Automated Spore Analysis using Bright-Field Imaging and Raman Microscopy

After the discovery of inadvertent shipments of viable B. anthracis spores by the United States Department of Defense in 2015, alternative and orthogonal methods were investigated to analyze spores to determine their viability. In this thesis we demonstrate a novel analysis technique that combines bright-field microscopy imaging with Raman chemical microscopy. We first developed an image segmentation routine based on the watershed method to locate individual spores within bright-field images. This routine was able to effectively demarcate 97.4% of the Bacillus spores within the bright-field images with minimal over-segmentation. Size and shape measurements, to include major and minor axis and area, were then extracted for 4048 viable spores which showed very good agreement with previously published values. When similar measurements were taken on 3627 gamma-irradiated spores, a statistically significant difference was noted for the minor axis length, ratio of major to minor axis, and total area when compared to the non-irradiated spores. Classification results show the ability to correctly classify 67% of viable spores with an 18% misclassification rate using the bright-field image by thresholding the minimum classification length. Raman chemical imaging microscopy (RCIM) was then used to measure populations of viable, gamma irradiated, and autoclaved spores of B. anthracis Sterne, B. atrophaeus. B. megaterium, and B. thuringiensis kurstaki. Significant spectral differences were observed between viable and inactivated spores due to the disappearance of features associated with calcium dipicolinate after irradiation. Principal component analysis was used which showed the ability to distinguish viable spores of B. anthracis Sterne and B. atrophaeus from each other and the other two Bacillus species. Finally, Raman microscopy was used to classify mixtures of viable and gamma inactivated spores. A technique was developed that fuses the size and shape characteristics obtained from the bright-field image to preferentially target viable spores. Simulating a scenario of a A practical demonstration of the technique was performed on a field of view containing approximately 7,000 total spores of which are only 12 were viable to simulate a sample that was not fully irradiated. Ten of these spores are properly classified while interrogating just 25% of the total spores

A bioinformatics workflow for detecting signatures of selection in genomic data

The detection of “signatures of selection” is now possible on a genome-wide scale in many plant and animal species, and can be performed in a population-specific manner due to the wealth of per-population genome-wide genotype data that is available. With genomic regions that exhibit evidence of having been under selection shown to also be enriched for genes associated with biologically important traits, detection of evidence of selective pressure is emerging as an additional approach for identifying novel gene-trait associations. While high-density genotype data is now relatively easy to obtain, for many researchers it is not immediately obvious how to go about identifying signatures of selection in these data sets. Here we describe a basic workflow, constructed from open source tools, for detecting and examining evidence of selection in genomic data. Code to install and implement the pipeline components, and instructions to run a basic analysis using the workflow described here, can be downloaded from our public GitHub repository: http://www.github.com/smilefreak/selectionTools

Te Mata Ira: Guidelines for Genomic Research with Māori.: Te Mata Ira: Guidelines for Genomic Research with Māori.

Māori ethical frameworks recognise that all research in New Zealand is of interest to Māori and outline community expectations of appropriate behavior in research to deliver the best outcomes for Māori. Research contributes to the broader development objectives of society. Ethics has a specific role in guiding key behaviours, processes and methodologies used in research. This document outlines a framework for addressing Māori ethical issues within the context of genetic or genomic research. It draws on a foundation of mātauranga (Māori knowledge) and tikanga Māori (Māori protocols and practices) and will be useful for researchers, ethics committee members and those who engage in consultation or advice about genomic research with Māori in local, regional, national or international settings

Te Mata Ira—Faces of the Gene: Developing a cultural foundation for biobanking and genomic research involving Māori

Te Mata Ira was a three-year research project (2012–2015) that explored Māori views on genomic research and biobanking for the development of culturally appropriate guidelines. A key component of this process has been to identify Māori concepts that provide cultural reference points for engaging with biobanking and genomic research. These cultural cues provide the basis for describing the cultural logic that underpins engagement in this context in a culturally acceptable manner. This paper outlines the role of two wānanga (workshops) conducted as part of the larger project that were used to make sense of the Māori concepts that emerged from other data-collection activities. The wānanga involved six experts who worked with the research team to make sense of the Māori concepts. The wānanga process created the logic behind the cultural foundation for biobanking and genomic research, providing a basis for understanding Māori concepts, Māori ethical principles and their application to biobanking and genomic research

