HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm.

Genome reconstruction and comparative genomics of pneumocystis jirovecii

Pneumocystis jirovecii is a fungus belonging to a basal lineage of the Ascomycotina, the Taphrinomycotina subphylum. It is a parasite specific to humans that dwells primarily in the lung and can cause severe pneumonia in individuals with debilitated immune system. Despite its clinical importance, many aspects of its biology remain poorly understood, at least in part because of the lack of a continuous in vitro cultivation system. The present thesis consists in the genome reconstruction and comparative genomics of P. jirovecii. It is made of three parts: (i) the de novo sequencing of P. jirovecii genome starting from a single broncho- alveolar lavage fluid of a single patient (ii) the de novo sequencing of the genome of the plant pathogen Taphrina deformans, a fungus closely related to P. jirovecii, and (iii) the genome scale comparison of P. jirovecii to other Taphrinomycotina members. Enrichment in P. jirovecii cells by immuno-precipitation, whole DNA random amplification, two complementary high throughput DNA sequencing methods, and in silico sorting and assembly of sequences were used for the de novo reconstruction of P. jirovecii genome from the microbiota of a single clinical specimen. An iterative ad hoc pipeline as well as numerical simulations was used to recover P. jirovecii sequences while purging out contaminants and assembly or amplification chimeras. This strategy produced a 8.1 Mb assembly, which encodes 3,898 genes. Homology searches, mapping on biochemical pathways atlases, and manual validations revealed that this genome lacks (i) most of the enzymes dedicated to the amino acids biosyntheses, and (ii) most virulence factors observed in other fungi, e.g. the glyoxylate shunt pathway and specific peptidases involved in the degradation of the host cell membrane. The same analyses applied to the available genomic sequences from Pneumocystis carinii the species infecting rats and Pneumocystis murina the species infecting mice revealed the same deficiencies. The genome sequencing of T. deformans yielded a 13 Mb assembly, which encodes 5,735 genes. T. deformans possesses enzymes involved plant cell wall degradation, secondary metabolism, the glyoxylate cycle, detoxification, sterol biosynthesis, as well as the biosyntheses of plant hormones such as abscisic acid or indole-3-acetic acid. T. deformans also harbors gene subsets that have counterparts in plant saprophytes or pathogens, which is consistent with its alternate saprophytic and pathogenic lifestyles. Mating genes were also identified. The homothallism of this fungus suggests a mating-type switching mechanism. Comparative analyses indicated that 81% of P. jirovecii genes are shared with eight other Taphrinomycotina members, including T. deformans, P. carinii and P. murina. These genes are mostly involved in housekeeping activities. The genes specific to the Pneumocystis genus represent 8%, and are involved in RNA metabolism and signaling. The signaling is known to be crucial for interaction of Pneumocystis spp with their environment. Eleven percent are unique to P. jirovecii and encode mostly proteins of unknown function. These genes in conjunction with other ones (e.g. the major surface glycoproteins) might govern the interaction of P. jirovecii with its human host cells, and potentially be responsible of the host specificity. P. jirovecii exhibits a reduced genome in size with a low GC content, and most probably scavenges vital compounds such as amino acids and cholesterol from human lungs. Consistently, its genome encodes a large set of transporters (ca. 22% of its genes), which may play a pivotal role in the acquisition of these compounds. All these features are generally observed in obligate parasite of various kingdoms (bacteria, protozoa, fungi). Moreover, epidemiological studies failed to evidence a free-living form of the fungus and Pneumocystis spp were shown to co-evolved with their hosts. Given also the lack of virulence factors, our observations strongly suggest that P. jirovecii is an obligate parasite specialized in the colonization of human lungs, and which causes disease only in individuals with compromised immune system. The same conclusion is most likely true for all other Pneumocystis spp in their respective mammalian host. - Pneumocystis jirovecii est un champignon appartenant à ine branche basale des Ascomycotina, le sous-embranchement des Taphrinomycotina. C'est un parasite spécifique aux humains qui réside principalement dans les poumons, et qui peut causer des pneumonies sévères