Roadway Design Standards for Rural and Suburban Subdivisions Final Report, June 2007

In Iowa, there are currently no uniform design standards for rural and suburban subdivision development roadways. Without uniform design standards, many counties are unable to provide adequate guidance for public facilities, particularly roadways, to be constructed as part of a rural subdivision development. If a developer is not required to install appropriate public improvements or does not do so properly, significant liability and maintenance expenses can be expected, along with the potential for major project costs to correct the situation. Not having uniform design standards for rural and suburban subdivision development improvements in Iowa creates situations where there is potential for inconsistency and confusion. Differences in the way development standards are applied also create incentives or disincentives for developers to initiate subdivision platting in a particular county. With the wide range of standards or lack of standards for local roads in development areas, it is critical that some level of uniformity is created to address equity in development across jurisdictional lines. The standards must be effective in addressing the problem, but they must not be so excessive as to curtail development activities within a local jurisdiction. In order to address the concerns, cities and counties have to work together to identify where growth is going to be focused. Within that long-term growth area, the roadways should be constructed to urban standards to provide an easier transition to traditional urban facilities as the area is developed. Developments outside of the designated growth area should utilize a rural cross section since it is less likely to have concentrated urban development. The developers should be required to develop roadways that are designed for a minimum life of 40 years, and the county should accept dedication of the roadway and be responsible for its maintenance.

Integrated methodologies to study human transcriptional regulation from functional genomics data

Abstract : The human body is composed of a huge number of cells acting together in a concerted manner. The current understanding is that proteins perform most of the necessary activities in keeping a cell alive. The DNA, on the other hand, stores the information on how to produce the different proteins in the genome. Regulating gene transcription is the first important step that can thus affect the life of a cell, modify its functions and its responses to the environment. Regulation is a complex operation that involves specialized proteins, the transcription factors. Transcription factors (TFs) can bind to DNA and activate the processes leading to the expression of genes into new proteins. Errors in this process may lead to diseases. In particular, some transcription factors have been associated with a lethal pathological state, commonly known as cancer, associated with uncontrolled cellular proliferation, invasiveness of healthy tissues and abnormal responses to stimuli. Understanding cancer-related regulatory programs is a difficult task, often involving several TFs interacting together and influencing each other's activity. This Thesis presents new computational methodologies to study gene regulation. In addition we present applications of our methods to the understanding of cancer-related regulatory programs. The understanding of transcriptional regulation is a major challenge. We address this difficult question combining computational approaches with large collections of heterogeneous experimental data. In detail, we design signal processing tools to recover transcription factors binding sites on the DNA from genome-wide surveys like chromatin immunoprecipitation assays on tiling arrays (ChIP-chip). We then use the localization about the binding of TFs to explain expression levels of regulated genes. In this way we identify a regulatory synergy between two TFs, the oncogene C-MYC and SP1. C-MYC and SP1 bind preferentially at promoters and when SP1 binds next to C-NIYC on the DNA, the nearby gene is strongly expressed. The association between the two TFs at promoters is reflected by the binding sites conservation across mammals, by the permissive underlying chromatin states 'it represents an important control mechanism involved in cellular proliferation, thereby involved in cancer. Secondly, we identify the characteristics of TF estrogen receptor alpha (hERa) target genes and we study the influence of hERa in regulating transcription. hERa, upon hormone estrogen signaling, binds to DNA to regulate transcription of its targets in concert with its co-factors. To overcome the scarce experimental data about the binding sites of other TFs that may interact with hERa, we conduct in silico analysis of the sequences underlying the ChIP sites using the collection of position weight matrices (PWMs) of hERa partners, TFs FOXA1 and SP1. We combine ChIP-chip and ChIP-paired-end-diTags (ChIP-pet) data about hERa binding on DNA with the sequence information to explain gene expression levels in a large collection of cancer tissue samples and also on studies about the response of cells to estrogen. We confirm that hERa binding sites are distributed anywhere on the genome. However, we distinguish between binding sites near promoters and binding sites along the transcripts. The first group shows weak binding of hERa and high occurrence of SP1 motifs, in particular near estrogen responsive genes. The second group shows strong binding of hERa and significant correlation between the number of binding sites along a gene and the strength of gene induction in presence of estrogen. Some binding sites of the second group also show presence of FOXA1, but the role of this TF still needs to be investigated. Different mechanisms have been proposed to explain hERa-mediated induction of gene expression. Our work supports the model of hERa activating gene expression from distal binding sites by interacting with promoter bound TFs, like SP1. hERa has been associated with survival rates of breast cancer patients, though explanatory models are still incomplete: this result is important to better understand how hERa can control gene expression. Thirdly, we address the difficult question of regulatory network inference. We tackle this problem analyzing time-series of biological measurements such as quantification of mRNA levels or protein concentrations. Our approach uses the well-established penalized linear regression models where we impose sparseness on the connectivity of the regulatory network. We extend this method enforcing the coherence of the regulatory dependencies: a TF must coherently behave as an activator, or a repressor on all its targets. This requirement is implemented as constraints on the signs of the regressed coefficients in the penalized linear regression model. Our approach is better at reconstructing meaningful biological networks than previous methods based on penalized regression. The method is tested on the DREAM2 challenge of reconstructing a five-genes/TFs regulatory network obtaining the best performance in the "undirected signed excitatory" category. Thus, these bioinformatics methods, which are reliable, interpretable and fast enough to cover large biological dataset, have enabled us to better understand gene regulation in humans.

