Math 412 - Topology with Applications

Highlights of Data Expedition: • Students explored daily observations of local climate data spanning the past 35 years. • Topological Data Analysis, or TDA for short, provides cutting-edge tools for studying the geometry of data in arbitrarily high dimensions. • Using TDA tools, students discovered intrinsic dynamical features of the data and learned how to quantify periodic phenomenon in a time-series. • Since nature invariably produces noisy data which rarely has exact periodicity, students also considered the theoretical basis of almost-periodicity and even invented and tested new mathematical definitions of almost-periodic functions. Summary The dataset we used for this data expedition comes from the Global Historical Climatology Network. “GHCN (Global Historical Climatology Network)-Daily is an integrated database of daily climate summaries from land surface stations across the globe.” Source: https://www.ncdc.noaa.gov/oa/climate/ghcn-daily/ We focused on the daily maximum and minimum temperatures from January 1, 1980 to April 1, 2015 collected from RDU International Airport. Through a guided series of exercises designed to be performed in Matlab, students explore these time-series, initially by direct visualization and basic statistical techniques. Then students are guided through a special sliding-window construction which transforms a time-series into a high-dimensional geometric curve. These high-dimensional curves can be visualized by projecting down to lower dimensions as in the figure below (Figure 1), however, our focus here was to use persistent homology to directly study the high-dimensional embedding. The shape of these curves has meaningful information but how one describes the “shape” of data depends on which scale the data is being considered. However, choosing the appropriate scale is rarely an obvious choice. Persistent homology overcomes this obstacle by allowing us to quantitatively study geometric features of the data across multiple-scales. Through this data expedition, students are introduced to numerically computing persistent homology using the rips collapse algorithm and interpreting the results. In the specific context of sliding-window constructions, 1-dimensional persistent homology can reveal the nature of periodic structure in the original data. I created a special technique to study how these high-dimensional sliding-window curves form loops in order to quantify the periodicity. Students are guided through this construction and learn how to visualize and interpret this information. Climate data is extremely complex (as anyone who has suffered from a bad weather prediction can attest) and numerous variables play a role in determining our daily weather and temperatures. This complexity coupled with imperfections of measuring devices results in very noisy data. This causes the annual seasonal periodicity to be far from exact. To this end, I have students explore existing theoretical notions of almost-periodicity and test it on the data. They find that some existing definitions are also inadequate in this context. Hence I challenged them to invent new mathematics by proposing and testing their own definition. These students rose to the challenge and suggested a number of creative definitions. While autocorrelation and spectral methods based on Fourier analysis are often used to explore periodicity, the construction here provides an alternative paradigm to quantify periodic structure in almost-periodic signals using tools from topological data analysis.

In Whose Image: The Emergence, Development, and Challenge of African-American Evangelicalism

The current era of American Christianity marks the transition from a Western, white-dominated U.S. Evangelicalism to an ethnically diverse demographic for evangelicalism. Despite this increasing diversity, U.S. Evangelicalism has demonstrated a stubborn inability to address the entrenched assumption of white supremacy. The 1970s witnessed the rise in prominence of Evangelicalism in the United States. At the same time, the era witnessed a burgeoning movement of African-American evangelicals, who often experienced marginalization from the larger movement. What factors prevented the integration between two seemingly theologically compatible movements? How do these factors impact the challenge of integration and reconciliation in the changing demographic reality of early twenty-first Evangelicalism?

The question is examined through the unpacking of the diseased theological imagination rooted in U.S. Evangelicalism. The theological categories of Creation, Anthropology, Christology, Soteriology, and Ecclesiology are discussed to determine specific deficiencies that lead to assumptions of white supremacy. The larger history of U.S. Evangelicalism and the larger story of the African-American church are explored to provide a context for the unique expression of African-American evangelicalism in the last third of the twentieth century. Through the use of primary sources — personal interviews, archival documents, writings by principals, and private collection documents — the specific history of African-American evangelicals in the 1960s and 1970s is described. The stories of the National Black Evangelical Association, Tom Skinner, John Perkins, and Circle Church provide historical snapshots that illuminate the relationship between the larger U.S. Evangelical movement and African-American evangelicals.

