The Use of Remote Sensing Techniques Compared to Traditional Archaeological Phase II Testing Methods: A Cost-Benefit Analysis, HR-524, 1986

Remote sensing was utilized in the Phase II Cultural Resources Investigation for this project in lieu of extensive excavations. The purpose of the present report is to compare the costs and benefits of the use of remote sensing to the hypothetical use of traditional excavation methods for this project. Estimates for this hypothetical situation are based on the project archaeologist's considerable past experience in conducting similar investigations. Only that part of the Phase II investigation involving field investigations is addressed in this report. Costs for literature review, laboratory analysis, report preparation, etc., are not included. The project manager proposed the use of this technique for the fol lowing logistic, safety and budgetary reasons.

Development of In Situ Detection Methods for Materials-Related Distress (MRD) in Concrete Pavements: Phase 2, HR-1081, 2005

This project utilized information from ground penetrating radar (GPR) and visual inspection via the pavement profile scanner (PPS) in proof-of-concept trials. GPR tests were carried out on a variety of portland cement concrete pavements and laboratory concrete specimens. Results indicated that the higher frequency GPR antennas were capable of detecting subsurface distress in two of the three pavement sites investigated. However, the GPR systems failed to detect distress in one pavement site that exhibited extensive cracking. Laboratory experiments indicated that moisture conditions in the cracked pavement probably explain the failure. Accurate surveys need to account for moisture in the pavement slab. Importantly, however, once the pavement site exhibits severe surface cracking, there is little need for GPR, which is primarily used to detect distress that is not observed visually. Two visual inspections were also conducted for this study by personnel from Mandli Communications, Inc., and the Iowa Department of Transportation (DOT). The surveys were conducted using an Iowa DOT video log van that Mandli had fitted with additional equipment. The first survey was an extended demonstration of the PPS system. The second survey utilized the PPS with a downward imaging system that provided high-resolution pavement images. Experimental difficulties occurred during both studies; however, enough information was extracted to consider both surveys successful in identifying pavement surface distress. The results obtained from both GPR testing and visual inspections were helpful in identifying sites that exhibited materials-related distress, and both were considered to have passed the proof-of-concept trials. However, neither method can currently diagnose materials-related distress. Both techniques only detected the symptoms of materials-related distress; the actual diagnosis still relied on coring and subsequent petrographic examination. Both technologies are currently in rapid development, and the limitations may be overcome as the technologies advance and mature.

Sieve Analysis of Combined Aggregate Samples by Different Test Methods, MLR-84-05, 1982

This past winter the sieve analysis of combined aggregate was investigated. This study was given No. 26 by the Central Laboratory. The purpose of this work was to try and develop a sieve analysis procedure for combined aggregate which is less time consuming and has the same accuracy as the method described in I.M. 304. In an attempt to use a variety of aggregates for this investigation, a request was made to each District Materials Office to obtain at least 3 different combined aggregate samples in their respective districts. At the same time it was also requested that the field technician test these samples, prior to submitting them to the Central Laboratory. The field technician was instructed to test each sample as described in method I.M. 304 and also by a modified AASHTO T27 method which will be identified in the report as Method A. The modified AASHTO Method A was identical to T27 with the exception that a smaller sample is used for testing. The field technicians submitted the samples, test results and also comments regarding the modified AASHTO procedure. The general comments of the modified AASHTO procedure were: The method was much simpler to follow; however, it took about the same amount of time so there was no real advantage. After reviewing AASHTO T27, T164, I.M. 304 and Report No. FHWA-RD-77-53 another test method was purposed. Report No. FHWA-RD-77-53 is a report prepared by FHWA from data they gathered concerning control practices and shortcut or alternative test methods for aggregate gradation. A second test method was developed which also was very similar to AASHTO T27, The test procedure for this method is attached and is identified as Method B. The following is a summary of test results submitted by the Field Technicians and obtained by the aggregate section of the Central Laboratory.

