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open access

Syntheses, X-ray Diffraction Structures, and Kinetics on New Formamidinate-Substituted Triosmium Clusters

Description: The reaction between the formamidine ligand PriN=CHNHPri and the activated cluster Os3(CO)10(MeCN)2 has been studied. A rapid reaction is observed at room temperature, yielding the hydride clusters HOs3(CO)9[μ-OCNPriC(H)NPri] and HOs3(CO)10[μ-NPriC(H)NPri] as the principal products. The spectroscopic data and X-ray diffraction structures of those formamidinate-substituted clusters will be present. The thermal reactivity of the clusters has been investigated, with the face-capped cluster HOs3(CO)9[μ-NPriC(H)NPri] found as the sole observable product. The relationship between these three clusters has been established by kinetic studies, the results of which will be discussed.
Date: December 2010
Creator: Yang, Li
Partner: UNT Libraries
open access

Building an Intelligent Filtering System Using Idea Indexing

Description: The widely used vector model maintains its popularity because of its simplicity, fast speed, and the appeal of using spatial proximity for semantic proximity. However, this model faces a disadvantage that is associated with the vagueness from keywords overlapping. Efforts have been made to improve the vector model. The research on improving document representation has been focused on four areas, namely, statistical co-occurrence of related items, forming term phrases, grouping of related words, and representing the content of documents. In this thesis, we propose the idea-indexing model to improve document representation for the filtering task in IR. The idea-indexing model matches document terms with the ideas they express and indexes the document with these ideas. This indexing scheme represents the document with its semantics instead of sets of independent terms. We show in this thesis that indexing with ideas leads to better performance.
Date: August 2003
Creator: Yang, Li
Partner: UNT Libraries
open access

Improving Topic Tracking with Domain Chaining

Description: Topic Detection and Tracking (TDT) research has produced some successful statistical tracking systems. While lexical chaining, a non-statistical approach, has also been applied to the task of tracking by Carthy and Stokes for the 2001 TDT evaluation, an efficient tracking system based on this technology has yet to be developed. In thesis we investigate two new techniques which can improve Carthy's original design. First, at the core of our system is a semantic domain chainer. This chainer relies not only on the WordNet database for semantic relationships but also on Magnini's semantic domain database, which is an extension of WordNet. The domain-chaining algorithm is a linear algorithm. Second, to handle proper nouns, we gather all of the ones that occur in a news story together in a chain reserved for proper nouns. In this thesis we also discuss the linguistic limitations of lexical chainers to represent textual meaning.
Date: August 2003
Creator: Yang, Li
Partner: UNT Libraries
open access

The form, distribution and mobility of arsenic in soilscontaminated by arsenic trioxide, at sites in southeast USA

Description: Soils from many industrial sites in southeastern USA arecontaminated with As because of the application of herbicide containingAs2O3. Among those contaminated sites, two industrial sites, FW and BH,which are currently active and of most serious environmental concerns,were selected to characterize the occurrence of As in the contaminatedsoils and to evaluate its environmental leachability. The soils are bothsandy loams with varying mineralogical and organic matter contents.Microwave-assisted acid digestion (EPA method 3051) of the contaminatedsoils indicated As levels of up to 325 mg/kg and 900 mg/kg (dry weightbasis) for FW and BH soils, respectively. However, bulk X-ray powderdiffraction (XRD) analysis failed to find any detectable As-bearingphases in either of the studied soil samples. Most of the soil As wasobserved by scanning electron microscopy, coupled with energy dispersiveX-ray spectroscopy (SEM/EDX), to be disseminated on the surfaces offine-grained soil particles in close association with Al and Fe. A fewAs-bearing particles were detected in BH soil using electron microprobeanalysis (EMPA). Synchrotron micro-XRD and X-ray absorption near-edgestructure (XANES) analyses indicated that these As-rich particles werepossibly phaunouxite, a mineral similar to calcium arsenate, which couldhave been formed by natural weathering after the application of As2O3.However, the scarcity of those particles eliminated them from playing anyimportant role in Assequestration.Synthetic acid rain sequential batchleaching experiments showed distinct As leaching behaviors of the twostudied soil samples: BH soil, which has the higher As content, showed aslow, steady release of As, while FW soil, with a lower As content,showed a much quicker release and lower overall retention of As uponleaching. Sequential chemical extraction experiments were carried outusing a simplified 4-step sequential chemical extraction procedure (SCEP)previously developed to characterize the fractionation of As and betterunderstand the different leaching behaviors of the two studied soils. Itwas shown that only about 50 percent of the total extractable As wasremoved by the first two extraction …
Date: March 4, 2005
Creator: Yang, Li & Donahoe, Rona J.
Partner: UNT Libraries Government Documents Department
open access

