CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes.

BACKGROUND: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries 1 to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. RESULTS: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. CONCLUSION: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.

Vascular dysfunction in children conceived by assisted reproductive technologies: underlying mechanisms and future implications.

Epidemiological studies in humans have demonstrated a relationship between pathological events during fetal development and increased cardiovascular risk later in life and have led to the so called "Fetal programming of cardiovascular disease hypothesis". The recent observation of generalised vascular dysfunction in young apparently healthy children conceived by assisted reproductive technologies (ART) provides a novel and potentially very important example of this hypothesis. This review summarises recent data in ART children demonstrating premature subclinical atherosclerosis in the systemic circulation and pulmonary vascular dysfunction predisposing to exaggerated hypoxia-induced pulmonary hypertension. These problems appear to be related to the ART procedure per se. Studies in ART mice demonstrating premature vascular aging and arterial hypertension further demonstrate the potential of ART to increase cardiovascular risk and have allowed to unravel epigenetic alterations of the eNOS gene as an underpinning mechanism. The roughly 25% shortening of the life span in ART mice challenged with a western style high-fat-diet demonstrates the potential importance of these alterations for the long-term outcome. Given the young age of the ART population, data on cardiovascular endpoints will not be available before 20 to 30 years from now. However, already now cohort studies of the ART population are needed to early detect cardiovascular alterations with the aim to prevent or at least optimally treat cardiovascular complications. Finally, a debate needs to be engaged on the future of ART and the consequences of its exponential growth for public health.

Steel Diaphragms in Prestressed Concrete Girder Bridges, September 2004

Over the years, bridge engineers have been concerned about the response of prestressed concrete (PC) girder bridges that had been hit by over-height vehicles or vehicle loads. When a bridge is struck by an over-height vehicle or vehicle load, usually the outside and in some instances one of the interior girders are damaged in a bridge. The effect of intermediate diaphragms in providing damage protection to the PC girders of a bridge is not clearly defined. This analytical study focused on the role of intermediate diaphragms in reducing the occurrence of damage in the girders of a PC-girder bridge that has been struck by an over-height vehicle or vehicle load. The study also investigated whether a steel, intermediate diaphragm would essentially provide the same degree of impact protection for PC girders as that provided by a reinforced-concrete diaphragm. This investigation includes the following: a literature search and a survey questionnaire to determine the state-of-the-art in the use and design of intermediate diaphragms in PC-girder bridges. Comparisons were made between the strain and displacement results that were experimentally measured for a large-scale, laboratory, model bridge during previously documented work and those results that were obtained from analyses of the finite-element models that were developed during this research for that bridge. These comparisons were conducted to calibrate the finite element models used in the analyses for this research on intermediate diaphragms. Finite-element models were developed for non-skewed and skewed PC-girder bridges. Each model was analyzed with either a reinforced concrete or two types of steel, intermediate diaphragms that were located at mid-span of an interior span for a PC-girder bridge. The bridge models were analyzed for lateral-impact loads that were applied to the bottom flange of the exterior girders at the diaphragms location and away from the diaphragms location. A comparison was conducted between the strains and displacements induced in the girders for each intermediate-diaphragm type. These results showed that intermediate diaphragms have an effect in reducing impact damage to the PC girders. When the lateral impact-load was applied at the diaphragm location, the reinforced-concrete diaphragms provided more protection for the girders than that provided by the two types of steel diaphragms. The three types of diaphragms provided essentially the same degree of protection to the impacted, PC girder when the lateral-impact load was applied away from the diaphragm location.

Prevalence of comedications and effect of potential drug-drug interactions in the Swiss HIV Cohort Study.

BACKGROUND: Potential drug-drug interactions (PDDIs) might expand with new combination antiretroviral therapies (ART) and polypharmacy related to increasing age and comorbidities. We investigated the prevalence of comedications and PDDIs within a large HIV cohort, and their effect on ART efficacy and tolerability. METHODS: All medications were prospectively recorded in 1,497 ART-treated patients and screened for PDDIs using a customized version of the Liverpool drug interactions database. RESULTS: Overall, 68% (1,013/1,497) of patients had a comedication and 40% (599/1,497) had > or = 1 PDDI. Among patients with comedication, 2% (21/1,013) had red-flag interactions (contraindicated) and 59% (597/1,013) had orange-flag interactions (potential dose adjustment and/or close monitoring required). The latter involved mainly central nervous system drugs (49%), cardiovascular drugs (34%) and methadone (19%). In the multivariate analysis, factors associated with having a comedication were advanced age, female gender, obesity and HCV infection. Independent risk factors for PDDIs were regimens combining protease inhibitors and non-nucleoside reverse transcriptase inhibitors (odds ratio [OR] 3.06, 95% confidence interval [CI] 1.44-6.48), > or = 2 comedications (OR 1.89, 95% CI 1.32-2.70), current illicit drug use (OR 2.00, 95% CI 1.29-3.10) and patients with HCV infection (OR 1.74, 95% CI 1.19-2.56). Viral response was similar in patients with and without PDDIs (84.5% versus 86.4%; P=0.386). During follow-up, ART was modified in 134 patients with comedication regardless of the presence of PDDIs (P=0.524). CONCLUSIONS: PDDIs increase with complex ART and comorbidities. No adverse effect was noted on ART efficacy or tolerability; however, most PDDIs affected comedication but were manageable through dose adjustment or monitoring.

