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https://www.readbyqxmd.com/read/28088843/evaluating-surrogate-marker-information-using-censored-data
#1
Layla Parast, Tianxi Cai, Lu Tian
Given the long follow-up periods that are often required for treatment or intervention studies, the potential to use surrogate markers to decrease the required follow-up time is a very attractive goal. However, previous studies have shown that using inadequate markers or making inappropriate assumptions about the relationship between the primary outcome and surrogate marker can lead to inaccurate conclusions regarding the treatment effect. Currently available methods for identifying and validating surrogate markers tend to rely on restrictive model assumptions and/or focus on uncensored outcomes...
January 15, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28088842/unbiased-split-variable-selection-for-random-survival-forests-using-maximally-selected-rank-statistics
#2
Marvin N Wright, Theresa Dankowski, Andreas Ziegler
The most popular approach for analyzing survival data is the Cox regression model. The Cox model may, however, be misspecified, and its proportionality assumption may not always be fulfilled. An alternative approach for survival prediction is random forests for survival outcomes. The standard split criterion for random survival forests is the log-rank test statistic, which favors splitting variables with many possible split points. Conditional inference forests avoid this split variable selection bias. However, linear rank statistics are utilized by default in conditional inference forests to select the optimal splitting variable, which cannot detect non-linear effects in the independent variables...
January 15, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28088840/evaluation-of-a-short-term-training-program-in-bedside-emergency-ultrasound-in-southwestern-tanzania
#3
Mark Shaffer, Heather A Brown, Chloé McCoy, Prosper Bashaka
OBJECTIVES: To evaluate the effect of a short-term training program in emergency ultrasound on physician skills and attitudes in southwestern Tanzania. METHODS: Eight registrar physicians at Mbeya Zonal Referral Hospital (Mbeya, Tanzania) underwent a 5-day course in bedside emergency ultrasound, focusing primarily on the focused assessment with sonography for trauma examination, including didactic sessions, practical sessions, and on-job training. The impact on ultrasound knowledge was assessed by pretest and posttest evaluations...
January 15, 2017: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/28088759/how-accurate-are-accurate-force-fields-for-b-dna
#4
Pablo D Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco
Last generation of force-fields are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as to the belief that theoretical models can substitute experimental ones in several cases. However these claims are based on limited benchmarks, where MD simulations have shown the ability to reproduce already existing 'experimental models', which in turn, have an unclear accuracy to represent DNA conformation in solution. In this work we explore the ability of different force-fields to predict the structure of two new B-DNA dodecamers, determined herein by means of (1)H nuclear magnetic resonance (NMR)...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28088651/limitations-in-biexponential-fitting-of-nmr-inversion-recovery-curves
#5
Mohammed Salman Shazeeb, Christopher H Sotak
NMR relaxation agents have long been employed as contrast agents in MRI. In many cases, the contrast agent is confined to either (i) the vascular and/or extracellular compartment (EC), as is the case with gadolinium(III)-based agents, or (ii) the intracellular compartment (IC), as is the case with manganese(II) ions. The compartmentalization of contrast agents often results in tissue-water (1)H relaxation profiles that are well modeled as biexponential. It has long been recognized that water exchange between compartments modifies the biexponential relaxation parameters (amplitudes and rate constants) from those that would be found in the absence of exchange...
January 6, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28088643/molecular-mechanisms-of-bio-catalysis-of-heme-extraction-from-hemoglobin
#6
Serzhan Sakipov, Olga Rafikova, Maria G Kurnikova, Ruslan Rafikov
Red blood cell hemolysis in sickle cell disease (SCD) releases free hemoglobin. Extracellular hemoglobin and its degradation products, free heme and iron, are highly toxic due to oxidative stress induction and decrease in nitric oxide availability. We propose an approach that helps to eliminate extracellular hemoglobin toxicity in SCD by employing a bacterial protein system that evolved to extract heme from extracellular hemoglobin. NEAr heme Transporter (NEAT) domains from iron-regulated surface determinant proteins from Staphylococcus aureus specifically bind free heme as well as facilitate its extraction from hemoglobin...
January 7, 2017: Redox Biology
https://www.readbyqxmd.com/read/28088633/quantitative-analysis-of-lab-to-lab-variability-in-caco-2-permeability-assays
#7
Jong Bong Lee, Atheer Zgair, Dhiaa A Taha, Xiaowei Zang, Leonid Kagan, Tae Hwan Kim, Min Gi Kim, Hwi-Yeol Yun, Peter M Fischer, Pavel Gershkovich
In this study, Caco-2 permeability results from different laboratories were compared. Six different sets of apparent permeability coefficient (Papp) values reported in the literature were compared to experimental Papp obtained in our laboratory. The differences were assessed by determining the root mean square error (RMSE) values between the datasets, which reached levels as high as 0.581 for the training set compounds, i.e. ten compounds with known effective human permeability (Peff). The consequences of these differences in Papp for prediction of oral drug absorption were demonstrated by introducing the Papp into the absorption and pharmacokinetics simulation software application GastroPlus(TM) for prediction of the fraction absorbed (Fa) in humans using calibrated "user-defined permeability models"...
