iProClass: an integrated, comprehensive and annotated protein classification database

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200 000 non-redundant PIR and SWISS-PROT proteins organized with more than 28 000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at http://pir.georgetow n.edu/iproclass/.

RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression

The RECODE database is a compilation of ‘programmed’ translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding. The database is freely available at http://recode.genetics.utah.edu/.

Republican Scientific-Medical Library, The Republic of Armenia: progress and programs*

In 1990, the Republican Scientific-Medical Library (RSML) of the Ministry of Health of Armenia in collaboration with the Fund for Armenian Relief created a vision of a national library network supported by information technology. This vision incorporated four goals: (1) to develop a national resource collection of biomedical literature accessible to all health professionals, (2) to develop a national network for access to bibliographic information, (3) to develop a systematic mechanism for sharing resources, and (4) to develop a national network of health sciences libraries. During the last decade, the RSML has achieved significant progress toward all four goals and has realized its vision of becoming a fully functional national library. The RSML now provides access to the literature of the health sciences including access to the Armenian medical literature, provides education and training to health professionals and health sciences librarians, and manages a national network of libraries of the major health care institutions in Armenia. The RSML is now able to provide rapid access to the biomedical literature and train health professionals and health sciences librarians in Armenia in information system use. This paper describes the evolution of the RSML and how it was accomplished.

Interaction of Cryptochrome 1, Phytochrome, and Ion Fluxes in Blue-Light-Induced Shrinking of Arabidopsis Hypocotyl Protoplasts1

Protoplasts isolated from red-light-adapted Arabidopsis hypocotyls and incubated under red light exhibited rapid and transient shrinking within a period of 20 min in response to a blue-light pulse and following the onset of continuous blue light. Long-persisting shrinkage was also observed during continuous stimulation. Protoplasts from a hy4 mutant and the phytochrome-deficient phyA/phyB double mutant of Arabidopsis showed little response, whereas those from phyA and phyB mutants showed a partial response. It is concluded that the shrinking response itself is mediated by the HY4 gene product, cryptochrome 1, whereas the blue-light responsiveness is strictly controlled by phytochromes A and B, with a greater contribution by phytochrome B. It is shown further that the far-red-absorbing form of phytochrome (Pfr) was not required during or after, but was required before blue-light perception. Furthermore, a component that directly determines the blue-light responsiveness was generated by Pfr after a lag of 15 min over a 15-min period and decayed with similar kinetics after removal of Pfr by far-red light. The anion-channel blocker 5-nitro-2-(3-phenylpropylamino)-benzoic acid prevented the shrinking response. This result, together with those in the literature and the kinetic features of shrinking, suggests that anion channels are activated first, and outward-rectifying cation channels are subsequently activated, resulting in continued net effluxes of Cl− and K+. The postshrinking volume recovery is achieved by K+ and Cl− influxes, with contribution by the proton motive force. External Ca2+ has no role in shrinking and the recovery. The gradual swelling of protoplasts that prevails under background red light is shown to be a phytochrome-mediated response in which phytochrome A contributes more than phytochrome B.

Post T Tauri stars in the solar neighborhood: isolated or members of young associations and moving groups

Post T Tauri stars (PTTS) are late-type stars in the age range between 10 and 100 Myr filling the gap between T Tauri (TTs) and zero-age: main sequence phases. This period of evolution remains ambiguous and until now different studies of young stars have failed to find the numbers of PTTS that are expected. In the last years, some PTTS have been identified among the X-ray detected pre-main sequence stars in some star-forming regions. More recently, additional PTTS have been identified in young associations and moving groups (β Pic, TW Hya, Tucana/Horologium, and the AB Dor). However, many isolated PTTS still remain undiscovered. In this contribution, we compiled the PTTS previously identified in the literature, and identified new candidates using the information provided by the high resolution spectra obtained during our surveys of late-type stars possible members to young moving groups, FGK stars in the solar neighborhood, and RasTyc sample. To identify PTTS we applied an age-oriented definition using relative age indicators (Li abundance, chromospheric and coronal emission and the kinematics) as well as color-magnitude diagrams and pre-main sequence isochrones.