Reconciliation of metabolites and biochemical reactions for metabolic networks.

Genome-scale metabolic network reconstructions are now routinely used in the study of metabolic pathways, their evolution and design. The development of such reconstructions involves the integration of information on reactions and metabolites from the scientific literature as well as public databases and existing genome-scale metabolic models. The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic network reconstructions. In this work, we discuss some of the major difficulties encountered in the mapping and reconciliation of metabolic resources and review three recent initiatives that aim to accelerate this process, namely BKM-react, MetRxn and MNXref (presented in this article). Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources. By reducing the time required for manual curation of metabolite and reaction discrepancies, these resources aim to accelerate the development and application of high-quality genome-scale metabolic network reconstructions and models.

Competition and cost overruns. Optimal misspecification of procurement contracts

Most cases of cost overruns in public procurement are related to important changes in the initial project design. This paper deals with the problem of design specification in public procurement and provides a rationale for design misspecification. We propose a model in which the sponsor decides how much to invest in design specification and awards competitively the project to a contractor. After the project has been awarded the sponsor engages in bilateral renegotiation with the contractor, in order to accommodate changes in the initial project s design that new information makes desirable. When procurement takes place in the presence of horizontally differentiated contractors, the design s specification level is seen to affect the resulting degree of competition. The paper highlights this interaction between market competition and design specification and shows that the sponsor s optimal strategy, when facing an imperfectly competitive market supply, is to underinvest in design specification so as to make significant cost overruns likely. Since no such misspecification occurs in a perfectly competitive market, cost overruns are seen to arise as a consequence of lack of competition in the procurement market.

Competition and cost overruns in procurement

Most cases of cost overruns in public procurement are related to important changes in theinitial project design. This paper deals with the problem of design speciffication in public procurement and provides a rationale for design misspeciffication. We propose a model in which the sponsor decides how much to invest in design speciffication and awards competitively the project to a contractor. After the project has been awarded the sponsor engages in bilateral renegotiation with the contractor, in order to accommodate changes in the initial project's design that new information makes desirable. When procurement takes place in the presence of horizontally differentiated contractors, the design's speciffication level is seen to affect the resulting degree of competition. The paper highlights this interaction between market competition and design speciffication and shows that the sponsor's optimal strategy, when facing an imperfectly competitive market supply, is to underinvest in design speciffication so as to make signifficant cost overrunslikely. Since no such misspeciffication occurs in a perfectly competitive market, cost overruns are seen to arise as a consequence of lack of competition in the procurement market.

Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection.

Human immunodeficiency virus type 1 (HIV-1) isolates from 20 chronically infected patients who participated in a structured treatment interruption (STI) trial were studied to determine whether viral fitness influences reestablishment of viremia. Viruses derived from individuals who spontaneously controlled viremia had significantly lower in vitro replication capacities than viruses derived from individuals that did not control viremia after interruption of antiretroviral therapy (ART), and replication capacities correlated with pre-ART and post-STI viral set points. Of note, no clinically relevant improvement of viral loads upon STI occurred. Virus isolates from controlling and noncontrolling patients were indistinguishable in terms of coreceptor usage, genetic subtype, and sensitivity to neutralizing antibodies. In contrast, viruses from controlling patients exhibited increased sensitivity to inhibition by chemokines. Sensitivity to inhibition by RANTES correlated strongly with slower replication kinetics of the virus isolates, suggesting a marked dependency of these virus isolates on high coreceptor densities on the target cells. In summary, our data indicate that viral fitness is a driving factor in determining the magnitude of viral rebound and viral set point in chronic HIV-1 infection, and thus fitness should be considered as a parameter influencing the outcome of therapeutic intervention in chronic infection.

