Search Results

Utilizing Emerging Technologies to Enhance Students' Engagement and Learning

Description: This poster discusses using clickers to improve students' classroom engagement and gauge students' understanding of the course materials during lecture classes, introducing emerging technologies to improve students' learning experiences, and introducing exergames such as Wii Sports and Wii Fit to promote students' motivation and engagement.
Date: April 12, 2013
Creator: Zhang, Tao
Partner: UNT College of Education

Changes of Children's Motivation in Physical Education and Physical Activity: A Longitudinal Perspective

Description: This article attempts to examine the relationship between changes of children's motivation to changes in children's intention for future participation in physical education and physical activity over an academic year, guided by the expectancy-value model.
Date: August 8, 2016
Creator: Gu, Xiangli & Zhang, Tao
Partner: UNT College of Education

Durable, Low-cost, Improved Fuel Cell Membranes

Description: The development of low cost, durable membranes and membranes electrode assemblies (MEAs) that operate under reduced relative humidity (RH) conditions remain a critical challenge for the successful introduction of fuel cells into mass markets. It was the goal of the team lead by Arkema, Inc. to address these shortages. Thus, this project addresses the following technical barriers from the fuel cells section of the Hydrogen Fuel Cells and Infrastructure Technologies Program Multi-Year Research, Development and Demonstration Plan: (A) Durability (B) Cost Arkema’s approach consisted of using blends of polyvinylidenefluoride (PVDF) and proprietary sulfonated polyelectrolytes. In the traditional approach to polyelectrolytes for proton exchange membranes (PEM), all the required properties are “packaged” in one macromolecule. The properties of interest include proton conductivity, mechanical properties, durability, and water/gas transport. This is the case, for example, for perfluorosulfonic acid-containing (PFSA) membranes. However, the cost of these materials is high, largely due to the complexity and the number of steps involved in their synthesis. In addition, they suffer other shortcomings such as mediocre mechanical properties and insufficient durability for some applications. The strength and originality of Arkema’s approach lies in the decoupling of ion conductivity from the other requirements. Kynar® PVDF provides an exceptional combination of properties that make it ideally suited for a membrane matrix (Kynar® is a registered trademark of Arkema Inc.). It exhibits outstanding chemical resistance in highly oxidative and acidic environments. In work with a prior grant, a membrane known as M41 was developed by Arkema. M41 had many of the properties needed for a high performance PEM, but had a significant deficiency in conductivity at low RH. In the first phase of this work, the processing parameters of M41 were explored as a means to increase its proton conductivity. Optimizing the processing of M41 was found to increase its ...
Date: March 17, 2011
Creator: Roger, Chris; Mountz, David; He, Wensheng & Zhang, Tao
Partner: UNT Libraries Government Documents Department

Defining the maize transcriptome de novo using deep RNA-Seq

Description: De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.
Date: June 1, 2011
Creator: Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin et al.
Partner: UNT Libraries Government Documents Department

Defining the maize transcriptome de novo using deep RNA-Seq

Description: De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.
Date: June 2, 2011
Creator: Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin et al.
Partner: UNT Libraries Government Documents Department

Metagenomic gene annotation by a homology-independent approach

Description: Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.
Date: June 2, 2011
Creator: Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong et al.
Partner: UNT Libraries Government Documents Department

Final Report - Inspection Limit Confirmation for Upper Head Penetration Nozzle Cracking

Description: The ASME Code Case N-729-1 defines alternative examination requirements for the Control Rod Drive Mechanism (CRDM) upper head penetration nozzle welds. The basis for these examination requirements was developed as part of an Industry program conducted by the Materials Reliability Program (MRP) through the Electric Power Research Institute (EPRI). The results of this program were published in MRP-95 Rev. 1 and document a set of finite element weld residual stress analyses conducted on a variety of upper head penetration nozzles. The inspection zone selected by the industry was based on the stress where it was assumed that primary water stress corrosion cracking (PWSCC) would not initiate. As explained in MRP-95 Rev. 1, it has been illustrated that PWSCC does not occur in the Alloy 600 tube when the stresses are below the yield strength of that tube. Typical yield strengths at operating conditions for Alloy 600 range from 35 ksi to 65 ksi. A stress less than 20-ksi tension was chosen as a conservative range where PWSCC would not initiate. Over the last several years, Engineering Mechanics Corporation of Columbus (Emc2) has conducted welding residual stress analyses on upper head penetration J-welds made from Alloy 182 weld metal for the U.S. Nuclear Regulatory Commission (NRC) staff. These efforts were performed as a confirmatory evaluation of the industry’s analyses conducted as part of their MRP-95 Rev. 1 effort. To this point, the analyses conducted by Emc2 have not been compared to the MRP-95 Rev. 1 results or the examination zones defined in the Code Case. Therefore, this report summarizes the past Emc2 CRDM welding analyses and investigates the regions where the welding stresses may be sufficiently high to promote stress corrosion cracking (SCC). In all, 90 welding residual stress analyses were conducted by Emc2 and the largest distance below the weld ...
Date: August 22, 2008
Creator: Anderson, Michael T.; Rudland, David L.; Zhang, Tao & Wilkowski, Gery M.
Partner: UNT Libraries Government Documents Department