Discursive constructions of social and environmental accounting in Brazil: the case of Petrobras.

In the 29 years following \"Our Common Future\" by the United Nations, there is considerable debate among governments, civil society, interest groups and business organisations about what constitutes sustainable development, which constitutes evidence for a contested discourse concerning sustainability. The purpose of this study is to understand this debate in the developing economic context of Brazil, and in particular, to understand and critique the social and environmental accounting [SEA] discursive constructions relating to the State-owned, Petrobras as well as to understand the Brazilian literature on SEA. The discourse theory [DT]-based analysis employs rhetorical redescription to analyse twenty-two reports from Petrobras from 2004-2013. I investigate the political notions by employing the methodological framework of the Logics of Critical Explanation [LCE]. LCE engenders five methodological steps: problematisation, retroduction, logics (social, political and fantasmatic), articulation and critique. The empirical discussion suggests that the hegemony of economic development operates to obfuscate, rhetorically, the development of sustainability, so as to maintain the core business of Petrobras conceived as capital accumulation. Equally, these articulations also illustrate how the constructions of SEA operate to serve the company\'s purpose with few (none) profound changes in integration of sustainability. The Brazilian literature on SEA sustains the status quo of neo-liberal market policies that operate to protect the dominant business case approach to maintain an agenda of wealth-creation in relation to social and environmental needs. The articulations of the case manifested in policies regarding, for example, corruption, which involved over-payments for contracts and unsustainable practices relating to the use of fossil fuels and demonstrated that there was antagonism between action and disclosure. The corruption scandal that emerged after SEA disclosures highlighted the rhetorical nature of disclosure when financial resources were subtracted from the company for political parties and engineering contractors hid facts through incomplete disclosures. The articulations of SEA misrepresent a broader context of the meanings associated with sustainability, which restricted the constructions of SEA to principally serve and represent the intention of the most powerful groups. The significance of SEA, then is narrowed to represent particular interests. The study argues for more critical studies as limited Brazilian literature concerning SEA kept a \'safe distance\' from substantively critiquing the constructions of SEA and its articulations in the Brazilian context. The literature review and the Petrobras\' case illustrate a variety of naming, instituting and articulatory practices that endeavour to maintain the current hegemony of development in an emerging economy, which allows Petrobras to continue to exercise significant profit at the expense of the social and environmental. The constructed idea of development in Petrobras\' discourses emphasises a rhetoric of wider development, but, in reality, these discourses were the antithesis of political, social and ethical developmental issues. These constructions aim to hide struggles between social inequalities and exploitation of natural resources and constitute excuses about a fanciful notion of rhetorical and hegemonic neo-liberal development. In summary, this thesis contributes to the prior literature in five ways: (i) the addition of DT to the analysis of SEA enhances the discussion of political elements such as hegemony, antagonism, logic of equivalence/difference, ideology and articulation; (ii) the analysis of an emerging economy such as Brazil incorporates a new perspective of the discussion of the discourses of SEA and development; (iii) this thesis includes a focus on rhetoric to discuss the maintenance of the status quo; (iv) the holistic structure of the LCE approach enlarges the understanding of the social, political and fantasmatic logics of SEA studies and; (v) this thesis combines an analysis of the literature and the case of Petrobras to characterise and critique the state of the Brazilian academy and its impacts and reflections on the significance of SEA. This thesis, therefore, argues for more critical studies in the Brazilian academy due to the persistence of idea of SEA and development that takes-for-granted deep exclusions and contradictions and provide little space for critiques.

