Matching Items (348)
Description
Sulfadiazine (SD), one of broad-spectrum antibiotics, exhibits limited biodegradation in wastewater treatment due to its chemical structure, which requires initial mono-oxygenation reactions to initiate its biodegradation. Intimately coupling UV photolysis with biodegradation, realized with the internal loop photobiodegradation reactor, accelerated SD biodegradation and mineralization by 35 and 71 %, respectively. The main organic products from photolysis were 2-aminopyrimidine (2-AP), p-aminobenzenesulfonic acid (ABS), and aniline (An), and an SD-photolysis pathway could be identified using C, N, and S balances. Adding An or ABS (but not 2-AP) into the SD solution during biodegradation experiments (no UV photolysis) gave SD removal and mineralization rates similar to intimately coupled photolysis and biodegradation. An SD biodegradation pathway, based on a diverse set of the experimental results, explains how the mineralization of ABS and An (but not 2-AP) provided internal electron carriers that accelerated the initial mono-oxygenation reactions of SD biodegradation. Thus, multiple lines of evidence support that the mechanism by which intimately coupled photolysis and biodegradation accelerated SD removal and mineralization was through producing co-substrates whose oxidation produced electron equivalents that stimulated the initial mono-oxygenation reactions for SD biodegradation.
ContributorsPan, Shihui (Author) / Yan, Ning (Author) / Liu, Xinyue (Author) / Wang, Wenbing (Author) / Zhang, Yongming (Author) / Liu, Rui (Author) / Rittmann, Bruce (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor)
Created2014-11-01
Description
Heterochromatin is a repressive chromatin compartment essential for maintaining genomic integrity. A hallmark of heterochromatin is the presence of specialized nonhistone proteins that alter chromatin structure to inhibit transcription and recombination. It is generally assumed that heterochromatin is highly condensed. However, surprisingly little is known about the structure of heterochromatin or its dynamics in solution. In budding yeast, formation of heterochromatin at telomeres and the homothallic silent mating type loci require the Sir3 protein. Here, we use a combination of sedimentation velocity, atomic force microscopy and nucleosomal array capture to characterize the stoichiometry and conformation of Sir3 nucleosomal arrays. The results indicate that Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome. We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres. We suggest that heterochromatin proteins promote silencing by ‘coating’ nucleosomal arrays, stabilizing interactions between nucleosomal histones and DNA.
ContributorsSwygert, Sarah G. (Author) / Manning, Benjamin J. (Author) / Senapati, Subhadip (Author) / Kaur, Parminder (Author) / Lindsay, Stuart (Author) / Demeler, Borries (Author) / Peterson, Craig L. (Author) / Biodesign Institute (Contributor) / Single Molecule Biophysics (Contributor)
Created2014-08-01
Description
We studied the microbial community structure of pilot two-stage membrane biofilm reactors (MBfRs) designed to reduce nitrate (NO[subscript 3]–) and perchlorate (ClO[subscript 4]–) in contaminated groundwater. The groundwater also contained oxygen (O[subscript 2]) and sulfate (SO[2 over 4]–), which became important electron sinks that affected the NO[subscript 3]– and ClO[subscript 4]– removal rates. Using pyrosequencing, we elucidated how important phylotypes of each “primary” microbial group, i.e., denitrifying bacteria (DB), perchlorate-reducing bacteria (PRB), and sulfate-reducing bacteria (SRB), responded to changes in electron-acceptor loading. UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. Diminished acceptor loading led to SO[2 over 4]– reduction in the lag MBfR, which allowed Desulfovibrionales (an SRB) and Thiothrichales (sulfur-oxidizers) to thrive through S cycling. As a result of this cooperative relationship, they competed effectively with DB/PRB phylotypes such as Xanthomonadales and Rhodobacterales. Thus, pyrosequencing illustrated that while DB, PRB, and SRB responded predictably to changes in acceptor loading, a decrease in total acceptor loading led to important shifts within the “primary” groups, the onset of other members (e.g., Thiothrichales), and overall greater diversity.
