Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

Background: The trithorax group (trxG) and Polycomb group (PcG) proteins are responsible for the maintenance of stable transcriptional patterns of many developmental regulators. They bind to specific regions of DNA and direct the post-translational modifications of histones, playing a role in the dynamics of chromatin structure.Results: We have performed genome-wide expression studies of trx and ash2 mutants in Drosophila melanogaster. Using computational analysis of our microarray data, we have identified 25 clusters of genes potentially regulated by TRX. Most of these clusters consist of genes that encode structural proteins involved in cuticle formation. This organization appears to be a distinctive feature of the regulatory networks of TRX and other chromatin regulators, since we have observed the same arrangement in clusters after experiments performed with ASH2, as well as in experiments performed by others with NURF, dMyc, and ASH1. We have also found many of these clusters to be significantly conserved in D. simulans, D. yakuba, D. pseudoobscura and partially in Anopheles gambiae.Conclusion: The analysis of genes governed by chromatin regulators has led to the identification of clusters of functionally related genes conserved in other insect species, suggesting this chromosomal organization is biologically important. Moreover, our results indicate that TRX and other chromatin regulators may act globally on chromatin domains that contain transcriptionally co-regulated genes.

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.

Data-driven clustering : new methods and applications

Abstract : This work is concerned with the development and application of novel unsupervised learning methods, having in mind two target applications: the analysis of forensic case data and the classification of remote sensing images. First, a method based on a symbolic optimization of the inter-sample distance measure is proposed to improve the flexibility of spectral clustering algorithms, and applied to the problem of forensic case data. This distance is optimized using a loss function related to the preservation of neighborhood structure between the input space and the space of principal components, and solutions are found using genetic programming. Results are compared to a variety of state-of--the-art clustering algorithms. Subsequently, a new large-scale clustering method based on a joint optimization of feature extraction and classification is proposed and applied to various databases, including two hyperspectral remote sensing images. The algorithm makes uses of a functional model (e.g., a neural network) for clustering which is trained by stochastic gradient descent. Results indicate that such a technique can easily scale to huge databases, can avoid the so-called out-of-sample problem, and can compete with or even outperform existing clustering algorithms on both artificial data and real remote sensing images. This is verified on small databases as well as very large problems. Résumé : Ce travail de recherche porte sur le développement et l'application de méthodes d'apprentissage dites non supervisées. Les applications visées par ces méthodes sont l'analyse de données forensiques et la classification d'images hyperspectrales en télédétection. Dans un premier temps, une méthodologie de classification non supervisée fondée sur l'optimisation symbolique d'une mesure de distance inter-échantillons est proposée. Cette mesure est obtenue en optimisant une fonction de coût reliée à la préservation de la structure de voisinage d'un point entre l'espace des variables initiales et l'espace des composantes principales. Cette méthode est appliquée à l'analyse de données forensiques et comparée à un éventail de méthodes déjà existantes. En second lieu, une méthode fondée sur une optimisation conjointe des tâches de sélection de variables et de classification est implémentée dans un réseau de neurones et appliquée à diverses bases de données, dont deux images hyperspectrales. Le réseau de neurones est entraîné à l'aide d'un algorithme de gradient stochastique, ce qui rend cette technique applicable à des images de très haute résolution. Les résultats de l'application de cette dernière montrent que l'utilisation d'une telle technique permet de classifier de très grandes bases de données sans difficulté et donne des résultats avantageusement comparables aux méthodes existantes.

Iowa Traffic Control Devices and Pavement Markings: A Manual for Cities and Counties April 2001

Iowa Traffic Control Devices and Pavement Markings: A Manual for Cities and Counties has been developed to provide state and local transportation agencies with suggestions and examples related to traffic control devices and pavement markings. Both rural and urban applications are included. The primary source of information for this document is the Manual on Uniform Traffic Control Devices (MUTCD), but many additional references have also been used. A complete listing of these is included in the appendix to this manual, and the reader is invited to consult these references for more in-depth information. The contents of this manual are not intended to represent standard practice or to imply legal requirements for installation in any particular manner. This document should be used as a supplement to the MUTCD, not as a substitute for any requirements contained therein. Engineering judgement should be applied to all decisions regarding traffic control devices and pavement markings. All references to the MUTCD in this manual apply to the millennium edition. The reader should be aware that many millennium revisions are allowed phase-in periods by the Federal Highway Administration (FHWA), ranging from two to ten years. These extended compliance periods should be considered when making decisions regarding traffic control devices and pavement markings. A new addition to the MUTCD, Part 5, “Traffic Control Devices for Low-Volume Roads,” also contains valuable recommendations for signing and marking low volume roads. This manual is presented in an easy to use threering format. Topics included in the complete guide manual may not apply to all jurisdictions and can easily be removed or modified as desired. Desired millennium MUTCD sections may be added for quick reference using the divider at the end of this document. Contents may also be available on CD-ROM in the future.

