Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs

The HIV Reverse Transcriptase and Protease Sequence Database is an on-line relational database that catalogs evolutionary and drug-related sequence variation in the human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease enzymes, the molecular targets of anti-HIV therapy (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protease sequences, including submissions from International Collaboration databases and sequences published in journal articles. Sequences are linked to data about the source of the sequence sample and the antiretroviral drug treatment history of the individual from whom the isolate was obtained. During the past year 3500 sequences have been added and the data model has been expanded to include drug susceptibility data on sequenced isolates. Database content has also been integrated with didactic text and the output of two sequence analysis programs.

Genetic heterogeneity in cystinuria: the SLC3A1 gene is linked to type I but not to type III cystinuria.

Cystinuria is an autosomal recessive amino-aciduria where three urinary phenotypes have been described (I, II, and III). An amino acid transporter gene, SLC3A1 (formerly rBAT), was found to be responsible for this disorder. To assess whether mutations in SLC3A1 are involved in different cystinuria phenotypes, linkage with this gene and its nearest marker (D2S119) was analyzed in 22 families with type I and/or type III cystinuria. Linkage with heterogeneity was proved (alpha = 0.45; P < 0.008). Type I/I families showed homogeneous linkage to SLC3A1 (Zmax > 3.0 at theta = 0.00; alpha = 1), whereas types I/III and III/III were not linked. Our data suggest that type I cystinuria is due to mutations in the SLC3A1 gene, whereas another locus is responsible for type III. This result establishes genetic heterogeneity for cystinuria, classically considered as a multiallelic monogenic disease.

Volunteer Engagement: Does Engagement Predict the Degree of Satisfaction among New Volunteers and the Commitment of Those who have been Active Longer?

This study examines the concept of engagement in samples of volunteers from different non-profit organisations. Study 1 analyzes the psychometric properties of the abbreviated version of the Utrecht Work Engagement Scale (UWES) (Schaufeli, Bakker, & Salanova, 2006a). Two factorial structures are examined: one-dimensional and three-dimensional structures. Based on the Three-Stage Model of Volunteers’ Duration of Service (Chacón, Vecina, & Dávila, 2007), Study 2 investigates the relationship between engagement, volunteer satisfaction, and intention to remain in a sample of new volunteers and the relationship between engagement, organisational commitment, and intention to remain in a sample of veteran volunteers. Moderated mediation analysis is provided using duration of service as a moderator in order to set a splitting point between new and veteran volunteers. The results of the confirmatory factor analysis suggest that the three-factor model fits better to the data. Regarding the structural models, the first one shows that engagement is crucial to volunteer satisfaction during the first stage, while volunteer satisfaction is the key variable in explaining intention to continue. The second structural model shows that engagement reinforces the participant’s commitment to the organisation, while organizational commitment predicts intention to continue. Both models demonstrate a notable decline when samples are changed.

An Independent Art Movement: The Independent Artist, Community Television, and the Age of Information

The history of community television shows that it has been a home to activist and non-profit organizations that have created programs focused on freedom of speech. This project proposes that community television is also a place where artists can have freedom of artistic expression. The reflective paper reviews the creation of my film designed to inform and attract artists to community television. In it I critically reflect on the artistic, technical, artistic/technical, and production changes made throughout my journey from being a visual artist to becoming a video-artist. The reflective paper, along with the film, act as a wake-up call to artists who are unaware of community television and the advantages it has to offer them.

Privacy in the Smart City: Implications of Sensor Network Design, Law, and Policy for Locational Privacy

Thesis (Master's)--University of Washington, 2016-06

DESEMPENHO DE ORGANIZAÇÃO SOCIAL (OS) NO GERENCIAMENTO DE ORGANISMOS PÚBLICOS: ESTUDO DESCRITIVO-EXPLORATÓRIO DO CENTRO NACIONAL DE PESQUISA EM ENERGIA E MATERIAIS - CNPEM

