Identification of Novel Craniofacial Regulatory Domains Located far Upstream of SOX9 and Disrupted in Pierre Robin Sequence.

Mutations in the coding sequence of SOX9 cause campomelic dysplasia (CD), a disorder of skeletal development associated with 46,XY disorders of sex development (DSDs). Translocations, deletions, and duplications within a ∼2 Mb region upstream of SOX9 can recapitulate the CD-DSD phenotype fully or partially, suggesting the existence of an unusually large cis-regulatory control region. Pierre Robin sequence (PRS) is a craniofacial disorder that is frequently an endophenotype of CD and a locus for isolated PRS at ∼1.2-1.5 Mb upstream of SOX9 has been previously reported. The craniofacial regulatory potential within this locus, and within the greater genomic domain surrounding SOX9, remains poorly defined. We report two novel deletions upstream of SOX9 in families with PRS, allowing refinement of the regions harboring candidate craniofacial regulatory elements. In parallel, ChIP-Seq for p300 binding sites in mouse craniofacial tissue led to the identification of several novel craniofacial enhancers at the SOX9 locus, which were validated in transgenic reporter mice and zebrafish. Notably, some of the functionally validated elements fall within the PRS deletions. These studies suggest that multiple noncoding elements contribute to the craniofacial regulation of SOX9 expression, and that their disruption results in PRS.

Fructose and glucose co-ingestion during prolonged exercise increases lactate and glucose fluxes and oxidation compared with an equimolar intake of glucose

BACKGROUND: When fructose is ingested together with glucose (GLUFRU) during exercise, plasma lactate and exogenous carbohydrate oxidation rates are higher than with glucose alone. OBJECTIVE: The objective was to investigate to what extent GLUFRU increased lactate kinetics and oxidation rate and gluconeogenesis from lactate (GNG(L)) and from fructose (GNG(F)). DESIGN: Seven endurance-trained men performed 120 min of exercise at approximately 60% VOmax (maximal oxygen consumption) while ingesting 1.2 g glucose/min + 0.8 g of either glucose or fructose/min (GLUFRU). In 2 trials, the effects of glucose and GLUFRU on lactate and glucose kinetics were investigated with glucose and lactate tracers. In a third trial, labeled fructose was added to GLUFRU to assess fructose disposal. RESULTS: In GLUFRU, lactate appearance (120 +/- 6 mumol . kg(1) . min(1)), lactate disappearance (121 +/- 7 mumol . kg(1) . min(1)), and oxidation (127 +/- 12 mumol . kg(1) . min(1)) rates increased significantly (P < 0.001) in comparison with glucose alone (94 +/- 16, 95 +/- 16, and 97 +/- 16 mumol . kg(1) . min(1), respectively). GNG(L) was negligible in both conditions. In GLUFRU, GNG(F) and exogenous fructose oxidation increased with time and leveled off at 18.8 +/- 3.7 and 38 +/- 4 mumol . kg(1) . min(1), respectively, at 100 min. Plasma glucose appearance rate was significantly higher (P < 0.01) in GLUFRU (91 +/- 6 mumol . kg(1) . min(1)) than in glucose alone (82 +/- 9 mumol . kg(1) . min(1)). Carbohydrate oxidation rate was higher (P < 0.05) in GLUFRU. CONCLUSIONS: Fructose increased total carbohydrate oxidation, lactate production and oxidation, and GNG(F). Fructose oxidation was explained equally by fructose-derived lactate and glucose oxidation, most likely in skeletal and cardiac muscle. This trial was registered at clinicaltrials.gov as NCT01128647.

