Modelling hydrodynamics in the Rio Parana, Argentina : an evaluation and inter-comparison of reduced-complexity and physics based models applied to a large sand-bed river

Depth-averaged velocities and unit discharges within a 30 km reach of one of the world's largest rivers, the Rio Parana, Argentina, were simulated using three hydrodynamic models with different process representations: a reduced complexity (RC) model that neglects most of the physics governing fluid flow, a two-dimensional model based on the shallow water equations, and a three-dimensional model based on the Reynolds-averaged Navier-Stokes equations. Row characteristics simulated using all three models were compared with data obtained by acoustic Doppler current profiler surveys at four cross sections within the study reach. This analysis demonstrates that, surprisingly, the performance of the RC model is generally equal to, and in some instances better than, that of the physics based models in terms of the statistical agreement between simulated and measured flow properties. In addition, in contrast to previous applications of RC models, the present study demonstrates that the RC model can successfully predict measured flow velocities. The strong performance of the RC model reflects, in part, the simplicity of the depth-averaged mean flow patterns within the study reach and the dominant role of channel-scale topographic features in controlling the flow dynamics. Moreover, the very low water surface slopes that typify large sand-bed rivers enable flow depths to be estimated reliably in the RC model using a simple fixed-lid planar water surface approximation. This approach overcomes a major problem encountered in the application of RC models in environments characterised by shallow flows and steep bed gradients. The RC model is four orders of magnitude faster than the physics based models when performing steady-state hydrodynamic calculations. However, the iterative nature of the RC model calculations implies a reduction in computational efficiency relative to some other RC models. A further implication of this is that, if used to simulate channel morphodynamics, the present RC model may offer only a marginal advantage in terms of computational efficiency over approaches based on the shallow water equations. These observations illustrate the trade off between model realism and efficiency that is a key consideration in RC modelling. Moreover, this outcome highlights a need to rethink the use of RC morphodynamic models in fluvial geomorphology and to move away from existing grid-based approaches, such as the popular cellular automata (CA) models, that remain essentially reductionist in nature. In the case of the world's largest sand-bed rivers, this might be achieved by implementing the RC model outlined here as one element within a hierarchical modelling framework that would enable computationally efficient simulation of the morphodynamics of large rivers over millennial time scales. (C) 2012 Elsevier B.V. All rights reserved.

Asphalt Resurfacing Structural Research, HR-556, Construction Report, 1995

Discarded tires present major disposal and environmental problems. One method of recycling tires is to use finely ground rubber from tires in asphalt cement concrete (ACC). This process has been researched in Iowa since 1991. There are currently eight projects being researched. This project involved using crumb rubber modifier (CRM) in ACC using a dry process. This project is located on US 63 in Howard County. It involved 17 test sections. There were five test sections using 20 lb of CRM per ton, four test sections using 10 lb of CRM per ton and eight test sections using a conventional mix. Not only were different mixes used, but the overlay was also placed in various thicknesses ranging from 2 in. to 8 in. (5 cm to 20 cm). The project was completed in August 1994. The project construction went well with only minor problems. This report contains information about procedures and tests that were completed and those that will be completed. Evaluation on the project will continue for five years.

Protection of Structural Concrete Substructures, HR-220, Progress Report, 1984

The corrosion of reinforcing steel within concrete has always been a problem in construction of bridge decks. With low slump concrete and epoxy rebar, progress has been made in controlling the corrosion. There is concern, however, that the chloride also attacks the substructures, specifically the pier columns. They are subject to chloride attack by chemical deicers in the drainage from the bridge deck. Piers supporting grade separation bridges are also subject to chlorides contained in the direct splash from the lower level traffic. In this project, a field evaluation was conducted to evaluate the effectiveness of commercially available products in preventing chloride intrusion.

Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices.

