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independent component analysis

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https://www.readbyqxmd.com/read/29345800/haplotype-based-genotyping-by-sequencing-in-oat-genome-research
#1
Wubishet A Bekele, Charlene P Wight, Shiaoman Chao, Catherine J Howarth, Nicholas A Tinker
In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel...
January 18, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29344954/mixed-ductal-lobular-carcinomas-evidence-for-progression-from-ductal-to-lobular-morphology
#2
Amy E McCart Reed, Jamie R Kutasovic, Katia Nones, Jodi M Saunus, Leonard Da Silva, Felicity Newell, Stephen Kazakoff, Lewis Melville, Janani Jayanthan, Ana Cristina Vargas, Lynne E Reid, Jonathan Beesley, Xiao Qing Chen, Anne Marie Patch, D David Clouston, Alan Porter, Elizabeth Evans, John V Pearson, Georgia Chenevix-Trench, Margaret C Cummings, Nic Waddell, Sunil R Lakhani, Peter T Simpson
Mixed ductal-lobular carcinomas (MDL) display both ductal and lobular morphology, and are an archetypal example of intra-tumour morphological heterogeneity. The mechanisms underlying coexistence of these different morphologic entities are poorly understood, although theories include that these components either represent 'collision' of independent tumours or evolve from a common ancestor. We performed comprehensive clinico-pathological analysis of a cohort of 82 MDLs and found: i) MDLs more frequently co-exist with ductal carcinoma in situ (DCIS) than lobular carcinoma in situ (LCIS); ii) the E-cadherin-catenin complex was normal in the ductal component in 77...
January 18, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344832/mitogen-activated-protein-kinase-6-and-map-kinase-phosphatase-1-are-involved-in-the-response-of-arabidopsis-roots-to-l-glutamate
#3
Jesús Salvador López-Bucio, Javier Raya-González, Gustavo Ravelo-Ortega, León Francisco Ruiz-Herrera, Maricela Ramos-Vega, Patricia León, José López-Bucio, Ángel Arturo Guevara-García
The function and components of L-glutamate signaling pathways in plants have just begun to be elucidated. Here, using a combination of genetic and biochemical strategies, we demonstrated that a MAPK module is involved in the control of root developmental responses to this amino acid. Root system architecture plays an essential role in plant adaptation to biotic and abiotic factors via adjusting signal transduction and gene expression. L-Glutamate (L-Glu), an amino acid with neurotransmitter functions in animals, inhibits root growth, but the underlying genetic mechanisms are poorly understood...
January 17, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29344167/analysis-of-imp3-expression-in-primary-tumor-and-stromal-cells-in-patients-with-colorectal-cancer
#4
Xiaoping Huang, Qingzhu Wei, Jianghuan Liu, Hongling Niu, Gang Xiao, Lixin Liu
Insulin-like growth factor II mRNA-binding protein 3 (IMP3) is an oncofetal protein upregulated in tumor cells during carcinogenesis. The aim of the present study was to investigate the expression status of IMP3 in colorectal cancer (CRC) tissues and its clinical significance. Immunostaining was performed in 130 CRC samples, the association of IMP3 expression with clinicopathological characteristics was assessed and 58 patients were selected for survival analysis. To the best of our knowledge, the present study describes for the first time the expression of IMP3 in tumor stromal components of CRC...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29342432/pharmacists-scope-of-practice-in-travel-health-a-review-of-state-laws-and-regulations
#5
Keri Hurley-Kim, Rebecca Snead, Karl M Hess
OBJECTIVES: The primary objective of this study was to assess pharmacists' authority to provide travel health services in each state and Washington, DC. Secondary objectives were to determine the need for collaborative practice agreements (CPAs), protocols, or prescriptions for this type of pharmacy practice and to identify jurisdictions where pharmacists are able to practice as travel health providers independent of CPAs or individual physician protocols. METHODS: An online survey was developed to assess pharmacists' authority to administer travel immunizations, furnish travel-related medications, and order travel-related laboratory tests...
