Formalizing Mathematical Knowledge as a Biform Theory Graph: A Case Study

A biform theory is a combination of an axiomatic theory and an algorithmic theory that supports the integration of reasoning and computation. These are ideal for formalizing algorithms that manipulate mathematical expressions. A theory graph is a network of theories connected by meaning-preserving theory morphisms that map the formulas of one theory to the formulas of another theory. Theory graphs are in turn well suited for formalizing mathematical knowledge at the most convenient level of abstraction using the most convenient vocabulary. We are interested in the problem of whether a body of mathematical knowledge can be effectively formalized as a theory graph of biform theories. As a test case, we look at the graph of theories encoding natural number arithmetic. We used two different formalisms to do this, which we describe and compare. The first is realized in ${\rm CTT}_{\rm uqe}$, a version of Church's type theory with quotation and evaluation, and the second is realized in Agda, a dependently typed programming language.Comment: 43 pages; published without appendices in: H. Geuvers et al., eds, Intelligent Computer Mathematics (CICM 2017), Lecture Notes in Computer Science, Vol. 10383, pp. 9-24, Springer, 201

First Foods Nutrition Curriculum for New Immigrant Families: A Pilot Study

Background: Immigrant families arrive in the US from a variety of nutritional landscapes and educational experiences. Early childhood is a key time to intervene to set children on a healthy path. Creating nutritional education programs tailored for immigrant families may improve nutrition and health outcomes. Objective: To evaluate the First Foods curriculum as a tool for knowledge and behavior change for new immigrant families of young children. Methods: Immigrant caregivers of children less than 2 years old were invited to attend First Foods, a 4-class series. Each series was offered in 1 of 5 different languages (Arabic, Dari, Somali, Burmese, and Nepali). Recruitment occurred through community organizations, primary care clinics and Women, Infants, and Children (WIC), and classes were held in King County, Washington. The curriculum was developed and taught by a registered pediatric dietitian with input from general pediatricians, all experienced in the care of immigrant families. Classes were interpreted in the relevant language and course materials were translated. The classes were based on 4 themes -- 1) Child Eating and Development, 2) Eating Together, 3) Food Safety, and 4) Health Living -- and incorporated positive parenting and child development. Attendees completed pre- and post-surveys in their respective languages or in English. Descriptive statistics, chi-squared analyses, t-tests, and a multi-level linear regression model were conducted in Stata v14.0. Results: Participants in the classes included 47 caregivers (91% mothers). Nearly one-third had previously lived in a refugee camp. They had lived in the US a mean 5.5 years (95% CI: 3.8-7.2 years), attended a mean 8.6 years of school (95% CI: 7.1-10.1 years), and had a mean of 2.8 children (95% CI: 2.3-3.3 children). Classes ranged in size from 5 to 14 caregivers. Caregivers reported an improved understanding of 2 out of 4 methods to decrease risk of dental caries (drinking tap water, p = \u3c0.001; going to the dentist, p=0.02). They reported a decreased use of food as a reward from the pre- to the post-survey (p=0.027). Additionally, the caregivers reported increased frequency of considering sugar content in family foods (p=0.033), and decreased frequency of purchasing food at a convenience store, after participating in the curriculum (p=0.001). Conversely, there were several domains where caregivers did not show a change in their response. Conclusion: First Foods, a community-tailored, early childhood feeding curriculum for immigrant parents of young children, improved knowledge and behavior among caregivers from a variety of immigrant communities in some domains. In the other domains, there may be opportunities to further optimize the educational messages and approach

Joining the conspiracy? Negotiating ethics and emotions in researching (around) AIDS in southern Africa

AIDS is an emotive subject, particularly in southern Africa. Among those who have been directly affected by the disease, or who perceive themselves to be personally at risk, talking about AIDS inevitably arouses strong emotions - amongst them fear, distress, loss and anger. Conventionally, human geography research has avoided engagement with such emotions. Although the ideal of the detached observer has been roundly critiqued, the emphasis in methodological literature on 'doing no harm' has led even qualitative researchers to avoid difficult emotional encounters. Nonetheless, research is inevitably shaped by emotions, not least those of the researchers themselves. In this paper, we examine the role of emotions in the research process through our experiences of researching the lives of 'Young AIDS migrants' in Malawi and Lesotho. We explore how the context of the research gave rise to the production of particular emotions, and how, in response, we shaped the research, presenting a research agenda focused more on migration than AIDS. This example reveals a tension between universalised ethics expressed through ethical research guidelines that demand informed consent, and ethics of care, sensitive to emotional context. It also demonstrates how dualistic distinctions between reason and emotion, justice and care, global and local are unhelpful in interpreting the ethics of research practice

Correlation of X-ray diffraction signatures of breast tissue and their histopathological classification

This pilot study examines the correlation of X-ray diffraction (XRD) measurements with the histopathological analysis of breast tissue. Eight breast cancer samples were investigated. Each sample contained a mixture of normal and cancerous tissues. In total, 522 separate XRD measurements were made at different locations across the samples (8 in total). The resulting XRD spectra were subjected to principal component analysis (PCA) in order to determine if there were any distinguishing features that could be used to identify different tissue components. 99.0% of the variation between the spectra were described by the first two principal components (PC). Comparing the location of points in PC space with the classification determined by histopathology indicated correlation between the shape/magnitude of the XRD spectra and the tissue type. These results are encouraging and suggest that XRD could be used for the intraoperative or postoperative classification of bulk tissue samples

Favourable ten-year overall survival in a Caucasian population with high probability of hereditary breast cancer