Road Use Tax Fund Efficiency Report, January 2012

In the November 2011 report issued by the Governor’s Transportation 2020 Citizen Advisory Commission (CAC), the commission recommended the Iowa Department of Transportation (DOT), at least annually, convene meetings with the cities and counties to review the operation, maintenance and improvement of Iowa’s public roadway system to identify ways to jointly increase efficiency. In response to this recommendation, Gov. Branstad directed the Iowa DOT to begin this effort immediately with a target of identifying $50 million of efficiency savings that can be captured from the $1.2 billion of Road Use Tax Funds (RUTF) provided to the Iowa DOT, cities and counties to administer, maintain and improve the public roadway system. This would build upon past joint and individual actions that have reduced administrative costs and resulted in increased funding for system improvements. Efficiency actions should be quantified, measured and reported to the public on a regular basis. Beyond the discussion of identifying funding solutions to our road and bridge needs, it is critical that all jurisdictions that own, maintain and improve the nation’s road and bridge systems demonstrate to the public these funds are utilized in the most efficient and effective manner. This requires continual innovation in all aspects of transportation planning, design, construction and maintenance - done in a transparent manner to clearly demonstrate to the public how their funds are being utilized. The Iowa DOT has identified 13 efficiency measures separated into two distinct categories – Program Efficiencies and Partnership Efficiencies. The total value of the efficiency measures is $50 million. Many of the efficiency items will need input, refinement and partnership from cities, counties, other local jurisdictions, and stakeholder interest groups. The Iowa DOT has begun meetings with many of these groups to help identify potential efficiency measures and strategies for moving forward. These partnerships and discussions will continue through implementation of the efficiency measures. Dependent on the measures identified, additional action may be required by the legislature, Iowa Transportation Commission, and/or other bodies to implement the action. In addition, a formal process will be developed to quantify, measure and report the results of actions taken on a regular basis.

Documents : Dating a document

The determination of the age of a document is a very frequent query, however it is also one of the most challenging and controversial areas of questioned document examination. Several approaches were defined to address this problem. The first is based on the introduction date of raw constituents (like paper or ink) on the market. The second approach is based on the aging of documents, which is unfortunately not only influenced by passing time, but also by storage conditions and document composition. The third approach considers the relative age of documents and aims at reconstructing their chronology. The three approaches are equally complex to develop and encounter quantity of problems which are not negligible. This article aims to expose the potential applications and limitations of current ink dating methods. Method development and validation and the interpretation of evidence prove to be essential criteria for the dating of documents.

Evolution of proteins after whole-genome duplication

Evolution of proteins after whole-genome duplicationGene and genome duplication are considered major mechanisms in the creation of newfunctions in genomes, or in the refinement of networks by the division of function amongmore genes. In animals, the best demonstrated whole genome duplication occurred at theorigin of Teleost fishes. This makes fishes an ideal model to study the consequences ofgenome duplication, particularly since we have a good sampling of genome sequences,abundant functional information, and a very well studied outgroup: the tetrapodes (includinghuman). More specifically, I studied the consequences of duplication on proteins usingevolutionary models to infer adaptive events. I analysed the influence of positive selection invertebrate genes, by contrasting singleton genes and duplicated genes. The conclusion of theanalyses was threefold: (i) positive selection affects diverse phylogenetic branches anddiverse gene categories during vertebrate evolution; (ii) it concerns only a small proportion ofsites (1%-5%); and (iii) whole genome duplication had no detectable impact on theprevalence of this positive selection.I also studied evolution at the amino acid level with different methods to detect functionalshifts (covarion process and constant-but-different process). As in my previous research, Ifound similar numbers of functional shifts between duplicates and between orthologs.The accepted framework for studies of molecular evolution is that orthologs share the samefunction, whereas the function of paralogs diverges. This framework gives a special place togene duplication in evolution, as the main mechanism for generating novelty. With myprevious results showing that duplication and speciation are not so different, we investigatedthe literature to question the evidence for similar or divergent evolution of gene function afterduplication relative to speciation genes. This led us to propose a more rigorous design offuture studies of gene duplication.Finally, based on my automated protocol, we built a database of positive selection invertebrates' genes, Selectome. This database is freely available on the web and will helpfuture evolutionary as well as biochemical studies.

CATMA: a complete Arabidopsis GST database.

The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as well as primer sequences for GST amplification and a wide range of supplementary information. All CATMA GST sequences are specific to the gene for which they were designed, and all gene models were predicted from a complete reannotation of the genome using uniform parameters. The database is searchable by sequence name, sequence homology or direct SQL query, and is available through the CATMA website at http://www.catma.org/.

Assessing the impact of DRGs on patient care and professional practice in Switzerland (IDoC) : a potential model for monitoring and evaluating healthcare reform.