Este trabalho discutiu o desempenho do Centro Nacional de Pesquisa em Energia e Materiais CNPEM, que deu início às suas atividades como Associação Brasileira de Tecnologia de Luz Síncrotron - ABTLuS, Organização Social (OS), entidade da sociedade civil, sem fins lucrativos, disciplinada pela Lei 9.637 de 15 de maio de 1998, para gerir organismos públicos mediante a assinatura de contrato de gestão baseado em metas a serem cumpridas. O modelo nasceu concomitantemente com a criação do Ministério da Administração e Reforma do Estado MARE, na gestão do ministro Luiz Carlos Bresser Pereira, no governo do presidente Fernando Henrique Cardoso - FHC, tendo como princípio básico a prestação de serviços sociais, nas áreas de cultura, educação, pesquisa científica, proteção e preservação do meio ambiente e saúde, na expectativa de que ele pudesse prestar melhores serviços do que as empresas estatais e as entidades da administração direta. Hoje, dez anos se passaram e o CNPEM continua prestando serviços na área de pesquisa científica ao CNPq e ao MCT, apesar de não haver apoio para a criação de novas OS na esfera do governo federal, o que indicou ameaças ao seu ciclo de vida. A pesquisa desenvolveu-se através de estudo descritivo-exploratório, interpretando dados por intermédio do processo de hermenêutica para interpretação de dados retirados dos documentos institucionais, com conclusão favorável à continuidade do modelo, tendo em vista que a pesquisa demonstra que ele é legal, legítimo e competente no cumprimento das metas e missão, bem como está em plena forma física, sem ameaças ao seu ciclo de vida, demonstrando que tem muito a oferecer para a ciência brasileira e, como não poderia deixar de ser, a milhares de usuários espalhados pelo Brasil e o mundo.

XBRL:an (open) source of enlightenment or disillusion?

Extensible Business Reporting Language (XBRL) is being adopted by European regulators as a data standard for the exchange of business information. This paper examines the approach of XBRL International (XII) to the meta-data standard's development and diffusion. We theorise the development of XBRL using concepts drawn from a model of successful open source projects. Comparison of the open source model to XBRL enables us to identify a number of interesting similarities and differences. In common with open source projects, the benefits and progress of XBRL have been overstated and 'hyped' by enthusiastic participants. While XBRL is an open data standard in terms of access to the equivalent of its 'source code' we find that the governance structure of the XBRL consortium is significantly different to a model open source approach. The barrier to participation that is created by requiring paid membership and a focus on transacting business at physical conferences and meetings is identified as particularly critical. Decisions about the technical structure of XBRL, the regulator-led pattern of adoption and the organisation of XII are discussed. Finally areas for future research are identified.

Zero weights and non-zero slacks:different solution to the same problem

This paper re-assesses three independently developed approaches that are aimed at solving the problem of zero-weights or non-zero slacks in Data Envelopment Analysis (DEA). The methods are weights restricted, non-radial and extended facet DEA models. Weights restricted DEA models are dual to envelopment DEA models with restrictions on the dual variables (DEA weights) aimed at avoiding zero values for those weights; non-radial DEA models are envelopment models which avoid non-zero slacks in the input-output constraints. Finally, extended facet DEA models recognize that only projections on facets of full dimension correspond to well defined rates of substitution/transformation between all inputs/outputs which in turn correspond to non-zero weights in the multiplier version of the DEA model. We demonstrate how these methods are equivalent, not only in their aim but also in the solutions they yield. In addition, we show that the aforementioned methods modify the production frontier by extending existing facets or creating unobserved facets. Further we propose a new approach that uses weight restrictions to extend existing facets. This approach has some advantages in computational terms, because extended facet models normally make use of mixed integer programming models, which are computationally demanding.

Characterization of a microbial transglutaminase cross-linked type II collagen scaffold

This study investigated the effect on the mechanical and physicochemical properties of type II collagen scaffolds after cross-linking with microbial transglutaminase (mTGase). It is intended to develop a collagen-based scaffold to be used for the treatment of degenerated intervertebral discs. By measuring the amount of ε-(γ-glutamyl)lysine isodipeptide formed after cross-linking, it was determined that the optimal enzyme concentration was 0.005% (w/v). From the production of covalent bonds induced by mTGase cross-linking, the degradation resistance of type II collagen scaffolds can be enhanced. Rheological analysis revealed an almost sixfold increase in storage modulus (G') with 0.005% (w/v) mTGase cross-linked scaffolds (1.31 ± 0.03 kPa) compared to controls (0.21 ± 0.01 kPa). There was a significant reduction in the level of cell-mediated contraction of scaffolds with increased mTGase concentrations. Cell proliferation assays showed that mTGase cross-linked scaffolds exhibited similar cytocompatibility properties in comparison to non-cross-linked scaffolds. In summary, cross-linking type II collagen with mTGase imparted more desirable properties, making it more applicable for use as a scaffold in tissue engineering applications. © Mary Ann Liebert, Inc.

