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https://www.readbyqxmd.com/read/28087895/crohn-disease-risk-prediction-best-practices-and-pitfalls-with-exome-data
#1
Manuel Giollo, David T Jones, Marco Carraro, Emanuela Leonardi, Carlo Ferrari, Silvio C E Tosatto
The Critical Assessment of Genome Interpretation (CAGI) experiment is the first attempt to evaluate the state-of-the-art in genetic data interpretation. Among the proposed challenges, Crohn disease (CD) risk prediction has become the most classic problem spanning three editions. The scientific question is very hard: can anybody assess the risk to develop CD given the exome data alone? This is one of the ultimate goals of genetic analysis, which motivated most CAGI participants to look for powerful new methods...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28081299/ultrasound-detection-of-regional-oxidative-stress-in-deep-tissues-using-novel-enzyme-loaded-nanoparticles
#2
Emilia S Olson, Inanc Ortac, Christopher Malone, Sadik Esener, Robert Mattrey
Oxidative stress is a powerful tool that is critical to immune mediated responses in healthy individuals, yet additionally plays a crucial role in development of cancer, inflammatory pathologies, and tissue ischemia. Despite this, there remain relatively few molecular tools to study oxidative stress, particularly in living mammals. To develop an intravenously injectable probe capable of labeling sites of oxidative stress in vivo, 200 nm catalase synthetic hollow enzyme loaded nanospheres (catSHELS) are designed and fabricated using a versatile enzyme nanoencapsulation method...
January 12, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28079956/an-exonuclease-iii-powered-on-particle-stochastic-dna-walker
#3
Xiangmeng Qu, Dan Zhu, Guangbao Yao, Shao Su, Jie Chao, Huajie Liu, Xiaolei Zuo, Lihua Wang, Jiye Shi, Lianhui Wang, Wei Huang, Hao Pei, Chunhai Fan
DNA-based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)-powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)-based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt-bridge mechanism. The operation of this Exo III-propelled DNA walker was monitored in real time and at the single-particle resolution using total internal reflection fluorescence microscopy (TIRF)...
January 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28077669/preparatory-alpha-band-oscillations-reflect-spatial-gating-independently-of-predictions-regarding-target-identity
#4
Theresa Wildegger, Freek van Ede, Mark W Woolrich, Celine R Gillebert, Anna Christina Nobre
Preparatory modulations of cortical alpha-band oscillations are a reliable index of the voluntary allocation of covert spatial attention. It is currently unclear whether attentional cues containing information about a target's identity (such as its visual orientation), in addition to its location, might additionally shape preparatory alpha modulations. Here, we explore this question by directly comparing spatial and feature-based attention in the same visual detection task while recording brain activity using magneto-encephalography (MEG)...
January 11, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28070278/entanglement-is-a-costly-life-history-stage-in-large-whales
#5
Julie van der Hoop, Peter Corkeron, Michael Moore
Individuals store energy to balance deficits in natural cycles; however, unnatural events can also lead to unbalanced energy budgets. Entanglement in fishing gear is one example of an unnatural but relatively common circumstance that imposes energetic demands of a similar order of magnitude and duration of life-history events such as migration and pregnancy in large whales. We present two complementary bioenergetic approaches to estimate the energy associated with entanglement in North Atlantic right whales, and compare these estimates to the natural energetic life history of individual whales...
January 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28069236/recent-advancements-in-the-sonophotocatalysis-spc-and-doped-sonophotocatalysis-dspc-for-the-treatment-of-recalcitrant-hazardous-organic-water-pollutants
#6
REVIEW
Debabrata Panda, Sivakumar Manickam
: Sonophotocatalysis (SPC) is considered to be one of the important wastewater treatment techniques and hence attracted the attention of researchers to eliminate recalcitrant hazardous organic pollutants from aqueous phase. In general, SPC refers to the integrated use of ultrasonic sound waves, ultraviolet radiation and the addition of a semiconductor material which functions as a photocatalyst. Current research has brought numerous improvements in the SPC based treatment by opting visible light irradiation, nanocomposite catalysts and numerous catalyst supports for better stability and performance...