An Empirical Comparison of Reuse in Embedded and Nonembedded Systems

High-quality software, delivered on time and budget, constitutes a critical part of most products and services in modern society. Our government has invested billions of dollars to develop software assets, often to redevelop the same capability many times. Recognizing the waste involved in redeveloping these assets, in 1992 the Department of Defense issued the Software Reuse Initiative. The vision of the Software Reuse Initiative was "To drive the DoD software community from its current "re-invent the software" cycle to a process-driven, domain-specific, architecture-centric, library-based way of constructing software.'' Twenty years after issuing this initiative, there is evidence of this vision beginning to be realized in nonembedded systems. However, virtually every large embedded system undertaken has incurred large cost and schedule overruns. Investigations into the root cause of these overruns implicates reuse. Why are we seeing improvements in the outcomes of these large scale nonembedded systems and worse outcomes in embedded systems? This question is the foundation for this research. The experiences of the Aerospace industry have led to a number of questions about reuse and how the industry is employing reuse in embedded systems. For example, does reuse in embedded systems yield the same outcomes as in nonembedded systems? Are the outcomes positive? If the outcomes are different, it may indicate that embedded systems should not use data from nonembedded systems for estimation. Are embedded systems using the same development approaches as nonembedded systems? Does the development approach make a difference? If embedded systems develop software differently from nonembedded systems, it may mean that the same processes do not apply to both types of systems. What about the reuse of different artifacts? Perhaps there are certain artifacts that, when reused, contribute more or are more difficult to use in embedded systems. Finally, what are the success factors and obstacles to reuse? Are they the same in embedded systems as in nonembedded systems? The research in this dissertation is comprised of a series of empirical studies using professionals in the aerospace and defense industry as its subjects. The main focus has been to investigate the reuse practices of embedded systems professionals and nonembedded systems professionals and compare the methods and artifacts used against the outcomes. The research has followed a combined qualitative and quantitative design approach. The qualitative data were collected by surveying software and systems engineers, interviewing senior developers, and reading numerous documents and other studies. Quantitative data were derived from converting survey and interview respondents' answers into coding that could be counted and measured. From the search of existing empirical literature, we learned that reuse in embedded systems are in fact significantly different from nonembedded systems, particularly in effort in model based development approach and quality where the development approach was not specified. The questionnaire showed differences in the development approach used in embedded projects from nonembedded projects, in particular, embedded systems were significantly more likely to use a heritage/legacy development approach. There was also a difference in the artifacts used, with embedded systems more likely to reuse hardware, test products, and test clusters. Nearly all the projects reported using code, but the questionnaire showed that the reuse of code brought mixed results. One of the differences expressed by the respondents to the questionnaire was the difficulty in reuse of code for embedded systems when the platform changed. The semistructured interviews were performed to tell us why the phenomena in the review of literature and the questionnaire were observed. We asked respected industry professionals, such as senior fellows, fellows and distinguished members of technical staff, about their experiences with reuse. We learned that many embedded systems used heritage/legacy development approaches because their systems had been around for many years, before models and modeling tools became available. We learned that reuse of code is beneficial primarily when the code does not require modification, but, especially in embedded systems, once it has to be changed, reuse of code yields few benefits. Finally, while platform independence is a goal for many in nonembedded systems, it is certainly not a goal for the embedded systems professionals and in many cases it is a detriment. However, both embedded and nonembedded systems professionals endorsed the idea of platform standardization. Finally, we conclude that while reuse in embedded systems and nonembedded systems is different today, they are converging. As heritage embedded systems are phased out, models become more robust and platforms are standardized, reuse in embedded systems will become more like nonembedded systems.

Transgender Group Therapy: Process and Issues with Male to Female Clients

Transgender issues are garnering more attention within the mental health field. With the increased social awareness of transgender issues, the mental health field is recognizing the need for effective psychological services for this population. Transgender individuals face unique challenges related to gender non-conformity, the coming-out and transitioning processes, and in society at large, all of which can lead to a number mental health concerns. Group therapy is a promising treatment modality for transgender individuals. The purpose of this paper is to offer a rationale for the effectiveness of group therapy, and recommendations for best practices utilizing the current literature and my experience with facilitating a Male to Female transgender therapy group.

Narrative Therapy and Stigma Management: Restorying the Patient Experience of Being Told, “You have MS

The purpose of this investigation was to determine if the way patients are informed of the diagnosis of multiple sclerosis (MS) affects their feelings about themselves as people with MS. Building on illness narrative, I hoped to examine how patients “storied” their experience of being informed of the diagnosis of MS and whether this “storying” had a lasting impact on their self-concept. The alternative would be that no connection exists between how a neurologist informs a patient of the diagnosis and how a person makes sense of their diagnosis and life with MS. Due to study limitations (e.g., small sample size, threat of response bias), the results are unclear about whether the way in which the news is broken has a lasting effect on patients' perceptions. However, review of the literature and patient responses indicate that there is a need for psychological intervention when patients are diagnosed with MS.

