Topological comparison of methods for predicting transcriptional cooperativity in yeast

Background: The cooperative interaction between transcription factors has a decisive role in the control of the fate of the eukaryotic cell. Computational approaches for characterizing cooperative transcription factors in yeast, however, are based on different rationales and provide a low overlap between their results. Because the wealth of information contained in protein interaction networks and regulatory networks has proven highly effective in elucidating functional relationships between proteins, we compared different sets of cooperative transcription factor pairs (predicted by four different computational methods) within the frame of those networks. Results: Our results show that the overlap between the sets of cooperative transcription factors predicted by the different methods is low yet significant. Cooperative transcription factors predicted by all methods are closer and more clustered in the protein interaction network than expected by chance. On the other hand, members of a cooperative transcription factor pair neither seemed to regulate each other nor shared similar regulatory inputs, although they do regulate similar groups of target genes. Conclusion: Despite the different definitions of transcriptional cooperativity and the different computational approaches used to characterize cooperativity between transcription factors, the analysis of their roles in the framework of the protein interaction network and the regulatory network indicates a common denominator for the predictions under study. The knowledge of the shared topological properties of cooperative transcription factor pairs in both networks can be useful not only for designing better prediction methods but also for better understanding the complexities of transcriptional control in eukaryotes.

Developing an Effective Construction Training Program for Hispanic Supervisors and Craft Workers, January 2004

Hispanics make up a growing percentage of the craft workers entering the construction industry, and this has created several challenges for American construction companies. This study addresses the situation by investigating training needs for Hispanic construction craft workers and developing a training program for them within the industry. In order to evaluate current craft workers’ conditions within the construction industry, Iowa State University researchers conducted a survey, with 98 Hispanic craft workers as respondents from 10 construction companies, to determine current working conditions. The results confirm that the language barrier is an obstacle for both the Hispanic workers and the English-speaking employees involved in construction projects. As a part of this research, two training courses were designed to help both American construction companies and their Hispanic labor force to overcome the barriers that keep them from succeeding safely and productively. A training course titled English as a Second Language Survival Course was developed to facilitate basic communication between Hispanic workers and their American supervisors using construction-focused terminology. This course was delivered once as a trial run for a two-hour duration and twice for a full-length duration of eight hours. Important feedback was obtained from participants as part of the evaluations of the course. “How much of the course contents will be useful in your working environment” was asked; 40% of workers said “all of it” and 60% said “most of it.” Another question was “Was it worth taking the time to attend the course?” to which 94% answered “definitely” and 6% answered “yes.” A second training course titled Stepping Up to Supervisor Course for Hispanic Construction Workers was also developed to provide an effective tool to help companies promote those Hispanic craft workers whose willingness and skills meet the requirements to advance to a supervisory position in an American construction company. This course will be offered in the spring of 2004.

Investigating Gaze of Children with ASD in Naturalistic Settings.

BACKGROUND: Visual behavior is known to be atypical in Autism Spectrum Disorders (ASD). Monitor-based eye-tracking studies have measured several of these atypicalities in individuals with Autism. While atypical behaviors are known to be accentuated during natural interactions, few studies have been made on gaze behavior in natural interactions. In this study we focused on i) whether the findings done in laboratory settings are also visible in a naturalistic interaction; ii) whether new atypical elements appear when studying visual behavior across the whole field of view. METHODOLOGY/PRINCIPAL FINDINGS: Ten children with ASD and ten typically developing children participated in a dyadic interaction with an experimenter administering items from the Early Social Communication Scale (ESCS). The children wore a novel head-mounted eye-tracker, measuring gaze direction and presence of faces across the child's field of view. The analysis of gaze episodes to faces revealed that children with ASD looked significantly less and for shorter lapses of time at the experimenter. The analysis of gaze patterns across the child's field of view revealed that children with ASD looked downwards and made more extensive use of their lateral field of view when exploring the environment. CONCLUSIONS/SIGNIFICANCE: The data gathered in naturalistic settings confirm findings previously obtained only in monitor-based studies. Moreover, the study allowed to observe a generalized strategy of lateral gaze in children with ASD when they were looking at the objects in their environment.

