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https://www.readbyqxmd.com/read/28437479/conformational-dynamics-of-bacterial-trigger-factor-in-apo-and-ribosome-bound-states
#1
Mehmet Tarik Can, Zeynep Kurkcuoglu, Gokce Ezeroglu, Arzu Uyar, Ozge Kurkcuoglu, Pemra Doruker
The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and chloroplasts. In this study, we aim to investigate the functional dynamics of fully-atomistic apo TF and its complex with 50S. As TF accomodates a high percentage of charged residues on its surface, the effect of ionic strength on TF dynamics is assessed here by performing five independent molecular dynamics (MD) simulations (total of 1.3 micro-second duration) at 29 mM and 150 mM ionic strengths...
2017: PloS One
https://www.readbyqxmd.com/read/28435505/inter-rater-agreement-of-end-of-shift-evaluations-based-on-a-single-encounter
#2
Steven Warrington, Michael Beeson, Amber Bradford
INTRODUCTION: End-of-shift evaluation (ESE) forms, also known as daily encounter cards, represent a subset of encounter-based assessment forms. Encounter cards have become prevalent for formative evaluation, with some suggesting a potential for summative evaluation. Our objective was to evaluate the inter-rater agreement of ESE forms using a single scripted encounter at a conference of emergency medicine (EM) educators. METHODS: Following institutional review board exemption, we created a scripted video simulating an encounter between an intern and a patient with an ankle injury...
April 2017: Western Journal of Emergency Medicine
https://www.readbyqxmd.com/read/28432786/the-comprehensive-connectome-of-a-neural-substrate-for-on-motion-detection-in-drosophila
#3
Shin-Ya Takemura, Aljoscha Nern, Dmitri B Chklovskii, Louis K Scheffer, Gerald M Rubin, Ian A Meinertzhagen
Analysing computations in neural circuits often uses simplified models because the actual neuronal implementation is not known. For example, a problem in vision, how the eye detects image motion, has long been analysed using Hassenstein-Reichardt (HR) detector or Barlow-Levick (BL) models. These both simulate motion detection well, but the exact neuronal circuits undertaking these tasks remain elusive. We reconstructed a comprehensive connectome of the circuits of Drosophila's motion-sensing T4 cells using a novel EM technique...
April 22, 2017: ELife
https://www.readbyqxmd.com/read/28431087/a-method-for-learning-a-sparse-classifier-in-the-presence-of-missing-data-for-high-dimensional-biological-datasets
#4
Kristen Severson, Brinda Monian, J Christopher Love, Richard D Braatz
Motivation: This work addresses two common issues in building classification models for biological or medical studies: learning a sparse model, where only a subset of a large number of possible predictors is used, and training in the presence of missing data. This work focuses on supervised generative binary classification models, specifically linear discriminant analysis (LDA). The parameters are determined using an expectation maximization algorithm to both address missing data and introduce priors to promote sparsity...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28407218/incorporating-covariates-into-integrated-factor-analysis-of-multi-view-data
#5
Gen Li, Sungkyu Jung
In modern biomedical research, it is ubiquitous to have multiple data sets measured on the same set of samples from different views (i.e., multi-view data). For example, in genetic studies, multiple genomic data sets at different molecular levels or from different cell types are measured for a common set of individuals to investigate genetic regulation. Integration and reduction of multi-view data have the potential to leverage information in different data sets, and to reduce the magnitude and complexity of data for further statistical analysis and interpretation...
April 13, 2017: Biometrics
https://www.readbyqxmd.com/read/28403371/development-of-a-theoretical-practical-script-for-clinical-simulation
#6
Renata Paula Fabri, Alessandra Mazzo, José Carlos Amado Martins, Ariadne da Silva Fonseca, César Eduardo Pedersoli, Fernanda Berchelli Girão Miranda, Laís Fumincelli, Rui Carlos Negrão Baptista
OBJECTIVE: To develop a theoretical-practical script based on the opinion of experts to be used in simulated clinical activities. METHOD: Qualitative study through analysis of content of interviews with experts on the theme in order to develop the proposed script. Of the 24 invited experts, 12 specialists from educational institutions in Brazil and abroad participated in the study in compliance with the ethical precepts. The experts responded to questions on the characterization of their study attributes and described the items required for the development of a simulated scenario...