Traumatic Brain Injury in Iowa: Iowa Brain Injury Resource Network Outcome Evaluation 2007-2009, August 2011

Termed the “silent epidemic,” traumatic brain injury (TBI) is the most debilitating outcome of injury, and is characterized by the irreversibility of its damages, long-term effects on quality of life and healthcare costs. The latest data available from the CDC estimate that nationally, 52,000 people die each year from TBI2. In Iowa, TBI is a major public health problem. The numbers and rates of hospitalizations and emergency department (ED) visits due to TBIs are steadily increasing. From 2006 to 2008, there were on average 545 injury deaths per year. Among the injured Iowans, TBI constituted nearly 30 percent (545) of all injury deaths, ten percent (1,591) of people hospitalized and seven percent (17,696) of ED visitors. 3 The state of Iowa has been supporting secondary prevention services to TBI survivors for several years. An Iowa organization that has made a significant effort in assisting TBI survivors is the Brain Injury Association of Iowa (BIAIA). The BIAIA administers the IBIRN program in cooperation with the Iowa Department of Public Health (IDPH) through HRSA TBI Implementation grant funding and state appropriations.

Monitoring network optimisation for spatial data classification using support vector machines

The paper presents a novel method for monitoring network optimisation, based on a recent machine learning technique known as support vector machine. It is problem-oriented in the sense that it directly answers the question of whether the advised spatial location is important for the classification model. The method can be used to increase the accuracy of classification models by taking a small number of additional measurements. Traditionally, network optimisation is performed by means of the analysis of the kriging variances. The comparison of the method with the traditional approach is presented on a real case study with climate data.

A Mixed-method Social Networks Study Design for Research on Transnational Families

This paper advocates the adoption of a mixed-methods research design to describe and analyze ego-centered social networks in transnational family research. Drawing on the experience of the Social Networks Influences on Family Formation project (2004-2005), I show how the combined use of network generators and semistructured interviews (N = 116) produces unique data on family configurations and their impact on life course choices. A mixed-methods network approach presents specific advantages for research on children in transnational families. On the one hand, quantitative analyses are crucial for reconstructing and measuring the potential and actual relational support available to children in a context where kin interactions may be hindered by temporary and prolonged periods of separation. On the other hand, qualitative analyses can address strategies and practices employed by families to maintain relationships across international borders and geographic distance, as well as the implications of those strategies for children's well-being.

Development of a New Process for Determining Design Year Traffic Demands, TR-528, 2007