January 13, 2018: Journal of the American Pharmacists Association: JAPhA
https://www.readbyqxmd.com/read/29341912/quantitative-estimation-of-phenytoin-sodium-disproportionation-in-the-formulations-using-vibration-spectroscopies-and-multivariate-methodologies
#6
Sathish Dharani, Ziyaur Rahman, Sogra F Barakh Ali, Hamideh Afrooz, Mansoor A Khan
Phenytoin sodium (PS) has tendency to convert to its base form; phenytoin base (PHT) during manufacturing, packaging, shelf life and in-use conditions that can influence its clinical performance. The objective of the present work was to develop a non-destructive, quick and easy analytical method for quantification of PHT in the drug product. A formulation was prepared containing the excipients present in the commercial capsule formulation of PS. Formulation containing either 100% PHT or PS was prepared and these formulations were mixed in different proportion to achieve 0-100% PHT matrices...
January 13, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29340220/multilocus-analysis-of-genetic-susceptibility-to-myocardial-infarction-in-russians-replication-study
#7
N G Kukava, B V Titov, G J Osmak, N A Matveeva, O G Kulakova, A V Favorov, R M Shakhnovich, M Ya Ruda, O O Favorova
In search of genetic markers of myocardial infarction (MI) risk, which have prognostic significance for Russians, we performed a replication study of MI association with genetic variants of PCSK9 (rs562556), APOE (epsilon polymorphism, rs7412 and rs429358), LPL (rs320), MTHFR (rs1801133), eNOS (rs2070744), and the 9p21 region (rs1333049) in 405 patients with MI and 198 controls. Significant MI association was observed with variants of the lipid metabolism genes (PCSK9, APOE and LPL), and of eNOS. The SNPs in the MTHFR gene and the 9p21 region were not significantly associated with MI one by one but were included in several different MI-associated allelic combinations identified by multilocus analysis...
October 2017: Acta Naturae
https://www.readbyqxmd.com/read/29340065/integrating-gene-and-lncrna-expression-to-infer-subpathway-activity-for-tumor-analyses
#8
Chunlong Zhang, Yanjun Xu, Haixiu Yang, Yingqi Xu, Qun Dong, Siyao Liu, Tan Wu, Yunpeng Zhang
LncRNAs acting as miRNA sponges to indirectly regulate mRNAs is a novel layer of gene regulation, therefore, it is necessary to integrate lncRNA and gene levels for interpreting tumor biological mechanism. In this study, we developed a lncRNA-gene integrated strategy to infer functional activities for tumor analyses at the subpathway level. In this strategy, we reconstructed subpathway graphs by embedding lncRNA components and considered the expression levels of both genes and lncRNAs to infer subpathway activities for each tumor sample...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339477/ebola-virus-proteins-np-vp35-and-vp24-are-essential-and-sufficient-to-mediate-nucleocapsid-transport
#9
Yuki Takamatsu, Larissa Kolesnikova, Stephan Becker
The intracytoplasmic movement of nucleocapsids is a crucial step in the life cycle of enveloped viruses. Determination of the viral components necessary for viral nucleocapsid transport competency is complicated by the dynamic and complex nature of nucleocapsid assembly and the lack of appropriate model systems. Here, we established a live-cell imaging system based on the ectopic expression of fluorescent Ebola virus (EBOV) fusion proteins, allowing the visualization and analysis of the movement of EBOV nucleocapsid-like structures with different protein compositions...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339406/genetic-diversity-molecular-phylogeny-and-selection-evidence-of-jinchuan-yak-revealed-by-whole-genome-resequencing
#10
Daoliang Lan, Xianrong Xiong, Tserang-Donko Mipam, Changxiu Fu, Qiang Li, Yi Ai, Dingchao Hou, Zhixin Chai, Jincheng Zhong, Jian Li
Jinchuan yak, a newly discovered yak breed, not only possesses a large proportion of multi-ribs but also exhibits many good characteristics, such as high meat production, milk yield and reproductive performance. However, information about their overall genetic structure, relationship with yaks in other areas, and possible origins and evolutionary processes is limited. In this study, 7,693,689 high-quality single-nucleotide polymorphisms were identified by resequencing the genome of Jinchuan yak. Principal component and population genetic structure analyses showed that Jinchuan yak was distinguished as an independent population among the domestic yak population...