chez des individus ayant un système immunitaire déficient. En dépit de son importance clinique, de nombreux aspects de sa biologie demeurent,largement méconnus, au moins en partie à cause de l'absence d'un système de culture in vitro continu. Cette thèse traite de la reconstruction du génome et de la génomique comparative de P. jirovecii. Elle comporte trois parties: (i) le séquençage de novo du génome de P. jirovecii à partir d'un lavage broncho-alvéolaire provenant d'un seul patient, (ii) le séquençage de novo du génome d'un champignon pathogène de plante Taphrina deformans qui est phylogénétiquement proche de P. jirovecii, et (iii) la comparaison du génome de P. jirovecii à celui d'autres membres du sous-embranchement des Taphrinomycotina. Un enrichissement en cellules de P. jirovecii par immuno-précipitation, une amplification aléatoire des molécules d'ADN, deux méthodes complémentaires de séquençage à haut débit, un tri in silico et un assemblage des séquences ont été utilisés pour reconstruire de novo le génome de P. jirovecii à partir du microbiote d'un seul échantillon clinique. Un pipeline spécifique ainsi que des simulations numériques ont été utilisés pour récupérer les séquences de P. jirovecii tout en éliminant les séquences contaminants et les chimères d'amplification ou d'assemblage. Cette stratégie a produit un assemblage de 8.1 Mb, qui contient 3898 gènes. Les recherches d'homologies, de cartographie des voies métaboliques et des validations manuelles ont révélé que ce génome est dépourvu (i) de la plupart des enzymes dédiées à la biosynthèse des acides aminés, et (ii) de la plupart des facteurs de virulence observés chez d'autres champignons, par exemple, le cycle du glyoxylate ainsi que des peptidases spécifiques impliquées dans la dégradation de la membrane de la cellule hôte. Les analyses appliquées aux données génomiques disponibles de Pneumocystis carinii, l'espèce infectant les rats, et de Pneumocystis murina, l'espèce infectant les souris, ont révélé les mêmes déficiences. Le séquençage du génome de T. deformans a généré un assemblage de 13.3 Mb qui contient 5735 gènes. T. deformans possède les gènes codant pour les enzymes impliquées dans la dégradation des parois cellulaires des plantes, le métabolisme secondaire, le cycle du glyoxylate, la détoxification, la biosynthèse des stérols ainsi que la biosynthèse d'hormones de plantes telles que l'acide abscissique ou l'acide indole 3-acétique. T. deformans possède également des sous-ensembles de gènes présents exclusivement chez des saprophytes ou des pathogènes de plantes, ce qui est consistent avec son mode de vie alternatif saprophyte et pathogène. Des gènes impliqués dans la conjugaison ont été identifiés. L'homothallisme de ce champignon suggère mécanisme de permutation du type conjuguant. Les analyses comparatives ont démontré que 81% des gènes de P. jirovecii sont présent chez les autres membres du sous-embranchement des Taphrinomycotina. Ces gènes sont essentiellement impliqués dans le métabolisme basai. Les gènes spécifiques au genre Pneumocystis représentent 8%, et sont impliqués dans le métabolisme de l'ARN et la signalisation. La signalisation est connue pour être cruciale pour l'interaction des espèces de Pneumocystis avec leur environnement. Les gènes propres à P. jirovecii représentent 11% et codent en majorité pour des protéines dont la fonction est inconnue. Ces gènes en conjonction avec d'autres (par exemple, les glycoprotéines de surface), pourraient être déterminants dans l'interaction de P. jirovecii avec les cellules de l'hôte humain, et être potentiellement responsable de la spécificité d'hôte. P. jirovecii possède un génome de taille réduite à faible pourcentage en GC et récupère très probablement des composés vitaux comme les acides aminés et le cholestérol à partir des poumons humains. De manière consistante, son génome code pour de nombreux transporteurs (22% de ses gènes), qui pourraient jouer un rôle essentiel dans l'acquisition de ces composés. Ces caractéristiques sont généralement observées chez les parasites obligatoires de plusieurs règnes (bactéries, protozoaires, champignons). De plus, les études épidémiologiques n'ont pas réussi à prouver l'existence d'ime forme vivant librement du champignon. Etant donné également l'absence de facteurs de virulence, nos observations suggèrent que P. jirovecii est un parasite obligatoire spécialisé dans la colonisation des poumons humains, ne causant une maladie que chez des individus ayant un système immunitaire compromis. La même conclusion est très probablement applicable à toutes les autres espèces de Pneumocystis dans leur hôte mammifère respectif.

