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Hierarchical clustering

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https://www.readbyqxmd.com/read/28734161/evaluation-of-the-effect-of-extraction-solvent-and-organ-selection-on-the-chemical-profile-of-astragalus-spinosus-using-hptlc-multivariate-image-analysis
#1
Eman Shawky, Dina A Selim
The evaluation of extraction protocols for untargeted and targeted metabolomics was implemented for root and aerial organs of Astragalus spinosus in this work. The efficiency and complementarity of commonly used extraction solvents, namely petroleum ether, methylene chloride, ethyl acetate and n-butanol were considered for method evaluation using chemometric techniques in conjunction with new, simple, and fast high performance thin layer chromatography (HPTLC) method for fingerprint analysis by extracting information from a digitalized HPTLC plate using ImageJ software...
July 15, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28728577/integrating-data-from-randomized-controlled-trials-and-observational-studies-to-predict-the-response-to-pregabalin-in-patients-with-painful-diabetic-peripheral-neuropathy
#2
Joe Alexander, Roger A Edwards, Alberto Savoldelli, Luigi Manca, Roberto Grugni, Birol Emir, Ed Whalen, Stephen Watt, Marina Brodsky, Bruce Parsons
BACKGROUND: More patient-specific medical care is expected as more is learned about variations in patient responses to medical treatments. Analytical tools enable insights by linking treatment responses from different types of studies, such as randomized controlled trials (RCTs) and observational studies. Given the importance of evidence from both types of studies, our goal was to integrate these types of data into a single predictive platform to help predict response to pregabalin in individual patients with painful diabetic peripheral neuropathy (pDPN)...
July 20, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28728573/splicing-arrays-reveal-novel-rbm10-targets-including-smn2-pre-mrna
#3
Leslie C Sutherland, Philippe Thibault, Mathieu Durand, Elvy Lapointe, Jose M Knee, Ariane Beauvais, Irina Kalatskaya, Sarah C Hunt, Julie J Loiselle, Justin G Roy, Sarah J Tessier, Gustavo Ybazeta, Lincoln Stein, Rashmi Kothary, Roscoe Klinck, Benoit Chabot
BACKGROUND: RBM10 is an RNA binding protein involved in message stabilization and alternative splicing regulation. The objective of the research described herein was to identify novel targets of RBM10-regulated splicing. To accomplish this, we downregulated RBM10 in human cell lines, using small interfering RNAs, then monitored alternative splicing, using a reverse transcription-PCR screening platform. RESULTS: RBM10 knockdown (KD) provoked alterations in splicing events in 10-20% of the pre-mRNAs, most of which had not been previously identified as RBM10 targets...
July 20, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28728128/radionuclide-biokinetics-in-the-russian-sturgeon-and-phylogenetic-consistencies-with-cartilaginous-and-bony-marine-fishes
#4
Ross A Jeffree, Scott J Markich, Francois Oberhaensli, Jean-Louis Teyssie
The biokinetics of eight radionuclides ((241)Am, (109)Cd, (134)Cs, (75)Se, (54)Mn, (110m)Ag, (65)Zn, (60)Co) absorbed from the aquatic medium by juvenile Russian sturgeon (Acipenser gueldenstaedtii) were experimentally determined in fresh (0.42‰) and brackish (9.0‰) waters, of a similar salinity range to the Caspian Sea, and in conjunction with chemical speciation modelling. Uptake and loss rate constants were determined for each radionuclide for a 14 day exposure at each salinity and during 28 days of exposure to radionuclide-free conditions...
July 17, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28725990/molecular-characterization-of-the-indigenous-stingless-bees-tetragonula-spp-complex-using-issr-marker-from-southern-peninsular-india
#5
P P Nayak, J Prakash
India is a country bestowed enormously with stingless bees, but genetic information about them is extremely minimal. This study focused to tap the geographic allocation, genetic variability, and differentiation among Tetragonula species complexes from natural and semi-urban habitats. Genetic analyses were assessed among 36 contrasting genotypes utilizing 20 ISSR primers. The dual combination exquisitely and productively amplified 245 DNA fragments at the loci, of which 240 bands were polymorphic (97.95%). Low to moderate level of genetic differentiation was detected from different estimators (Ht 0...
