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Refinement validation structure

Roshanak Farhoodi, Bahar Akbal-Delibas, Nurit Haspel
Discriminating native-like structures from false positives with high accuracy is one of the biggest challenges in protein-protein docking. While there is an agreement on the existence of a relationship between various favorable intermolecular interactions (e.g., Van der Waals, electrostatic, and desolvation forces) and the similarity of a conformation to its native structure, the precise nature of this relationship is not known. Existing protein-protein docking methods typically formulate this relationship as a weighted sum of selected terms and calibrate their weights by using a training set to evaluate and rank candidate complexes...
October 17, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Charlotte Martineau, Mathieu Allix, Matthew R Suchomel, Florence Porcher, François Vivet, Christophe Legein, Monique Body, Dominique Massiot, Francis Taulelle, Franck Fayon
The room temperature structure of Ba5AlF13 has been investigated by coupling electron, synchrotron and neutron powder diffraction, solid-state high-resolution NMR ((19)F and (27)Al) and first principles calculations. An initial structural model has been obtained from electron and synchrotron powder diffraction data, and its main features have been confirmed by one- and two-dimensional NMR measurements. However, DFT GIPAW calculations of the (19)F isotropic shieldings revealed an inaccurate location of one fluorine site (F3, site 8a), which exhibited unusual long F-Ba distances...
October 4, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Jin Han, Philip J Batterham, Alison L Calear, Yang Wu, Yiyun Shou, Bregje A J van Spijker
This paper reports the validation of the Chinese versions of the Suicidal Ideation Attributes Scale (SIDAS), Stigma of Suicide Scale (short form, SOSS), and Literacy of Suicide Scale (short form, LOSS) among 57 Chinese and English bilinguals and 224 Chinese university students. All the translated scales showed high correlations with the original versions. The translated SIDAS and refined SOSS demonstrated robust factor structures, good internal consistency and convergent validity. Chinese students with self-reported depression symptoms tended to have higher glorification of suicide and lower suicide literacy...
August 11, 2016: Death Studies
Michael G Kahn, Tiffany J Callahan, Juliana Barnard, Alan E Bauck, Jeff Brown, Bruce N Davidson, Hossein Estiri, Carsten Goerg, Erin Holve, Steven G Johnson, Siaw-Teng Liaw, Marianne Hamilton-Lopez, Daniella Meeker, Toan C Ong, Patrick Ryan, Ning Shang, Nicole G Weiskopf, Chunhua Weng, Meredith N Zozus, Lisa Schilling
OBJECTIVE: Harmonized data quality (DQ) assessment terms, methods, and reporting practices can establish a common understanding of the strengths and limitations of electronic health record (EHR) data for operational analytics, quality improvement, and research. Existing published DQ terms were harmonized to a comprehensive unified terminology with definitions and examples and organized into a conceptual framework to support a common approach to defining whether EHR data is 'fit' for specific uses...
2016: EGEMS
Wouter G Touw, Bart van Beusekom, Jochem M G Evers, Gert Vriend, Robbie P Joosten
Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn-Cys distances and Cys-Zn-Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Rhiannon B Parker, Philip D Parker, Theresa Larkin, Jon Cockburn
BACKGROUND: Gender bias within medical education is gaining increasing attention. However, valid and reliable measures are needed to adequately address and monitor this issue. This research conducts a psychometric evaluation of a short multidimensional scale that assesses medical students' awareness of gender bias, beliefs that gender bias should be addressed, and experience of gender bias during medical education. METHODS: Using students from the University of Wollongong, one pilot study and two empirical studies were conducted...
September 29, 2016: BMC Medical Education
Attila G Császár, Tibor Furtenbacher, Péter Árendás
Quantum mechanics builds large-scale graphs (networks): the vertices are the discrete energy levels the quantum system possesses, and the edges are the (quantum-mechanically allowed) transitions. Parts of the complete quantum mechanical networks can be probed experimentally via high-resolution, energy-resolved spectroscopic techniques. The complete rovibronic line list information for a given molecule can only be obtained through sophisticated quantum-chemical computations. Experiments as well as computations yield what we call spectroscopic networks (SN)...