Toward integrated management of cerebral aneurysms

In the last few years, some of the visionary concepts behind the virtual physiological human began to be demonstrated on various clinical domains, showing great promise for improving healthcare management. In the current work, we provide an overview of image- and biomechanics-based techniques that, when put together, provide a patient-specific pipeline for the management of intracranial aneurysms. The derivation and subsequent integration of morphological, morphodynamic, haemodynamic and structural analyses allow us to extract patient-specific models and information from which diagnostic and prognostic descriptors can be obtained. Linking such new indices with relevant clinical events should bring new insights into the processes behind aneurysm genesis, growth and rupture. The development of techniques for modelling endovascular devices such as stents and coils allows the evaluation of alternative treatment scenarios before the intervention takes place and could also contribute to the understanding and improved design of more effective devices. A key element to facilitate the clinical take-up of all these developments is their comprehensive validation. Although a number of previously published results have shown the accuracy and robustness of individual components, further efforts should be directed to demonstrate the diagnostic and prognostic efficacy of these advanced tools through large-scale clinical trials.

Mining and exploiting domain-specific corpora in the PANACEA platform

The objective of the PANACEA ICT-2007.2.2 EU project is to build a platform that automates the stages involved in the acquisition,production, updating and maintenance of the large language resources required by, among others, MT systems. The development of a Corpus Acquisition Component (CAC) for extracting monolingual and bilingual data from the web is one of the most innovative building blocks of PANACEA. The CAC, which is the first stage in the PANACEA pipeline for building Language Resources, adopts an efficient and distributed methodology to crawl for web documents with rich textual content in specific languages and predefined domains. The CAC includes modules that can acquire parallel data from sites with in-domain content available in more than one language. In order to extrinsically evaluate the CAC methodology, we have conducted several experiments that used crawled parallel corpora for the identification and extraction of parallel sentences using sentence alignment. The corpora were then successfully used for domain adaptation of Machine Translation Systems.

Nationalisme économique et réalisme mercantile : la politique énergétique russe sous Poutine (2000-2008)

Mon travail met en évidence la restructuration de l'industrie énergétique russe sous les deux mandats Poutine (2000-2008) via le rôle prédominant de l'État dans une perspective historique. Une nouvelle élite politique russe (les Silovikis) issue des structures de force de l'Etat favorise le nationalisme économique axé sur le rétablissement de l'autorité du gouvernement central au sein de l'industrie énergétique nationale au détriment des pouvoirs régionaux, des sociétés privées étrangères et des oligarques indépendants. Dans cette perspective, on peut citer "l'affaire Youkos" en 2003 caractérisée par l'arrestation de l'oligarque Mikhaïl Khodorkhovsky; les tentatives silovikiennes de reprendre l'ascendant sur les compagnies pétrolières régionales Tatneft et Bachneft gérées par les gouvernements tatar et bachkir, la pression fiscale envers les majors pétrolières étrangères à l'instar du conflit russo- britannique relatif à la joint-venture TNK-BP. Quant à la politique énergétique étrangère russe, elle est inspirée par line vision réaliste mercantile; le gouvernement silovikien vise à défendre l'intérêt national, le prestige et la puissance de la Russie via ses "champions" énergétiques Rosneft et Gazprom utilisés comme levier politique, notamment à l'égard des pays de la CEI considéré par Moscou comme sa sphère d'influence historique. Dans cette perspective, nous pouvons mentionner l'interruption des approvisionnements pétroliers et gaziers russes à l'Ukraine, aux Etats baltes ou encore à la Géorgie; la concurrence entre les majors russes et étrangères en Asie centrale / Caucase pour les champs pétrolifères et les tracés de pipelines (nouveau «Grand Jeu»); la diversification des marchés russes à l'exportation à travers la promotion de nouveaux pipelines partant des champs pétrolifères sibériens vers la Chine et l'océan Pacifique.¦My work highlights the restructuration of the Russian energy industry under the 2 Putin madates (2000-2008) by the predominant role of the state in a historical perspective. A new Russian politic elite (Siloviki) from state structure forces promotes the economic nationalism focused on the reestablishment of the central governmental authority in the national energy industry against regional powers, private foreign companies and independent oligarchs. In this perspective, we can mention the "Yukos Affair" in 2003 with the arrest of the oligarch Mikhail Khodorkhovsky; the silovikian attempts to take over the regional oil companies Tatneft and Bachneft handled by the Tatar and Bashkir governments; the fiscal silovikian pressure against foreign companies such as the Russo-Britannic joint- venture TNK-BP. As for the Russian energy Foreign policy, it is inspired by a mercantile realism vision; the silovikian government aims to defend the national interest, the prestige and the power of Russia through its energy companies Rosneft and Gazprom as a political leverage especially toward the CEI Countries considered by Moscow as it historical sphere of influence. In this perspective, we can mention the interruption of Russian oil&gas supply toward Ukraine, Baltic states or Georgia; the competition between Russian and foreign companies in Central Asia/Caucasus for oil and gas fields and pipeline routes (new "Great Game"); the diversification of Russian export markets through the promotion ο new pipelines from Siberian oil&gas fields to China and the Pacific Ocean.