July 19, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/28725670/fatty-acid-and-lipidomic-data-in-normal-and-tumor-colon-tissues-of-rats-fed-diets-with-and-without-fish-oil
#6
Zora Djuric, Muhammad Nadeem Aslam, Becky R Simon, Ananda Sen, Yan Jiang, Jianwei Ren, Rena Chan, Tanu Soni, Thekkelnaycke M Rajendiran, William L Smith, Dean E Brenner
Data is provided to show the detailed fatty acid and lipidomic composition of normal and tumor rat colon tissues. Rats were fed either a Western fat diet or a fish oil diet, and half the rats from each diet group were treated with chemical carcinogens that induce colon cancer (azoxymethane and dextran sodium sulfate). The data show total fatty acid profiles of sera and of all the colon tissues, namely normal tissue from control rats and both normal and tumor tissues from carcinogen-treated rats, as obtained by gas chromatography with mass spectral detection...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28725622/authentication-of-piper-betle-l-folium-and-quantification-of-their-antifungal-activity
#7
I Made Agus Gelgel Wirasuta, I Gusti Ayu Made Srinadi, Ida Bagus Gede Dwidasmara, Ni Luh Putu Putri Ardiyanti, I Gusti Ayu Arya Trisnadewi, Ni Luh Putu Vidya Paramita
The TLC profiles of intra- and inter-day precision for Piper betle L. (PBL) folium methanol extract was studied for their peak marker recognition and identification. The Numerical chromatographic parameters (NCPs) of the peak markers, the hierarchical clustering analysis (HCA) and the principal component analysis (PCA) were applied to authenticate the PBL. folium extract from other Piper species folium extract and to ensure the antifungal activity quality of the PBL essential oil. The spotted extract was developed with the mobile phase of toluene: ethyl acetate; 93:7, (v/v)...
July 2017: Journal of Traditional and Complementary Medicine
https://www.readbyqxmd.com/read/28724069/a-distinct-genetic-cluster-in-cultivated-chickpea-as-revealed-by-genome-wide-marker-discovery-and-genotyping
#8
Stefano Pavan, Concetta Lotti, Angelo R Marcotrigiano, Rosa Mazzeo, Nicoletta Bardaro, Valentina Bracuto, Francesca Ricciardi, Francesca Taranto, Nunzio D'Agostino, Adalgisa Schiavulli, Claudio De Giovanni, Cinzia Montemurro, Gabriella Sonnante, Luigi Ricciardi
The accurate description of plant biodiversity is of utmost importance to efficiently address efforts in conservation genetics and breeding. Herein, we report the successful application of a genotyping-by-sequencing (GBS) approach in chickpea ( L.), resulting in the characterization of a cultivated germplasm collection with 3187 high-quality single nucleotide polymorphism (SNP) markers. Genetic structure inference, principal component analysis, and hierarchical clustering all indicated the identification of a genetic cluster corresponding to black-seeded genotypes traditionally cultivated in Southern Italy...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28721670/extending-a-tandem-mass-spectral-library-to-include-ms-2-spectra-of-fragment-ions-produced-in-source-and-ms-n-spectra
#9
Xiaoyu Yang, Pedatsur Neta, Stephen E Stein
Tandem mass spectral library searching is finding increased use as an effective means of determining chemical identity in mass spectrometry-based omics studies. We previously reported on constructing a tandem mass spectral library that includes spectra for multiple precursor ions for each analyte. Here we report our method for expanding this library to include MS(2) spectra of fragment ions generated during the ionization process (in-source fragment ions) as well as MS(3) and MS(4) spectra. These can assist the chemical identification process...