Various attempts at integration and shared leadership were made in the 1970s as African-American evangelicals engaged with white Evangelical institutions. However, the failure of these attempts point to the challenges to diversity for U.S. Evangelicalism and the failure of the Evangelical theological imagination. The diseased theological imagination of U.S. Evangelical Christianity prevented engagement with the needed challenge of African American evangelicalism, resulting in dysfunctional racial dynamics evident in twenty-first century Evangelical Christianity. The historical problem of situating African American evangelicals reveals the theological problem of white supremacy in U.S. Evangelicalism.

Investigating relative clauses in children with specific language impairment

Background: It is well documented that children with Specific Language Impairment (SLI) experience significant grammatical deficits. While much of the focus in the past has been on their morphosyntactic difficulties, less is known about their acquisition of complex syntactic structures such as relative clauses. The role of memory in language performance has also become increasingly prominent in the literature. Aims: This study aims to investigate the control of an important complex syntactic structure, the relative clause, by school age children with SLI in Ireland, using a newly devised sentence recall task. It also aims to explore the role of verbal and short-termworking memory in the performance of children with SLI on the sentence recall task, using a standardized battery of tests based on Baddeley’s model of working memory. Methods and Procedures: Thirty two children with SLI, thirty two age matched typically developing children (AM-TD) between the ages of 6 and 7,11 years and twenty younger typically developing (YTD) children between 4,7 and 5 years, completed the task. The sentence recall (SR) task included 52 complex sentences and 17 fillers. It included relative clauses that are used in natural discourse and that reflect a developmental hierarchy. The relative clauses were also controlled for length and varied in syntactic complexity, representing the full range of syntactic roles. There were seven different relative clause types attached to either the predicate nominal of a copular clause (Pn), or to the direct object of a transitive clause (Do). Responses were recorded, transcribed and entered into a database for analysis. TheWorkingMemory Test Battery for children (WMTB-C—Pickering & Gathercole, 2001) was administered in order to explore the role of short-term memory and working memory on the children’s performance on the SR task. Outcomes and Results: The children with SLI showed significantly greater difficulty than the AM-TD group and the YTD group. With the exception of the genitive subject clauses, the children with SLI scored significantly higher on all sentences containing a Pn main clause than those containing a transitive main clause. Analysis of error types revealed the frequent production of a different type of relative clause than that presented in the task—with a strong word order preference in the NVN direction indicated for the children with SLI. The SR performance for the children with SLI was most highly correlated with expressive language skills and digit recall. Conclusions and Implications: Children with SLI have significantly greater difficulty with relative clauses than YTD children who are on average two years younger—relative clauses are a delay within a delay. Unlike the YTD children they show a tendency to simplify relative clauses in the noun verb noun (NVN) direction. They show a developmental hierarchy in their production of relative clause constructions and are highly influenced by the frequency distribution of the relative clauses in the ambient language.

Proving My Competency One Test at a Time: Internationally Educated Nurses and the Canadian English Language Benchmark Assessment for Nurses

Abstract Professional language assessment is a new concept that has great potential to benefit Internationally Educated Professionals and the communities they serve. This thesis reports on a qualitative study that examined the responses of 16 Canadian English Language Benchmark Assessment for Nurses (CELBAN) test-takers on the topic of their perceptions of the CELBAN test-taking experience in Ontario in the winter of 2015. An Ontario organization involved in registering participants distributed an e-mail through their listserv. Thematic analyses of focus group and interview transcripts identified 7 themes from the data. These themes were used to inform conclusions to the following questions: (1) How do IENs characterize their assessment experience? (2) How do IENs describe the testing constructs measured by the CELBAN? (3) What, if any, potential sources of construct irrelevant variance (CIV) do the test-takers describe based on their assessment experience? (4) Do IENs feel that the CELBAN tasks provide a good reflection of the types of communicative tasks required of a nurse? Overall, participants reported positive experiences with the CELBAN as an assessment of their language skills, and noted some instances in which they felt some factors external to the assessment impacted their demonstration of their knowledge and skill. Lastly, some test-takers noted the challenge of completing the CELBAN where the types of communicative nursing tasks included in the assessment differed from nursing tasks typical of an IENs country or origin. The findings are discussed in relation to literature on high-stakes large-scale assessment and IEPs, and a set of recommendations are offered to future CELBAN administration. These recommendations include (1) the provision of a webpage listing all licensure requirements (2) monitoring of CELBAN location and dates in relation to the wider certification timeline for applicants (3) The provision of additional CELBAN preparatory materials (4) Minor changes to the CELBAN administrative protocols. Given that the CELBAN is a relatively new assessment format and its widespread use for high-stakes decisions (a component of nursing certification and licensure), research validating IEN-test-taker responses to construct representation and construct irrelevant variance is critical to our understanding of the role of competency testing for IENs.

