Poincar-Cartan integral invariant and canonical transformation for singular lagrangians

In this work we develop the canonical formalism for constrained systems with a finite number of degrees of freedom by making use of the PoincarCartan integral invariant method. A set of variables suitable for the reduction to the physical ones can be obtained by means of a canonical transformation. From the invariance of the PoincarCartan integral under canonical transformations we get the form of the equations of motion for the physical variables of the system.

Discretized integral hydrodynamics

Using an interpolant form for the gradient of a function of position, we write an integral version of the conservation equations for a fluid. In the appropriate limit, these become the usual conservation laws of mass, momentum, and energy. We also discuss the special cases of the Navier-Stokes equations for viscous flow and the Fourier law for thermal conduction in the presence of hydrodynamic fluctuations. By means of a discretization procedure, we show how the integral equations can give rise to the so-called particle dynamics of smoothed particle hydrodynamics and dissipative particle dynamics.

Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

Background: The trithorax group (trxG) and Polycomb group (PcG) proteins are responsible for the maintenance of stable transcriptional patterns of many developmental regulators. They bind to specific regions of DNA and direct the post-translational modifications of histones, playing a role in the dynamics of chromatin structure.Results: We have performed genome-wide expression studies of trx and ash2 mutants in Drosophila melanogaster. Using computational analysis of our microarray data, we have identified 25 clusters of genes potentially regulated by TRX. Most of these clusters consist of genes that encode structural proteins involved in cuticle formation. This organization appears to be a distinctive feature of the regulatory networks of TRX and other chromatin regulators, since we have observed the same arrangement in clusters after experiments performed with ASH2, as well as in experiments performed by others with NURF, dMyc, and ASH1. We have also found many of these clusters to be significantly conserved in D. simulans, D. yakuba, D. pseudoobscura and partially in Anopheles gambiae.Conclusion: The analysis of genes governed by chromatin regulators has led to the identification of clusters of functionally related genes conserved in other insect species, suggesting this chromosomal organization is biologically important. Moreover, our results indicate that TRX and other chromatin regulators may act globally on chromatin domains that contain transcriptionally co-regulated genes.

ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins

Background: Annotations of completely sequenced genomes reveal that nearly half of the genes identified are of unknown function, and that some belong to uncharacterized gene families. To help resolve such issues, information can be obtained from the comparative analysis of homologous genes in model organisms. Results: While characterizing genes from the retinitis pigmentosa locus RP26 at 2q31-q33, we have identified a new gene, ORMDL1, that belongs to a novel gene family comprising three genes in humans (ORMDL1, ORMDL2 and ORMDL3), and homologs in yeast, microsporidia, plants, Drosophila, urochordates and vertebrates. The human genes are expressed ubiquitously in adult and fetal tissues. The Drosophila ORMDL homolog is also expressed throughout embryonic and larval stages, particularly in ectodermally derived tissues. The ORMDL genes encode transmembrane proteins anchored in the endoplasmic reticulum (ER). Double knockout of the two Saccharomyces cerevisiae homologs leads to decreased growth rate and greater sensitivity to tunicamycin and dithiothreitol. Yeast mutants can be rescued by human ORMDL homologs. Conclusions: From protein sequence comparisons we have defined a novel gene family, not previously recognized because of the absence of a characterized functional signature. The sequence conservation of this family from yeast to vertebrates, the maintenance of duplicate copies in different lineages, the ubiquitous pattern of expression in human and Drosophila, the partial functional redundancy of the yeast homologs and phenotypic rescue by the human homologs, strongly support functional conservation. Subcellular localization and the response of yeast mutants to specific agents point to the involvement of ORMDL in protein folding in the ER.

Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions

Background: The trithorax group (trxG) genes absent, small or homeotic discs 1 (ash1) and 2 (ash2) were isolated in a screen for mutants with abnormal imaginal discs. Mutations in either gene cause homeotic transformations but Hox genes are not their only targets. Although analysis of double mutants revealed that ash2 and ash1 mutations enhance each other's phenotypes, suggesting they are functionally related, it was shown that these proteins are subunits of distinct complexes.Results: The analysis of wing imaginal disc transcriptomes from ash2 and ash1 mutants showed that they are highly similar. Functional annotation of regulated genes using Gene Ontology allowed identification of severely affected groups of genes that could be correlated to the wing phenotypes observed. Comparison of the differentially expressed genes with those from other genome-wide analyses revealed similarities between ASH2 and Sin3A, suggesting a putative functional relationship. Coimmunoprecipitation studies and immunolocalization on polytene chromosomes demonstrated that ASH2 and Sin3A interact with HCF (host-cell factor). The results of nucleosome western blots and clonal analysis indicated that ASH2 is necessary for trimethylation of the Lys4 on histone 3 (H3K4).Conclusion: The similarity between the transcriptomes of ash2 and ash1 mutants supports a model in which the two genes act together to maintain stable states of transcription. Like in humans, both ASH2 and Sin3A bind HCF. Finally, the reduction of H3K4 trimethylation in ash2 mutants is the first evidence in Drosophila regarding the molecular function of this trxG gene.

