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https://www.readbyqxmd.com/read/28922607/antdas-automatic-data-analysis-strategy-for-uplc-qtof-based-nontargeted-metabolic-profiling-analysis
#1
Hai-Yan Fu, Xiao-Ming Guo, Yue-Ming Zhang, Jing-Jing Song, Qing-Xia Zheng, Ping-Ping Liu, Peng Lu, Qian-Si Chen, Yong-Jie Yu, Yuanbin She
High-quality data analysis methodology remains a bottleneck for metabolic profiling analysis based on ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. The present work aims to address this problem by proposing a novel data analysis strategy wherein (1) chromatographic peaks in the UPLC-QTOF dataset are automatically extracted by using an advanced multiscale Gaussian smoothing-based peak extraction strategy. (2) A peak annotation stage is used to cluster fragment ions that belong to the same compound...
September 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28921901/structureselector-a-web-based-software-to-select-and-visualize-the-optimal-number-of-clusters-by-using-multiple-methods
#2
Yu-Long Li, Jin-Xian Liu
Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program STUCTURE has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (MedMedK, MedMeaK, MaxMedK, MaxMeaK) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data...
September 16, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28919358/perfused-human-hepatocyte-microtissues-identify-reactive-metabolite-forming-and-mitochondria-perturbing-hepatotoxins
#3
Cliff Rowe, Mohsen Shaeri, Emma Large, Terri Cornforth, Angela Robinson, Tomasz Kostrzewski, Rowena Sison-Young, Christopher Goldring, Kevin Park, David Hughes
Hepatotoxins cause liver damage via many mechanisms but the formation of reactive metabolites and/or damage to liver mitochondria are commonly implicated. We assess 3D human primary hepatocyte microtissues as a platform for hepatotoxicity studies with reactive metabolite-forming and mitochondria-perturbing compounds. We show that microtissues formed from cryopreserved human hepatocytes had bile canaliculi, transcribed mRNA from genes associated with xenobiotic metabolism and expressed functional cytochrome P450 enzymes...
September 15, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28912300/-18-f-av-1451-binding-in-vivo-mirrors-the-expected-distribution-of-tdp-43-pathology-in-the-semantic-variant-of-primary-progressive-aphasia
#4
W R Bevan-Jones, Thomas E Cope, P Simon Jones, Luca Passamonti, Young T Hong, Tim D Fryer, Robert Arnold, Kieren S J Allinson, Jonathan P Coles, Franklin I Aigbirhio, Karalyn Patterson, John T O'Brien, James B Rowe
INTRODUCTION: Semantic dementia, including the semantic variant of primary progressive aphasia (svPPA), is strongly associated with TAR-DNA binding protein 43 (TDP-43) type C pathology. It provides a useful model in which to test the specificity of in vivo binding of the putative tau ligand [(18)F]AV-1451, which is elevated in frontotemporal lobar degeneration tauopathies. METHODS AND RESULTS: Seven patients (five with svPPA and two with 'right' semantic dementia) and 12 healthy controls underwent positron emission tomography brain imaging with [(18)F]AV-1451...
September 14, 2017: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/28910606/multivariate-analysis-as-a-key-tool-in-chemotaxonomy-of-brinjal-eggplant-african-eggplants-and-wild-related-species
#5
Łukasz P Haliński, John Samuels, Piotr Stepnowski
The brinjal eggplant (Solanum melongena L.) is an important vegetable species worldwide, while African eggplants (S. aethiopicum L., S. macrocarpon L.) are indigenous vegetable species of local significance. Taxonomy of eggplants and their wild relatives is complicated and still unclear. Hence, the objective of the study was to clarify taxonomic position of cultivars and landraces of brinjal, its wild relatives and African eggplant species and their wild ancestors using chemotaxonomic markers and multivariate analysis techniques for data processing, with special attention paid to the recognition of markers characteristic for each group of the plants...
