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Search Results: 1 - 10 of 406795 matches for " Edward M. Fox "
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Real-Time, Variable-Depth Tillage for Managing Soil Compaction in Cotton Production  [PDF]
Jonathan W. Fox, Ahmad Khalilian, Young J. Han, Phillip B. Williams, Ali Mirzakhani Nafchi, Joe Mari Maja, Michael W. Marshall, Edward M. Barnes
Open Journal of Soil Science (OJSS) , 2018, DOI: 10.4236/ojss.2018.86012
Abstract: Cotton root growth is often hindered in the Southeastern U.S. due to the presence of root-restricting soil layers. Tillage must be used to temporarily remove this compacted soil layer to allow root growth to depths needed to sustain plants during periods of drought. However, the use of a uniform depth of tillage may be an inefficient use of energy due to the varying depth of this root-restricting layer. Therefore, the objective of this project was to develop and test equipment for controlling tillage depth “on-the-go” to match the soil physical parameters, and to determine the effects of site-specific tillage on soil physical properties, energy requirements, and plant responses in cotton production. Site-specific tillage operations reduced fuel consumption by 45% compared to conventional constant-depth tillage. Only 20% of the test field required tillage at recommended depth of 38-cm deep for Coastal Plain soils. Cotton taproot length in the variable-depth tillage plots was 96% longer than those in the no-till plots (39 vs. 19.8 cm). Statistically, there was no difference in cotton lint yield between conventional and the variable-depth tillage. Deep tillage (conventional or variable-rate) increased cotton lint yields by 20% compared to no-till.
Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility
Aidan Casey,Edward M. Fox,Stephan Schmitz-Esser,Aidan Coffey,Olivia McAuliffe,Kieran Jordan
Frontiers in Microbiology , 2014, DOI: 10.3389/fmicb.2014.00068
Abstract: Listeria monocytogenes is a virulent food-borne pathogen most often associated with the consumption of “ready-to-eat” foods. The organism is a common contaminant of food processing plants where it may persist for extended periods of time. A commonly used approach for the control of Listeria monocytogenes in the processing environment is the application of biocides such as quaternary ammonium compounds. In this study, the transcriptomic response of a persistent strain of L. monocytogenes (strain 6179) on exposure to a sub-lethal concentration of the quaternary ammonium compound benzethonium chloride (BZT) was assessed. Using RNA-Seq, gene expression levels were quantified by sequencing the transcriptome of L. monocytogenes 6179 in the presence (4 ppm) and absence of BZT, and mapping each data set to the sequenced genome of strain 6179. Hundreds of differentially expressed genes were identified, and subsequent analysis suggested that many biological processes such as peptidoglycan biosynthesis, bacterial chemotaxis and motility, and carbohydrate uptake, were involved in the response of L. monocyotogenes to the presence of BZT. The information generated in this study further contributes to our understanding of the response of bacteria to environmental stress. In addition, this study demonstrates the importance of using the bacterium's own genome as a reference when analysing RNA-Seq data.
Rubber Tree Distribution Mapping in Northeast Thailand  [PDF]
Zhe Li, Jefferson M. Fox
International Journal of Geosciences (IJG) , 2011, DOI: 10.4236/ijg.2011.24060
Abstract: In many parts of mainland Southeast Asia rubber plantations are expanding rapidly in areas where the crop was not historically found. Monitoring and mapping the distribution of rubber trees in the region is necessary for developing a better understanding of the consequences of land-cover and land-use change on carbon and water cycles. In this study, we conducted rubber tree growth mapping in Northeast Thailand using Landsat 5 TM data. A Mahalanobis typicality method was used to identify different age rubber trees. Landsat 5 TM 30 m non-thermal reflective bands, NDVI and tasseled cap transformation components were selected as the model input metrics. The validation was carried out using provincial level agricultural statistical data on the rubber tree growth area. At regional (Northeast Thailand) and provincial scales, the estimates of mature and middle-age rubber stands produced from 30 m Landsat 5 TM data compared well (high statistical significance) with the provincial rubber tree growth statistical data.