Water tanks as ecosystems. Local ecosystemic perception for integral management of water tanks in Tamil Nadu, South India

Water tanks offer from many centuries ago solutions in South India for several problems related with water scarcity. They are a traditional water harvesting system wide spread in this territory, allowing a potential decentralized and participatory management of the local population on their own resources. Although water tanks¿ main function is irrigation, they have many other uses, functions and natural resources associated, involving stakeholders in the villages apart from those farmers making use of the irrigation. Water tanks provide a variety of landscapes and biodiversity that creates a valuable heterogeneous territory. The complexity of such an ecosystem should be managed with an integral perspective, considering all the elements involved and their relations, and understanding that water tanks are not just water deposits. This multidisciplinary study tries to demonstrate the idea of water tanks as ecosystems, describing and analyzing deeply and in an unprecedentedly way the functions, uses, natural resources and stakeholders. The research also focuses in the assessment of the ecosystemic perception of the local population of some villages in Tamil Nadu, employing diverse anthropological methodology.

Integral Bridge Abutment-to-Approach Slab Connection Final Report, June 2008

The Iowa Department of Transportation has long recognized that approach slab pavements of integral abutment bridges are prone to settlement and cracking, which manifests as the “bump at the end of the bridge”. A commonly recommended solution is to integrally attach the approach slab to the bridge abutment. Two different approach slabs, one being precast concrete and the other being cast-inplace concrete, were integrally connected to side-by-side bridges and investigated. The primary objective of this investigation was to evaluate the approach slab performance and the impacts the approach slabs have on the bridge. To satisfy the research needs, the project scope involved a literature review, survey of Midwest Department of Transportation current practices, implementing a health monitoring system on the bridge and approach slab, interpreting the data obtained during the evaluation, and conducting periodic visual inspections. Based on the information obtained from the testing the following general conclusions were made: The integral connection between the approach slabs and the bridges appear to function well with no observed distress at this location and no relative longitudinal movement measured between the two components; Tying the approach slab to the bridge appears to impact the bridge; The two different approach slabs, the longer precast slab and the shorter cast-in-place slab, appear to impact the bridge differently; The measured strains in the approach slabs indicate a force exists at the expansion joint and should be taken into consideration when designing both the approach slab and the bridge; The observed responses generally followed an annual cyclic and/or short term cyclic pattern over time.

Mapping the transcription start points of the Staphylococcus aureus eap, emp, and vwb promoters reveals a conserved octanucleotide sequence that is essential for expression of these genes.

Mapping the transcription start points of the eap, emp, and vwb promoters revealed a conserved octanucleotide sequence (COS). Deleting this sequence abolished the expression of eap, emp, and vwb. However, electrophoretic mobility shift assays gave no evidence that this sequence was a binding site for SarA or SaeR, known regulators of eap and emp.

The evolutionary conserved BER1 gene is involved in microtubule stability in yeast

In yeast, microtubules are dynamic filaments necessary for spindle and nucleus positioning, as well as for proper chromosome segregation. We identify a function for the yeast gene BER1 (Benomyl REsistant 1) in microtubule stability. BER1 belongs to an evolutionary conserved gene family whose founding member Sensitivity to Red light Reduced is involved in red-light perception and circadian rhythms in Arabidopsis. Here, we present data showing that the ber1Delta mutant is affected in microtubule stability, particularly in presence of microtubule-depolymerising drugs. The pattern of synthetic lethal interactions obtained with the ber1Delta mutant suggests that Ber1 may function in N-terminal protein acetylation. Our work thus suggests that microtubule stability might be regulated through this post-translational modification on yet-to-be determined proteins

Power variation of some integral fractional processes

We consider the asymptotic behaviour of the realized power variation of processes of the form ¿t0usdBHs, where BH is a fractional Brownian motion with Hurst parameter H E(0,1), and u is a process with finite q-variation, q<1/(1¿H). We establish the stable convergence of the corresponding fluctuations. These results provide new statistical tools to study and detect the long-memory effect and the Hurst parameter.

Instrumentation and Monitoring of Precast Bridge Approach Tied to an Integral Abutment Bridge in Bremer County, SPR 0000-005, 2010

Approach slab pavement at integral abutment (I-A) bridges are prone to settlement and cracking, which has been long recognized by the Iowa Department of Transportation (DOT). A commonly recommended solution is to integrally attach the approach slab to the bridge abutment. This study sought to supplement a previous project by instrumenting, monitoring, and analyzing the behavior of an approach slab tied to a integral abutment bridge. The primary objective of this investigation was to evaluate the performance of the approach slab. To satisfy the research needs, the project scope involved reviewing a similar previous study, implementing a health monitoring system on the approach slab, interpreting the data obtained during the evaluation, and conducting periodic visual inspections of the bridge and approach slab. Based on the information obtained from the testing, the following general conclusions were made: the integral connection between the approach slab and the bridge appears to function well with no observed distress at this location and no relative longitudinal movement measured between the two components; the measured strains in the approach slabs indicate a force exists at the expansion joint and should be taken into consideration when designing both the approach slab and the bridge and the observed responses generally followed an annual cyclic and/or short term cyclic pattern over time; the expansion joint at one side of the approach slab does not appear to be functioning as well as elsewhere; much larger frictional forces were observed in this study compared to the previous study.

