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Refinement validation structure

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https://www.readbyqxmd.com/read/28815771/molstack-interactive-visualization-tool-for-presentation-interpretation-and-validation-of-macromolecules-and-electron-density-maps
#1
Przemyslaw J Porebski, Piotr Sroka, Heping Zheng, David R Cooper, Wladek Minor
Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼ 90% are themselves the interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric...
August 17, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28809817/synthesis-and-physicochemical-characterization-of-the-process-related-impurities-of-eplerenone-an-antihypertensive-drug
#2
Iwona Dams, Agata Białońska, Piotr Cmoch, Małgorzata Krupa, Anita Pietraszek, Anna Ostaszewska, Michał Chodyński
Two unknown impurities were observed during the process development for multigram-scale synthesis of eplerenone (Inspra(®)). The new process-related impurities were identified and fully characterized as the corresponding (7β,11α,17α)-11-hydroxy- and (7α,11β,17α)-9,11-dichloroeplerenone derivatives 12a and 13. Seven other known but poorly described in the literature eplerenone impurities, including four impurities A, B, C and E listed in the European Pharmacopoeia 8.4 were also detected, identified and fully characterized...
August 15, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28802223/silver-and-gold-in-the-protein-data-bank
#3
Oliviero Carugo
The structural features of the silver and gold sites in protein crystal structures extracted from the Protein Data Bank have been investigated. It is observed that both cations have nearly always low oxidations states (+1) and low coordination numbers, adopt standard stereochemistries, and interact preferentially (particularly gold) with sulfur donor atoms of cysteine and methionine side-chains. Interestingly, gold cation have been very often refined with occupancy minor than 1.0 and are very often "naked", in the sense that no donor atoms are sufficiently close to the metal cation...
July 27, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28800485/validation-of-site-specific-soil-ni-toxicity-thresholds-with-independent-ecotoxicity-and-biogeochemistry-data-for-elevated-soil-ni
#4
Beverley Hale, Yamini Gopalapillai, Amanda Pellegrino, Tyson Jennett, Julie Kikkert, Wilson Lau, Christian Schlekat, Mike J McLaughlin
The Existing Substances Regulation Risk Assessments by the European Union (EU RA) generated new toxicity data for soil organisms exposed to Ni added to sixteen field-collected soils with low background concentration of metals and varying physico-chemical soil characteristics. Using only effective cation exchange capacity (eCEC) as a bioavailability correction, chronic toxicity of Ni in soils with a wide range of characteristics could be predicted within a factor of two. The objective of the present study was to determine whether this was also the case for three independent data sets of Ni toxicity thresholds...
August 8, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28796609/piecewise-planar-stereoscan-sequential-structure-and-motion-using-plane-primitives
#5
Carolina Raposo, Michel Antunes, Joao P Barreto
The article describes a pipeline that receives as input a sequence of stereo images, and outputs the camera motion and a Piecewise-Planar Reconstruction (PPR) of the scene. The pipeline, named Piecewise-Planar StereoScan (PPSS), works as follows: the planes in the scene are detected for each stereo view using semi-dense depth estimation; the relative pose is computed by a new closed-form minimal algorithm that only uses point correspondences whenever plane detections do not fully constrain the motion; the camera motion and the PPR are jointly refined by alternating between discrete optimization and continuous bundle adjustment; and, finally, the detected 3D planes are segmented in images using a new framework that handles low texture and visibility issues...
August 9, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28790989/a-proposal-for-a-structural-model-of-the-feline-calicivirus-protease-bound-to-the-substrate-peptide-under-physiological-conditions
#6
Masaru Yokoyama, Tomoichiro Oka, Hirotaka Takagi, Hirotatsu Kojima, Takayoshi Okabe, Tetsuo Nagano, Yukinobu Tohya, Hironori Sato
Feline calicivirus (FCV) protease functions to cleave viral precursor proteins during productive infection. Previous studies have mapped a protease-coding region and six cleavage sites in viral precursor proteins. However, how the FCV protease interacts with its substrates remains unknown. To gain insights into the interactions, we constructed a molecular model of the FCV protease bound with the octapeptide containing a cleavage site of the capsid precursor protein by homology modeling and docking simulation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28780192/a-novel-hpv-prophylactic-peptide-vaccine-designed-by-immunoinformatics-and-structural-vaccinology-approaches
#7
Manica Negahdaripour, Mahboobeh Eslami, Navid Nezafat, Nasim Hajighahramani, Mohammad Bagher Ghoshoon, Eskandar Shoolian, Ali Dehshahri, Nasrollah Erfani, Mohammad Hossein Morowvat, Younes Ghasemi
Human papillomavirus (HPV)-caused cervical cancer is the fourth common female cancer globally. Despite availability of three effective vaccines in market, development of HPV prophylactic vaccines is still pursued due to affordability issues and type-restricted protection of the marketed vaccines. Investigational second generation prophylactic HPV vaccines are mostly exploiting epitopes from the virus minor capsid protein (L2), which despite many advantages suffer from low immunogenicity, a common problem of epitope vaccines...
