The Pratt Pouch Provides a Three-Fold Access Increase to Antiretroviral Medication for Births outside Health Facilities in Southern Zambia.

INTRODUCTION: Modern day antiretroviral therapy allows HIV+ pregnant women to lower the likelihood of viral transmission to their infants before, during, and after birth from 20-45% to less than 5%. In developing countries, where non-facility births may outnumber facility births, infant access to safe antiretroviral medication during the critical first three days after birth is often limited. A single-dose, polyethylene pouch ("Pratt Pouch") addresses this challenge by allowing the medication to be distributed to mothers during antenatal care. METHODS: The Pratt Pouch was introduced as part of a one year clinical feasibility study in two districts in Southern Province, Zambia. Participating nurses, community health workers, and pharmacists were trained before implementation. Success in achieving improved antiretroviral medication access was assessed via pre intervention and post intervention survey responses by HIV+ mothers. RESULTS: Access to medication for HIV-exposed infants born outside of a health facility increased from 35% (17/51) before the introduction of the pouch to 94% (15/16) after (p<0.05). A non-significant increase in homebirth rates from 33% (pre intervention cohort) to 50% (post intervention cohort) was observed (p>0.05). Results remained below the national average homebirth rate of 52%. Users reported minimal spillage and a high level of satisfaction with the Pratt Pouch. CONCLUSION: The Pratt Pouch enhances access to infant antiretroviral medication in a rural, non-facility birth setting. Wide scale implementation could have a substantial global impact on HIV transmission rates from mother to child.

Men's knowledge and attitudes about cervical cancer screening in Kenya.

BACKGROUND: A number of studies have identified male involvement as an important factor affecting reproductive health outcomes, particularly in the areas of family planning, antenatal care, and HIV care. As access to cervical cancer screening programs improves in resource-poor settings, particularly through the integration of HIV and cervical cancer services, it is important to understand the role of male partner support in women's utilization of screening and treatment. METHODS: We administered an oral survey to 110 men in Western Kenya about their knowledge and attitudes regarding cervical cancer and cervical cancer screening. Men who had female partners eligible for cervical cancer screening were recruited from government health facilities where screening was offered free of charge. RESULTS: Specific knowledge about cervical cancer risk factors, prevention, and treatment was low. Only half of the men perceived their partners to be at risk for cervical cancer, and many reported that a positive screen would be emotionally upsetting. Nevertheless, all participants said they would encourage their partners to get screened. CONCLUSIONS: Future interventions should tailor cervical cancer educational opportunities towards men. Further research is needed among both men and couples to better understand barriers to male support for screening and treatment and to determine how to best involve men in cervical cancer prevention efforts.

A Framework for Citizen-Centred Social Statistics and Analysis (Working Paper 48)

Economic policy-making has long been more integrated than social policy-making in part because the statistics and much of the analysis that supports economic policy are based on a common conceptual framework – the system of national accounts. People interested in economic analysis and economic policy share a common language of communication, one that includes both concepts and numbers. This paper examines early attempts to develop a system of social statistics that would mirror the system of national accounts, particular the work on the development of social accounts that took place mainly in the 60s and 70s. It explores the reasons why these early initiatives failed but argues that the preconditions now exist to develop a new conceptual framework to support integrated social statistics – and hence a more coherent, effective social policy. Optimism is warranted for two reasons. First, we can make use of the radical transformation that has taken place in information technology both in processing data and in providing wide access to the knowledge that can flow from the data. Second, the conditions exist to begin to shift away from the straight jacket of government-centric social statistics, with its implicit assumption that governments must be the primary actors in finding solutions to social problems. By supporting the decision-making of all the players (particularly individual citizens) who affect social trends and outcomes, we can start to move beyond the sterile, ideological discussions that have dominated much social discourse in the past and begin to build social systems and structures that evolve, almost automatically, based on empirical evidence of ‘what works best for whom’. The paper describes a Canadian approach to developing a framework, or common language, to support the evolution of an integrated, citizen-centric system of social statistics and social analysis. This language supports the traditional social policy that we have today; nothing is lost. However, it also supports a quite different social policy world, one where individual citizens and families (not governments) are seen as the central players – a more empirically-driven world that we have referred to as the ‘enabling society’.