April 10, 2017: Revista da Escola de Enfermagem da U S P
https://www.readbyqxmd.com/read/28380783/vectorial-eigenvector-method-for-simulating-the-polarization-dependent-resonator
#7
Youyou Hu, Xiaofeng He, Sisi Liu, Xiahui Tang, Bo Li
Derived from the eigenvector method (EM), a vectorial eigenvector method (VEM) for the mode calculation of polarization dependent resonator is presented. New transfer matrices of laser resonant cavities with polarization-selective devices are built by using Jones matrix representation. The eigenvectors computed by solving the matrix eigenequation manifest the mode characteristics of resonators, including cylindrical vector (CV) modes. Comparing with EM, the VEM inherits EM's superiorities and extends scalar models to vector models...
March 6, 2017: Optics Express
https://www.readbyqxmd.com/read/28370077/flexible-fitting-to-cryo-em-density-map-using-ensemble-molecular-dynamics-simulations
#8
Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama
Flexible fitting is a computational algorithm to derive a new conformational model that conforms to low-resolution experimental data by transforming a known structure. A common application is against data from cryo-electron microscopy to obtain conformational models in new functional states. The conventional flexible fitting algorithms cannot derive correct structures in some cases due to the complexity of conformational transitions. In this study, we show the importance of conformational ensemble in the refinement process by performing multiple fittings trials using a variety of different force constants...
April 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28367256/investigating-differences-in-brain-functional-networks-using-hierarchical-covariate-adjusted-independent-component-analysis
#9
Ran Shi, Ying Guo
Human brains perform tasks via complex functional networks consisting of separated brain regions. A popular approach to characterize brain functional networks in fMRI studies is independent component analysis (ICA), which is a powerful method to reconstruct latent source signals from their linear mixtures. In many fMRI studies, an important goal is to investigate how brain functional networks change according to specific clinical and demographic variabilities. Existing ICA methods, however, cannot directly incorporate covariate effects in ICA decomposition...
December 2016: Annals of Applied Statistics
https://www.readbyqxmd.com/read/28344722/assessment-of-emergency-medicine-residents-a-systematic-review
#10
REVIEW
Isabelle N Colmers-Gray, Kieran Walsh, Teresa M Chan
BACKGROUND: Competency-based medical education is becoming the new standard for residency programs, including Emergency Medicine (EM). To inform programmatic restructuring, guide resources and identify gaps in publication, we reviewed the published literature on types and frequency of resident assessment. METHODS: We searched MEDLINE, EMBASE, PsycInfo and ERIC from Jan 2005 - June 2014. MeSH terms included "assessment," "residency," and "emergency medicine." We included studies on EM residents reporting either of two primary outcomes: 1) assessment type and 2) assessment frequency per resident...
February 2017: Canadian Medical Education Journal
https://www.readbyqxmd.com/read/28336911/2d-hybrid-analysis-approach-for-building-three-dimensional-atomic-model-by-electron-microscopy-image-matching
#11
Atsushi Matsumoto, Naoyuki Miyazaki, Junichi Takagi, Kenji Iwasaki
In this study, we develop an approach termed "2D hybrid analysis" for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334132/maximum-likelihood-estimation-and-em-algorithm-of-copas-like-selection-model-for-publication-bias-correction
#12
Jing Ning, Yong Chen, Jin Piao
Publication bias occurs when the published research results are systematically unrepresentative of the population of studies that have been conducted, and is a potential threat to meaningful meta-analysis. The Copas selection model provides a flexible framework for correcting estimates and offers considerable insight into the publication bias. However, maximizing the observed likelihood under the Copas selection model is challenging because the observed data contain very little information on the latent variable...
February 25, 2017: Biostatistics
https://www.readbyqxmd.com/read/28332159/electromagnetically-tracked-personalized-templates-for-surgical-navigation
#13
Andrew W L Dickinson, Michelle L Zec, David R Pichora, Brian J Rasquinha, Randy E Ellis
PURPOSE: An electromagnetic (EM) surgical tracking system was developed for orthopedic navigation. The reportedly poor accuracy of point-based EM navigation was improved by using anatomical impressions, which were EM-tracked personalized templates. Lines, rather than points, were consistently used for calibration and error evaluation. METHODS: Technical accuracy was tested using models derived from CT scans of ten cadaver shoulders. Tracked impressions were first designed, calibrated, and tested using lines as fiducial objects...