2000-2001 The Lynn University Philharmonia

Program Concerto for 3 Keyboards and Orchestra / J. S. Bach Roberta Rust, Phillip Evans, and Ying Huang, piano Adagio & Allegro Molto for French Horn, Trombone and Orchestra / M. Haydn Gregory Miller, horn and Mark Hetzler, trombone Sinfonia Concertante for Winds and Orchestra / W. A. Mozart Ray Still, oboe, Paul Green, clarinet, Arthur Weisberg, bassoon, and Gregory Miller, horn Concerto for Two Cellos / D. Ott Johanne Perron and Claudio Jaffe, cello Sinfonia Concertante for Strings and Orchestra / W. A. Mozart Sergiu Schwartz, violin and Laura Wilcox, violahttps://spiral.lynn.edu/conservatory_philharmonia/1122/thumbnail.jp

He Tangata Kei Tua: Guidelines for biobanking with Māori.

Māori ethical frameworks recognise that all research in New Zealand is of interest to Māori and outline community expectations of appropriate behavior in research to deliver the best outcomes for Māori. Research contributes to the broader development objectives of society and this endeavor is being supported by biobanking infrastructure. Ethics has a specific role in guiding key behaviours, processes and methodologies used in research. This document outlines a framework for addressing Māori ethical issues within the context of biobanking. It draws on a foundation of mātauranga (Indigenous knowledge) and tikanga Māori (Māori protocols and practices) and will be useful for researchers, ethics committee members and those who engage in consultation or advice about biobanking with Māori in local, regional, national or international settings

The risk of menstrual abnormalities after tubal sterilization: a case control study

BACKGROUND: Tubal sterilization is the method of family planning most commonly used. The existence of the post-tubal-ligation syndrome of menstrual abnormalities has been the subject of debate for decades. METHODS: In a cross-sectional study, 112 women with the history of Pomeroy type of tubal ligation achieved by minilaparatomy as the case group and 288 women with no previous tubal ligation as the control group were assessed for menstrual abnormalities. RESULTS: Menstrual abnormalities were not significantly different between the case and control groups (p = 0.824). The abnormal uterine bleeding frequency differences in two different age groups (30–39 and 40–45 years old) were statistically significant (p = 0.0176). CONCLUSION: Tubal sterilization does not cause menstrual irregularities

Challenges in quantifying changes in the global water cycle

Human influences have likely already impacted the large-scale water cycle but natural variability and observational uncertainty are substantial. It is essential to maintain and improve observational capabilities to better characterize changes. Understanding observed changes to the global water cycle is key to predicting future climate changes and their impacts. While many datasets document crucial variables such as precipitation, ocean salinity, runoff, and humidity, most are uncertain for determining long-term changes. In situ networks provide long time-series over land but are sparse in many regions, particularly the tropics. Satellite and reanalysis datasets provide global coverage, but their long-term stability is lacking. However, comparisons of changes among related variables can give insights into the robustness of observed changes. For example, ocean salinity, interpreted with an understanding of ocean processes, can help cross-validate precipitation. Observational evidence for human influences on the water cycle is emerging, but uncertainties resulting from internal variability and observational errors are too large to determine whether the observed and simulated changes are consistent. Improvements to the in situ and satellite observing networks that monitor the changing water cycle are required, yet continued data coverage is threatened by funding reductions. Uncertainty both in the role of anthropogenic aerosols, and due to large climate variability presently limits confidence in attribution of observed changes

Effect of Sotagliflozin on Total Hospitalizations in Patients With Type 2 Diabetes and Worsening Heart Failure A Randomized Trial

In the SOLOIST-WHF (Effect of Sotagliflozin on Cardiovascular Events in Patients With Type 2 Diabetes Post Worsening Heart Failure) trial, sotagliflozin, a sodium-glucose cotransporter-1 and sodium-glucose cotransporter-2 inhibitor, reduced total occurrences of cardiovascular deaths, hospitalizations for heart failure, and urgent visits for heart failure relative to placebo by 33%