ContributorsOntiveros-Valencia, Aura (Author) / Tang, Youneng (Author) / Zhao, Heping (Author) / Friese, David (Author) / Overstreet, Ryan (Author) / Smith, Jennifer (Author) / Evans, Patrick (Author) / Rittmann, Bruce (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor)
Created2014-07-01
Description
The Combined Activated Sludge-Anaerobic Digestion Model (CASADM) quantifies the effects of recycling anaerobic-digester (AD) sludge on the performance of a hybrid activated sludge (AS)-AD system. The model includes nitrification, denitrification, hydrolysis, fermentation, methanogenesis, and production/utilization of soluble microbial products and extracellular polymeric substances (EPS). A CASADM example shows that, while effluent COD and N are not changed much by hybrid operation, the hybrid system gives increased methane production in the AD and decreased sludge wasting, both caused mainly by a negative actual solids retention time in the hybrid AD. Increased retention of biomass and EPS allows for more hydrolysis and conversion to methane in the hybrid AD. However, fermenters and methanogens survive in the AS, allowing significant methane production in the settler and thickener of both systems, and AD sludge recycle makes methane formation greater in the hybrid system.
ContributorsYoung, Michelle (Author) / Marcus, Andrew (Author) / Rittmann, Bruce (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor)
Created2013-08-13
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 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
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 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
Description
Background
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
ContributorsZhang, Wenlu (Author) / Feng, Daming (Author) / Li, Rongjian (Author) / Chernikov, Andrey (Author) / Chrisochoides, Nikos (Author) / Osgood, Christopher (Author) / Konikoff, Charlotte (Author) / Newfeld, Stuart (Author) / Kumar, Sudhir (Author) / Ji, Shuiwang (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2013-12-28
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Description
Background
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
ContributorsYuan, Lei (Author) / Woodard, Alexander (Author) / Ji, Shuiwang (Author) / Jiang, Yuan (Author) / Zhou, Zhi-Hua (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / Ira A. Fulton Schools of Engineering (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2012-05-23
Description
The importance of second language learning in today’s ever-increasing globalized world is becoming ever more paramount. Despite seeming trends which indicate aversion to globalization, the international phenomenon which describes the connection made between peoples and cultures, will only increase its influence in coming years. With the advances globalization has made, it is becoming more important to learn and study foreign languages in order to keep abreast of this trend and not be left behind by globalization. Why electronic translation is not so viable in the long run (at least currently) is that culture and syntax are not things which can be simply ascertained via mediums such as application use. Due to the fact that advanced language proficiency is considered to be an integral piece towards stronger sentiments of “integration” (i.e. Syrian refugees integrating into EU and US) it is of more importance that increasing second language proficiency receives the adequate study and implementation to reflect a more cohesive globalized world. Accompanying this necessity is the simple fact that adult second language learners often struggle to overcome difficulty to the challenging yet rewarding task of learning and eventually mastering a second language.
To truly understand the difficulty some adult second language learners have with learning a second language it can be helpful to compare second language acquisition to how one naturally, and seemingly effortlessly in many cases, acquires their native language. How can a comparative analysis of how native speakers and adult second language learners each learn their first and second language respectively be successfully converted to a specific means of assisting adult second language learners achieve the highest level of possible fluency? In order to more accurately propose a viable solution to the overarching question, the following three questions have been proposed as a means to springboard into better understanding the nature of the main topic.
The points to consider while analyzing the main question throughout this analysis are as follows: How would it be best for an adult second language learner to achieve the same level off proficiency as a native speaker of a given language whom has been exposed to all of its intricacies since birth? At what point exactly is someone considered to have the same level of proficiency which a native speaker of a given language would have and how does that differ from being a heritage speaker? With the final supporting question being: What type of learning would be best suited in helping a heritage speaker (someone who learns a language in the home by virtue of their heritage) or adult second language learner to become highly proficient in a second language?
In order to propose a wide variety of integration between these questions with the conjoined purpose of answering the inquiry of this thesis, many different sources supporting each of the above questions will contain certain overlap, providing a clear basis for constructing a tri-fold argument in answering the thesis question as acutely as possible. In regards to the first question, the question of “proficiency” will be a subsection committed to understanding the nature of how language proficiency works and at what point (if ever) one can ever be considered “highly proficient” in a second language.
All three exploratory questions are compatible with a theory known as Critical Period Theory, a theory in linguistics proposed by Montreal neurologist Wilder Penfield, which states, “There is a critical age, before puberty, that one must learn language. If one has not learned to speak before puberty it is much more difficult, and sometimes impossible, to learn language and speak in a meaningful way.” The overlap which this method binds to Universal Grammar is a rather close-knit relationship. Research composed by certain linguists suggest that “children are born with a certain universal grammar wired into their brains.” This will be compared and cross-examined to a higher degree in a later section of the paper.