Relatório Final - Consultoria Nacional de Cabo Verde

No âmbito do Projecto de Cooperação Técnica CPLP/FAO, foi criado, por despacho do MADRRM, um Comité Nacional de Coordenação para apresentar um Quadro de Demandas e Propostas do país com vistas ao desenvolvimento de um Programa Regional de Cooperação Sul-Sul e Norte-Sul envolvendo os países da CPLP no domínio da Gestão Sustentável das Terras (GST), no âmbito da UNCCD, com Assessoria Técnica da FAO e do Secretariado da CPLP, e com o apoio de uma Equipa de Consultores Nacionais. A estrutura do Relatório Nacional foi baseada no historial da implementação da UNCCD em Cabo Verde, integrando a problemática da Gestão Sustentável das Terras, e apresenta diferentes temáticas, nomeadamente: O Quadro Institucional e Legislativo relevante, os Actores chaves, as necessidades de reforço de capacidades, os domínios de intervenção relevantes, os arranjos institucionais pertinentes. A degradação das terras e o avanço da desertificação representam um risco real e significativo para as populações nos países da CPLP, incluindo Cabo Verde, as quais enfrentam a ameaça da desertificação com diferentes níveis de intensidade e incidência territorial. Da mesma forma, os países apresentam em diferentes estágios de implementação da UNCCD, reflexos das suas dificuldades em termos de capacidades, estratégias e recursos financeiros para o envolvimento dos diferentes intervenientes. Os Relatórios Nacionais sobre a situação da Desertificação destacam uma sequência de riscos e situações de vulnerabilidades, seguidos de impactos socioeconómicos e estratégias de Adaptação. A análise aponta as possíveis estratégias de adaptação e busca de soluções em Cabo Verde. No contexto da Desertificação e Degradação das Terras, a aptidão dos solos tem uma importância determinante na Gestão Sustentável das Terras. A Identificação do tipo de uso actual das terras deverá ser feita de acordo com as prioridades de intervenção quanto a aptidão dos solos (Agricultura, Biodiversidade, etc…). A delimitação das terras facilita a implementação de políticas e programas de desenvolvimento sustentável. Esse processo tem vindo a tomar corpo em Cabo Verde através do Programa das Áreas Protegidas Terrestres e Marinhas, o que significa um primeiro passo para a implementação de um Programa Nacional de Gestão Sustentável das Terras. O contexto político caracteriza-se por uma evolução positiva a nível de tomada de consciência sobre a sustentabilidade ambiental. Cabo Verde dispõe de um quadro normativo, amplo e abrangente no Sector do Ambiente. No entanto, as leis e seus regulamentos são acentuadamente complexos, com um elevado grau de tecnicidade, o que os torna de difícil entendimento para grande parte da comunidade que chega a ter acesso a um ou outro instrumento legal de protecção do ambiente e da natureza. Da análise das políticas seguidas durante os últimos anos constata-se que a problemática ambiental ganhou uma nova dimensão, a partir de 1995. Assim, ganhos positivos foram conseguidos, essencialmente no que concerne ao enquadramento institucional e legal. A problemática fundiária reveste-se de grande complexidade em Cabo Verde decorrente não apenas da forma como se dá o acesso à terra como também das relações sociais e de produção do campo, num contexto de um ecossistema frágil e de uma sociedade com graves problemas de pobreza e vulnerabilidade, acentuando os mecanismos de dependência à terra e à actividade agrícola bem como de sujeição no quadro de determinadas relações sociais. No programa do governo e outros instrumentos atribui-se ao ordenamento do território e a gestão integrada dos recursos naturais um lugar estratégico no processo de desenvolvimento de Cabo Verde. O Governo objectiva estimular o surgimento de fileiras competitivas, incluindo a prestação de serviços, em especial o turismo rural, em particular através da articulação com o processo de desenvolvimento de parques naturais e de valorização dos recursos ambientais e conservação da natureza. O Desenvolvimento das Capacidades é um processo de longo prazo que privilegia o fortalecimento endógeno das estruturas nacionais, por conseguinte a