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https://www.readbyqxmd.com/read/28733595/how-cholesteryl-ester-transfer-protein-can-also-be-a-potential-triglyceride-transporter
#1
Venkat R Chirasani, Sanjib Senapati
CETP transfers cholesteryl esters (CEs) and triglycerides (TGs) between different lipoproteins and came in limelight as a drug-target against CVD. In the search for detailed mechanism of lipid transfer through CETP, enormous effort is devoted employing crystallographic, cryo-EM, and Molecular Dynamics (MD) studies. However, these studies primarily focused on CE-bound CETP structure and CE transfer mechanism. With the reported correlation that CETP looses significant CE transfer activity upon inhibiting TG transfer, it is of tremendous importance to understand the structure and dynamics of TG-bound CETP...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28731828/geographical-variation-in-community-divergence-insights-from-tropical-forest-monodominance-by-ectomycorrhizal-trees
#2
Tadashi Fukami, Mifuyu Nakajima, Claire Fortunel, Paul V A Fine, Christopher Baraloto, Sabrina E Russo, Kabir G Peay
Convergence occurs in both species traits and community structure, but how convergence at the two scales influences each other remains unclear. To address this question, we focus on tropical forest monodominance, in which a single, often ectomycorrhizal (EM) tree species occasionally dominates forest stands within a landscape otherwise characterized by diverse communities of arbuscular mycorrhizal (AM) trees. Such monodominance is a striking potential example of community divergence resulting in alternative stable states...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28728147/efficient-maximum-likelihood-estimation-for-pedigree-data-with-the-sum-product-algorithm
#3
Alexander Engelhardt, Anna Rieger, Achim Tresch, Ulrich Mansmann
OBJECTIVE: We analyze data sets consisting of pedigrees with age at onset of colorectal cancer (CRC) as phenotype. The occurrence of familial clusters of CRC suggests the existence of a latent, inheritable risk factor. We aimed to compute the probability of a family possessing this risk factor as well as the hazard rate increase for these risk factor carriers. Due to the inheritability of this risk factor, the estimation necessitates a costly marginalization of the likelihood. METHODS: We propose an improved EM algorithm by applying factor graphs and the sum-product algorithm in the E-step...
July 21, 2017: Human Heredity
https://www.readbyqxmd.com/read/28704285/cricothyroidotomy-in-situ-simulation-curriculum-cric-study-training-residents-for-rare-procedures
#4
Andrew Petrosoniak, Agnes Ryzynski, Gerald Lebovic, Karen Woolfrey
INTRODUCTION: Technical skill acquisition for rare procedures can be challenging given the few real-life training opportunities. In situ simulation (ISS), a training technique that takes place in the actual workplace, is a promising method to promote environmental fidelity for rare procedures. This study evaluated a simulation-based technical skill curriculum for cricothyroidotomy using deliberate practice, followed by an ISS evaluation session. METHODS: Twenty emergency medicine residents participated in a two-part curriculum to improve cricothryoidotomy performance...
April 2017: Simulation in Healthcare: Journal of the Society for Simulation in Healthcare
https://www.readbyqxmd.com/read/28700924/mesoscopic-adaptive-resolution-scheme-toward-understanding-of-interactions-between-sickle-cell-fibers
#5
Lu Lu, He Li, Xin Bian, Xuejin Li, George Em Karniadakis
Understanding of intracellular polymerization of sickle hemoglobin (HbS) and subsequent interaction with the membrane of a red blood cell (RBC) is important to predict the altered morphologies and mechanical properties of sickle RBCs in sickle cell anemia. However, modeling the integrated processes of HbS nucleation, polymerization, HbS fiber interaction, and subsequent distortion of RBCs is challenging as they occur at multispatial scales, ranging from nanometers to micrometers. To make progress toward simulating the integrated processes, we propose a hybrid HbS fiber model, which couples fine-grained and coarse-grained HbS fiber models through a mesoscopic adaptive resolution scheme (MARS)...
July 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28699975/the-expected-cardiovascular-benefit-of-plasma-cholesterol-lowering-with-or-without-ldl-c-targets-in-healthy-individuals-at-higher-cardiovascular-risk
#6
Fernando Henpin Yue Cesena, Antonio Gabriele Laurinavicius, Viviane A Valente, Raquel D Conceição, Raul D Santos, Marcio S Bittencourt
Background: There is controversy whether management of blood cholesterol should be based or not on LDL-cholesterol (LDL-c) target concentrations. Objectives: To compare the estimated impact of different lipid-lowering strategies, based or not on LDL-c targets, on the risk of major cardiovascular events in a population with higher cardiovascular risk. Methods: We included consecutive individuals undergoing a routine health screening in a single center who had a 10-year risk for atherosclerotic cardiovascular disease (ASCVD) ≥ 7...