Nanotechnology in food industry II: risk assessment and legislation

Currently, there is increasing use of nanomaterials in the food industry thanks to the many advantages offered and make the products that contain them more competitive in the market. Their physicochemical properties often differ from those of bulk materials, which require specialized risk assessment. This should cover the risks to the health of workers and consumers as well as possible environmental risks. The risk assessment methods must go updating due to more widespread use of nanomaterials, especially now that are making their way down to consumer products. Today there is no specific legislation for nanomaterials, but there are several european dispositions and regulations that include them. This review gives an overview of the risk assessment and the existing current legislation regarding the use of nanotechnology in the food industry.

Creating New Design-Build-Test Experiences as Outputs of Undergraduate Design-Build-Test Projects

This paper describes a methodology of using individual engineering undergraduate student projects as a means of effectively and efficiently developing new Design-Build-Test (DBT) learning experiences and challenges.
A key aspect of the rationale for this approach is that it benefits all parties. The student undertaking the individual project gets an authentic experience of producing a functional artefact, which has been the result of a design process that addresses conception, design, implementation and operation. The supervising faculty member benefits from live prototyping of new curriculum content and resources with a student who is at a similar level of knowledge and experience as the intended end users of the DBT outputs. The multiple students who ultimately undertake the DBT experiences / challenges benefit from the enhanced nature of a learning experience which has been “road tested” and optimised.
To demonstrate the methodology the paper will describe a case study example of an individual project completed in 2015. This resulted in a DBT design challenge with a theme of designing a catapult for throwing table tennis balls, the device being made from components laser cut from medium density fibreboard (MDF). Further three different modes of operation will be described which use the same resource materials but operate over different timescales and with different learning outcomes, from an icebreaker exercise focused on developing team dynamics through to full DBT where students get an opportunity to experience the full impact of their design decisions by competing against other students with a catapult they have designed and built themselves.

Toward A Reliable Quality Control Test For Microneedle Insertion

Microneedles (MNs) are emerging devices that can be used for the delivery of drugs at specific locations1. Their performance is primarily judged by different features and the penetration through tissue is one of the most important aspects to evaluate. For detailed studies of MN performance different kind of in-vitro, exvivo and in-vivo tests should be performed. The main limitation of some of these tests is that biological tissue is too heterogeneous, unstable and difficult to obtain. In addition the use of biological materials sometimes present legal issues. There are many studies dealing with artificial membranes for drug diffusion2, but studies of artificial membranes for Microneedle mechanical characterization are scarce3. In order to overcome these limitations we have developed tests using synthetic polymeric membranes instead of biological tissue. The selected artificial membrane is homogeneous, stable, and readily available. This material is mainly composed of a roughly equal blend of a hydrocarbon wax and a polyolefin and it is commercially available under the brand name Parafilm®. The insertion of different kind of MN arrays prepared from crosslinked polymers were performed using this membrane and correlated with the insertion of the MN arrays in ex-vivo neonatal porcine skin. The insertion depth of the MNs was evaluated using Optical coherence tomography (OCT). The implementation of MN transdermal patches in the market can be improved by make this product user-friendly and easy to use. Therefore, manual insertion is preferred to other kind of procedures. Consequently, the insertion studies were performed in neonatal porcine skin and the artificial membrane using a manual insertion force applied by human volunteers. The insertion studies using manual forces correlated very well with the same studies performed with a Texture Analyzer equipment. These synthetic membranes seem to mimic closely the mechanical properties of the skin for the insertion of MNs using different methods of insertion. In conclusion, this artificial membrane substrate offers a valid alternative to biological tissue for the testing of MN insertion and can be a good candidate for developing a reliable quality control MN insertion test.

