Matching Items (90)
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Description
The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern

The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern web development technologies, Genie was developed as a simulator to help educators in biology, genetics, and evolution classrooms teach their students about population genetics. Because Genie was designed for the modern web, it is highly accessible to both educators and students, who can access the web application using any modern web browser on virtually any device. Genie demonstrates the efficacy of web devel- opment technologies for demonstrating and simulating complex processes, and it will be a unique educational tool for educators who teach population genetics.
ContributorsRoos, Benjamin Hirsch (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Mayron, Liam (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
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Description
Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS,

Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
ContributorsSchwartz, Rachel (Author) / Harkins, Kelly (Author) / Stone, Anne (Author) / Cartwright, Reed (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-06-11
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Description
Background
Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D,

Background
Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria.
Methodology
We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure.
Principal Findings
We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations.
Conclusions
Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the value of automated quantitative 3D nuclear morphometry as an objective tool to enable development of sensitive and specific nuclear grade classification in breast cancer diagnosis.
Created2012-01-05
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Description
Callithrix penicillata, also known as the Black-tufted marmoset primarily lives in the Brazilian highlands and has had little research conducted on it. For this project I performed a genome curation on the newly assembled genome of this species. The scaffolds obtained by the Dovetail Genomics reads were organized and labeled

Callithrix penicillata, also known as the Black-tufted marmoset primarily lives in the Brazilian highlands and has had little research conducted on it. For this project I performed a genome curation on the newly assembled genome of this species. The scaffolds obtained by the Dovetail Genomics reads were organized and labeled into chromosomes using the 2014 Callithrix jacchus genome as a reference. Then, using that same genome as a reference, 13 of the chromosomes were reverse complimented to be continuous with the 2014 Callithrix jacchus genome. The N50 statistics of the assembly were calculated and found to be 124 Mb. Quality scores were run for the final genome using referee and visualized with a bar plot, with 99% of sites scoring above 0. Heterozygosity was also calculated and found to be 0.3%. Finally, the final version of the genome was visually compared to the 2017 Callithrix jacchus genome and the GRCh38 human genome. This genome was submitted to the NCBIs database to await further approval.
ContributorsJohnson, Joelle Genevieve (Author) / Cartwright, Reed (Thesis director) / Stone, Anne (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
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Description

This study aims to examine the relationship between urban densification and pedestrian thermal comfort at different times of the year, and to understand how this can impact patterns of activity in downtown areas. The focus of the research is on plazas in the urban core of downtown Tempe, given their

This study aims to examine the relationship between urban densification and pedestrian thermal comfort at different times of the year, and to understand how this can impact patterns of activity in downtown areas. The focus of the research is on plazas in the urban core of downtown Tempe, given their importance to the pedestrian landscape. With that in mind, the research question for the study is: how does the microclimate of a densifying urban core affect thermal comfort in plazas at different times of the year? Based on the data, I argue that plazas in downtown Tempe are not maximally predisposed to pedestrian thermal comfort in the summer or the fall. Thus, the proposed intervention to improve thermal comfort in downtown Tempe’s plazas is the implementation of decision support tools focused on education, community engagement, and thoughtful building designs for heat safety.

ContributorsCox, Nicole (Author) / Redman, Charles (Thesis director) / Hondula, David M. (Committee member) / School of Social Transformation (Contributor) / School of Sustainability (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description

Arizona is a unique state in that rain is not a normal occurrence throughout most of the year (NWS). Arizona averages from less than three months to half a month of measurable precipitation days per year (WRCC). With that, it is important to know the public’s understanding as well as

Arizona is a unique state in that rain is not a normal occurrence throughout most of the year (NWS). Arizona averages from less than three months to half a month of measurable precipitation days per year (WRCC). With that, it is important to know the public’s understanding as well as their general trend of likeness towards the weather forecasts they receive. A questionnaire was distributed to 426 people in the state of Arizona to review what they understand from the forecasts and what they would like to see on social media and television.

ContributorsHermansen, Alexis Nicole (Author) / Alvarez, Melanie (Thesis director) / Cerveny, Randall (Committee member) / Hondula, David M. (Committee member) / Walter Cronkite School of Journalism & Mass Comm (Contributor) / School of Geographical Sciences and Urban Planning (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description
Since its discovery in 1524, many people have characterized the vermiform appendix. Charles Darwin considered the human appendix to be a vestige and a useless structure. Others at the time opposed this hypothesis. However, Darwin's hypothesis became prevalent one until recently when there became a renewed interest in the appendix

Since its discovery in 1524, many people have characterized the vermiform appendix. Charles Darwin considered the human appendix to be a vestige and a useless structure. Others at the time opposed this hypothesis. However, Darwin's hypothesis became prevalent one until recently when there became a renewed interest in the appendix because of advancements in microscopes, knowledge of the immune system, and phylogenetics. In this review, I will argue that the vermiform appendix, although still not completely understood, has important functions. First, I will give the anatomy of the appendix. I will discuss the comparative anatomy between different animals and also primates. I will address the effects of appendicitis and appendectomy. I will give background on vestigial structures and will discuss if the appendix is a vestige. Following, I will review the evolution of the appendix. Finally, I will argue that the function of the appendix is as an immune organ, including discussion of gut-associated lymphoid tissue (GALT), development of lymphoid follicles in GALT and their comparison within different organs, Immunoglobulin A (IgA) function in the gut, biofilms as evidence that the appendix is a safe-house for beneficial bacteria, re-inoculation of the bowel, and protection against recurring infection. I will conclude with future studies that should be conducted to further our understanding of the vermiform appendix.
ContributorsPrestwich, Shelby Elizabeth (Author) / Cartwright, Reed (Thesis director) / Lynch, John (Committee member) / Furstenau, Tara (Committee member) / School of Geographical Sciences and Urban Planning (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description