January 11, 2017: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/28088594/the-number-of-primary-events-per-variable-affects-estimation-of-the-subdistribution-hazard-competing-risks-model
#8
Peter C Austin, Arthur Allignol, Jason P Fine
OBJECTIVE: To examine the effect of the number of events per variable (EPV) on the accuracy of estimated regression coefficients, standard errors, empirical coverage rates of estimated confidence intervals and empirical estimates of statistical power when using the Fine-Gray subdistribution hazard regression model to assess the effect of covariates on the incidence of events that occur over time in the presence of competing risks. STUDY DESIGN AND SETTING: Monte Carlo simulations were used...
January 11, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28088591/specific-agreement-on-dichotomous-outcomes-in-the-situation-of-more-than-two-raters
#9
Henrica C W de Vet, Rieky E Dikmans, Iris Eekhout
OBJECTIVE: For assessing inter-rater agreement the concepts of observed agreement and specific agreement have been proposed. The situation of two raters and dichotomous outcomes has been described, whereas often times multiple raters are involved. We aim to extend it for more than two raters and examine how to calculate agreement estimates and 95% confidence intervals (CIs). STUDY DESIGN AND SETTING: As an illustration we used a reliability study that includes the scores of 4 plastic surgeons classifying photographs of breasts of 50 women, after breast reconstruction into 'satisfied' or 'not satisfied'...
January 11, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28088576/lid-domain-plasticity-and-lipid-flexibility-modulate-enzyme-specificity-in-human-monoacylglycerol-lipase
#10
Laura Riccardi, Jose M Arencibia, Luca Bono, Andrea Armirotti, Stefania Girotto, Marco De Vivo
Human monoacylglycerol lipase (MAGL) is a membrane-interacting enzyme that generates pro-inflammatory signaling molecules. For this reason, MAGL inhibition is a promising strategy to treat pain, cancer, and neuroinflammatory diseases. MAGL can hydrolyze monoacylglycerols bearing an acyl chain of different lengths and degrees of unsaturation, cleaving primarily the endocannabinoid 2-arachidonoylglycerol. Importantly, the enzymatic binding site of MAGL is confined by a 75-amino-acid-long, flexible cap domain, named 'lid domain', which is structurally similar to that found in several other lipases...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088574/time-dependence-of-the-enhancement-effect-of-chemical-enhancers-molecular-mechanisms-of-enhancing-kinetics
#11
Xiaochang Liu, Peng Quan, Shanshan Li, Chao Liu, Yuan Zhao, Yongshan Zhao, Liang Fang
Chemical enhancers are widely used for facilitating drug penetration in transdermal drug delivery system (TDDS). However, there is a lack of knowledge about how the enhancement effect changes over time. In this study, on the basis of kinetic parameters of enhancement effect, molecular details of the dynamic enhancement process was described and a new hypothesis of the recovery mechanism of the skin barrier function was proposed. Using pretreated skin and flurbiprofen patch, the effects of Azone (AZ) and menthol decanoate (MT-10) were evaluated with in vitro permeation experiment and further confirmed by confocal laser scanning microscopy (CLSM) and TEWL...
January 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28088403/ginkgo-fruit-extract-as-an-additive-to-modify-rumen-microbiota-and-fermentation-and-to-mitigate-methane-production
#12
S Oh, R Shintani, S Koike, Y Kobayashi
Ginkgo fruit, an unused byproduct of the ginkgo nut industry, contains antimicrobial compounds known as anacardic acids. Two major cultivars of ginkgo, Kyuju (K) and Tokuro (T), were evaluated for their potential as a feed additive for ruminants. In batch culture, we incubated a mixture of hay and concentrate in diluted rumen fluid with or without 1.6% (fruit equivalent) ginkgo fruit extract. We conducted another series of batch culture studies to determine the dose response of fermentation. We also conducted continuous culture using the rumen simulation technique (RUSITEC) with cultivar K and carried out a pure culture study to monitor the sensitivity of 17 representative rumen bacterial species to ginkgo extract and component phenolics...