August 2, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28777575/quantifying-the-performances-of-dft-for-predicting-vibrationally-resolved-optical-spectra-asymmetric-fluoroborate-dyes-as-working-examples
#8
Joanna Bednarska, Robert Zalesny, Wojciech Bartkowiak, Borys Osmialowski, Miroslav Medved, Denis Jacquemin
This contribution aims at a quantitative assessment of the performances of a panel of exchange-correlation functionals, including semi-local (BLYP and PBE), global hybrids (B3LYP, PBE0, M06, BHandHLYP, M06-2X, and M06-HF) and range-separated hybrids (CAM-B3LYP, LC-ωPBE, LC-BLYP, ωB97X, and ωB97X-D), in predicting the vibrationally-resolved absorption spectra of BF2-carrying compounds. To this end, for 19 difluoroborates as examples, we use, as a metric, the vibrational reorganization energy (λvib) that can be determined based on the computationally efficient linear coupling model (aka...
August 4, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28774292/rosetta-broker-for-membrane-protein-structure-prediction-concentrative-nucleoside-transporter-3-and-corticotropin-releasing-factor-receptor-1-test-cases
#9
Dorota Latek
BACKGROUND: Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. In this work an example of such de novo method was used to structurally and functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors...
August 3, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28772310/development-and-initial-validation-of-a-consumer-questionnaire-to-predict-the-presence-of-ear-disease
#10
Samantha J Kleindienst, David A Zapala, Donald W Nielsen, James W Griffith, Dania Rishiq, Larry Lundy, Sumitrajit Dhar
Importance: The already large population of individuals with age- or noise-related hearing loss in the United States is increasing, yet hearing aids remain largely inaccessible. The recent decision by the US Food and Drug Administration to not enforce the medical examination prior to hearing aid fitting highlights the need to reengineer consumer protections when increasing accessibility. A self-administered tool to estimate ear disease risk would provide disease surveillance without posing an unreasonable barrier to hearing aid procurement...
August 3, 2017: JAMA Otolaryngology—Head & Neck Surgery
https://www.readbyqxmd.com/read/28762965/experimental-charge-density-studies-data-reduction-and-model-quality-the-more-the-better
#11
Regine Herbst-Irmer, Dietmar Stalke
In this review, recent developments concerning data and model quality in experimental charge-density investigations from a personal view-point are described. Data quality is not only achieved by the high resolution, high I/σ(I) values, low merging R values and high multiplicity. The quality of the innermost reflections especially is crucial for mapping the density distribution of the outermost valence electrons and can be monitored by (I/σ)(asymptotic). New detector technologies seem to be promising improvements...
August 1, 2017: Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials
https://www.readbyqxmd.com/read/28748106/a-feasibility-study-of-a-theory-based-intervention-to-improve-appropriate-polypharmacy-for-older-people-in-primary-care
#12
Cathal A Cadogan, Cristín Ryan, Gerard J Gormley, Jill J Francis, Peter Passmore, Ngaire Kerse, Carmel M Hughes
BACKGROUND: A general practitioner (GP)-targeted intervention aimed at improving the prescribing of appropriate polypharmacy for older people was previously developed using a systematic, theory-based approach based on the UK Medical Research Council's complex intervention framework. The primary intervention component comprised a video demonstration of a GP prescribing appropriate polypharmacy during a consultation with an older patient. The video was delivered to GPs online and included feedback emphasising the positive outcomes of performing the behaviour...
2018: Pilot and Feasibility Studies
https://www.readbyqxmd.com/read/28744791/automatic-allograft-bone-selection-through-band-registration-and-its-application-to-distal-femur
#13
Yu Zhang, Lei Qiu, Fengzan Li, Qing Zhang, Li Zhang, Xiaohui Niu
Clinical reports suggest that large bone defects could be effectively restored by allograft bone transplantation, where allograft bone selection acts an important role. Besides, there is a huge demand for developing the automatic allograft bone selection methods, as the automatic methods could greatly improve the management efficiency of the large bone banks. Although several automatic methods have been presented to select the most suitable allograft bone from the massive allograft bone bank, these methods still suffer from inaccuracy...
July 25, 2017: Cell and Tissue Banking
https://www.readbyqxmd.com/read/28739560/ontology-based-approach-to-social-data-sentiment-analysis-detection-of-adolescent-depression-signals
#14
Hyesil Jung, Hyeoun-Ae Park, Tae-Min Song
BACKGROUND: Social networking services (SNSs) contain abundant information about the feelings, thoughts, interests, and patterns of behavior of adolescents that can be obtained by analyzing SNS postings. An ontology that expresses the shared concepts and their relationships in a specific field could be used as a semantic framework for social media data analytics. OBJECTIVE: The aim of this study was to refine an adolescent depression ontology and terminology as a framework for analyzing social media data and to evaluate description logics between classes and the applicability of this ontology to sentiment analysis...
