Transient Heat Storage Systems

Phase change materials (PCM) have many applications in transient cooling systems, including those with high transient heat loads and low duty cycles. These materials allow a system to remain within a narrow temperature range with a relatively low weight compared to conventional heat sinks or high-power cooling systems. This senior capstone project includes the design of a PCM based thermal energy storage system to integrate into an existing cooling loop, as well as a determination of viable PCM’s for the application. This report contains the necessary information to build the test apparatus

CMS Pixel Telescope Addition to T-980 Bent Crystal Collimation Experiment at the Tevatron

An enhancement to the T-980 bent crystal collimation experiment at the Tevatron has been completed. The enhancement was the installation of a pixel telescope inside the vacuum-sealed beam pipe of the Tevatron. The telescope is comprised of six CMS PSI46 pixel plaquettes, arranged as three stations of horizontal and vertical planes, with the CAPTAN system for data acquisition and control. The purpose of the pixel telescope is to measure beam profiles produced by bent crystals under various conditions. The telescope electronics inside the beam pipe initially were not adequately shielded from the image current of the passing beams. A new shielding approach was devised and installed, which resolved the problem. The noise issues encountered and the mitigating techniques are presented herein, as well as some preliminary results from the telescope.Comment: 9 pp. 2nd International Conference on Technology and Instrumentation in Particle Physics 2011: TIPP 2011. 9-14 Jun 2011. Chicago, Illinoi

Phenex: Ontological Annotation of Phenotypic Diversity

Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge

The Teleost Taxonomy Ontology

The Teleost Taxonomy Ontology (TTO) is an ontology of taxonomic groups and associated names for fish (not just teleosts). This ontology has served as a source of names and taxonomic structure within the Phenoscape project since early 2008. Although the TTO is based on Eschmeyer's Catalog of Fishes (CoF) and incorporates all valid species and genus names, it is also extended by the curation needs of the Phenoscape project. Names of fossil taxa not included in the CoF as well as references to specimens identied only to genus (e.g., _Eigenmannia sp._ (Fink and Fink 1981)) are incorporated into the TTO as required by the curation needs of the Phenoscape project. As Phenoscape receives updates to the CoF, a tool called TTOUpdate merges the changes into the TTO

The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age

The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.This work was supported by the National Science Foundation (NSF DBI 0641025), National Institutes of Health (HG002659), and the National Evolutionary Synthesis Center (NSF EF-0423641)

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology

Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics