Revising the UMLS Semantic Network

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration

Special Libraries, Winter 1986

Volume 77, Issue 1https://scholarworks.sjsu.edu/sla_sl_1986/1000/thumbnail.jp

Sensors for biomedical applications

This paper considers the impact during the last decade of modern IC technology, microelectronics, thin- and thick-film technology, fibre optic technology, etc. on the development of sensors for biomedical applications

Integration of a failure monitoring within a hybrid dynamic simulation environment

The complexity and the size of the industrial chemical processes induce the monitoring of a growing number of process variables. Their knowledge is generally based on the measurements of system variables and on the physico-chemical models of the process. Nevertheless this information is imprecise because of process and measurement noise. So the research ways aim at developing new and more powerful techniques for the detection of process fault. In this work, we present a method for the fault detection based on the comparison between the real system and the reference model evolution generated by the extended Kalman filter. The reference model is simulated by the dynamic hybrid simulator, PrODHyS. It is a general object-oriented environment which provides common and reusable components designed for the development and the management of dynamic simulation of industrial systems. The use of this method is illustrated through a didactic example relating to the field of Chemical Process System Engineering

Was Germany ever united? Borders and domestic trade, 1885 - 1933

Was Germany ever united? Given the historical circumstances of Germanys unification in the 19th century there is no obvious answer to this question. But such an answer can affect the prospects of the post-1989 unification process, and beyond this of European integration. We provide an econometric analysis of Germanys economic integration across various internal borders from the foundation of the Kaiserreich until the end of the Weimar Republic. This analysis is based on a new comprehensive set of domestic trade flow data on railways and waterways, covering all parts of Germany 1885-1933. First, the disintegration effects by the separation of Alsace-Lorraine and Western Poland from Germany after the Versailles treaty were somewhat limited by previous disintegration of these regions. Second, while there is broad support for increasing integration across old political, administrative, and confessional borders between 1885 and 1933, a geographical divide between eastern and western parts of Germany had a persistent trade diverting effect well into the 1930s. --Germany,Economic Integration,Railways,Waterways

SkyNet: A modular nuclear reaction network library

Almost all of the elements heavier than hydrogen that are present in our solar system were produced by nuclear burning processes either in the early universe or at some point in the life cycle of stars. In all of these environments, there are dozens to thousands of nuclear species that interact with each other to produce successively heavier elements. In this paper, we present SkyNet, a new general-purpose nuclear reaction network that evolves the abundances of nuclear species under the influence of nuclear reactions. SkyNet can be used to compute the nucleosynthesis evolution in all astrophysical scenarios where nucleosynthesis occurs. SkyNet is free and open-source and aims to be easy to use and flexible. Any list of isotopes can be evolved and SkyNet supports various different types of nuclear reactions. SkyNet is modular so that new or existing physics, like nuclear reactions or equations of state, can easily be added or modified. Here, we present in detail the physics implemented in SkyNet with a focus on a self-consistent transition to and from nuclear statistical equilibrium (NSE) to non-equilibrium nuclear burning, our implementation of electron screening, and coupling of the network to an equation of state. We also present comprehensive code tests and comparisons with existing nuclear reaction networks. We find that SkyNet agrees with published results and other codes to an accuracy of a few percent. Discrepancies, where they exist, can be traced to differences in the physics implementations.Comment: 39 pages, 11 figures, published in ApJ Supplement Serie

A Minimal Model of Metabolism Based Chemotaxis

Since the pioneering work by Julius Adler in the 1960's, bacterial chemotaxis has been predominantly studied as metabolism-independent. All available simulation models of bacterial chemotaxis endorse this assumption. Recent studies have shown, however, that many metabolism-dependent chemotactic patterns occur in bacteria. We hereby present the simplest artificial protocell model capable of performing metabolism-based chemotaxis. The model serves as a proof of concept to show how even the simplest metabolism can sustain chemotactic patterns of varying sophistication. It also reproduces a set of phenomena that have recently attracted attention on bacterial chemotaxis and provides insights about alternative mechanisms that could instantiate them. We conclude that relaxing the metabolism-independent assumption provides important theoretical advances, forces us to rethink some established pre-conceptions and may help us better understand unexplored and poorly understood aspects of bacterial chemotaxis

Mapping the Human Exposome to Uncover the Causes of Breast Cancer.

Breast cancer is an important cause of morbidity and mortality for women, yet a significant proportion of variation in individual risk is unexplained. It is reasonable to infer that unexplained breast cancer risks are caused by a myriad of exposures and their interactions with genetic factors. Most epidemiological studies investigating environmental contribution to breast cancer risk have focused on a limited set of exposures and outcomes based on a priori knowledge. We hypothesize that by measuring a rich set of molecular information with omics (e.g., metabolomics and adductomics) and comparing these profiles using a case-control design we can pinpoint novel environmental risk factors. Specifically, exposome-wide association study approaches can be used to compare molecular profiles between controls and either breast cancer cases or participants with phenotypic measures associated with breast cancer (e.g., high breast density, chronic inflammation). Current challenges in annotating compound peaks from biological samples can be addressed by creating libraries of environmental chemicals that are breast cancer relevant using publicly available high throughput exposure and toxicity data, and by mass spectra fragmentation. This line of discovery and innovation will extend understanding of how environmental exposures interact with genetics to affect health, and provide evidence to support new breast cancer prevention strategies

From discretization to regularization of composite discontinuous functions

Discontinuities between distinct regions, described by different equation sets, cause difficulties for PDE/ODE solvers. We present a new algorithm that eliminates integrator discontinuities through regularizing discontinuities. First, the algorithm determines the optimum switch point between two functions spanning adjacent or overlapping domains. The optimum switch point is determined by searching for a “jump point” that minimizes a discontinuity between adjacent/overlapping functions. Then, discontinuity is resolved using an interpolating polynomial that joins the two discontinuous functions. This approach eliminates the need for conventional integrators to either discretize and then link discontinuities through generating interpolating polynomials based on state variables or to reinitialize state variables when discontinuities are detected in an ODE/DAE system. In contrast to conventional approaches that handle discontinuities at the state variable level only, the new approach tackles discontinuity at both state variable and the constitutive equations level. Thus, this approach eliminates errors associated with interpolating polynomials generated at a state variable level for discontinuities occurring in the constitutive equations. Computer memory space requirements for this approach exponentially increase with the dimension of the discontinuous function hence there will be limitations for functions with relatively high dimensions. Memory availability continues to increase with price decreasing so this is not expected to be a major limitation