visão linear e descontinua dos projectos que tiram recursos/proveitos das estruturas deve ceder o lugar à uma visão mais integrada onde é o projecto que deve se adaptar a estrutura para reforça-la. Assim a implementação de uma Estratégia para o Desenvolvimento das Capacidades na GST deverá passar pela identificação de sequências, nomeadamente: - As capacidades necessárias; - Os tipos de actividades por realizar; - Os actores a serem envolvidos; - As modalidades de desenvolvimento das capacidades. A identificação das Instituições-Chave e definição das competências da Coordenação Nacional do Programa resultou de uma estreita concertação e negociação de todas as partes envolvidas, tendo em consideração o carácter pluridisciplinar e multi-sectorial e transversal da UNCCD. As instituições e/ou equipas nacionais serão envolvidas na implementação das actividades no âmbito da Gestão Sustentável das Terras, e integram um processo de aprendizagem de “Job-training” favorecendo a aquisição de conhecimentos e saber - fazer, através de trabalhos sobre os diferentes engajamentos da UNCCD. A degradação dos solos e práticas de gestão insustentável das terras estão entre os maiores desafios ambientais do mundo de hoje, o que constitui também um importante obstáculo para a satisfação das necessidades básicas da humanidade, especialmente em zonas áridas. A Degradação das Terras aumenta a vulnerabilidade das populações perante as alterações e mudanças climáticas, reduzindo as actividades rurais, diminuindo a produtividade agrícola, favorecendo a vulnerabilidade nas produções, reduzindo os recursos naturais locais; A Gestão Sustentável das Terras pode reduzir a vulnerabilidade às Mudanças Climáticas, aumentar as capacidades das populações na adaptação às Mudanças Climáticas, e em muitos casos, pode contribuir para a mitigação das Mudanças Climáticas através do aumento da sequestração do carbono e redução da emissão de gases. No contexto actual não existem Programas/Projectos específicos para a Gestão Sustentável das Terras, mas há Programas/Projectos Maiores que integram a Componente Luta contra a Desertificação como estratégia de implementação. A visão linear e descontínua dos projectos que tiram recursos/proveitos das estruturas deve ceder o lugar para uma visão mais integrada onde é o projecto que deve se adaptar a estrutura para reforça-la. Considerando um vasto leque de Programas/Projectos em “Pipeline”, em varias áreas relacionadas com UNCCD/GST no país, optou-se por fazer uma Priorização dos Domínios de intervenção de acordo com os Recursos Financeiros e Capacidades Nacionais. Foram propostos 5 Eixos (Gestão Sustentável dos Recursos Naturais, Fortalecimento Institucional, Comunicação e Cidadania, Parcerias e Sinergias, Desenvolvimento Cientifico e Tecnológico), estruturados em 7 Domínios de intervenção (Apoio na GST, Desenvolvimento Agrosilvo- pastoril, Ordenamento do Território, Sistema de Monitorização e Avaliação, IEC Ambiental, Desenvolvimento das Capacidades para mobilização de fundos e Investigação Inter-disciplinar e Integrada) que integram Projectos de Desenvolvimento. O Desenvolvimento das Capacidades necessita de arranjos institucionais que respondem directamente aos objectivos definidos no Programa GST em Cabo Verde. A elaboração e implementação de um Programa de Gestão Sustentável das Terras exigem um esforço conjunto de articulação e concertação entre os actores/parceiros chaves, e uma intervenção eficiente e eficaz por parte dos mesmos. Perspectiva-se que o alcance dos objectivos traçados no âmbito do Programa só será possível através de uma actuação eficaz de cada actor envolvido e da sinergia resultante da interacção entre as instituições. A parceria é fundamental tendo em conta a transversalidade da Gestão Sustentável das Terras (GST). Em consequência, as diferentes instituições (actores/parceiros) devem ser implicadas de modo a participarem nas actividades habilitantes de planificação e criação de capacidades endógenas, nos diferentes domínios prioritários da GST que facilitarão a aplicação de medidas de reacção eficazes, conforme o estabelecido nas Convenções do Rio, nomeadamente a UNCCD.