BACKGROUND: The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K+, Ca2+ and Na2+ concentrations. The presence of P-type II gene subfamilies that are specific for certain kingdoms has been reported but was sometimes contradicted by discovery of previously unknown homologous sequences in newly sequenced genomes. Members of this gene family have been sampled in all of the fungal phyla except the arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), which are known to play a key-role in terrestrial ecosystems and to be genetically highly variable within populations. Here we used highly degenerate primers on AMF genomic DNA to increase the sampling of fungal P-Type II ATPases and to test previous predictions about their evolution. In parallel, homologous sequences of the P-type II ATPases have been used to determine the nature and amount of polymorphism that is present at these loci among isolates of Glomus intraradices harvested from the same field. RESULTS: In this study, four P-type II ATPase sub-families have been isolated from three AMF species. We show that, contrary to previous predictions, P-type IIC ATPases are present in all basal fungal taxa. Additionally, P-Type IIE ATPases should no longer be considered as exclusive to the Ascomycota and the Basidiomycota, since we also demonstrate their presence in the Zygomycota. Finally, a comparison of homologous sequences encoding P-type IID ATPases showed unexpectedly that indel mutations among coding regions, as well as specific gene duplications occur among AMF individuals within the same field. CONCLUSION: On the basis of these results we suggest that the diversification of P-Type IIC and E ATPases followed the diversification of the extant fungal phyla with independent events of gene gains and losses. Consistent with recent findings on the human genome, but at a much smaller geographic scale, we provided evidence that structural genomic changes, such as exonic indel mutations and gene duplications are less rare than previously thought and that these also occur within fungal populations.

Review: Contact sport-related chronic traumatic encephalopathy in the elderly: clinical expression and structural substrates.

A. Costanza, K. Weber, S. Gandy, C. Bouras, P. R. Hof, P. Giannakopoulos and A. Canuto (2011) Neuropathology and Applied Neurobiology37, 570-584 Contact sport-related chronic traumatic encephalopathy in the elderly: clinical expression and structural substrates Professional boxers and other contact sport athletes are exposed to repetitive brain trauma that may affect motor functions, cognitive performance, emotional regulation and social awareness. The term of chronic traumatic encephalopathy (CTE) was recently introduced to regroup a wide spectrum of symptoms such as cerebellar, pyramidal and extrapyramidal syndromes, impairments in orientation, memory, language, attention, information processing and frontal executive functions, as well as personality changes and behavioural and psychiatric symptoms. Magnetic resonance imaging usually reveals hippocampal and vermis atrophy, a cavum septum pellucidum, signs of diffuse axonal injury, pituitary gland atrophy, dilated perivascular spaces and periventricular white matter disease. Given the partial overlapping of the clinical expression, epidemiology and pathogenesis of CTE and Alzheimer's disease (AD), as well as the close association between traumatic brain injuries (TBIs) and neurofibrillary tangle formation, a mixed pathology promoted by pathogenetic cascades resulting in either CTE or AD has been postulated. Molecular studies suggested that TBIs increase the neurotoxicity of the TAR DNA-binding protein 43 (TDP-43) that is a key pathological marker of ubiquitin-positive forms of frontotemporal dementia (FTLD-TDP) associated or not with motor neurone disease/amyotrophic lateral sclerosis (ALS). Similar patterns of immunoreactivity for TDP-43 in CTE, FTLD-TDP and ALS as well as epidemiological correlations support the presence of common pathogenetic mechanisms. The present review provides a critical update of the evolution of the concept of CTE with reference to its neuropathological definition together with an in-depth discussion of the differential diagnosis between this entity, AD and frontotemporal dementia.

Dynamic Deflections for Determining Structural Rating of Flexible Pavements, HR-178, 1979

The Road Rater is a dynamic deflection measuring apparatus for flexible base pavements. The Road Rater replaces the Benkelman Beam which was last used by the Iowa DOT in 1977. Road Rater test results correlate reasonably well (correlation coefficient = 0.83) with Benkelman Beam test data. The basic differences between the Road Rater and Benkelman Beam are as follows: 1. The Benkelman Beam uses a static 18,000 lb. load while the Road Rater uses a dynamic 800 to 2,000 lb. loading. 2. The Road Rater tests much faster and more economically than the Benkelman Beam. 3. The Road Rater better simulates a moving truck than the Benkelman Beam. The basic operating principle of the Road Rater is to impart a dynamic loading and measure the resultant movement of the pavement with velocity sensors. This data, when properly adjusted for temperature by use of a nomograph included in this report, can be used to determine pavement life expectancy and estimate overlay thickness required. Road Rater testing will be conducted in the spring, when pavements are in their weakest condition, until seasonal correction factors can be developed. The Road Rater does not have sufficient ram weight to effectively evaluate load carrying capacity of rigid pavements. All rigid pavements react similarly to Road Rater testing and generally deflect from 0.65 to 1.30 mils. Research will be contined to evaluate rigid pavements with the Road Rater, however. The Road Rater has proven to be a reliable, troublefree pavement evaluation machine. The deflection apparatus was originally front-mounted,but was rear-mounted during the winter of 1977-78. Since that time, van handling has greatly improved, and front suspension parts are no longer overstressed due to improper weight distribution.