January 11, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28088371/a-quality-by-design-qbd-study-on-enoxaparin-sodium-loaded-polymeric-microspheres-for-colon-specific-delivery
#13
Dana Hales, Laurian Vlase, Sebastian Alin Porav, Andreea Bodoki, Lucian Barbu-Tudoran, Marcela Achim, Ioan Tomuță
The aim of this study was to apply quality by design (QbD) for pharmaceutical development of enoxaparin sodium microspheres for colon-specific delivery. The Process Parameters (CPPs) and Critical Quality Attributes (CQAs) were identified. A central composite experimental design was used in order to develop the design space of microspheres for colon-specific delivery that have the desired Quality Target Product Profile (QTPP). The CPPs studied were Eudragit® FS-30D/Eudragit® RS-PO ratio, poly(vinyl alcohol) (PVA) concentration and sodium chloride (NaCl) concentration...
January 11, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28088357/joint-genome-wide-prediction-in-several-populations-accounting-for-randomness-of-genotypes-a-hierarchical-bayes-approach-ii-multivariate-spike-and-slab-priors-for-marker-effects-and-derivation-of-approximate-bayes-and-fractional-bayes-factors-for-the-complete
#14
Carlos Alberto Martínez, Kshitij Khare, Arunava Banerjee, Mauricio A Elzo
This study corresponds to the second part of a companion paper devoted to the development of Bayesian multiple regression models accounting for randomness of genotypes in across population genome-wide prediction. This family of models considers heterogeneous and correlated marker effects and allelic frequencies across populations, and has the ability of considering records from non-genotyped individuals and individuals with missing genotypes in any subset of loci without the need for previous imputation, taking into account uncertainty about imputed genotypes...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28088325/molecular-dynamics-simulations-of-ternary-lipid-bilayers-containing-plant-sterol-and-glucosylceramide
#15
Shiva Emami, Sodeif Azadmard-Damirchi, Seyed Hadi Peighambardoust, Javad Hesari, Hadi Valizadeh, Roland Faller
An atomic-level molecular dynamics simulation was carried out to study the effects of a plant sterol (sitosterol) and glucosylceramide (GlcCer) on a 1,2-dilinoleoylposphocholine (DLiPC) membrane. Initially, a membrane containing 50mol % sitosterol was compared with that containing the same ratio of cholesterol. These simulations showed differential condensing and ordering effects of sitosterol and cholesterol, with cholesterol being slightly more efficient than sitosterol in packing the membrane more tightly to a liquid ordered phase...
January 11, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/28088300/cytoplasmic-rna-protein-particles-exhibit-non-gaussian-subdiffusive-behavior
#16
Thomas J Lampo, Stella Stylianidou, Mikael P Backlund, Paul A Wiggins, Andrew J Spakowitz
The cellular cytoplasm is a complex, heterogeneous environment (both spatially and temporally) that exhibits viscoelastic behavior. To further develop our quantitative insight into cellular transport, we analyze data sets of mRNA molecules fluorescently labeled with MS2-GFP tracked in real time in live Escherichia coli and Saccharomyces cerevisiae cells. As shown previously, these RNA-protein particles exhibit subdiffusive behavior that is viscoelastic in its origin. Examining the ensemble of particle displacements reveals a Laplace distribution at all observed timescales rather than the Gaussian distribution predicted by the central limit theorem...
January 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28088170/application-of-a-bayesian-dominance-model-improves-power-in-quantitative-trait-genome-wide-association-analysis
#17
Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H E Meuwissen, Robin Wellmann
BACKGROUND: Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset...
January 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28088161/efficient-free-energy-calculations-by-combining-two-complementary-tempering-sampling-methods
#18
Liangxu Xie, Lin Shen, Zhe-Ning Chen, Mingjun Yang
Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088151/phase-transition-of-a-symmetric-diblock-copolymer-induced-by-nanorods-with-different-surface-chemistry
#19
Yu-Qi Guo, Jun-Xing Pan, Min-Na Sun, Jin-Jun Zhang
We investigate the phase transition of a symmetric diblock copolymer induced by nanorods with different surface chemistry. The results demonstrate that the system occurs the phase transition from a disordered structure to ordered parallel lamellae and then to the tilted layered structure as the number of rods increases. The dynamic evolution of the domain size and the order parameter of the microstructure are also examined. Furthermore, the influence of rod property, rod-phase interaction, rod-rod interaction, rod length, and polymerization degree on the behavior of the polymer system is also investigated systematically...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088150/optimal-orientation-of-an-asymmetric-top-molecule-with-terahertz-pulses
#20
L H Coudert
Terahertz pulses effects are investigated in an asymmetric top C2v molecule using numerical simulations. The average value of the direction cosine ΦZx is computed solving the time dependent Schrödinger equation for several types of pulses. The H2S molecule taken as a test case is first subject to two short terahertz pulses with a duration smaller than 5 ps, an identical maximum value of the electric field of 2 MV/cm, but a different shape. The thermal average ⟨⟨ΦZx⟩⟩ is calculated for several temperatures, and non-periodic time variations are found even for the lowest temperature...
January 14, 2017: Journal of Chemical Physics
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