Analysis of the human cytomegalovirus genomic region from UL146 through UL147A reveals sequence hypervariability, genotypic stability, and overlapping transcripts
Nell S Lurain, Andrea M Fox, Heather M Lichy, Sangeeta M Bhorade, Carl F Ware, Diana D Huang, Sau-Ping Kwan, Edward R Garrity, Sunwen Chou
Virology Journal , 2006, DOI: 10.1186/1743-422x-3-4
Abstract: The region of the HCMV genome from UL146 through UL147A was analyzed in clinical strains for sequence variability, genotypic stability, and transcriptional expression. The UL146 sequences in clinical strains from two geographically distant sites were assigned to 12 sequence groups that differ by over 60% at the amino acid level. The same groups were generated by sequences from the UL146-UL147 intergenic region and the UL147 ORF. In contrast to the high level of sequence variability among unrelated clinical strains, the sequences of UL146 through UL147A from isolates of the same strain were highly stable after repeated passage both in vitro and in vivo. Riboprobes homologous to these ORFs detected multiple overlapping transcripts differing in temporal expression. UL146 sequences are present only on the largest transcript, which also contains all of the downstream ORFs including UL148 and UL132. The sizes and hybridization patterns of the transcripts are consistent with a common 3'-terminus downstream of the UL132 ORF. Early-late expression of the transcripts associated with UL146 and UL147 is compatible with the potential role of CXC chemokines in pathogenesis associated with viral replication.Clinical isolates from two different geographic sites cluster in the same groups based on the hypervariability of the UL146, UL147, or the intergenic sequences, which provides strong evidence for linkage and no evidence for interstrain recombination within this region. The sequence of individual strains was absolutely stable in vitro and in vivo, which indicates that sequence drift is not a mechanism for the observed sequence hypervariability. There is also no evidence of transcriptional splicing, although multiple overlapping transcripts extending into the adjacent UL148 and UL132 open reading frames were detected using gene-specific probes.Human cytomegalovirus (HCMV) has a double-stranded linear DNA genome of approximately 235 kbp in length making it the largest of the human
Next-Generation cDNA Screening for Oncogene and Resistance Phenotypes
Nobuaki Shindoh,Akinori Yoda,Yuka Yoda,Timothy J. Sullivan,Oliver Weigert,Andrew A. Lane,Nadja Kopp,Liat Bird,Scott J. Rodig,Edward A. Fox,David M. Weinstock
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049201
Abstract: There is a pressing need for methods to define the functional relevance of genetic alterations identified by next-generation sequencing of cancer specimens. We developed new approaches to efficiently construct full-length cDNA libraries from small amounts of total RNA, screen for transforming and resistance phenotypes, and deconvolute by next-generation sequencing. Using this platform, we screened a panel of cDNA libraries from primary specimens and cell lines in cytokine-dependent murine Ba/F3 cells. We demonstrate that cDNA library-based screening can efficiently identify DNA and RNA alterations that confer either cytokine-independent proliferation or resistance to targeted inhibitors, including RNA alterations and intergenic fusions. Using barcoded next-generation sequencing, we simultaneously deconvoluted cytokine-independent clones recovered after transduction of 21 cDNA libraries. This approach identified multiple gain-of-function alleles, including KRAS G12D, NRAS Q61K and an activating splice variant of ERBB2. This approach has broad applicability for identifying transcripts that confer proliferation, resistance and other phenotypes in vitro and potentially in vivo.
A multicenter, retrospective chart review study comparing index therapy change rates in open-angle glaucoma or ocular hypertension patients newly treated with latanoprost or travoprost-Z monotherapy
Joel M Fain, Sameer Kotak, Jack Mardekian, Jason Bacharach, Deepak P Edward, Steven Rauchman, Teresa Brevetti, Janet L Fox, Cherie Lovelace
BMC Ophthalmology , 2011, DOI: 10.1186/1471-2415-11-13
Abstract: At 14 clinical practice sites, medical records were abstracted for patients with a diagnosis of open-angle glaucoma or ocular hypertension and who were ≥40 years of age, had a baseline and at least one follow-up visit, and had no prior history of ocular prostaglandin use. Data regarding demographics, ocular/systemic medical histories, clinical variables, therapy initiations and reasons for changes, adverse events, and resource utilization were recorded from randomly chosen eligible charts. Primary outcomes were rates of and reasons for changing from the initial therapy within six months and across the full study period (1000 days).Data from 900 medical charts (latanoprost, 632; travoprost-Z, 268) were included. For both cohorts, average follow-up was >1 year. Cohorts were similar with regard to age (median ~67 years), gender distribution (>50% female), and diagnosis (~80% with open-angle glaucoma). Within six months, rates of index therapy change for latanoprost versus travoprost-Z were 21.2% (134/632) and 28.7% (77/268), respectively (p = 0.0148); across the full study period, rates were 34.5% (218/632) and 45.2% (121/268), respectively (p = 0.0026). Among those who changed their index therapy, insufficient IOP control was the most commonly reported reason followed by adverse events; hyperemia was the most commonly reported adverse event at index therapy change.In this "real world" study of changes in therapy in patients prescribed initial monotherapy with latanoprost with BAK or travoprost-Z with SofZia, medication changes were common in both treatment groups but statistically significantly more frequent with travoprost-Z.Research has demonstrated that progression of ocular hypertension to glaucoma and progression of glaucomatous damage can be delayed or halted with the use of topical ocular hypotensive agents [1-4]. Patients can benefit from these therapies only if they are taken as directed over the long term; however, medication discontinuation and changes may