Kaolinite dissolution and precipitation kinetics at 22oC and pH4

Description: Dissolution and precipitation rates of low defect Georgia kaolinite (KGa-1b) as a function of Gibbs free energy of reaction (or reaction affinity) were measured at 22 C and pH 4 in continuously stirred flow through reactors. Steady state dissolution experiments showed slightly incongruent dissolution, with a Si/Al ratio of about 1.12 that is attributed to the re-adsorption of Al on to the kaolinite surface. No inhibition of the kaolinite dissolution rate was apparent when dissolved aluminum was varied from 0 and 60 {micro}M. The relationship between dissolution rates and the reaction affinity can be described well by a Transition State Theory (TST) rate formulation with a Temkin coefficient of 2 R{sub diss} (mol/m{sup 2}s) = 1.15 x 10{sup -13} [1-exp(-{Delta}G/2RT)]. Stopping of flow in a close to equilibrium dissolution experiment yielded at solubility constant for kaolinite at 22 C of 10{sup 7.57}. Experiments on the precipitation kinetics of kaolinite showed a more complex behavior. One conducted using kaolinite seed that had previously undergone extensive dissolution under far from equilibrium conditions for 5 months showed a quasi-steady state precipitation rate for 105 hours that was compatible with the TST expression above. After this initial period, however, precipitation rates decreased by an order of magnitude, and like other precipitation experiments conducted at higher supersaturation and without kaolinite seed subjected to extensive prior dissolution, could not be described with the TST law. The initial quasi-steady state rate is interpreted as growth on activated sites created by the dissolution process, but this reversible growth mechanism could not be maintained once these sites were filled. Long-term precipitation rates showed a linear dependence on solution saturation state that is generally consistent with a two dimensional nucleation growth mechanism following the equation R{sub ppt}(mol/m{sup 2}s) = 3.38 x 10{sup -14} exp[181776/T{sup 2}1n{Omega}]. Further analysis using Synchrotron Scanning …
Date: July 16, 2007
Creator: Yang, Li & Steefel, Carl I.
Partner: UNT Libraries Government Documents Department
open access

Kinetic Studies on C‐h Bond Activation in the Reaction of Triosmium Clusters with Diphosphine and Amidine Ligands

Description: The reaction of 1-(diphenylphosphino)-2-(diphenylphosphito)benzene (PP*) and Os3(CO)10(ACN) has been investigated. A combined experimental and computational study on the isomerization of 1,2-Os3(CO)10[μ-1,2-Ph2P(C6H4)P(OPh)2] (A) and 1,1-Os3(CO)10[μ-1,2-Ph2P(C6H4)P(OPh)2] (B) and reversible ortho-metalation exhibited by the triosmium cluster B are reported. The subsequent conversion of cluster B to the hydrido cluster HOs3(CO)9[μ-1,2-PhP(C6H4-η1)C6H4P(OPh)2] (E) and the benzyne-substituted cluster HOs3(CO)8(µ3-C6H4)[μ-1,2-PhP(C6H4)P(OPh)2] (N) has been established. All of these new clusters have been isolated and fully characterized in solution by IR and NMR spectroscopy; in addition, X-ray diffraction analyses have been performed on the clusters A, B, J, and N. The ortho-metalation reaction that gives cluster E is shown to be reversible, and the mechanism has been probed using selectively deuterated PP* isotopomers. Kinetic and thermodynamic isotope data, in conjunction with DFT calculations, are presented that support the existence of an intermediate unsaturated cluster in the ortho-metalation reaction. Due to interest in the coordination chemistry of formamidines, the non-symmetric amidine ligands PhNC(Me)NHPri, PhNC(Et)NHPri, and (2,4,6-Me3C6H2)NC(Me)NHPri, have been synthesized, and their reaction with Os3(CO)10(MeCN)2 has been investigated. Of the twelve new clusters prepared in section, seven have been structurally characterized by X-ray crystallography.
Date: December 2014
Creator: Yang, Li
Partner: UNT Libraries
open access

