World Wide Web Robot for Extreme Datamining with Swiss-Tx Supercomputers

This paper discusses the software and hardware issues of designing a highly parallel robot for extreme datamining on the Internet. As a sample application, a World Wide Web server count experiment for Switzerland and Thailand is presented. Our platform of choice is the SwissTx, a supercomputer built from commodity components that runs NT and COMPAQ tru64 UNIX. Hardware and software of this machine are discussed and benchmark results presented. They show that NT is a feasible choice even under the given extreme conditions. Using statistical modelling for optimizing the search process, the inevitable bandwidth problem is reduced to some extent to a computation problem. We suggest that our approach to Web robots is a robust bet for a multitude of future Internet applications which might lead to a large-scale and cost-efficient usage of Web robots

The Failure or Future of American Archival History: A Somewhat Unorthodox View

The quality of research on American archival history has been uneven and the quantity not very impressive. This essay reviews some of the highlights of American archival history research, especially the growing interest in cultural and public history that has produced some studies of interest to scholars curious about the history of archives. The essay also focuses more on why such research still seems so far removed from the interests of most archivists. The essay will consider some hopeful signs, such as the re-emergence of records and record-keeping systems as a core area for study, for a renewed emphasis on American archival history. While much needs to be done, I am optimistic that the golden age of historical research on American archives lies ahead

Information Outlook, August 2006

Volume 10, Issue 8https://scholarworks.sjsu.edu/sla_io_2006/1007/thumbnail.jp

Length, Protein-Protein Interactions, and Complexity

The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein interactions has driven the selection of longer proteins, as longer proteins are more able to distinguish among a larger number of distinct interactions due to their greater average surface area. Annotated protein sequences available from the SWISS-PROT database were analyzed for thirteen eukaryotes, eight bacteria, and two archaea species. The number of subcellular locations to which each protein is associated is used as a measure of the number of interactions to which a protein participates. Two databases of yeast protein-protein interactions were used as another measure of the number of interactions to which each \emph{S. cerevisiae} protein participates. Protein length is shown to correlate with both number of subcellular locations to which a protein is associated and number of interactions as measured by yeast two-hybrid experiments. Protein length is also shown to correlate with the probability that the protein is encoded by an essential gene. Interestingly, average protein length and number of subcellular locations are not significantly different between all human proteins and protein targets of known, marketed drugs. Increased protein length appears to be a significant mechanism by which the increasing complexity of protein-protein interaction networks is accommodated within the natural evolution of species. Consideration of protein length may be a valuable tool in drug design, one that predicts different strategies for inhibiting interactions in aberrant and normal pathways.Comment: 13 pages, 5 figures, 2 tables, to appear in Physica

Role of the Fractalkine Receptor in CNS Autoimmune Inflammation: New Approach Utilizing a Mouse Model Expressing the Human CX3CR1

Multiple sclerosis (MS), an inflammatory demyelinating disease of the central nervous system (CNS) is the leading cause of non-traumatic neurological disability in young adults. Immune mediated destruction of myelin and oligodendrocytes is considered the primary pathology of MS, but progressive axonal loss is the major cause of neurological disability. In an effort to understand microglia function during CNS inflammation, our laboratory focuses on the fractalkine/CX3CR1 signaling as a regulator of microglia neurotoxicity in various models of neurodegeneration. Fractalkine (FKN) is a transmembrane chemokine expressed in the CNS by neurons and signals through its unique receptor CX3CR1 present in microglia. During experimental autoimmune encephalomyelitis (EAE), CX3CR1 deficiency confers exacerbated disease defined by severe inflammation and neuronal loss. The CX3CR1 human polymorphism I249/M280 present in ∼20% of the population exhibits reduced adhesion for FKN conferring defective signaling whose role in microglia function and influence on neurons during MS remains unsolved. The aim of this study is to assess the effect of weaker signaling through hCX3CR1I249/M280 during EAE. We hypothesize that dysregulated microglial responses due to impaired CX3CR1 signaling enhance neuronal/axonal damage. We generated an animal model replacing the mouse CX3CR1 locus for the hCX3CR1I249/M280 variant. Upon EAE induction, these mice exhibited exacerbated EAE correlating with severe inflammation and neuronal loss. We also observed that mice with aberrant CX3CR1 signaling are unable to produce FKN and ciliary neurotrophic factor during EAE in contrast to wild type mice. Our results provide validation of defective function of the hCX3CR1I249/M280 variant and the foundation to broaden the understanding of microglia dysfunction during neuroinflammation. © 2018 Cardona et al

Knowledge Transfer Needs and Methods

INE/AUTC 12.3

GridCertLib: a Single Sign-on Solution for Grid Web Applications and Portals

This paper describes the design and implementation of GridCertLib, a Java library leveraging a Shibboleth-based authentication infrastructure and the SLCS online certificate signing service, to provide short-lived X.509 certificates and Grid proxies. The main use case envisioned for GridCertLib, is to provide seamless and secure access to Grid/X.509 certificates and proxies in web applications and portals: when a user logs in to the portal using Shibboleth authentication, GridCertLib can automatically obtain a Grid/X.509 certificate from the SLCS service and generate a VOMS proxy from it. We give an overview of the architecture of GridCertLib and briefly describe its programming model. Its application to some deployment scenarios is outlined, as well as a report on practical experience integrating GridCertLib into portals for Bioinformatics and Computational Chemistry applications, based on the popular P-GRADE and Django softwares.Comment: 18 pages, 1 figure; final manuscript accepted for publication by the "Journal of Grid Computing