Genome-Wide Analysis of Neuroblastomas using High-Density Single Nucleotide Polymorphism Arrays
Rani E. George, Edward F. Attiyeh, Shuli Li, Lisa A. Moreau, Donna Neuberg, Cheng Li, Edward A. Fox, Matthew Meyerson, Lisa Diller, Paolo Fortina, A. Thomas Look, John M. Maris
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000255
Abstract: Background Neuroblastomas are characterized by chromosomal alterations with biological and clinical significance. We analyzed paired blood and primary tumor samples from 22 children with high-risk neuroblastoma for loss of heterozygosity (LOH) and DNA copy number change using the Affymetrix 10K single nucleotide polymorphism (SNP) array. Findings Multiple areas of LOH and copy number gain were seen. The most commonly observed area of LOH was on chromosome arm 11q (15/22 samples; 68%). Chromosome 11q LOH was highly associated with occurrence of chromosome 3p LOH: 9 of the 15 samples with 11q LOH had concomitant 3p LOH (P = 0.016). Chromosome 1p LOH was seen in one-third of cases. LOH events on chromosomes 11q and 1p were generally accompanied by copy number loss, indicating hemizygous deletion within these regions. The one exception was on chromosome 11p, where LOH in all four cases was accompanied by normal copy number or diploidy, implying uniparental disomy. Gain of copy number was most frequently observed on chromosome arm 17q (21/22 samples; 95%) and was associated with allelic imbalance in six samples. Amplification of MYCN was also noted, and also amplification of a second gene, ALK, in a single case. Conclusions This analysis demonstrates the power of SNP arrays for high-resolution determination of LOH and DNA copy number change in neuroblastoma, a tumor in which specific allelic changes drive clinical outcome and selection of therapy.
ETDs, NDLTD, and open access: a 5S perspective
Fox, Edward A.;Yang, Seungwon;Kim, Seonho;
Ciência da Informa??o , 2006, DOI: 10.1590/S0100-19652006000200009
Abstract: worldwide initiatives toward digital library (dl) support for electronic theses and dissertations (etds), facilitated by the work of the networked digital library of theses and dissertations (ndltd), are a key part of the move toward open access. when all graduate students learn to use openly available etds, and have experience with authoring and submission in connection with their own research results, it will be easy for them to continue these efforts through other contributions to open access. when all universities support etd activities, they will be key participants in institutional repositories and open access, and will have engaged in discussion and infrastructure development supportive of further open access activities. understanding of open access also can be facilitated through modeling of all of these efforts using the 5s framework, considering the key aspects of dl development: societies, scenarios, spaces, structures, and streams.
Technology and research in a global Networked University Digital Library (NUDL)
Gon?alves, Marcos André;Fox, Edward A.;
Ciência da Informa??o , 2001, DOI: 10.1590/S0100-19652001000300003
Abstract: digital libraries (dls) are extremely complex information systems that support the creation, management, distribution, and preservation of complex information resources, while allowing effective and efficient interaction among the several societies that benefit from dl content and services. in this paper, we focus on our experience facing challenges of building, maintaining, and developing the networked university digital library (www.nudl.org), an extension of the networked digital library of theses and dissertations (www.ndltd.org). nudl is a worldwide initiative that addresses making the intellectual property produced in universities more accessible, stimulating international collaboration across all disciplines. we detail technological aspects of our solutions and research activities carried out to provide powerful and enriched services for the communities served by this initiative.
Automatically Generating Interfaces for Personalized Interaction with Digital Libraries
Saverio Perugini,Naren Ramakrishnan,Edward A. Fox
Computer Science , 2004,
Abstract: We present an approach to automatically generate interfaces supporting personalized interaction with digital libraries; these interfaces augment the user-DL dialog by empowering the user to (optionally) supply out-of-turn information during an interaction, flatten or restructure the dialog, and enquire about dialog options. Interfaces generated using this approach for CITIDEL are described.
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