In situ chemical fixation of arsenic-contaminated soils: Anexperimental study

Description: This paper reports the results of an experimentalstudytesting a low-cost in situ chemical fixation method designed to reclaimarsenic-contaminated subsurface soils. Subsurface soils from severalindustrial sites in southeastern U.S. were contaminated with arsenicthrough heavy application of herbicide containing arsenic trioxide. Themean concentrations of environmentally available arsenic in soilscollected from the two study sites, FW and BH, are 325 mg/kg and 900mg/kg, respectively. The soils are sandy loams with varying mineralogicaland organic contents. The previous study [Yang L, Donahoe RJ. The form,distribution and mobility of arsenic in soils contaminated by arsenictrioxide, at sites in Southeast USA. Appl Geochem 2007;22:320 341]indicated that a large portion of the arsenic in both soils is associatedwith amorphous aluminum and iron oxyhydroxides and shows very slowrelease against leaching by synthetic precipitation. The soil's amorphousaluminum and iron oxyhydroxides content was found to have the mostsignificant effect on its ability to retain arsenic.Based on thisobservation, contaminated soils were reacted with different treatmentsolutions in an effort to promote the formation of insolublearsenic-bearing phases and thereby decrease the leachability of arsenic.Ferrous sulfate, potassium permanganate and calcium carbonate were usedas the reagents for the chemical fixation solutions evaluated in threesets of batch experiments: (1) FeSO4; (2) FeSO4 and KMnO4; (3) FeSO4,KMnO4 and CaCO3. The optimum treatment solutions for each soil wereidentified based on the mobility of arsenic during sequential leaching oftreated and untreated soils using the fluids described in EPA Method 1311[USEPA. Method 1311: toxicity characteristic leaching procedure. Testmethods for evaluating solid waste, physical/chemical methods. 3rd ed.Washington, DC: U.S. Environmental Protection Agency, Office of SolidWaste. U.S. Government Printing Office; 1992]toxic characteristicsleaching procedure (TCLP) and EPA Method 1312 [USEPA.Method 1312:synthetic precipitation leaching procedure. Test methods for evaluatingsolid waste, physical/chemical methods. 3rd ed. Washington, DC: U.S.Environmental Protection Agency, Office of Solid Waste. U.S. GovernmentPrinting Office; 1994]synthetic precipitation leaching procedure(SPLP).Both FW and BH soils showed …
Date: March 27, 2007
Creator: Yang, Li; Donahoe, Rona J. & Redwine, James C.
Partner: UNT Libraries Government Documents Department
open access

The Role of Filtration in Maintaining Clean Heat Exchanger Coils

Description: The main purpose of the study was to investigate the role of filtration in maintaining clean heat exchanger coils and overall performance. Combinations of 6 different levels of filtration (MERV 14, 11, 8, 6, 4, and no filter) and 4 different coils (an eight-row lanced-fin coil, HX8L), (an eight-row wavy-fin coil, HX8W), (a four-row lanced-fin coil, HX4L) and (a two-row lanced-fin coil, HX2L) were tested at 4 different air velocities (1.52, 2.03, 2.54,3.05 m/s (300, 400, 500, 600 ft/min)). The fouled conditions were obtained after injection of 600 grams of ASHRAE standard dust upstream of the filter/coil combination. This magnitude of dust is representative of a year of normal operation for an air conditioning system. The air-side pressure drops of the coils and filters and air-side heat transfer coefficients of the coils were determined from the measurements under the clean and fouled conditions. Depending upon the filter and coil test, the coil pressure drops increased in the range of 6%-30% for an air velocity at 2.54 m/s (500 ft/min). The impact was significantly greater for tests performed without a filter. The largest relative effect of fouling on pressure drop occurs for coils with fewer rows and having lanced fins. Coils with a greater number of rows can hold more dust so that a fixed amount of dust has a relatively smaller impact. The impact of fouling on air-side heat transfer coefficients was found to be relatively small. In some cases, heat transfer was actually enhanced due to additional turbulence caused by the presence of dust. The experimental results for pressure drops and heat transfer coefficients were correlated and the correlations were implemented within computer models of prototypical rooftop air conditioners and used to evaluate the impact of fouling on cooling capacity and EER. The equipment cooling capacity is reduced with …
Date: June 30, 2004
Creator: Yang, Li; Braun, James E. & Groll, Eckhard A.
Partner: UNT Libraries Government Documents Department
open access