July 18, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28720886/spatio-temporal-variations-of-typhoid-and-paratyphoid-fevers-in-zhejiang-province-china-from-2005-to-2015
#10
Hua Gu, Wenjie Fan, Kui Liu, Shuwen Qin, Xiuyang Li, Jianmin Jiang, Enfu Chen, Yibiao Zhou, Qingwu Jiang
Typhoid and paratyphoid are two common enteric infectious diseases with serious gastrointestinal symptoms. Data was collected of the registered cases in Zhejiang Province from 2005 to 2015. The epidemiological characteristics were investigated and high-risk regions were detected with descriptive epidemiological methods and in-depth spatio-temporal statistics. A sharp decline in the incidences of both diseases was observed. The seasonal patterns were identified with typhoid and paratyphoid, one in summer from May to September was observed from 2005 to 2010 and the other lesser one in spring from January to March only observed from 2005 to 2007...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28718784/investigation-of-the-effect-of-the-degree-of-processing-of-radix-rehmanniae-preparata-shu-dihuang-on-shu-dihuangtan-carbonization-preparation-technology
#11
Xianglong Meng, Meijing He, Rui Guo, Rui Duan, Fengxian Huo, Chenzi Lv, Bo Wang, Shuosheng Zhang
Carbonization of Radix Rehmanniae Preparata (Shu Dihuangtan) via stir-frying could increase its homeostasis maintaining and antidiarrheal effects. To ensure these pharmacological functions, the quality of the raw material (processed Rehmanniae Radix) must be well controlled. Therefore, we analyzed the effects of different degrees of processing and adjuvants on processed Rehmanniae Radix (Shu Dihuang) by High Performance Liquid Chromatography (HPLC) chromatographic fingerprints, thermal gravimetric analysis and Fourier transform infrared spectroscopy (FTIR)...
July 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28718724/black-raspberries-and-their-anthocyanin-and-fiber-fractions-alter-the-composition-and-diversity-of-gut-microbiota-in-f-344-rats
#12
Pan Pan, Vy Lam, Nita Salzman, Yi-Wen Huang, Jianhua Yu, Jianying Zhang, Li-Shu Wang
Natural compounds can alter the diversity and composition of the gut microbiome, potentially benefiting our health. We previously demonstrated chemopreventive effects of black raspberries (BRBs) in colorectal cancer, which is associated with gut dysbiosis. To investigate the effects of whole BRBs and their fractions on gut microbiota, we fed F-344 rats a control diet, 5% BRBs, the BRB anthocyanin fraction, or the BRB residue fraction for 6 weeks. Feces were collected at baseline and at weeks 3 and 6, and bacterial sequence counts were analyzed...
July 18, 2017: Nutrition and Cancer
https://www.readbyqxmd.com/read/28717653/individual-social-and-environmental-correlates-of-active-transportation-patterns-in-french-women
#13
Camille Perchoux, Christophe Enaux, Jean-Michel Oppert, Mehdi Menai, Hélène Charreire, Paul Salze, Christiane Weber, Serge Hercberg, Thierry Feuillet, Franck Hess, Célina Roda, Chantal Simon, Julie-Anne Nazare
The objectives were (1) to define physical activity (PA) and sedentary behaviors (SB) patterns in daily life contexts (work, leisure, and transportation) in French working women from NutriNet-Santé web-cohort and (2) to identify pattern(s) of active transportation and their individual, social, and environmental correlates. 23,432 participants completed two questionnaires to evaluate PA and SB in daily life contexts and individual representations of residential neighborhood and transportation modes. Hierarchical cluster analysis was performed which identified 6 distinct movement behavior patterns: (i) active occupation, high sedentary leisure, (ii) sedentary occupation, low leisure, (iii) sedentary transportation, (iv) sedentary occupation and leisure, (v) active transportation, and (vi) active leisure...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28717649/circular-rna-profiling-and-bioinformatic-modeling-identify-its-regulatory-role-in-hepatic-steatosis
#14
Xing-Ya Guo, Chong-Xin He, Yu-Qin Wang, Chao Sun, Guang-Ming Li, Qing Su, Qin Pan, Jian-Gao Fan
Circular RNAs (circRNAs) exhibit a wide range of physiological and pathological activities. To uncover their role in hepatic steatosis, we investigated the expression profile of circRNAs in HepG2-based hepatic steatosis induced by high-fat stimulation. Differentially expressed circRNAs were subjected to validation using QPCR and functional analyses using principal component analysis, hierarchical clustering, target prediction, gene ontology (GO), and pathway annotation, respectively. Bioinformatic integration established the circRNA-miRNA-mRNA regulatory network so as to identify the mechanisms underlying circRNAs' metabolic effect...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28717101/mechanism-based-risk-assessment-strategy-for-drug-induced-cholestasis-using-the-transcriptional-benchmark-dose-derived-by-toxicogenomics
#15
Taisuke Kawamoto, Yuichi Ito, Osamu Morita, Hiroshi Honda
Cholestasis is one of the major causes of drug-induced liver injury (DILI), which can result in withdrawal of approved drugs from the market. Early identification of cholestatic drugs is difficult due to the complex mechanisms involved. In order to develop a strategy for mechanism-based risk assessment of cholestatic drugs, we analyzed gene expression data obtained from the livers of rats that had been orally administered with 12 known cholestatic compounds repeatedly for 28 days at three dose levels. Qualitative analyses were performed using two statistical approaches (hierarchical clustering and principle component analysis), in addition to pathway analysis...