Researchers should continuously ask how to improve the models we rely on to make financial decisions in terms of the planning, design, construction, and maintenance of roadways. This project presents an alternative tool that will supplement local decision making but maintain a full appreciation of the complexity and sophistication of today’s regional model and local traffic impact study methodologies. This alternative method is tailored to the desires of local agencies, which requested a better, faster, and easier way to evaluate land uses and their impact on future traffic demands at the sub-area or project corridor levels. A particular emphasis was placed on scenario planning for currently undeveloped areas. The scenario planning tool was developed using actual land use and roadway information for the communities of Johnston and West Des Moines, Iowa. Both communities used the output from this process to make regular decisions regarding infrastructure investment, design, and land use planning. The City of Johnston case study included forecasting future traffic for the western portion of the city within a 2,600-acre area, which included 42 intersections. The City of West Des Moines case study included forecasting future traffic for the city’s western growth area covering over 30,000 acres and 331 intersections. Both studies included forecasting a.m. and p.m. peak-hour traffic volumes based upon a variety of different land use scenarios. The tool developed took goegraphic information system (GIS)-based parcel and roadway information, converted the data into a graphical spreadsheet tool, allowed the user to conduct trip generation, distribution, and assignment, and then to automatically convert the data into a Synchro roadway network which allows for capacity analysis and visualization. The operational delay outputs were converted back into a GIS thematic format for contrast and further scenario planning. This project has laid the groundwork for improving both planning and civil transportation decision making at the sub-regional, super-project level.

Development of Self-Cleaning Box Culvert Design – Phase II, TR-619, 2013

Culverts are common means to convey flow through the roadway system for small streams. In general, larger flows and road embankment heights entail the use of multibarrel culverts (a.k.a. multi-box) culverts. Box culverts are generally designed to handle events with a 50-year return period, and therefore convey considerably lower flows much of the time. While there are no issues with conveying high flows, many multi-box culverts in Iowa pose a significant problem related to sedimentation. The highly erosive Iowa soils can easily lead to the situation that some of the barrels can silt-in early after their construction, becoming partially filled with sediment in few years. Silting can reduce considerably the capacity of the culvert to handle larger flow events. Phase I of this Iowa Highway Research Board project (TR-545) led to an innovative solution for preventing sedimentation. The solution was comprehensively investigated through laboratory experiments and numerical modeling aimed at screening design alternatives and testing their hydraulic and sediment conveyance performance. Following this study phase, the Technical Advisory Committee suggested to implement the recommended sediment mitigation design to a field site. The site selected for implementation was a 3-box culvert crossing Willow Creek on IA Hwy 1W in Iowa City. The culvert was constructed in 1981 and the first cleanup was needed in 2000. Phase II of the TR 545 entailed the monitoring of the site with and without the selfcleaning sedimentation structure in place (similarly with the study conducted in laboratory). The first monitoring stage (Sept 2010 to December 2012) was aimed at providing a baseline for the operation of the as-designed culvert. In order to support Phase II research, a cleanup of the IA Hwy 1W culvert was conducted in September 2011. Subsequently, a monitoring program was initiated to document the sedimentation produced by individual and multiple storms propagating through the culvert. The first two years of monitoring showed inception of the sedimentation in the first spring following the cleanup. Sedimentation continued to increase throughout the monitoring program following the depositional patterns observed in the laboratory tests and those documented in the pre-cleaning surveys. The second part of Phase II of the study was aimed at monitoring the constructed self-cleaning structure. Since its construction in December 2012, the culvert site was continuously monitored through systematic observations. The evidence garnered in this phase of the study demonstrates the good performance of the self-cleaning structure in mitigating the sediment deposition at culverts. Besides their beneficial role in sediment mitigation, the designed self-cleaning structures maintain a clean and clear area upstream the culvert, keep a healthy flow through the central barrel offering hydraulic and aquatic habitat similar with that in the undisturbed stream reaches upstream and downstream the culvert. It can be concluded that the proposed self-cleaning structural solution “streamlines” the area upstream the culvert in a way that secures the safety of the culvert structure at high flows while producing much less disturbance in the stream behavior compared with the current constructive approaches.

The TREAT-NMD Duchenne Muscular Dystrophy Registries: Conception, Design, and Utilization by Industry and Academia.

Duchenne muscular dystrophy (DMD) is an X-linked genetic disease, caused by the absence of the dystrophin protein. Although many novel therapies are under development for DMD, there is currently no cure and affected individuals are often confined to a wheelchair by their teens and die in their twenties/thirties. DMD is a rare disease (prevalence <5/10,000). Even the largest countries do not have enough affected patients to rigorously assess novel therapies, unravel genetic complexities, and determine patient outcomes. TREAT-NMD is a worldwide network for neuromuscular diseases that provides an infrastructure to support the delivery of promising new therapies for patients. The harmonized implementation of national and ultimately global patient registries has been central to the success of TREAT-NMD. For the DMD registries within TREAT-NMD, individual countries have chosen to collect patient information in the form of standardized patient registries to increase the overall patient population on which clinical outcomes and new technologies can be assessed. The registries comprise more than 13,500 patients from 31 different countries. Here, we describe how the TREAT-NMD national patient registries for DMD were established. We look at their continued growth and assess how successful they have been at fostering collaboration between academia, patient organizations, and industry.