Transcription, tagging and coding of bilingual corpora via LIDES

L'objectiu d'aquest informe és presentar l'aplicació d'una sèrie de propostes sobre transcripció, etiquetatge i codificació a dos corpus: el corpus bilingüe LC (La Canonja (Català-Espanyol)) i el corpus trilingüe CSCD (Code-switching as Communicative Design (Català-Espanyol-Anglès)). Aquestes propostes, que constitueixen l'aportació de l'equip IULA-LIPPS (Language Interaction in Plurilingual and Plurilectal Speakers) al manual de codificació del sistema LIDES (Language Interaction Database Exchange System), adoptat pel grup europeu LIPPS, poden ser útils per transcriure, etiquetar i codificar dades provinents de llengües tipològicament properes i distants.

Presence of an oligodendroglioma-like component in newly diagnosed glioblastoma identifies a pathogenetically heterogeneous subgroup and lacks prognostic value: central pathology review of the EORTC_26981/NCIC_CE.3 trial.

Glioblastoma (GBM) is a morphologically heterogeneous tumor type with a median survival of only 15 months in clinical trial populations. However, survival varies greatly among patients. As part of a central pathology review, we addressed the question if patients with GBM displaying distinct morphologic features respond differently to combined chemo-radiotherapy with temozolomide. Morphologic features were systematically recorded for 360 cases with particular focus on the presence of an oligodendroglioma-like component and respective correlations with outcome and relevant molecular markers. GBM with an oligodendroglioma-like component (GBM-O) represented 15% of all confirmed GBM (52/339) and was not associated with a more favorable outcome. GBM-O encompassed a pathogenetically heterogeneous group, significantly enriched for IDH1 mutations (19 vs. 3%, p = 0.003) and EGFR amplifications (71 vs. 48%, p = 0.04) compared with other GBM, while co-deletion of 1p/19q was found in only one case and the MGMT methylation frequency was alike (47 vs. 46%). Expression profiles classified most of the GBM-O into two subtypes, 36% (5/14 evaluable) as proneural and 43% as classical GBM. The detection of pseudo-palisading necrosis (PPN) was associated with benefit from chemotherapy (p = 0.0002), while no such effect was present in the absence of PPN (p = 0.86). In the adjusted interaction model including clinical prognostic factors and MGMT status, PPN was borderline nonsignificant (p = 0.063). Taken together, recognition of an oligodendroglioma-like component in an otherwise classic GBM identifies a pathogenetically mixed group without prognostic significance. However, the presence of PPN may indicate biological features of clinical relevance for further improvement of therapy.

Referencial para o ensino em português língua segunda em Cabo Verde no contexto da oficialização da língua cabo-verdiana

A qualidade do ensino depende da língua em que é ministrado, conforme o domínio que dela têm os aprendentes. Historicamente, nas escolas de Cabo Verde, o Português tem sido a língua veicular e de alfabetização e é assumido como instrumento de comunicação escrita e meio de acesso a diferentes áreas de saber, já que usufrui do estatuto de língua recomendada para o ensino das diferentes disciplinas. No entanto, a UNESCO recomenda ou reconhece que o ensino deve ser iniciado e/ou realizado em língua materna, de acordo com a Declaração Universal dos Direitos Linguísticos. Todavia, a Língua Cabo-Verdiana (LCV), que tem o estatuto de Língua materna (LM), é ainda predominantemente oral, embora seja utilizada à escala nacional, a nível do quotidiano. A LCV ainda não é ensinada nas escolas, pelo que a instituição de um modelo de ensino que favoreça a situação actual de Cabo Verde exige uma complexa e reflectida decisão a tomar pelas autoridades educativas. O ensino será ministrado na Língua Cabo-Verdiana? Continuará a sê-lo em Português, como se fosse língua materna, ou como língua estrangeira, língua segunda? Ou será melhor um ensino bilingue? As respostas a estas e outras questões serão procuradas junto dos professores do Ensino Básico, alguns do Secundário que ensinam em Cabo Verde e altos responsáveis pelo sistema educativo caracterizarão o ensino, a língua de ensino no processo pedagógico, a hipótese de introdução da língua materna. É nossa perspectiva reunir ideias que justifiquem a proposta de um planeamento educativo, onde sobressaem aspectos relacionados com a escolha de língua (s) de ensino, visando introduzir melhoria na qualidade das aprendizagens, de modo a satisfazer as necessidades do país.