An Evidence-Based Approach to Access Reform (Working Paper 22)

In August 2000, the federal government began an internal review of the Access to Information Act (ATIA). The ATIA gives Canadians a qualified right of access to records held by federal institutions. Decisions about reform should be based on good evidence about the operation of the Act and the likely impact of proposed reforms. This paper describes how data on ATIA operations is collected by federal institutions and provides a guide to academic researchers interested in conducting empirical research on the operation of the law. It constructs a small dataset that describes the processing of a sample of 663 requests received in 1999, and uses this dataset to illustrate the potential of an evidence-based approach to ATIA reform. The dataset can be downloaded from http://evidence.foilaw.net. The project was supported by a $4,800 grant from the Principal’s Development Fund of Queen’s University awarded in May 2001. Comments should be sent to the principal investigator, Alasdair Roberts, at roberts@policystudies.ca.

Newcomer Integration in Online Knowledge Communities: Exploring the Role of Dialogic Textual Complexity

Using online knowledge communities (OKCs) as informal learning environments poses the question how likely these will integrate newcomers as peripheral participants. Previous research has identified surface characteristics of the OKC dialog as integrativity predictors. Yet, little is known about the role of dialogic textual complexity. This contribution proposes a comprehensive approach based on previously validated textual complexity indexes and applies it to predict OKC integrativity. The dialog analysis of N = 14 blogger communities with a total of 1937 participants identified three main components of textual complexity: dialog participation, structure and cohesion. From these, dialog cohesion was higher in integrative OKCs, thus significantly predicting OKC integrativity. This result adds to previous OKC research by uncovering the depth of OKC discourse. For educational practice, the study suggests a way of empowering learners by automatically assessing the integrativity of OKCs in which they may attempt to participate and access community knowledge.

Designing an interactive laboratory experiment to investigate buoyancy

Laboratory classes provide a visual and practical way of supplementing traditional teaching through lectures and tutorial classes. A criticism of laboratories in our School is that they are largely based on demonstration with insufficient participation by students. This provided the motivation to create a new laboratory experiment which would be interactive, encourage student enthusiasm with the subject and improve the quality of student learning.

The topic of the laboratory is buoyancy. While this is a key topic in the first-year fluids module, the laboratory has been designed in such a way that prior knowledge of the topic is unnecessary and therefore it would be accessible by secondary school pupils. The laboratory climaxes in a design challenge. However, it begins with a simple task involving students identifying some theoretical background information using given websites. They then have to apply their knowledge by developing some equations. Next, given some materials (a sheet of tinfoil, card and blu-tack), they have to design a vessel to carry the greatest mass without sinking. Thus, they are given an open-ended problem and have to provide a mathematical justification for their design. Students are expected to declare the maximum mass for their boat in advance of it being tested to create a sense of competition and fun. Overall, the laboratory involves tasks which begin at a low level and progressively get harder, incorporating understanding, applying, evaluating and designing (with reference to Bloom’s taxonomy).

The experiment has been tested in a modern laboratory with wall-mounted screens and access to the internet. Students enjoyed the hands-on aspect and thought the format helped their learning.

The use of cheap materials which are readily available means that many students can be involved at one time. Support documentation has been produced, both for the student participants and the facilitator. The latter is given advice on how to guide the students (without simply giving them the answer) and given some warning about potential problems the students might have.

The authors believe that the laboratory can be adapted for use by secondary school pupils and hope that it will be used to promote engineering in an engaging and enthusing way to a wider audience. To this end, contact has already been made with the Widening Participation Unit at the University to gain advice on possible next steps.

Modelling responses to spatially fractionated radiation fields using preclinical image-guided radiotherapy

OBJECTIVES: Radiotherapy is planned to achieve the optimal physical dose distribution to the target tumour volume whilst minimising dose to the surrounding normal tissue. Recent in vitro experimental evidence has demonstrated an important role for intercellular communication in radiobiological responses following non-uniform exposures. This study aimed to model the impact of these effects in the context of techniques involving highly modulated radiation fields or spatially fractionated treatments such as GRID therapy.