Sensitive and specific detection of viable Mycobacterium avium subsp. paratuberculosis in raw milk by the Peptide-mediated magnetic separation (PMS)-phage assay

This study describes further validation of a previously described Peptide-mediated magnetic separation (PMS)-Phage assay, and its application to test raw cows’ milk for presence of viable Mycobacterium avium subsp. paratuberculosis (MAP). The inclusivity and exclusivity of the PMS-phage assay were initially assessed, before the 50% limit of detection (LOD50) was determined and compared with those of PMS-qPCR (targeting both IS900 and f57) and PMS-culture. These methods were then applied in parallel to test 146 individual milk samples and 22 bulk tank milk samples from Johne’s affected herds. Viable MAP were detected by the PMS-phage assay in 31 (21.2%) of 146 individual milk samples (mean plaque count of 228.1 PFU/50 ml, range 6-948 PFU/50 ml), and 13 (59.1%) of 22 bulk tank milks (mean plaque count of 136.83 PFU/50 ml, range 18-695 PFU/50 ml). In contrast, only 7 (9.1%) of 77 individual milks and 10 (45.4%) of 22 bulk tank milks tested PMS-qPCR positive, and 17 (11.6%) of 146 individual milks and 11 (50%) of 22 bulk tank milks tested PMS-culture positive. The mean 50% limits of detection (LOD50) of the PMS-phage, PMS-IS900 qPCR and PMS-f57 qPCR assays, determined by testing MAP-spiked milk, were 0.93, 135.63 and 297.35 MAP CFU/50 ml milk, respectively. Collectively, these results demonstrate that, in our laboratory, the PMS-phage assay is a sensitive and specific method to quickly detect the presence of viable MAP cells in milk. However, due to its complicated, multi-step nature, the method would not be a suitable MAP screening method for the dairy industry.

Activation of STING-Dependent Innate Immune Signaling By S-Phase-Specific DNA Damage in Breast Cancer

BACKGROUND: Previously we identified a DNA damage response-deficient (DDRD) molecular subtype within breast cancer. A 44-gene assay identifying this subtype was validated as predicting benefit from DNA-damaging chemotherapy. This subtype was defined by interferon signaling. In this study, we address the mechanism of this immune response and its possible clinical significance.

METHODS: We used immunohistochemistry (IHC) to characterize immune infiltration in 184 breast cancer samples, of which 65 were within the DDRD subtype. Isogenic cell lines, which represent DDRD-positive and -negative, were used to study the effects of chemokine release on peripheral blood mononuclear cell (PBMC) migration and the mechanism of immune signaling activation. Finally, we studied the association between the DDRD subtype and expression of the immune-checkpoint protein PD-L1 as detected by IHC. All statistical tests were two-sided.

RESULTS: We found that DDRD breast tumors were associated with CD4+ and CD8+ lymphocytic infiltration (Fisher's exact test P < .001) and that DDRD cells expressed the chemokines CXCL10 and CCL5 3.5- to 11.9-fold more than DNA damage response-proficient cells (P < .01). Conditioned medium from DDRD cells statistically significantly attracted PBMCs when compared with medium from DNA damage response-proficient cells (P < .05), and this was dependent on CXCL10 and CCL5. DDRD cells demonstrated increased cytosolic DNA and constitutive activation of the viral response cGAS/STING/TBK1/IRF3 pathway. Importantly, this pathway was activated in a cell cycle-specific manner. Finally, we demonstrated that S-phase DNA damage activated expression of PD-L1 in a STING-dependent manner.

CONCLUSIONS: We propose a novel mechanism of immune infiltration in DDRD tumors, independent of neoantigen production. Activation of this pathway and associated PD-L1 expression may explain the paradoxical lack of T-cell-mediated cytotoxicity observed in DDRD tumors. We provide a rationale for exploration of DDRD in the stratification of patients for immune checkpoint-based therapies.

Development of a Laboratory Durability Test for Asphalts, HR-124, 1967

Fruitful research on durability of paving asphalts may come from two approaches: The improvement of the asphalt for durability; The development of relatively rapid laboratory tests which will enable the design engineer to select or to specify an asphalt based on quality and to make a correct estimate of the service life of a selected asphalt when used in a specific paving mixture. Research Project HR-124, "Development of a Laboratory Durability Test for Asphalts," sponsored by the Iowa Highway Research Board is in the second category and was intended to be the initial stage of an overall study in the development of a durability test for paving asphalts.

