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- Solution structure of apamin determined by nuclear magnetic resonance and distance geometryWemmer ; Pease (1988-11-01)The solution structure of the bee venom neurotoxin apamin has been determined with a distance geometry program using distance constraints derived from NMR. Twenty embedded structures were generated and refined by using the program DSPACE. After error minimization using both conjugate gradient and dynamics algorithms, six structures had very low residual error. Comparisons of these show that the backbone of the peptide is quite well-defined with the largest rms difference between backbone atoms in these structures of 1.34 A. The side chains have far fewer constraints and show greater variability in their positions. The structure derived here is generally consistent with the qualitative model previously described, with most differences occurring in the loop between the beta-turn (residues 2-5) and the C-terminal alpha-helix (residues 9-17). Comparisons are made with previously derived models from NMR data and other methods.
- Science, institutional archives and open access: an overview and a pilot survey on the Italian cancer research institutionsCastelli, Mauro ; Cognetti, Gaetana ; Truccolo, Ivana ; Poltronieri, Elisabetta ; Di Benedetto, Corrado ; Mazzocut, Mauro (2010-12-20)BACKGROUND: The Open Archive Initiative (OAI) refers to a movement started around the '90 s to guarantee free access to scientific information by removing the barriers to research results, especially those related to the ever increasing journal subscription prices. This new paradigm has reshaped the scholarly communication system and is closely connected to the build up of institutional repositories (IRs) conceived to the benefit of scientists and research bodies as a means to keep possession of their own literary production. The IRs are high-value tools which permit authors to gain visibility by enabling rapid access to scientific material (not only publications) thus increasing impact (citation rate) and permitting a multidimensional assessment of research findings. METHODS: A survey was conducted in March 2010 to mainly explore the managing system in use for archiving the research finding adopted by the Italian Scientific Institutes for Research, Hospitalization and Health Care (IRCCS) of the oncology area within the Italian National Health Service (Servizio Sanitario Nazionale, SSN). They were asked to respond to a questionnaire intended to collect data about institutional archives, metadata formats and posting of full-text documents. The enquiry concerned also the perceived role of the institutional repository DSpace ISS, built up by the Istituto Superiore di Sanità (ISS) and based on a XML scheme for encoding metadata. Such a repository aims at acting as a unique reference point for the biomedical information produced by the Italian research institutions. An in-depth analysis has also been performed on the collection of information material addressed to patients produced by the institutions surveyed. RESULTS: The survey respondents were 6 out of 9. The results reveal the use of different practices and standard among the institutions concerning: the type of documentation collected, the software adopted, the use and format of metadata and the conditions of accessibility to the IRs. CONCLUSIONS: The Italian research institutions in the field of oncology are moving the first steps towards the philosophy of OA. The main effort should be the implementation of common procedures also in order to connect scientific publications to researchers curricula. In this framework, an important effort is represented by the project of ISS aimed to set a common interface able to allow migration of data from partner institutions to the OA compliant repository DSpace ISS.
- Chaotic extension neural network theory-based XXY stage collision fault detection using a single accelerometer sensorHsieh, Chin-Tsung ; Lin, Huo-Cheng ; Yau, Her-Terng ; Wu, Shang-Yi (2014-11-14)The collision fault detection of a XXY stage is proposed for the first time in this paper. The stage characteristic signals are extracted and imported into the master and slave chaos error systems by signal filtering from the vibratory magnitude of the stage. The trajectory diagram is made from the chaos synchronization dynamic error signals E1 and E2. The distance between characteristic positive and negative centers of gravity, as well as the maximum and minimum distances of trajectory diagram, are captured as the characteristics of fault recognition by observing the variation in various signal trajectory diagrams. The matter-element model of normal status and collision status is built by an extension neural network. The correlation grade of various fault statuses of the XXY stage was calculated for diagnosis. The dSPACE is used for real-time analysis of stage fault status with an accelerometer sensor. Three stage fault statuses are detected in this study, including normal status, Y collision fault and X collision fault. It is shown that the scheme can have at least 75% diagnosis rate for collision faults of the XXY stage. As a result, the fault diagnosis system can be implemented using just one sensor, and consequently the hardware cost is significantly reduced.