METHODS: Using the small animal radiotherapy research platform (SARRP) as a key enabling technology to deliver precision imaged-guided radiotherapy, it is possible to achieve spatially modulated dose distributions that model typical clinical scenarios. In this work, we planned uniform and spatially fractionated dose distributions using multiple isocentres with beam sizes of 0.5 - 5 mm to obtain 50% volume coverage in a subcutaneous murine tumour model, and applied a model of cellular response that incorporates intercellular communication to assess the potential impact of signalling effects with different ranges.

RESULTS: Models of GRID treatment plans which incorporate intercellular signalling showed increased cell killing within the low dose region. This results in an increase in the Equivalent Uniform Dose (EUD) for GRID exposures compared to standard models, with some GRID exposures being predicted to be more effective than uniform delivery of the same physical dose.

CONCLUSIONS: This study demonstrates the potential impact of radiation induced signalling on tumour cell response for spatially fractionated therapies and identifies key experiments to validate this model and quantify these effects in vivo.

ADVANCES IN KNOWLEDGE: This study highlights the unique opportunities now possible using advanced preclinical techniques to develop a foundation for biophysical optimisation in radiotherapy treatment planning.

Learning to Interpret and Generate Instructional Recipes

Thesis (Ph.D.)--University of Washington, 2016-08

A Game of Horns: Transnational Flows of Rhino Horn

A multi-sectorial regime of protection including international treaties, conservation and security measures, demand reduction campaigns and quasi-military interventions has been established to protect rhinos. Despite these efforts, the poaching of rhinos and trafficking of rhino horn continue unabated. This dissertation asks why the illegal market in rhinoceros horn is so resilient in spite of the myriad measures employed to disrupt it. A theoretical approach grounded in the sociology of markets is applied to explain the structure and functioning of the illegal market. The project follows flows of rhino horn from the source in southern Africa to illegal markets in Southeast Asia. The multi-sited ethnography included participant observations, interviews and focus groups with 416 informants during fourteen months of fieldwork. The sample comprised of, amongst others, convicted and active rhino poachers, smugglers and kingpins, private rhino breeders and hunting outfitters, African and Asian law enforcement officials, as well as affected local communities and Asian consumers. Court files, CITES trade data, archival materials, newspaper reports and social media posts were also analysed to supplement findings and to verify and triangulate data from interviews, focus groups and observations. Central to the analysis is the concept of “contested illegality”, a legitimization mechanism employed by market participants along the different segments of the horn supply chain. These actors' implicit or explicit contestation of the state-sponsored label of illegality serves as a legitimising and enabling mechanism, facilitating participation in gray or illegal markets for rhino horn. The research identified fluid interfaces between legal, illegal and gray markets, with recurring actors who have access to transnational trade structures, and who also possess market and product knowledge, as well as information about the regulatory regime and its loopholes. It is against the background of colonial, apartheid and neoliberal exploitation and marginalization of local communities that a second argument is introduced: the path dependency of conservation paradigms. Underpinning rhino conservation and regulation are archaic and elitist conservation regimes that discount the potential for harmonious relationships between local communities and wildlife. The increasing militarization of anti-poaching measures and green land grabs are exacerbating the rhino problem by alienating communities further from conservation areas and wild animals. The third argument looks at how actors deal with coordination problems in transnational illegal markets. Resolving the coordination problems of cooperation, value and competition are considered essential to the operation of formal markets. It is argued that the problem of security provides an additional and crucial obstacle to actors transacting in markets. The systematic analysis of flows between the researched sites of production, distribution and consumption of rhino horn shows that the social embeddedness of actors facilitates the flourishing of illegal markets in ways that escape an effective enforcement of CITES regulations.

