2009 Iowa’s Rail System Background Prepared by the Office of Systems Planning December 2010

Iowa’s Rail Environment Iowa’s rail transportation system provides both freight and passenger service. Rail serves a variety of trips, including those within Iowa and those to other states as well as to foreign markets. While rail competes with other modes, it also cooperates with those modes to provide intermodal services to Iowans. In 2009 Iowa’s rail transportation system could be described as follows: Freight Iowa’s 130,000-mile freight transportation system includes an extensive railroad network, a well-developed highway system, two bordering navigable waterways, and a pipeline network as well as air cargo facilities. While rail accounts for only 3 percent of the freight network, it carries 43 percent of Iowa’s freight tonnage. A great variety of commodities ranging from fresh fish to textiles to optical products are moved by rail. However, most of the Iowa rail shipments consist of bulk commodities, including grain, grain products, coal, ethanol, and fertilizers. The railroad network performs an important role in moving bulk commodities produced and consumed in the state to local processors, livestock feeders, river terminals and ports for foreign export. The railroad’s ability to haul large volumes, long distances at low costs will continue to be a major factor in moving freight and improving the economy of Iowa. Key 2008 Facts • 3,945 miles of track • 18 railroads • 49.5 million tons shipped • 39.7 million tons received • 2 Amtrak routes • 6 Amtrak stations • 66,286 rail passenger rides Key Rail Trends • slightly fewer miles being operated; • railroads serving Iowa has remained the same; • more rail freight traffic; • more tons hauled per car; • higher average rail rates per ton-mile since 2002; • more car and tons hauled per locomotive; and • more ton miles per gallon of fuel consumed. Iowa’s rail system and service has been evolving over time relative to its size, financial conditions, and competition from other modes.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

Council Bluffs Interstate System Improvements Project Pottawatomie County, Iowa and Douglas County, Nebraska Project Number: IM-029-3(62)54-13-78, November 2004

The Iowa Department of Transportation (Iowa DOT), Nebraska Department of Roads (NDOR), and the Federal Highway Administration (FHWA) are proposing to improve the interstate system around Council Bluffs with improvements extending across the Missouri River on I-80 to east of the I-480 interchange in Omaha, Nebraska, see Figure 1-1. The study considers long-term, broad-based transportation improvements along I-80, I-29, and I-480, including approximately 18 mainline miles of interstate and 14 interchanges (3 system1, 11 service), that would add capacity and correct functional issues along the mainline and interchanges and upgrade the I-80 Missouri River Crossing. These improvements, once implemented, would bring the segments of I-80 and I-29 up to current engineering standards and modernize the roadway to accommodate future traffic needs. In 2001, Iowa DOT and FHWA initiated the Council Bluffs Interstate System (CBIS) Improvements Project. The agencies concluded that the environmental study process would be conducted in two stages; that is, a tiered approach would be applied. The project is being conducted pursuant to the National Environmental Policy Act (NEPA) regulations issued by the Council on Environmental Quality (CEQ), 40 Code of Federal Regulations (CFR) Part 1502.20, and FHWA 23 CFR Part 771.111, that permit tiering for large, complex NEPA studies. Tier 1 is an examination of the overall interstate system improvement needs, including a clear explanation of the area’s transportation needs, a study of alternatives to satisfy them, and broad consideration of potential environmental and social impacts. The Tier 1 evaluation is at a sufficient level of engineering and environmental detail to assist decision makers in selecting a preferred transportation strategy. Tier 1 includes preparation of a draft and final Environmental Impact Statement (EIS) that would disclose the potential environmental and social effects (evaluated at a planning level that considers a variety of conceptual designs) of the proposed improvements. The final EIS will conclude with a Record of Decision (ROD) that states the preferred plan for improvements to be implemented. Essentially, the Tier 1 document will establish the planning framework for the needed improvements. Because the scope of the overall system improvements is large, the interstate improvements would be implemented as a series of individual projects that fit into the overall planning framework. The Tier 1 Area of Potential Impact, which is discussed in detail in Section 4 is an alternative that considers a combination of the most reasonable concepts that have been developed, buffered by approximately 100 or more feet to ensure that any Tier 2 design modifications would remain inside the outer boundary.

Neuromodulation by oxytocin and vasopressin in the central nervous system as a basis for their rapid behavioral effects.