Os manuais de língua portuguesa e o desenvolvimento da expressão oral no ensino secundário de Cabo Verde

Na elaboração do presente trabalho, que tem como tema “Os manuais de língua portuguesa e o desenvolvimento da expressão oral no ensino secundário de Cabo Verde”, procurou-se investigar, a partir da perspectiva dos manuais de Língua Portuguesa, até que ponto os mesmos podem servir ou não para o desenvolvimento da competência comunicativa dos alunos do ensino secundário, na modalidade de expressão oral. Para isso foi adoptada uma metodologia situada no campo da investigação educacional, sem pôr de lado os métodos da pesquisa qualitativa e quantitativa, o que permitiu abordar as questões relacionadas com as constantes situações de insucesso na aprendizagem da Língua Portuguesa, cujas causas têm sido atribuídas, quase sempre, aos factores como as metodológicas, aos problemas linguísticos, decorrentes da forte presença da língua materna no quotidiano dos aprendentes e ao uso de materiais desajustados da realidade nacional. Assim, para o cumprimento dos objectivos propostos, foi possível trabalhar sobre dois corpora; por um lado analisaram-se os manuais do ensino secundário, por outro, foi examinado o inquérito aplicado tanto aos professores como aos alunos, e cujo tratamento dos dados permitiu confirmar a aceitação entusiástica dos manuais escolares no contexto pedagógico, apesar da descrença na potencialidade dos exercícios propostos em desenvolver a capacidade de expressão oral dos alunos. Outro aspecto digno de registo foi o desejo manifestado pelos informantes em ter outros materiais capazes de melhorar o ensino do Português como língua segunda. Em termos do ensino da citada disciplina, foram apresentadas algumas sugestões para que a sua melhoria reverta a favor do sucesso de aprendizagem de todos os alunos

O ensino e o uso do conjuntivo no terceiro ciclo em Cabo Verde: estudo de caso realizado na escola secundaria Manuel Lopes - Praia

Neste trabalho analisamos um conteúdo gramatical - o modo conjuntivo num contexto de aprendizagem formal, seguindo duas vias: a teórica, em que fizemos uma abordagem sobre as perspectivas de vários gramáticos; a prática, que se traduz na análise de um corpus. Desenvolvemos esta análise com base nas produções escritas dos aprendentes do terceiro ciclo, na Escola Secundária Manuel Lopes, Praia, com o objectivo de fazer uma abordagem crítica respeitante ao ensino do Português Língua Segunda, em particular, ao ensino e uso do conjuntivo na supracitada língua em Cabo Verde. Com efeito, foram abordadas questões relativas às teorias de aquisição/aprendizagem segundo as perspectivas de diversos autores. A análise dos textos escritos orientou-nos para o levantamento e estudo dos erros de uso do conjuntivo e para termos uma noção do perfil sociolinguístico dos aprendentes. A descrição linguística efectuada conduziu-nos a uma reflexão sobre as formas de tratamento e de recuperação dos erros . Os resultados sugerem que o insucesso na aprendizagem do Português Língua Segunda deve-se a factores vários, entre os quais, sociolinguísticos e políticos. Nesta sequência, perspectivamos a superação de erros mediante estratégias e sugestões metodológicas para um ensino eficaz do conjuntivo em Português Língua Segunda, neste país.

A leverage theory of reputation building with co-branding: Complementarity in reputation building

We present a leverage theory of reputation building with co-branding. We showthat under certain conditions, co-branding that links unknown firms in a new sectorwith established firms in a mature sector allows the unknown firms to signal a highproduct quality and establish their own reputation. We compare this situationwith a benchmark in which both sectors are new and firms signal their qualityonly with prices. We investigate how this comparison is affected by the nature ofthe technology linking the two sectors and a cross-sector inference problem thatconsumers might face in identifying the true cause of product failure. We find thatco-branding facilitates the process in which a Þrm in the new sector to signal itsproduct quality only if the co-branding sectors produce complementary inputs andconsumers face a cross-sector inference problem. We apply our insight to economicsof superstars, multinational firms and co-authorship.

