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Refinement validation structure

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https://www.readbyqxmd.com/read/28345622/comprehensive-track-structure-based-evaluation-of-dna-damage-by-light-ions-from-radiotherapy-relevant-energies-down-to-stopping
#1
W Friedland, E Schmitt, P Kundrát, M Dingfelder, G Baiocco, S Barbieri, A Ottolenghi
Track structures and resulting DNA damage in human cells have been simulated for hydrogen, helium, carbon, nitrogen, oxygen and neon ions with 0.25-256 MeV/u energy. The needed ion interaction cross sections have been scaled from those of hydrogen; Barkas scaling formula has been refined, extending its applicability down to about 10 keV/u, and validated against established stopping power data. Linear energy transfer (LET) has been scored from energy deposits in a cell nucleus; for very low-energy ions, it has been defined locally within thin slabs...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#2
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28341584/development-of-videogrammetry-as-a-tool-for-gas-particle-fluidization-research
#3
S Anweiler
Many industries use fluidization of solid particles for energy efficiency or environmental friendly process development, and this paper introduces research techniques developed for investigating gas-particle systems At present there is plenty of room for refining gas-particle fluidization process. With the rapidly rising application of mathematical modelling, real time visualization of processes will be widely used for validation of those models in the near future. In presented research, photogrammetry, as a part of close range vision metrology, has been expanded to allow dynamic space and time analysis of the phase concentration distribution inside fluidization devices...
March 21, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28319851/-31-p-dephased-13-c-detected-redor-for-nmr-crystallography-at-natural-isotopic-abundance
#4
Alexander I Greenwood, Mary C Clay, Chad M Rienstra
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one...
February 28, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28291758/using-more-than-801%C3%A2-296-small-molecule-crystal-structures-to-aid-in-protein-structure-refinement-and-analysis
#5
Jason C Cole, Ilenia Giangreco, Colin R Groom
The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal-organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein-ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28286364/considerations-in-the-development-of-a-sound-tolerance-interview-and-questionnaire-instrument
#6
REVIEW
LaGuinn P Sherlock, Craig Formby
Most clinicians approach the objective fitting of hearing aids with three goals in mind: audibility, comfort, and tolerance. When these three amplification goals have been met, the hearing aid user is more likely to adapt to and perceive benefit from hearing aid use. However, problems related to the loudness of sounds and reduced sound tolerance, which may or may not be reported by the aided user, can adversely impact adaptation to amplification and the individual's quality of life. Although there are several standardized questionnaires available to evaluate hearing aid benefit and satisfaction, there is no standardized questionnaire or interview tool for evaluating reduced sound tolerance and the related impact on hearing aid use...
February 2017: Seminars in Hearing
https://www.readbyqxmd.com/read/28280472/measuring-responsible-gambling-amongst-players-development-of-the-positive-play-scale
#7
Richard T A Wood, Michael J A Wohl, Nassim Tabri, Kahlil Philander
The modern gambling industry has, by-in-large, assumed a duty of care to minimize the risks associated with gambling, which has manifested in responsible gambling (RG) programming (e.g., educating players about the odds of success). The current study fills a void in gambling operators, regulators, and researchers ability to measure RG beliefs and behavior in their player-base, with the development and validation of the Positive Play Scale (PPS). In Study 1, we reviewed the literature and consulted 30 players as well as 10 RG experts to help generate a definition of RG beliefs and behavior that helped guide item generation...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28272524/atomistic-structural-ensemble-refinement-reveals-non-native-structure-stabilizes-a-sub-millisecond-folding-intermediate-of-chey
#8
Jade Shi, R Paul Nobrega, Christian Schwantes, Sagar V Kathuria, Osman Bilsel, C Robert Matthews, T J Lane, Vijay S Pande
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28259528/structural-insights-of-smkdac8-inhibitors-targeting-schistosoma-epigenetics-through-a-combined-structure-based-3d-qsar-in-vitro-and-synthesis-strategy
#9
Flavio Ballante, D Rajasekhar Reddy, Nancy J Zhou, Garland R Marshall
A predictive structure-based 3D QSAR (COMBINEr 2.0) model of the Schistosoma mansoni lysine deacetylase 8 enzyme (SmKDAC8) was developed, validated and used to perform virtual screening (VS) of the NCI Diversity Set V database (1593 compounds). Three external datasets (with congeneric structures to those experimentally resolved in complexes by X-ray and previously reported as SmKDAC8 inhibitors) were employed to compose and validate the most predictive model. Two series characterized by 104 benzodiazepine derivatives (BZDs) and 60 simplified largazole analogs (SLAs), recently reported by our group as human KDAC inhibitors, were tested for their inhibition potency against SmKDAC8 to probe the predictive capability of the quantitative models against compounds with diverse structures...