The last several years have seen an increasing number of studies that describe effects of oxytocin and vasopressin on the behavior of animals or humans. Studies in humans have reported behavioral changes and, through fMRI, effects on brain function. These studies are paralleled by a large number of reports, mostly in rodents, that have also demonstrated neuromodulatory effects by oxytocin and vasopressin at the circuit level in specific brain regions. It is the scope of this review to give a summary of the most recent neuromodulatory findings in rodents with the aim of providing a potential neurophysiological basis for their behavioral effects. At the same time, these findings may point to promising areas for further translational research towards human applications.

Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

2009 Iowa Railroad System Plan, 2009

The 2009 Iowa Railroad System Plan is intended to guide the Iowa Department of Transportation (DOT) in its activities of promoting access to rail transportation, helping to improve the freight railroad transportation system, expanding passenger rail service, and promoting improved safety both on the rail system and where the rail system interacts with people and other transportation modes. The Iowa DOT has been developing railroad transportation plans since the late 1970s. The original plan was prepared in 1978 during a time of crisis in the Iowa railroad system. Several large Iowa railroad carriers had filed for bankruptcy and were reorganizing both their businesses and physical systems. The 1978 plan was a guide for determining which railroad lines the state would partner with to preserve and improve the lines. In the 1970s, 1980s and 1990s, the railroad system mileage in Iowa was reduced from about

Stable alpha-synuclein oligomers strongly inhibit chaperone activity of the Hsp70 system by weak interactions with J-domain co-chaperones.

α-Synuclein aggregation and accumulation in Lewy bodies are implicated in progressive loss of dopaminergic neurons in Parkinson disease and related disorders. In neurons, the Hsp70s and their Hsp40-like J-domain co-chaperones are the only known components of chaperone network that can use ATP to convert cytotoxic protein aggregates into harmless natively refolded polypeptides. Here we developed a protocol for preparing a homogeneous population of highly stable β-sheet enriched toroid-shaped α-Syn oligomers with a diameter typical of toxic pore-forming oligomers. These oligomers were partially resistant to in vitro unfolding by the bacterial Hsp70 chaperone system (DnaK, DnaJ, GrpE). Moreover, both bacterial and human Hsp70/Hsp40 unfolding/refolding activities of model chaperone substrates were strongly inhibited by the oligomers but, remarkably, not by unstructured α-Syn monomers even in large excess. The oligomers acted as a specific competitive inhibitor of the J-domain co-chaperones, indicating that J-domain co-chaperones may preferably bind to exposed bulky misfolded structures in misfolded proteins and, thus, complement Hsp70s that bind to extended segments. Together, our findings suggest that inhibition of the Hsp70/Hsp40 chaperone system by α-Syn oligomers may contribute to the disruption of protein homeostasis in dopaminergic neurons, leading to apoptosis and tissue loss in Parkinson disease and related neurodegenerative diseases.

Non-Destructive Evaluation of Iowa Pavements Phase 2: Development of a Fully Automated Software System for Rapid Analysis/Processing of the Falling Weight Deflectometer Data, 2009

The Office of Special Investigations at Iowa Department of Transportation (DOT) collects FWD data on regular basis to evaluate pavement structural conditions. The primary objective of this study was to develop a fully-automated software system for rapid processing of the FWD data along with a user manual. The software system automatically reads the FWD raw data collected by the JILS-20 type FWD machine that Iowa DOT owns, processes and analyzes the collected data with the rapid prediction algorithms developed during the phase I study. This system smoothly integrates the FWD data analysis algorithms and the computer program being used to collect the pavement deflection data. This system can be used to assess pavement condition, estimate remaining pavement life, and eventually help assess pavement rehabilitation strategies by the Iowa DOT pavement management team. This report describes the developed software in detail and can also be used as a user-manual for conducting simulation studies and detailed analyses. *********************** Large File ***********************

Mynodbcsv: Lightweight Zero-Config Database Solution for Handling Very Large CSV Files.

