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Refinement validation structure

Lim Heo, Michael Feig
Summary: Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. Availability: PREFMD is freely available as a web server at http://feiglab...
November 8, 2017: Bioinformatics
Tobias Todsen
Surgeons are increasingly using ultrasonography (US) in their clinical management of patients. However, US is a very user-dependent imaging modality and proper skills of the US operator are needed to ensure quality in patient care. This thesis explores the validity evidence for assessment of competence in abdominal and head & neck ultrasonography using the Objective Structured Assessment of Ultrasound Skills (OSAUS) scale. With the use of Messick's unitary framework of validity, five sources of validity evidence were explored: test content, response processes, inter-nal structure, relations to other variables, and consequences...
November 2017: Danish Medical Journal
Elisabete Sónia Carmo Ferreira, Iuliia V Voroshylova, Volodymyr A Koverga, Carlos M Pereira, M Natalia Dias Soeiro Cordeiro
In this work we developed a new force field model (FFM) for propylene glycol (PG) based on the OPLS all-atom potential. The OPLS potential was refined using quantum chemical calculations, taking into account the densities and self-diffusion values. The validation of this new FFM was carried out based on a wide range of physicochemical properties, such as density, enthalpy of vaporization, self-diffusion coefficients, isothermal compressibility, surface tension and shear viscosity. The molecular dynamics (MD) simulations were performed over a large range of temperatures (293...
November 7, 2017: Journal of Physical Chemistry. B
Angela J Beck, Fátima Coronado, Matthew L Boulton, Jacqueline A Merrill
Public health workforce size and composition have been difficult to accurately determine because of the wide variety of methods used to define job title terms, occupational categories, and worker characteristics. In 2014, a preliminary consensus-based public health workforce taxonomy was published to standardize the manner in which workforce data are collected and analyzed by outlining uniform categories and terms. We summarize development of the taxonomy's 2017 iteration and provide guidelines for its implementation in public health workforce development efforts...
November 2, 2017: Journal of Public Health Management and Practice: JPHMP
Yingzhou Xie, Yiqing Wei, Yue Shen, Xiaobin Li, Hao Zhou, Cui Tai, Zixin Deng, Hong-Yu Ou
TADB2.0 ( is an updated database that provides comprehensive information about bacterial type II toxin-antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences...
November 2, 2017: Nucleic Acids Research
Sophie Cleanthous, Stefan Cano, Elizabeth Kinter, Patrick Marquis, Jennifer Petrillo, Xiaojun You, Craig Wakeford, Guido Sabatella
Background: Study objectives were to evaluate the Multiple Sclerosis Impact Scale (MSIS-29) and explore an optimized scoring structure based on empirical post-hoc analyses of data from the Phase III ADVANCE clinical trial. Methods: ADVANCE MSIS-29 data from six time-points were analyzed in a sample of patients with relapsing-remitting multiple sclerosis (RRMS). Rasch Measurement Theory (RMT) analysis was undertaken to examine three broad areas: sample-to-scale targeting, measurement scale properties, and sample measurement validity...
July 2017: Multiple Sclerosis Journal—Experimental, Translational and Clinical
Renfeng Wang, Liesbeth De Donder, Free De Backer, Tao He, Sofie Van Regenmortel, Shihua Li, Koen Lombaerts
This study describes the development and validation of the Elder Learning Barriers (ELB) scale, which seeks to identify the obstacles that affect the level of educational participation of older adults. The process of item pool design and scale development is presented, as well as the testing and scale refinement procedure. The data were collected from a sample of 579 older Chinese adults (aged over 55) in the Xi'an region of China. After randomly splitting the sample for cross-validation purposes, the construct validity of the ELB scale was confirmed containing five dimensions: dispositional, informational, physical, situational, and institutional barriers...
December 2017: International Journal of Aging & Human Development
Alana McEvoy, Maxwell B Sauder, Katherine McDonald, Phillipe Suter, Annie Pouliot, Roger Zemek, Nordau Kanigsberg, Regis Vaillancourt, Michele L Ramien
BACKGROUND: Current eczema action plans (EAP) are based on written instructions without illustrations. Incorporating validated illustrations into EAPs can significantly improve comprehension and usability. OBJECTIVE: To produce and validate a set of illustrations for key counselling points of a pediatric EAP. METHODS: Illustrations were developed using key graphic elements and refined by subject experts. Illustrations were evaluated during one-on-one structured interviews with parents/caregivers of children ages 9 and younger, as well as with children ages 10 to 17 years between September 2015 and June 2016...
November 1, 2017: Journal of Cutaneous Medicine and Surgery
Elena Szefer, Donghuan Lu, Farouk Nathoo, Mirza Faisal Beg, Jinko Graham
Using publicly-available data from the Alzheimer's Disease Neuroimaging Initiative, we investigate the joint association between single-nucleotide polymorphisms (SNPs) in previously established linkage regions for Alzheimer's disease (AD) and rates of decline in brain structure. In an initial, discovery stage of analysis, we applied a weighted RV test to assess the association between 75,845 SNPs in the Alzgene linkage regions and rates of change in structural MRI measurements for 56 brain regions affected by AD, in 632 subjects...
November 1, 2017: Statistical Applications in Genetics and Molecular Biology
Sebastian Gohr, Peter Hrobarik, Martin Kaupp
For a closer validation of four-component relativistic DFT methods within the matrix Dirac-Kohn-Sham (mDKS) framework with global hybrid functionals for EPR parameter calculations to be applied in the modeling of tungsten enzymes, we refine a previously suggested protocol [Gohr et al. \textit{J. Chem. Phys. A}, \textbf{2015}, \textit{119}, 12892-12905] for computations on 5d systems. This is done for a series of larger, unsymmetrical W(V) complexes thought to closely resemble enzyme active sites in this oxidation state...
October 27, 2017: Journal of Physical Chemistry. A
Madelynn R D Stackhouse, Rachel W Jones Ross, Susan D Boon
This research presents a multidimensional conceptualization of unforgiveness and the development and validation of the unforgiveness measure (UFM). The scale was developed based on a qualitative study of people's experiences of unforgiven interpersonal offences (Study 1). Three dimensions of unforgiveness emerged (Study 2): emotional-ruminative unforgiveness, cognitive-evaluative unforgiveness, and offender reconstrual. We supported the scale's factor structure, reliability, and validity (Study 3). We also established the convergent and discriminant validity of the UFM with measures of negative affect, rumination, forgiveness, cognitive reappraisal, and emotional suppression (Study 4)...
October 25, 2017: British Journal of Social Psychology
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen, Swati Jain, Steven M Lewis, W Bryan Arendall, Jack Snoeyink, Paul D Adams, Simon C Lovell, Jane S Richardson, David C Richardson
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix...
October 25, 2017: Protein Science: a Publication of the Protein Society
Joshua L Howard, Marylène Gagné, Julien S Bureau
Self-determination theory proposes a multidimensional representation of motivation comprised of several factors said to fall along a continuum of relative autonomy. The current meta-analysis examined the relationships between these motivation factors in order to demonstrate how reliably they conformed to a predictable continuum-like pattern. Based on data from 486 samples representing over 205,000 participants who completed 1 of 13 validated motivation scales, the results largely supported a continuum-like structure of motivation and indicate that self-determination is central in explaining human motivation...
October 19, 2017: Psychological Bulletin
Heike Schütze, Melvin Chin, David Weller, Mark F Harris
Background: The rising incidence of cancer and increasing number of cancer survivors place competing demands on specialist oncology clinics. This has led to a need to consider collaborative care between primary and secondary care for the long-term post-treatment care of cancer survivors. Objective: To explore the views of breast and colorectal cancer survivors, their oncologist and GP about GPs taking a more active role in long-term cancer follow-up care. Methods: Semi-structured interviews using a thematic analysis framework...
October 14, 2017: Family Practice
Roman Shevchuk, Jochen S Hub
Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching...
October 2017: PLoS Computational Biology
Jiawei Wang, Bingren Zhang, Chanchan Shen, Jinhua Zhang, Wei Wang
BACKGROUND: Headache symptoms self-reported by migraine patients are largely congruent with the clinician-used diagnostic criteria, but not always so. Patients' self-reports of headache symptoms might offer additional clues to characterize migraine with (MA) and without (MO) aura more precisely. METHODS: Firstly, we invited 324 participants with a life-long headache attack to answer an item-matrix measuring symptoms of primary headaches, then we performed both exploratory and confirmatory factor analyses to their answers and refined a headache symptom questionnaire...
October 12, 2017: BMC Neurology
Horia Jalily Hasani, Marawan Ahmed, Khaled Barakat
The voltage-gated KCNQ1/KCNE1 potassium ion channel complex, forms the slow delayed rectifier (IKs) current in the heart, which plays an important role in heart signaling. The importance of KCNQ1/KCNE1 channel's function is further implicated by the linkage between loss-of-function and gain-of-function mutations in KCNQ1 or KCNE1, and long QT syndromes, congenital atrial fibrillation, and short QT syndrome. Also, KCNQ1/KCNE1 channels are an off-target for many non-cardiovascular drugs, leading to fatal cardiac irregularities...
September 29, 2017: Journal of Molecular Graphics & Modelling
Begonya Garcia-Zapirain, Ahmed Shalaby, Ayman El-Baz, Adel Elmaghraby
Ulcer tissue segmentation is of immense importance in helping medical personnel to assess wounds. This paper introduces a new computational framework employing state-of-the-art image processing techniques to segment pressure ulcer tissue structures from color images. The framework integrates a visual appearance model of an observed input image with prior color information from an available database of previously stored color RGB images. The following four processing steps are performed. First, to minimize the execution time and enhance the segmentation accuracy, a region-of-interest (ROI) of the whole ulcer area is automatically identified based on contrast changes...
September 22, 2017: Computers in Biology and Medicine
Giuseppe Sciortino, Daniele Sanna, Valeria Ugone, Giovanni Micera, Agustí Lledós, Jean-Didier Maréchal, Eugenio Garribba
This study presents an implementation of the protein-ligand docking program GOLD and a generalizable method to predict the binding site and orientation of potential vanadium drugs. Particularly, theoretical methods were applied to the study of the interaction of two V(IV)O complexes with antidiabetic activity, [V(IV)O(pic)2(H2O)] and [V(IV)O(ma)2(H2O)], where pic is picolinate and ma is maltolate, with lysozyme (Lyz) for which electron paramagnetic resonance spectroscopy suggests the binding of the moieties VO(pic)2 and VO(ma)2 through a carboxylate group of an amino acid residue (Asp or Glu)...
November 6, 2017: Inorganic Chemistry
Seunghwa Jeong, Jungjin Lee, Bumki Kim, Younghui Kim, Junyong Noh
We present a hybrid approach that segments an object by using both color and depth information obtained from views captured from a low-cost RGBD camera and sparsely-located color cameras. Our system begins with generating dense depth information of each target image by using Structure from Motion and joint bilateral upsampling. We formulate the multi-view object segmentation as the Markov Random Field energy optimization on the graph constructed from the superpixels. To ensure inter-view consistency of the segmentation results between color images that have too few color features, our local mapping method generates dense inter-view geometric correspondences by using the dense depth images...
September 29, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
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