The usability of semantic search tools:a review

The goal of semantic search is to improve on traditional search methods by exploiting the semantic metadata. In this paper, we argue that supporting iterative and exploratory search modes is important to the usability of all search systems. We also identify the types of semantic queries the users need to make, the issues concerning the search environment and the problems that are intrinsic to semantic search in particular. We then review the four modes of user interaction in existing semantic search systems, namely keyword-based, form-based, view-based and natural language-based systems. Future development should focus on multimodal search systems, which exploit the advantages of more than one mode of interaction, and on developing the search systems that can search heterogeneous semantic metadata on the open semantic Web.

Almost Separable Data Aggregation by Layers of Formal Neurons

Information extraction or knowledge discovery from large data sets should be linked to data aggregation process. Data aggregation process can result in a new data representation with decreased number of objects of a given set. A deterministic approach to separable data aggregation means a lesser number of objects without mixing of objects from different categories. A statistical approach is less restrictive and allows for almost separable data aggregation with a low level of mixing of objects from different categories. Layers of formal neurons can be designed for the purpose of data aggregation both in the case of deterministic and statistical approach. The proposed designing method is based on minimization of the of the convex and piecewise linear (CPL) criterion functions.

Importance and Benefits of OPEN SCIENCE for Ubiquitous Sharing, Dissemination and Impact

While openness is well applied to software development and exploitation (open sources), and successfully applied to new business models (open innovation), fundamental and applied research seems to lag behind. Even after decades of advocacy, in 2011 only 50% of the public-funded research was freely available and accessible (Archambault et al., 2013). The current research workflows, stemming from a pre-internet age, result in loss of opportunity not only for the researchers themselves (cf. extensive literature on topic at Open Access citation project, http://opcit.eprints.org/), but also slows down innovation and application of research results (Houghton & Swan, 2011). Recent studies continue to suggest that lack of awareness among researchers, rather than lack of e-infrastructure and methodology, is a key reason for this loss of opportunity (Graziotin 2014). The session will focus on why Open Science is ideally suited to achieving tenure-relevant researcher impact in a “Publish or Perish” reality. Open Science encapsulates tools and approaches for each step along the research cycle: from Open Notebook Science to Open Data, Open Access, all setting up researchers for capitalising on social media in order to promote and discuss, and establish unexpected collaborations. Incorporating these new approaches into a updated personal research workflow is of strategic beneficial for young researchers, and will prepare them for expected long term funder trends towards greater openness and demand for greater return on investment (ROI) for public funds.

A versenyképesség társadalmi környezete

Kutatásunk alapvetése, hogy egy ország versenyképessége az értékteremtő munkamegosztást támogató teljes közösségi intézményrendszer sikeres működésén múlik. Munkánkkal arra kerestük a választ, milyen értékek és motivációk alakítják a magyar gazdaság intézményrendszerét. Nem a hivatalos magatartási szabályok statikus elemzésére koncentráltunk, hanem a normák, konvenciók és innovációk világára, az intézményrendszer jövőjét befolyásoló dinamikus elemekre. Elemzésünk fókuszában a társadalmi és vállalkozói értékek, a gazdaságpolitika formálók versenyképességi narratívái, a helyi gazdaságok versenyképességi tényezői, a versenyképesség javítását szolgáló magánkezdeményezések és a nonprofit szektor működése álltak. Fő eredményünk, hogy a Magyarország jövőbeli versenyképességét befolyásoló tudati elemek - a gazdasági döntéshozók motivációi és normái – megfelelő alapot teremtenek a gazdaságunk versenyképességét megerősítő üzleti, civil és kormányzati kezdeményezések számára. Magas közösségi és morális elvárások jellemzik a lakosság és a vállalkozók értékrendjét. A gazdaságpolitika-alkotók nyitottak az intézményi problémákra, a magyar véleményformálók körében egyetértés van a fő versenyképességi kihívásokat illetően. Jól azonosíthatóak a szervezők erőfeszítéseit kompenzálni képes versenyképességi összefogások keretei. A helyi gazdaságfejlesztés intézményei alakulóban vannak. A nonprofit szektor működési viszonyainak bizonytalansága ellenére a közcélúság és a versenyképesség közös területein (mint az atipikus foglalkoztatás) jól teljesít. Ezek az eredmények egyszerre nyitnak perspektívát a tudományos vizsgálódás és a gyakorlati cselekvés számára. Az önérdek és a közösségi értékteremtő képesség javításának motivációja közötti kapcsolat tudományos vizsgálata, a társadalmi innovációk kutatása a versenyképesség javíthatóságának kereteit tárhatja fel. Az üzleti, civil vagy kormányzati szereplők pedig akkor tudják a fogyasztói, közösségi elvárásokat sikeresen összeegyeztetni stratégiai céljaikkal, ha a gazdasági és társadalmi szereplők normáihoz, konvencióihoz igazítva alakítják ki intézményformáló stratégiáikat. __________ The competitiveness of nations is based on the successful function of the institutions that support the division of labor on value creation – this is the basic principle of this research. Our project investigates what values and motivations shape the institutional setting of Hungarian economy. We study the world of norms, conventions and innovations – the elements that shape the institutions. The static analysis of official rules has only a minor role in this approach. Research focuses (1) on the value system of entrepreneurs (2), on the mind setting of public managers and executives of economic policy (3) on the factors of local economic competitiveness, (4) on the actions of private and non-profit sector in order to enhance competitiveness. The main finding of this research is that the cognitive factors that shape the competitiveness of Hungary – the norms and motivations of decision makers in the economy – give a positive support for the competitiveness strengthening initiatives of business, non-profit and public sectors. The studies on the values system of entrepreneurs and citizens show that expectations and moral values connected to competitiveness are strong. The public managers of economic policy are open-minded and there is a general consensus of experts, business and politics on the key competitiveness challenges of Hungary. There are well defined frameworks to conceptualize the schemes that make organizers’ efforts affordable in private initiatives for competitiveness. There are various developments on the field of institutions for local economic development. The nonprofit sector has good results on the common fields of competiveness and equity (like atypical forms of employment) despite the uncertainties in the background of the sector. These results open perspectives both for scientific research and practical applications. The research on connection between individual goals and motivation to improve value creating ability of the society and the study of social innovation reveal new aspects of competitiveness. Business, non-profit or public leaders can better synchronize their strategies with the expectation of consumers, communities and constituencies if their intentions to shape institutional settings fit better to the norms and conventions of the social and economic stakeholders.