September 11, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28910577/subnuclear-distribution-of-proteins-links-with-genome-architecture
#6
Fouziya R Shah, Younus A Bhat, Ajazul H Wani
Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28904803/comparative-transcriptome-analysis-during-early-fruit-development-between-three-seedy-citrus-genotypes-and-their-seedless-mutants
#7
Shujian Zhang, Qingchun Shi, Ute Albrecht, Robert G Shatters, Ric Stange, Greg McCollum, Shuo Zhang, Chengming Fan, Ed Stover
Identification of genes with differential transcript abundance (GDTA) in seedless mutants may enhance understanding of seedless citrus development. Transcriptome analysis was conducted at three time points during early fruit development (Phase 1) of three seedy citrus genotypes: Fallglo (Bower citrus hybrid (Citrus reticulata×C. reticulata×C. paradisi)×Temple (C. reticulata×C. sinensis)), grapefruit (C. paradisi), Pineapple sweet orange (C. sinensis), and their seedless mutants. Seed abortion in seedless mutants was observed at 26 days post anthesis (Time point 2)...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28903341/apobec3g-acts-as-a-therapeutic-target-in-mesenchymal-gliomas-by-sensitizing-cells-to-radiation-induced-cell-death
#8
Yu Wang, Shaofang Wu, Siyuan Zheng, Shuzhen Wang, Arjun Wali, Ravesanker Ezhilarasan, Erik P Sulman, Dimpy Koul, W K Alfred Yung
Genomic, transcriptional, and proteomic analyses of brain tumors reveal that subtypes differ in their pathway activity, progression, and response to therapy. We performed an expression profiling of Glioma Initiating Cells (GICs) and comparative analysis between different groups of GICs indicates major variations in gene expression. Hierarchical clustering analysis revealed groups of GICs reflecting their heterogeneity, and among some of the genes as major regulators of mesenchymal phenotype, we identified ABOBEC3G as one of the most discriminating genes in mesenchymal group...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28901285/a-case-study-for-a-psychographic-behavioral-segmentation-approach-for-targeted-demand-generation-in-voluntary-medical-male-circumcision
#9
Sema K Sgaier, Maria Eletskaya, Elisabeth Engl, Owen Mugurungi, Bushimbwa Tambatamba, Gertrude Ncube, Sinokuthemba Xaba, Alice Nanga, Svetlana Gogolina, Patrick Odawo, Sehlulekile Gumede-Moyo, Steve Kretschmer
Public health programs are starting to recognize the need to move beyond a one-size-fits-all approach in demand generation, and instead tailor interventions to the heterogeneity underlying human decision making. Currently, however, there is a lack of methods to enable such targeting. We describe a novel hybrid behavioral-psychographic segmentation approach to segment stakeholders on potential barriers to a target behavior. We then apply the method in a case study of demand generation for voluntary medical male circumcision (VMMC) among 15-29-year-old males in Zambia and Zimbabwe...
September 13, 2017: ELife
https://www.readbyqxmd.com/read/28901009/sample-size-determination-for-multilevel-hierarchical-designs-using-generalized-linear-mixed-models
#10
Anup Amatya, Dulal K Bhaumik
A unified statistical methodology of sample size determination is developed for hierarchical designs that are frequently used in many areas, particularly in medical and health research studies. The solid foundation of the proposed methodology opens a new horizon for power analysis in presence of various conditions. Important features such as joint significance testing, unequal allocations of clusters across intervention groups, and differential attrition rates over follow up time points are integrated to address some useful questions that investigators often encounter while conducting such studies...
September 12, 2017: Biometrics
https://www.readbyqxmd.com/read/28899361/interactive-visual-exploration-and-refinement-of-cluster-assignments
#11
Michael Kern, Alexander Lex, Nils Gehlenborg, Chris R Johnson
BACKGROUND: With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear...
September 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28898531/synergistic-hepatoprotective-and-antioxidant-effect-of-artichoke-fig-mulberry-herbal-mixture-on-hepg2-cells-and-their-metabolic-profiling-using-nmr-coupled-with-chemometrics
#12
Fadia S Youssef, Rola M Labib, Omayma A Eldahshan, Abdel Nasser B Singab
The edible plants have long been reported to possess a lot of biological activities. Herein, the hepatoprotective and the antioxidant activity of the aqueous infusion of the edible parts of Cynara cardunculus, Ficus carica and Morus nigra and their herbal mixture (CFM) was investigated in vitro using CCl4 induced damage in HepG2 cells. The highest amelioration was observed via the consumption of CFM at 1 mg/ml showing 47.00, 37.09% decline in AST (Aspartate Transaminase) and ALT (Alanine Transaminase) and 77...
