637 research outputs found

    An Ontology for Description of Drug Discovery Investigations

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    SummaryThe paper presents an ontology for the description of Drug Discovery Investigation (DDI). This has been developed through the use of a Robot Scientist “Eve”, and in consultation with industry. DDI aims to define the principle entities and the relations in the research and development phase of the drug discovery pipeline. DDI is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. This enables DDI to be integrated with such related ontologies as the Vaccine Ontology, the Advancing Clinico-Genomic Trials on Cancer Master Ontology, etc. DDI is available at http://purl.org/ddi/wikipedia or http://purl.org/ddi/home</jats:p

    Meta-QSAR: a large-scale application of meta-learning to drug design and discovery.

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    We investigate the learning of quantitative structure activity relationships (QSARs) as a case-study of meta-learning. This application area is of the highest societal importance, as it is a key step in the development of new medicines. The standard QSAR learning problem is: given a target (usually a protein) and a set of chemical compounds (small molecules) with associated bioactivities (e.g. inhibition of the target), learn a predictive mapping from molecular representation to activity. Although almost every type of machine learning method has been applied to QSAR learning there is no agreed single best way of learning QSARs, and therefore the problem area is well-suited to meta-learning. We first carried out the most comprehensive ever comparison of machine learning methods for QSAR learning: 18 regression methods, 3 molecular representations, applied to more than 2700 QSAR problems. (These results have been made publicly available on OpenML and represent a valuable resource for testing novel meta-learning methods.) We then investigated the utility of algorithm selection for QSAR problems. We found that this meta-learning approach outperformed the best individual QSAR learning method (random forests using a molecular fingerprint representation) by up to 13%, on average. We conclude that meta-learning outperforms base-learning methods for QSAR learning, and as this investigation is one of the most extensive ever comparisons of base and meta-learning methods ever made, it provides evidence for the general effectiveness of meta-learning over base-learning

    Kolmogorov-Sinai entropy in field line diffusion by anisotropic magnetic turbulence

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    The Kolmogorov-Sinai (KS) entropy in turbulent diffusion of magnetic field lines is analyzed on the basis of a numerical simulation model and theoretical investigations. In the parameter range of strongly anisotropic magnetic turbulence the KS entropy is shown to deviate considerably from the earlier predicted scaling relations [Rev. Mod. Phys. {\bf 64}, 961 (1992)]. In particular, a slowing down logarithmic behavior versus the so-called Kubo number R1R\gg 1 (R=(δB/B0)(ξ/ξ)R = (\delta B / B_0) (\xi_\| / \xi_\bot), where δB/B0\delta B / B_0 is the ratio of the rms magnetic fluctuation field to the magnetic field strength, and ξ\xi_\bot and ξ\xi_\| are the correlation lengths in respective dimensions) is found instead of a power-law dependence. These discrepancies are explained from general principles of Hamiltonian dynamics. We discuss the implication of Hamiltonian properties in governing the paradigmatic "percolation" transport, characterized by RR\to\infty, associating it with the concept of pseudochaos (random non-chaotic dynamics with zero Lyapunov exponents). Applications of this study pertain to both fusion and astrophysical plasma and by mathematical analogy to problems outside the plasma physics. This research article is dedicated to the memory of Professor George M. ZaslavskyComment: 15 pages, 2 figures. Accepted for publication on Plasma Physics and Controlled Fusio

    The prognosis of allocentric and egocentric neglect : evidence from clinical scans

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    We contrasted the neuroanatomical substrates of sub-acute and chronic visuospatial deficits associated with different aspects of unilateral neglect using computed tomography scans acquired as part of routine clinical diagnosis. Voxel-wise statistical analyses were conducted on a group of 160 stroke patients scanned at a sub-acute stage. Lesion-deficit relationships were assessed across the whole brain, separately for grey and white matter. We assessed lesions that were associated with behavioural performance (i) at a sub-acute stage (within 3 months of the stroke) and (ii) at a chronic stage (after 9 months post stroke). Allocentric and egocentric neglect symptoms at the sub-acute stage were associated with lesions to dissociated regions within the frontal lobe, amongst other regions. However the frontal lesions were not associated with neglect at the chronic stage. On the other hand, lesions in the angular gyrus were associated with persistent allocentric neglect. In contrast, lesions within the superior temporal gyrus extending into the supramarginal gyrus, as well as lesions within the basal ganglia and insula, were associated with persistent egocentric neglect. Damage within the temporo-parietal junction was associated with both types of neglect at the sub-acute stage and 9 months later. Furthermore, white matter disconnections resulting from damage along the superior longitudinal fasciculus were associated with both types of neglect and critically related to both sub-acute and chronic deficits. Finally, there was a significant difference in the lesion volume between patients who recovered from neglect and patients with chronic deficits. The findings presented provide evidence that (i) the lesion location and lesion size can be used to successfully predict the outcome of neglect based on clinical CT scans, (ii) lesion location alone can serve as a critical predictor for persistent neglect symptoms, (iii) wide spread lesions are associated with neglect symptoms at the sub-acute stage but only some of these are critical for predicting whether neglect will become a chronic disorder and (iv) the severity of behavioural symptoms can be a useful predictor of recovery in the absence of neuroimaging findings on clinical scans. We discuss the implications for understanding the symptoms of the neglect syndrome, the recovery of function and the use of clinical scans to predict outcome

    Italian standardization of the Apples Cancellation Test

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    Hemispatial neglect due to right parieto-temporo-frontal lesions has a negative impact on the success of rehabilitation, resulting in poor functional gain. Recent research has shown that different types of neglect can impact in a different way on rehabilitation outcomes. The availability of a sensitive test, useful for distinguishing egocentric and allocentric forms of neglect, may be clinically important as all current clinical instruments fail to distinguish between these forms of disturbance, yet they differentially predict outcome. The Apples Test is a new instrument useful to evaluate both egocentric and allocentric forms of neglect. In order to establish Italian norms for this diagnostic instrument the test was administered to a sample of 412 healthy people of both genders (201 M and 211 F), aged from 20 to 80 years enrolled from 14 different rehabilitation centers in Italy. Based on the data, we established pathological performance cut-offs for the accuracy score (total omission errors), the asymmetry score for egocentric neglect (omission error difference), the asymmetry score for allocentric neglect (commission error difference) and execution time. The usefulness of the Apples Test for diagnostic purposes is illustrated by presenting three patients with different forms of neglect (egocentric, allocentric and mixed neglect)
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