QUESTIONS UNDER STUDY: The starting point of the interdisciplinary project "Assessing the impact of diagnosis related groups (DRGs) on patient care and professional practice" (IDoC) was the lack of a systematic ethical assessment for the introduction of cost containment measures in healthcare. Our aim was to contribute to the methodological and empirical basis of such an assessment. METHODS: Five sub-groups conducted separate but related research within the fields of biomedical ethics, law, nursing sciences and health services, applying a number of complementary methodological approaches. The individual research projects were framed within an overall ethical matrix. Workshops and bilateral meetings were held to identify and elaborate joint research themes. RESULTS: Four common, ethically relevant themes emerged in the results of the studies across sub-groups: (1.) the quality and safety of patient care, (2.) the state of professional practice of physicians and nurses, (3.) changes in incentives structure, (4.) vulnerable groups and access to healthcare services. Furthermore, much-needed data for future comparative research has been collected and some early insights into the potential impact of DRGs are outlined. CONCLUSIONS: Based on the joint results we developed preliminary recommendations related to conceptual analysis, methodological refinement, monitoring and implementation.

An adaptive multiscale method for density-driven instabilities

Accurate modeling of flow instabilities requires computational tools able to deal with several interacting scales, from the scale at which fingers are triggered up to the scale at which their effects need to be described. The Multiscale Finite Volume (MsFV) method offers a framework to couple fine-and coarse-scale features by solving a set of localized problems which are used both to define a coarse-scale problem and to reconstruct the fine-scale details of the flow. The MsFV method can be seen as an upscaling-downscaling technique, which is computationally more efficient than standard discretization schemes and more accurate than traditional upscaling techniques. We show that, although the method has proven accurate in modeling density-driven flow under stable conditions, the accuracy of the MsFV method deteriorates in case of unstable flow and an iterative scheme is required to control the localization error. To avoid large computational overhead due to the iterative scheme, we suggest several adaptive strategies both for flow and transport. In particular, the concentration gradient is used to identify a front region where instabilities are triggered and an accurate (iteratively improved) solution is required. Outside the front region the problem is upscaled and both flow and transport are solved only at the coarse scale. This adaptive strategy leads to very accurate solutions at roughly the same computational cost as the non-iterative MsFV method. In many circumstances, however, an accurate description of flow instabilities requires a refinement of the computational grid rather than a coarsening. For these problems, we propose a modified iterative MsFV, which can be used as downscaling method (DMsFV). Compared to other grid refinement techniques the DMsFV clearly separates the computational domain into refined and non-refined regions, which can be treated separately and matched later. This gives great flexibility to employ different physical descriptions in different regions, where different equations could be solved, offering an excellent framework to construct hybrid methods.

TrkB and TrkC signaling are required for maturation and synaptogenesis of hippocampal connections

Recent studies have suggested a role for neurotrophins in the growth and refinement of neural connections, in dendritic growth, and in activity-dependent adult plasticity. To unravel the role of endogenous neurotrophins in the development of neural connections in the CNS, we studied the ontogeny of hippocampal afferents intrkB (¿/¿) and trkC (¿/¿) mice. Injections of lipophilic tracers in the entorhinal cortex and hippocampus of newborn mutant mice showed that the ingrowth of entorhinal and commissural/associational afferents to the hippocampus was not affected by these mutations. Similarly, injections of biocytin in postnatal mutant mice (P10¿P16) did not reveal major differences in the topographic patterns of hippocampal connections. In contrast, quantification of biocytin-filled axons showed that commissural and entorhinal afferents have a reduced number of axon collaterals (21¿49%) and decreased densities of axonal varicosities (8¿17%) in both trkB (¿/¿) and trkC (¿/¿) mice. In addition, electron microscopic analyses showed thattrkB (¿/¿) and trkC (¿/¿) mice have lower densities of synaptic contacts and important structural alterations of presynaptic boutons, such as decreased density of synaptic vesicles. Finally, immunocytochemical studies revealed a reduced expression of the synaptic-associated proteins responsible for synaptic vesicle exocytosis and neurotransmitter release (v-SNAREs and t-SNAREs), especially in trkB (¿/¿) mice. We conclude that neither trkB nor trkC genes are essential for the ingrowth or layer-specific targeting of hippocampal connections, although the lack of these receptors results in reduced axonal arborization and synaptic density, which indicates a role for TrkB and TrkC receptors in the developmental regulation of synaptic inputs in the CNS in vivo. The data also suggest that the genes encoding for synaptic proteins may be targets of TrkB and TrkC signaling pathways.