Modelling and Verification of a Correction Factor to Evaluate the Efficiency of Solar Thermal Collectors with the Rapid Test Method

A new method for the evaluation of the efficiency of parabolic trough collectors, called Rapid Test Method, is investigated at the Solar Institut Jülich. The basic concept is to carry out measurements under stagnation conditions. This allows a fast and inexpensive process due to the fact that no working fluid is required. With this approach, the temperature reached by the inner wall of the receiver is assumed to be the stagnation temperature and hence the average temperature inside the collector. This leads to a systematic error which can be rectified through the introduction of a correction factor. A model of the collector is simulated with COMSOL Multipyisics to study the size of the correction factor depending on collector geometry and working conditions. The resulting values are compared with experimental data obtained at a test rig at the Solar Institut Jülich. These results do not match with the simulated ones. Consequentially, it was not pos-sible to verify the model. The reliability of both the model with COMSOL Multiphysics and of the measurements are analysed. The influence of the correction factor on the rapid test method is also studied, as well as the possibility of neglecting it by measuring the receiver’s inner wall temperature where it receives the least amount of solar rays. The last two chapters analyse the specific heat capacity as a function of pressure and tem-perature and present some considerations about the uncertainties on the efficiency curve obtained with the Rapid Test Method.

The Effect of Carbohydrate Mouth Rinsing On Skill Specific Performance and Cognitive Function Following a Fatigue Inducing Bout of Fencing

The aim of this study was to investigate whether rinsing the mouth with a carbohydrate solution could improve skill-specific fencing performance and cognitive function following a fatigue inducing simulated bout of fencing in epee fencers. Eleven healthy, competitive epee fencers (three female; eight male; 33.9 ± 14.7 years; body mass 79 ± 16 kg; height 162 ± 54 cm) volunteered to participant in a single-blind crossover design study. During visit 1 participants completed a 1-minute lunge test and stroop test pre and post fatigue inducing fencing protocol. A 30 second electroencephalography (EEG) recording was taken pre-protocol participants were instructed stay in a seated stationary position with their eyes closed. Heart rate and ratings of perceived exertion were recorded following each fight during the fatiguing protocol. Participants mouth rinsed (10 seconds) either 25ml of a 6.7% maltodextrin solution (CHO) or 25ml of water (placebo) between fights and during the EEG recording. Blood lactate and glucose measurements were taken at baseline, pre and post protocol. All measurements and tests were repeated during a 2nd visit to the laboratory, except participants were given a different solution to mouth rinse, separated by a minimum of 5 days. The results showed an increase in heart rate (P < 0.05) and overall RPE (P < 0.001) over time in both trials. There were no recorded differences in blood glucose (F(1,8) = 0.634, P = 0.4, ηp 0.07) or blood lactate levels (F(1,8) = 0.123, P = 0.7, ηp 0.01) between trials. There was a significant improvement in lunge test accuracy in the CHO trial (F(1,8) = 5.214, P = 0.05, ηp 0.40). However, there was no recorded difference in response time to congruent (F(1,8) = 0.326, P = 0.58, ηp 0.04) or incongruent (F(1,8) = 0.189, P = 0.68, ηp 0.02) stimuli between trials. In conclusion mouth rinsing a CHO solution significantly improves accuracy of skill-specific fencing performance but does not affect cognitive function following a fatigue inducing fencing protocol in epee fencers.

Age-Specific Fertility Dynamics: Sub-Saharan African Fertility in a Global Context

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

Distribuição dos metais nas poeiras colhidas em Estarreja: estudo da mobilidade e impacto potencial dos metais no ambiente