O aprender em ambientes de aprendizagem configurando uma cultura escolar

Nesta tese problematizamos o aprender, a partir do olhar dos estudantes do 7º e 8º anos, em uma escola da rede pública de ensino do município do Rio Grande/RS/Brasil. A escola, em 2011, optou por realizar um trabalho coletivo e cooperativo e modificou sua dinâmica de funcionamento transformando as salas de aula convencionais em Ambientes de Aprendizagem, nos quais os estudantes têm acesso a uma maior diversidade de recursos e a interação com os colegas é permanente, possibilitando o desenvolvimento de estratégias diferenciadas motivando o aluno a estabelecer relações entre o conhecimento escolar, a sua vida e o mundo. Nesta escola, são os estudantes que se deslocam de um ambiente para outro, a cada duas horas, os professores permanecem com a sala organizada, conforme as necessidades e materiais pedagógicos e tecnológicos por área de conhecimento. Para conhecer como os estudantes aprendem neste novo ambiente realizamos diversos questionamentos como: o que significa aprender em Ambientes de Aprendizagem, como eram as aulas nas salas de aulas convencionais e como são as aulas nos Ambientes de Aprendizagem. Adotamos o Discurso do Sujeito Coletivo (DSC) como metodologia de análise, buscando a recursividade nos discursos individuais o que permitiu a construção dos discursos coletivos que denominamos Aprender “ontem” nas salas de aula, Aprender “hoje” nos Ambientes de Aprendizagem e Aprender com o material pedagógico. Os discursos evidenciam mudanças no aprender, em decorrência da transformação das salas de aula convencionais em Ambientes de Aprendizagem. Mostram ainda que os estudantes percebem as aulas mais dinâmicas e que agora tem liberdade para levantar e dialogar com os colegas e/ou para usar o material didático disponível no ambiente. Destacam um maior interesse de ambas as partes evidenciando que a ação docente está mais acolhedora e que acreditam em uma grande mudança na educação. A análise dos discursos nos possibilitou compreender que trabalhos realizados em ambientes coletivos e desafiadores modificam o aprender pela liberdade de ação, de expressão e pelo respeito ao outro como legítimo outro na convivência.

Study into licences used by Open Access journals

The Knowledge Exchange Licensing Expert Group has commissioned a study which examined which licences or licence provisions are being used by open access and hybrid publishers when making their publications available in open access. The study intended to identify a ‘best practice’ licence model framework and to formulate recommendations with respect to an OA licence structure, taking into account the commercial and non-commercial needs of authors as well as the publishers. The study was undertaken by Maverick Outsource Services Ltd. This led to the following recommendations for an optimum licence in an open access journal: The author retains copyright; The author or rightholder grants to all users a free, irrevocable, worldwide, perpetual right of access to the work, and besides a licence to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works in any digital medium for any reasonable purpose, subject to proper attribution of authorship; A complete version of the work and all supplemental materials is deposited immediately upon initial publication in at least one online repository. This includes the permission as stated under 2, in a suitable standard electronic format; The copyright holder can retain the right to restrict commercial use if they wish; The copyright holder provides the publisher with permission to publish, subject to open accessibility of the work in online published form.

Meeting on Provisions in Licensing Incorporating new developments in daily licensing practice: Setting conditions for open access, patron driven access, and data & text mining

Following the workshop on new developments in daily licensing practice in November 2011, we brought together fourteen representatives from national consortia (from Denmark, Germany, Netherlands and the UK) and publishers (Elsevier, SAGE and Springer) met in Copenhagen on 9 March 2012 to discuss provisions in licences to accommodate new developments. The one day workshop aimed to: present background and ideas regarding the provisions KE Licensing Expert Group developed; introduce and explain the provisions the invited publishers currently use;ascertain agreement on the wording for long term preservation, continuous access and course packs; give insight and more clarity about the use of open access provisions in licences; discuss a roadmap for inclusion of the provisions in the publishers’ licences; result in report to disseminate the outcome of the meeting. Participants of the workshop were: United Kingdom: Lorraine Estelle (Jisc Collections) Denmark: Lotte Eivor Jørgensen (DEFF), Lone Madsen (Southern University of Denmark), Anne Sandfær (DEFF/Knowledge Exchange) Germany: Hildegard Schaeffler (Bavarian State Library), Markus Brammer (TIB) The Netherlands: Wilma Mossink (SURF), Nol Verhagen (University of Amsterdam), Marc Dupuis (SURF/Knowledge Exchange) Publishers: Alicia Wise (Elsevier), Yvonne Campfens (Springer), Bettina Goerner (Springer), Leo Walford (Sage) Knowledge Exchange: Keith Russell The main outcome of the workshop was that it would be valuable to have a standard set of clauses which could used in negotiations, this would make concluding licences a lot easier and more efficient. The comments on the model provisions the Licensing Expert group had drafted will be taken into account and the provisions will be reformulated. Data and text mining is a new development and demand for access to allow for this is growing. It would be easier if there was a simpler way to access materials so they could be more easily mined. However there are still outstanding questions on how authors of articles that have been mined can be properly attributed.