An analysis of teachers' perceptions of informal science professional development

Science professional development, which is fundamental to science education improvement, has been described as being weak and fragmentary. The purpose of this study was to investigate teachers' perceptions of informal science professional development to gain an in-depth understanding of the essence of the phenomenon and related science-teaching dispositions. Based on the frameworks of phenomenology, constructivism, and adult learning theory, the focus was on understanding how the phenomenon was experienced within the context of teachers' everyday world. ^ Data were collected from eight middle-school teachers purposefully selected because they had participated in informal programs during Project TRIPS (Teaching Revitalized Through Informal Programs in Science), a collaboration between the Miami-Dade school district, government agencies (including NASA), and non-profit organizations (including Audubon of Florida). In addition, the teachers experienced hands-on labs offered through universities (including the University of Arizona), field sites, and other agencies. ^ The study employed Seidman's (1991) three-interview series to collect the data. Several methods were used to enhance the credibility of the research, including using triangulation of the data. The interviews were transcribed, color-coded and organized into six themes that emerged from the data. The themes included: (a) internalized content knowledge, (b) correlated hands-on activities, (c) enhanced science-teaching disposition, (d) networking/camaraderie, (e) change of context, and (f) acknowledgment as professionals. The teachers identified supportive elements and constraints related to each theme. ^ The results indicated that informal programs offering experiential learning opportunities strengthened understanding of content knowledge. Teachers implemented hands-on activities that were explicitly correlated to their curriculum. Programs that were conducted in a relaxed context enhanced teachers' science-teaching dispositions. However, a lack of financial and administrative support, perceived safety risks, insufficient reflection time, and unclear itineraries impeded program implementation. The results illustrated how informal educators can use this cohesive model as they develop programs that address the supports and constraints to teachers' science instruction needs. This, in turn, can aid teachers as they strive to provide effective science instruction to students; notions embedded in reforms. Ultimately, this can affect how learners develop the ability to make informed science decisions that impact the quality of life on a global scale. ^

The capacity challenges of nonprofit, community-based organizations

This mixed method case study explored the capacity challenges of neighbourhood based community centres related to the areas of governance and leadership, program delivery, financial management and human resources. The study involved the examination of three community centres with multi-mandates (i.e., provide programs and services to individuals from pre-school to seniors in the areas of social, educational, recreational and health) and utilized three phases of data collection: 1) surveys with board members; 2) focus groups with all boards and staff; and 3) document review which examined pertinent organizational policies and procedures. Questions were aimed at gaining an understanding of some of the challenges faced by staff and administrators of neighbourhood based community centres, as there a gap in the research in this particular area. Research findings identified a number of related challenges facing non-profit organizations specifically in the areas of funding and staffing and how these challenges impact both day to day operations and longer term sustainability. More research is needed with nonprofit organizations that have these broader mandates and diverse operational challenges, hence greater capacity building challenges.