Measuring Party Positions and Issue Salience from Media Coverage: Introducing and Cross-Validating New Indicators

Recent studies have started to use media data to measure party positions and issue salience. The aim of this article is to compare and cross-validate this alternative approach with the more commonly used party manifestos, expert judgments and mass surveys. To this purpose, we present two methods to generate indicators of party positions and issue salience from media coverage: the core sentence approach and political claims analysis. Our cross-validation shows that with regard to party positions, indicators derived from the media converge with traditionally used measurements from party manifestos, mass surveys and expert judgments, but that salience indicators measure different underlying constructs. We conclude with a discussion of specific research questions for which media data offer potential advantages over more established methods.

Architectural features of bacterial genomes and their applications

Résumé -Caractéristiques architecturales des génomes bactériens et leurs applications Les bactéries possèdent généralement un seul chromosome circulaire. A chaque génération, ce chromosome est répliqué bidirectionnellement, par deux complexes enzymatiques de réplication se déplaçant en sens opposé depuis l'origine de réplication jusqu'au terminus, situé à l'opposé. Ce mode de réplication régit l'architecture du chromosome -l'orientation des gènes par rapport à la réplication, notamment - et est en grande partie à l'origine des pressions qui provoquent la variation de la composition en nucléotides du génome, hors des contraintes liées à la structure et à la fonction des protéines codées sur le chromosome. Le but de cette thèse est de contribuer à quantifier les effets de la réplication sur l'architecture chromosomique, en s'intéressant notamment aux gènes des ARN ribosomiques, cruciaux pour la bactérie. D'un autre côté, cette architecture est spécifique à l'espèce et donne ainsi une «identité génomique » aux gènes. Il est démontré ici qu'il est possible d'utiliser des marqueurs «naïfs » de cette identité pour détecter, notamment dans le génome du staphylocoque doré, des îlots de pathogénicité, qui concentrent un grand nombre de facteurs de virulence de la bactérie. Ces îlots de pathogénicité sont mobiles, et peuvent passer d'une bactérie à une autre, mais conservent durant un certain temps l'identité génomique de leur hôte précédent, ce qui permet de les reconnaître dans leur nouvel hôte. Ces méthodes simples, rapides et fiables seront de la plus haute importance lorsque le séquençage des génomes entiers sera rapide et disponible à très faible coût. Il sera alors possible d'analyser instantanément les déterminants pathogéniques et de résistance aux antibiotiques des agents pathogènes. Summary The bacterial genome is a highly organized structure, which may be referred to as the genome architecture, and is mainly directed by DNA replication. This thesis provides significant insights in the comprehension of the forces that shape bacterial chromosomes, different in each genome and contributing to confer them an identity. First, it shows the importance of the replication in directing the orientation of prokaryotic ribosomal RNAs, and how it shapes their nucleotide composition in a tax on-specific manner. Second, it highlights the pressure acting on the orientation of the genes in general, a majority of which are transcribed in the same direction as replication. Consequently, apparent infra-arm genome rearrangements, involving an exchange of the leading/lagging strands and shown to reduce growth rate, are very likely artifacts due to an incorrect contig assembly. Third, it shows that this genomic identity can be used to detect foreign parts in genomes, by establishing this identity for a given host and identifying the regions that deviate from it. This property is notably illustrated with Staphylococcus aureus: known pathogenicity islands and phages, and putative ancient pathogenicity islands concentrating many known pathogenicity-related genes are highlighted; the analysis also detects, incidentally, proteins responsible for the adhesion of S. aureus to the hosts' cells. In conclusion, the study of nucleotide composition of bacterial genomes provides the opportunity to better understand the genome-level pressures that shape DNA sequences, and to identify genes and regions potentially related to pathogenicity with fast, simple and reliable methods. This will be of crucial importance when whole-genome sequencing will be a rapid, inexpensive and routine tool.

Feasibility of Visualization and Simulation Applications to Improve Work Zone Safety and Mobility

Visualization is a relatively recent tool available to engineers for enhancing transportation project design through improved communication, decision making, and stakeholder feedback. Current visualization techniques include image composites, video composites, 2D drawings, drive-through or fly-through animations, 3D rendering models, virtual reality, and 4D CAD. These methods are used mainly to communicate within the design and construction team and between the team and external stakeholders. Use of visualization improves understanding of design intent and project concepts and facilitates effective decision making. However, visualization tools are typically used for presentation only in large-scale urban projects. Visualization is not widely accepted due to a lack of demonstrated engineering benefits for typical agency projects, such as small- and medium-sized projects, rural projects, and projects where external stakeholder communication is not a major issue. Furthermore, there is a perceived high cost of investment of both financial and human capital in adopting visualization tools. The most advanced visualization technique of virtual reality has only been used in academic research settings, and 4D CAD has been used on a very limited basis for highly complicated specialty projects. However, there are a number of less intensive visualization methods available which may provide some benefit to many agency projects. In this paper, we present the results of a feasibility study examining the use of visualization and simulation applications for improving highway planning, design, construction, and safety and mobility.