Somatosensory motor bodily representation cortical thinning in Tourette : effects of tic severity, age and gender

Introduction: Tourette syndrome (TS) implicates the disinhibition of the cortico-striatal-thalamic-cortical circuitry (CSTC). Previous studies used a volumetric approach to investigate this circuitry with inconsistent findings. Cortical thickness may represent a more reliable measure than volume due to the low variability in the cytoarchitectural structure of the grey matter. Methods: 66 magnetic resonance imaging scans were acquired from 34 TS (age range 10-25, mean 17.19±4.1) and 32 normal controls (NC) (age range 10-20, mean 16.33±3.56). Brain morphology was assessed using the fully automated Civet pipeline at the Montreal Neurological Institute. Results: We report (1) significant cortical thinning in the fronto-parietal and somatosensory-motor cortices in TS relative to NC (p<0.05); (2) TS boys showed thinner cortex relative to TS girls in the fronto-parietal cortical regions (p<0.05); (3) significant decrease in the fronto-parietal mean cortical thickness in TS with age relative to NC and in the pre-central cortex in TS boys relative to TS girls; (4) significant negative correlations between tic severity and the somatosensory-motor cortical thickness. Conclusions: TS revealed important thinning in brain regions particularly involved in the somatosensory/motor bodily representations which may play an important role in tics. Our findings are in agreement with Leckman et al. (1991) hypothesis stating that facial tics would be associated with dysfunction in an orofacial subset of the motor circuit, eye blinking with the occulo-motor circuit, whereas lack of inhibition to a dysfunction in the prefrontal cortex. Gender and age differences may reflect differential etiological factors, which have significant clinical relevance in TS and should be considered in developing and using diagnostic and therapeutic interventions.

High-performance payload data handling system for Gaia

Gaia is the most ambitious space astrometry mission currently envisaged and is a technological challenge in all its aspects. We describe a proposal for the payload data handling system of Gaia, as an example of a high-performance, real-time, concurrent, and pipelined data system. This proposal includes the front-end systems for the instrumentation, the data acquisition and management modules, the star data processing modules, and the payload data handling unit. We also review other payload and service module elements and we illustrate a data flux proposal.

A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.

BACKGROUND: The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as the International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely used in mouse genetics studies. Here we perform a comprehensive genomic and phenotypic analysis of the two strains to identify differences that may influence their underlying genetic mechanisms. RESULTS: We undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. We annotate 34 SNPs and 2 indels that distinguish C57BL/6J and C57BL/6N coding sequences, as well as 15 structural variants that overlap a gene. In parallel we assess the comparative phenotypes of the two inbred lines utilizing the EMPReSSslim phenotyping pipeline, a broad based assessment encompassing diverse biological systems. We perform additional secondary phenotyping assessments to explore other phenotype domains and to elaborate phenotype differences identified in the primary assessment. We uncover significant phenotypic differences between the two lines, replicated across multiple centers, in a number of physiological, biochemical and behavioral systems. CONCLUSIONS: Comparison of C57BL/6J and C57BL/6N demonstrates a range of phenotypic differences that have the potential to impact upon penetrance and expressivity of mutational effects in these strains. Moreover, the sequence variants we identify provide a set of candidate genes for the phenotypic differences observed between the two strains.

