Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.

Cancer genomes frequently contain somatic copy number alterations (SCNA) that can significantly perturb the expression level of affected genes and thus disrupt pathways controlling normal growth. In melanoma, many studies have focussed on the copy number and gene expression levels of the BRAF, PTEN and MITF genes, but little has been done to identify new genes using these parameters at the genome-wide scale. Using karyotyping, SNP and CGH arrays, and RNA-seq, we have identified SCNA affecting gene expression ('SCNA-genes') in seven human metastatic melanoma cell lines. We showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. Since few of these alterations were recurrent across our samples, we used a protein network-guided approach to determine whether any pathways were enriched in SCNA-genes in one or more samples. From this unbiased genome-wide analysis, we identified 28 significantly enriched pathway modules. Comparison with two large, independent melanoma SCNA datasets showed less than 10% overlap at the individual gene level, but network-guided analysis revealed 66% shared pathways, including all but three of the pathways identified in our data. Frequently altered pathways included WNT, cadherin signalling, angiogenesis and melanogenesis. Additionally, our results emphasize the potential of the EPHA3 and FRS2 gene products, involved in angiogenesis and migration, as possible therapeutic targets in melanoma. Our study demonstrates the utility of network-guided approaches, for both large and small datasets, to identify pathways recurrently perturbed in cancer.

2004 Annual Report of the Iowa Communications Network, 2004

This is the Annual Report for Fiscal Year 2004 (July 1, 2003-June 30, 2004) for the Iowa Communications Network.

Evaluation of the Iowa Department of Transportation's Compensatory Wetland Mitgation Program, August 30, 2004

The purpose of this investigation was to evaluate the Compensatory Wetland Mitigation Program at the Iowa Department of Transportation (DOT) in terms of regulatory compliance. Specific objectives included: 1) Determining if study sites meet the definition of a jurisdictional wetland. 2) Determining the degree of compliance with requirements specified in Clean Water Act Section 404 permits. A total of 24 study sites, in four age classes were randomly selected from over 80 sites currently managed by the Iowa DOT. Wetland boundaries were delineated in the field and mitigation compliance was determined by comparing the delineated wetland acreage at each study site to the total wetland acreage requirements specified in individual CWA Section 404 permits. Of the 24 sites evaluated in this study, 58 percent meet or exceed Section 404 permit requirements. Net gain ranged from 0.19 acre to 27.2 acres. Net loss ranged from 0.2 acre to 14.6 acres. The Denver Bypass 1 site was the worst performer, with zero acres of wetland present on the site and the Akron Wetland Mitigation Site was the best performer with slightly more than 27 acres over the permit requirement. Five of the 10 under-performing sites are more than five years post construction, two are five years post construction, one is three years post construction and the remaining two are one year post construction. Of the sites that meet or exceed permit requirements, approximately 93 percent are five years or less post construction and approximately 43 percent are only one year old. Only one of the 14 successful sites is more than five years old. Using Section 404 permit acreage requirements as the criteria for measuring success, 58 percent of the wetland mitigation sites investigated as part of this study are successful. Using net gain/loss as the measure of success, the Compensatory Wetland Mitigation Program has been successful in creating/restoring nearly 44 acres of wetland over what was required by permits.

A regulatory network for coordinated flower maturation.

For self-pollinating plants to reproduce, male and female organ development must be coordinated as flowers mature. The Arabidopsis transcription factors AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8 regulate this complex process by promoting petal expansion, stamen filament elongation, anther dehiscence, and gynoecium maturation, thereby ensuring that pollen released from the anthers is deposited on the stigma of a receptive gynoecium. ARF6 and ARF8 induce jasmonate production, which in turn triggers expression of MYB21 and MYB24, encoding R2R3 MYB transcription factors that promote petal and stamen growth. To understand the dynamics of this flower maturation regulatory network, we have characterized morphological, chemical, and global gene expression phenotypes of arf, myb, and jasmonate pathway mutant flowers. We found that MYB21 and MYB24 promoted not only petal and stamen development but also gynoecium growth. As well as regulating reproductive competence, both the ARF and MYB factors promoted nectary development or function and volatile sesquiterpene production, which may attract insect pollinators and/or repel pathogens. Mutants lacking jasmonate synthesis or response had decreased MYB21 expression and stamen and petal growth at the stage when flowers normally open, but had increased MYB21 expression in petals of older flowers, resulting in renewed and persistent petal expansion at later stages. Both auxin response and jasmonate synthesis promoted positive feedbacks that may ensure rapid petal and stamen growth as flowers open. MYB21 also fed back negatively on expression of jasmonate biosynthesis pathway genes to decrease flower jasmonate level, which correlated with termination of growth after flowers have opened. These dynamic feedbacks may promote timely, coordinated, and transient growth of flower organs.

