FastEpistasis: a high performance computing solution for quantitative trait epistasis.

Motivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously. Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism ( SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.

Optimizing Pavement Base, Subbase, and Subgrade Layers for Cost and Performance of Local Roads, TR-640

This report is one of two products for this project with the other being a design guide. This report describes test results and comparative analysis from 16 different portland cement concrete (PCC) pavement sites on local city and county roads in Iowa. At each site the surface conditions of the pavement (i.e., crack survey) and foundation layer strength, stiffness, and hydraulic conductivity properties were documented. The field test results were used to calculate in situ parameters used in pavement design per SUDAS and AASHTO (1993) design methodologies. Overall, the results of this study demonstrate how in situ and lab testing can be used to assess the support conditions and design values for pavement foundation layers and how the measurements compare to the assumed design values. The measurements show that in Iowa, a wide range of pavement conditions and foundation layer support values exist. The calculated design input values for the test sites (modulus of subgrade reaction, coefficient of drainage, and loss of support) were found to be different than typically assumed. This finding was true for the full range of materials tested. The findings of this study support the recommendation to incorporate field testing as part of the process to field verify pavement design values and to consider the foundation as a design element in the pavement system. Recommendations are provided in the form of a simple matrix for alternative foundation treatment options if the existing foundation materials do not meet the design intent. The PCI prediction model developed from multi-variate analysis in this study demonstrated a link between pavement foundation conditions and PCI. The model analysis shows that by measuring properties of the pavement foundation, the engineer will be able to predict long term performance with higher reliability than by considering age alone. This prediction can be used as motivation to then control the engineering properties of the pavement foundation for new or re-constructed PCC pavements to achieve some desired level of performance (i.e., PCI) with time.

Guidance for Improving Foundation Layers to Increase Pavement Performance on Local Roads, TR-640, 2014

This document is the second of two deliverables for the project Optimizing Pavement Base, Subbase, and Subgrade Layers for Cost and Performance on Local Roads (TR-640). The first deliverable is the 454-page Final Field Data Report. The field data report describes test results and comparative analysis from 16 different portland cement concrete (PCC) pavement sites on local city and county roads in Iowa. At each site the surface conditions of the pavement (i.e., crack survey) and foundation layer strength, stiffness, and hydraulic conductivity properties were documented. The field test results were used to calculate in situ parameters used in pavement design methodologies for AASHTO (1993) and Iowa’s Statewide Urban Design and Specifications (SUDAS). Overall, the results of the study demonstrate how in situ and lab testing can be used to assess the support conditions and design values for pavement foundation layers and how the measurements compare to the assumed design values. This guide summarizes the study results and outlines general guidelines for applying them to optimize pavement bases, subbases, and subgrade layers of local roads with PCC pavements and thus their performance.

Assessment of Nondestructive Testing Technologies for Quality Control/Quality Assurance of Asphalt Mixtures, TR-653, 2015

Asphalt pavements suffer various failures due to insufficient quality within their design lives. The American Association of State Highway and Transportation Officials (AASHTO) Mechanistic-Empirical Pavement Design Guide (MEPDG) has been proposed to improve pavement quality through quantitative performance prediction. Evaluation of the actual performance (quality) of pavements requires in situ nondestructive testing (NDT) techniques that can accurately measure the most critical, objective, and sensitive properties of pavement systems. The purpose of this study is to assess existing as well as promising new NDT technologies for quality control/quality assurance (QC/QA) of asphalt mixtures. Specifically, this study examined field measurements of density via the PaveTracker electromagnetic gage, shear-wave velocity via surface-wave testing methods, and dynamic stiffness via the Humboldt GeoGauge for five representative paving projects covering a range of mixes and traffic loads. The in situ tests were compared against laboratory measurements of core density and dynamic modulus. The in situ PaveTracker density had a low correlation with laboratory density and was not sensitive to variations in temperature or asphalt mix type. The in situ shear-wave velocity measured by surface-wave methods was most sensitive to variations in temperature and asphalt mix type. The in situ density and in situ shear-wave velocity were combined to calculate an in situ dynamic modulus, which is a performance-based quality measurement. The in situ GeoGauge stiffness measured on hot asphalt mixtures several hours after paving had a high correlation with the in situ dynamic modulus and the laboratory density, whereas the stiffness measurement of asphalt mixtures cooled with dry ice or at ambient temperature one or more days after paving had a very low correlation with the other measurements. To transform the in situ moduli from surface-wave testing into quantitative quality measurements, a QC/QA procedure was developed to first correct the in situ moduli measured at different field temperatures to the moduli at a common reference temperature based on master curves from laboratory dynamic modulus tests. The corrected in situ moduli can then be compared against the design moduli for an assessment of the actual pavement performance. A preliminary study of microelectromechanical systems- (MEMS)-based sensors for QC/QA and health monitoring of asphalt pavements was also performed.