Computer-Aided Business Model Design

There is a lack of dedicated tools for business model design at a strategic level. However, in today's economic world the need to be able to quickly reinvent a company's business model is essential to stay competitive. This research focused on identifying the functionalities that are necessary in a computer-aided design (CAD) tool for the design of business models in a strategic context. Using design science research methodology a series of techniques and prototypes have been designed and evaluated to offer solutions to the problem. The work is a collection of articles which can be grouped into three parts: First establishing the context of how the Business Model Canvas (BMC) is used to design business models and explore the way in which CAD can contribute to the design activity. The second part extends on this by proposing new technics and tools which support elicitation, evaluation (assessment) and evolution of business models design with CAD. This includes features such as multi-color tagging to easily connect elements, rules to validate coherence of business models and features that are adapted to the correct business model proficiency level of its users. A new way to describe and visualize multiple versions of a business model and thereby help in addressing the business model as a dynamic object was also researched. The third part explores extensions to the business model canvas such as an intermediary model which helps IT alignment by connecting business model and enterprise architecture. And a business model pattern for privacy in a mobile environment, using privacy as a key value proposition. The prototyped techniques and proposition for using CAD tools in business model modeling will allow commercial CAD developers to create tools that are better suited to the needs of practitioners.

Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases

AbstractBACKGROUND: Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult.PRINCIPAL FINDINGS: We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell.CONCLUSIONS: For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases.AVAILABILITY: The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download

On the tractability of the piecewise-linear approximation for general discrete-choice network revenue management

The choice network revenue management (RM) model incorporates customer purchase behavioras customers purchasing products with certain probabilities that are a function of the offeredassortment of products, and is the appropriate model for airline and hotel network revenuemanagement, dynamic sales of bundles, and dynamic assortment optimization. The underlyingstochastic dynamic program is intractable and even its certainty-equivalence approximation, inthe form of a linear program called Choice Deterministic Linear Program (CDLP) is difficultto solve in most cases. The separation problem for CDLP is NP-complete for MNL with justtwo segments when their consideration sets overlap; the affine approximation of the dynamicprogram is NP-complete for even a single-segment MNL. This is in contrast to the independentclass(perfect-segmentation) case where even the piecewise-linear approximation has been shownto be tractable. In this paper we investigate the piecewise-linear approximation for network RMunder a general discrete-choice model of demand. We show that the gap between the CDLP andthe piecewise-linear bounds is within a factor of at most 2. We then show that the piecewiselinearapproximation is polynomially-time solvable for a fixed consideration set size, bringing itinto the realm of tractability for small consideration sets; small consideration sets are a reasonablemodeling tradeoff in many practical applications. Our solution relies on showing that forany discrete-choice model the separation problem for the linear program of the piecewise-linearapproximation can be solved exactly by a Lagrangian relaxation. We give modeling extensionsand show by numerical experiments the improvements from using piecewise-linear approximationfunctions.

Learning about Bayesian networks for forensic interpretation : An example based on the "the problem of multiple propositions"

Both, Bayesian networks and probabilistic evaluation are gaining more and more widespread use within many professional branches, including forensic science. Notwithstanding, they constitute subtle topics with definitional details that require careful study. While many sophisticated developments of probabilistic approaches to evaluation of forensic findings may readily be found in published literature, there remains a gap with respect to writings that focus on foundational aspects and on how these may be acquired by interested scientists new to these topics. This paper takes this as a starting point to report on the learning about Bayesian networks for likelihood ratio based, probabilistic inference procedures in a class of master students in forensic science. The presentation uses an example that relies on a casework scenario drawn from published literature, involving a questioned signature. A complicating aspect of that case study - proposed to students in a teaching scenario - is due to the need of considering multiple competing propositions, which is an outset that may not readily be approached within a likelihood ratio based framework without drawing attention to some additional technical details. Using generic Bayesian networks fragments from existing literature on the topic, course participants were able to track the probabilistic underpinnings of the proposed scenario correctly both in terms of likelihood ratios and of posterior probabilities. In addition, further study of the example by students allowed them to derive an alternative Bayesian network structure with a computational output that is equivalent to existing probabilistic solutions. This practical experience underlines the potential of Bayesian networks to support and clarify foundational principles of probabilistic procedures for forensic evaluation.

