Interfacial separation between elastic solids with randomly rough surfaces: comparison between theory and numerical techniques

We study the distribution of interfacial separations P(u) at the contact region between two elastic solids with randomly rough surfaces. An analytical expression is derived for P(u) using Persson's theory of contact mechanics, and is compared to numerical solutions obtained using (a) a half-space method based on the Boussinesq equation, (b) a Green's function molecular dynamics technique and (c) smart-block classical molecular dynamics. Overall, we find good agreement between all the different approaches.Comment: 25 pages, 12 figure

The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers

This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information’s (NCBI’s) Entrez system. The NLB collects these links from each resource and passes them to the NCBI which incorporates them into its Entrez LinkOut service. In this way, an Entrez user looking at a specific Entrez entry can LinkOut directly to related neuroscience information. The information stored in the NLB can also be utilized in other ways. A second approach, which is operational on a pilot basis, is for the NLB Web server to create dynamically its own Web page of LinkOut links for each NCBI identifier in the NLB database. This approach can allow other resources (in addition to the NCBI Entrez) to LinkOut to related neuroscience information. The paper describes the current NLB system and discusses certain design issues that arose during its implementation

Automatic Pulmonary Nodule Detection in CT Scans Using Convolutional Neural Networks Based on Maximum Intensity Projection

Accurate pulmonary nodule detection is a crucial step in lung cancer screening. Computer-aided detection (CAD) systems are not routinely used by radiologists for pulmonary nodule detection in clinical practice despite their potential benefits. Maximum intensity projection (MIP) images improve the detection of pulmonary nodules in radiological evaluation with computed tomography (CT) scans. Inspired by the clinical methodology of radiologists, we aim to explore the feasibility of applying MIP images to improve the effectiveness of automatic lung nodule detection using convolutional neural networks (CNNs). We propose a CNN-based approach that takes MIP images of different slab thicknesses (5 mm, 10 mm, 15 mm) and 1 mm axial section slices as input. Such an approach augments the two-dimensional (2-D) CT slice images with more representative spatial information that helps discriminate nodules from vessels through their morphologies. Our proposed method achieves sensitivity of 92.67% with 1 false positive per scan and sensitivity of 94.19% with 2 false positives per scan for lung nodule detection on 888 scans in the LIDC-IDRI dataset. The use of thick MIP images helps the detection of small pulmonary nodules (3 mm-10 mm) and results in fewer false positives. Experimental results show that utilizing MIP images can increase the sensitivity and lower the number of false positives, which demonstrates the effectiveness and significance of the proposed MIP-based CNNs framework for automatic pulmonary nodule detection in CT scans. The proposed method also shows the potential that CNNs could gain benefits for nodule detection by combining the clinical procedure.Comment: Submitted to IEEE TM

Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealisations of biochemically reacting systems must be able to capture stochastic phenomena. While robust theory exists to describe such stochastic models, the computational challenges in exploring these models can be a significant burden in practice since realistic models are analytically intractable. Determining the expected behaviour and variability of a stochastic biochemical reaction network requires many probabilistic simulations of its evolution. Using a biochemical reaction network model to assist in the interpretation of time course data from a biological experiment is an even greater challenge due to the intractability of the likelihood function for determining observation probabilities. These computational challenges have been subjects of active research for over four decades. In this review, we present an accessible discussion of the major historical developments and state-of-the-art computational techniques relevant to simulation and inference problems for stochastic biochemical reaction network models. Detailed algorithms for particularly important methods are described and complemented with MATLAB implementations. As a result, this review provides a practical and accessible introduction to computational methods for stochastic models within the life sciences community

From techno-scientific grammar to organizational syntax. New production insights on the nature of the firm

The paper aims at providing the conceptual building blocks of a theory of the firm which addresses its "ontological questions" (existence,boundaries and organization) by placing production at its core. We draw on engineering for a more accurate description of the production process itself, highlighting its inner complexity and potentially chaotic nature, and on computational linguistics for a production-based account of the nature of economic agents and of the mechanisms through which they build ordered production sets. In so doing, we give a "more appropriate" production basis to the crucial issues of how firm's boundaries are set, how its organisational structure is defined, and how it changes over time. In particular, we show how economic agents select some tasks to be performed internally, while leaving some other to external suppliers, on the basis of criteria based on both the different degrees of internal congruence of the tasks to be performed (i.e. the internal environment), and on the outer relationships carried out with other agents (i.e. the external environment)

Brittle porous material mesovolume structure models and simulation of their mechanical properties

To study the mechanical response of brittle porous materials at mesoscale, porous samples were generated and their deformation was numerically modelled. Two types of pore space morphology such as overlapping spherical pores and overlapping spherical solids were explicitly considered. For deformation modelling, an evolutionary approach including the nonlinear constitutive equations used to describe damage accumulation and its impact on the degradation of the solid frame strength properties was applied. The numerical results have shown that an average stress-strain diagram is sensitive to pore morphology as well as porosity

The Data Big Bang and the Expanding Digital Universe: High-Dimensional, Complex and Massive Data Sets in an Inflationary Epoch

Recent and forthcoming advances in instrumentation, and giant new surveys, are creating astronomical data sets that are not amenable to the methods of analysis familiar to astronomers. Traditional methods are often inadequate not merely because of the size in bytes of the data sets, but also because of the complexity of modern data sets. Mathematical limitations of familiar algorithms and techniques in dealing with such data sets create a critical need for new paradigms for the representation, analysis and scientific visualization (as opposed to illustrative visualization) of heterogeneous, multiresolution data across application domains. Some of the problems presented by the new data sets have been addressed by other disciplines such as applied mathematics, statistics and machine learning and have been utilized by other sciences such as space-based geosciences. Unfortunately, valuable results pertaining to these problems are mostly to be found only in publications outside of astronomy. Here we offer brief overviews of a number of concepts, techniques and developments, some "old" and some new. These are generally unknown to most of the astronomical community, but are vital to the analysis and visualization of complex datasets and images. In order for astronomers to take advantage of the richness and complexity of the new era of data, and to be able to identify, adopt, and apply new solutions, the astronomical community needs a certain degree of awareness and understanding of the new concepts. One of the goals of this paper is to help bridge the gap between applied mathematics, artificial intelligence and computer science on the one side and astronomy on the other.Comment: 24 pages, 8 Figures, 1 Table. Accepted for publication: "Advances in Astronomy, special issue "Robotic Astronomy

The Missing Link between Morphemic Assemblies and Behavioral Responses:a Bayesian Information-Theoretical model of lexical processing

We present the Bayesian Information-Theoretical (BIT) model of lexical processing: A mathematical model illustrating a novel approach to the modelling of language processes. The model shows how a neurophysiological theory of lexical processing relying on Hebbian association and neural assemblies can directly account for a variety of effects previously observed in behavioural experiments. We develop two information-theoretical measures of the distribution of usages of a morpheme or word, and use them to predict responses in three visual lexical decision datasets investigating inflectional morphology and polysemy. Our model offers a neurophysiological basis for the effects of morpho-semantic neighbourhoods. These results demonstrate how distributed patterns of activation naturally result in the arisal of symbolic structures. We conclude by arguing that the modelling framework exemplified here, is a powerful tool for integrating behavioural and neurophysiological results