Feasibility of Visualization and Simulation Applications, Tech Transfer Summary, 2008

Visualization is a relatively recent tool available to engineers for enhancing transportation project design through improved communication, decision making, and stakeholder feedback. Current visualization techniques include image composites, video composites, 2D drawings, drive-through or fly-through animations, 3D rendering models, virtual reality, and 4D CAD. These methods are used mainly to communicate within the design and construction team and between the team and external stakeholders. Use of visualization improves understanding of design intent and project concepts and facilitates effective decision making. However, visualization tools are typically used for presentation only in large-scale urban projects. Visualization is not widely accepted due to a lack of demonstrated engineering benefits for typical agency projects, such as small- and medium-sized projects, rural projects, and projects where external stakeholder communication is not a major issue. Furthermore, there is a perceived high cost of investment of both financial and human capital in adopting visualization tools. The most advanced visualization technique of virtual reality has only been used in academic research settings, and 4D CAD has been used on a very limited basis for highly complicated specialty projects. However, there are a number of less intensive visualization methods available which may provide some benefit to many agency projects. In this paper, we present the results of a feasibility study examining the use of visualization and simulation applications for improving highway planning, design, construction, and safety and mobility.

Evolutionary footprint of coevolving positions in genes.

MOTIVATION: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson-Crick constraint, are usually considered a priori in current measures of coevolution. RESULTS: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 × 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of 'independent' evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution.

Sooty blotch and flyspeck control with fungicide applications based on calendar, local IPM, and warning system

The objective of this work was to compare fungicide application timing for the control of sooty blotch and flyspeck (SBFS) of 'Fuji' apples in Rio Grande do Sul state, Brazil. The following treatments were evaluated in two growing seasons: two warning system-based (modified version of the Brown-Sutton-Hartmann system) spray of captan plus thiophanate methyl, with or without summer pruning; two calendar/rain-based spray of captan or a mixture of captan plus thiophanate methyl; fungicide spray timing based on a local integrated pest management (IPM) for the control of summer diseases; and a check without spraying. Sooty blotch and flyspeck incidence over time and their severity at harvest were evaluated. The highest number of spray was required by calendar/rain-based treatments (eight and seven sprays in the sequential years). The warning system recommended five and three sprays, in the sequential years, which led to the highest SBFS control efficacy expressed by the reduced initial inoculum and disease progress rate. Summer pruning enhanced SBFS control efficacy, especially by suppressing SBFS signs which tended to be restrained to the peduncle region of the fruit. Sooty blotch and flyspeck can be managed both with calendar and the grower-based IPM practices in Brazil, but a reduced number of sprays is required when the warning system is used.

Intraocular implants for extended drug delivery: therapeutic applications.

An overview of ocular implants with therapeutic application potentials is provided. Various types of implants can be used as slow release devices delivering locally the needed drug for an extended period of time. Thus, multiple periocular or intraocular injections of the drug can be circumvented and secondary complications minimized. The various compositions of polymers fulfilling specific delivery goals are described. Several of these implants are undergoing clinical trials while a few are already commercialized. Despite the paramount progress in design, safety and efficacy, the place of these implants in our clinical therapeutic arsenal remains limited. Miniaturization of the implants allowing for their direct injection without the need for a complicated surgery is a necessary development avenue. Particulate systems which can be engineered to target specifically certain cells or tissues are another promising alternative. For ocular diseases affecting the choroid and outer retina, transscleral or intrasscleral implants are gaining momentum.

The CD4-like molecule LAG-3, biology and therapeutic applications.

IMPORTANCE OF THE FIELD: Promising immunotherapeutic agents targeting co-stimulatory pathways are currently being tested in clinical trials. One player in this array of regulatory pathways is the LAG-3/MHC class II axis. The lymphocyte activation gene-3 (LAG-3) is a negative co-stimulatory receptor that modulates T cell homeostasis, proliferation and activation. A recombinant soluble dimeric form of LAG-3 (sLAG-3-Ig, IMP321) shows adjuvant properties and enhances immunogenicity of tumor vaccines. Recent clinical trials produced encouraging results, especially when the human dimeric soluble form of LAG-3 (hLAG-3-Ig) was used in combination with chemotherapy. AREAS COVERED IN THIS REVIEW: The biological relevance of LAG-3 in vivo. Pre-clinical data demonstrating adjuvant properties, as well as the improvement of tumor immunity by sLAG-3-Ig. Recent advances in the clinical development of the therapeutic reagent IMP321, hLAG-3-Ig, for cancer treatment. WHAT THE READER WILL GAIN: This review summarizes preclinical and clinical data on the biological functions of LAG-3. TAKE HOME MESSAGE: The LAG-3 inhibitory pathway is attracting attention, in the light of recent studies demonstrating its role in T cell unresponsiveness, and Treg function after chronic antigen stimulation. As a soluble recombinant dimer, the sLAG-3-Ig protein acts as an adjuvant for therapeutic induction of T cell responses, and may be beneficial to cancer patients when used in combination therapies.