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Refinement validation structure

Krishnendu Bera, Priyanka Rani, Gaurav Kishor, Shikha Agarwal, Antresh Kumar, Durg Vijay Singh
ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known...
September 20, 2017: Journal of Biomolecular Structure & Dynamics
Walter G O'Dell, Anne K Gormaley, David A Prida
PURPOSE: Detailed characterization of changes in vessel size is crucial for the diagnosis and management of a variety of vascular diseases. Because clinical measurement of vessel size is typically dependent on the radiologist's subjective interpretation of the vessel borders, it is often prone to high inter- and intra-user variability. Automatic methods of vessel sizing have been developed for two-dimensional images but a fully three-dimensional (3D) method suitable for vessel sizing from volumetric X-ray computed tomography (CT) or magnetic resonance imaging has heretofore not been demonstrated and validated robustly...
September 14, 2017: Medical Physics
Sk Abdul Amin, Nilanjan Adhikari, Shovanlal Gayen, Tarun Jha
A number of people worldwide have been suffering from ocular neovascularization that may be treated by a variety of drugs but these may possess adverse effects. Therefore, small antiangiogenic molecules with higher potency and lower toxic effects are intended. However, homoisoflavonoids of natural origin show the potential antiangiogenic effect in ocular neovascularization. These homoisoflavonoids are judged quantitatively in terms of statistical validation through multi-chemometric modeling approaches for the betterment and refinement of their structures required for higher antiangiogenic activity targeted to ocular neovascularization...
September 8, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Elaheh Maleki, Farouk Belkadi, Mathieu Ritou, Alain Bernard
The longtime productivity of an industrial machine is improved by condition-based maintenance strategies. To do this, the integration of sensors and other cyber-physical devices is necessary in order to capture and analyze a machine's condition through its lifespan. Thus, choosing the best sensor is a critical step to ensure the efficiency of the maintenance process. Indeed, considering the variety of sensors, and their features and performance, a formal classification of a sensor's domain knowledge is crucial...
September 8, 2017: Sensors
Florian Ganglberger, Joanna Kaczanowska, Josef M Penninger, Andreas Hess, Katja Bühler, Wulf Haubensak
Functional neuroanatomical maps provide a mesoscale reference framework for studies from molecular to systems neuroscience and psychiatry. The underlying structure-function relationships are typically derived from functional manipulations or imaging approaches. Although highly informative, these are experimentally costly. The increasing amount of publicly available brain and genetic data offers a rich source that could be mined to address this problem computationally. Here, we developed an algorithm that fuses gene expression and connectivity data with functional genetic meta data and exploits cumulative effects to derive neuroanatomical maps related to multi-genic functions...
September 3, 2017: NeuroImage
D Ellen K Tarr
Related proteins that have been studied in different labs using varying organisms may lack a uniform system of nomenclature and classification, making it difficult to discuss the group as a whole and to place new sequences into the appropriate context. Developing a reference that prioritizes important sequence features related to structure and/or activity can be used in addition to established names to add some coherency to a diverse group of proteins. This paper uses the cysteine-stabilized alpha-helix (CS-αβ) superfamily as an example to show how a reference generated in spreadsheet software can clarify relationships between existing proteins in the superfamily, as well as facilitate the addition of new sequences...
August 16, 2017: Journal of Visualized Experiments: JoVE
Bonnie A Clough, Michael J Ireland, Sonja March
BACKGROUND: Occupational stress and burnout are highly prevalent among doctors, with stigma identified as a barrier to help-seeking in this population. However, there has been a lack of a standardised tool to measure stigma of occupational stress and burnout among doctors. AIMS: The aim of the current study was to develop and investigate the psychometric properties of the Stigma of Occupational Stress Scale for Doctors (SOSS-D). METHOD: An online questionnaire package was completed by 200 (38 male, 162 female) doctors...
