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independent component analysis

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https://www.readbyqxmd.com/read/28097046/molecular-classification-of-tissue-from-a-transformed-non-hogkin-s-lymphoma-case-with-unexpected-long-time-remission
#1
Julie Støve Bødker, Marianne Tang Severinsen, Tarec Christoffer El-Galaly, Rasmus Froberg Brøndum, Maria Bach Laursen, Steffen Falgreen, Mette Nyegaard, Alexander Schmitz, Lasse Hjort Jakobsen, Anna Amanda Schönherz, Hanne Due, Linn Reinholdt, Martin Bøgsted, Karen Dybkær, Hans Erik Johnsen
BACKGROUND: The concept of precision medicine in cancer includes individual molecular studies to predict clinical outcomes. In the present N = 1 case we retrospectively have analysed lymphoma tissue by exome sequencing and global gene expression in a patient with unexpected long-term remission following relaps. The goals were to phenotype the diagnostic and relapsed lymphoma tissue and evaluate its pattern. Furthermore, to identify mutations available for targeted therapy and expression of genes to predict specific drug effects by resistance gene signatures (REGS) for R-CHOP as described at http://www...
2017: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/28095989/prolonged-k-deficiency-increases-intracellular-atp-cell-cycle-arrest-and-cell-death-in-renal-tubular-cells
#2
Kedsarin Fong-Ngern, Nardtaya Ausakunpipat, Nilubon Singhto, Kanyarat Sueksakit, Visith Thongboonkerd
BACKGROUND: Chronic potassium (K(+)) deficiency can cause renal damage namely hypokalemic nephropathy with unclear pathogenic mechanisms. In the present study, we investigated expression and functional alterations in renal tubular cells induced by prolonged K(+) deficiency. METHODS: MDCK cells were maintained in normal-K(+) (CNK) (K(+)=5.3mmol/L), low-K(+) (CLK) (K(+)=2.5mmol/L), or K(+)-depleted (CKD) (K(+)=0mmol/L) medium for 10days (n=5 independent cultures/condition)...
January 4, 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28095800/diet-gonadal-sex-and-sex-chromosome-complement-influence-white-adipose-tissue-mirna-expression
#3
Jenny C Link, Yehudit Hasin-Brumshtein, Rita M Cantor, Xuqi Chen, Arthur P Arnold, Aldons J Lusis, Karen Reue
BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by targeting specific mRNA species for degradation or interfering with translation. Specific miRNAs are key regulators of adipogenesis, and are expressed at different levels in adipose tissue from lean and obese mice. The degree of lipid accumulation and distribution of white adipose tissue differs between males and females, and it is unknown whether sex differences in adipose tissue-specific miRNA expression may contribute to this dimorphism...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28093799/computing-the-z-score-and-centiles-for-cross-sectional-analysis-a-practical-approach
#4
REVIEW
Greggory R DeVore
Although Z scores have been reported in the literature, one of the problems for the nonstatistician is understanding the systematic approach used to compute the predicted mean and standard deviation, components of the Z score equation, which may vary as the independent variable changes over time (eg, gestational age). This review focuses on a step-by-step analysis using linear, quadratic, and fractional polynomials to compute the mean and standard deviation as a function of a continuous independent variable...
January 17, 2017: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/28093358/mapping-the-functional-connectome-traits-of-levels-of-consciousness
#5
Enrico Amico, Daniele Marinazzo, Carol Di Perri, Lizette Heine, Jitka Annen, Charlotte Martial, Mario Dzemidzic, Murielle Kirsch, Vincent Bonhomme, Steven Laureys, Joaquín Goñi
Examining task-free functional connectivity (FC) in the human brain offers insights on how spontaneous integration and segregation of information relate to human cognition, and how this organization may be altered in different conditions, and neurological disorders. This is particularly relevant for patients in disorders of consciousness (DOC) following severe acquired brain damage and coma, one of the most devastating conditions in modern medical care. We present a novel data-driven methodology, connICA, which implements Independent Component Analysis (ICA) for the extraction of robust independent FC patterns (FC-traits) from a set of individual functional connectomes, without imposing any a priori data stratification into groups...