Utilization of Remote Traffic Monitoring Devices for Urban Freeway Work Zone Assessment Final Report, January 2012

The objective of this project was to promote and facilitate analysis and evaluation of the impacts of road construction activities in Smart Work Zone Deployment Initiative (SWZDI) states. The two primary objectives of this project were to assess urban freeway work-zone impacts through use of remote monitoring devices, such as radar-based traffic sensors, traffic cameras, and traffic signal loop detectors, and evaluate the effectiveness of using these devices for such a purpose. Two high-volume suburban freeway work zones, located on Interstate 35/80 (I-35/I-80) through the Des Moines, Iowa metropolitan area, were evaluated at the request of the Iowa Department of Transportation (DOT).

Development of a Traffic Control Devices and Pavement Markings Manual for Iowa's Cities and Counties with a Survery of Common Practices, April 2001

Transportation agencies in Iowa are responsible for a significant public investment with the installation and maintenance of traffic control devices and pavement markings. Included in this investment are thousands of signs and other inventory items, equipment, facilities, and staff. The proper application of traffic control devices and pavement markings is critical to public safety on streets and highways, and local governments have a prescribed responsibility under the Code of Iowa to properly manage these assets. This research report addresses current traffic control and pavement marking application, maintenance, and management in Iowa.

Revision to the SUDAS Traffic Signal Standards – Phase 2, Final Report, May 2012

This report provides a summary of the updates to the traffic signal content within the Iowa Statewide Urban Design and Specifications (SUDAS) Design Manual Chapter 13 and Standard Specifications Division 8. Major focal points included pole footing design, cabinets and controllers, monitoring systems, communications systems, and figure updates. This work was completed through a project task force with a variety of participants (contractors, Iowa Department of Transportation, city traffic engineers, consultant, vendors, and University research and support staff).

Concrete Overlay Field Application Program Iowa Task Report US 18 Concrete Overlay Construction Under Traffic, May 2012

The National Concrete Pavement Technology Center, Iowa Department of Transportation, and Federal Highway Administration set out to demonstrate and document the design and construction of portland cement concrete (PCC) overlays on two-lane roadways while maintaining two-way traffic. An 18.82 mile project was selected for 2011 construction in northeast Iowa on US 18 between Fredericksburg and West Union. This report documents planning, design, and construction of the project and lessons learned. The work included the addition of subdrains, full-depth patching, bridge approach replacement, and drainage structural repair and cleaning prior to overlay construction. The paving involved surface preparation by milling to grade and the placement of a 4.5 inch PCC overlay and 4 foot of widening to the existing pavement. In addition, the report makes recommendations on ways to improve the process for future concrete overlays.

Iowa Railroad Traffic Density, July 1, 2011

Iowa railroad traffic density.

Traffic map, Iowa,1984.

Traffic volumes represented on this map are average volumes between major traffic generators: highway junctions, cities, recreational areas or high volume secondary roads.

Evaluation of Low Cost Traffic Calming for Rural Communities – Phase II, April 2013

The main goal of the research described in this report was to evaluate countermeasures that agencies can use to reduce speeds as drivers enter rural communities located on high-speed roadways. The objectives of this study were as follows: * Identify and summarize countermeasures used to manage speeds in transition zones * Demonstrate the effectiveness of countermeasures that are practical for high- to low-speed transition zones * Acquire additional information about countermeasures that may show promise but lack sufficient evidence of effectiveness * Develop an application toolbox to assist small communities in selecting appropriate transition zones and effective countermeasures for entrances to small rural communities The team solicited small communities that were interested in participating in the Phase II study and several communities were also recommended. The treatments evaluated were selected by carefully considering traffic-calming treatments that have been used effectively in other countries for small rural communities, as well as the information gained from the first phase of the project. The treatments evaluated are as follows: * Transverse speed bars * Colored entrance treatment * Temporary island * Radar-activated speed limit sign * Speed feedback sign The toolbox publication and four focused tech briefs also cover the results of this work.

Annual Average Daily Traffic on the Interstate System, 2012

Vehicle Traffic Map produced by the Iowa Department of Transportation.

Vehicle Traffic Map, 2012

Vehicle Traffic Map produced by the Iowa Department of Transportation.