Experimental and Computational Studies of the Isomerization Reactions of Bidentate Phosphine Ligands in Triosmium Clusters: Kinetics of the Rearrangements from Bridged to Chelated Isomers and X-ray Structures of the Clusters Os3 (CO)10 (dppbz), 1,1-Os3 (CO)10 (dppbzF4), HOs3 (CO)9 [μ -1,2-PhP (C6H4-ɳ1) C6H4PPh2], and HOs3 (CO)9- [μ-1,2-PhP (C6H4-ɳ 1) C6F4PPh2]

Description: Article on experimental and computational studies of the isomerization reactions of bidentate phosphine ligands in triosmium clusters.
Date: February 22, 2011
Creator: Zhang, Xue; Kandala, Srikanth; Yang, Li; Watson, William H.; Wang, Xiaoping; Hrovat, David A. et al.
Partner: UNT College of Arts and Sciences
open access

Experimental and Computational Preference for Phosphine Regioselectivity and Stereoselective Tripodal Rotation in Hos₃(Co)₈(PPh₃)₂(μ-1,2-N,Cη-¹,ᴋ¹-C₇H₄NS)

Description: This article investigates the site preference for ligand substitution in the benzothiazolate-bridged cluster HOs₃(CO)₁₀(μ-1,2-N,Cη-¹,ᴋ¹-C₇H₄NS) using PPh₃.
Date: September 12, 2018
Creator: Begum, Shahin A.; Chowdhury, Md. Arshad H.; Ghosh, Shishir; Tocher, Derek A.; Richmond, Michael G.; Yang, Li et al.
Partner: UNT College of Science
open access

Genome-wide analysis of promoter architecture in Drosophila melanogaster

Description: Core promoters are critical regions for gene regulation in higher eukaryotes. However, the boundaries of promoter regions, the relative rates of initiation at the transcription start sites (TSSs) distributed within them, and the functional significance of promoter architecture remain poorly understood. We produced a high-resolution map of promoters active in the Drosophila melanogaster embryo by integrating data from three independent and complementary methods: 21 million cap analysis of gene expression (CAGE) tags, 1.2 million RNA ligase mediated rapid amplification of cDNA ends (RLMRACE) reads, and 50,000 cap-trapped expressed sequence tags (ESTs). We defined 12,454 promoters of 8037 genes. Our analysis indicates that, due to non-promoter-associated RNA background signal, previous studies have likely overestimated the number of promoter-associated CAGE clusters by fivefold. We show that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases. This suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications. Transcription factor binding motifs are differentially enriched as a function of promoter shape, and peaked promoter shape is correlated with both temporal and spatial regulation of gene expression. Our results contribute to the emerging view that core promoters are functionally diverse and control patterning of gene expression in Drosophila and mammals.
Date: October 20, 2010
Creator: Hoskins, Roger A.; Landolin, Jane M.; Brown, James B.; Sandler, Jeremy E.; Takahashi, Hazuki; Lassmann, Timo et al.
Partner: UNT Libraries Government Documents Department
open access

High Throughput Identification, Purification and Structural Characterization of Water Soluble Protein Complexes in Desulfovibrio vulgaris

