Improved oil recovery in Mississippian carbonate reservoirs of Kansas near term Class 2. Annual report, September 18, 1994--March 15, 1997

This annual report describes progress during the second year of the project entitled {open_quotes}Improved Oil Recovery in Mississippian Carbonate Reservoirs in Kansas{close_quotes}. This project funded under the Department of Energy`s Class 2 program targets improving the reservoir performance of mature oil fields located in shallow shelf carbonate reservoirs. The focus of this project is development and demonstration of cost-effective reservoir description and management technologies to extend the economic life of mature reservoirs in Kansas and the mid-continent. As part of the project, several tools and techniques for reservoir description and management were developed, modified and demonstrated. These include: (1) a new approach to subsurface visualization using electric logs ({open_quotes}Pseudoseismic{open_quotes}); (2) a low-cost easy-to-use spreadsheet log analysis software (PfEFFER); and (3) an extension of the BOAST-3 computer program for full field reservoir simulation. The world-wide-web was used to provide rapid and flexible dissemination of the project results through the Internet. Included in this report is a summary of significant project results at the demonstration site (Schaben Field, Ness County, Kansas). These results include an outline of the reservoir description based on available and newly acquired data and reservoir simulation results. Detailed information is available on-line through the Internet. Based on the reservoir simulation, three infill wells will be drilled to validate the reservoir description and demonstrate the effectiveness of the proposed reservoir management strategies. The demonstration phase of the project has just begun and will be presented in the next annual report

Observational diagnostics of gas in protoplanetary disks

Protoplanetary disks are composed primarily of gas (99% of the mass). Nevertheless, relatively few observational constraints exist for the gas in disks. In this review, I discuss several observational diagnostics in the UV, optical, near-IR, mid-IR, and (sub)-mm wavelengths that have been employed to study the gas in the disks of young stellar objects. I concentrate in diagnostics that probe the inner 20 AU of the disk, the region where planets are expected to form. I discuss the potential and limitations of each gas tracer and present prospects for future research.Comment: Review written for the proceedings of the conference "Origin and Evolution of Planets 2008", Ascona, Switzerland, June 29 - July 4, 2008. Date manuscript: October 2008. 17 Pages, 6 graphics, 134 reference

Proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction

Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies

A systematic review of the effects of exercise interventions on body composition in HIV+ adults

Over the years, physical activity and exercise have been used to positively impact the health and quality of life of persons infected with HIV and, more recently, has been associated with a spectrum of body composition changes. The aim of this review was to examine the effects of various exercise interventions on body composition in HIV positive adults, using a search strategy of randomized, controlled trials (RCTs). A systematic review was performed by five independent reviewers using a predetermined protocol adapted from previous research for assessing the articles for inclusion, the extracted data, and methodological quality. Eight RCTs involving 430 (26% female) HIV positive adults performing exercise a minimum of thrice weekly for at least six weeks were finally selected: Four were progressive resistance training (PRT) studies, three were aerobic training (AT) studies, and one involved yoga. In the PRT studies, there were significant increases in three anthropometric measures, namely, body mass, sum of skinfolds and sum of limb girths. In the AT studies, significant decreases were found in seven anthropometric measures, namely, body mass index, waist-hip ratio, body mass, triceps skinfold, waist circumference and sum of skinfolds. With yoga, the changes were nonsignificant. Exercise contributes to improved body composition and, when applied safely, appears to be beneficial for adults living with HIV/AIDS. However, these findings should be interpreted cautiously due to the relatively few RCTs published to date. Future studies would benefit from increased attention to sample size, female participants, participant follow-up, complete statistical analysis and intention-to-treat analysis.Scopu

Fabrication of electron beam generated, chirped, phase mask (1070 . 11 – 1070 . 66 nm) for fiber Bragg grating dispersion compensator

We report on the fabrication of a chirped, phase mask that was used to create a fiber Bragg grating(FBG)device for the compensation of chromatic dispersion in longhaul optical transmission networks.Electron beamlithography was used to expose the grating onto a resist-coated quartz plate. After etching, this phase mask was used to holographically expose an index grating into the fiber core [K. O. Hill, F. Bilodeau, D. C. Johnson, and J. Albert, Appl. Phys. Lett.62, 1035 (1993)]. The linear increase in the grating period, “chirp,” is only 0.55 nm over the 10 cm grating. This is too small to be defined by computer aided design and a digital deflection system. Instead, the chirp was incorporated by repeatedly rescaling the analog electronics used for field size calibration. Special attention must be paid to minimize any field stitching and exposure artifacts. This was done by using overlapping fields in a “voting” method. As a result, each grating line is exposed by the accumulation of three overlapping exposures at 1/3 dose. This translates any abrupt stitching error into a small but uniform change in the line-to-space ratio of the grating. The phase mask was used with the double-exposure photoprinting technique [K. O. Hill, F. Bilodeau, B. Malo, T. Kitagawa, S. Thériault, D. C. Johnson, J. Albert, and K. Takiguchi, Opt. Lett. 19, 1314 (1994)]: a KrF excimer laser holograp

Transverse Beam Spin Asymmetries in Forward-Angle Elastic Electron-Proton Scattering

We have measured the beam-normal single-spin asymmetry in elastic scattering of transversely-polarized 3 GeV electrons from unpolarized protons at Q^2 = 0.15, 0.25 (GeV/c)^2. The results are inconsistent with calculations solely using the elastic nucleon intermediate state, and generally agree with calculations with significant inelastic hadronic intermediate state contributions. A_n provides a direct probe of the imaginary component of the 2-gamma exchange amplitude, the complete description of which is important in the interpretation of data from precision electron-scattering experiments.Comment: 5 pages, 3 figures, submitted to Physical Review Letters; shortened to meet PRL length limit, clarified some text after referee's comment

Strange Quark Contributions to Parity-Violating Asymmetries in the Forward G0 Electron-Proton Scattering Experiment

We have measured parity-violating asymmetries in elastic electron-proton scattering over the range of momentum transfers 0.12 < Q^2 < 1.0 GeV^2. These asymmetries, arising from interference of the electromagnetic and neutral weak interactions, are sensitive to strange quark contributions to the currents of the proton. The measurements were made at JLab using a toroidal spectrometer to detect the recoiling protons from a liquid hydrogen target. The results indicate non-zero, Q^2 dependent, strange quark contributions and provide new information beyond that obtained in previous experiments.Comment: 5 pages, 2 figure