Le plafond de fer de l'université : femmes et carrières

Pourquoi les femmes n'ont-elles pas « l'étoffe du chercheur » ? Le modèle unique imposé par le monde académique pénalise les femmes dans leur ascension professionnelle et sa rigidité qui perdure au sein des universités nous a conduites à revisiter les travaux réalisés dans le monde de l'entreprise sur le « plafond de verre », le « ciel de plomb » ou le « leaky pipeline », pour nous intéresser à ces processus pernicieux. Du fait de son mode de recrutement prétendument fondé sur le seul mérite (et son alliée l'excellence), le monde académique pourrait garantir une certaine égalité entre hommes et femmes, mais il n'en n'est rien. Afin de faire émerger les processus complexes qui conduisent à l'exclusion des femmes du sommet des hiérarchies universitaires, cet ouvrage mêle des textes académiques à des contributions plus personnelles qui prennent la forme de témoignages ou de réflexions illustrant les aléas des parcours féminins dans l'université (S. Boes, A. Casini, C. Carvalho, V. Cossy, S. Da Rin, F. Fassa, S. Kradolfer, N. Le Feuvre, R.J. Leeman, C. Marry, M. Sanchez-Mazas, E. Ollagnier, S. Paroz, M. Rosende, I. Stengers, G. Theurillat).

2009 Iowa’s Rail System Background Prepared by the Office of Systems Planning December 2010

Iowa’s Rail Environment Iowa’s rail transportation system provides both freight and passenger service. Rail serves a variety of trips, including those within Iowa and those to other states as well as to foreign markets. While rail competes with other modes, it also cooperates with those modes to provide intermodal services to Iowans. In 2009 Iowa’s rail transportation system could be described as follows: Freight Iowa’s 130,000-mile freight transportation system includes an extensive railroad network, a well-developed highway system, two bordering navigable waterways, and a pipeline network as well as air cargo facilities. While rail accounts for only 3 percent of the freight network, it carries 43 percent of Iowa’s freight tonnage. A great variety of commodities ranging from fresh fish to textiles to optical products are moved by rail. However, most of the Iowa rail shipments consist of bulk commodities, including grain, grain products, coal, ethanol, and fertilizers. The railroad network performs an important role in moving bulk commodities produced and consumed in the state to local processors, livestock feeders, river terminals and ports for foreign export. The railroad’s ability to haul large volumes, long distances at low costs will continue to be a major factor in moving freight and improving the economy of Iowa. Key 2008 Facts • 3,945 miles of track • 18 railroads • 49.5 million tons shipped • 39.7 million tons received • 2 Amtrak routes • 6 Amtrak stations • 66,286 rail passenger rides Key Rail Trends • slightly fewer miles being operated; • railroads serving Iowa has remained the same; • more rail freight traffic; • more tons hauled per car; • higher average rail rates per ton-mile since 2002; • more car and tons hauled per locomotive; and • more ton miles per gallon of fuel consumed. Iowa’s rail system and service has been evolving over time relative to its size, financial conditions, and competition from other modes.

Fourmidable: a database for ant genomics.

BACKGROUND: Fourmidable is an infrastructure to curate and share the emerging genetic, molecular, and functional genomic data and protocols for ants. DESCRIPTION: The Fourmidable assembly pipeline groups nucleotide sequences into clusters before independently assembling each cluster. Subsequently, assembled sequences are annotated via Interproscan and BLAST against general and insect-specific databases. Gene-specific information can be retrieved using gene identifiers, searching for similar sequences or browsing through inferred Gene Ontology annotations. The database will readily scale as ultra-high throughput sequence data and sequences from additional species become available. CONCLUSION: Fourmidable currently houses EST data from two ant species and microarray gene expression data for one of these. Fourmidable is publicly available at http://fourmidable.unil.ch.

Midwest Transportation Consortium Annual Report, 2004-2005

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2005-2006

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2006-2007

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.