War so terrible : the informal theory of interstate warfare and the determinants of interstate war outcomes

Title from PDF of title page; abstract from research PDF (University of Missouri--Columbia, viewed on June 26, 2014).This thesis puts forth a theory of how interstate wars are fought and how certain outcomes and their determinants occur. It begins with an overview of military theory and military science, followed by an overview of the relevant literature in political science. Next the Informal Theory of Interstate Warfare is put forth, along with its implications for how interstate wars are fought and won, lost, or fought to a draw. The theory and its several hypotheses are then tested qualitatively in two case studies, that of the Russo-Japanese War, and World War II. The theory and its hypotheses are further tested quantitatively using a data set that contains strategic level, operational level, doctrinal, economic, population, and political variables with an emphasis on ground, naval, and air warfare in order to determine how and why certain war outcomes occur, the determinants of those war outcomes, and the overall validity of the Informal Theory of Interstate Warfare

Optimizing the Evaluation of Finite Element Matrices

Assembling stiffness matrices represents a significant cost in many finite element computations. We address the question of optimizing the evaluation of these matrices. By finding redundant computations, we are able to significantly reduce the cost of building local stiffness matrices for the Laplace operator and for the trilinear form for Navier-Stokes. For the Laplace operator in two space dimensions, we have developed a heuristic graph algorithm that searches for such redundancies and generates code for computing the local stiffness matrices. Up to cubics, we are able to build the stiffness matrix on any triangle in less than one multiply-add pair per entry. Up to sixth degree, we can do it in less than about two. Preliminary low-degree results for Poisson and Navier-Stokes operators in three dimensions are also promising

A Survey of the Humoral Immune Response of Cancer Patients to a Panel of Human Tumor Antigens

Evidence is growing for both humoral and cellular immune recognition of human tumor antigens. Antibodies with specificity for antigens initially recognized by cytotoxic T lymphocytes (CTLs), e.g., MAGE and tyrosinase, have been detected in melanoma patient sera, and CTLs with specificity for NY-ESO-1, a cancer-testis (CT) antigen initially identified by autologous antibody, have recently been identified. To establish a screening system for the humoral response to autoimmunogenic tumor antigens, an enzyme-linked immunosorbent assay (ELISA) was developed using recombinant NY-ESO-1, MAGE-1, MAGE-3, SSX2, Melan-A, and tyrosinase proteins. A survey of sera from 234 cancer patients showed antibodies to NY-ESO-1 in 19 patients, to MAGE-1 in 3, to MAGE-3 in 2, and to SSX2 in 1 patient. No reactivity to these antigens was found in sera from 70 normal individuals. The frequency of NY-ESO-1 antibody was 9.4% in melanoma patients and 12.5% in ovarian cancer patients. Comparison of tumor NY-ESO-1 phenotype and NY-ESO-1 antibody response in 62 stage IV melanoma patients showed that all patients with NY-ESO-1+ antibody had NY-ESO-1+ tumors, and no patients with NY-ESO-1− tumors had NY-ESO-1 antibody. As the proportion of melanomas expressing NY-ESO-1 is 20–40% and only patients with NY-ESO-1+ tumors have antibody, this would suggest that a high percentage of patients with NY-ESO-1+ tumors develop an antibody response to NY-ESO-1

The Scientific Investigation of Unidentified Aerial Phenomena (UAP) Using Multimodal Ground-based Observatories

Peer reviewedPublisher PD

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology

HLA-DM Mediates Epitope Selection by a “Compare-Exchange” Mechanism when a Potential Peptide Pool Is Available

BACKGROUND: HLA-DM (DM) mediates exchange of peptides bound to MHC class II (MHCII) during the epitope selection process. Although DM has been shown to have two activities, peptide release and MHC class II refolding, a clear characterization of the mechanism by which DM facilitates peptide exchange has remained elusive. METHODOLOGY/PRINCIPAL FINDINGS: We have previously demonstrated that peptide binding to and dissociation from MHCII in the absence of DM are cooperative processes, likely related to conformational changes in the peptide-MHCII complex. Here we show that DM promotes peptide release by a non-cooperative process, whereas it enhances cooperative folding of the exchange peptide. Through electron paramagnetic resonance (EPR) and fluorescence polarization (FP) we show that DM releases prebound peptide very poorly in the absence of a candidate peptide for the exchange process. The affinity and concentration of the candidate peptide are also important for the release of the prebound peptide. Increased fluorescence energy transfer between the prebound and exchange peptides in the presence of DM is evidence for a tetramolecular complex which resolves in favor of the peptide that has superior folding properties. CONCLUSION/SIGNIFICANCE: This study shows that both the peptide releasing activity on loaded MHCII and the facilitating of MHCII binding by a candidate exchange peptide are integral to DM mediated epitope selection. The exchange process is initiated only in the presence of candidate peptides, avoiding possible release of a prebound peptide and loss of a potential epitope. In a tetramolecular transitional complex, the candidate peptides are checked for their ability to replace the pre-bound peptide with a geometry that allows the rebinding of the original peptide. Thus, DM promotes a "compare-exchange" sorting algorithm on an available peptide pool. Such a "third party"-mediated mechanism may be generally applicable for diverse ligand recognition in other biological systems

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits

How Mathematicians Obtain Conviction: Implications for Mathematics Instruction and Research on Epistemic Cognition

This is an Accepted Manuscript of an article published by Taylor & Francis in Educational Psychologist on 16th January 2014, available online: http://wwww.tandfonline.com/10.1080/00461520.2013.865527The received view of mathematical practice is that mathematicians gain certainty in mathematical assertions by deductive evidence rather than empirical or authoritarian evidence. This assumption has influenced mathematics instruction where students are expected to justify assertions with deductive arguments rather than by checking the assertion with specific examples or appealing to authorities. In this paper, we argue that the received view about mathematical practice is too simplistic; some mathematicians sometimes gain high levels of conviction with empirical or authoritarian evidence and sometimes do not gain full conviction from the proofs that they read. We discuss what implications this might have, both for for mathematics instruction and theories of epistemic cognition