Testing the effects of genetic crossing distance on embryo survival within a metapopulation of brown trout (Salmo trutta)

Predicting progeny performance from parental genetic divergence can potentially enhance the efficiency of supportive breeding programmes and facilitate risk assessment. Yet, experimental testing of the effects of breeding distance on offspring performance remains rare, especially in wild populations of vertebrates. Recent studies have demonstrated that embryos of salmonid fish are sensitive indicators of additive genetic variance for viability traits. We therefore used gametes of wild brown trout (Salmo trutta) from five genetically distinct populations of a river catchment in Switzerland, and used a full factorial design to produce over 2,000 embryos in 100 different crosses with varying genetic distances (FST range 0.005-0.035). Customized egg capsules allowed recording the survival of individual embryos until hatching under natural field conditions. Our breeding design enabled us to evaluate the role of the environment, of genetic and nongenetic parental contributions, and of interactions between these factors, on embryo viability. We found that embryo survival was strongly affected by maternal environmental (i.e. non-genetic) effects and by the microenvironment, i.e. by the location within the gravel. However, embryo survival was not predicted by population divergence, parental allelic dissimilarity, or heterozygosity, neither in the field nor under laboratory conditions. Our findings suggest that the genetic effects of inter-population hybridization within a genetically differentiated meta-population can be minor in comparison to environmental effects.

Alkali Content of Fly Ash – Measuring and Testing Strategies for Compliance, TR-628, 2015

Sodium and potassium are the common alkalis present in fly ash. Excessive amounts of fly ash alkalis can cause efflorescence problems in concrete products and raise concern about the effectiveness of the fly ash to mitigate alkali-silica reaction (ASR). The available alkali test, which is commonly used to measure fly ash alkali, takes approximately 35 days for execution and reporting. Hence, in many instances the fly ash has already been incorporated into concrete before the test results are available. This complicates the job of the fly ash marketing agencies and it leads to disputes with fly ash users who often are concerned with accepting projects that contain materials that fail to meet specification limits. The research project consisted of a lab study and a field study. The lab study focused on the available alkali test and how fly ash alkali content impacts common performance tests (mortar-bar expansion tests). Twenty-one fly ash samples were evaluated during the testing. The field study focused on the inspection and testing of selected, well documented pavement sites that contained moderately reactive fine aggregate and high-alkali fly ash. A total of nine pavement sites were evaluated. Two of the sites were control sites that did not contain fly ash. The results of the lab study indicated that the available alkali test is prone to experimental errors that cause poor agreement between testing labs. A strong (linear) relationship was observed between available alkali content and total alkali content of Class C fly ash. This relationship can be used to provide a quicker, more precise method of estimating the available alkali content. The results of the field study failed to link the use of high-alkali fly ash with the occurrence of ASR in the various concrete sites. Petrographic examination of the pavement cores indicated that Wayland sand is an ASR-sensitive aggregate. This was in good agreement with Iowa DOT field service records. It was recommended that preventative measures should be used when this source of sand is used in concrete mixtures.

Portland Cement Concrete Curing Compound Performance Phase I and Phase II, MLR-02-03, 2003

Testing the efficiency of Portland Cement Concrete (PCC) curing compounds is currently done following Test Method Iowa 901-D, May 2002. Concrete test specimens are prepared from mortar materials and are wet cured 5 hours before the curing compound is applied. All brands of curing compound submitted to the Iowa Department of Transportation are laboratory tested for comparative performance under the same test conditions. These conditions are different than field PCC paving conditions. Phase I tests followed Test Method Iowa 901-D, but modified the application amounts of the curing compound. Test results showed that the application of two coats of one-half thickness each increased efficiency compared to one full thickness coat. Phase II tests also used the modified application amounts, used a concrete mix (instead of a mortar mix) and applied curing compound a few minutes after molding. Measurements of losses, during spraying of the curing compound, were noted and were found to be significant. Test results showed that application amounts, testing techniques, concrete specimen mix design and spray losses do influence the curing compound efficiency. The significance of the spray losses indicates that the conventional test method being used (Iowa 901 D) should be revised.

Performance of Reinforcement Fabric Used Under Asphaltic Concrete Overlays, MLR-83-03, 1983

The 1982 cost of a two-inch asphaltic concrete overlay, with fabric, was an average of 85% of the cost of a three-inch overlay (see attached calculations). A structural number can be assigned to the extra inch of overlay, whereas it is doubtful that any number can be assigned to the fabric. The observations made on the projects in this report leave little reason to be optimistic on the use of fabrics under asphalt overlays. This is especially true of the Floyd, Dallas and Clarke county projects. A great amount of fabric is being used nationwide for this purpose, probably more from sales promotion than from actual documented performance. Full scale field testing is continuing each time a project is let utilizing fabric reinforcement under asphaltic concrete overlays. It has already become apparent that the use of fabrics in AC overlays is not always cost effective.

