Made available in DSpace on 2014-12-17T14:53:19Z (GMT). No. of bitstreams: 1 VaniaSCC_DISSERT.pdf: 1266430 bytes, checksum: bb0efc87ad098a7372a42a87a2cdce0a (MD5) Previous issue date: 2013-11-20 / Funda??o de Apoio ? Pesquisa do Estado do Rio Grande do Norte / Knowledge and innovation were seen as major forces, both for survival, as the acquisition of competitive advantages in the Brazilian economy, as well as adding value to the product as a market differentiator. The Triple Helix model is directed toward the knowledge-based economy. Over the past six years, the Federal Government through the Financier of Studies and Projects ( FINEP ) invested in technological innovation projects, economic subsidies, about U.S. $ 1 billion supporting more than 800 projects with these resources. According to the MCTI , the Northeast, over the years 2000 to 2010 increased spending on Science and Technology (considering the activities of research and development more scientific and related activities) of the State Government in relation to its total revenue In 2000, 0.51% of total revenues were invested in Science & Technology, while in 2010 this figure increased to 1.31%. Among the nine Northeast states, Para?ba is highlighted. In 2000, 0.33% of its total revenues were directed to innovation, reaching 2.04% in 2010, the largest increase in the region while the RN invested 0.24% in 2000 and in 2010 reached the level of 1.42 %. According to IBGE, in the period 2000-2011, the micro and small enterprises surpassed the barrier of 6 million establishments. In 2000, there were 4.2 million establishments while in 2011 were 6.3 million active establishments. Therefore, throughout the period, there was a creation of approximately 2.1 million new establishments. Between 2000 and 2011, micro and small businesses have created 7.0 million formal jobs, 8.6 million jobs in 2000 to 15.6 million in 2011. This scenario shows the importance of this study in relation to the investment of governments in RD & I in micro and small enterprises. This study aims to analyze the interaction Universities - Business - Government in the development of innovation in micro and small companies in Rio Grande do Norte participants of the edicts of Inova FAPERN. We chose to adopt as a research method case study concerning the procedure of the research, exploratory, descriptive, and on documents with engineers and researchers of innovation projects approved by PAPPE Subsidy (Inova -RN I, II and III). Data collection was done through the report made by FAPERN entitled: " Evaluation of companies financed and supported by the Grant Program for Technological Innovation for Micro and Small Enterprises RN - INOVA -RN " (2010) and a questionnaire with 40 closed questions and 1 opened to 30 affirmative composed based on a 5-point Likert scale. The analysis of data was qualitative and quantitative. The study provided to identify the importance and barriers arising from the relation between Government Enterprise (micro and small) and University as essential to the economic development of the region. It was also identified that, in the innovation projects, 70% of the goods or services originating from research were to market these, 50% resulted in a patent for the company and 80% publications of scientific articles / O conhecimento e a inova??o passaram a ser vistos como importantes for?as, tanto de sobreviv?ncia, quanto de aquisi??o de vantagens competitivas na economia brasileira, al?m de agregar valor ao produto como diferencial de mercado. O modelo da Tr?plice H?lice ? direcionado para a economia baseada no conhecimento. Nos ?ltimos seis anos o Governo Federal, atrav?s da Financiadora de Estudos e Projetos (FINEP), investiu em projetos de inova??o tecnol?gica, subven??o econ?mica, cerca de R$ 1 bilh?o, apoiando mais de 800 projetos com estes recursos. Segundo dados do MCTI, a regi?o Nordeste, ao longo dos anos 2000 a 2010, aumentou os disp?ndios em Ci?ncia e Tecnologia (considerando as atividades de pesquisa e desenvolvimento mais atividades cient?ficas e correlatas) dos Governos estaduais em rela??o ?s suas receitas totais. Em 2000, 0,51% das receitas totais eram investidos em C&T, enquanto em 2010 este valor passou a ser de 1,31%. Entre os nove Estados, a Para?ba tem destaque. Em 2000, 0,33% de suas receitas totais foram direcionadas para inova??o, alcan?ando 2,04% em 2010, o maior aumento da regi?o. Enquanto o RN investiu 0,24% em 2000 e em 2010, alcan?ou a marca de 1,42%. Segundo o