2017: Journal of Toxicological Sciences
https://www.readbyqxmd.com/read/28715507/independent-component-analysis-ica-based-clustering-of-temporal-rna-seq-data
#16
Moysés Nascimento, Fabyano Fonseca E Silva, Thelma Sáfadi, Ana Carolina Campana Nascimento, Talles Eduardo Maciel Ferreira, Laís Mayara Azevedo Barroso, Camila Ferreira Azevedo, Simone Eliza Faccione Guimarães, Nick Vergara Lopes Serão
Gene expression time series (GETS) analysis aims to characterize sets of genes according to their longitudinal patterns of expression. Due to the large number of genes evaluated in GETS analysis, an useful strategy to summarize biological functional processes and regulatory mechanisms is through clustering of genes that present similar expression pattern over time. Traditional cluster methods usually ignore the challenges in GETS, such as the lack of data normality and small number of temporal observations...
2017: PloS One
https://www.readbyqxmd.com/read/28714074/altered-metabolomic-genomic-signature-a-potential-noninvasive-biomarker-of-epilepsy
#17
Helen C Wu, Fabien Dachet, Farhad Ghoddoussi, Shruti Bagla, Darren Fuerst, Jeffrey A Stanley, Matthew P Galloway, Jeffrey A Loeb
OBJECTIVE: This study aimed to identify noninvasive biomarkers of human epilepsy that can reliably detect and localize epileptic brain regions. Having noninvasive biomarkers would greatly enhance patient diagnosis, patient monitoring, and novel therapy development. At the present time, only surgically invasive, direct brain recordings are capable of detecting these regions with precision, which severely limits the pace and scope of both clinical management and research progress in epilepsy...
July 17, 2017: Epilepsia
https://www.readbyqxmd.com/read/28714002/identification-of-key-genes-in-gram%C3%A2-positive-and-gram%C3%A2-negative-sepsis-using-stochastic-perturbation
#18
Zhenliang Li, Ying Zhang, Yaling Liu, Yanchun Liu, Youyi Li
Sepsis is an inflammatory response to pathogens (such as Gram‑positive and Gram‑negative bacteria), which has high morbidity and mortality in critically ill patients. The present study aimed to identify the key genes in Gram‑positive and Gram‑negative sepsis. GSE6535 was downloaded from Gene Expression Omnibus, containing 17 control samples, 18 Gram‑positive samples and 25 Gram‑negative samples. Subsequently, the limma package in R was used to screen the differentially expressed genes (DEGs). Hierarchical clustering was conducted for the specific DEGs in Gram‑negative and Gram‑negative samples using cluster software and the TreeView software...
July 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28712626/public-preferences-for-lung-cancer-screening-policies
#19
Henk Broekhuizen, Catharina G M Groothuis-Oudshoorn, Rozemarijn Vliegenthart, Harry Groen, Maarten J IJzerman
BACKGROUND: Because early detection of lung cancer can substantially improve survival, there is increasing attention for lung cancer screening. OBJECTIVES: To estimate public preferences for lung cancer screening and to identify subgroups in preferences. METHODS: Seven important attributes were selected using the literature, interviews, and a panel session. Preferences were elicited using a swing weighting questionnaire. The resulting attribute weights indicate the relative importance of swings from the worst to the best level between attributes...
July 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28712417/holding-the-body-in-mind-interoceptive-awareness-dispositional-mindfulness-and-psychological-well-being
#20
Adam W Hanley, Wolf E Mehling, Eric L Garland
Objective Recent dialogue between Western and Eastern traditions has stimulated novel explorations of the relationship between mind and body. Many of these cross-cultural, mind-body dialogues have proven productive in identifying more adaptive forms of embodiment. Prior studies suggest that dispositional mindfulness (DM) and interoceptive awareness (IA) are associated but distinct, key constructs in mind-body approaches that are conceptualized in a variety of ways with imprecisely characterized relationship...
August 2017: Journal of Psychosomatic Research
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