Remote collaborative multi-user informal learning experiences: design and evaluation

This paper presents a customizable system used to develop a collaborative multi-user problem solving game. It addresses the increasing demand for appealing informal learning experiences in museum-like settings. The system facilitates remote collaboration by allowing groups of learners tocommunicate through a videoconferencing system and by allowing them to simultaneously interact through a shared multi-touch interactive surface. A user study with 20 user groups indicates that the game facilitates collaboration between local and remote groups of learners. The videoconference and multitouch surface acted as communication channels, attracted students’ interest, facilitated engagement, and promoted inter- and intra-group collaboration—favoring intra-group collaboration. Our findings suggest that augmentingvideoconferencing systems with a shared multitouch space offers newpossibilities and scenarios for remote collaborative environments and collaborative learning.

Design Methodology for Corrugated Metal Pipe Tiedowns, HR-362, Phase II, 1995

This investigation is the final phase of a three part study whose overall objectives were to determine if a restraining force is required to prevent inlet uplift failures in corrugated metal pipe (CMP) installations, and to develop a procedure for calculating the required force when restraint is required. In the initial phase of the study (HR-306), the extent of the uplift problem in Iowa was determined and the forces acting on a CMP were quantified. In the second phase of the study (HR- 332), laboratory and field tests were conducted. Laboratory tests measured the longitudinal stiffness ofCMP and a full scale field test on a 3.05 m (10 ft) diameter CMP with 0.612 m (2 ft) of cover determined the soil-structure interaction in response to uplift forces. Reported herein are the tasks that were completed in the final phase of the study. In this phase, a buried 2.44 m (8 ft) CMP was tested with and without end-restraint and with various configurations of soil at the inlet end of the pipe. A total of four different soil configurations were tested; in all tests the soil cover was constant at 0.61 m (2 ft). Data from these tests were used to verify the finite element analysis model (FEA) that was developed in this phase of the research. Both experiments and analyses indicate that the primary soil contribution to uplift resistance occurs in the foreslope and that depth of soil cover does not affect the required tiedown force. Using the FEA, design charts were developed with which engineers can determine for a given situation if restraint force is required to prevent an uplift failure. If an engineer determines restraint is needed, the design charts provide the magnitude of the required force. The design charts are applicable to six gages of CMP for four flow conditions and two types of soil.

Identification of Practices, Design, Construction, and Repair Using Trenchless Technology, TR-570, 2010

Trenchless technologies are methods used for the construction and rehabilitation of underground utility pipes. These methods are growing increasingly popular due to their versatility and their potential to lower project costs. However, the use of trenchless technologies in Iowa and their effects on surrounding soil and nearby structures has not been adequately documented. Surveys of and interviews with professionals working in trenchless-related industries in Iowa were conducted, and the results were analyzed and compared to survey results from the United States as a whole. The surveys focused on method familiarity, pavement distress observed, reliability of trenchless methods, and future improvements. Results indicate that the frequency of pavement distress or other trenchless-related issues are an ongoing problem in the industry. Inadequate soil information and quality control/quality assurance (QC/QA) are partially to blame. Fieldwork involving the observation of trenchless construction projects was undertaken with the purpose of documenting current practices and applications of trenchless technology in the United States and Iowa. Field tests were performed in which push-in pressure cells were used to measure the soil stresses induced by trenchless construction methods. A program of laboratory soil testing was carried out in conjunction with the field testing. Soil testing showed that the installations were made in sandy clay or well-graded sand with silt and gravel. Pipes were installed primarily using horizontal directional drilling with pipe diameters from 3 to 12 inches. Pressure cell monitoring was conducted during the following construction phases: pilot bore, pre-reaming, and combined pipe pulling and reaming. The greatest increase in lateral earth pressure was 5.6 psi and was detected 2.1 feet from the centerline of the bore during a pilot hole operation in sandy lean clay. Measurements from 1.0 to 2.5 psi were common. Comparisons were made between field measurements and analytical and finite element calculation methods.