Iowa Communications Network, Independent Auditor's Reports, Basic Financial Statements and Supplementary Information, Schedule of Findings, June 30, 2004

State Agency Audit Report

A WiMAX-based implementation of network MIMO for indoor wireless systems

It is well known that multiple-input multiple-output (MIMO) techniques can bring numerous benefits, such as higher spectral efficiency, to point-to-point wireless links. More recently, there has been interest in extending MIMO concepts tomultiuser wireless systems. Our focus in this paper is on network MIMO, a family of techniques whereby each end user in a wireless access network is served through several access points within its range of influence. By tightly coordinating the transmission and reception of signals at multiple access points, network MIMO can transcend the limits on spectral efficiency imposed by cochannel interference. Taking prior information-theoretic analyses of networkMIMO to the next level, we quantify the spectral efficiency gains obtainable under realistic propagation and operational conditions in a typical indoor deployment. Our study relies on detailed simulations and, for specificity, is conducted largely within the physical-layer framework of the IEEE 802.16e Mobile WiMAX system. Furthermore,to facilitate the coordination between access points, we assume that a high-capacity local area network, such as Gigabit Ethernet,connects all the access points. Our results confirm that network MIMO stands to provide a multiple-fold increase in spectralefficiency under these conditions.

Report of Recommendations to the Iowa Department of Transportation, June 30, 2004

State Audit Reports

Free-and open source software for a course on network management: authoring and enactment of scripts based on collaborative learning strategies

This paper describes a Computer-Supported Collaborative Learning (CSCL) case study in engineering education carried out within the context of a network management course. The case study shows that the use of two computing tools developed by the authors and based on Free- and Open-Source Software (FOSS) provide significant educational benefits over traditional engineering pedagogical approaches in terms of both concepts and engineering competencies acquisition. First, the Collage authoring tool guides and supports the course teacher in the process of authoring computer-interpretable representations (using the IMS Learning Design standard notation) of effective collaborative pedagogical designs. Besides, the Gridcole system supports the enactment of that design by guiding the students throughout the prescribed sequence of learning activities. The paper introduces the goals and context of the case study, elaborates onhow Collage and Gridcole were employed, describes the applied evaluation methodology, anddiscusses the most significant findings derived from the case study.

Development of the Iowa Drainage Law Manual, March 2005

Although Iowa has some of the most productive agricultural land in the nation, it also maintains a very extensive road network.Consequently, landowners and roadway officials often must deal with drainage issues affecting private lands and public highways. However, many individuals are unfamiliar with legal drainage requirements, practices, and procedures, which can result in misunderstandings concerning maintenance responsibilities for drainage facilities, sometimes leading to litigation. To assist propertyowners, public agencies, and others with interest in better understanding drainage maintenance responsibilities, a reference manual was developed to describe Iowa’s drainage laws and offer interpretations in a clear and concise manner. To develop a comprehensive drainage manual, researchers identified and reviewed current available literature. These resources described pertinent drainage issues and presented explanations of legal responsibilities. The literature review included manuals and guides from Iowa, surrounding states, and federal agencies. Researchers developed a survey to assess the needs and interestsof potential users of an Iowa drainage law manual. Survey responses were used to identify common problems and concerns among individuals who encounter drainage issues on a regular basis. Issues mentioned in the survey responses included interpretation of drainage laws and commonly encountered questions relating to public improvements and private interests. Many individuals, including county engineers, stated interest in specific topics such as maintenance and/or diversion of drainage, landowner issues, and upstream and downstream impacts. Overall, the survey provided researchers with valuable information regarding drainage issues, problems, current policies, and concerns. A comprehensive manual of Iowa drainage law will assist agencies and individuals in interpreting current code requirements and in implementing effective and beneficial solutions when dealing with drainage issues.

2006-2010 Iowa Transportation Improvement Program

This document provides the planned investments in Iowa's transportation system for the five-year period of 2006-2010. It encompasses aviation, railroads, rivers, trails, state parks and institutional roads, roadways, and public transit.

2005 Annual Report of the Iowa Communications Network

This is the Annual Report for Fiscal Year 2005 (July 1, 2004-June 30, 2005) for the Iowa Communications Network.

Iowa Department of Transportation Office of Contracts Letting Summary - July 1, 2004 through June 30, 2005

A summary of the regularly scheduled lettings and emergency/special lettings held by the Iowa Department of Transportation for construction and maintenance work during the period July 1, 2004, through June 30, 2005.