Mynodbcsv: Lightweight Zero-Config Database Solution for Handling Very Large CSV Files.

Volumes of data used in science and industry are growing rapidly. When researchers face the challenge of analyzing them, their format is often the first obstacle. Lack of standardized ways of exploring different data layouts requires an effort each time to solve the problem from scratch. Possibility to access data in a rich, uniform manner, e.g. using Structured Query Language (SQL) would offer expressiveness and user-friendliness. Comma-separated values (CSV) are one of the most common data storage formats. Despite its simplicity, with growing file size handling it becomes non-trivial. Importing CSVs into existing databases is time-consuming and troublesome, or even impossible if its horizontal dimension reaches thousands of columns. Most databases are optimized for handling large number of rows rather than columns, therefore, performance for datasets with non-typical layouts is often unacceptable. Other challenges include schema creation, updates and repeated data imports. To address the above-mentioned problems, I present a system for accessing very large CSV-based datasets by means of SQL. It's characterized by: "no copy" approach - data stay mostly in the CSV files; "zero configuration" - no need to specify database schema; written in C++, with boost [1], SQLite [2] and Qt [3], doesn't require installation and has very small size; query rewriting, dynamic creation of indices for appropriate columns and static data retrieval directly from CSV files ensure efficient plan execution; effortless support for millions of columns; due to per-value typing, using mixed text/numbers data is easy; very simple network protocol provides efficient interface for MATLAB and reduces implementation time for other languages. The software is available as freeware along with educational videos on its website [4]. It doesn't need any prerequisites to run, as all of the libraries are included in the distribution package. I test it against existing database solutions using a battery of benchmarks and discuss the results.

Jevons et Walras : entre philosophie morale et économie sociale, un jalon dans la compréhension de la décision publique

This PhD dissertation deals with the question of evaluating social welfare and public policy making through the works of William Stanley Jevons (1835-1882) and Léon Walras (1834-1910), two economists who lived in the 19th century. These authors, well-known for their analyses on pure economics, were also deeply interested in the social problems of their time and proposed solutions to remedy them. In accordance with utilitarianism, Jevons was convinced that the reforms implemented by public authorities should improve social welfare (viewed as dependant on individual utilities). As for Walras, he defined a justice criterion based on a particular definition of natural law, and the reforms he proposed had the objective of restoring the rights following from this definition. We have drawn two principal conclusions from our work. First, the analyses of Jevons and Walras, who are often considered marginalise, are different not only in pure economics (as suggested by Jaffé in the seventies), but also from the point of view of welfare economics (defined as a science dealing with the evaluation of different social states). Secondly, these authors propose two different ways of justifying social reforms which have similarities with modern theory even though neither Jevons nor Walras are considered pioneers of welfare economics or public economics. Based on these two conclusions, we claim that studying these authors' theories might be of interest for the evaluation of public projects by the economists of today. Not only were their problems similar to ours, but also the original ideas present in their analyses may lead to the refinement of modern methods.Résumé en françaisCette these de doctorat porte sur les manières dont deux économistes du XIXe siècle, William Stanley Jevons (1835-1882) et Léon Walras (1834-1910), abordent la question du bien- etre collectif et la prise de décision publique. Connus principalement pour leurs travaux en économie pure, ces auteurs s'intéressent également à la question sociale et proposent des solutions pour y remédier. Jevons, conformément à son adhésion à la tradition utilitariste, estime que les interventions des autorités publiques doivent avoir pour objectif l'amélioration du bien- être collectif. Quant à Walras, il adopte un critère de justice qui relève du « droit naturel » et les propositions sociales qu'il préconise sont justifiées sur la base de leur conformité avec ce dernier. A l'issue du travail effectué dans le cadre de cette thèse, nous avons abouti à deux résultats principaux : (1) Les analyses de Jevons et Walras, deux économistes qui sont souvent considérés comme des « marginalistes » diffèrent fondamentalement non seulement dans leur analyse de l'économie pure, comme Jaffé le soulignait (1976), mais également en termes d'économie du bien-être (comprise comme une science ayant pour objectif l'évaluation des différents états sociaux). (2) Il existe deux voies originales pour justifier les réformes sociales dans les oeuvres de Jevons et Walras qui partagent des similarités importantes avec les théories modernes bien que ces auteurs ne fassent pas partie des jalons généralement retenus de l'histoire de l'économie du bien-être et de l'économie publique. Ces deux résultats nous conduisent à avancer que l'étude des approches de Jevons et de Walras peut contribuer à la formulation de nouvelles solutions à des problèmes rencontrés dans l'évaluation des différentes politiques publiques, car non seulement les préoccupations de ces auteurs était similaires aux nôtres, mais vu les éléments originaux que leurs propositions comportent, elles peuvent permettre de nuancer certaines aspects des méthodes modernes.