Costs and Benefits of Open Access

In June 2009 a study was completed that had been commissioned by Knowledge Exchange and written by Professor John Houghton, Victoria University, Australia. This report on the study was titled: "Open Access – What are the economic benefits? A comparison of the United Kingdom, Netherlands and Denmark." This report was based on the findings of studies in which John Houghton had modelled the costs and benefits of Open Access in three countries. These studies had been undertaken in the UK by JISC, in the Netherlands by SURF and in Denmark by DEFF. In the three national studies the costs and benefits of scholarly communication were compared based on three different publication models. The modelling revealed that the greatest advantage would be offered by the Open Access model, which means that the research institution or the party financing the research pays for publication and the article is then freely accessible. Adopting this model could lead to annual savings of around EUR 70 million in Denmark, EUR 133 million in The Netherlands and EUR 480 in the UK. The report concludes that the advantages would not just be in the long term; in the transitional phase too, more open access to research results would have positive effects. In this case the benefits would also outweigh the costs.

Collection-Level Subject Access in Aggregations of Digital Collections: Metadata Application and Use

Problems in subject access to information organization systems have been under investigation for a long time. Focusing on item-level information discovery and access, researchers have identified a range of subject access problems, including quality and application of metadata, as well as the complexity of user knowledge required for successful subject exploration. While aggregations of digital collections built in the United States and abroad generate collection-level metadata of various levels of granularity and richness, no research has yet focused on the role of collection-level metadata in user interaction with these aggregations. This dissertation research sought to bridge this gap by answering the question “How does collection-level metadata mediate scholarly subject access to aggregated digital collections?” This goal was achieved using three research methods: • in-depth comparative content analysis of collection-level metadata in three large-scale aggregations of cultural heritage digital collections: Opening History, American Memory, and The European Library • transaction log analysis of user interactions, with Opening History, and • interview and observation data on academic historians interacting with two aggregations: Opening History and American Memory. It was found that subject-based resource discovery is significantly influenced by collection-level metadata richness. The richness includes such components as: 1) describing collection’s subject matter with mutually-complementary values in different metadata fields, and 2) a variety of collection properties/characteristics encoded in the free-text Description field, including types and genres of objects in a digital collection, as well as topical, geographic and temporal coverage are the most consistently represented collection characteristics in free-text Description fields. Analysis of user interactions with aggregations of digital collections yields a number of interesting findings. Item-level user interactions were found to occur more often than collection-level interactions. Collection browse is initiated more often than search, while subject browse (topical and geographic) is used most often. Majority of collection search queries fall within FRBR Group 3 categories: object, concept, and place. Significantly more object, concept, and corporate body searches and less individual person, event and class of persons searches were observed in collection searches than in item searches. While collection search is most often satisfied by Description and/or Subjects collection metadata fields, it would not retrieve a significant proportion of collection records without controlled-vocabulary subject metadata (Temporal Coverage, Geographic Coverage, Subjects, and Objects), and free-text metadata (the Description field). Observation data shows that collection metadata records in Opening History and American Memory aggregations are often viewed. Transaction log data show a high level of engagement with collection metadata records in Opening History, with the total page views for collections more than 4 times greater than item page views. Scholars observed viewing collection records valued descriptive information on provenance, collection size, types of objects, subjects, geographic coverage, and temporal coverage information. They also considered the structured display of collection metadata in Opening History more useful than the alternative approach taken by other aggregations, such as American Memory, which displays only the free-text Description field to the end-user. The results extend the understanding of the value of collection-level subject metadata, particularly free-text metadata, for the scholarly users of aggregations of digital collections. The analysis of the collection metadata created by three large-scale aggregations provides a better understanding of collection-level metadata application patterns and suggests best practices. This dissertation is also the first empirical research contribution to test the FRBR model as a conceptual and analytic framework for studying collection-level subject access.