February 13, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28256337/psychometric-properties-of-the-chinese-version-of-the-attitudes-towards-cardiopulmonary-resuscitation-with-defibrillation-acprd-c-among-female-hospital-nurses-in-taiwan
#10
Hsing-Long Lin, Mei-Hsiang Lin, Chao-Chung Ho, Chin-Hua Fu, Malcolm Koo
INTRODUCTION: Nurses are often the first responders to in-hospital cardiac emergencies. A positive attitude towards cardiopulmonary resuscitation with defibrillation may contribute to early cardiopulmonary resuscitation and rapid defibrillation, which are associated with enhanced long-term survival. The aim of this study was to translate and adapt the 31-item attitudes towards cardiopulmonary resuscitation with defibrillation and the national resuscitation guidelines (ACPRD) instrument into Chinese and to evaluate its psychometric properties in a sample of Taiwanese hospital nurses...
February 27, 2017: International Emergency Nursing
https://www.readbyqxmd.com/read/28255197/confirmatory-factor-analyses-of-self-and-parent-report-inventory-of-callous-unemotional-traits-in-8-to-10-year-olds
#11
Yu Gao, Wei Zhang
The factorial structure of the Inventory of Callous-Unemotional Traits (ICU; Frick 2004) has been inconsistent across various studies using different rater versions and samples. In this study the factorial structure of the self- and parent-report versions of the ICU was examined in a community sample of 340 boys and girls aged 8- to 10-years. A series of confirmatory factor analyses revealed that (1) for self-report ICU, a two-factor model comprising one Uncaring and one Callousness factor fit the data best; the factorial structure was invariant across sex, although boys showed higher scores than girls on the Uncaring factor; (2) for the parent-report ICU, a three-factor structure was supported, and boys and girls did not differ on factor structure or levels of the factors...
September 2016: Journal of Psychopathology and Behavioral Assessment
https://www.readbyqxmd.com/read/28251442/documentation-of-pharmaceutical-care-development-of-an-intervention-oriented-classification-system
#12
Karen A Maes, Sophia Bruch, Kurt E Hersberger, Markus L Lampert
Background A standardised classification system of pharmaceutical interventions (PI) is in use in several Swiss hospitals, whereas none exists for community pharmacies to date. To promote information exchange between both settings, a compatible structure of the classification system is needed. Objective To develop an intervention oriented classification system for community pharmacies named PharmDISC based on the hospital system; to test it on interrater reliability, appropriateness, interpretability, and face and content validity; to assess pharmacists' opinions...
March 2, 2017: International Journal of Clinical Pharmacy
https://www.readbyqxmd.com/read/28249240/identification-of-novel-dual-specificity-phosphatase-26-inhibitors-by-a-hybrid-virtual-screening-approach-based-on-pharmacophore-and-molecular-docking
#13
Ji-Xia Ren, Zhong Cheng, Yu-Xin Huang, Jing-Feng Zhao, Peng Guo, Zhong-Mei Zou, Yong Xie
Dual-specificity phosphatase 26 (DUSP26) has recently emerged as a target for treatment of human cancers. However, only two small-molecule inhibitors of DUSP26 are known so far, namely NSC-87877 and ethyl-3, 4-dephostatin. DUSP26 contains an N-terminal region (residues 1-60) and a conserved C-terminal catalytic domain (residues 61-211, DUSP26-C). The crystal structure of DUSP26-C, showing a catalytically inactive conformation of the active site, was reported in a previous study. However, the detailed catalytic mechanism of DUSP26 cannot be described based on that structure...
February 26, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28241391/princeton_tigress-2-0-high-refinement-consistency-and-net-gains-through-support-vector-machines-and-molecular-dynamics-in-double-blind-predictions-during-the-casp11-experiment
#14
George A Khoury, James Smadbeck, Chris A Kieslich, Alexandra J Koskosidis, Yannis A Guzman, Phanourios Tamamis, Christodoulos A Floudas
Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during the last four CASP experiments, a majority of the methods continue to degrade models rather than improve them. Princeton_TIGRESS (Khoury et al., Proteins 2014;82:794-814) was developed previously and utilizes separate sampling and selection stages involving Monte Carlo and molecular dynamics simulations and classification using an SVM predictor...