Volumes of data used in science and industry are growing rapidly. When researchers face the challenge of analyzing them, their format is often the first obstacle. Lack of standardized ways of exploring different data layouts requires an effort each time to solve the problem from scratch. Possibility to access data in a rich, uniform manner, e.g. using Structured Query Language (SQL) would offer expressiveness and user-friendliness. Comma-separated values (CSV) are one of the most common data storage formats. Despite its simplicity, with growing file size handling it becomes non-trivial. Importing CSVs into existing databases is time-consuming and troublesome, or even impossible if its horizontal dimension reaches thousands of columns. Most databases are optimized for handling large number of rows rather than columns, therefore, performance for datasets with non-typical layouts is often unacceptable. Other challenges include schema creation, updates and repeated data imports. To address the above-mentioned problems, I present a system for accessing very large CSV-based datasets by means of SQL. It's characterized by: "no copy" approach - data stay mostly in the CSV files; "zero configuration" - no need to specify database schema; written in C++, with boost [1], SQLite [2] and Qt [3], doesn't require installation and has very small size; query rewriting, dynamic creation of indices for appropriate columns and static data retrieval directly from CSV files ensure efficient plan execution; effortless support for millions of columns; due to per-value typing, using mixed text/numbers data is easy; very simple network protocol provides efficient interface for MATLAB and reduces implementation time for other languages. The software is available as freeware along with educational videos on its website [4]. It doesn't need any prerequisites to run, as all of the libraries are included in the distribution package. I test it against existing database solutions using a battery of benchmarks and discuss the results.

Origin of a restraining bend in an evolving strike-slip system: The Cenozoic As Pontes basin (NW Spain)

The As Pontes basin (12 km2), NW Iberian Peninsula, is bounded by a double restraining bend of a dextral strike-slip fault, which is related to the western onshore end of the Pyrenean belt. Surface and subsurface data obtained from intensive coal exploration and mining in the basin since the 1960s together with additional structural and stratigraphic sequence analysis allowed us to determine the geometric relationships between tectonic structures and stratigraphic markers. The small size of the basin and the large amount of quality data make the As Pontes basin a unique natural laboratory for improving our understanding of the origin and evolution of restraining bends. The double restraining bend is the end stage of the structural evolution of a compressive underlapping stepover, where the basin was formed. During the first stage (stepover stage), which began ca. 30 Ma ago (latest Rupelian) and lasted 3.4 My, two small isolated basins bounded by thrusts and normal faults were formed. For 1.3 My, the strike-slip faults, which defined the stepover, grew towards each other until joining and forming the double restraining bend, which bounds one large As Pontes basin (transition stage). The history of the basin was controlled by the activity of the double restraining bend for a further 3.4 My (restraining bend stage) and ended in mid-Aquitanian times (ca. 22 Ma).

The Economics of Reducing the County Road System: Three Case Studies in Iowa, HR-242, 1986

This research project looked at the economic benefits and costs associated with alternative strategies for abandoning low volume rural highways and bridges. Three test counties in Iowa were studied, each 100 square miles in size: Hamilton County having a high agricultural tax base and a high percentage of paved roads and few bridges; Shelby County having a relatively low agricultural tax base, hilly terrain and a low percentage of paved road and many bridges; and Linn County having a high agricultural tax base, a high percentage of paved roads and a large number of non-farm households. A questionnaire survey was undertaken to develop estimates of farm and household travel patterns. Benefits and costs associated with the abandonment of various segments of rural highway and bridge mileages in each county were calculated. "Benefits" calculated were reduced future reconstruction and maintenance costs, whereas "costs" were the added cost of travel resulting from the reduced mileage. Some of the findings suggest limited cost savings from abandonment of county roads with no property access in areas with large non-farm rural population; relatively high cost savings from the abandonment of roads with no property access in areas with small rural population; and the largest savings from the conversion of public dead-end gravel roads with property or residence accesses to private drives.