Evaluation of Transverse Joint Forming Methods for PCC Pavement, TR-532, 2006

The members of the Iowa Concrete Paving Association, the National Concrete Pavement Technology Center Research Committee, and the Iowa Highway Research Board commissioned a study to examine alternative ways of developing transverse joints in portland cement concrete pavements. The present study investigated six separate variations of vertical metal strips placed above and below the dowels in conventional baskets. In addition, the study investigated existing patented assemblies and a new assembly developed in Spain and used in Australia. The metal assemblies were placed in a new pavement and allowed to stay in place for 30 days before the Iowa Department of Transportation staff terminated the test by directing the contractor to saw and seal the joints. This report describes the design, construction, testing, and conclusions of the project.

Rehabilitation of Concrete Pavements Utilizing Rubblization and Crack and Seat Methods (Phase II): Performance Evaluation of Rubblized Pavements in Iowa, TR-550, 2008

This Phase II follow-up study of IHRB Project TR-473 focused on the performance evaluation of rubblized pavements in Iowa. The primary objective of this study was to evaluate the structural condition of existing rubblized concrete pavements across Iowa through Falling Weight Deflectometer (FWD) tests, Dynamic Cone Penetrometer (DCP) tests, visual pavement distress surveys, etc. Through backcalculation of FWD deflection data using the Iowa State University's advanced layer moduli backcalculation program, the rubblized layer moduli were determined for various projects and compared with each other for correlating with the long-term pavement performance. The AASHTO structural layer coefficient for rubblized layer was also calculated using the rubblized layer moduli. To validate the mechanistic-empirical (M-E) hot mix asphalt (HMA) overlay thickness design procedure developed during the Phase I study, the actual HMA overlay thicknesses from the rubblization projects were compared with the predicted thicknesses obtained from the design software. The results of this study show that rubblization is a valid option to use in Iowa in the rehabilitation of portland cement concrete pavements provided the foundation is strong enough to support construction operations during the rubblization process. The M-E structural design methodology developed during Phase I can estimate the HMA overlay thickness reasonably well to achieve long-lasting performance of HMA pavements. The rehabilitation strategy is recommended for continued use in Iowa under those conditions conducive for rubblization.

Determination and Evaluation of Alternate Methods for Managing and Controlling Highway-Related Dust, TR-449, 2002

Road dust is caused by wind entraining fine material from the roadway surface and the main source of Iowa road dust is attrition of carbonate rock used as aggregate. The mechanisms of dust suppression can be considered as two processes: increasing particle size of the surface fines by agglomeration and inhibiting degradation of the coarse material. Agglomeration may occur by capillary tension in the pore water, surfactants that increase bonding between clay particles, and cements that bind the mineral matter together. Hygroscopic dust suppressants such as calcium chloride have short durations of effectiveness because capillary tension is the primary agglomeration mechanism. Somewhat more permanent methods of agglomeration result from chemicals that cement smaller particles into a mat or larger particles. The cements include lignosulfonates, resins, and asphalt products. The duration of the cements depend on their solubility and the climate. The only dust palliative that decreases aggregate degradation is shredded shingles that act as cushions between aggregate particles. It is likely that synthetic polymers also provide some protection against coarse aggregate attrition. Calcium chloride and lignosulfonates are widely used in Iowa. Both palliatives have a useful duration of about 6 months. Calcium chloride is effective with surface soils of moderate fine content and plasticity whereas lignin works best with materials that have high fine content and high plasticity indices. Bentonite appears to be effective for up to two years and works well with surface materials having low fines and plasticity and works well with limestone aggregate. Selection of appropriate dust suppressants should be based on characterization of the road surface material. Estimation of dosage rates for potential palliatives can be based on data from this report, from technical reports, information from reliable vendors, or laboratory screening tests. The selection should include economic analysis of construction and maintenance costs. The effectiveness of the treatment should be evaluated by any of the field performance measuring techniques discussed in this report. Novel dust control agents that need research for potential application in Iowa include; acidulated soybean oil (soapstock), soybean oil, ground up asphalt shingles, and foamed asphalt. New laboratory evaluation protocols to screen additives for potential effectiveness and determine dosage are needed. A modification of ASTM D 560 to estimate the freeze-thaw and wet-dry durability of Portland cement stabilized soils would be a starting point for improved laboratory testing of dust palliatives.