January 13, 2017: NeuroImage
https://www.readbyqxmd.com/read/28092203/machine-learning-of-three-dimensional-right-ventricular-motion-enables-outcome-prediction-in-pulmonary-hypertension-a-cardiac-mr-imaging-study
#6
Timothy J W Dawes, Antonio de Marvao, Wenzhe Shi, Tristan Fletcher, Geoffrey M J Watson, John Wharton, Christopher J Rhodes, Luke S G E Howard, J Simon R Gibbs, Daniel Rueckert, Stuart A Cook, Martin R Wilkins, Declan P O'Regan
Purpose To determine if patient survival and mechanisms of right ventricular failure in pulmonary hypertension could be predicted by using supervised machine learning of three-dimensional patterns of systolic cardiac motion. Materials and Methods The study was approved by a research ethics committee, and participants gave written informed consent. Two hundred fifty-six patients (143 women; mean age ± standard deviation, 63 years ± 17) with newly diagnosed pulmonary hypertension underwent cardiac magnetic resonance (MR) imaging, right-sided heart catheterization, and 6-minute walk testing with a median follow-up of 4...
January 16, 2017: Radiology
https://www.readbyqxmd.com/read/28089951/bzr1-positively-regulates-freezing-tolerance-via-cbf-dependent-and-cbf-independent-pathways-in-arabidopsis
#7
Hui Li, Keyi Ye, Yiting Shi, Jinkui Cheng, Xiaoyan Zhang, Shuhua Yang
Cold stress is a major environmental factor that adversely affects plant growth and development. The C-repeat Binding Factor/DRE Binding Factor 1 (CBF/DREB1) transcriptional regulatory cascade has been shown to play important roles in plant response to cold. Here we demonstrate that two key components of BR signaling modulate freezing tolerance of plants. The loss-of-function mutant of the GSK3-like kinases involved in BR signaling, bin2-3 bil1 bil2, showed increased freezing tolerance, whereas overexpression of BIN2 resulted in hypersensitivity to freezing stress under both non-acclimated and acclimated conditions...
January 13, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28088482/combined-spatiotemporal-ica-stica-for-continuous-and-dynamic-lag-structure-analysis-of-mreg-data
#8
Ville Raatikainen, Niko Huotari, Vesa Korhonen, Aleksi Rasila, Janne Kananen, Lauri Raitamaa, Tuija Keinänen, Jussi Kantola, Osmo Tervonen, Vesa Kiviniemi
This study investigated lag structure in the resting-state fMRI by applying a novel independent component (ICA) method to magnetic resonance encephalography (MREG) data. Briefly, the spatial ICA (sICA) was used for defining the frontal and back nodes of the default mode network (DMN), and the temporal ICA (tICA), which is enabled by the high temporal resolution of MREG (TR=100ms), was used to separate both neuronal and physiological components of these two spatial map regions. Subsequently, lag structure was investigated between the frontal (DMNvmpf) and posterior (DMNpcc) DMN nodes using both conventional method with all-time points and a sliding-window approach...
January 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/28087176/carotid-plaque-detection-improves-the-predictive-value-of-cha2ds2-vasc-score-in-patients-with-non-valvular-atrial-fibrillation-the-arapacis-study
#9
Stefania Basili, Lorenzo Loffredo, Daniele Pastori, Marco Proietti, Alessio Farcomeni, Anna Rita Vestri, Pasquale Pignatelli, Giovanni Davì, William R Hiatt, Gregory Y H Lip, Gino R Corazza, Francesco Perticone, Francesco Violi
BACKGROUND AND AIMS: Vascular disease (VD), as assessed by history of myocardial infarction or peripheral artery disease or aortic plaque, increases stroke risk in atrial fibrillation (AF), and is a component of risk assessment using the CHA2DS2-VASc score. We investigated if systemic atherosclerosis as detected by ultrasound carotid plaque (CP) could improve the predictive value of the CHA2DS2-VASc score. METHODS: We analysed data from the ARAPACIS study, an observational study including 2027 Italian patients with non-valvular AF, in whom CP was detected using Doppler Ultrasonography...