January 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29337243/intratumoral-morphological-heterogeneity-can-be-an-indicator-of-genetic-heterogeneity-in-colorectal-cancer
#11
Juliane Büttner, Korinna Jöhrens, Frederick Klauschen, Michael Hummel, Dido Lenze, Wolfgang Saeger, Annika Lehmann
Anti-EGFR-targeted therapy is used to treat metastatic colorectal cancers with RAS wild-type. However, resistance to targeted therapy is often observed and can be primary or acquired. One reason for primary resistance is the presence of mutations that are undetected due to genetic heterogeneity, which can be expressed by differences present in primary tumor and distant metastasis or recurrence or by an intratumoral heterogeneity (presence of different subclones in the investigated tumor sample). The aim of our study was to investigate if morphological heterogeneity can be an indicator of intratumoral heterogeneity...
January 11, 2018: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/29335878/antioxidant-compounds-recovery-from-ju%C3%A3-ara-residue-by-thermal-assisted-extraction
#12
Leilson O Ribeiro, Ricardo N C Pereira, Renata V Tonon, Lourdes Maria C Cabral, Manuela Cristina P A Santiago, António A Vicente, José António C Teixeira, Virgínia M Matta, Suely P Freitas
This study aimed to recover bioactive compounds by solid-liquid extraction from the agro-industrial residue obtained during juçara fruits processing into pulp. A preliminary study using different solvents (methanol, ethanol and water) indicated ethanol in aqueous solution as the best solvent for antioxidants recovery. Then, a Box-Behnken design was applied considering as independent variables the solvent composition (30-70% ethanol in water), temperature (30-70 °C) and time (30-60 min), in order to evaluate the effects of these factors on antioxidant activity in juçara extract...
January 15, 2018: Plant Foods for Human Nutrition
https://www.readbyqxmd.com/read/29335847/diabetes-obesity-and-the-metabolic-syndrome-as-prognostic-factors-in-stages-i-to-iii-colorectal-cancer-patients
#13
Brianna Croft, Melissa Reed, Caitlyn Patrick, Natalie Kovacevich, Ioannis A Voutsadakis
BACKGROUND: Attempts to introduce prognostic factors for survival outcomes in localized colorectal cancer patients receiving surgical treatment with or without adjuvant therapies, beyond the classic staging parameters, have been met with limited success. Obesity and diabetes mellitus are among the conditions that predispose to colorectal cancer but their value as prognostic markers once the disease is diagnosed is controversial. PATIENTS AND METHODS: This study examines the prognostic value of the components of metabolic syndrome in a retrospective series of colorectal cancer patients with stages I to III disease followed in a single center...
January 15, 2018: Journal of Gastrointestinal Cancer
https://www.readbyqxmd.com/read/29335614/reliability-of-pulse-waveform-separation-analysis-responses-to-an-orthostatic-challenge
#14
Lee Stoner, Keeron Stone, Erik D Hanson, James Faulkner, Simon Fryer, Daniel Credeur
Cardiovascular autonomic nervous system function can be assessed using an orthostatic challenge to induce arterial wave reflection. While arterial reflection is typically estimated using a central augmentation index, a superior estimation can be obtained using pulse wave separation analysis to estimate the aortic backward pressure wave (Pb). However, to be of value in a clinical or research setting, an assessment tool must be precise (reliable). Therefore, this study sought to determine the measurement precision of Pb responses to a modified tilt-table test...
January 15, 2018: Hypertension Research: Official Journal of the Japanese Society of Hypertension
https://www.readbyqxmd.com/read/29334845/neutrophil-to-lymphocyte-ratio-and-mural-nodule-height-as-predictive-factors-for-malignant-intraductal-papillary-mucinous-neoplasms
#15
Yusuke Watanabe, Yusuke Niina, Kazuyoshi Nishihara, Takafumi Okayama, Sadafumi Tamiya, Toru Nakano
BACKGROUND: Accurate preoperative prediction for malignant IPMN is still challenging. The aim of this study was to investigate the validity of neutrophil-to-lymphocyte ratio (NLR) and mural nodule height (MNH) for predicting malignant intraductal papillary mucinous neoplasm (IPMN). METHODS: The medical records of 60 patients who underwent pancreatectomy for IPMN were retrospectively reviewed. RESULTS: NLR tended to be higher in malignant IPMN (median: 2...