Evaluation of Long-Term Field Performance of Cold In-Place Recycled Roads: Summary Report, TR-502, 2007

Cold in-place recycling (CIR) has become an attractive method for rehabilitating asphalt roads that have good subgrade support and are suffering distress related to non-structural aging and cracking of the pavement layer. Although CIR is widely used, its use could be expanded if its performance were more predictable. Transportation officials have observed roads that were recycled under similar circumstances perform very differently for no clear reason. Moreover, a rational mix design has not yet been developed, design assumptions regarding the structural support of the CIR layer remain empirical and conservative, and there is no clear understanding of the cause-effect relationships between the choices made during the design/construction process and the resulting performance. The objective of this project is to investigate these relationships, especially concerning the age of the recycled pavement, cumulative traffic volume, support conditions, aged engineering properties of the CIR materials, and road performance. Twenty-four CIR asphalt roads constructed in Iowa from 1986 to 2004 were studied: 18 were selected from a sample of roads studied in a previous research project (HR-392), and 6 were selected from newer CIR projects constructed after 1999. This report summarizes the results of a comprehensive program of field distress surveys, field testing, and laboratory testing for these CIR asphalt roads. The results of this research can help identify changes that should be made with regard to design, material selection, and construction in order to lengthen the time between rehabilitation cycles and improve the performance and cost-effectiveness of future recycled roads.

Iowa State Highway 92 Over Drainage Ditch #25: Performance Evaluation - Galvanized Reinforcing Bars -- Louisa County, Iowa, 2015

Several strategies are available to the Iowa Department of Transportation (IaDOT) for limiting deterioration due to chloride-induced corrosion of embedded reinforcing bars in concrete bridge decks. While the method most commonly used throughout the Midwestern United States is to construct concrete bridge decks with fusion-bonded epoxy-coated reinforcing bars, galvanized reinforcing bars are an available alternative. Previous studies of the in situ performance of galvanized reinforcing bars in service in bridge decks have been limited. IaDOT requested that Wiss, Janney, Elstner Associates, Inc. (WJE) perform this study to gain further understanding of the long-term performance of an Iowa bridge deck reinforced with galvanized reinforcing bars. This study characterized the condition of a bridge deck with galvanized reinforcing bars after about 36 years of service and compared that performance to the expected performance of epoxy-coated or uncoated reinforcing bars in similar bridge construction. For this study, IaDOT selected the Iowa State Highway 92 bridge across Drainage Ditch #25 in Louisa County, Iowa (Structure No. 5854.5S092), which was constructed using galvanized reinforcing bars as the main deck reinforcing. The scope of work for this study included: field assessment, testing, and sampling; laboratory testing and analysis; analysis of findings; service life modeling; and preparation of this report. In addition, supplemental observations of the condition of the galvanized reinforcing bars were made during a subsequent project to repair the bride deck.

Field Testing of Abrasive Delivery Systems in Winter Maintenance, TR-458, 2009

The key goals in winter maintenance operations are preserving the safety and mobility of the traveling public. To do this, it is in general necessary to try to increase the friction of the road surface above the typical friction levels found on a snow or ice covered roadway. Because of prior work on the performance of abrasives (discussed in greater detail in chapter 2) a key concern when using abrasives has become how to ensure the greatest increase in pavement friction when using abrasives for the longest period of time. There are a number of ways in which the usage of abrasives can be optimized, and these methods are discussed and compared in this report. In addition, results of an Iowa DOT test of zero-velocity spreaders are presented. Additionally in this study the results of field studies conducted in Johnson County Iowa on the road surface friction of pavements treated with abrasive applications using different modes of delivery are presented. The experiments were not able to determine any significant difference in material placement performance between a standard delivery system and a chute based delivery system. The report makes a number of recommendations based upon the reviews and the experiments.