Description: Our scheme for the tagless purification of water soluble complexes. 10 g of protein from a crude bacterial extract is first fractionated by ammonium sulfate precipitation and then by a series of chromatographic steps: anion exchange (IEX), hydrophobic interaction (HIC), and finally size exclusion (Gel Filtration). Fractions from the last chromatography step are trypsin digested and peptides labeled with iTRAQ reagents to allow multiplexing and quantitation during mass spectrometric analysis. Elution profiles of identified proteins are then subjected to clustering analysis.
Date: May 17, 2010
Creator: Dong,, Ming; Han, Bong-Gyoon; Liu, Hui-Hai; Malik, J.; Geller, Jil; Yang, Li et al.
Partner: UNT Libraries Government Documents Department
open access

The transcriptional diversity of 25 Drosophila cell lines

Description: Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are ‘‘off’’ and survival/growth pathways ‘‘on.’’ Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal discderived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common ‘‘cell line‘‘ gene expression pattern. Wereport the transcriptional profiles of 25 Drosophila melanogaster cell lines, principally by whole-genome tiling microarray analysis of total RNA, carried out as part of the modENCODE project. The data produced in this study add to our knowledge of the cell lines and of the Drosophila transcriptome in several ways. We summarize the expression of previously annotated genes in each of the 25 lines with emphasis on what those patterns reveal about …
Date: November 15, 2010
Creator: Cherbas, Lucy; Willingham, Aarron; Zhang, Dayu; Yang, Li; Zou, Yi; Eads, Brian D. et al.
Partner: UNT Libraries Government Documents Department
open access

The developmental transcriptome of Drosophila melanogaster

Description: Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development. Drosophila melanogaster is an important non-mammalian model system that has had a critical role in basic biological discoveries, such as identifying chromosomes as the carriers of genetic information and uncovering the role of genes in development. Because it shares a substantial genic content with humans, Drosophila is increasingly used as a translational model for human development, homeostasis and disease. High-quality maps are needed for all functional genomic elements. Previous studies demonstrated that a rich collection of genes is deployed during the life cycle of the fly. Although expression profiling using microarrays has revealed the expression of, 13,000 annotated genes, it is difficult to map splice junctions and individual base modifications generated by RNA editing using such approaches. Single-base resolution is essential to define precisely the elements that comprise the Drosophila transcriptome. Estimates of the number of transcript isoforms are less accurate than estimates of the number of genes. Whereas, 20% of Drosophila genes are annotated as encoding alternatively spliced premRNAs, splice-junction microarray experiments indicate that this number is at least 40% (ref. 7). …
Date: December 2, 2010
Creator: Connecticut, University of; Graveley, Brenton R.; Brooks, Angela N.; Carlson, Joseph W.; Duff, Michael O.; Landolin, Jane M. et al.
Partner: UNT Libraries Government Documents Department
open access

Identification of functional elements and regulatory circuits by Drosophila modENCODE

Description: To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. Several years after the complete genetic sequencing of many species, it is still unclear how to translate genomic information into a functional map of cellular and developmental programs. The Encyclopedia of DNA Elements (ENCODE) (1) and model organism ENCODE (modENCODE) (2) projects use diverse genomic assays to comprehensively annotate the Homo sapiens (human), Drosophila melanogaster (fruit fly), and Caenorhabditis elegans (worm) genomes, through systematic generation and computational integration of functional genomic data sets. Previous genomic studies in flies have made seminal contributions to our understanding of basic biological mechanisms and genome functions, facilitated by genetic, experimental, computational, and manual annotation of the euchromatic and heterochromatic genome (3), small genome size, short life cycle, and a deep knowledge of development, gene function, and chromosome biology. The functions of {approx}40% of the protein and nonprotein-coding genes [FlyBase 5.12 (4)] have been determined from cDNA collections (5, 6), manual curation of gene models (7), gene mutations and comprehensive genome-wide RNA interference screens (8-10), and comparative genomic analyses …
Date: December 22, 2010
Creator: Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V.; Kheradpour, Pouya; Negre, Nicolas; Eaton, Matthew L. et al.
Partner: UNT Libraries Government Documents Department
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