January 4, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28087161/effect-of-acetabular-position-on-polyethylene-liner-wear-measured-using-simultaneous-biplanar-acquisition
#10
Prateek Goyal, James L Howard, Xunhua Yuan, Matthew G Teeter, Brent A Lanting
BACKGROUND: Studies that have previously examined the relationship between acetabular component inclination angle and polyethylene wear have shown increased wear of conventional polyethylene with high inclination angles. To date, there are no long-term in vivo studies examining the correlation between cup position and polyethylene wear with highly crosslinked polyethylene. METHODS: An institutional arthroplasty database was used to identify patients who had metal-on-highly crosslinked polyethylene primary total hip arthroplasty using the same component design with a minimum follow-up of 10 years...
December 14, 2016: Journal of Arthroplasty
https://www.readbyqxmd.com/read/28086752/single-genome-retrieval-of-context-dependent-variability-in-mutation-rates-for-human-germline
#11
Aleksandr B Sahakyan, Shankar Balasubramanian
BACKGROUND: Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. RESULTS: The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081448/the-relationships-among-fear-of-hypoglycaemia-diabetes-related-quality-of-life-and-psychological-well-being-in-norwegian-adults-with-type-1-diabetes
#12
Ragnhild B Strandberg, Marit Graue, Tore Wentzel-Larsen, Mark Peyrot, Astrid K Wahl, Berit Rokne
AIMS: To examine the associations among fear of hypoglycaemia, diabetes-related quality of life and psychological well-being, and determine whether diabetes-related quality of life is a mediator of the relationship between fear of hypoglycaemia and psychological well-being in adults with Type 1 diabetes. METHODS: A total of 235 of 319 invited adults (18-69years) with Type 1 diabetes agreed to participate. Hierarchical linear regression was applied to 188 individuals with complete data...
December 27, 2016: Diabetes Research and Clinical Practice
https://www.readbyqxmd.com/read/28081171/a-higher-proportion-of-metabolic-syndrome-in-chinese-subjects-with-sleep-disordered-breathing-a-case-control-study-based-on-electrocardiogram-derived-sleep-analysis
#13
Ping-Huei Tseng, Pei-Lin Lee, Wei-Chung Hsu, Yan Ma, Yi-Chia Lee, Han-Mo Chiu, Yi-Lwun Ho, Ming-Fong Chen, Ming-Shiang Wu, Chung-Kang Peng
OBJECTIVE: The prevalence of metabolic syndrome (MS) has increased rapidly in Taiwan and worldwide. We aim to determine the association between sleep-disordered breathing (SDB) and MS in a Chinese general population. METHODS: This case-control study recruited subjects who have undergone a prospective electrocardiogram-based cardiopulmonary coupling (CPC) sleep spectrogram as part of the periodic health check-ups at the National Taiwan University Hospital. Comprehensive anthropometrics, blood biochemistry, prevalence of MS and its individual components were compared with Bonferroni correction between 40 subjects with SDB, defined as the CPC-derived apnea-hypopnea index (CPC-AHI) >5 event/hour and 80 age- and sex-matched controls, defined as CPC-AHI <1 event/hour...
2017: PloS One
https://www.readbyqxmd.com/read/28079701/ex-vivo-assessment-of-coronary-atherosclerotic-plaque-by-grating-based-phase-contrast-computed-tomography-correlation-with-optical-coherence-tomography
#14
Christopher Habbel, Holger Hetterich, Marian Willner, Julia Herzen, Kristin Steigerwald, Sigrid Auweter, Ulrich Schüller, Jörg Hausleiter, Steffen Massberg, Maximilian Reiser, Franz Pfeiffer, Tobias Saam, Fabian Bamberg
OBJECTIVES: The aim of this study was to determine the diagnostic accuracy of grating-based phase-contrast computed tomography (gb-PCCT) to classify and quantify coronary vessel characteristics in comparison with optical coherence tomography (OCT) and histopathology in an ex vivo setting. MATERIALS AND METHODS: After excision from 5 heart specimens, 15 human coronary arteries underwent gb-PCCT examination using an experimental imaging setup consisting of a rotating molybdenum anode x-ray tube, a Talbot-Lau grating interferometer, and a single photon counting detector...