October 12, 2016: Journal of Physical Chemistry. A
Goutam Chandra, Subhamay Panda
Protein three-dimensional structures are very much important in terms of functional and evolutionary context. Present study deals with the evaluation of snake venom constituent cytotoxin, short neurotoxin and related non-toxin proteins of other chordates with reference to structure prediction, validation of the models, distribution of secondary structural elements, hydrophobicity molecular surface analysis, functional annotation and functionally critical binding site identification with the assistance of different bioinformatical tools...
September 23, 2016: Current Drug Discovery Technologies
Bin Deng, Cristina Lento, Derek J Wilson
Protein therapeutics have emerged as a major class of biopharmaceuticals over the past several decades, a trend that has motivated the advancement of bioanalytical technologies for protein therapeutic characterization. Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful and sensitive technique that can probe the higher order structure of proteins and has been used in the assessment and development of monoclonal antibodies (mAbs), antibody-drug conjugates (ADCs) and biosimilar antibodies. It has also been used to quantify protein-ligand, protein-receptor and other protein-protein interactions involved in signaling pathways...
October 12, 2016: Analytica Chimica Acta
Jessica Aijia Liu, Martin Cheung
The neural crest (NC) is a remarkable transient structure generated during early vertebrate development. The neural crest progenitors have extensive migratory capacity and multipotency, harboring stem cell-like characteristics such as self-renewal. They can differentiate into a variety of cell types from craniofacial skeletal tissues to the trunk peripheral nervous system (PNS). Multiple regulators such as signaling factors, transcription factors, and migration machinery components are expressed at different stages of NC development...
September 14, 2016: Developmental Biology
Daniel R Lueders, Jacob L Sellon, Jay Smith, Jonathan T Finnoff
BACKGROUND: Chronic exertional compartment syndrome (CECS) is a common cause of exertional leg pain. It is commonly treated with a surgical fasciotomy, which has a surgical complication rate of up to 16% and takes approximately 6-12 weeks to return to preprocedure activity levels. Therefore, the development of a less invasive, effective outpatient intervention to treat CECS is desirable. OBJECTIVE: To describe and validate an ultrasound-guided (USG) fasciotomy technique for the anterior and lateral compartments of the lower limb in an unembalmed cadaveric model...
September 14, 2016: PM & R: the Journal of Injury, Function, and Rehabilitation
Arturo Nicola Natali, Emanuele Luigi Carniel, Chiara Giulia Fontanella, Alessandro Frigo, Silvia Todros, Alessandro Rubini, Giulia Maria De Benedictis, Maria Angela Cerruto, Walter Artibani
Urinary incontinence, often related to sphincter damage, is found in male patients, leading to a miserable quality of life and to huge costs for the healthcare system. The most effective surgical solution currently considered for men is the artificial urinary sphincter that exerts a pressure field on the urethra, occluding the duct. The evaluation of this device is currently based on clinical and surgical competences. The artificial sphincter design and mechanical action can be investigated by a biomechanical model of the urethra under occlusion, evaluating the interaction between tissues and prosthesis...
September 16, 2016: Biomechanics and Modeling in Mechanobiology
Xu Zhang, Fang Lu, Yan-Kun Chen, Gang-Gang Luo, Lu-di Jiang, Lian-Sheng Qiao, Yan-Ling Zhang, Yu-Hong Xiang
P2Y1 receptor (P2Y1R), which belongs to G protein-coupled receptors (GPCRs), is an important target in ADP-induced platelet aggregation. The crystal structure of P2Y1R has been solved recently, which revealed orthosteric and allosteric ligand-binding sites with the details of ligand-protein binding modes. And it suggests that P2Y1R antagonists, which recognize two distinct sites, could potentially provide an efficacious and safe antithrombotic profile. In present paper, 2D similarity search, pharmacophore based screening, and molecular docking were used to explore the potential natural P2Y1R antagonists...
2016: Evidence-based Complementary and Alternative Medicine: ECAM
Deborah L Snell, Rachelle Martin, Lois J Surgenor, Richard J Siegert, E Jean C Hay-Smith
PURPOSE: Qualitative research examining experiences of recovering from mild traumatic brain injury (MTBI) is limited. Findings from quantitative studies regarding predictors of persisting symptoms are inconsistent with limited attention directed to capturing broad perspectives and priorities of the wider stakeholders. More flexible research approaches may help advance the field. We used a mixed method design to generate patient perspectives of MTBI recovery, integrating these with quantitative investigation to isolate factors that might contribute to divergent MTBI outcomes...