As poeiras urbanas, vulgarmente designadas na literatura por street dusts ou road dusts, são misturas heterogêneas de partículas minerais do solo e partículas resultantes do tráfego, formando um material com características únicas e específicas de cada local. Estas partículas, geralmente enriquecidas com elementos potencialmente tóxicos, quando inaladas ou ingeridas poderão ser um risco para a saúde das populações. Neste trabalho foram recolhidas 21 amostras de poeiras urbanas na cidade de Estarreja assim como amostras representativas de partículas relacionados com o tráfego (poeiras resultante do desgaste dos travões e das marcações dos pavimentos e estradas) com o objetivo de investigar a contribuição relativa destas partículas no comportamento geoquímico dessas amostras e o risco associado para as populações locais. Para a concretização do objetivo proposto caracterizou-se química e mineralogicamente as amostras de poeiras urbanas e as partículas relacionadas com o tráfego e avaliou-se a disponibilidade e bioacessibilidade para três elementos considerados potencialmente tóxicos (Cu, Pb e Zn) usando uma combinação de ensaios: (a) digestão ácida; (b) extração sequencial para identificar o fracionamento do Cu, Pb e Zn nas diferentes fases-suporte dos metais, e (c) bioaccessibilidade oral in vitro. Os resultados da análise química mostram que as poeiras dos travões apresentam concentrações elevadas em Fe, Cu, Zn, Mn, Ba, Sb, Cr e Ni sendo de referir diferenças composicionais significativas entre as amostras estudadas. A amostra de tinta contém teores elevados de Ba, Ca, Ti e Pb e também pode conter outros elementos tais como Co, Cr, Cu, Mn. Mineralogicamente constata-se que as amostras de poeiras dos travões tem uma composição mineralógica semelhante mostrando que são constituídas por uma elevada percentagem de material de baixa cristalinidade, grafite e óxidos/hidróxidos de Fe amorfos. A amostra de tinta de marcação dos pavimentos das estradas é composta por material mais cristalino do que a poeira dos travões e é essencialmente constituída por carbonatos (maioritariamente dolomite) e também por barite (em menor quantidade). Os resultados obtidos nas amostras de poeiras urbanas indicam a existência de associações de elementos que definem claramente a componente geogénica e/ou antropogénica e apontam para diferenças entre essas associações nas duas frações estudadas (250 m e 63 m). A heterogeneidade das poeiras é revelada pela existência de partículas com origem geogénica (por exemplo quartzo e aluminossilicatos), de partículas com características marcadamente antropogénicas (partículas enriquecidas em Fe, Pb, Zn e Cu) ou ainda de partículas com origem mista (óxidos de Fe e Ti). Os resultados da extração química seletiva sequencial permitiu concluir que, nas amostras em estudo, as fases de troca e ácido-solúveis são as fases suporte mais importantes para o Cu, Pb e Zn Os resultados dos ensaios de bioacessibilidade mostraram também que uma percentagem significativa de Cu, Pb e Zn total está disponível para absorção gástrica. Este estudo destaca também a necessidade de se caracterizar em detalhe as propriedades intrínsecas das partículas antrópicas presentes nas poeiras urbanas, de forma a compreender as variações da fração bioacessível nos diferentes elementos estudados assim como nas diferentes frações.

'Danger Theory: The Link between AIS and IDS?'

Abstract We present ideas about creating a next generation Intrusion Detection System (IDS) based on the latest immunological theories. The central challenge with computer security is determining the difference between normal and potentially harmful activity. For half a century, developers have protected their systems by coding rules that identify and block specific events. However, the nature of current and future threats in conjunction with ever larger IT systems urgently requires the development of automated and adaptive defensive tools. A promising solution is emerging in the form of Artificial Immune Systems (AIS): The Human Immune System (HIS) can detect and defend against harmful and previously unseen invaders, so can we not build a similar Intrusion Detection System (IDS) for our computers? Presumably, those systems would then have the same beneficial properties as HIS like error tolerance, adaptation and self-monitoring. Current AIS have been successful on test systems, but the algorithms rely on self-nonself discrimination, as stipulated in classical immunology. However, immunologist are increasingly finding fault with traditional self-nonself thinking and a new 'Danger Theory' (DT) is emerging. This new theory suggests that the immune system reacts to threats based on the correlation of various (danger) signals and it provides a method of 'grounding' the immune response, i.e. linking it directly to the attacker. Little is currently understood of the precise nature and correlation of these signals and the theory is a topic of hot debate. It is the aim of this research to investigate this correlation and to translate the DT into the realms of computer security, thereby creating AIS that are no longer limited by self-nonself discrimination. It should be noted that we do not intend to defend this controversial theory per se, although as a deliverable this project will add to the body of knowledge in this area. Rather we are interested in its merits for scaling up AIS applications by overcoming self-nonself discrimination problems.