Vulnerabilities of Fingerprint Reader to Fake Fingerprint Attacks

The purpose of this research is to assess the vulnerabilities of a high resolution fingerprint sensor when confronted with fake fingerprints. The study has not been focused on the decision outcome of the biometric device, but essentially on the scores obtained following the comparison between a query (genuine or fake) and a template using an AFIS system. To do this, fake fingerprints of 12 subjects have been produced with and without their cooperation. These fake fingerprints have been used alongside with real fingers. The study led to three major observations: First, genuine fingerprints produced scores higher than fake fingers (translating a closer proximity) and this tendency is observed considering each subject separately. Second, scores are however not sufficient as a single measure to differentiate these samples (fake from genuine) given the variation due to the donors themselves. That explains why fingerprint readers without vitality detection can be fooled. Third, production methods and subjects greatly influence the scores obtained for fake fingerprints.

Self reported physical activity, public health, and perceived environment: results from a comparative European study

The focus of physical activity promotion is moving from methods for increasing health enhancing physical activity on the individual level to higher level strategies including environmental and policy approaches. Scientific inquiry, traditionally related to individual-based strategies, requires adaptation and refinement when environmental and policy changes become more relevant. The objective of this study is to investigate the significance for behaviour and health of community-based environments that encourage physical activity. DESIGN AND SETTING The article presents data and results from a cross sectional comparative survey of the general population in six European countries (Belgium, Finland, Germany (East and West), Netherlands, Spain, Switzerland). Specifically, the relation between perceived community-based opportunities for physical activity, self reported physical activity, and self rated health status is investigated. PARTICIPANTS Representative samples of general populations (adults 18 years or older). Overall response rate: 53.5%. Sample sizes realised: Belgium: n=389; Finland: n=400; Germany (East): n = 913; Germany (West): n=489; Netherlands: n=366; Spain: n=380; Switzerland: n=406. MAIN RESULTS Analyses show that best opportunities are reported by people who are lightly to moderately physically active. People's self rated health is moderately, but significantly associated with both perceived opportunities, and physical activity itself. These predictors interact in that especially for women, the health impact of physical activity is more pronounced in case of good opportunities. CONCLUSIONS The paper shows the potential of opportunities within residential and community environments with regard to physical activity, both for behaviour and health. Opportunities may enable the population, especially women, to develop an active lifestyle, and thus improve their health. Future studies with objective indicators for physical activity related environments should test the findings that are based on perceptions.

Etude clinique et analyse de liaison au locus 3q28 de deux familles suisses avec atrophie optique dominante de Kjer (OPA1) [Clinical study and genetic 3q28 locus linkage in 2 Swiss families with Kjer dominant optic atrophy (OPA1)]

METHODS: We examined 20 patients from 2 unrelated Swiss families to describe their clinical phenotype. In addition, a linkage analysis was performed in an attempt to confirm the reported genetic homogeneity of this condition as well as to refine its genomic localization. RESULTS: Two point analysis provided a cumulative LOD-score of 3.03 with marker D3S 2305. The absence of recombination precluded further refinement of the disease interval. CONCLUSIONS: Our data confirm the genetic homogeneity and the extreme variability of expression, occasionally mimicking low tension glaucoma.