Laboratory Performance Evaluation of CIR-Emulsion and its Comparison Against CIR-Foam Test Results from Phase 2, TR-474, 2009

Currently, no standard mix design procedure is available for CIR-emulsion in Iowa. The CIR-foam mix design process developed during the previous phase is applied for CIR-emulsion mixtures with varying emulsified asphalt contents. Dynamic modulus test, dynamic creep test, static creep test and raveling test were conducted to evaluate the short- and long-term performance of CIR-emulsion mixtures at various testing temperatures and loading conditions. A potential benefit of this research is a better understanding of CIR-emulsion material properties in comparison with those of CIR-foam material that would allow for the selection of the most appropriate CIR technology and the type and amount of the optimum stabilization material. Dynamic modulus, flow number and flow time of CIR-emulsion mixtures using CSS- 1h were generally higher than those of HFMS-2p. Flow number and flow time of CIR-emulsion using RAP materials from Story County was higher than those from Clayton County. Flow number and flow time of CIR-emulsion with 0.5% emulsified asphalt was higher than CIR-emulsion with 1.0% or 1.5%. Raveling loss of CIR-emulsion with 1.5% emulsified was significantly less than those with 0.5% and 1.0%. Test results in terms of dynamic modulus, flow number, flow time and raveling loss of CIR-foam mixtures are generally better than those of CIR-emulsion mixtures. Given the limited RAP sources used for this study, it is recommended that the CIR-emulsion mix design procedure should be validated against several RAP sources and emulsion types.

Effects of Implements of Husbandry (Farm Equipment) on Pavement Performance, TR-563, 2012

The effects of farm equipment on the structural behavior of flexible and rigid pavements were investigated in this study. The project quantified the difference in pavement behavior caused by heavy farm equipment as compared to a typical 5-axle, 80 kip semi-truck. This research was conducted on full scale pavement test sections designed and constructed at the Minnesota Road Research facility (MnROAD). The testing was conducted in the spring and fall seasons to capture responses when the pavement is at its weakest state and when agricultural vehicles operate at a higher frequency, respectively. The flexible pavement sections were heavily instrumented with strain gauges and earth pressure cells to measure essential pavement responses under heavy agricultural vehicles, whereas the rigid pavement sections were instrumented with strain gauges and linear variable differential transducers (LVDTs). The full scale testing data collected in this study were used to validate and calibrate analytical models used to predict relative damage to pavements. The developed procedure uses various inputs (including axle weight, tire footprint, pavement structure, material characteristics, and climatic information) to determine the critical pavement responses (strains and deflections). An analysis was performed to determine the damage caused by various types of vehicles to the roadway when there is a need to move large amounts agricultural product.

Carbonate Rock Pore Size Distribution Determination through Iowa Pore Index Testing, MLR-15-01, 2015

The Iowa Pore Index (IPI) measures the pore system of carbonate (limestone and dolomite) rocks using pressurized water to infiltrate the pore system. This technique provides quantitative results for the primary and capillary (secondary) pores in carbonate rocks. These results are used in conjunction with chemical and mineralogical test results to calculate a quality number, which is used as a predictor of aggregate performance in Portland cement concrete (PCC) leading to the durability classification of the aggregate. This study had two main objectives: to determine the effect different aggregate size has on IPI test results and to establish the precision of IPI test and test apparatus. It was found that smaller aggregate size fractions could be correlated to the standard 1/2”-3/4” size sample. Generally, a particle size decrease was accompanied by a slight decrease in IPI values. The IPI testing also showed fairly good agreement of the secondary pore index number between the 1/2”-3/4”and the 3/8”-1/2” fraction. The #4-3/8” showed a greater difference of the secondary number from the 1/2”-3/4” fraction. The precision of the IPI test was established as a standard deviation (Sr) of 2.85 (Primary) and 0.87 (Secondary) with a repeatability limit (%r) of 8.5% and 14.9% for the primary and secondary values, respectively.

Field Evaluation of Elliptical Steel Dowel Performance, 2006

Joints are always a concern in the construction and long-term performance of concrete pavements. Research has shown that we need some type of positive load transfer across transverse joints. The same research has directed pavement designers to use round dowels spaced at regular intervals across the transverse joint to distribute the vehicle loads both longitudinally and transversely across the joint. The goal is to reduce bearing stresses on the dowels and the two pavement slab edges and erosion of the underlying surface, hence improved long-term joint and pavement structure performance. Road salts cause metal corrosion in doweled joints, excessive bearing stresses hollow dowel ends, and construction processes are associated with cracking pavement at the end of dowels. Dowels are also a cost factor in the pavement costs when joint spacing is reduced to control curling and warping distress in pavements. Designers desire to place adequate numbers of dowels spaced at the proper locations to handle the anticipated loads and bearing stresses for the design life of the pavement. This interim report is the second of three reports on the evaluation of elliptical steel dowels. This report consists of an update on the testing and performance of the various shapes and sizes of dowels. It also documents the results of the first series of performance surveys and draws interim conclusions about the performance of various bar shapes, sizes, spacings, and basket configurations. In addition to the study of elliptical steel dowel performance, fiber reinforced polymers (FRP) are also tested as elliptical dowel material (in contrast to steel) on a section of the highway construction north of the elliptical steel test sections.