Pile Design and Tests for Integral Abutment Bridges, HR-273, 1987

Expansion joints increase both the initial cost and the maintenance cost of bridges. Integral abutment bridges provide an attractive design alternative because expansion joints are eliminated from the bridge itself. However, the piles in these bridges are subjected to horizontal movement as the bridge expands and contracts during temperature changes. The objective of this research was to develop a method of designing piles for these conditions. Separate field tests simulating a pile and a bridge girder were conducted for three loading cases: (1) vertical load only, (2) horizontal displacement of pile head only, and (3) combined horizontal displacement of pile head with subsequent vertical load. Both tests (1) and (3) reached the same ultimate vertical load, that is, the horizontal displacement had no effect on the vertical load capacity. Several model tests were conducted in sand with a scale factor of about 1:10. Experimental results from both the field and model tests were used to develop the vertical and horizontal load-displacement properties of the soil. These properties were input into the finite element computer program Integral Abutment Bridge Two-Dimensional (IAB2D), which was developed under a previous research contract. Experimental and analytical results compared well for the test cases. Two alternative design methods, both based upon the American Association of State Highway and Transportation Officials (AASHTO) Specification, were developed. Alternative One is quite conservative relative to IAB2D results and does not permit plastic redistribution of forces. Alternative Two is also conservative when compared to IAB2D, but plastic redistribution is permitted. To use Alternative Two, the pile cross section must have sufficient inelastic rotation capacity before local buckling occurs. A design example for a friction pile and an end-bearing pile illustrates both alternatives.

A conserved transcript pattern in response to a specialist and a generalist herbivore.

Transcript patterns elicited in response to attack reveal, at the molecular level, how plants respond to aggressors. These patterns are fashioned both by inflicted physical damage as well as by biological components displayed or released by the attacker. Different types of attacking organisms might therefore be expected to elicit different transcription programs in the host. Using a large-scale DNA microarray, we characterized gene expression in damaged as well as in distal Arabidopsis thaliana leaves in response to the specialist insect, Pieris rapae. More than 100 insect-responsive genes potentially involved in defense were identified, including genes involved in pathogenesis, indole glucosinolate metabolism, detoxification and cell survival, and signal transduction. Of these 114 genes, 111 were induced in Pieris feeding, and only three were repressed. Expression patterns in distal leaves were markedly similar to those of local leaves. Analysis of wild-type and jasmonate mutant plants, coupled with jasmonate treatment, showed that between 67 and 84% of Pieris-regulated gene expression was controlled, totally or in part, by the jasmonate pathway. This was correlated with increased larval performance on the coronatine insensitive1 glabrous1 (coi1-1 gl1) mutant. Independent mutations in COI1 and GL1 led to a faster larval weight gain, but the gl1 mutation had relatively little effect on the expression of the insect-responsive genes examined. Finally, we compared transcript patterns in Arabidopis in response to larvae of the specialist P. rapae and to a generalist insect, Spodoptera littoralis. Surprisingly, given the complex nature of insect salivary components and reported differences between species, almost identical transcript profiles were observed. This study also provides a robustly characterized gene set for the further investigation of plant-insect interaction.

Validation of Design Recommendations for Integral Abutment Piles, HR-292, 1989

Since integral abutment bridges decrease the initial and maintenance costs of bridges, they provide an attractive alternative for bridge designers. The objective of this project is to develop rational and experimentally verified design recommendations for these bridges. Field testing consisted of instrumenting two bridges in Iowa to monitor air and bridge temperatures, bridge displacements, and pile strains. Core samples were also collected to determine coefficients of thermal expansion for the two bridges. Design values for the coefficient of thermal expansion of concrete are recommended, as well as revised temperature ranges for the deck and girders of steel and concrete bridges. A girder extension model is developed to predict the longitudinal bridge displacements caused by changing bridge temperatures. Abutment rotations and passive soil pressures behind the abutment were neglected. The model is subdivided into segments that have uniform temperatures, coefficients of expansion, and moduli of elasticity. Weak axis pile strains were predicted using a fixed-head model. The pile is idealized as an equivalent cantilever with a length determined by the surrounding soil conditions and pile properties. Both the girder extension model and the fixed-head model are conservative for design purposes. A longitudinal frame model is developed to account for abutment rotations. The frame model better predicts both the longitudinal displacement and weak axis pile strains than do the simpler models. A lateral frame model is presented to predict the lateral motion of skewed bridges and the associated strong axis pile strains. Full passive soil pressure is assumed on the abutment face. Two alternatives for the pile design are presented. Alternative One is the more conservative and includes thermally induced stresses. Alternative Two neglects thermally induced stresses but allows for the partial formation of plastic hinges (inelastic redistribution of forces). Ductility criteria are presented for this alternative. Both alternatives are illustrated in a design example.