Methods for Estimating Annual Exceedance-Probability Discharges for Streams in Iowa, Based on Data through Water Year 2010, TR-519, 2013

A statewide study was performed to develop regional regression equations for estimating selected annual exceedance- probability statistics for ungaged stream sites in Iowa. The study area comprises streamgages located within Iowa and 50 miles beyond the State’s borders. Annual exceedanceprobability estimates were computed for 518 streamgages by using the expected moments algorithm to fit a Pearson Type III distribution to the logarithms of annual peak discharges for each streamgage using annual peak-discharge data through 2010. The estimation of the selected statistics included a Bayesian weighted least-squares/generalized least-squares regression analysis to update regional skew coefficients for the 518 streamgages. Low-outlier and historic information were incorporated into the annual exceedance-probability analyses, and a generalized Grubbs-Beck test was used to detect multiple potentially influential low flows. Also, geographic information system software was used to measure 59 selected basin characteristics for each streamgage. Regional regression analysis, using generalized leastsquares regression, was used to develop a set of equations for each flood region in Iowa for estimating discharges for ungaged stream sites with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities, which are equivalent to annual flood-frequency recurrence intervals of 2, 5, 10, 25, 50, 100, 200, and 500 years, respectively. A total of 394 streamgages were included in the development of regional regression equations for three flood regions (regions 1, 2, and 3) that were defined for Iowa based on landform regions and soil regions. Average standard errors of prediction range from 31.8 to 45.2 percent for flood region 1, 19.4 to 46.8 percent for flood region 2, and 26.5 to 43.1 percent for flood region 3. The pseudo coefficients of determination for the generalized leastsquares equations range from 90.8 to 96.2 percent for flood region 1, 91.5 to 97.9 percent for flood region 2, and 92.4 to 96.0 percent for flood region 3. The regression equations are applicable only to stream sites in Iowa with flows not significantly affected by regulation, diversion, channelization, backwater, or urbanization and with basin characteristics within the range of those used to develop the equations. These regression equations will be implemented within the U.S. Geological Survey StreamStats Web-based geographic information system tool. StreamStats allows users to click on any ungaged site on a river and compute estimates of the eight selected statistics; in addition, 90-percent prediction intervals and the measured basin characteristics for the ungaged sites also are provided by the Web-based tool. StreamStats also allows users to click on any streamgage in Iowa and estimates computed for these eight selected statistics are provided for the streamgage.

Evaluation of Design Flood Frequency Methods for Iowa Streams, TR-533, 2009

The objective of this project was to assess the predictive accuracy of flood frequency estimation for small Iowa streams based on the Rational Method, the NRCS curve number approach, and the Iowa Runoff Chart. The evaluation was based on comparisons of flood frequency estimates at sites with sufficiently long streamgage records in the Midwest, and selected urban sites throughout the United States. The predictive accuracy and systematic biases (under- or over-estimation) of the approaches was evaluated based on forty-six Midwest sites and twenty-one urban sites. The sensitivity of several watershed characteristics such as soil properties, slope, and land use classification was also explored. Recommendations on needed changes or refinements for applications to Iowa streams are made.

Improved Methods for Determining Wind Loads on Highway Sign and Traffic-Signal Structures, TR-559, 2007

The main objective of the proposed study is to use Computational Fluid Dynamics (CFD) tools to determine the wind loads by accurate numerical simulations of air flow characteristics around large highway sign structures under severe wind speeds conditions. Fully three-dimensional Reynolds- Averaged Navier-Stokes (RANS) simulations are used to estimate the total force on different panels, as well as the actual pressure distribution on the front and back faces of the panels. In particular, the present study investigates the effects of aspect ratio and sign spacing for regular panels, the effect of sign depth for the dynamic message signs that are now being used on Iowa highways, the effect induced by the presence of back-to-back signs, the effect of the presence of add-on exit signs, and the effect of the presence of trucks underneath the signs potentially creating “wind tunnel” effect.