September 12, 2017: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/28893273/food-parenting-practices-for-5-to-12%C3%A2-year-old-children-a-concept-map-analysis-of-parenting-and-nutrition-experts-input
#13
Teresia M O'Connor, Louise C Mâsse, Andrew W Tu, Allison W Watts, Sheryl O Hughes, Mark R Beauchamp, Tom Baranowski, Truc Pham, Jerica M Berge, Barbara Fiese, Rebecca Golley, Melanie Hingle, Stef P J Kremers, Kyung E Rhee, Helen Skouteris, Amber Vaughn
BACKGROUND: Parents are an important influence on children's dietary intake and eating behaviors. However, the lack of a conceptual framework and inconsistent assessment of food parenting practices limits our understanding of which food parenting practices are most influential on children. The aim of this study was to develop a food parenting practice conceptual framework using systematic approaches of literature reviews and expert input. METHOD: A previously completed systematic review of food parenting practice instruments and a qualitative study of parents informed the development of a food parenting practice item bank consisting of 3632 food parenting practice items...
September 11, 2017: International Journal of Behavioral Nutrition and Physical Activity
https://www.readbyqxmd.com/read/28892803/characterization-of-the-key-odorants-of-fennel-essential-oils-of-different-regions-using-gc-ms-and-gc-o-combined-with-partial-least-squares-regression
#14
Zuobing Xiao, Jiaying Chen, Yunwei Niu, Feng Chen
The key odorants and the aroma profile of six fennel essential oils from different regions were investigated by using gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS) and sensory evaluation. A total of 30 volatile compounds were determined by GC-O with aroma extract dilution analysis (AEDA) and the odor activity values (OAV) of them were calculated. Among these compounds, α-pinene, α-phellandrene, limonene, α-cubebene, β-caryophyllene, estragole, α-humulene, trans-anethole, δ-cadinene and p-anisaldehyde contributed greatly to the aroma of fennel essential oil due to their high flavor dilution (FD) factors and high OAVs...
August 5, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28891999/underdetermined-blind-source-separation-of-synchronous-orthogonal-frequency-hopping-signals-based-on-single-source-points-detection
#15
Chaozhu Zhang, Yu Wang, Fulong Jing
This paper considers the complex-valued mixing matrix estimation and direction-of-arrival (DOA) estimation of synchronous orthogonal frequency hopping (FH) signals in the underdetermined blind source separation (UBSS). A novel mixing matrix estimation algorithm is proposed by detecting single source points (SSPs) where only one source contributes its power. Firstly, the proposed algorithm distinguishes the SSPs by the comparison of the normalized coefficients of time frequency (TF) points, which is more effective than existing detection algorithms...
September 11, 2017: Sensors
https://www.readbyqxmd.com/read/28888224/long-term-patient-reported-outcomes-following-radiation-therapy-for-oropharyngeal-cancer-cross-sectional-assessment-of-a-prospective-symptom-survey-in-patients-%C3%A2-65%C3%A2-years-old
#16
Salman A Eraj, Mona K Jomaa, Crosby D Rock, Abdallah S R Mohamed, Blaine D Smith, Joshua B Smith, Theodora Browne, Luke C Cooksey, Bowman Williams, Brandi Temple, Kathryn E Preston, Jeremy M Aymar, Neil D Gross, Randal S Weber, Amy C Hessel, Renata Ferrarotto, Jack Phan, Erich M Sturgis, Ehab Y Hanna, Steven J Frank, William H Morrison, Ryan P Goepfert, Stephen Y Lai, David I Rosenthal, Tito R Mendoza, Charles S Cleeland, Kate A Hutcheson, Clifton D Fuller, Adam S Garden, G Brandon Gunn
BACKGROUND: Given the potential for older patients to experience exaggerated toxicity and symptoms, this study was performed to characterize patient reported outcomes in older patients following definitive radiation therapy (RT) for oropharyngeal cancer (OPC). METHODS: Cancer-free head and neck cancer survivors (>6 months since treatment completion) were eligible for participation in a questionnaire-based study. Participants completed the MD Anderson Symptom Inventory-Head and Neck module (MDASI-HN)...