Rotten Symbol Mongering: Scapegoating in Post-9/11 American War Literature

A rhetorical approach to the fiction of war offers an appropriate vehicle by which one may encounter and interrogate such literature and the cultural metanarratives that exist therein. My project is a critical analysis—one that relies heavily upon Kenneth Burke’s dramatistic method and his concepts of scapegoating, the comic corrective, and hierarchical psychosis—of three war novels published in 2012 (The Yellow Birds by Kevin Powers, FOBBIT by David Abrams, and Billy Lynn’s Long Halftime Walk by Ben Fountain). This analysis assumes a rhetorical screen in order to subvert and redirect the grand narratives the United States perpetuates in art form whenever it goes to war. Kenneth Burke’s concept of ad bellum purificandum (the purification of war) sought to bridge the gap between war experience and the discourse that it creates in both art and criticism. My work extends that project. I examine the symbolic incongruity of convenient symbols that migrate from war to war (“Geronimo” was used as code for Osama bin Laden’s death during the S.E.A.L team raid; “Indian Country” stands for any dangerous land in Iraq; hajji is this generation’s epithet for the enemy other). Such an examination can weaken our cultural “symbol mongering,” to borrow a phrase from Walker Percy. These three books, examined according to Burke’s methodology, exhibit a wide range of approaches to the soldier’s tale. Notably, however, whether they refigure the grand narratives of modern culture or recast the common redemptive war narrative into more complex representations, this examination shows how one can grasp, contend, and transcend the metanarrative of the typical, redemptive war story.

On the development of advanced techniques for mixed-elastohydrodynamic lubrification modelling of journal and sliding bearing systems.

The present thesis is focused on the development of a thorough mathematical modelling and computational solution framework aimed at the numerical simulation of journal and sliding bearing systems operating under a wide range of lubrication regimes (mixed, elastohydrodynamic and full film lubrication regimes) and working conditions (static, quasi-static and transient conditions). The fluid flow effects have been considered in terms of the Isothermal Generalized Equation of the Mechanics of the Viscous Thin Films (Reynolds equation), along with the massconserving p-Ø Elrod-Adams cavitation model that accordingly ensures the so-called JFO complementary boundary conditions for fluid film rupture. The variation of the lubricant rheological properties due to the viscous-pressure (Barus and Roelands equations), viscous-shear-thinning (Eyring and Carreau-Yasuda equations) and density-pressure (Dowson-Higginson equation) relationships have also been taken into account in the overall modelling. Generic models have been derived for the aforementioned bearing components in order to enable their applications in general multibody dynamic systems (MDS), and by including the effects of angular misalignments, superficial geometric defects (form/waviness deviations, EHL deformations, etc.) and axial motion. The bearing exibility (conformal EHL) has been incorporated by means of FEM model reduction (or condensation) techniques. The macroscopic in fluence of the mixedlubrication phenomena have been included into the modelling by the stochastic Patir and Cheng average ow model and the Greenwood-Williamson/Greenwood-Tripp formulations for rough contacts. Furthermore, a deterministic mixed-lubrication model with inter-asperity cavitation has also been proposed for full-scale simulations in the microscopic (roughness) level. According to the extensive mathematical modelling background established, three significant contributions have been accomplished. Firstly, a general numerical solution for the Reynolds lubrication equation with the mass-conserving p - Ø cavitation model has been developed based on the hybridtype Element-Based Finite Volume Method (EbFVM). This new solution scheme allows solving lubrication problems with complex geometries to be discretized by unstructured grids. The numerical method was validated in agreement with several example cases from the literature, and further used in numerical experiments to explore its exibility in coping with irregular meshes for reducing the number of nodes required in the solution of textured sliding bearings. Secondly, novel robust partitioned techniques, namely: Fixed Point Gauss-Seidel Method (PGMF), Point Gauss-Seidel Method with Aitken Acceleration (PGMA) and Interface Quasi-Newton Method with Inverse Jacobian from Least-Squares approximation (IQN-ILS), commonly adopted for solving uid-structure interaction problems have been introduced in the context of tribological simulations, particularly for the coupled calculation of dynamic conformal EHL contacts. The performance of such partitioned methods was evaluated according to simulations of dynamically loaded connecting-rod big-end bearings of both heavy-duty and high-speed engines. Finally, the proposed deterministic mixed-lubrication modelling was applied to investigate the in fluence of the cylinder liner wear after a 100h dynamometer engine test on the hydrodynamic pressure generation and friction of Twin-Land Oil Control Rings.

Art influences on Mark Z. Danielewski's House of Leaves and Los Angeles's influence on Johnny Truant

"...is a novel that combines literature and art to create a unique postmodern object. It was published just over a decade ago, and in that time numerous scholars and students have written papers and articles on it. Within these articles, the themes are usually about deconstruction, the house as a digital object, the house's lack of homeliness, or characters who claim authorial presence. Danielewski distance himself from that role. The house and its impossible labyrinth are the central feature of the book. A house should provide stability, but this house shifts its rooms and walls at random. A house should protect its occupants, but this one kills people. This house links itself into an infinite amount of information through its use of the internet as an influence and a stylistic device, but it has nothing but an absence in its very foundation, an empty labyrinth with an unseen monster."

Does the scientific evidence support the advertising claims made for products containing Lactobacillus casei and Bifidobacterium lactis? A systematic review

Background To analyse the scientific evidence that exists for the advertising claims made for two products containing Lactobacillus casei and Bifidobacterium lactis and to conduct a comparison between the published literature and what is presented in the corporate website. Methods Systematic review, using Medline through Pubmed and Embase. We included human clinical trials that exclusively measured the effect of Lactobacillus casei or Bifidobacterium lactis on a healthy population, and where the objective was related to the health claims made for certain products in advertising. We assessed the levels of evidence and the strength of the recommendation according to the classification criteria established by the Oxford Centre for Evidence Based Medicine (CEBM). We also assessed the outcomes of the studies published on the website that did not appear in the search. Results Of the 440 articles identified, 16 met the inclusion criteria. Only four (25%) of these presented a level of evidence of 1b and a recommendation grade of A, all corresponding to studies on product containing Bifidobacterium lactis, and only 12 of the 16 studies were published on the corporate website (47). Conclusions There is insufficient scientific evidence to support the health claims made for these products, especially in the case of product containing Lactobacillus casei.

Youth Sport Programs: An Avenue to Foster Positive Youth Development

Concern about the growth in adolescent problem behaviours (e.g. delinquency, drug use) has led to increased interest in positive youth development, and a surge in funding for ‘after school programs.’ We evaluate the potential of youth sport programs to foster positive development, while decreasing the risk of problem behaviours. Literature on the positive and negative outcomes of youth sport is presented. We propose that youth sport programs actively work to assure positive outcomes through developmentally appropriate designs and supportive child–adult (parent/coach) relationships. We also highlight the importance of sport programs built on developmental assets (Benson, 1997 ) and appropriate setting features (National Research Council and Institute of Medicine, 2002 ) in bringing about the five ‘C’s of positive development (competence, confidence, character, connections, and compassion/caring: Lerner et al., 2000 ). An applied sport-programming model, which highlights the important roles of policy-makers, sport organizations, coaches and parents in fostering positive youth development is presented as a starting point for further applied and theoretical research.

Developing an Analytical Framework on Social Cohesion in Singapore. Reflections from the framing of social cohesion debates in the OECD and Europe. EU Centre Singapore Working Paper No. 17, November 2013

Official discourse in Singapore on social cohesion is often framed along the broad parameters of achieving racial and religious harmony. Many policies – formal and informal – and several laws evolved to manage these two aspects of society. Yet, as Singapore developed and with a much more complex socioeconomic environment both domestically and externally, there is perhaps a need to re-look the discourse and framework for discussing social cohesion. This paper takes a critical look at how the issue of social cohesion is framed in academic literature and policy discussions in Europe and the OECD, and tries to develop a broader analytical framework that could be useful in the Singapore context as it struggles with the multiple fault lines in society (beyond race and religion) that have emerged in the last decade or so.