Thrombin-sensitive photodynamic agents: a novel strategy for selective synovectomy in rheumatoid arthritis.

Protease-sensitive macromolecular prodrugs have attracted interest for bio-responsive drug delivery to sites with up-regulated proteolytic activities such as inflammatory or cancerous lesions. Here we report the development of a novel polymeric photosensitizer prodrug (T-PS) to target thrombin, a protease up-regulated in synovial tissues of rheumatoid arthritis (RA) patients, for minimally invasive photodynamic synovectomy. In T-PS, multiple photosensitizer units are tethered to a polymeric backbone via short, thrombin-cleavable peptide linkers. Photoactivity of the prodrug is efficiently impaired due to energy transfer between neighbouring photosensitizer units. T-PS activation by exogenous and endogenous thrombin induced an increase in fluorescence emission by a factor of 16 after in vitro digestion and a selective fluorescence enhancement in arthritic lesions in vivo, in a collagen-induced arthritis mouse model. In vitro studies on primary human synoviocytes showed a phototoxic effect only after enzymatic digestion of the prodrug and light irradiation, thus demonstrating the functionality of T-PS induced PDT. The developed photosensitizer prodrugs combine the passive targeting capacity of macromolecular drug delivery systems with site-selective photosensitizer release and activation. They illuminate lesions with pathologically enhanced proteolytic activity and induce cell death, subsequent to irradiation.