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

Description: Background: Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. While high throughput mRNA sequencing (RNA-Seq) has emerged as a powerful tool for addressing these problems, its success is dependent upon the availability and quality of reference genome sequences, thus limiting the organisms to which it can be applied. Results: Here, we describe Rnnotator, an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. We have applied the Rnnotator assembly pipeline to two yeast transcriptomes and compared the results to the reference gene catalogs of these organisms. The contigs produced by Rnnotator are highly accurate (95percent) and reconstruct full-length genes for the majority of the existing gene models (54.3percent). Furthermore, our analyses revealed many novel transcribed regions that are absent from well annotated genomes, suggesting Rnnotator serves as a complementary approach to analysis based on a reference genome for comprehensive transcriptomics. Conclusions: These results demonstrate that the Rnnotator pipeline is able to reconstruct full-length transcripts in the absence of a complete reference genome.
Date: November 19, 2010
Creator: Martin, Jeffrey; Bruno, Vincent M.; Fang, Zhide; Meng, Xiandong; Blow, Matthew; Zhang, Tao et al.
Partner: UNT Libraries Government Documents Department

The Airborne Metagenome in an Indoor Urban Environment

Description: The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens.
Date: February 12, 2008
Creator: Tringe, Susannah; Zhang, Tao; Liu, Xuguo; Yu, Yiting; Lee, Wah Heng; Yap, Jennifer et al.
Partner: UNT Libraries Government Documents Department

ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers

Description: A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed reproducible enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.
Date: February 1, 2009
Creator: Visel, Axel; Blow, Matthew J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy et al.
Partner: UNT Libraries Government Documents Department

Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance

Description: Some ionic liquids (ILs) have been shown to be very effective solvents for biomass pretreatment. It is known that some ILs can have a strong inhibitory effect on fungal cellulases, making the digestion of cellulose inefficient in the presence of ILs. The identification of IL-tolerant enzymes that could be produced as a cellulase cocktail would reduce the costs and water use requirements of the IL pretreatment process. Due to their adaptation to high salinity environments, halophilic enzymes are hypothesized to be good candidates for screening and identifying IL-resistant cellulases. Using a genome-based approach, we have identified and characterized a halophilic cellulase (Hu-CBH1) from the halophilic archaeon, Halorhabdus utahensis. Hu-CBH1 is present in a gene cluster containing multiple putative cellulolytic enzymes. Sequence and theoretical structure analysis indicate that Hu-CBH1 is highly enriched with negatively charged acidic amino acids on the surface, which may form a solvation shell that may stabilize the enzyme, through interaction with salt ions and/or water molecules. Hu-CBH1 is a heat tolerant haloalkaliphilic cellulase and is active in salt concentrations up to 5 M NaCl. In high salt buffer, Hu-CBH1 can tolerate alkali (pH 11.5) conditions and, more importantly, is tolerant to high levels (20percent w/w) of ILs, including 1-allyl-3-methylimidazolium chloride ([Amim]Cl). Interestingly, the tolerances to heat, alkali and ILs are found to be salt-dependent, suggesting that the enzyme is stabilized by the presence of salt. Our results indicate that halophilic enzymes are good candidates for the screening of IL-tolerant cellulolytic enzymes.
Date: February 17, 2011
Creator: Zhang, Tao; Datta, Supratim; Eichler, Jerry; Ivanova, Natalia; Axen, Seth D.; Kerfeld, Cheryl A. et al.
Partner: UNT Libraries Government Documents Department