IBGE, no per?odo 2000-2011, as micro e pequenas empresas suplantaram a barreira dos 6 milh?es de estabelecimentos. Em 2000, havia 4,2 milh?es de estabelecimentos, enquanto em 2011 eram 6,3 milh?es de estabelecimentos em atividade. Portanto, em todo o per?odo, houve uma cria??o de aproximadamente 2,1 milh?es de novos estabelecimentos. Entre 2000 e 2011, as micro e pequenas empresas criaram 7,0 milh?es de empregos com carteira assinada, 8,6 milh?es de postos de trabalho em 2000, para 15,6 milh?es em 2011. Diante deste cen?rio, mostra-se a import?ncia deste estudo no que se refere ao investimento dos Governos em PD&I em micro e pequenas empresas. Este trabalho tem como objetivo analisar a intera??o Universidades Empresas - Governo no desenvolvimento da inova??o em micro e pequenas empresas do Rio Grande do Norte participantes dos editais do Inova da FAPERN. Optou-se por adotar como m?todo de pesquisa o estudo de caso, quanto ao procedimento da pesquisa, explorat?ria-descritiva, sobre documentos e com coordenadores e pesquisadores dos projetos de inova??o aprovados pelo PAPPE Subven??o (Inova-RN I, II e III). A coleta de dados foi feita atrav?s do relat?rio confeccionado pela FAPERN intitulado: Avalia??o das empresas financiadas e apoiadas pelo Programa Subven??o ? Inova??o Tecnol?gica para Micro e Pequenas Empresas do RN - INOVA-RN (2010) e aplica??o de question?rio com 40 perguntas fechadas e 1 aberta, para 30 afirmativas compostas com base na escala Likert de 5 pontos. Quanto ? an?lise dos dados foi qualitativa e quantitativa. O estudo proporcionou identificar a import?ncia e os entraves oriundos da rela??o Governo, Empresa (micro e pequena) e Universidade como essencial para o desenvolvimento econ?mico da regi?o. Foi identificado tamb?m que dos projetos de inova??o, 70% dos produtos ou servi?os originados das pesquisas foram para o mercado, destes, 50% geraram patente para a empresa e 80% publica??es de artigos cient?ficos

Receptores nucleares formam uma superfamília de proteínas responsáveis pela regulação da expressão de genes. Estruturalmente, são formados por três domínios: um domínio N-terminal bastante variável, um domínio altamente conservado de ligação com o DNA e um domínio C-terminal, menos conservado, denominado domínio de ligação com o ligante (LDB). Diversos experimentos mostram que a interação com o ligante afeta a estrutura e a mobilidade da hélice C-terminal dos receptores nucleares (hélice 12 do domínio de ligação com o ligante), sendo o principal mecanismo de ativação e repressão da transcrição. As primeiras estruturas de LBDs de receptores nucleares revelaram importantes diferenças entre estruturas contendo ligantes (holo) e estruturas apo, principalmente no que diz respeito a posição da hélice 12: em estruturas apo, foi observada a H12 em uma conformação aberta, expondo o sítio de ligação com o ligante, enquanto que em estruturas holo, foi observada a H12 em uma conformação fechada, dobrada sobre o corpo do LBD e envolvendo completamente o ligante. Essa diferença sugeriu um mecanismo para a entrada e saída de ligantes do sítio de ligação denominado modelo da ratoeira, entretanto, esse modelo apresenta diversas inconsistências e tem sido desacreditado. Estudos experimentais e teóricos recentes mostram que a hélice 12 é mais móvel na ausência de ligantes, entretanto, esses estudos não fornecem evidencias de que o aumento da mobilidade da está associado com o deslocamento da H12 em relação ao corpo do LBD, como sugerido pelo modelo da ratoeira. Embora esteja claro que a hélice 12 é mais móvel na ausência de ligantes, a dimensão da variação conformacional sofrida pela hélice 12 ainda não está clara. Nesse trabalho buscamos a construção de um modelo capaz de dimensionar a mobilidade da hélice 12 através da comparação direta entre simulações de dinâmica molecular e experimentos de anisotropia de fluorescência resolvida no tempo. Utilizando simulações de dinâmica molecular reproduzimos experimentos de anisotropia de fluorescência acoplando a sonda cys-flúor a hélice 12 do PPARγ para estudar sua mobilidade. Mostramos que as observações experimentais só podem ser explicadas por conformações onde a sonda fluorescente permanece presa a superfície do LBD. Foi mostrado também que curvas de anisotropia com decaimentos comparáveis com os decaimentos experimentais estão associados a pequenas variações conformacionais de hélice 12. Simulações para dois modelos de apo-PPARγ com a H12 aberta em relação ao corpo do LBD e para