<p>Abstract</p> <p>Background</p> <p>The purpose of our study was to compare differences in the prognosis of breast cancer (BC) patients at high (H) risk or intermediate slightly (IS) increased risk based on family history and those without a family history of BC, and to evaluate whether ten-year overall survival can be considered a good indicator of <it>BRCA1 </it>gene mutation.</p> <p>Methods</p> <p>We classified 5923 breast cancer patients registered between 1988 and 2006 at the Department of Oncology and Haematology in Modena, Italy, into one of three different risk categories according to Modena criteria. One thousand eleven patients at H and IS increased risk were tested for <it>BRCA1/2 </it>mutations. The overall survival (OS) and disease free survival (DFS) were the study end-points.</p> <p>Results</p> <p>Eighty <it>BRCA1 </it>carriers were identified. A statistically significantly better prognosis was observed for patients belonging to the H risk category with respect to women in the IS and sporadic groups (82% vs.75% vs.73%, respectively; p < 0.0001). Comparing only <it>BRCA1 </it>carriers with <it>BRCA-</it>negative and sporadic BC (77% vs.77% vs.73%, respectively; p < 0.001) an advantage in OS was seen.</p> <p>Conclusions</p> <p>Patients belonging to a population with a high probability of being <it>BRCA1 </it>carriers had a better prognosis than those with sporadic BC. Considering these results, women who previously had BC and had survived ten years could be selected for <it>BRCA1 </it>analysis among family members at high risk of hereditary BC during genetic counselling. Since only 30% of patients with a high probability of having hereditary BC have <it>BRCA1 </it>mutations, selecting women with a long term survival among this population could increase the rate of positive analyses, avoiding the use of expensive tests.</p

Citizen Science Case Studies and Their Impacts on Social Innovation

Social innovation brings social change and aims to address societal challenges and social needs in a novel way. We therefore consider citizen science as both (1) social innovation in research and (2) an innovative way to develop and foster social innovation. In this chapter, we discuss how citizen science contributes to society’s goals and the development of social innovation, and we conceptualise citizen science as a process that creates social innovation. We argue that both citizen science and social innovation can be analysed using three dimensions – content, process, and empowerment (impact). Using these three dimensions as a framework for our analysis, we present five citizen science cases to demonstrate how citizen science leads to social innovation. As a result of our case study analysis, we identify the major challenges for citizen science in stimulating social innovation

Functional Connection between Rad51 and PML in Homology-Directed Repair

The promyelocytic leukemia protein (PML) is a tumor suppressor critical for formation of nuclear bodies (NBs) performing important functions in transcription, apoptosis, DNA repair and antiviral responses. Earlier studies demonstrated that simian virus 40 (SV40) initiates replication near PML NBs. Here we show that PML knockdown inhibits viral replication in vivo, thus indicating a positive role of PML early in infection. SV40 large T antigen (LT) induces DNA damage and, consequently, nuclear foci of the key homologous recombination repair protein Rad51 that colocalize with PML. PML depletion abrogates LT-induced Rad51 foci. LT may target PML NBs to gain access to DNA repair factors like Rad51 that are required for viral replication. We have used the SV40 model to gain insight to DNA repair events involving PML. Strikingly, even in normal cells devoid of viral oncoproteins, PML is found to be instrumental for foci of Rad51, Mre11 and BRCA1, as well as homology-directed repair after double-strand break (DSB) induction. Following LT expression or external DNA damage, PML associates with Rad51. PML depletion also causes a loss of RPA foci following γ-irradiation, suggesting that PML is required for processing of DSBs. Immunofluorescent detection of incorporated BrdU without prior denaturation indicates a failure to generate ssDNA foci in PML knockdown cells upon γ-irradiation. Consistent with the lack of RPA and BrdU foci, γ-irradiation fails to induce Chk1 activation, when PML is depleted. Taken together, we have discovered a novel functional connection between PML and the homologous recombination-mediated repair machinery, which might contribute to PML tumor suppressor activity

Presence of genes for type III secretion system 2 in Vibrio mimicus strains

<p>Abstract</p> <p>Background</p> <p>Vibrios, which include more than 100 species, are ubiquitous in marine and estuarine environments, and several of them e.g. <it>Vibrio cholerae</it>, <it>V. parahaemolyticus</it>, <it>V. vulnificus </it>and <it>V. mimicus</it>, are pathogens for humans. Pathogenic <it>V. parahaemolyticus </it>strains possess two sets of genes for type III secretion system (T3SS), T3SS1 and T3SS2. The latter are critical for virulence of the organism and be classified into two distinct phylogroups, T3SS2α and T3SS2β, which are reportedly also found in pathogenic <it>V. cholerae </it>non-O1/non-O139 serogroup strains. However, whether T3SS2-related genes are present in other <it>Vibrio </it>species remains unclear.</p> <p>Results</p> <p>We therefore examined the distribution of the genes for T3SS2 in vibrios other than <it>V. parahaemolyticus </it>by using a PCR assay targeting both T3SS2α and T3SS2β genes. Among the 32 <it>Vibrio </it>species tested in our study, several T3SS2-related genes were detected in three species, <it>V. cholerae</it>, <it>V. mimicus </it>and <it>V. hollisae</it>, and most of the essential genes for type III secretion were present in T3SS2-positive <it>V. cholerae </it>and <it>V. mimicus </it>strains. Moreover, both <it>V. mimicus </it>strains possessing T3SS2α and T3SS2β were identified. The gene organization of the T3SS2 gene clusters in <it>V. mimicus </it>strains was fundamentally similar to that of <it>V. parahaemolyticus </it>and <it>V. cholerae </it>in both T3SS2α- and T3SS2β-possessing strains.</p> <p>Conclusions</p> <p>This study is the first reported evidence of the presence of T3SS2 gene clusters in <it>V. mimicus </it>strains. This finding thus provides a new insight into the pathogenicity of the <it>V. mimicus </it>species.</p