June 2017: Arquivos Brasileiros de Cardiologia
https://www.readbyqxmd.com/read/28693507/estimating-parameters-for-probabilistic-linkage-of-privacy-preserved-datasets
#7
Adrian P Brown, Sean M Randall, Anna M Ferrante, James B Semmens, James H Boyd
BACKGROUND: Probabilistic record linkage is a process used to bring together person-based records from within the same dataset (de-duplication) or from disparate datasets using pairwise comparisons and matching probabilities. The linkage strategy and associated match probabilities are often estimated through investigations into data quality and manual inspection. However, as privacy-preserved datasets comprise encrypted data, such methods are not possible. In this paper, we present a method for estimating the probabilities and threshold values for probabilistic privacy-preserved record linkage using Bloom filters...
July 10, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28660954/electromagnetic-theories-of-surface-enhanced-raman-spectroscopy
#8
REVIEW
Song-Yuan Ding, En-Ming You, Zhong-Qun Tian, Martin Moskovits
Surface-enhanced Raman spectroscopy (SERS) and related spectroscopies are powered primarily by the concentration of the electromagnetic (EM) fields associated with light in or near appropriately nanostructured electrically-conducting materials, most prominently, but not exclusively high-conductivity metals such as silver and gold. This field concentration takes place on account of the excitation of surface-plasmon (SP) resonances in the nanostructured conductor. Optimizing nanostructures for SERS, therefore, implies optimizing the ability of plasmonic nanostructures to concentrate EM optical fields at locations where molecules of interest reside, and to enhance the radiation efficiency of the oscillating dipoles associated with these molecules and nanostructures...
June 29, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28660223/development-and-evaluation-of-image-reconstruction-algorithms-for-a-novel-desktop-spect-system
#9
Navid Zeraatkar, Arman Rahmim, Saeed Sarkar, Mohammad Reza Ay
OBJECTIVE S: Various iterative reconstruction algorithms in nuclear medicine have been introduced in the last three decades. For each new imaging system, it is wise to select appropriate image reconstruction algorithms and evaluate their performance. In this study, three approaches of image reconstruction were developed for a novel desktop open-gantry SPECT system, PERSPECT, to assess their performance in terms of the quality of the resultant reconstructed images. METHODS: In the present work, a proposed image reconstruction algorithm for the PERSPECT, referred to as quasi-simultaneous multiplicative algebraic reconstruction technique (qSMART), together with two popular image reconstruction methods, maximum-likelihood expectation-maximization (MLEM) and ordered-subsets EM (OSEM), were implemented and compared...
2017: Asia Oceania Journal of Nuclear Medicine & Biology
https://www.readbyqxmd.com/read/28657312/molecular-dynamics-flexible-fitting-simulations-identify-new-models-of-the-closed-state-of-the-cystic-fibrosis-transmembrane-conductance-regulator-protein
#10
Luba Simhaev, Nael A McCarty, Robert C Ford, Hanoch Senderowitz
Cystic fibrosis (CF) is a lethal, genetic disease found in particular in humans of European origin which is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel. The search for CF therapies acting by modulating the impaired function of mutant CFTR will be greatly advanced by high resolution structures of CFTR in different states. To date, two medium resolution electron microscopy (EM) structures of CFTR are available (one of a distant zebrafish (Danio rerio) CFTR ortholog and one of human CFTR)...
July 18, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28644798/joint-alignment-of-multiple-point-sets-with-batch-and-incremental-expectation-maximization
#11
Dimitrios Georgios Evangelidis, Radu Horaud
This paper addresses the problem of registering multiple point sets. Solutions to this problem are often approximated by repeatedly solving for pairwise registration, which results in an uneven treatment of the sets forming a pair: a model set and a data set. The main drawback of this strategy is that the model set may contain noise and outliers, which negatively affects the estimation of the registration parameters. In contrast, the proposed formulation treats all the point sets on an equal footing. Indeed, all the points are drawn from a central Gaussian mixture, hence the registration is cast into a clustering problem...
June 21, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28643694/simultaneous-maximum-a-i-posteriori-i-longitudinal-pet-image-reconstruction
#12
Sam Ellis, Andrew J Reader
Positron emission tomography (PET) is frequently used to monitor functional changes that occur over extended time scales, for example in longitudinal oncology PET protocols that include routine clinical follow-up scans to assess the efficacy of a course of treatment. In these contexts PET datasets are currently reconstructed into images using single-dataset reconstruction methods. Inspired by recently proposed joint PET-MR reconstruction methods, we propose to reconstruct longitudinal datasets simultaneously by using a joint penalty term in order to exploit the high degree of similarity between longitudinal images...
