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independent component analysis

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https://www.readbyqxmd.com/read/28339467/a-non-canonical-rna-degradation-pathway-suppresses-rnai-dependent-epimutations-in-the-human-fungal-pathogen-mucor-circinelloides
#1
Silvia Calo, Francisco E Nicolás, Soo Chan Lee, Ana Vila, Maria Cervantes, Santiago Torres-Martinez, Rosa M Ruiz-Vazquez, Maria E Cardenas, Joseph Heitman
Mucorales are a group of basal fungi that includes the casual agents of the human emerging disease mucormycosis. Recent studies revealed that these pathogens activate an RNAi-based pathway to rapidly generate drug-resistant epimutant strains when exposed to stressful compounds such as the antifungal drug FK506. To elucidate the molecular mechanism of this epimutation pathway, we performed a genetic analysis in Mucor circinelloides that revealed an inhibitory role for the non-canonical RdRP-dependent Dicer-independent silencing pathway, which is an RNAi-based mechanism involved in mRNA degradation that was recently identified...
March 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28338849/a-preventative-lifestyle-intervention-for-older-adults-lifestyle-matters-a-randomised-controlled-trial
#2
Gail Mountain, Gill Windle, Daniel Hind, Stephen Walters, Anju Keertharuth, Robin Chatters, Kirsty Sprange, Claire Craig, Sarah Cook, Ellen Lee, Tim Chater, R Woods, Louise Newbould, Lauren Powell, Katy Shortland, Jennifer Roberts
Objectives: to test whether an occupation-based lifestyle intervention can sustain and improve the mental well-being of adults aged 65 years or over compared to usual care, using an individually randomised controlled trial. Participants: 288 independently living adults aged 65 years or over, with normal cognition, were recruited from two UK sites between December 2011 and November 2015. Interventions: lifestyle Matters is a National Institute for Health and Care Excellence recommended multi-component preventive intervention designed to improve the mental well-being of community living older people at risk of decline...
February 25, 2017: Age and Ageing
https://www.readbyqxmd.com/read/28338651/dichotomy-in-intrahepatic-cholangiocarcinomas-based-on-histologic-similarities-to-hilar-cholangiocarcinomas
#3
Masayuki Akita, Kohei Fujikura, Tetsuo Ajiki, Takumi Fukumoto, Kyoko Otani, Takeshi Azuma, Tomoo Itoh, Yonson Ku, Yoh Zen
Intrahepatic cholangiocarcinomas were classified into two types based on their microscopic appearance. Tumors with histologic similarities to hilar cholangiocarcinomas (predominantly ductal adenocarcinomas with minor tubular components, if present, restricted to the invasive front) were defined as the perihilar type, whereas the others were classified as peripheral cholangiocarcinomas. Among the 47 cases examined in the present study, 26 (55%) were classified as the perihilar type, whereas 21 (45%) were the peripheral type...
March 24, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28338052/dissociable-diffusion-mri-patterns-of-white-matter-microstructure-and-connectivity-in-alzheimer-s-disease-spectrum
#4
Nhat Trung Doan, Andreas Engvig, Karin Persson, Dag Alnæs, Tobias Kaufmann, Jaroslav Rokicki, Aldo Córdova-Palomera, Torgeir Moberget, Anne Brækhus, Maria Lage Barca, Knut Engedal, Ole A Andreassen, Geir Selbæk, Lars T Westlye
Recent efforts using diffusion tensor imaging (DTI) have documented white matter (WM) alterations in Alzheimer's disease (AD). The full potential of whole-brain DTI, however, has not been fully exploited as studies have focused on individual microstructural indices independently. In patients with AD (n = 79), mild (MCI, n = 55) and subjective (SCI, n = 30) cognitive impairment, we applied linked independent component analysis (LICA) to model inter-subject variability across five complementary DTI measures (fractional anisotropy (FA), axial/radial/mean diffusivity, diffusion tensor mode), two crossing fiber measures estimated using a multi-compartment crossing-fiber model reflecting the volume fraction of the dominant (f1) and non-dominant (f2) diffusion orientation, and finally, connectivity density obtained from full-brain probabilistic tractography...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334758/n1-methyl-pseudouridine-in-mrna-enhances-translation-through-eif2%C3%AE-dependent-and-independent-mechanisms-by-increasing-ribosome-density
#5
Yuri V Svitkin, Yi Min Cheng, Tirtha Chakraborty, Vladimir Presnyak, Matthias John, Nahum Sonenberg