as estruturas cristalográficas de apo-RXR e apo-ER, onde a H12 também adota uma conformação aberta, revelaram curvas de anisotropia com decaimentos mais rápidos que os experimentais. Esses resultados implicam em um modelo onde a H12 sofre alterações conformacionais locais, não apresentando variações tão dramáticas como o proposto pelo modelo da ratoeira. / Nuclear Hormone Receptors comprise a protein superfamily responsible for regulation of gene expression. Structurally, they are composed by three domains: a variable N-terminal domain, a highly conserved DNA-binding domain (DBD), and a less conserved C-terminal domain, known as ligand binding domain (LBD). Many experiments have shown that the interaction with ligands affects the structure and the mobility of nuclear receptors C-terminal helix (LBDs Helix 12), being the main mechanism of transcription activation and repression. The first nuclear receptor LBDs structures revealed important differences between ligand bound (holo) and apo-structures concerning the position of the H12: in apo structures, H12 adopted an open conformation, exposing the ligand binding pocket, whereas in holo structures, the H12 was closed, packed over the body of the LBD, burying completely the ligand. This difference suggested a mechanism for ligand entry and exit from the binding pocket called mouse-trap model, however this model has several inconsistencies and has been discredited. Recent experimental and theoretical studies have shown that H12 is more labile in the absence of ligand, but these studies dont provide evidences that the increase in the mobility is associated with the detachment of H12 from the body of the LBD as suggested by the mouse-trap model. Although its clear that H12 is more flexible in the absence of ligands, the size of the conformational changes undergone by H12 is not yet clear. In this work we seek to construct a definitive model for the range of motions that H12 may undergo in the presence or absence of ligand using molecular dynamics simulations. Through direct comparison between molecular dynamics simulations and time-resolved fluorescence anisotropy experiments, we show that experimental observation can only be explained by conformations where the fluorescent probe is interacting with the surface of the PPARγ surface. We also show that simulations with anisotropy decay rates comparable to the experimental decay are associated with small helix 12 conformational changes. Simulations with two models of apo-PPARγ with H12 detached from the body of the LBD and with crystallographic structures of apo-RXR and apo-ER, where the H12 also is in an open conformation, display anisotropy decay rates significantly faster than the experimental ones. These results imply a model for the molecular mobility of the LBD where H12 undergoes local conformational changes and should exhibit dynamic properties less dramatic than proposed by the mouse trap model.

This master’s thesis is focused on the properties and types of helical antennas. The helical antenna work in the different modes. These modes are described in this thesis. There are also discussed possibility for design a dual-band helical antennas. The main aim of this work is the selection of a suitable solution and design a dual-band helical antenna for the WiFi band working at resonance frequencies of 2,4 GHz and 5 GHz. The simulation of this antenna was performed in the program CST Microwave studio.

Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs) and signal peptides (SPs) where sequence similarity is necessarily a consequence of physical requirements rather than common ancestry. Since the matching of SPs/TMs creates the illusion of matching hydrophobic cores, the inclusion of SPs/TMs into domain models can give rise to wrong annotations. More than 1001 domains among the 10,340 models of Pfam release 23 and 18 domains of SMART version 6 (out of 809) contain SP/TM regions. As expected, fragment mode HMM searches generate promiscuous hits limited to solely the SP/TM part among clearly unrelated proteins. More worryingly, this work shows explicit examples that the scores of clearly false-positive hits, even in globalmode searches, can be elevated into the significance range just by matching the hydrophobic runs. In the PIR iProClass database v3.74 using conservative criteria, this study finds that at least between 2.1% and 13.6% of its annotated Pfam hits appear unjustified for a set of validated domain models. Thus, false