May 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28063313/desulfurization-critical-step-towards-enhanced-selenium-removal-from-industrial-effluents
#7
Lucian C Staicu, Nadia Morin-Crini, Grégorio Crini
Selenium (Se) removal from synthetic solutions and from real Flue Gas Desulfurization (FGD) wastewater generated by a coal-fired power plant was studied for the first time using a commercial iron oxide impregnated strong base anion exchange resin, Purolite(®) FerrIX A33E. In synthetic solutions, the resin showed high affinity for selenate and selenite, while sulfate exhibited a strong competition for both oxyanions. The FGD wastewater investigated is a complex system that contains Se (∼1200 μg L(-1)), SO4(2-) (∼1...
December 29, 2016: Chemosphere
https://www.readbyqxmd.com/read/28061369/employing-image-processing-techniques-for-cancer-detection-using-microarray-images
#8
Nastaran Dehghan Khalilabad, Hamid Hassanpour
Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes...
December 21, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28060759/a-potential-prognostic-lncrna-signature-for-predicting-survival-in-patients-with-bladder-urothelial-carcinoma
#9
Zhenyu Bao, Weitao Zhang, Dong Dong
Increasing evidence has highlighted the critical roles of long non-coding RNA (lncRNA) in cancer development and progression. However, the prognostic power of expression-based lncRNA signature for predicting overall survival in patients with Bladder Urothelial Carcinoma (BLCA) has not been investigated. Here, we performed a comprehensive analysis for lncRNA expression profiles and corresponding clinical information of 234 BLCA patients from The Cancer Genome Atlas (TCGA). We established a set of four-lncRNAs that were significantly associated with BLCA patients' survival...
January 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060701/perisomatic-gabaergic-synapses-of-basket-cells-effectively-control-principal-neuron-activity-in-amygdala-networks
#10
Judit M Veres, Gergő A Nagy, Norbert Hájos
Efficient control of principal neuron firing by basket cells is critical for information processing in cortical microcircuits, however, the relative contribution of their perisomatic and dendritic synapses to spike inhibition is still unknown. Using in vitro electrophysiological paired recordings we reveal that in the mouse basal amygdala cholecystokinin- and parvalbumin-containing basket cells provide equally potent control of principal neuron spiking. We performed pharmacological manipulations, light and electron microscopic investigations to show that, although basket cells innervate the entire somato-denditic membrane surface of principal neurons, the spike controlling effect is achieved primarily via the minority of synapses targeting the perisomatic region...
January 6, 2017: ELife
https://www.readbyqxmd.com/read/28060344/visualizing-the-interrenal-steroidogenic-tissue-and-its-vascular-microenvironment-in-zebrafish
#11
Chih-Wei Chou, Jamie Lin, Hsin-Yu Hou, Yi-Wen Liu
This protocol introduces how to detect differentiated interrenal steroidogenic cells through a simple whole-mount enzymatic activity assay. Identifying differentiated steroidogenic tissues through chromogenic histochemical staining of 3-β-Hydroxysteroid dehydrogenase /Δ(5-4) isomerase (3β-Hsd) activity-positive cells is critical for monitoring the morphology and differentiation of adrenocortical and interrenal tissues in mammals and teleosts, respectively. In the zebrafish model, the optical transparency and tissue permeability of the developing embryos and larvae allow for whole-mount staining of 3β-Hsd activity...
December 21, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28059578/a-bayesian-meta-analytic-approach-for-safety-signal-detection-in-randomized-clinical-trials
#12
Motoi Odani, Satoru Fukimbara, Tosiya Sato
BACKGROUND/AIM: Meta-analyses are frequently performed on adverse event data and are primarily used for improving statistical power to detect safety signals. However, in the evaluation of drug safety for New Drug Applications, simple pooling of adverse event data from multiple clinical trials is still commonly used. We sought to propose a new Bayesian hierarchical meta-analytic approach based on consideration of a hierarchical structure of reported individual adverse event data from multiple randomized clinical trials...