September 4, 2017: Journal of Mental Health
Bin Yang, Yuri Knyazikhin, Matti Mõttus, Miina Rautiainen, Pauline Stenberg, Lei Yan, Chi Chen, Kai Yan, Sungho Choi, Taejin Park, Ranga B Myneni
This paper presents the theoretical basis of the algorithm designed for the generation of leaf area index and diurnal course of its sunlit portion from NASA's Earth Polychromatic Imaging Camera (EPIC) onboard NOAA's Deep Space Climate Observatory (DSCOVR). The Look-up-Table (LUT) approach implemented in the MODIS operational LAI/FPAR algorithm is adopted. The LUT, which is the heart of the approach, has been significantly modified. First, its parameterization incorporates the canopy hot spot phenomenon and recent advances in the theory of canopy spectral invariants...
September 1, 2017: Remote Sensing of Environment
Anup Arunrao Deshpande, Monika Sharma, Anand Kumar Bachhawat
Cystine transporters are a clinically important class of transporters found in bacteria, pathogenic fungi and mammalian cells. Despite their significance, very little is known about the mechanism of substrate recognition and transport. We have carried out studies on the plasma membrane Candida glabrata cystine transporter, CgCYN1 a member of the amino acid-polyamine-organocation (APC) transporter superfamily. A homology model of CgCYN1 was generated by using crystal structures of three known bacterial APC transporters followed by further refinement using molecular dynamics simulations...
September 1, 2017: Biochimica et Biophysica Acta
Giulio Alberini, Fabio Benfenati, Luca Maragliano
Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains...
2017: PloS One
Bryan J Weiner, Cara C Lewis, Cameo Stanick, Byron J Powell, Caitlin N Dorsey, Alecia S Clary, Marcella H Boynton, Heather Halko
BACKGROUND: Implementation outcome measures are essential for monitoring and evaluating the success of implementation efforts. Yet, currently available measures lack conceptual clarity and have largely unknown reliability and validity. This study developed and psychometrically assessed three new measures: the Acceptability of Intervention Measure (AIM), Intervention Appropriateness Measure (IAM), and Feasibility of Intervention Measure (FIM). METHODS: Thirty-six implementation scientists and 27 mental health professionals assigned 31 items to the constructs and rated their confidence in their assignments...
August 29, 2017: Implementation Science: IS
Ruida Cheng, Holger R Roth, Nathan Lay, Le Lu, Baris Turkbey, William Gandler, Evan S McCreedy, Tom Pohida, Peter A Pinto, Peter Choyke, Matthew J McAuliffe, Ronald M Summers
Accurate automatic segmentation of the prostate in magnetic resonance images (MRI) is a challenging task due to the high variability of prostate anatomic structure. Artifacts such as noise and similar signal intensity of tissues around the prostate boundary inhibit traditional segmentation methods from achieving high accuracy. We investigate both patch-based and holistic (image-to-image) deep-learning methods for segmentation of the prostate. First, we introduce a patch-based convolutional network that aims to refine the prostate contour which provides an initialization...
October 2017: Journal of Medical Imaging
Benjamin R Mackie, Andrea Marshall, Marion Mitchell, Michael J Ireland
BACKGROUND: The validity of instruments is crucial in ensuring that data collected are sound and that these data represents what the instrument claims to measure. When an instrument is revised or used in a different population it is useful to re-examine its construct validity. AIM: To test the psychometrics properties of an instrument - the revised Families' Importance In Nursing Care - Nurses' Attitudes, designed to measure nurse' attitudes towards involving family in nursing care in an adult acute care setting...
August 23, 2017: Journal of Advanced Nursing
Marawan Ahmed, Horia Jalily Hasani, Aravindhan Ganesan, Michael Houghton, Khaled Barakat
Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer...
2017: Drug Design, Development and Therapy
Ying Cui, Xiuming Xi, Jinsheng Zhang, Jiang Feng, Xiaoxiao Deng, Ang Li, Jianxin Zhou
BACKGROUND: In China, increasing attention has been devoted to the patient safety culture within health administrative departments and healthcare organizations. However, no official version of a patient safety culture assessment tool has been published or is widely used, and little is known about the status of the safety culture in Chinese hospitals. The aims of this study were to examine the reliability and validity of the Safety Attitudes Questionnaire in Chinese and to establish benchmark data on the safety culture in Beijing...
August 23, 2017: BMC Health Services Research
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
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
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
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
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
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