positive domain hits enforced by SP/TM regions can lead to dramatic annotation errors where the hit has nothing in common with the problematic domain model except the SP/TM region itself. A workflow of flagging problematic hits arising from SP/TM-containing models for critical reconsideration by annotation users is provided. While E-value guided extrapolation of protein domain annotation from libraries such as Pfam with the HMMER suite is indispensable for hypothesizing about the function of experimentally uncharacterized protein sequences, it can also complicate the annotation problem. In HMMER2, the E-value is computed from the score via a logistic function or via a domain model-specific extreme value distribution (EVD); the lower of the two is returned as E-value for the domain hit in the query sequence. We demonstrated that, for thousands of domain models, this treatment results in switching from the EVD to the statistical model with the logistic function when scores grow (for Pfam release 23, 99% in the global mode and 75% in the fragment mode). If the score corresponding to the breakpoint results in an E-value above a user-defined threshold (e.g., 0.1), a critical score region with conflicting E-values from the logistic function (below the threshold) and from EVD (above the threshold) does exist. Thus, this switch will affect E-value guided annotation decisions in an automated mode. To emphasize, switching in the fragment mode is of no practical relevance since it occurs only at E-values far below 0.1. Unfortunately, a critical score region does exist for 185 domain models in the hmmpfam and 1748 domain models in the hmmsearch global-search mode. For 145 out the respective 185 models, the critical score region is indeed populated by actual sequences. In total, 24.4% of their hits have a logistic function-derived E-value<0.1 when the EVD provides an E-value>0.1. Examples of false annotations are provided and the appropriateness of a logistic function as alternative to the EVD is critically discussed. This work shows that misguided E-value computation coupled with non-globular regions embedded in domain model library not only causes annotation errors in public databases but also limits the extrapolation power of protein function prediction tasks. So far, the preceding work has demonstrated that sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches from non-polar residues. We found that there are two types of transmembrane helices (TMs) in membrane-associated proteins. On the one hand, there are so-called simple TMs with elevated hydrophobicity, low sequence complexity and extraordinary enrichment in long aliphatic residues. They merely serve as membrane-anchoring device. In contrast, so-called complex TMs have lower hydrophobicity, higher sequence complexity and some functional residues. These TMs have additional roles besides membrane anchoring such as intramembrane complex formation, ligand binding or a catalytic role. Simple and complex TMs can occur both in single- and multi-membrane-spanning proteins essentially in any type of topology. Whereas simple TMs have the potential to confuse searches for sequence homologues and to generate unrelated hits with seemingly convincing statistical significance, complex TMs contain essential evolutionary information. For extending the homologyconcept onto membrane proteins, we provide a necessary quantitative criterion to distinguish simple TMs in query sequences prior to their usage in homology searches based on assessment of hydrophobicity and sequence complexity of the TM sequence segments. Theoretical insights from this work were applied to problems of function prediction for specific uncharacterized gene/protein sequences (for example, APMAP and ARXES) and for the functional classification of TM-containing proteins.

No description available.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19261号 / 理博第4116号 / 新制||理||1592(附属図書館) / 32263 / 京都大学大学院理学研究科化学専攻 / (主査)教授 杉山 弘, 教授 三木 邦夫, 教授 藤井 紀子 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

ACP interacts with diverse proteins in an unknown way. Possibly there is a similar mode of interaction between ACP and all ACP-binding proteins, the amphiphilic helix. The hydrophobicities of helices from 4 different ACPs were compared. Hydrophobic moment plots were prepared for ACP helices and those of many EF hand calcium-binding proteins. Both groups of proteins occupied the same region of the plot.

No description available.