January 1, 2017: Clinical Trials: Journal of the Society for Clinical Trials
https://www.readbyqxmd.com/read/28057680/an-informative-approach-on-differential-abundance-analysis-for-time-course-metagenomic-sequencing-data
#13
Dan Luo, Sara Ziebell, Lingling An
MOTIVATION: The advent of high-throughput next generation sequencing technology has greatly promoted the field of metagenomics where previously unattainable information about microbial communities can be discovered. Detecting differentially abundant features (e.g., species or genes) plays a critical role in revealing the contributors (i.e., pathogens) to the biological or medical status of microbial samples. However, currently available statistical methods lack power in detecting differentially abundant features contrasting different biological or medical conditions, in particular, for time series metagenomic sequencing data...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28054252/a-risk-factor-analysis-for-in-hospital-mortality-after-surgery-for-infective-endocarditis-and-a-proposal-of-a-new-predictive-scoring-system
#14
Giuseppe Gatti, Bernardo Benussi, Florida Gripshi, Alessio Della Mattia, Alberto Proclemer, Antonio Cannatà, Lorella Dreas, Roberto Luzzati, Gianfranco Sinagra, Aniello Pappalardo
PURPOSE: Risk stratification is of utmost importance for patients with infective endocarditis (IE) who need surgery. However, for these critically ill patients, aspecific scoring systems are used to predict the risk of death after surgery. The aim of this study was both to analyze the risk factors for in-hospital death, which complicates surgery for IE and to create a mortality risk score based on the results of this analysis. METHODS: Outcomes of 138 consecutive patients (mean age 60...
January 4, 2017: Infection
https://www.readbyqxmd.com/read/28052783/statistical-tests-of-differential-susceptibility-performance-limitations-and-improvements
#15
Marco Del Giudice
Statistical tests of differential susceptibility have become standard in the empirical literature, and are routinely used to adjudicate between alternative developmental hypotheses. However, their performance and limitations have never been systematically investigated. In this paper I employ Monte Carlo simulations to explore the functioning of three commonly used tests proposed by Roisman et al. (2012). Simulations showed that critical tests of differential susceptibility require considerably larger samples than standard power calculations would suggest...
January 5, 2017: Development and Psychopathology
https://www.readbyqxmd.com/read/28048739/tu-ab-207a-03-image-quality-dose-and-clinical-applications
#16
F Dong
: Practicing medical physicists are often time charged with the tasks of evaluating and troubleshooting complex image quality issues related to CT scanners. This course will equip them with a solid and practical understanding of common CT imaging chain and its major components with emphasis on acquisition physics and hardware, reconstruction, artifacts, image quality, dose, and advanced clinical applications. The core objective is to explain the effects of these major system components on the image quality...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048020/tu-ab-207a-00-ct-systems-course
#17
Baojun Li
: Practicing medical physicists are often time charged with the tasks of evaluating and troubleshooting complex image quality issues related to CT scanners. This course will equip them with a solid and practical understanding of common CT imaging chain and its major components with emphasis on acquisition physics and hardware, reconstruction, artifacts, image quality, dose, and advanced clinical applications. The core objective is to explain the effects of these major system components on the image quality...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047355/tu-ab-207a-01-image-acquisition-physics-and-hardware
#18
B Li
: Practicing medical physicists are often time charged with the tasks of evaluating and troubleshooting complex image quality issues related to CT scanners. This course will equip them with a solid and practical understanding of common CT imaging chain and its major components with emphasis on acquisition physics and hardware, reconstruction, artifacts, image quality, dose, and advanced clinical applications. The core objective is to explain the effects of these major system components on the image quality...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047308/tu-ab-brc-09-fast-dose-averaged-let-and-biological-dose-calculations-for-proton-therapy-using-graphics-cards
#19
H Wan, Chan Tseung, C Beltran
PURPOSE: To demonstrate fast and accurate Monte Carlo (MC) calculations of proton dose-averaged linear energy transfer (LETd) and biological dose (BD) on a Graphics Processing Unit (GPU) card. METHODS: A previously validated GPU-based MC simulation of proton transport was used to rapidly generate LETd distributions for proton treatment plans. Since this MC handles proton-nuclei interactions on an event-by-event using a Bertini intranuclear cascade-evaporation model, secondary protons were taken into account...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046685/tu-ab-207a-02-image-reconstruction-and-artifact-reduction
#20
J Hsieh
: Practicing medical physicists are often time charged with the tasks of evaluating and troubleshooting complex image quality issues related to CT scanners. This course will equip them with a solid and practical understanding of common CT imaging chain and its major components with emphasis on acquisition physics and hardware, reconstruction, artifacts, image quality, dose, and advanced clinical applications. The core objective is to explain the effects of these major system components on the image quality...
June 2016: Medical Physics
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