June 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28640808/transmembrane-helical-interactions-in-the-cftr-channel-pore
#13
Jhuma Das, Andrei A Aleksandrov, Liying Cui, Lihua He, John R Riordan, Nikolay V Dokholyan
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF). Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28638320/membrane-fusion-involved-in-neurotransmission-glimpse-from-electron-microscope-and-molecular-simulation
#14
REVIEW
Zhiwei Yang, Lu Gou, Shuyu Chen, Na Li, Shengli Zhang, Lei Zhang
Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28636906/flexible-fitting-of-atomic-models-into-cryo-em-density-maps-guided-by-helix-correspondences
#15
Hang Dou, Derek W Burrows, Matthew L Baker, Tao Ju
Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28631295/an-em-algorithm-for-nonparametric-estimation-of-the-cumulative-incidence-function-from-repeated-imperfect-test-results
#16
Birgit I Witte, Johannes Berkhof, Marianne A Jonker
In screening and surveillance studies, event times are interval censored. Besides, screening tests are imperfect so that the interval at which an event takes place may be uncertain. We describe an expectation-maximization algorithm to find the nonparametric maximum likelihood estimator of the cumulative incidence function of an event based on screening test data. Our algorithm has a closed-form solution for the combined expectation and maximization step and is computationally undemanding. A simulation study indicated that the bias of the estimator tends to zero for large sample size, and its mean squared error is in general lower than the mean squared error of the estimator that assumes the screening test is perfect...
June 20, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28630393/sample-size-re-estimation-without-un-blinding-for-time-to-event-outcomes-in-oncology-clinical-trials
#17
Huang Lihong, Bai Jianling, Yu Hao, Chen Feng
Sample size re-estimation is essential in oncology studies. However, the use of blinded sample size reassessment for survival data has been rarely reported. Based on the density function of the exponential distribution, an expectation-maximization (EM) algorithm of the hazard ratio was derived, and several simulation studies were used to verify its applications. The method had obvious variation in the hazard ratio estimates and overestimation for the relatively small hazard ratios. Our studies showed that the stability of the EM estimation results directly correlated with the sample size, the convergence of the EM algorithm was impacted by the initial values, and a balanced design produced the best estimates...
June 20, 2017: Journal of Biomedical Research
https://www.readbyqxmd.com/read/28623479/fast-calibration-of-electromagnetically-tracked-oblique-viewing-rigid-endoscopes
#18
Xinyang Liu, Christina E Rice, Raj Shekhar
PURPOSE: The oblique-viewing (i.e., angled) rigid endoscope is a commonly used tool in conventional endoscopic surgeries. The relative rotation between its two moveable parts, the telescope and the camera head, creates a rotation offset between the actual and the projection of an object in the camera image. A calibration method tailored to compensate such offset is needed. METHODS: We developed a fast calibration method for oblique-viewing rigid endoscopes suitable for clinical use...
June 16, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28610694/preconditioned-alternating-projection-algorithm-for-solving-the-penalized-likelihood-spect-reconstruction-problem
#19
Si Li, Jiahan Zhang, Andrzej Krol, C Ross Schmidtlein, David Feiglin, Yuesheng Xu
PURPOSE: The authors recently developed a preconditioned alternating projection algorithm (PAPA) for solving the penalized-likelihood SPECT reconstruction problem. The proposed algorithm can solve a wide variety of non-differentiable optimization models. This work is dedicated to comparing the performance of PAPA with total variation (TV) regularization (TV-PAPA) and a novel forward-backward algorithm with nested expectation maximization (EM)-TV iteration scheme (FB-EM-TV). METHODS: Monte Carlo technique was used to simulate multiple noise realizations of the fan-beam collimated SPECT data for a piecewise constant phantom with warm background, and hot and cold spheres with uniform activities at two noise levels...
June 2017: Physica Medica: PM
https://www.readbyqxmd.com/read/28607082/interface-induced-multiferroism-by-design-in-complex-oxide-superlattices
#20
Hangwen Guo, Zhen Wang, Shuai Dong, Saurabh Ghosh, Mohammad Saghayezhian, Lina Chen, Yakui Weng, Andreas Herklotz, Thomas Z Ward, Rongying Jin, Sokrates T Pantelides, Yimei Zhu, Jiandi Zhang, E W Plummer
Interfaces between materials present unique opportunities for the discovery of intriguing quantum phenomena. Here, we explore the possibility that, in the case of superlattices, if one of the layers is made ultrathin, unexpected properties can be induced between the two bracketing interfaces. We pursue this objective by combining advanced growth and characterization techniques with theoretical calculations. Using prototype La2/3Sr1/3MnO3 (LSMO)/BaTiO3 (BTO) superlattices, we observe a structural evolution in the LSMO layers as a function of thickness...
June 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
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