March 22, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28322338/flexible-frequency-selective-metamaterials-for-microwave-applications
#14
Bo Gao, Matthew M F Yuen, Terry Tao Ye
Metamaterials have attracted more and more research attentions recently. Metamaterials for electromagnetic applications consist of sub-wavelength structures designed to exhibit particular responses to an incident EM (electromagnetic) wave. Traditional EM (electromagnetic) metamaterial is constructed from thick and rigid structures, with the form-factor suitable for applications only in higher frequencies (above GHz) in microwave band. In this paper, we developed a thin and flexible metamaterial structure with small-scale unit cell that gives EM metamaterials far greater flexibility in numerous applications...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28304348/an-em-induction-hi-speed-rotation-angular-rate-sensor
#15
Kai Li, Yuan Li, Yan Han
A hi-speed rotation angular rate sensor based on an electromagnetic induction signal is proposed to provide a possibility of wide range measurement of high angular rates. An angular rate sensor is designed that works on the principle of electromagnetism (EM) induction. In addition to a zero-phase detection technique, this sensor uses the feedback principle of magnetic induction coils in response to a rotating magnetic field. It solves the challenge of designing an angular rate sensor that is suitable for both low and high rotating rates...
March 17, 2017: Sensors
https://www.readbyqxmd.com/read/28302724/genetically-introduced-hydrogen-bond-interactions-reveal-an-asymmetric-charge-distribution-on-the-radical-cation-of-the-special-pair-chlorophyll-p680
#16
Ryo Nagao, Motoki Yamaguchi, Shin Nakamura, Hanayo Ueoka-Nakanishi, Takumi Noguchi
The special-pair chlorophyll (Chl) P680 in photosystem II has an extremely high redox potential (Em) to enable water oxidation in photosynthesis. Significant positive charge localization on one of the Chl constituents, PD1 or PD2, in P680(+) has been proposed to contribute to this high Em To identify the Chl molecule on which the charge is mainly localized, we genetically introduced a hydrogen bond to the 13(1)-keto C=O group of PD1 and PD2 by changing the nearby D1-V157 and D2-V156 residues to His, respectively...
March 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28288152/patient-specific-modeling-of-individual-sickle-cell-behavior-under-transient-hypoxia
#17
Xuejin Li, E Du, Ming Dao, Subra Suresh, George Em Karniadakis
Sickle cell disease (SCD) is a highly complex genetic blood disorder in which red blood cells (RBC) exhibit heterogeneous morphology changes and decreased deformability. We employ a kinetic model for cell morphological sickling that invokes parameters derived from patient-specific data. This model is used to investigate the dynamics of individual sickle cells in a capillary-like microenvironment in order to address various mechanisms associated with SCD. We show that all RBCs, both hypoxia-unaffected and hypoxia-affected ones, regularly pass through microgates under oxygenated state...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28281878/joint-modeling-of-time-to-recurrence-and-cancer-stage-at-recurrence-in-oncology-trials
#18
Olga Marchenko, Alex Tsodikov, Robert Keener, Natallia Katenka, Yngvil Kloster Thomas
This research was motivated by a clinical trial with bladder cancer patients who went through a surgery and were followed up for cancer recurrence. One of the main objectives of the trial was to evaluate the time to cancer recurrence in patients in control and experimental groups. At the time of recurrence, the disease stage was also evaluated. Because the stage of cancer at recurrence significantly impacts future treatment and patient prognosis of survival, analyzing the time to cancer recurrence and the stage at recurrence jointly provides more clinically relevant information than analyzing the time to recurrence alone...
2017: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/28269677/radio-frequency-induced-heating-of-an-insulated-wire-during-magnetic-resonance-imaging
#19
Mikhail Kozlov, Gregor Schaefers
Radio frequency (RF) induced power deposition near straight insulated leads excited by different incident electrical field profiles was investigated. 3-D electromagnetic (EM) simulations were used to obtain implant models as well as RF-induced power depositions calculated as the integral of power loss density. For the investigated setups up to 400% discrepancy between the implant model predictions and EM simulation values was observed.
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28269599/simultaneous-reconstruction-and-segmentation-with-the-mumford-shah-functional-for-electron-tomography
#20
Li Shen, Eric Todd Quinto, Shiqiang Wang, Ming Jiang
Electron micrography (EM) is an important method for determining the three-dimensional (3D) structure of macromolecular complexes and biological specimens. But there are several limitations such as poor signal-to-noise, limitation on range of tilt angles and sub-region subject to electron exposure, unintentional movements of the specimen, with EM systems that make the reconstruction procedure a severely ill-posed problem. A different choice of reconstruction method may lead to different results and create different additional artifacts in reconstructed images...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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