February 27, 2017: Proteins
https://www.readbyqxmd.com/read/28241011/the-burden-of-typhoid-fever-in-low-and-middle-income-countries-a-meta-regression-approach
#15
Marina Antillón, Joshua L Warren, Forrest W Crawford, Daniel M Weinberger, Esra Kürüm, Gi Deok Pak, Florian Marks, Virginia E Pitzer
BACKGROUND: Upcoming vaccination efforts against typhoid fever require an assessment of the baseline burden of disease in countries at risk. There are no typhoid incidence data from most low- and middle-income countries (LMICs), so model-based estimates offer insights for decision-makers in the absence of readily available data. METHODS: We developed a mixed-effects model fit to data from 32 population-based studies of typhoid incidence in 22 locations in 14 countries...
February 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28231266/an-examination-of-the-factorial-and-convergent-validity-of-four-measures-of-conspiracist-ideation-with-recommendations-for-researchers
#16
Viren Swami, David Barron, Laura Weis, Martin Voracek, Stefan Stieger, Adrian Furnham
A number scales have been developed to measure conspiracist ideation, but little attention has been paid to the factorial validity of these scales. We reassessed the psychometric properties of four widely-used scales, namely the Belief in Conspiracy Theories Inventory (BCTI), the Conspiracy Mentality Questionnaire (CMQ), the Generic Conspiracist Beliefs Scale (GCBS), and the One-Item Conspiracy Measure (OICM). Eight-hundred-and-three U.S. adults completed all measures, along with measures of endorsement of 9/11 and anti-vaccination conspiracy theories...
2017: PloS One
https://www.readbyqxmd.com/read/28223945/toward-respiratory-assessment-using-depth-measurements-from-a-time-of-flight-sensor
#17
Charles Sharp, Vahid Soleimani, Sion Hannuna, Massimo Camplani, Dima Damen, Jason Viner, Majid Mirmehdi, James W Dodd
Introduction: There is increasing interest in technologies that may enable remote monitoring of respiratory disease. Traditional methods for assessing respiratory function such as spirometry can be expensive and require specialist training to perform and interpret. Remote, non-contact tracking of chest wall movement has been explored in the past using structured light, accelerometers and impedance pneumography, but these have often been costly and clinical utility remains to be defined. We present data from a 3-Dimensional time-of-flight camera (found in gaming consoles) used to estimate chest volume during routine spirometry maneuvres...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28210925/prospective-associations-between-depressive-symptoms-and-the-metabolic-syndrome-the-spirited-life-study-of-methodist-pastors-in-north-carolina
#18
Timothy W Smith, David E Eagle, Rae Jean Proeschold-Bell
BACKGROUND: Metabolic syndrome (Met-S) has a robust concurrent association with depression. A small, methodologically limited literature suggests that Met-S and depression are reciprocally related over time, an association that could contribute to their overlapping influences on morbidity and mortality in cardiovascular disease, diabetes, and cancer. PURPOSE: Using a refined approach to the measurement of Met-S as a continuous latent variable comprising continuous components, this study tested the prospective associations between Met-S and depression...
February 16, 2017: Annals of Behavioral Medicine: a Publication of the Society of Behavioral Medicine
https://www.readbyqxmd.com/read/28198721/the-chronic-otitis-media-benefit-inventory-combi-development-and-validation-of-a-dynamic-quality-of-life-questionnaire-for-chronic-ear-disease
#19
John S Phillips, Mark Haggard, Helen Spencer, Matthew Yung
OBJECTIVE: This study introduces a change-oriented short-form health-related quality of life questionnaire suited to symptoms of adult chronic middle ear disease and its consequences, and describes its properties. STUDY DESIGN: Two-centre prospective correlational study primarily for instrument development. SETTING: Two otology secondary care centers in England. PATIENTS: Fifty-two consecutive adult patients with active chronic otitis media undergoing surgery...
February 14, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28198676/global-transcriptome-analysis-reveals-extensive-gene-remodeling-alternative-splicing-and-differential-transcription-profiles-in-non-seed-vascular-plant-selaginella-moellendorffii
#20
Yan Zhu, Longxian Chen, Chengjun Zhang, Pei Hao, Xinyun Jing, Xuan Li
BACKGROUND: Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome of S. moellendorffii revealed many conserved genes and pathways, as well as specialized genes different from flowering plants. Despite the progress made, little is known about long noncoding RNAs (lncRNA) and the alternative splicing (AS) of coding genes in S. moellendorffii. Its coding gene models have not been fully validated with transcriptome data...
January 25, 2017: BMC Genomics
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