Standard General Relativity from Chern-Simons Gravity

Chern-Simons models for gravity are interesting because they provide with a truly gauge-invariant action principle in the fiber-bundle sense. So far, their main drawback has largely been the perceived remoteness from standard General Relativity, based on the presence of higher powers of the curvature in the Lagrangian (except, remarkably, for three-dimensional spacetime). Here we report on a simple model that suggests a mechanism by which standard General Relativity in five-dimensional spacetime may indeed emerge at a special critical point in the space of couplings, where additional degrees of freedom and corresponding "anomalous" Gauss-Bonnet constraints drop out from the Chern-Simons action. To achieve this result, both the Lie algebra g and the symmetric g-invariant tensor that define the Chern-Simons Lagrangian are constructed by means of the Lie algebra S-expansion method with a suitable finite abelian semigroup S. The results are generalized to arbitrary odd dimensions, and the possible extension to the case of eleven-dimensional supergravity is briefly discussed.Comment: 6 pages, no figures; v2: published versio

Supersymmetry, quark confinement and the harmonic oscillator

We study some quantum systems described by noncanonical commutation relations formally expressed as [q,p]=ihbar(I + chi H), where H is the associated (harmonic oscillator-like) Hamiltonian of the system, and chi is a Hermitian (constant) operator, i.e. [H,chi]=0 . In passing, we also consider a simple (chi=0 canonical) model, in the framework of a relativistic Klein-Gordon-like wave equation.Comment: To be published in Journal of Physics A: Mathematical and Theoretical (2007

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources. Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous data stored at different locations. Therefore, we develop a semantic problem solving environment (SPSE) that allows parasitologists to query their lab data integrated with public resources using ontologies. An ontology specifies a common vocabulary and formal relationships among the terms that describe an organism, and experimental data and processes in this case. SPSE supports capturing and querying provenance information, which is metadata on the experimental processes and data recorded for reproducibility, and includes a visual query-processing tool to formulate complex queries without learning the query language syntax. We demonstrate the significance of SPSE in identifying gene knockout targets for T. cruzi. The overall goal of SPSE is to help researchers discover new or existing knowledge that is implicitly present in the data but not always easily detected. Results demonstrate improved usefulness of SPSE over existing lab systems and approaches, and support for complex query design that is otherwise difficult to achieve without the knowledge of query language syntax

The Evolution of Amastin Surface Glycoproteins in Trypanosomatid Parasites

Amastin is a transmembrane glycoprotein found on the cell surfaces of trypanosomatid parasites. Encoded by a large, diverse gene family, amastin was initially described from the intracellular, amastigote stage of Trypanosoma cruzi and Leishmania donovani. Genome sequences have subsequently shown that the amastin repertoire is much larger in Leishmania relative to Trypanosoma. However, it is not known when this expansion occurred, whether it is associated with the origins of Leishmania and vertebrate parasitism itself, or prior to this. To examine the timing of amastin diversification, as well as the evolutionary mechanisms regulating gene repertoire and sequence diversity, this study sequenced the genomic regions containing amastin loci from two related insect parasites (Leptomonas seymouri and Crithidia sp.) and estimated a phylogeny for these and other amastin sequences. The phylogeny shows that amastin includes four subfamilies with distinct genomic positions, secondary structures, and evolution, which were already differentiated in the ancestral trypanosomatid. Diversification in Leishmania was initiated from a single ancestral locus on chromosome 34, with rapid derivation of novel loci through transposition and accelerated sequence divergence. This is absent from related organisms showing that diversification occurred after the origin of Leishmania. These results describe a substantial elaboration of amastin repertoire directly associated with the origin of Leishmania, suggesting that some amastin genes evolved novel functions crucial to cell function in leishmanial parasites after the acquisition of a vertebrate host