July 24, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28720133/developing-a-questionnaire-to-determine-the-impact-of-self-management-in-diabetes-giving-people-with-diabetes-a-voice
#15
J Carlton, J Elliott, D Rowen, K Stevens, H Basarir, K Meadows, J Brazier
BACKGROUND: The prevalence of diabetes mellitus (DM) is increasing dramatically, placing considerable financial burden on the healthcare budget of each country. Patient self-management is crucial for the control of blood glucose, which largely determines the chances of developing diabetes-related complications. Self-management interventions vary widely, and a method is required for assessing the impact of self-management. This paper describes the development of a questionnaire intended for use to measure the impact of self-management in diabetes...
July 18, 2017: Health and Quality of Life Outcomes
https://www.readbyqxmd.com/read/28715587/a-quantitative-and-qualitative-exploration-of-photoaversion-in-achromatopsia
#16
Jonathan Aboshiha, Neruban Kumaran, Angelos Kalitzeos, Chris Hogg, Gary Rubin, Michel Michaelides
Purpose: Photoaversion (PA) is a disabling and ubiquitous feature of achromatopsia (ACHM). We aimed to help define the characteristics of this important symptom, and present the first published assessment of its impact on patients' lives, as well as quantitative and qualitative PA assessments. Methods: Molecularly confirmed ACHM subjects were assessed for PA using four tasks: structured survey of patient experience, novel quantitative subjective measurement of PA, visual acuities in differing ambient lighting, and objective palpebral aperture-related PA testing...
July 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28700701/development-and-validation-of-the-maugeri-sleep-quality-and-distress-inventory-masqudi-17
#17
Elisa Morrone, Cinzia Sguazzin, Giorgio Bertolotti, Andrea Giordano, Alberto Braghiroli, Gian Luigi Balestroni, Raffaele Manni, Luigi Ferini Strambi, Vincenza Castronovo, Marco Zucconi, Fabrizio De Carli, Eleonora Pinna, Marcella Ottonello, Ines Giorgi, Michele Terzaghi, Sara Marelli, Francesco Fanfulla
OBJECTIVES: The aim of this study was to develop and validate a questionnaire designed to measure the impact of sleep impairment on emotional distress in patients with various sleep disorders. METHODS: Five experts created an item data-bank pertaining to sleep-related psychological symptoms and somatic perceptions. Fifty patients in two focus groups examined each item for: a) word clarity (indicating any ambiguity of interpretation) and b) appropriateness for the target population...
2017: PloS One
https://www.readbyqxmd.com/read/28700088/standardizing-bimanual-vaginal-examination-using-cognitive-task-analysis
#18
Isabella Plumptre, Omar Mulki, Alejandro Granados, Claudine Gayle, Shahla Ahmed, Naomi Low-Beer, Jenny Higham, Fernando Bello
OBJECTIVE: To create a standardized universal list of procedural steps for bimanual vaginal examination (BVE) for teaching, assessment, and simulator development. METHODS: This observational study, conducted from June-July 2012 and July-December 2014, collected video data of 10 expert clinicians performing BVE in a nonclinical environment. Video data were analyzed to produce a cognitive task analysis (CTA) of the examination steps performed. The CTA was further refined through structured interviews to make it suitable for teaching or assessment...
July 12, 2017: International Journal of Gynaecology and Obstetrics
https://www.readbyqxmd.com/read/28699318/high-resolution-anorectal-manometry-an-expensive-hobby-or-worth-every-penny
#19
REVIEW
G Basilisco, A E Bharucha
Introduced approximately 10 years ago, high-resolution manometry catheters have fostered interest in anorectal manometry. This review, which accompanies two articles in this issue of Neurogastroenterology and Motility, reviews the methods, clinical indications, utility, and pitfalls of anorectal manometry and revisits the American Gastroenterological Association (AGA) Medical Position Statement on Anorectal Testing Techniques, which was last published in 1999. High-resolution manometry provides a refined assessment of the anorectal pressure profile, obviates the need for station pull-through maneuvers, and minimizes movement artifacts...
August 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/28684885/a-state-space-based-approach-to-localizing-single-molecules-from-multi-emitter-images
#20
Milad R Vahid, Jerry Chao, E Sally Ward, Raimund J Ober
Single molecule super-resolution microscopy is a powerful tool that enables imaging at sub-diffraction-limit resolution. In this technique, subsets of stochastically photoactivated fluorophores are imaged over a sequence of frames and accurately localized, and the estimated locations are used to construct a high-resolution image of the cellular structures labeled by the fluorophores. Available localization methods typically first determine the regions of the image that contain emitting fluorophores through a process referred to as detection...
January 28, 2017: Proceedings of SPIE
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