Structural Analysis and Overlay Design of Pavements Using the Road Rater, MLR-84-3, 1986

In recent years the Iowa DOT has shifted emphasis from the construction of new roads to the maintenance and preservation of existing highways. A need has developed for analyzing pavements structurally to select the correct rehabilitation strategy and to properly design a pavement overlay if necessary. This need has been fulfilled by Road Rater testing which has been used successfully on all types of pavements to evaluate pavement and subgrade conditions and to design asphaltic concrete overlays. The Iowa Road Rater Design Method has been simplified so that it may be easily understood and used by the widely diverse groups of individuals which may be involved in pavement restoration and management. Road Rater analysis techniques have worked well to date and have been verified by pavement coring, soils sampling and testing, and pavement removal by block sampling. Void detection testing has also been performed experimentally in Iowa, and results indicate that the Road Rater can be used to locate pavement voids and that Road Rater analysis techniques are reasonably accurate. The success of Road Rater research and development has made deflection test data one of the most important pavement management inputs.

Antigen binding to secretory immunoglobulin A results in decreased sensitivity to intestinal proteases and increased binding to cellular Fc receptors.

In intestinal secretions, secretory IgA (SIgA) plays an important sentinel and protective role in the recognition and clearance of enteric pathogens. In addition to serving as a first line of defense, SIgA and SIgA x antigen immune complexes are selectively transported across Peyer's patches to underlying dendritic cells in the mucosa-associated lymphoid tissue, contributing to immune surveillance and immunomodulation. To explain the unexpected transport of immune complexes in face of the large excess of free SIgA in secretions, we postulated that SIgA experiences structural modifications upon antigen binding. To address this issue, we associated specific polymeric IgA and SIgA with antigens of various sizes and complexity (protein toxin, virus, bacterium). Compared with free antibody, we found modified sensitivity of the three antigens assayed after exposure to proteases from intestinal washes. Antigen binding further impacted on the immunoreactivity toward polyclonal antisera specific for the heavy and light chains of the antibody, as a function of the antigen size. These conformational changes promoted binding of the SIgA-based immune complex compared with the free antibody to cellular receptors (Fc alphaRI and polymeric immunoglobulin receptor) expressed on the surface of premyelocytic and epithelial cell lines. These data reveal that antigen recognition by SIgA triggers structural changes that confer to the antibody enhanced receptor binding properties. This identifies immune complexes as particular structural entities integrating the presence of bound antigens and adds to the known function of immune exclusion and mucus anchoring by SIgA.

Structural development accounting

We construct and estimate a unified model combining three of the main sources ofcross-country income disparities: differences in factor endowments, barriers to technologyadoption and the inappropriateness of frontier technologies to local conditions. The keycomponents are different types of workers, distortions to capital accumulation, directedtechnical change, costly adoption and spillovers from the world technology frontier. Despiteits parsimonious parametrization, our empirical model provides a good fit of GDP data forup to 86 countries in 1970 and 122 countries in 2000. Removing barriers to technologyadoption would increase the output per worker of the average non-OECD country relativeto the US from 0.19 to 0.61, while increasing skill premia in all countries. Removing barriersto trade in goods amplifies income disparities, induces skill-biased technology adoptionand increases skill premia in the majority of countries. These results are reverted if tradeliberalization is coupled with international IPR protection.