Radiating Effectiveness of Annular-Finned Space Radiators, Including Mutual Irradiation between Radiator Elements

the authors also provide an approximate quantitative number for the accuracy of the numerical results. Based on the authors' results of Figs. 8 and 9, the fully developed periodic flow is achieved at x/L = 4 and 30 for Re = 200 and 1600 respectively for L/H = 1. Would the authors first quantitatively define the periodic fully developed flow, and then provide the tabular values of x/L as functions of L/H and Re for L/H = 0.2,0.5,1,2 and 5, and the covered range of Re. A research task remains further refining the analytical model to correlate better the performance of interrupted wall surface with the experimental results. Subsequently, the more complex heat exchanger surfaces could be analyzed. In the meanwhile, this paper by Prof. Sparrow and his colleagues serves as a reminder that the flow and heat transfer phenomena in a compact heat exchanger are too complex to analyze. A better quantitative understanding of the flow phenomena is essential for better correlations and improved heat exchanger design. Additional Reference Authors' Closure We are appreciative of the perspectives conveyed by Dr. Shah's Discussion. With regard to the role of vortices and wakes, there are, assuredly, conditions where they will affect both the heat transfer and friction. On the other hand, there are conditions for which no significant effect will be felt. Perspectives on these conditions are conveyed in references [11] and [12]. In connection with the identification of the periodically developed regime in Figs. 8 and 9, there is considerable latitude depending on the selected criterion. Since all portions of a velocity or temperature profile do not develop with equal rapidity, there are various criteria that can be employed. It was for this reason that we did not quote development lengths in the paper. Additional References 11 Kottke, V., Blenke, H., and Schmidt, K. G., "The Influence of Nose Section and Turbulence Intensity on the Flow Around Thick Plates in Parallel Flow," Warme-und Stoffubertragung, Vol. 10,1977, pp. 159-174. 12 Loehrke, R. I., Roadman, R. E., and Read, G. W" ASME Paper The purpose of this discussion is to point out how one of Minning's results can be generalized. In his analysis of the inverted conical frustrum, Minning has chosen to express his results in terms of four variables-the cone half angle fi, the height of the frustrum h, the radial location of the differential element p, and the vertical distance from the differential element to the extended frustrums' vertex s. In my view, this last choice is not the natural one and indeed it obscures the generality of the result expressed by equation It appears that a better choice of variable would be the radius of the frustrum in the plane of the element or ring, which is given by r = -s tan fi. If s is thereby eliminated from equation With respect to this latter point, one may note, as was done for a cylinder by Sparrow, et al. [1] that the shape factor in question can be considered as the sum of two parts-one being a circular segment and, in this case, the other being a tilted triangular plate frustrum. 1 By C. P. Minning, published in the August, 1977 issue of the JOURNAL OP HEAT TRANSFER, Vol. 99, No. 3, The Aerospace Corporation, El Segundo, CA 90245. Since the former is known [2], the latter can be readily obtained and subsequently expressed in variables more suitable for that configuration. This, of course, introduces new possibilities too numerous to mention. Finally, since Minning does not mention any analytical checks of his result, it is pointed out that, when /3 = 0, it reduces to a form equivalent to that for the cylinder [1]. Additional References 1 Sparrow, E. M., Miller, G. B., and Jonsson, V. K., "Radiating Effectiveness of Annular-Finned Space Radiators, Including Mutual Irradiation between Radiator Elements," Journal Aerospace Sciences, Vol. 29, 1962, pp. 1291-1299 2 Sparrow, E. M., "A New and Simpler Formulation for Radiative Angle Factors," ASME JOURNAL OF HEAT TRANSFER, Vol. 85,1963, pp. 81-88. Author's Closure I appreciate Dr. Nelson's pointing out that the applicability of equation An alternate expression that avoids this confusion can be derived by substitution of the relation r = -s tanjtf, as suggested by Dr. Nelson, and the relation a = (7r/2) -fi into equation C^)] [(h cot a + r) -In this expression, a is the angle between the plane of dAi and the sloping side of the conical frustrum. Values of a are always positive and lie in the range 0 < « < TT. For 0 < « < 7r/2, the frustrum opens upward away from the plane of dA\. For 7r/2 < a < w, the frustrum opens downward toward the plane of dAi. The special case, a = it 12

A unified framework for managing provenance information in translational research

<p>Abstract</p> <p>Background</p> <p>A critical aspect of the NIH <it>Translational Research </it>roadmap, which seeks to accelerate the delivery of "bench-side" discoveries to patient's "bedside," is the management of the <it>provenance </it>metadata that keeps track of the origin and history of data resources as they traverse the path from the bench to the bedside and back. A comprehensive provenance framework is essential for researchers to verify the quality of data, reproduce scientific results published in peer-reviewed literature, validate scientific process, and associate trust value with data and results. Traditional approaches to provenance management have focused on only partial sections of the translational research life cycle and they do not incorporate "domain semantics", which is essential to support domain-specific querying and analysis by scientists.</p> <p>Results</p> <p>We identify a common set of challenges in managing provenance information across the <it>pre-publication </it>and <it>post-publication </it>phases of data in the translational research lifecycle. We define the semantic provenance framework (SPF), underpinned by the Provenir upper-level provenance ontology, to address these challenges in the four stages of provenance metadata:</p> <p>(a) Provenance <b>collection </b>- during data generation</p> <p>(b) Provenance <b>representation </b>- to support interoperability, reasoning, and incorporate domain semantics</p> <p>(c) Provenance <b>storage </b>and <b>propagation </b>- to allow efficient storage and seamless propagation of provenance as the data is transferred across applications</p> <p>(d) Provenance <b>query </b>- to support queries with increasing complexity over large data size and also support knowledge discovery applications</p> <p>We apply the SPF to two exemplar translational research projects, namely the Semantic Problem Solving Environment for <it>Trypanosoma cruzi </it>(<it>T.cruzi </it>SPSE) and the Biomedical Knowledge Repository (BKR) project, to demonstrate its effectiveness.</p> <p>Conclusions</p> <p>The SPF provides a unified framework to effectively manage provenance of translational research data during pre and post-publication phases. This framework is underpinned by an upper-level provenance ontology called Provenir that is extended to create domain-specific provenance ontologies to facilitate provenance interoperability, seamless propagation of provenance, automated querying, and analysis.</p

The steady-state transcriptome of the four major life-cycle stages of Trypanosoma cruzi

<p>Abstract</p> <p>Background</p> <p>Chronic chagasic cardiomyopathy is a debilitating and frequently fatal outcome of human infection with the protozoan parasite, <it>Trypanosoma cruzi</it>. Microarray analysis of gene expression during the <it>T. cruzi </it>life-cycle could be a valuable means of identifying drug and vaccine targets based on their appropriate expression patterns, but results from previous microarray studies in <it>T. cruzi </it>and related kinetoplastid parasites have suggested that the transcript abundances of most genes in these organisms do not vary significantly between life-cycle stages.</p> <p>Results</p> <p>In this study, we used whole genome, oligonucleotide microarrays to globally determine the extent to which <it>T. cruzi </it>regulates mRNA relative abundances over the course of its complete life-cycle. In contrast to previous microarray studies in kinetoplastids, we observed that relative transcript abundances for over 50% of the genes detected on the <it>T. cruzi </it>microarrays were significantly regulated during the <it>T. cruzi </it>life-cycle. The significant regulation of 25 of these genes was confirmed by quantitative reverse-transcriptase PCR (qRT-PCR). The <it>T. cruzi </it>transcriptome also mirrored published protein expression data for several functional groups. Among the differentially regulated genes were members of paralog clusters, nearly 10% of which showed divergent expression patterns between cluster members.</p> <p>Conclusion</p> <p>Taken together, these data support the conclusion that transcript abundance is an important level of gene expression regulation in <it>T. cruzi</it>. Thus, microarray analysis is a valuable screening tool for identifying stage-regulated <it>T. cruzi </it>genes and metabolic pathways.</p

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets