Recommendations for the use of ultrasound in rheumatoid arthritis: literature review and SONAR score experience.

Ultrasound (US) has become a useful tool in the detection of early disease, differential diagnosis, guidance of treatment decisions and treatment monitoring of rheumatoid arthritis (RA). In 2008, the Swiss Sonography in Arthritis and Rheumatism (SONAR) group was established to promote the use of US in inflammatory arthritis in clinical practice. A scoring system was developed and taught to a large number of Swiss rheumatologists who already contributed to the Swiss Clinical Quality Management (SCQM) database, a national patient register. This paper intends to give a Swiss consensus about best clinical practice recommendations for the use of US in RA on the basis of the current literature knowledge and experience with the Swiss SONAR score. Literature research was performed to collect data on current evidence. The results were discussed among specialists of the Swiss university centres and private practice, following a structured procedure. Musculoskelatal US was found to be very helpful in establishing the diagnosis and monitoring the evolution of RA, and to be a reliable tool if used by experienced examiners. It influences treatment decisions such as continuing, intensifying or stepping down therapy. The definite modalities of integrating US into the diagnosis and monitoring of RA treatments will be defined within a few years. There are, however, strong arguments to use US findings as of today in daily clinical care. Some practical recommendations about the use of US in RA, focusing on the diagnosis and the use of the SONAR score, are proposed.

The new culture of electronic publishing

Local conditions in the past often limited opportunities for scholarly exchange. But now these limits are gone and the global workplace has replaced them. It is important to react to these changes. Every academic department must now adopt new methods and rethink processes. Another is the intense national and international debate about open access to scholarly knowledge. The Open Access Initiative shows that a change is taking place in the communication process. This change is also important for service departments within research institutions. Libraries, computer centers and related units have to ask themselves how to react appropriately to the new conditions. What services must be changed or redeveloped, and in what quality and quantity should they be offered? This article focuses on changes in the scholarly publication process. It describes both technological changes and the changes needed in people's attitudes.

The Brazilian electronic theses and dissertations digital library: providing open access for scholarly information

This paper describes a project led by the Instituto Brasileiro de Informações em Ciência e Tecnologia (Ibict), a government institution, to build a national digital library for electronic theses and dissertations - Bibliteca Digital de Teses e Dissertações (BDTD). The project has been a collaborative effort among Ibict, universities and other research centers in Brazil. The developers adopted a system architecture based on the Open Archives Initiative (OAI) in which universities and research centers act as data providers and Ibict as a service provider. A Brazilian metadata standard for electronic theses and dissertations was developed for the digital library. A toolkit including open source package was also developed by Ibict to be distributed to potential data providers. BDTD has been integrated with the international initiative: the Networked Digital Library of Thesis and Dissertation (NDLTD). Discussions in the paper address various issues related to project design, development and management as well as the role played by Ibict. Conclusions highlight some important lessons learned to date and challenges for the future in expanding the BDTD project.

Mortality of patients with COPD participating in chronic disease management programmes: a happy end?

BACKGROUND: Concerns about increased mortality could question the role of COPD chronic disease management (CDM) programmes. We aimed at extending a recent Cochrane review to assess the effects of CDM on mortality in patients with COPD. METHODS: Mortality data were available for 25 out of 29 trials identified in a COPD integrated care systematic review. Meta-analysis using random-effects models was performed, followed by subgroup analyses according to study length (3-12 months vs >12 months), main intervention component (exercise, self-management, structured follow-up) and use of an action plan. RESULTS: The meta-analysis showed no impact of CDM on mortality (pooled OR: 1.00, 95% CI 0.79 to 1.28). CONCLUSIONS: These results do not suggest that CDM programmes expose patients with COPD to excessive mortality risk.

The Gene Ontology in 2010: extensions and refinements.

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

The co-evolution of social institutions, demography, and large-scale human cooperation.

Human cooperation is typically coordinated by institutions, which determine the outcome structure of the social interactions individuals engage in. Explaining the Neolithic transition from small- to large-scale societies involves understanding how these institutions co-evolve with demography. We study this using a demographically explicit model of institution formation in a patch-structured population. Each patch supports both social and asocial niches. Social individuals create an institution, at a cost to themselves, by negotiating how much of the costly public good provided by cooperators is invested into sanctioning defectors. The remainder of their public good is invested in technology that increases carrying capacity, such as irrigation systems. We show that social individuals can invade a population of asocials, and form institutions that support high levels of cooperation. We then demonstrate conditions where the co-evolution of cooperation, institutions, and demographic carrying capacity creates a transition from small- to large-scale social groups.

Electronic Bulletin Board System, HR-345, 1998

The primary objectives of the Electronic Bulletin Board System (BBS) project were to: (1) Provide an electronic communication tool which would link city and county engineering offices to each other and to other governmental agencies for messaging and data sharing; (2) Provide a dial-up site for reference information or files accessible on-demand; and (3) Provide a "stepping stone" to the world of electronic data transfer, recognizing that most local government employees face a huge complex of technology with limited knowledge of computers and communications tools. The system was designed to be as simple as possible, and to require minimal equipment and software cost to the users. The original system was an Apex 386/25 computer with MS-DOS 5.0 software and the final configuration was an HP Vectra XM Pentium 90 with MS-NT 3.51 and Mustang - Wildcat 5.0 software. The users of the BBS were county engineers and their staff, offices in the central office of the Iowa Department of Transportation (DOT) and Resident Construction Engineers at the Iowa DOT. Much of the activity was between the county engineers, and their staffs, and the Iowa DOT offices with which they have ongoing business activities. The BBS contained files for mapping, Internet e-mail service, Accident Location Analysis System (ALAS) data, Iowa DOT bid lettings, and Autocad and Intergraph maps and standards. The 800 line calls were recorded and gave the best indication of the usage and the trends that were being followed. The usage tended to be higher in the winter months when design activities are occurring and lower in the summer months when the construction is in progress. The project was judged a success. The BBS did provide a "stepping stone" to the world of electronic data transfer.

The evolution of social discounting in hierarchically clustered populations.

The expression of a social behaviour may affect the fitness of actors and recipients living in the present and in the future of the population. When there is a risk that a future reward will not be experienced in such a context, the value of that reward should be discounted; but by how much? Here, we evaluate social discount rates for delayed fitness rewards to group of recipients living at different positions in both space and time than the actor in a hierarchically clustered population. This is a population where individuals are grouped into families, families into villages, villages into clans, and so on, possibly ad infinitum. The group-wide fitness effects are assumed to either increase or decrease the fecundity or the survival of recipients and can be arbitrarily extended in space and time. We find that actions changing the survival of individuals living in the future are generally more strongly discounted than fecundity-changing actions for all future times and that the value of future rewards increases as individuals live longer. We also find that delayed fitness effects may not only be discounted by a constant factor per unit delay (exponential discounting), but that, as soon as there is localized dispersal in a population, discounting per unit delay is likely to fall rapidly for small delays and then slowly for longer delays (hyperbolic discounting). As dispersal tends to be localized in natural populations, our results suggest that evolution is likely to favour individuals that express present-biased behaviours and that may be time-inconsistent with respect to their group-wide effects.

HIV rebounds from latently infected cells, rather than from continuing low-level replication.

Rapid rebound of plasma viremia in patients after interruption of long-term combination antiretroviral therapy (cART) suggests persistence of low-level replicating cells or rapid reactivation of latently infected cells. To further characterize rebounding virus, we performed extensive longitudinal clonal evolutionary studies of HIV env C2-V3-C3 regions and exploited the temporal relationships of rebounding plasma viruses with regard to pretreatment sequences in 20 chronically HIV-1-infected patients having undergone multiple 2-week structured treatment interruptions (STI). Rebounding virus during the short STI was homogeneous, suggesting mono- or oligoclonal origin during reactivation. No evidence for a temporal structure of rebounding virus in regard to pretreatment sequences was found. Furthermore, expansion of distinct lineages at different STI cycles emerged. Together, these findings imply stochastic reactivation of different clones from long-lived latently infected cells rather than expansion of viral populations replicating at low levels. After treatment was stopped, diversity increased steadily, but pretreatment diversity was, on average, achieved only >2.5 years after the start of STI when marked divergence from preexisting quasispecies also emerged. In summary, our results argue against persistence of ongoing low-level replication in patients on suppressive cART. Furthermore, a prolonged delay in restoration of pretreatment viral diversity after treatment interruption demonstrates a surprisingly sustained evolutionary bottleneck induced by punctuated antiretroviral therapy.

Electronic Construction Collaboration System – Final Phase, SPR RB02-008, 2014

This phase of the research project involved two major efforts: (1) Complete the implementation of AEC-Sync (formerly known as Attolist) on the Iowa Falls Arch Bridge project and (2) develop a web-based project management system (WPMS) for projects under $10 million. For the first major effort, AEC-Sync was provided for the Iowa Department of Transportation (DOT) in a software as a service agreement, allowing the Iowa DOT to rapidly implement the solution with modest effort. During the 2010 fiscal year, the research team was able to help with the implementation process for the solution. The research team also collected feedback from the Broadway Viaduct project team members before the start of the project and implementation of the solution. For the 2011 fiscal year, the research team collected the post-project surveys from the Broadway Viaduct project members and compared them to the pre-project survey results. The result of the AEC-Sync implementation in the Broadway Viaduct project was a positive one. The project members were satisfied with the performance of AEC-Sync and how it facilitated document management and transparency. In addition, the research team distributed, collected, and analyzed the pre-project surveys for the Iowa Falls Arch Bridge project. During the 2012 fiscal year, the research team analyzed the post-project surveys for the Iowa Falls Arch Bridge project AEC-Sync implementation and found a positive outcome when compared to the pre-project surveys. The second major effort for this project involved the identification and implementation of a WPMS solution for smaller bridge and highway projects. During the 2011 fiscal year, Microsoft SharePoint was selected to be implemented on these smaller highway projects. In this year, workflows for the shop/working drawings for the smaller highway projects specified in Section 1105 of the Iowa DOT Specifications were developed. These workflows will serve as the guide for the development of the SharePoint pages. In order to implement the Microsoft SharePoint pages, the effort of an integrated team proved to be vital because it brought together the expertise required from researchers, programmers, and webpage developers to develop the SharePoint pages.