Many people use public transportation in their daily lives, which is often praised at as a healthy and sustainable choice to make. However, in extreme temperatures this also puts people at a greater risk for negative consequences resulting from such exposure to heat. In Phoenix, public transportation riders are faced

Many people use public transportation in their daily lives, which is often praised at as a healthy and sustainable choice to make. However, in extreme temperatures this also puts people at a greater risk for negative consequences resulting from such exposure to heat. In Phoenix, public transportation riders are faced with extreme heat in the summer along with the increased internal heat production caused by the physical activity required to use public transportation. In this study, I estimated total exposure and average exposure per rider for six stops in Phoenix. To do this I used City of Phoenix ridership data, weather data, and survey responses from an ASU City of Phoenix Bus Stop Survey conducted in summer 2016. These data sets were combined by multiplying different metrics to produce various exposure values. During analysis two sets of calculations were made. One keeping weather constant and another keeping ridership constant. I found that there was a large range of exposure between the selected stops and that the thermal environment influences the amount of exposure depending on the time of day the exposure is occurring. During the morning a greener location leads to less exposure, while in the afternoon an urban location leads to less exposure. Know detailed information about exposure at these stops I was also able to evaluate survey participants' thermal comfort at each stop and how it may relate to exposure. These findings are useful in making educated transportation planning decisions and improving the quality of life for people living in places with extreme summer temperatures.

ContributorsGerster, Katrina Ashley (Author) / Hondula, David M. (Thesis director) / Watkins, Lance (Committee member) / School of Geographical Sciences and Urban Planning (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
With the rising data output and falling costs of Next Generation Sequencing technologies, research into data compression is crucial to maintaining storage efficiency and costs. High throughput sequencers such as the HiSeqX Ten can produce up to 1.8 terabases of data per run, and such large storage demands are even

With the rising data output and falling costs of Next Generation Sequencing technologies, research into data compression is crucial to maintaining storage efficiency and costs. High throughput sequencers such as the HiSeqX Ten can produce up to 1.8 terabases of data per run, and such large storage demands are even more important to consider for institutions that rely on their own servers rather than large data centers (cloud storage)1. Compression algorithms aim to reduce the amount of space taken up by large genomic datasets by encoding the most frequently occurring symbols with the shortest bit codewords and by changing the order of the data to make it easier to encode. Depending on the probability distribution of the symbols in the dataset or the structure of the data, choosing the wrong algorithm could result in a compressed file larger than the original or a poorly compressed file that results in a waste of time and space2. To test efficiency among compression algorithms for each file type, 37 open-source compression algorithms were used to compress six types of genomic datasets (FASTA, VCF, BCF, GFF, GTF, and SAM) and evaluated on compression speed, decompression speed, compression ratio, and file size using the benchmark test lzbench. Compressors that outpreformed the popular bioinformatics compressor Gzip (zlib -6) were evaluated against one another by ratio and speed for each file type and across the geometric means of all file types. Compressors that exhibited fast compression and decompression speeds were also evaluated by transmission time through variable speed internet pipes in scenarios where the file was compressed only once or compressed multiple times.
ContributorsHowell, Abigail (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Taylor, Jay (Committee member) / Barrett, The Honors College (Contributor)
Created2017-05
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Description
Many bacteria actively import environmental DNA and incorporate it into their genomes. This behavior, referred to as transformation, has been described in many species from diverse taxonomic backgrounds. Transformation is expected to carry some selective advantages similar to those postulated for meiotic sex in eukaryotes. However, the accumulation of loss-of-function

Many bacteria actively import environmental DNA and incorporate it into their genomes. This behavior, referred to as transformation, has been described in many species from diverse taxonomic backgrounds. Transformation is expected to carry some selective advantages similar to those postulated for meiotic sex in eukaryotes. However, the accumulation of loss-of-function alleles at transformation loci and an increased mutational load from recombining with DNA from dead cells create additional costs to transformation. These costs have been shown to outweigh many of the benefits of recombination under a variety of likely parameters. We investigate an additional proposed benefit of sexual recombination, the Red Queen hypothesis, as it relates to bacterial transformation. Here we describe a computational model showing that host-pathogen coevolution may provide a large selective benefit to transformation and allow transforming cells to invade an environment dominated by otherwise equal non-transformers. Furthermore, we observe that host-pathogen dynamics cause the selection pressure on transformation to vary extensively in time, explaining the tight regulation and wide variety of rates observed in naturally competent bacteria. Host-pathogen dynamics may explain the evolution and maintenance of natural competence despite its associated costs.
ContributorsPalmer, Nathan David (Author) / Cartwright, Reed (Thesis director) / Wang, Xuan (Committee member) / Sievert, Chris (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05