Variation in performance across Swiss mammography screening programmes: the influence of reading strategy and experience.

[Abstract] Reading volume and mammography screening performance appear positively correlated. Performance was compared across organised Swiss screening programmes, which target relatively small populations. Except for accreditation of 2nd readers radiologists (restrictive vs non-restrictive strategy), Swiss programmes have similar screening regimen/procedures and duration, which maximises comparability. Variation in performance was explored in order to improve mammography practice and optimise screening performance. Indicators of quality and effectiveness were evaluated for about 200,000 screens performed over 4 screening rounds in the 3 longest-standing Swiss cantonal programmes (of Vaud, Geneva and Valais). Interval cancers were identified by linkage with cancer registries records. Most European standards of performance were met with a favourable cancer stage shift. Several performance indicators showed substantial variation across programmes. In subsequent rounds, compared with programmes (Vaud and Geneva) which accredited few 2nd readers to increase their individual reading volume, proportions of in situ lesions and of small cancers (? 1cm) were one third lower and halved, respectively, and the proportion of advanced lesions (stage II+) nearly 50% higher in the programme without a restrictive selection strategy. Discrepancy in second-year proportional incidence of interval cancers appears to be multicausal. Differences in performance could partly be explained by a selective strategy for 2nd readers and a prior experience in service screening, but not by the levels of opportunistic screening and programme attendance. This study provides clues for enhancing mammography screening performance in low-volume Swiss programmes.

Evolutionary branching in deme-structured populations.

Adaptive dynamics shows that a continuous trait under frequency dependent selection may first converge to a singular point followed by spontaneous transition from a unimodal trait distribution into a bimodal one, which is called "evolutionary branching". Here, we study evolutionary branching in a deme-structured population by constructing a quantitative genetic model for the trait variance dynamics, which allows us to obtain an analytic condition for evolutionary branching. This is first shown to agree with previous conditions for branching expressed in terms of relatedness between interacting individuals within demes and obtained from mutant-resident systems. We then show this branching condition can be markedly simplified when the evolving trait affect fecundity and/or survival, as opposed to affecting population structure, which would occur in the case of the evolution of dispersal. As an application of our model, we evaluate the threshold migration rate below which evolutionary branching cannot occur in a pairwise interaction game. This agrees very well with the individual-based simulation results.

Processat de vídeo aplicat a la robòtica

Aquest projecte consisteix en acoblar una càmera web uEye en una de les extremitats d'un robot industrial (ABB Irc5). Aquest robot, es mourà en cas què es detecti una cara a través de la webcam. L'objectiu és intentar que la cara es situï sempre al mig de la imatge captada per la càmera. Podem dividir les tasques d'aquest projecte amb 4 fases diferents. A continuació expliquem les diferents etapes. La Càmera uEye s'encarrega de capturar imatges i passar-les a un PC utilitzant Python. La funció de Detecció de Cares ens indica la posició i dimensions de la cara. Tot seguit, la funció LabJack s'encarrega de canviar els valors digitals de les 5 senyals mitjançant programació amb Python. Per últim el Robot ABB interpreta el valor d'aquestes 5 senyals i es desplaça mitjançant petits increments amb l'objectiu de situar la cara al mig de la imatge capturada.

La Salut als diaris digitals, una qüestió de salut digital: les notícies de salut en els diaris digitals en llengua catalana: exploració i assaig metodològic per a l'anàlisi descriptiva