Disseny d’un sistema d’entrenament per l’escalada

El projecte proposa un sistema d’entrenament per l’escalada, donant noves solucions adaptades a les noves tendències socials i de mercat. La millora en la comunicació usuari-producte i el seguiment del progrés en l’entrenament són les bases d’aquest projecte, entorn a les quals giren totes les solucions plantejades. Donat l’increment exponencial dels usuaris de sales d’entrenament i aficionats a l’escalada en els últims deu anys, on m’incloc, aquest projecte pretén donar una nova visió més real de l’entrenament, plantejant un producte versàtil i canviant, el qual s’adequa a les necessitats concretes de cada usuari, a l’hora que proposa diferents muntatges segons les possibilitats de l’espai d’instal·lació. L’interès personal per l’escalada i l’experiència durants els últims anys en sales d’entrenament m’han fet plantejar-me la funció de diferents elements dins d’aquests espais. L’ús de noves tecnologies i de sistemes de programació específics donen a l’usuari l’oportunitat d’endinsar-se en tota una experiència diferent d’entrenament, on pot dissenyar el seu propi pla, tenir un seguiment estadístic de la seva evolució i ser partícip d’una xarxa social de contactes, recomanacions, actualitzacions d’exercicis i plantejament de nous reptes. Naixent les sales d’entrenament a la dècada dels seixanta, avui dia són més de 40 les empreses dedicades a la producció i fabricació de material per elles. Només un 11% inverteixen en innovació i disseny i, tot i així, els resultats, en la majoria dels casos, no es desmarquen gaire d’allò que ja existeix. Amb aquest projecte es vol obrir un nou paradigma en el sector, donar la volta a allò existent i mostrar que fent un bon estudi de necessitats es poden plantejar solucions molt més reals, adaptables i personalitzables.

Systemic and pulmonary vascular dysfunction in children conceived by assisted reproductive technologies.

BACKGROUND: Assisted reproductive technology (ART) involves the manipulation of early embryos at a time when they may be particularly vulnerable to external disturbances. Environmental influences during the embryonic and fetal development influence the individual's susceptibility to cardiovascular disease, raising concerns about the potential consequences of ART on the long-term health of the offspring. METHODS AND RESULTS: We assessed systemic (flow-mediated dilation of the brachial artery, pulse-wave velocity, and carotid intima-media thickness) and pulmonary (pulmonary artery pressure at high altitude by Doppler echocardiography) vascular function in 65 healthy children born after ART and 57 control children. Flow-mediated dilation of the brachial artery was 25% smaller in ART than in control children (6.7±1.6% versus 8.6±1.7%; P<0.0001), whereas endothelium-independent vasodilation was similar in the 2 groups. Carotid-femoral pulse-wave velocity was significantly (P<0.001) faster and carotid intima-media thickness was significantly (P<0.0001) greater in children conceived by ART than in control children. The systolic pulmonary artery pressure at high altitude (3450 m) was 30% higher (P<0.001) in ART than in control children. Vascular function was normal in children conceived naturally during hormonal stimulation of ovulation and in siblings of ART children who were conceived naturally. CONCLUSIONS: Healthy children conceived by ART display generalized vascular dysfunction. This problem does not appear to be related to parental factors but to the ART procedure itself. CLINICAL TRIAL REGISTRATION: URL: www.clinicaltrials.gov. Unique identifier: NCT00837642.

A Computerized Method for the Hydrologic Design of Culverts, February 1974

Nationwide, about five cents of each highway construction dollar is spent on culverts. In Iowa, average annual construction costs on the interstate, primary, and federal-aid secondary systems are about $120,000,000. Assuming the national figure applies to Iowa, about $6,000,000 are spent on culvert construction annually. For each one percent reduction in overall culvert costs, annual construction costs would be reduced by $60,000. One area of potential cost reduction lies in the sizing of the culvert. Determining the flow area and hydraulic capacity is accomplished in the initial design of the culvert. The normal design sequence is accomplished in two parts. The hydrologic portion consists of the determination of a design discharge in cubic feet per second using one of several available methods. This discharge is then used directly in the hydraulic portion of the design to determine the proper type, size, and shape of culvert to be used, based on various site and design restrictions. More refined hydrologic analyses, including rainfall-runoff analysis, flood hydrograph development, and streamflow routing techniques, are not pursued in the existing design procedure used by most county and state highway engineers.