Denna studie undersöker hur hybridorganisationer hanterar sin organisationsidentitet och dekonflikterande institutionella kraven från kontexten Triple Helix. Detta genomförs genom endeduktiv komparativ fallstudie av tre statligt ägda holdingbolag och ett privatägt holdingbolagvid svenska universitet. Vår studie visar hur organisationsidentiteten inom dessa hybrider tar enmer eller mindre hybrid karaktär bland grupper i olika organisationsnivåer. Detta stärker deutvalda hybridernas multivokalitet, definierat som dess förmåga att skaffa sig legitimitet blandintressentgrupper från olika institutionella ordningar. Hybridorganisationens multivokalitet kandärav ses som en nödvändighet eller krav för dess överlevnad. Våra resultat bekräftar tidigarelitteraturs resultat om att hybriditeten går att hantera aktivt, genom separering av logiker ochsamordning kring ett gemensamt mål. Uppsatsen påvisar hur i kontexten Triple Helix,hybridorganisationen har möjlighet att separera aktiviteterna mellan sin och universitetetsdominerande logik. Fördelningen och samarbetet med universitet etableras i en process för attskaffa sig legitimitet gentemot vissa huvudintressenter. Processen är tänkt för en gradvistransformering från en logik till en annan av intressentgrupper som stödjer universitetsdominerande logik. Detta kompletterar tidigare litteratur om hantering av hybriditet. Vår studiebidrar med empiriskt stöd att teorier om organisationsidentitet och den institutionella teorin kankomplettera varandra i analysen av hybrider. / This study explores how hybrid organizations manage their organizational identity and theconflicting institutional demands from the context of Triple Helix. We conducted a deductivecomparative case study of three state owned holding companies and one private holdingcompany managed by Swedish universities. Our study suggests that inside hybrids,organizational identity takes more or less hybrid form among groups of different organizationallevels. This strengthens these hybrids' multivocality, defined by its ability to gain legitimacyamong stakeholders from different institutional orders. For the survival of the hybridorganization multivocality may be viewed upon as a requirement. The results of the studyconfirm previous research that hybridity is manageable through separation of the logics and bycoordination of common goals. The study demonstrates that in the context of Triple Helix, thehybrid organization has the opportunity to collaborate with the university to divide and allocateactivities characterized by their dominating logics. The allocation and collaboration with theuniversity is established in a process in order for the hybrid to gain legitimacy towards groups ofmain stakeholders. The process is thought of as a gradual transformation from one logic to theother of stakeholders belonging to the dominating logic of the university. These findingscomplete previous findings about the management of organizational hybridity. Our study ingeneral contributes with empirical data that the organizational identity- and institutional theoryperspectives may complete each other in the analysis of hybrid organizations.

The digital development of the 1990s and early 2000s had a major effect on the Swedish media industry, including newspapers. Still, it is not clear what role academia had during this process. Therefore, the purpose of this thesis is to examine the role of the university in the digital development of the Swedish news media industry. To investigate this, a case study has been performed, focusing on the Swedish technical university KTH Royal Institute of Technology. A theoretical background was created, consisting of the three waves of digitalization by Yoo et al. (2010), the emerge of the entrepreneurial university, and the Triple Helix model. Data were collected through archival research consisting of the Swedish magazines Ny Teknik and Pressens Tidning, and semi-structured interviews with seven individuals. The results showed that the digital development of the Swedish news media industry was characterized by the rise of the Internet, which generated both new news channels and contributed to digitally develop the printing industry. The results indicate that KTH’s role in this development was to provide the industry with well-educated engineers as well as innovations through research projects, to help media companies handle the opportunities and the challenges the digital development offered. The results also indicate that KTH in some ways can be compared to an entrepreneurial university, since the university has contributed to economic activities in society. However, most of these activities would not have been possible without the participation of the media industry, demonstrating that the concept of the Triple Helix to some extent also can be applied to this case study. / Den digitala utvecklingen av 1990- och tidigt 2000-tal hade en stor effekt på den svenska medieindustrin, inklusive tidningsindustrin. Det är dock inte klart vad för roll universiteten hade under denna process. Syftet med denna uppsats är därför att undersöka universitetets roll i den digitala utvecklingen av den svenska nyhetsmedieindustrin. För att undersöka detta har en fallstudie genomförts, som fokuserar på det svenska tekniska universitetet KTH Kungliga Tekniska Högskolan. En teoretisk bakgrund togs fram, bestående av de tre vågorna av digitalisering av Yoo et al. (2010), framväxten av det entreprenöriella universitetet och modellen Triple Helix. Data samlades in genom arkivforsknings bestående av de svenska tidningarna Ny Teknik och Pressens Tidning, samt semistrukturerade intervjuer med sju personer. Resultaten visade att den digitala utvecklingen av den svenska nyhetsmedieindustrin karaktäriserades av uppkomsten av Internet, vilket genererade både nya nyhetskanaler och bidrog till en digital utveckling av tryckeribranschen. Resultaten indikerar att KTH:s roll i denna utveckling bestod av att bidra med välutbildade ingenjörer till industrin, likväl som innovation genom forskningsprojekt, vilket hjälpte industrin hantera möjligheterna och utmaningarna som den digitala utvecklingen medförde. Resultaten indikerar också att KTH i viss utsträckning kan jämföras med det entreprenöriella universitetet, eftersom universitetet har bidragit till ekonomiska aktiviteter i samhället. De flesta av dessa aktiviteter hade dock inte varit möjliga utan medieindustrins delaktighet, vilket demonstrerar att modellen Triple Helix i viss utsträckning kan appliceras på denna fallstudie.