Characterization of polyphosphate synthesis by isolated yeast vacuoles

Polyphosphate (iPOP) is a linear polymer of orthophosphate units linked together by high energy phosphoanhydride bonds. It is found in all organisms, localized in organelles called acidocalcisomes and ranges from a few to few hundred monomers in length. iPOP has been found to play a vast array of roles in all organisms, including phosphate and energy metabolism, regulation of enzymes, virulence, pathogenicity, bone remodelling and blood clotting, among many others. Recently it was found that iPOP levels were increased in myeloma cells. The growing interest in iPOP in human cell lines makes it an interesting molecule to study. However, not much is known about its metabolism in eukaryotes. Acidocalcisomes are electron dense, acidic organelles that belong to the group of Lysosome Related Organelles (LROs). The conservation of acidocalcisomes among all kingdoms of life is suggestive of their important roles for the organisms. However, they are difficult to analyse because of limited biochemical tools for investigation. Yeast vacuoles present remarkable similarities to acidocalcisomes in terms of their physiological and structural features, including synthesis and storage of iPOP, which make them an ideal candidate to study biological processes which are shared between vacuoles and acidocalcisomes. The availability of tools for genetic manipulation and isolation of vacuoles makes yeast a candidate of choice for the characterization of iPOP synthesis in eukaryotes. Our group has identified the Vacuolar Transporter Chaperone (VTC) complex as iPOP polymerase and identified the catalytic subunit (Vtc4). The goal of my study was to characterize the process of iPOP synthesis by isolated vacuoles and to reconstitute iPOP synthesis in liposomes. The first step was to develop a method for monitoring iPOP by isolated vacuoles over time and comparing it with previously known methods. Next, a detailed characterization was performed to determine the modulators of the process, both for intact as well as solubilized vacuoles. Finally, attempts were made to purify the VTC complex and reconstitute it in liposomes. A parallel line of study was the translocation and storage of synthesized iPOP in the lumen of the vacuoles. As a result of this study, it is possible to determine distinct pools of iPOP- inside and outside the vacuolar lumen. Additionally, I establish that the vacuolar lysate withstands harsh steps during reconstitution on liposomes and retains iPOP synthesizing activity. The next steps will be purification of the intact VTC complex and its structure determination by cryo-electron microscopy. - Les organismes vivants sont composés d'une ou plusieurs cellules responsables des processus biologiques élémentaires tels que la digestion, la respiration, la synthèse et la reproduction. Leur environnement interne est en équilibre et ils réalisent un très grand nombre de réactions chimiques et biochimiques pour maintenir cet équilibre. A différents compartiments cellulaires, ou organelles, sont attribuées des tâches spécifiques pour maintenir les cellules en vie. L'étude de ces fonctions permet une meilleure compréhension de la vie et des organismes vivants. De nombreux processus sont bien connus et caractérisés mais d'autres nécessitent encore des investigations détaillées. L'un de ces processus est le métabolisme des polyphosphates. Ces molécules sont des polymères linéaires de phosphate inorganique dont la taille peut varier de quelques dizaines à quelques centaines d'unités élémentaires. Ils sont présents dans tous les organismes, des bactéries à l'homme. Ils sont localisés principalement dans des compartiments cellulaires appelés acidocalcisomes, des organelles acides observés en microscopie électronique comme des structures denses aux électrons. Les polyphosphates jouent un rôle important dans le stockage et le métabolisme de l'énergie, la réponse au stress, la virulence, la pathogénicité et la résistance aux drogues. Chez l'homme, ils sont impliqués dans la coagulation du sang et le remodelage osseux. De nouvelles fonctions biologiques des polyphosphates sont encore découvertes, ce qui accroît l'intérêt des chercheurs pour ces molécules. Bien que des progrès considérables ont été réalisés afin de comprendre la fonction des polyphosphates chez les bactéries, ce qui concerne la synthèse, le stockage et la dégradation des polyphosphates chez les eucaryotes est mal connu. Les vacuoles de la levure Saccharomyces cerevisiae sont similaires aux acidocalcisomes des organismes supérieurs en termes de structure et de fonction. Les acidocalcisomes sont difficiles à étudier car il n'existe que peu d'outils génétiques et biochimiques qui permettent leur caractérisation. En revanche, les vacuoles peuvent être aisément isolées des cellules vivantes et manipulées génétiquement. Les vacuoles comme les acidocalcisomes synthétisent et stockent les polyphosphates. Ainsi, les découvertes faites grâce aux vacuoles de levures peuvent être extrapolées aux acidocalcisomes des organismes supérieurs. Le but de mon projet était de caractériser la synthèse des polyphosphates par des vacuoles isolées. Au cours de mon travail de thèse, j'ai mis au point une méthode de mesure de la synthèse des polyphosphates par des organelles purifés. Ensuite, j'ai identifié des composés qui modulent la réaction enzymatique lorsque celle-ci a lieu dans la vacuole ou après solubilisation