by this post-translational modification, we undertook an analysis of the X. laevis phosphoproteome at seven developmental stages beginning with stage VI oocytes and ending with two-cell embryos. Concurrent measurement of the proteome and phosphoproteome enabled measurement of phosphosite occupancy as a function of developmental stage...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142202/genomic-mosaicism-in-paternal-sperm-and-multiple-parental-tissues-in-a-dravet-syndrome-cohort
#20
Xiaoxu Yang, Aijie Liu, Xiaojing Xu, Xiaoling Yang, Qi Zeng, Adam Yongxin Ye, Zhe Yu, Sheng Wang, August Yue Huang, Xiru Wu, Qixi Wu, Liping Wei, Yuehua Zhang
Genomic mosaicism in parental gametes and peripheral tissues is an important consideration for genetic counseling. We studied a Chinese cohort affected by a severe epileptic disorder, Dravet syndrome (DS). There were 56 fathers who donated semen and 15 parents who donated multiple peripheral tissue samples. We used an ultra-sensitive quantification method, micro-droplet digital PCR (mDDPCR), to detect parental mosaicism of the proband's pathogenic mutation in SCN1A, the causal gene of DS in 112 families. Ten of the 56 paternal sperm samples were found to exhibit mosaicism of the proband's mutations, with mutant allelic fractions (MAFs) ranging from 0...
November 15, 2017: Scientific Reports
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