September 14, 2016: Disability and Rehabilitation
Elisabete S C Ferreira, Iuliia V Voroshylova, Carlos M Pereira, M Natália D S Cordeiro
In this work, we combined various parameters found in the literature for the choline cation, chloride anion, and ethylene glycol to set up force field models (FFMs) for a eutectic mixture, namely, ethaline (1:2 choline chloride/ethylene glycol (ChCl:2EG)). The validation of these models was carried out on the basis of physical and chemical properties, such as the density, expansion coefficient, enthalpy of vaporization, self-diffusion coefficients, isothermal compressibility, surface tension, and shear viscosity...
September 13, 2016: Journal of Physical Chemistry. B
Michele Peters, Caroline M Potter, Laura Kelly, Cheryl Hunter, Elizabeth Gibbons, Crispin Jenkinson, Angela Coulter, Julien Forder, Ann-Marie Towers, Christine A'Court, Ray Fitzpatrick
PURPOSE: To identify the main issues of importance when living with long-term conditions to refine a conceptual framework for informing the item development of a patient-reported outcome measure for long-term conditions. MATERIALS AND METHODS: Semi-structured qualitative interviews (n=48) were conducted with people living with at least one long-term condition. Participants were recruited through primary care. The interviews were transcribed verbatim and analyzed by thematic analysis...
2016: Patient related Outcome Measures
Patrick J Polsunas, Gwendolyn Sowa, Julie M Fritz, Angela Gentili, Natalia E Morone, Srinivasa Naga Raja, Eric Rodriguez, Kenneth Schmader, Joel D Scholten, Debra K Weiner
OBJECTIVE: To present an algorithm of sequential treatment options for managing sacroiliac joint (SIJ) pain in the setting of chronic low back pain (CLBP) in the older adult. This is the tenth part in a series, and includes an illustrative clinical case. METHODS: The stepped care drug table and evaluation and treatment algorithm were created following a thorough literature review of approaches and subsequent analysis through a modified Delphi process. The principal investigator developed the initial draft, which was refined for content by an interdisciplinary panel of five experts...
September 2016: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
Heather M Gilmartin, Karen H Sousa, Catherine Battaglia
BACKGROUND: The central line (CL) bundle interventions are important for preventing central line-associated bloodstream infections (CLABSIs), but a modeling method for testing the CL bundle interventions within a health systems framework is lacking. OBJECTIVES: Guided by the Quality Health Outcomes Model (QHOM), this study tested the CL bundle interventions in reflective and composite, latent, variable measurement models to assess the impact of the modeling approaches on an investigation of the relationships between adherence to the CL bundle interventions, organizational context, and CLABSIs...
September 2016: Nursing Research
P B Rosenthal
Single-particle electron cryomicroscopy may be used to determine the structure of biological assemblies by aligning and averaging low-contrast projection images recorded in the electron microscope. Recent progress in both experimental and computational methods has led to higher resolution three-dimensional maps, including for more challenging low molecular weight proteins, and this has highlighted the problems of model bias and over-fitting during iterative refinement that can potentially lead to incorrect map features at low or high resolution...
2016: Methods in Enzymology
Victoria Fallon, Jason Christian Grovenor Halford, Kate Mary Bennett, Joanne Allison Harrold
Perinatal symptoms of anxiety are increasingly recognised due to their high prevalence and impact. Studies using pregnancy-specific anxiety measures have found that they may predict perinatal outcomes more effectively than general measures. However, no such measure exists to assess anxieties specific to the postpartum. This study aimed to develop and validate a measure (Postpartum Specific Anxiety Scale; PSAS) that accurately represents the specific anxieties faced by postpartum women, using a four-stage methodology: (1) 51 items were generated from interviews conducted with a group of 19 postpartum women at two time points, (2) the scale was reviewed and refined by a diverse expert panel, (3) an online pilot study (n = 146) was conducted to assess comprehensibility and acceptability and (4) an online sample of 1282 mothers of infants up to 6 months old completed the PSAS against a battery of convergent measures...
August 29, 2016: Archives of Women's Mental Health
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