Non-optical Imaging of Flow, Boiling, and Salt Deposition in a Simulated Debris Bed

Determining flow and heat transfer characteristics in a debris bed or a packed bed is difficult due to the lack of optical access. Non-optical imaging methods, such as x-ray or neutron imaging, can be used to observe flow characteristics and particle deposition, as well as boiling in a packed bed. An amorphous Silicon detector based digital radiography camera can be used to image with either x-rays or neutrons at up to 100 frames per second. The digital radiography camera, coupled with digital image analysis techniques was used to characterize fluid fraction and flow rates in a simulated debris bed. A water percolation experiment was performed where a test section filled with 1-3 mm glass particles was used as a simulated debris bed, and properties such as packing fraction, volumetric flow rate, and evaporation rate were calculated both physically and using data from the images. The values obtained using the images were benchmarked against the physically calculated values and found to be in agreement, validating the image processing algorithms

Hepatitis C Virus Induces Regulatory T Cells by Naturally Occurring Viral Variants to Suppress T Cell Responses

Regulatory T cell markers are increased in chronically infected individuals with the hepatitis C virus (HCV), but to date, the induction and maintenance of Tregs in HCV infection has not been clearly defined. In this paper, we demonstrate that naturally occurring viral variants suppress T cell responses to cognate NS3358-375 in an antigen-specific manner. Of four archetypal variants, S370P induced regulatory T cell markers in comparison to NS3358-375-stimulated CD4 T cells. Further, the addition of variant-specific CD4 T cells back into a polyclonal culture in a dose-dependent manner inhibited the T cell response. These results suggest that HCV is able to induce antigen-specific regulatory T cells to suppress the antiviral T cell response in an antigen-specific manner, thus contributing to a niche within the host that could be conducive to HCV persistence

Continuous Mercury and Chloride Monitors for Coal Gasifiers

Ames Laboratory will develop an integrated sampling and analysis system suitable for on-line monitoring of Hg and HCl in advanced coal-based gasifiers. The objectives of this project are to 1) summarize current technology for monitoring Hg and HCl in gaseous effluents, 2) identify analytical techniques for such determinations in high-temperature, high-pressure gases from coal-based systems for producing electrical power, 3) evaluate promising analytical approaches, and 4) produce reliable on-line monitors which are adaptable to plant-scale diagnostics and process control. Project Description Commercially available instruments which were potentially suitable for monitoring Hg and HCl in coal gasifiers were screened and the most promising techniques were selected for laboratory evaluation. For Hg, the techniques selected for further consideration were atomic absorption (AA) and atomic fluorescence (AF). For HCl, gas-filter-correlation infrared spectroscopy (GFCIR), a dry calorimetric procedure, and ion mobility spectroscopy (IMS) were selected for testing in the laboratory. The analytical systems selected for use in on-line Hg and HCl analyzers will be adapted for application to monitoring hot pressurized gases from coal gasifiers. Additional work will involve developing suitable gas conditioning and sample introduction systems. That work may be as important as the development of the analytical detectors themselves. After the laboratory studies have been completed, prototype instruments will be tested and evaluated in the field

Testing of a Continuous Sampling Mercury CEM at the EPA-Rotary Kiln Incinerator Simulator Facility

This report has been prepared to document the performance of the continuous sampling mercury monitoring system developed by Ames Laboratory for use as a continuous emission monitor (CEM). This work was funded by the U.S. Department of Energy, Office of Environmental Management, Office of Science and Technology, through the Mixed Waste Focus Area. The purpose of the project is to develop instrumentation and methods for spectroscopic field-monitoring applications. During FY01 this included continued development and testing of an echelle spectrometer system for the detection of mercury (Hg) by atomic absorption. Due to the relatively poor limits of detection for Hg by optical emission techniques, the CEM has been designed for the detection of elemental Hg by optical absorption. The sampling system allows continuous introduction of stack gas into the CEM for analysis of elemental and total Hg in the gas stream. A heated pyrolysis tube is used in this system to convert oxidized Hg compounds to elemental Hg prior to analysis for total Hg. The pyrolysis tube is bypassed to measure elemental Hg. The CEM is designed to measure the elemental Hg concentration of the gas sample, measure the total Hg concentration, perform a zero check (analysis of room air), and then re-zero the system (to correct for any instrumental drift that occurs over time). This is done in an automated, sequential measurement cycle to provide continuous monitoring of Hg concentrations in the stack gas. The continuous sampling Hg CEM was tested at the EPA-Rotary Kiln in Durham, NC at the beginning of FY02. This report describes the characteristics and performance of the system and the results of the field tests performed at EPA. The Hg CEM system was developed in response to the need of DOE and other organizations to monitor Hg that may be released during the processing or combustion of hazardous or mixed-waste materials. The promulgation of regulations limiting the release of Hg and requiring continuous monitoring of stack gases from combustion and treatment processes would seriously impact the operations of DOE waste treatment facilities. Therefore, it is important to develop and validate techniques that adequately meet proposed sensitivity and accuracy requirements. The most likely form of validation for such a technique involves comparison of CEM results with a reference test method for a test combustion system. Therefore, the CEM system was tested at EPA by monitoring Hg emissions in a natural gas combustion exhaust (that was spiked with Hg) while simultaneously collecting samples using the Ontario-Hydro mercury speciation method as the reference method. The CEM results were available continuously during the on-line monitoring that was performed. The results of the reference method sampling were received a number of weeks after the testing at EPA. These results are discussed in this report, with a comparison and evaluation of the reference method and Hg CEM data

The dead shall be raised : Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut

In July 2011, renovations to Yale-New Haven Hospital inadvertently exposed the cemetery of Christ Church, New Haven, Connecticut’s first Catholic cemetery. While this cemetery was active between 1833 and 1851, both the church and its cemetery disappeared from public records, making the discovery serendipitous. Four relatively well-preserved adult skeletons were recovered with few artifacts. All four individuals show indicators of manual labor, health and disease stressors, and dental health issues. Two show indicators of trauma, with the possibility of judicial hanging in one individual. Musculoskeletal markings are consistent with physical stress, and two individuals have arthritic indicators of repetitive movement/specialized activities. Radiographic analyses show osteopenia, healed trauma, and other pathologies in several individuals. Dental calculus analysis did not identify any tuberculosis indicators, despite osteological markers. Isotopic analyses of teeth indicate that all four were likely recent immigrants to the Northeastern United States. Nuclear and mitochondrial DNA were recovered from three individuals, and these analyses identified ancestry, hair/eye color, and relatedness. Genetic and isotopic results upended our initial ancestry assessment based on burial context alone. These individuals provide biocultural evidence of New Haven’s Industrial Revolution and the plasticity of ethnic and religious identity in the immigrant experience. Their recovery and the multifaceted analyses described here illuminate a previously undescribed part of the city’s rich history. The collective expertise of biological, geochemical, archaeological, and historical researchers interprets socioeconomic and cultural identity better than any one could alone. Our combined efforts changed our initial assumptions of a poor urban Catholic cemetery’s membership, and provide a template for future discoveries and analyses

Efficient error correction for next-generation sequencing of viral amplicons

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing.</p> <p>Results</p> <p>In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones.</p> <p>Conclusions</p> <p>Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses.</p> <p>The implementations of the algorithms and data sets used for their testing are available at: <url>http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm</url></p

Potential for La Crosse virus segment reassortment in nature

The evolutionary success of La Crosse virus (LACV, family Bunyaviridae) is due to its ability to adapt to changing conditions through intramolecular genetic changes and segment reassortment. Vertical transmission of LACV in mosquitoes increases the potential for segment reassortment. Studies were conducted to determine if segment reassortment was occurring in naturally infected Aedes triseriatus from Wisconsin and Minnesota in 2000, 2004, 2006 and 2007. Mosquito eggs were collected from various sites in Wisconsin and Minnesota. They were reared in the laboratory and adults were tested for LACV antigen by immunofluorescence assay. RNA was isolated from the abdomen of infected mosquitoes and portions of the small (S), medium (M) and large (L) viral genome segments were amplified by RT-PCR and sequenced. Overall, the viral sequences from 40 infected mosquitoes and 5 virus isolates were analyzed. Phylogenetic and linkage disequilibrium analyses revealed that approximately 25% of infected mosquitoes and viruses contained reassorted genome segments, suggesting that LACV segment reassortment is frequent in nature

Hepatitis C Virus Antigenic Convergence

Vaccine development against hepatitis C virus (HCV) is hindered by poor understanding of factors defining cross-immunoreactivity among heterogeneous epitopes. Using synthetic peptides and mouse immunization as a model, we conducted a quantitative analysis of cross-immunoreactivity among variants of the HCV hypervariable region 1 (HVR1). Analysis of 26,883 immunological reactions among pairs of peptides showed that the distribution of cross-immunoreactivity among HVR1 variants was skewed, with antibodies against a few variants reacting with all tested peptides. The HVR1 cross-immunoreactivity was accurately modeled based on amino acid sequence alone. The tested peptides were mapped in the HVR1 sequence space, which was visualized as a network of 11,319 sequences. The HVR1 variants with a greater network centrality showed a broader cross-immunoreactivity. The entire sequence space is explored by each HCV genotype and subtype. These findings indicate that HVR1 antigenic diversity is extensively convergent and effectively limited, suggesting significant implications for vaccine development

Dengue Virus Infection and Virus-Specific HLA-A2 Restricted Immune Responses in Humanized NOD-scid IL2rγnull Mice

BACKGROUND:The lack of a suitable animal model to study viral and immunological mechanisms of human dengue disease has been a deterrent to dengue research. METHODOLOGY/PRINCIPAL FINDINGS:We sought to establish an animal model for dengue virus (DENV) infection and immunity using non-obese diabetic/severe combined immunodeficiency interleukin-2 receptor gamma-chain knockout (NOD-scid IL2rgamma(null)) mice engrafted with human hematopoietic stem cells. Human CD45(+) cells in the bone marrow of engrafted mice were susceptible to in vitro infection using low passage clinical and established strains of DENV. Engrafted mice were infected with DENV type 2 by different routes and at multiple time points post infection, we detected DENV antigen and RNA in the sera, bone marrow, spleen and liver of infected engrafted mice. Anti-dengue IgM antibodies directed against the envelope protein of DENV peaked in the sera of mice at 1 week post infection. Human T cells that developed following engraftment of HLA-A2 transgenic NOD-scid IL2rgamma(null) mice with HLA-A2(+) human cord blood hematopoietic stem cells, were able to secrete IFN-gamma, IL-2 and TNF-alpha in response to stimulation with three previously identified A2 restricted dengue peptides NS4b 2353((111-119)), NS4b 2423((181-189)), and NS4a 2148((56-64)). CONCLUSIONS/SIGNIFICANCE:This is the first study to demonstrate infection of human cells and functional DENV-specific T cell responses in DENV-infected humanized mice. Overall, these mice should be a valuable tool to study the role of prior immunity on subsequent DENV infections

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

<p>Abstract</p> <p>Background</p> <p>Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely.</p> <p>Results</p> <p>To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment.</p> <p>Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers.</p> <p>Conclusions</p> <p>Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at <url>http://www.labkey.org</url>. Documentation and source code are available under the Apache License 2.0.</p