January 15, 2018: Acta Chirurgica Belgica
https://www.readbyqxmd.com/read/29332738/body-composition-estimation-in-children-and-adolescents-by-bioelectrical-impedance-analysis-a-systematic-review
#16
REVIEW
João Antônio Chula de Castro, Tiago Rodrigues de Lima, Diego Augusto Santos Silva
BACKGROUND: Bioelectrical impedance analysis (BIA) has commonly been used to assess the body composition of children and adolescents. BIA validation studies have found distinct correlation values with reference methods. OBJECTIVES: To assess the reproducibility, correlation and mean differences in body composition estimated by BIA and reference methods, we systematically reviewed the literature in the pediatric population. METHOD: The search for articles was conducted in March 2016 and was limited to articles published from 2005 to 2015 in the PubMed, Embase, EBSCO, Web of Science, Scopus and SciELO databases...
January 2018: Journal of Bodywork and Movement Therapies
https://www.readbyqxmd.com/read/29332666/optimizing-reverse-shoulder-arthroplasty-component-position-in-the-setting-of-advanced-arthritis-with-posterior-glenoid-erosion-a-computer-enhanced-range-of-motion-analysis
#17
Jay D Keener, Brendan M Patterson, Nathan Orvets, Alexander W Aleem, Aaron M Chamberlain
BACKGROUND: Our study purpose was to determine the optimal glenoid and humeral reverse shoulder arthroplasty (RSA) component design and position in osteoarthritic shoulders with severe glenoid retroversion deformities. METHODS: Computed tomography scans from 10 subjects were analyzed with advanced software including RSA range of motion (ROM) analysis. Variables included glenoid component retroversion of 0°, 5°, 10°, 15°, and 20° and baseplate lateralization of 0, 5, and 10 mm...
February 2018: Journal of Shoulder and Elbow Surgery
https://www.readbyqxmd.com/read/29329580/evidence-for-the-activation-of-pyroptotic-and-apoptotic-pathways-in-rpe-cells-associated-with-nlrp3-inflammasome-in-the-rodent-eye
#18
Jiangyuan Gao, Jing Z Cui, Eleanor To, Sijia Cao, Joanne A Matsubara
BACKGROUND: Age-related macular degeneration (AMD) is a devastating eye disease causing irreversible vision loss in the elderly. Retinal pigment epithelium (RPE), the primary cell type that is afflicted in AMD, undergoes programmed cell death in the late stages of the disease. However, the exact mechanisms for RPE degeneration in AMD are still unresolved. The prevailing theories consider that each cell death pathway works independently and without regulation of each other. Building upon our previous work in which we induced a short burst of inflammasome activity in vivo, we now investigate the effects of prolonged inflammasome activity on RPE cell death mechanisms in rats...
January 12, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29329105/daily-sitting-time-associated-with-the-risk-of-metabolic-syndrome-in-korean-adolescents
#19
Ki Nam Bae, Hye Ryun Kim, Young-Jun Rhie, Kee-Hyoung Lee, Hyo-Kyoung Nam
BACKGROUND: This study aimed to investigate the relationship between daily sitting time and the risk of metabolic syndrome in Korean adolescents. METHODS: Data from 486 adolescents aged 12-18 years were obtained from national surveys. Daily sitting time was measured using questionnaires and divided into three intervals: <8 h; 8-12 h; and ≥12 h. RESULTS: The mean daily sitting time and prevalence of positive metabolic components were 620...
January 12, 2018: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/29328983/social-and-cognitive-control-skills-in-long-life-occupation-activities-modulate-the-brain-reserve-in-the-behavioural-variant-of-frontotemporal-dementia
#20
Alessandra Dodich, Giulia Carli, Chiara Cerami, Sandro Iannaccone, Giuseppe Magnani, Daniela Perani
BACKGROUND: Cognitive reserve may delay disease onset and mitigate symptoms presentation in neurodegenerative dementias. Although high occupation levels can be associated with higher cognitive reserve in the behavioural variant of frontotemporal dementia (bvFTD), it was never addressed how specific occupation profiles involving social interaction, executive and attention abilities can modulate neural reserve in bvFTD. MATERIALS AND METHODS: We retrospectively included thirty-seven bvFTD patients with clinical-neuropsychological and FDG-PET brain metabolic data...
December 19, 2017: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
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