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  • Solution structure of apamin determined by nuclear magnetic resonance and distance geometry
    Wemmer ; 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 institutions
    Castelli, 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 sensor
    Hsieh, 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.
  • The dubious value of cerebrospinal fluid adenosine deaminase measurement for the diagnosis of tuberculous meningitis
    George, 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.
  • The Effect of a Variable Disc Pad Friction Coefficient for the Mechanical Brake System of a Railway Vehicle
    Lee, 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.