Financial crisis: theory and practice

In the last 50 years, we have had approximately 40 events with characteristics related to financial crisis. The most severe crisis was in 1929, when the financial markets plummet and the US gross domestic product decline in more than 30 percent. Recently some years ago, a new crisis developed in the United States, but instantly caused consequences and effects in the rest of the world.This new economic and financial crisis has increased the interest and motivation for the academic community, professors and researchers, to understand the causes and effects of the crisis, to learn from it. This is the one of the main reasons for the compilation of this book, which begins with a meeting of a group of IAFI researchers from the University of Barcelona, where researchers form Mexico and Spain, explain causes and consequences of the crisis of 2007.For that reason, we believed this set of chapters related to methodologies, applications and theories, would conveniently explained the characteristics and events of the past and future financial crisisThis book consists in 3 main sections, the first one called "State of the Art and current situation", the second named "Econometric applications to estimate crisis time periods" , and the third one "Solutions to diminish the effects of the crisis". The first section explains the current point of view of many research papers related to financial crisis, it has 2 chapters. In the first one, it describe and analyzes the models that historically have been used to explain financial crisis, furthermore, it proposes to used alternative methodologies such as Fuzzy Cognitive Maps. On the other hand , Chapter 2 , explains the characteristics and details of the 2007 crisis from the US perspective and its comparison to 1929 crisis, presenting some effects in Mexico and Latin America.The second section presents two econometric applications to estimate possible crisis periods. For this matter, Chapter 3, studies 3 Latin-American countries: Argentina, Brazil and Peru in the 1994 crisis and estimates the multifractal characteristics to identify financial and economic distress.Chapter 4 explains the crisis situations in Argentina (2001), Mexico (1994) and the recent one in the United States (2007) and its effects in other countries through a financial series methodology related to the stock market.The last section shows an alternative to prevent the effects of the crisis. The first chapter explains the financial stability effects through the financial system regulation and some globalization standards. Chapter 6, study the benefits of the Investor activism and a way to protect personal and national wealth to face the financial crisis risks.

Art i ciència: converses

A la infància, Enric Canadell químic teòric i Àlex Nogué artista visual comparteixen pupitre i jocs de carrer a Castellfollit de la Roca, un poble de la Garrotxa, Girona. Segueixen trajectes vitals ben diferents i desenvolupen una ampla experiència professional internacional en la ciència i l'art. Quaranta-cinc anys més tard es retroben novament sota el projecte "En comptes de la revolució, converses" promogut per Cafè Central i l'Associació per les Arts Contemporànies H.ACC per tal de cercar coincidències en les seves activitats professionals aparentment tan dispars i en la seva forma de viure-les.

Assessment of Weathering Steel Bridge Performance in Iowa and Development of Inspection and Maintenance Techniques, RB17-012, 2013

Weathering steel is commonly used as a cost-effective alternative for bridge superstructures, as the costs and environmental impacts associated with the maintenance/replacement of paint coatings are theoretically eliminated. The performance of weathering steel depends on the proper formation of a surface patina, which consists of a dense layer of corrosion product used to protect the steel from further atmospheric corrosion. The development of the weathering steel patina may be hindered by environmental factors such as humid environments, wetting/drying cycles, sheltering, exposure to de-icing chlorides, and design details that permit water to pond on steel surfaces. Weathering steel bridges constructed over or adjacent to other roadways could be subjected to sufficient salt spray that would impede the development of an adequate patina. Addressing areas of corrosion on a weathering steel bridge superstructure where a protective patina has not formed is often costly and negates the anticipated cost savings for this type of steel superstructure. Early detection of weathering steel corrosion is important to extending the service life of the bridge structure; however, written inspection procedures are not available for inspectors to evaluate the performance or quality of the patina. This project focused on the evaluation of weathering steel bridge structures, including possible methods to assess the quality of the weathering steel patina and to properly maintain the quality of the patina. The objectives of this project are summarized as follows:  Identify weathering steel bridge structures that would be most vulnerable to chloride contamination, based on location, exposure, environment, and other factors.  Identify locations on an individual weathering steel bridge structure that would be most susceptible to chloride contamination, such as below joints, splash/spray zones, and areas of ponding water or debris.  Identify possible testing methods and/or inspection techniques for inspectors to evaluate the quality of the weathering steel patina at locations discussed above.  Identify possible methods to measure and evaluate the level of chloride contamination at the locations discussed above.  Evaluate the effectiveness of water washing on removing chlorides from the weathering steel patina.  Develop a general prioritization for the washing of bridge structures based on the structure’s location, environment, inspection observations, patina evaluation findings, and chloride test results.

MEPDG Work Plan Task No. 7: Existing Pavement Input Information for the Mechanistic-Empirical Pavement Design Guide, 2009

The objective of this study is to systematically evaluate the Iowa Department of Transportation’s (DOT’s) existing Pavement Management Information System (PMIS) with respect to the input information required for Mechanistic-Empirical Pavement Design Guide (MEPDG) rehabilitation analysis and design. To accomplish this objective, all of available PMIS data for interstate and primary roads in Iowa were retrieved from the Iowa DOT PMIS. The retrieved data were evaluated with respect to the input requirements and outputs for the latest version of the MEPDG software (version 1.0). The input parameters that are required for MEPDG HMA rehabilitation design, but currently unavailable in the Iowa DOT PMIS were identified. The differences in the specific measurement metrics used and their units for some of the pavement performance measures between the Iowa DOT PMIS and MEPDG were identified and discussed. Based on the results of this study, it is recommended that the Iowa DOT PMIS should be updated, if possible, to include the identified parameters that are currently unavailable, but are required for MEPDG rehabilitation design. Similarly, the measurement units of distress survey results in the Iowa DOT PMIS should be revised to correspond to those of MEPDG performance predictions. *******************Large File**************************