DATA DRIVEN APPROACHES TO IDENTIFY DETERMINANTS OF HEART DISEASES AND CANCER RESISTANCE

Cancer and cardio-vascular diseases are the leading causes of death world-wide. Caused by systemic genetic and molecular disruptions in cells, these disorders are the manifestation of profound disturbance of normal cellular homeostasis. People suffering or at high risk for these disorders need early diagnosis and personalized therapeutic intervention. Successful implementation of such clinical measures can significantly improve global health. However, development of effective therapies is hindered by the challenges in identifying genetic and molecular determinants of the onset of diseases; and in cases where therapies already exist, the main challenge is to identify molecular determinants that drive resistance to the therapies. Due to the progress in sequencing technologies, the access to a large genome-wide biological data is now extended far beyond few experimental labs to the global research community. The unprecedented availability of the data has revolutionized the capabilities of computational researchers, enabling them to collaboratively address the long standing problems from many different perspectives. Likewise, this thesis tackles the two main public health related challenges using data driven approaches. Numerous association studies have been proposed to identify genomic variants that determine disease. However, their clinical utility remains limited due to their inability to distinguish causal variants from associated variants. In the presented thesis, we first propose a simple scheme that improves association studies in supervised fashion and has shown its applicability in identifying genomic regulatory variants associated with hypertension. Next, we propose a coupled Bayesian regression approach -- eQTeL, which leverages epigenetic data to estimate regulatory and gene interaction potential, and identifies combinations of regulatory genomic variants that explain the gene expression variance. On human heart data, eQTeL not only explains a significantly greater proportion of expression variance in samples, but also predicts gene expression more accurately than other methods. We demonstrate that eQTeL accurately detects causal regulatory SNPs by simulation, particularly those with small effect sizes. Using various functional data, we show that SNPs detected by eQTeL are enriched for allele-specific protein binding and histone modifications, which potentially disrupt binding of core cardiac transcription factors and are spatially proximal to their target. eQTeL SNPs capture a substantial proportion of genetic determinants of expression variance and we estimate that 58% of these SNPs are putatively causal. The challenge of identifying molecular determinants of cancer resistance so far could only be dealt with labor intensive and costly experimental studies, and in case of experimental drugs such studies are infeasible. Here we take a fundamentally different data driven approach to understand the evolving landscape of emerging resistance. We introduce a novel class of genetic interactions termed synthetic rescues (SR) in cancer, which denotes a functional interaction between two genes where a change in the activity of one vulnerable gene (which may be a target of a cancer drug) is lethal, but subsequently altered activity of its partner rescuer gene restores cell viability. Next we describe a comprehensive computational framework --termed INCISOR-- for identifying SR underlying cancer resistance. Applying INCISOR to mine The Cancer Genome Atlas (TCGA), a large collection of cancer patient data, we identified the first pan-cancer SR networks, composed of interactions common to many cancer types. We experimentally test and validate a subset of these interactions involving the master regulator gene mTOR. We find that rescuer genes become increasingly activated as breast cancer progresses, testifying to pervasive ongoing rescue processes. We show that SRs can be utilized to successfully predict patients' survival and response to the majority of current cancer drugs, and importantly, for predicting the emergence of drug resistance from the initial tumor biopsy. Our analysis suggests a potential new strategy for enhancing the effectiveness of existing cancer therapies by targeting their rescuer genes to counteract resistance. The thesis provides statistical frameworks that can harness ever increasing high throughput genomic data to address challenges in determining the molecular underpinnings of hypertension, cardiovascular disease and cancer resistance. We discover novel molecular mechanistic insights that will advance the progress in early disease prevention and personalized therapeutics. Our analyses sheds light on the fundamental biological understanding of gene regulation and interaction, and opens up exciting avenues of translational applications in risk prediction and therapeutics.