The importance of Universal Grammar in relation to Critical Period Theory cannot be overstated. Universal Grammar in relation to the second language Critical Period Theory will help explain at which point, someone is considered to be a “native speaker” of a given language. The third question posed of how would it be best for heritage and second language learners to increase their proficiency in a second language really touches on both of these theories in regards to at which age someone is exposed to a specific language in addition to how Universal Grammar affects the development of second language acquisition. In the realm of perpetually working towards mitigating an answer to this analysis’s thesis, the connecting thread or “roter Faden”, as it is said in German, will be the integrative domain the above questions will have on arriving to a clearer understanding of the nature of how a comparative analysis of second language learners and mother-tongue speakers can expedite the language learning process of second language learners, using techniques of native speakers which they inherently pick-up.
To truly understand the difficulty some adult second language learners have with learning a second language it can be helpful to compare second language acquisition to how one naturally, and seemingly effortlessly in many cases, acquires their native language. How can a comparative analysis of how native speakers and adult second language learners each learn their first and second language respectively be successfully converted to a specific means of assisting adult second language learners achieve the highest level of possible fluency? In order to more accurately propose a viable solution to the overarching question, the following three questions have been proposed as a means to springboard into better understanding the nature of the main topic.
The points to consider while analyzing the main question throughout this analysis are as follows: How would it be best for an adult second language learner to achieve the same level off proficiency as a native speaker of a given language whom has been exposed to all of its intricacies since birth? At what point exactly is someone considered to have the same level of proficiency which a native speaker of a given language would have and how does that differ from being a heritage speaker? With the final supporting question being: What type of learning would be best suited in helping a heritage speaker (someone who learns a language in the home by virtue of their heritage) or adult second language learner to become highly proficient in a second language?
In order to propose a wide variety of integration between these questions with the conjoined purpose of answering the inquiry of this thesis, many different sources supporting each of the above questions will contain certain overlap, providing a clear basis for constructing a tri-fold argument in answering the thesis question as acutely as possible. In regards to the first question, the question of “proficiency” will be a subsection committed to understanding the nature of how language proficiency works and at what point (if ever) one can ever be considered “highly proficient” in a second language.
All three exploratory questions are compatible with a theory known as Critical Period Theory, a theory in linguistics proposed by Montreal neurologist Wilder Penfield, which states, “There is a critical age, before puberty, that one must learn language. If one has not learned to speak before puberty it is much more difficult, and sometimes impossible, to learn language and speak in a meaningful way.” The overlap which this method binds to Universal Grammar is a rather close-knit relationship. Research composed by certain linguists suggest that “children are born with a certain universal grammar wired into their brains.” This will be compared and cross-examined to a higher degree in a later section of the paper.
The importance of Universal Grammar in relation to Critical Period Theory cannot be overstated. Universal Grammar in relation to the second language Critical Period Theory will help explain at which point, someone is considered to be a “native speaker” of a given language. The third question posed of how would it be best for heritage and second language learners to increase their proficiency in a second language really touches on both of these theories in regards to at which age someone is exposed to a specific language in addition to how Universal Grammar affects the development of second language acquisition. In the realm of perpetually working towards mitigating an answer to this analysis’s thesis, the connecting thread or “roter Faden”, as it is said in German, will be the integrative domain the above questions will have on arriving to a clearer understanding of the nature of how a comparative analysis of second language learners and mother-tongue speakers can expedite the language learning process of second language learners, using techniques of native speakers which they inherently pick-up.
ContributorsRoselius, Thomas Jacob (Author) / Lee, Sara (Thesis director) / Reves, Christiane (Committee member) / College of Public Service and Community Solutions (Contributor) / College of Integrative Sciences and Arts (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
This study examined the type and frequency of questions asked by attorneys in cases of children alleging sexual abuse. Of interest was whether child age would affect the questions asked. The participants included 25 child witnesses testifying in criminal trials in Maricopa County over a recent ten-year period. Children were placed into two groups: younger (five to seven-year-olds) and older (eight to nine-year-olds). Every question asked, and answer provided, during children's testimony, was systematically and reliably coded for the content of the interaction. Attorneys exhibited developmental sensitivity, varying the amount of question they asked across content areas by the age of the child. In addition, attorneys varied in what they asked about: the prosecution focused more on the plausibility of abuse, whereas the defense focused more on how others may have suggestively influenced the child's report. Both attorneys were equally concerned about the consistency of narratives. The findings from the present study have direct policy implications for how attorneys structure their arguments, both in an attempt to establish, and question, children's credibility in these important cases. Keywords: children, age, suggestibility, consistency, inconsistency, plausibility
ContributorsHogan, Caitlyn Rose (Author) / Stolzenberg, Stacia (Thesis director) / Fradella, Hank (Committee member) / College of Public Service and Community Solutions (Contributor) / School of Criminology and Criminal Justice (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05