Certain chemical modifications confer increased stability and low immunogenicity to in vitro transcribed mRNAs, thereby facilitating expression of therapeutically important proteins. Here, we demonstrate that N1-methyl-pseudouridine (N1mΨ) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. Through extensive analysis of various modified transcripts in cell-free translation systems, we deconvolute the different components of the effect on protein expression independent of mRNA stability mechanisms...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334456/a-systematic-review-of-combined-student-and-parent-based-programs-to-prevent-alcohol-and-other-drug-use-among-adolescents
#6
REVIEW
Nicola C Newton, Katrina E Champion, Tim Slade, Cath Chapman, Lexine Stapinski, Ina Koning, Zoe Tonks, Maree Teesson
ISSUES: Alcohol and other drug use among adolescents is a serious concern, and effective prevention is critical. Research indicates that expanding school-based prevention programs to include parenting components could increase prevention outcomes. This paper aims to identify and describe existing combined student- and parent-based programs for the prevention of alcohol and other drug use to evaluate the efficacy of existing programs. APPROACH: The PsycINFO, Medline, Central Register of Controlled trials and Cochrane databases were searched in April 2015 and additional articles were obtained from reference lists...
March 23, 2017: Drug and Alcohol Review
https://www.readbyqxmd.com/read/28334131/pca-leverage-outlier-detection-for-high-dimensional-functional-magnetic-resonance-imaging-data
#7
Amanda F Mejia, Mary Beth Nebel, Ani Eloyan, Brian Caffo, Martin A Lindquist
Outlier detection for high-dimensional (HD) data is a popular topic in modern statistical research. However, one source of HD data that has received relatively little attention is functional magnetic resonance images (fMRI), which consists of hundreds of thousands of measurements sampled at hundreds of time points. At a time when the availability of fMRI data is rapidly growing-primarily through large, publicly available grassroots datasets-automated quality control and outlier detection methods are greatly needed...
February 27, 2017: Biostatistics
https://www.readbyqxmd.com/read/28333636/sequential-dictionary-learning-from-correlated-data-application-to-fmri-data-analysis
#8
Abd-Krim Seghouane, Asif Iqbal
Sequential dictionary learning via the K-SVD algorithm has been revealed as a successful alternative to conventional data driven methods such as independent component analysis (ICA) for functional magnetic resonance imaging (fMRI) data analysis. fMRI datasets are however structured data matrices with notions of spatio-temporal correlation and temporal smoothness. This prior information has not been included in the K-SVD algorithm when applied to fMRI data analysis. In this paper we propose three variants of the K-SVD algorithm dedicated to fMRI data analysis by accounting for this prior information...
March 22, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28333634/a-precision-analysis-of-camera-distortion-models
#9
Zhongwei Tang, Rafael Grompone von Gioi, Pascal Monasse, Jean-Michel Morel
This paper addresses the question of identifying the right camera direct or inverse distortion model permitting a high subpixel precision fit to real camera distortion. Five classic camera distortion models are reviewed and their precision compared for direct or inverse distortion. By definition, the three radially symmetric models can only model a distortion radially symmetric around some distortion center. They can be extended to deal with non-radially symmetric distortions by adding tangential distortion components, but still may be too simple for very accurate modeling of real cameras...
March 22, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28332867/age-related-changes-in-thoracic-skeletal-geometry-of-elderly-females
#10
Sven A Holcombe, Stewart C Wang, James B Grotberg
OBJECTIVE: Both females and the elderly have been identified as vulnerable populations with increased injury and mortality risk in multiple crash scenarios. Particularly in frontal impacts, older females show higher risk to the chest and thorax than their younger or male counterparts. Thoracic geometry plays a role in this increase, and this study aims to quantify key parts of that geometry in a way that can directly inform human body models that incorporate the concept of person age...