- Erratum to: DRR and portal image registration for automatic patient positioning in radiotherapy treatmentBastida-Jumilla, Ma Consuelo ; Verdú-Monedero, Rafael ; Larrey-Ruiz, Jorge ; Sancho-Gómez, José-Luis ; Morales-Sánchez, Juan (2015-04-01)
- QSAR DataBank repository: open and linked qualitative and quantitative structure-activity relationship modelsSild, S ; Maran, U ; Ruusmann, V (2015-06-25)BACKGROUND: Structure-activity relationship models have been used to gain insight into chemical and physical processes in biomedicine, toxicology, biotechnology, etc. for almost a century. They have been recognized as valuable tools in decision support workflows for qualitative and quantitative predictions. The main obstacle preventing broader adoption of quantitative structure-activity relationships [(Q)SARs] is that published models are still relatively difficult to discover, retrieve and redeploy in a modern computer-oriented environment. This publication describes a digital repository that makes in silico (Q)SAR-type descriptive and predictive models archivable, citable and usable in a novel way for most common research and applied science purposes. DESCRIPTION: The QSAR DataBank (QsarDB) repository aims to make the processes and outcomes of in silico modelling work transparent, reproducible and accessible. Briefly, the models are represented in the QsarDB data format and stored in a content-aware repository (a.k.a. smart repository). Content awareness has two dimensions. First, models are organized into collections and then into collection hierarchies based on their metadata. Second, the repository is not only an environment for browsing and downloading models (the QDB archive) but also offers integrated services, such as model analysis and visualization and prediction making. CONCLUSIONS: The QsarDB repository unlocks the potential of descriptive and predictive in silico (Q)SAR-type models by allowing new and different types of collaboration between model developers and model users. The key enabling factor is the representation of (Q)SAR models in the QsarDB data format, which makes it easy to preserve and share all relevant data, information and knowledge. Model developers can become more productive by effectively reusing prior art. Model users can make more confident decisions by relying on supporting information that is larger and more diverse than before. Furthermore, the smart repository automates most of the mundane work (e.g., collecting, systematizing, and reporting data), thereby reducing the time to decision.
- Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiersMcLean, Andrew ; Mason, Nicholas J ; Harvey, Matthew J ; Rzepa, Henry S (2015-08-08)BACKGROUND: We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the persistent identifier of the dataset with optional specification of the attributes of the data document such as filename or media type. RESULTS: The procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories. CONCLUSIONS: Our methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data. Graphical abstract.
- The Effect of a Variable Disc Pad Friction Coefficient for the Mechanical Brake System of a Railway VehicleLee, Nam-Jin ; Kang, Chul-Goo (2015-08-12)A brake hardware-in-the-loop simulation (HILS) system for a railway vehicle is widely applied to estimate and validate braking performance in research studies and field tests. When we develop a simulation model for a full vehicle system, the characteristics of all components are generally properly simplified based on the understanding of each component's purpose and interaction with other components. The friction coefficient between the brake disc and the pad used in simulations has been conventionally considered constant, and the effect of a variable friction coefficient is ignored with the assumption that the variability affects the performance of the vehicle braking very little. However, the friction coefficient of a disc pad changes significantly within a range due to environmental conditions, and thus, the friction coefficient can affect the performance of the brakes considerably, especially on the wheel slide. In this paper, we apply a variable friction coefficient and analyzed the effects of the variable friction coefficient on a mechanical brake system of a railway vehicle. We introduce a mathematical formula for the variable friction coefficient in which the variable friction is represented by two variables and five parameters. The proposed formula is applied to real-time simulations using a brake HILS system, and the effectiveness of the formula is verified experimentally by testing the mechanical braking performance of the brake HILS system.
- Standards-based curation of a decade-old digital repository dataset of molecular informationMurray-Rust, Peter ; Rzepa, Henry S ; Stewart, James J P ; Mason, Nicholas J ; Harvey, Matthew J ; McLean, Andrew (2015-08-27)The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported.The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools.We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the "supporting information") should be conducted in a manner that facilitates automatic periodic curation. Graphical abstractStandards and metadata-based curation of a decade-old digital repository dataset of molecular information.
- Modeling and Simulation of Control Actuation System with Fuzzy-PID Logic Controlled Brushless Motor Drives for Missiles Glider ApplicationsArulmozhiyal, Ramaswamy ; Muniraj, Murali (2015-11-03)A control actuation system has been used extensively in automotive, aerospace, and defense applications. The major challenges in modeling control actuation system are rise time, maximum peak to peak overshoot, and response to nonlinear system with percentage error. This paper addresses the challenges in modeling and real time implementation of control actuation system for missiles glider applications. As an alternative fuzzy-PID controller is proposed in BLDC motor drive followed by linkage mechanism to actuate fins in missiles and gliders. The proposed system will realize better rise time and less overshoot while operating in extreme nonlinear dynamic system conditions. A mathematical model of BLDC motor is derived in state space form. The complete control actuation system is modeled in MATLAB/Simulink environment and verified by performing simulation studies. A real time prototype of the control actuation is developed with dSPACE-1104 hardware controller and a detailed analysis is carried out to confirm the viability of the proposed system.