Structural Characterization of UHPC Waffle Bridge Deck and Connections, TR-614, 2014

The AASHTO strategic plan in 2005 for bridge engineering identified extending the service life of bridges and accelerating bridge construction as two of the grand challenges in bridge engineering. These challenges have the objective of producing safer and more economical bridges at a faster rate with a minimum service life of 75 years and reduced maintenance cost to serve the country’s infrastructure needs. Previous studies have shown that a prefabricated full-depth precast concrete deck system is an innovative technique that accelerates the rehabilitation process of a bridge deck, extending its service life with reduced user delays and community disruptions and lowering its life-cycle costs. Previous use of ultra-high performance concrete (UHPC) for bridge applications in the United States has been considered to be efficient and economical because of its superior structural characteristics and durability properties. Full-depth UHPC waffle deck panel systems have been developed over the past three years in Europe and the United States. Subsequently, a single span, 60-ft long and 33-ft wide prototype bridge with full-depth prefabricated UHPC waffle deck panels has been designed and built for a replacement bridge in Wapello County, Iowa. The structural performance characteristics and the constructability of the UHPC waffle deck system and its critical connections were studied through an experimental program at the structural laboratory of Iowa State University (ISU). Two prefabricated full-depth UHPC waffle deck (8 feet by 9 feet 9 inches by 8 inches) panels were connected to 24-ft long precast girders, and the system was tested under service, fatigue, overload, and ultimate loads. Three months after the completion of the bridge with waffle deck system, it was load tested under live loads in February 2012. The measured strain and deflection values were within the acceptable limits, validating the structural performance of the bridge deck. Based on the laboratory test results, observations, field testing of the prototype bridge, and experience gained from the sequence of construction events such as panel fabrication and casting of transverse and longitudinal joints, a prefabricated UHPC waffle deck system is found to be a viable option to achieve the goals of the AASHTO strategic plan.

Cellular source and mechanisms of high transcriptome complexity in the Mammalian testis.

Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.

Contribution of the Global Regulator Gene gacA to Persistence and Dissemination of Pseudomonas fluorescens Biocontrol Strain CHA0 Introduced into Soil Microcosms.

Structural and regulatory genes involved in the synthesis of antimicrobial metabolites are essential for the biocontrol activity of fluorescent pseudomonads and, in principle, amenable to genetic engineering for strain improvement. An eventual large-scale release of such bacteria raises the question of whether such genes also contribute to the persistence and dissemination of the bacteria in soil ecosystems. Pseudomonas fluorescens wild-type strain CHA0 protects plants against a variety of fungal diseases and produces several antimicrobial metabolites. The regulatory gene gacA globally controls antibiotic production and is crucial for disease suppression in CHA0. This gene also regulates the production of extracellular protease and phospholipase. The contribution of gacA to survival and vertical translocation of CHA0 in soil microcosms of increasing complexity was studied in coinoculation experiments with the wild type and a gacA mutant which lacks antibiotics and some exoenzymes. Both strains were marked with spontaneous resistance to rifampin. In a closed system with sterile soil, strain CHA0 and the gacA mutant multiplied for several weeks, whereas these strains declined exponentially in nonsterile soil of different Swiss origins. The gacA mutant was less persistent in nonrhizosphere raw soil than was the wild type, but no competitive disadvantage when colonizing the rhizosphere and roots of wheat was found in the particular soil type and during the period studied. Vertical translocation was assessed after strains had been applied to undisturbed, long (60-cm) or short (20-cm) soil columns, both planted with wheat. A smaller number of cells of the gacA mutant than of the wild type were detected in the percolated water and in different depths of the soil column. Single-strain inoculation gave similar results in all microcosms tested. We conclude that mutation in a single regulatory gene involved in antibiotic and exoenzyme synthesis can affect the survival of P. fluorescens more profoundly in unplanted soil than in the rhizosphere.

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few aminoacids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

Role of structural saturation and geometry in the luminescence of silicon-based nanostructured materials

The structural saturation and stability, the energy gap, and the density of states of a series of small, silicon-based clusters have been studied by means of the PM3 and some ab initio (HF/6-31G* and 6-311++G**, CIS/6-31G* and MP2/6-31G*) calculations. It is shown that in order to maintain a stable nanometric and tetrahedral silicon crystallite and remove the gap states, the saturation atom or species such as H, F, Cl, OH, O, or N is necessary, and that both the cluster size and the surface species affect the energetic distribution of the density of states. This research suggests that the visible luminescence in the silicon-based nanostructured material essentially arises from the nanometric and crystalline silicon domains but is affected and protected by the surface species, and we have thus linked most of the proposed mechanisms of luminescence for the porous silicon, e.g., the quantum confinement effect due to the cluster size and the effect of Si-based surface complexes.