Solar Powered Highway Delineator System, HR-367, 1993

Currently, many drivers experience some difficulty in viewing the road ahead of them during times of reduced visibility, such as rain, snow, fog, or the darkness of night- Recent studies done by the National Safety Council provide a detailed contrast between fatal accidents occurring during the day and night. Revealed was that the motor vehicle night death rate (4.41 deaths per 100 million miles driven) was sharply higher than the corresponding death rate during daylight hours (1.21). By providing a delineating system powered by the natural resource of solar power, a constant source of visibility may be maintained throughout the evening. Along with providing enough light to trace the outline of the road, other major goals defined in producing this delineator system are as follows: 1. A strong and durable design that would protect the internal components and survive extreme weather conditions. 2. A low maintenance system where components need few repairs or replacements. 3. A design which makes all components accessible in the event that maintenance is needed, but also prevents vandalism. 4. A design that provides greater visibility to drivers and will not harm a vehicle or its passengers in the event of a collision. This solar powered highway delineator consists of an adjustable solar array, a light fixture, and a standard delineator pole. The solar array houses and protects the solar panels, and can be easily adjusted to obtain a maximum amount of sunlight. The light fixture primarily houses the battery, the circuit and the light assembly. Both components allow for easy accessibility and reduce vandalism using internal connections for bolts and wires. The delineator mounting pole is designed to extensively deform in the event of a collision, therefore reducing any harm caused to the vehicle and/or the passengers. The cost of a single prototype to be produced is approximately $70.00 excluding labor costs. However, these material and labor costs will be greatly reduced if a large number of delineators are produced. It is recommended that the Iowa Department of Transportation take full advantage of the research and development put into this delineator design. The principles used in creating this delineator can be used to provide an outline for drivers to follow, or on a larger scale, provide actual roadway lighting in areas where it was never before possible or economically feasible. In either event, the number of fatal accidents will be decreased due to the improved driver visibility in the evening.

Development and Implementation of an Expert System for Forecasting Fog on US Highway 30 in Cedar Rapids, Iowa, HR-357, 1996

Several accidents, some involving fatalities, have occurred on U.S. Highway 30 near the Archer Daniels Midland Company (ADM) Corn Sweeteners plant in Cedar Rapids, Iowa. A contributing factor to many of these accidents has been the large amounts of water (vapor and liquid) emitted from multiple sources at ADM's facility located along the south side of the highway. Weather and road closure data acquired from IDOT have been used to develop a database of meteorological conditions preceding and accompanying closure of Highway 30 in Cedar Rapids. An expert system and a FORTRAN program were developed as aids in decision making with regard to closure of Highway 30 near the plant. The computer programs were used for testing, evaluation, and final deployment. Reports indicate the decision tools have been successfully implemented and were judged to be helpful in forecasting road closures and in reducing costs and personnel time in monitoring the roadway.

Comparison between a linear ion trap and a triple quadruple MS in the sensitive detection of large peptides at femtomole amounts on column.

In addition to the importance of sample preparation and extract separation, MS detection is a key factor in the sensitive quantification of large undigested peptides. In this article, a linear ion trap MS (LIT-MS) and a triple quadrupole MS (TQ-MS) have been compared in the detection of large peptides at subnanomolar concentrations. Natural brain natriuretic peptide, C-peptide, substance P and D-Junk-inhibitor peptide, a full D-amino acid therapeutic peptide, were chosen. They were detected by ESI and simultaneous MS(1) and MS(2) acquisitions. With direct peptide infusion, MS(2) spectra revealed that fragmentation was peptide dependent, milder on the LIT-MS and required high collision energies on the TQ-MS to obtain high-intensity product ions. Peptide adsorption on surfaces was overcome and peptide dilutions ranging from 0.1 to 25 nM were injected onto an ultra high-pressure LC system with a 1 mm id analytical column and coupled with the MS instruments. No difference was observed between the two instruments when recording in LC-MS(1) acquisitions. However, in LC-MS(2) acquisitions, a better sensitivity in the detection of large peptides was observed with the LIT-MS. Indeed, with the three longer peptides, the typical fragmentation in the TQ-MS resulted in a dramatic loss of sensitivity (> or = 10x).

IRM cardiaque en évolution: de grandes études multicentriques en 2012 [Cardiac MR in development: the large multicenter CMR studies in 2012].

The results of several large multicenter CMR studies were reported in 2012, thus, constantly corroborating the evidence on CMR performance. In this review, we present results of the MR-IMPACT programme and the CE-MARC study, which demonstrated the superiority of perfusion-CMR over gated SPECT for the workup of suspected CAD, the currently available data from the European CMR registry, comprising almost 30,000 patients from 57 participating centers in 15 European countries, and finally, the results of the Advisa-MRI study, which documented the safety of a MRI-compatible pacemaker system. These large trials and others set the basis for the recommendations in the new European guidelines on heart failure to use CMR as a first line method if echocardiographic quality is inadequate or the etiology of heart failure is unclear.