de l'organelle. J'ai ainsi pu mettre en évidence deux groupes distincts de polyphosphates dans le système : ceux au-dehors de la vacuole et ceux en-dedans de l'organelle. Cette observation suggère donc très fortement que les vacuoles non seulement synthétisent les polyphosphates mais aussi transfère les molécules synthétisées de l'extérieur vers l'intérieur de l'organelle. Il est très vraisemblable que les vacuoles régulent le renouvellement des polyphosphates qu'elles conservent, en réponse à des signaux cellulaires. Des essais de purification de l'enzyme synthétisant les polyphosphates ainsi que sa reconstitution dans des liposomes ont également été entrepris. Ainsi, mon travail présente de nouveaux aspects de la synthèse des polyphosphates chez les eucaryotes et les résultats devraient encourager l'élucidation de mécanismes similaires chez les organismes supérieurs. - Les polyphosphates (iPOP) sont des polymères linéaires de phosphates inorganiques liés par des liaisons phosphoanhydres de haute énergie. Ces molécules sont présentes dans tous les organismes et localisées dans des compartiments cellulaires appelés acidocalcisomes. Elles varient en taille de quelques dizaines à quelques centaines d'unités phosphate. Des fonctions nombreuses et variées ont été attribuées aux iPOP dont un rôle dans les métabolismes de l'énergie et du phosphate, dans la régulation d'activités enzymatiques, la virulence, la pathogénicité, le remodelage osseux et la coagulation sanguine. Il a récemment été montré que les cellules de myélome contiennent une grande quantité de iPOP. Il y donc un intérêt croissant pour les iPOP dans les lignées cellulaires humaines. Cependant, très peu d'informations sur le métabolisme des iPOP chez les eucaryotes sont disponibles. Les acidocalcisomes sont des compartiments acides et denses aux électrons. Ils font partie du groupe des organelles similaires aux lysosomes (LROs pour Lysosome Related Organelles). Le fait que les acidocalcisomes soient conservés dans tous les règnes du vivant montrent l'importance de ces compartiments pour les organismes. Cependant, l'analyse de ces organelles est rendue difficile par l'existence d'un nombre limité d'outils biochimiques permettant leur caractérisation. Les vacuoles de levures possèdent des aspects structuraux et physiologiques très similaires à ceux des acidocalcisomes. Par exemple, ils synthétisent et gardent en réserve les iPOP. Ceci fait des vacuoles de levure un modèle idéal pour l'étude de processus biologiques conservés chez les vacuoles et les acidocalcisomes. De plus, la levure est un organisme de choix pour l'étude de la synthèse des iPOP compte-tenu de l'existence de nombreux outils génétiques et la possibilité d'isoler des vacuoles fonctionnelles. Notre groupe a identifié le complexe VTC (Vacuole transporter Chaperone) comme étant responsable de la synthèse des iPOP et la sous-unité Vtc4p comme celle possédant l'activité catalytique. L'objectif de cette étude était de caractériser le processus de synthèse des iPOP en utilisant des vacuoles isolées et de reconstituer la synthèse des iPOP dans des liposomes. La première étape a consisté en la mise au point d'un dosage permettant la mesure de la quantité de iPOP synthétisés par les organelles isolés en fonction du temps. Cette nouvelle méthode a été comparée aux méthodes décrites précédemment dans la littérature. Ensuite, la caractérisation détaillée du processus a permis d'identifier des composés modulateurs de la réaction à la fois pour des vacuoles intactes et des vacuoles solubilisées. Enfin, des essais de purification du complexe VTC et sa reconstitution dans des liposomes ont été entrepris. De façon parallèle, une étude sur la translocation et le stockage des iPOP dans le lumen des vacuoles a été menée. Il a ainsi été possible de mettre en évidence différents groupes de iPOP : les iPOP localisés à l'intérieur et ceux localisés à l'extérieur des vacuoles isolées. De plus, nous avons observé que le lysat vacuolaire n'est pas détérioré par les étapes de reconstitution dans les liposomes et conserve l'activité de synthèse des iPOP. Les prochaines étapes consisteront en la purification du complexe intact et de la détermination de sa structure par cryo-microscopie électronique.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Inoculation methods under greenhouse conditions for evaluating soybean resistance to sudden death syndrome

The objectives of this work were to evaluate two greenhouse screening methods for sudden death syndrome (SDS) and to determine which one is best correlated with field resistance of soybean genotypes. The evaluations were done with three sets of genotypes that were classified as partially resistant, intermediate, and susceptible to SDS based on previous field evaluations. These three sets were independently evaluated for greenhouse SDS reactions using cone and tray inoculation methods. Plants were infected using grains of white sorghum [Sorghum bicolor (L.) Moench] infested with Fusarium solani f. sp. glycines. Foliar symptom severity was rated 21 days after emergence. The cone and field SDS ratings were significantly correlated and ranged from 0.69 for set 1 to 0.51 for set 3. Correlations of SDS ratings of genotypes between field and greenhouse tray ratings were significant for set 1 and not significant for set 2. The cone method showed the highest correlation with field results and is recommended to screen soybean genotypes for SDS resistance.