September 9, 2017: Radiation Oncology
https://www.readbyqxmd.com/read/28887896/lesion-evidence-for-a-critical-role-of-left-posterior-but-not-frontal-areas-in-alpha-beta-power-decreases-during-context-driven-word-production
#17
Vitória Piai, Joost Rommers, Robert T Knight
Different frequency bands in the electroencephalogram are postulated to support distinct language functions. Studies have suggested that alpha-beta power decreases may index word-retrieval processes. In context-driven word retrieval, participants hear lead-in sentences that either constrain the final word ("He locked the door with the") or not ("She walked in here with the"). The last word is shown as a picture to be named. Previous studies have consistently found alpha-beta power decreases prior to picture onset for constrained relative to unconstrained sentences, localised to the left lateral-temporal and lateral-frontal lobes...
September 9, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28886133/phylogeographic-pattern-suggests-a-general-northeastward-dispersal-in-the-distribution-of-machilus-pauhoi-in-south-china
#18
Qin Zhu, Bo-Yong Liao, Pei Li, Jun-Cheng Li, Xiao-Mei Deng, Xin-Sheng Hu, Xiao-Yang Chen
Machilus pauhoi Kanehira is an important timber species in China. A provenance trial was recently set up to evaluate the growth performance of trees from different localities, with the aim of designing seed transfer guidelines. Here, we tested twelve nuclear microsatellite markers derived from other species of the Lauraceae family and investigated population genetic structure in M. pauhoi. Both the number of observed alleles per locus (Na) and the polymorphic information content (PIC) significantly decreased against the latitude, but showed an insignificant decrease against the longitude...
2017: PloS One
https://www.readbyqxmd.com/read/28884295/dietary-patterns-nutrition-knowledge-lifestyle-and-health-related-quality-of-life-associations-with-anti-hypertension-medication-adherence-in-a-sample-of-australian-adults
#19
Saman Khalesi, Christopher Irwin, Jing Sun
INTRODUCTION: Poor anti-hypertension medication (AHT) adherence can increase disease costs and adverse outcomes. Hypertensive individuals who have a better nutrition knowledge may lead a healthier lifestyle, have a better health-related quality of life (HRQoL) and greater confidence to change behaviour. On this basis, they may have better treatment adherence. AIM: To explore the association between the above-mentioned variables and AHT adherence in a group of Australian adults with high blood pressure (BP) in a cross-sectional clinical and community-based study...
September 7, 2017: High Blood Pressure & Cardiovascular Prevention: the Official Journal of the Italian Society of Hypertension
https://www.readbyqxmd.com/read/28883080/phenotype-in-combination-with-genotype-improves-outcome-prediction-in-acute-myeloid-leukemia-a-report-from-children-s-oncology-group-protocol-aaml0531
#20
Andrew P Voigt, Lisa Eidenschink Brodersen, Todd A Alonzo, Robert B Gerbing, Andrew J Menssen, Elisabeth R Wilson, Samir Kahwash, Susana C Raimondi, Betsy A Hirsch, Alan S Gamis, Soheil Meshinchi, Denise A Wells, Michael R Loken
Diagnostic biomarkers can be used to determine relapse risk in acute myeloid leukemia, and certain genetic aberrancies have prognostic relevance. A diagnostic immunophenotypic expression profile, which quantifies the amounts of distinct gene products, not just their presence or absence, was established to improve outcome prediction for patients with acute myeloid leukemia. The immunophenotypic expression profile, which defines each patient's leukemia as a location in 15-dimensional space, was generated for 769 patients enrolled in the Children's Oncology Group AAML0531 protocol...
September 7, 2017: Haematologica
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