March 23, 2017: Traffic Injury Prevention
https://www.readbyqxmd.com/read/28332506/effectiveness-of-home-blood-pressure-telemonitoring-a-systematic-review-and-meta-analysis-of-randomised-controlled-studies
#11
REVIEW
Y Duan, Z Xie, F Dong, Z Wu, Z Lin, N Sun, J Xu
To summarise evidence about the effectiveness of home blood pressure telemonitoring (HBPT) and identify the key components of intervention. We comprehensively searched PubMed, EMBASE and the Cochrane Library for relevant studies. The authors were contacted for additional information. Two authors independently extracted the data and assessed the risk of bias. 46 randomised controlled trials including a total of 13 875 cases were identified. Compared with usual care, HBPT improved office systolic blood pressure (BP) and diastolic BP by 3...
March 23, 2017: Journal of Human Hypertension
https://www.readbyqxmd.com/read/28331964/the-hypomorphic-tert-a1062t-variant-is-associated-with-increased-treatment-related-toxicity-in-acute-myeloid-leukemia
#12
Anna Both, Jürgen Krauter, Frederik Damm, Felicitas Thol, Gudrun Göhring, Michael Heuser, Oliver Ottmann, Michael Lübbert, Mohammed Wattad, Lothar Kanz, Günter Schlimok, Aruna Raghavachar, Walter Fiedler, Hartmut Kirchner, Wolfram Brugger, Brigitte Schlegelberger, Gerhard Heil, Arnold Ganser, Katharina Wagner
Hypomorphic germline variants in TERT, the gene encoding the reverse transcriptase component of the human telomerase complex, occur with a frequency of 3-5% in acute myeloid leukemia. We analyzed the clinical and prognostic impact of the most common TERT A1062T variant in younger patients with acute myeloid leukemia intensively treated within two prospective multicenter trials. Four hundred and twenty patients (age 17-60 years) were analyzed for the TERT A1062T variant by direct sequencing. Fifteen patients (3...
March 22, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28329065/right-ventricular-outflow-tract-systolic-function-correlates-with-exercise-capacity-in-patients-with-severe-right-ventricle-dilatation-after-repair-of-tetralogy-of-fallot
#13
Shuhua Luo, Jianhua Li, Dan Yang, Yaxin Zhou, Qi An, Yucheng Chen
OBJECTIVES: The relationship between exercise capacity and right ventricular (RV) components function in repaired tetralogy of Fallot patients with severely dilated right ventricles is poorly understood. The aim of this study was to characterize the exercise capacity and its relationship to RV global and components function in repaired tetralogy of Fallot patients with RV end-diastolic volume index  >150 ml/m 2 , a currently accepted threshold for pulmonary valve replacement. METHODS: The medical records and results of cardiac magnetic resonance imaging and cardiopulmonary exercise testing of 25 consecutive eligible patients were reviewed...
February 16, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/28329030/protective-factors-in-the-intestinal-microbiome-against-clostridium-difficile-infection-in-recipients-of-allogeneic-hematopoietic-stem-cell-transplantation
#14
Yeon Joo Lee, Esther P Arguello, Robert R Jenq, Eric Littmann, Grace J Kim, Liza C Miller, Lilan Ling, Cesar Figueroa, Elizabeth Robilotti, Miguel-Angel Perales, Juliet N Barker, Sergio Giralt, Marcel R M van den Brink, Eric G Pamer, Ying Taur
Background.: Clostridium difficile infection (CDI) is a frequent complication in recipients of allogeneic hematopoietic stem cell transplantation (allo-HSCT), who receive intensive treatments that significantly disrupt the intestinal microbiota. In this study, we examined the microbiota composition of allo-HSCT recipients to identify bacterial colonizers that confer protection against CDI following engraftment. Methods.: Feces collected from adult recipients allo-HSCT at engraftment were analyzed; 16S rRNA genes were sequenced and analyzed from each sample...
January 30, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28328797/activation-senescence-and-inflammation-markers-in-hiv-patients-association-with-renal-function
#15
Alexandra Ozanne, Pierre Duffau, Frédéric-Antoine Dauchy, Claire Rigothier, Cécile Terrien, Estibaliz Lazaro, Charles Cazanave, Sylvie Lawson-Ayayi, Fabrice Bonnet, Patrick Blanco, Linda Wittkop, Isabelle Pellegrin
OBJECTIVES: To assess the association between immune-activation (IA), immune-senescence (IS), inflammation biomarkers and renal function measured by estimated glomerular function rate (eGFR) at inclusion and its evolution over a 3-years follow-up in HIV-infected patients with undetectable viral load. DESIGN: The CIADIS (Chronic Immune Activation anD Senescence) sub-study consecutively included patients between October 2011 and May 2013 enrolled in the ANRS CO3 Aquitaine observational cohort...