En l’actual context de la societat de la informació, les noves tecnologies de la comunicació i, específicament, el fenomen d’Internet, adquireixen una importància rellevant en tots els sectors socials i fan replantejar la comunicació de masses. Les característiques que ofereixen els mitjans digitals (multimedialitat, hipertextualitat, interactivitat) comporten una nova forma d’estructurar i llegir la informació. Així, capçaleres i periodistes s’han d’actualitzar en la producció de la informació i en la seva transmissió, i l’usuari ha d’aprendre noves formes de lectura per adaptar-se al nou paradigma comunicacional. D’altra banda, la societat del benestar en què vivim reclama cada cop més als mitjans de comunicació generals i també específicament als digitals que parlin de temes de salut. Aquests mitjans esdevenen fonts principals d’aquest tipus d’informació, després del metge, per a la gestió autònoma de la pròpia salut. És a partir d’aquesta convergència de mitjans digitals, periodisme i salut, de la necessitat d’explorar la situació actual i del desig d’aportar coneixements per a la millora de la pràctica professional del periodisme, que es desenvolupa el treball que es presenta en aquesta memòria. El projecte que es presenta és una anàlisi restrospectiva i descriptiva de les notícies de salut que es produeixen durant un mes als diaris digitals que publiquen en llengua catalana: El Periódico de Catalunya, l’Avui, i LaMalla.net.

Defective TNF-alpha-mediated hepatocellular apoptosis and liver damage in acidic sphingomyelinase knockout mice

This study addressed the contribution of acidic sphingomyelinase (ASMase) in TNF-alpha-mediated hepatocellular apoptosis. Cultured hepatocytes depleted of mitochondrial glutathione (mGSH) became sensitive to TNF-alpha, undergoing a time-dependent apoptotic cell death preceded by mitochondrial membrane depolarization, cytochrome c release, and caspase activation. Cyclosporin A treatment rescued mGSH-depleted hepatocytes from TNF-alpha-induced cell death. In contrast, mGSH-depleted hepatocytes deficient in ASMase were resistant to TNF-alpha-mediated cell death but sensitive to exogenous ASMase. Furthermore, although in vivo administration of TNF-alpha or LPS to galactosamine-pretreated ASMase(+/+) mice caused liver damage, ASMase(-/-) mice exhibited minimal hepatocellular injury. To analyze the requirement of ASMase, we assessed the effect of glucosylceramide synthetase inhibition on TNF-alpha-mediated apoptosis. This approach, which blunted glycosphingolipid generation by TNF-alpha, protected mGSH-depleted ASMase(+/+) hepatocytes from TNF-alpha despite enhancement of TNF-alpha-stimulated ceramide formation. To further test the involvement of glycosphingolipids, we focused on ganglioside GD3 (GD3) because of its emerging role in apoptosis through interaction with mitochondria. Analysis of the cellular redistribution of GD3 by laser scanning confocal microscopy revealed the targeting of GD3 to mitochondria in ASMase(+/+) but not in ASMase(-/-) hepatocytes. However, treatment of ASMase(-/-) hepatocytes with exogenous ASMase induced the colocalization of GD3 and mitochondria. Thus, ASMase contributes to TNF-alpha-induced hepatocellular apoptosis by promoting the mitochondrial targeting of glycosphingolipids.

NS4B Self-Interaction through Conserved C-Terminal Elements Is Required for the Establishment of Functional Hepatitis C Virus Replication Complexes.

Hepatitis C virus (HCV) is an important human pathogen, persistently infecting more than 170 million individuals worldwide. Studies of the HCV life cycle have become possible with the development of cell culture systems supporting the replication of viral RNA and the production of infectious virus. However, the exact functions of individual proteins, especially of nonstructural protein 4B (NS4B), remain poorly understood. NS4B triggers the formation of specific, vesicular membrane rearrangements, referred to as membranous webs, which have been reported to represent sites of HCV RNA replication. However, the mechanism of vesicle induction is not known. In this study, a panel of 15 mutants carrying substitutions in the highly conserved NS4B C-terminal domain was generated. Five mutations had only a minor effect on replication, but two of them enhanced assembly and release of infectious virus. Ten mutants were replication defective and used for selection of pseudoreversions. Most of the pseudoreversions also localized to the highly conserved NS4B C-terminal domain and were found to restore replication competence upon insertion into the corresponding primary mutant. Importantly, pseudoreversions restoring replication competence also restored heterotypic NS4B self-interaction, which was disrupted by the primary mutation. Finally, electron microscopy analyses of membrane alterations induced by NS4B mutants revealed striking morphological abnormalities, which were restored to wild-type morphology by the corresponding pseudoreversion. These findings demonstrate the important role of the C-terminal domain in NS4B self-interaction and the formation of functional HCV replication complexes.