January 10, 2017: Investigative Radiology
https://www.readbyqxmd.com/read/28079247/dynamic-location-changes-of-bub1-phosphorylated-h2athr133-with-cenh3-nucleosome-in-maize-centromeric-regions
#15
Handong Su, Yalin Liu, Qianhua Dong, Chao Feng, Jing Zhang, Yang Liu, James A Birchler, Fangpu Han
The genomic stability of all organisms requires precise cell division with proper chromosome orientation. The Bub1-H2Aph-Sgo1 pathway and spindle assembly checkpoint (SAC) components have been identified in yeast and mammals that are important for sister centromere orientation and chromosome segregation. However, their roles in plants are not clear. Maize meiotic mutants and minichromosomes were used to study the role of H2AThr133 phosphorylation and SAC components in sister centromere orientation and chromosome segregation...
January 12, 2017: New Phytologist
https://www.readbyqxmd.com/read/28076801/msmbuilder-statistical-models-for-biomolecular-dynamics
#16
Matthew P Harrigan, Mohammad M Sultan, Carlos X Hernández, Brooke E Husic, Peter Eastman, Christian R Schwantes, Kyle A Beauchamp, Robert T McGibbon, Vijay S Pande
MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076406/the-development-and-validation-of-the-empathy-components-questionnaire-ecq
#17
Laurie Batchelder, Mark Brosnan, Chris Ashwin
Key research suggests that empathy is a multidimensional construct comprising of both cognitive and affective components. More recent theories and research suggest even further factors within these components of empathy, including the ability to empathize with others versus the drive towards empathizing with others. While numerous self-report measures have been developed to examine empathy, none of them currently index all of these wider components together. The aim of the present research was to develop and validate the Empathy Components Questionnaire (ECQ) to measure cognitive and affective components, as well as ability and drive components within each...
2017: PloS One
https://www.readbyqxmd.com/read/28075219/how-do-assessments-of-activities-of-daily-living-address-executive-functions-a-scoping-review
#18
Frédérique Poncet, Bonnie Swaine, Elisabeth Dutil, Mathilde Chevignard, Pascale Pradat-Diehl
: Executive functions (EF) allow persons to adapt to situations arising in daily life and can be affected following acquired brain injury (ABI). Measuring the impact of EF impairments on the accomplishment of activities of daily living (ADL) requires specific assessment tools, but choosing the right tool may be difficult. PURPOSE: To conduct a scoping review on how assessments of ADL address EF and EF impairments in persons with ABI. METHOD: A scoping review of literature (peer-reviewed and grey literature) published until August 2014 was conducted...
January 11, 2017: Neuropsychological Rehabilitation
https://www.readbyqxmd.com/read/28075197/validation-of-an-established-prognostic-score-after-re-irradiation-of-recurrent-glioma
#19
Kerstin A Kessel, Josefine Hesse, Christoph Straube, Claus Zimmer, Friederike Schmidt-Graf, Jürgen Schlegel, Bernhard Meyer, Stephanie E Combs
BACKGROUND: Re-irradiation (Re-RT) is offered widely in clinical routine, and has been established as a key element in the treatment of recurrent gliomas. At our center, generally re-resection is performed widely by an experienced neurosurgical team. Thus, Re-RT mostly offered to patients with macroscopic residuals or irresectable lesions, is applied later compared to other centers. Therefore, we sought to validate the Combs Prognostic Score developed in 2012 using our independent patient cohort...
January 11, 2017: Acta Oncologica
https://www.readbyqxmd.com/read/28075001/-proposed-model-of-executive-functions-based-on-factorial-analyses
#20
REVIEW
J Tirapu-Ustarroz, P Cordero-Andres, P Luna-Lario, P Hernaez-Goni
INTRODUCTION: Since Lezak coined the term executive functions to refer to the mental capabilities that are considered essential for performing efficacious, creative and socially acceptable behaviour, they have gradually grown in importance in neuropsychological research. Different models have been proposed to explain their nature, but there is no general agreement as to whether we are dealing with a unitary construct or a multimodal processing system with independent, but interconnected, components...
January 16, 2017: Revista de Neurologia
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