March 21, 2017: AIDS
https://www.readbyqxmd.com/read/28328315/analysis-of-protein-target-interactions-of-synthetic-mixtures-by-affinity-lc-ms
#16
Prachi Singh, Kalaipriya Madhaiyan, Minh-Dao Duong-Thi, Brian W Dymock, Sten Ohlson
Analysis of interactions between molecules is of fundamental importance in life science research. In this study, we applied weak affinity chromatography, based on high-performance liquid chromatography and mass spectrometry, as a powerful tool for direct analysis of the components of a chemical reaction mixture for their binding to a target protein. As a demonstration of the potential of this method, we analyzed the binding of the compounds of the reaction mixture to the chaperone heat shock protein 90 (Hsp90)...
April 2017: SLAS Discov
https://www.readbyqxmd.com/read/28327972/orthogonal-decomposition-of-left-ventricular-remodelling-in-myocardial-infarction
#17
Xingyu Zhang, Pau Medrano-Gracia, Bharath Ambale-Venkatesh, David A Bluemke, Brett R Cowan, J Paul Finn, Alan H Kadish, Daniel C Lee, Joao A C Lima, Alistair A Young, Avan Suinesiaputra
Background: Left ventricular size and shape is important for quantifying cardiac remodelling in response to cardiovascular disease. Geometric remodelling indices have been shown to have prognostic value in predicting adverse events in the clinical literature, but these often describe interrelated shape changes. We developed a novel method for deriving orthogonal remodelling components directly from any (moderately independent) set of clinical remodelling indices. Results: Six clinical remodelling indices (end-diastolic volume index, sphericity, relative wall thickness, ejection fraction, apical conicity and longitudinal shortening) were evaluated using cardiac magnetic resonance images of 300 patients with myocardial infarction, and 1991 asymptomatic subjects, obtained from the Cardiac Atlas Project...
February 6, 2017: GigaScience
https://www.readbyqxmd.com/read/28327687/utilization-of-services-for-institutional-deliveries-in-gorkha-district
#18
G Paudel, U N Yadav, S J Thakuri, J P Singh, S B Marahatta
BACKGROUND: Adequate health services for improving maternal and neonatal health is an important global health issues. Institutional delivery is most important component to address maternal and neonatal issue. Institutional delivery service utilization assures safe birth and minimizes the maternal morbidity and mortality. This study was aimed to assess the utilization of institutional delivery service among the mothers of Gorkha district. METHODS: A cross sectional study of 180 mothers having child below 2 years residing in Palungtar municipality was done between March to July 2015...
September 2016: Journal of Nepal Health Research Council
https://www.readbyqxmd.com/read/28327648/comparison-of-multivariate-analysis-methods-for-extracting-the-paraffin-component-from-the-paraffin-embedded-cancer-tissue-spectra-for-raman-imaging
#19
Phiranuphon Meksiarun, Mika Ishigaki, Verena A C Huck-Pezzei, Christian W Huck, Kanet Wongravee, Hidetoshi Sato, Yukihiro Ozaki
This study aimed to extract the paraffin component from paraffin-embedded oral cancer tissue spectra using three multivariate analysis (MVA) methods; Independent Component Analysis (ICA), Partial Least Squares (PLS) and Independent Component - Partial Least Square (IC-PLS). The estimated paraffin components were used for removing the contribution of paraffin from the tissue spectra. These three methods were compared in terms of the efficiency of paraffin removal and the ability to retain the tissue information...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327454/collective-variables-for-the-study-of-long-time-kinetics-from-molecular-trajectories-theory-and-methods
#20
REVIEW
Frank Noé, Cecilia Clementi
Collective variables are an important concept to study high-dimensional dynamical systems, such as molecular dynamics of macromolecules, liquids, or polymers, in particular to define relevant metastable states and state-transition or phase-transition. Over the past decade, a rigorous mathematical theory has been formulated to define optimal collective variables to characterize slow dynamical processes. Here we review recent developments, including a variational principle to find optimal approximations to slow collective variables from simulation data, and algorithms such as the time-lagged independent component analysis...
March 16, 2017: Current Opinion in Structural Biology
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