- R. A. FISHER, LANCELOT HOGBEN, AND THE 'COMPETITION' FOR THE CHAIR OF SOCIAL BIOLOGY AT THE LONDON SCHOOL OF ECONOMICS IN 1930: CORRECTING THE LEGENDSarkar, Sahotra ; Tabery, James (2015-12-01)From 1930 to 1937 Lancelot Hogben FRS occupied the Chair of Social Biology at the London School of Economics and Political Science. According to standard histories of this appointment, he and R. A. Fisher FRS both applied for the position, but Hogben was selected over Fisher. The episode has received attention in large part because of the later prominence of the two figures involved. The surviving archival records, however, tell a remarkably different story. Neither Fisher nor Hogben was ever an official candidate for the chair. Indeed, Fisher seems not to have applied for the position at all, and Hogben was approached only behind the scenes of the official search. The purpose of this paper is to correct and complete the history of this episode.
- A Method to Simultaneously Detect the Current Sensor Fault and Estimate the State of Energy for Batteries in Electric VehiclesWang, Jing ; Li, Shiying ; Cao, Binggang ; Xu, Jun (2016-08-19)Recently, State of energy (SOE) has become one of the most fundamental parameters for battery management systems in electric vehicles. However, current information is critical in SOE estimation and current sensor is usually utilized to obtain the latest current information. However, if the current sensor fails, the SOE estimation may be confronted with large error. Therefore, this paper attempts to make the following contributions: Current sensor fault detection and SOE estimation method is realized simultaneously. Through using the proportional integral observer (PIO) based method, the current sensor fault could be accurately estimated. By taking advantage of the accurate estimated current sensor fault, the influence caused by the current sensor fault can be eliminated and compensated. As a result, the results of the SOE estimation will be influenced little by the fault. In addition, the simulation and experimental workbench is established to verify the proposed method. The results indicate that the current sensor fault can be estimated accurately. Simultaneously, the SOE can also be estimated accurately and the estimation error is influenced little by the fault. The maximum SOE estimation error is less than 2%, even though the large current error caused by the current sensor fault still exists.
- How to organize science and technology information in Latin America?Palacios, Mauricio (2016-09-30)
- Data files for ab initio calculations of the lattice parameter and elastic stiffness coefficients of bcc Fe with solutesFellinger, Michael R ; Trinkle, Dallas R ; Hector, Louis G ; xcvbbngfjf (2016-11-29)We present computed datasets on changes in the lattice parameter and elastic stiffness coefficients of bcc Fe due to substitutional Al, B, Cu, Mn, and Si solutes, and octahedral interstitial C and N solutes. The data is calculated using the methodology based on density functional theory (DFT) presented in Ref. (M.R. Fellinger, L.G. Hector Jr., D.R. Trinkle, 2017) . All the DFT calculations were performed using the Vienna Ab initio Simulations Package (VASP) (G. Kresse, J. Furthmüller, 1996) . The data is stored in the NIST dSpace repository (http://hdl.handle.net/11256/671).
- A metadata-driven approach to data repository designMcLean, Andrew ; Harvey, Matthew J ; Rzepa, Henry S (2017-01-24)The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with DataCite in accordance with their current metadata schema, in exchange for a persistent digital object identifier. Two examples of data preview are illustrated, including the demonstration of a method for integration with commercial software that confers rich domain-specific data analytics without introducing customisation into the repository itself.
- The dubious value of cerebrospinal fluid adenosine deaminase measurement for the diagnosis of tuberculous meningitisGeorge, Jaya ; Dusé, Adriano ; Ekermans, Pieter (2017-01-31)The diagnosis of tuberculous meningitis (TBM) can be extremely difficult in the absence of culture confirmation. Cerebrospinal fluid (CSF) adenosine deaminase (ADA) can potentially assist in this regard, although its current value remains unclear. The literature on the usefulness of CSF ADA in TBM diagnosis is inconsistent, especially from an analytical point of view.A retrospective analysis of clinical and laboratory data relating to all CSF ADA requests during 2009 and 2010 in a South African quaternary healthcare setting was performed. A CSF ADA cut-off for TBM diagnosis was calculated using receiver operating characteristic curve analysis. The performance of CSF ADA in different infective and non-infective categories was assessed.In total, 3548 CSF ADA requests were considered over the 2-year period. Of these, 1490 were for patients for whom both a CSF ADA and a mycobacterial culture were requested. The optimal cut-off was calculated at 2.0 U/L (AUC = 0.86; 95% CI = 0.82 - 0.89; p-value < 0.01; sensitivity of 85.9% (95% CI of 77.0 - 92.3) and specificity of 77.7% (95% CI of 75.4 - 79.8%); positive likelihood ratio = 3.85 and negative likelihood ratio = 0.18). At this cut-off 13 TBM cases were missed.An optimal cut-off for routine use could not be established as too many TBM cases were missed. Specimen integrity, lack of ADA assay standardisation and overlap in performance of the assay in different diagnostic categories affect interpretation.
- Practices of research data curation in institutional repositories: A qualitative view from repository staffStvilia, Besiki ; Lee, Dong Joon (2017-03-16)The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools.