Core Analysis Tools Research Articles

Cytokine profile of human limbal myofibroblasts: Key players in corneal antiviral response.

Corneal transparency may be compromised by viral infections causing corneal scarring, edema, and neovascularization. Ocular injury results from collateral damage induced by exacerbated immune response in corneal stroma. Myofibroblasts play a key role in this process by producing a disorganized extracellular matrix and inflammatory mediators. However, the immune response profile of myofibroblasts during viral infections is still under study. The aim of this work was to analyze the cytokine profile of human limbal myfibroblasts (HLMs) stimulated with the double-stranded RNA analog polyinosinic:polycytidylic acid (poly I:C) and to identify their signaling pathways. HLMs were isolated from cadaveric sclera-corneal rims and stimulated with poly I:C (10μg/ml) for 12h. The secretion of 36 cytokines was measured using the Human Cytokine Array Panel A. The secretion of IFN-β was quantified by ELISA. The expression of pattern recognition receptors (PRRs) such as TLR3, RIG-1 and MDA5 were analyzed by western blot assays. Furthermore, translocation of the nuclear factors NF-κB, IRF3, and IRF7 was assessed by fluorescence staining. In addition, the differentially expressed cytokines were analyzed using the Core Analysis Tool of the Ingenuity Pathway Analysis IPA software. HLMs stimulated with poly I:C increased (fold change>2) the secretion of G-CSF, sTREM-1, CXCL1, CCL1, CXCL8, CXCL10, CXCL11, CCL2, CCL5, IL-13, IL-6, IL-1ra, and IFN-β compared with HLMs under basal conditions. Poly I:C stimulation also induced the expression of RIG-1 (p<0.001), but the expression of TLR3 and MDA5 was unmodified. Finally, HLMs increased nuclear translocation of NF-κB, IRF3, and IRF7 after poly I:C stimulation. Bioinformatic analysis identified canonical signaling pathways associated with cell adhesion and diapedesis, chemokine signaling, and activation of IRFs by cytosolic pattern recognition receptors. These results demonstrate that HLMs secrete cytokines involved in immune cell activation and chemotaxis. The data suggest a key role for HLMs during viral infections in cornea and extend our knowledge about the signaling pathways they trigger.

BEAVRS BENCHMARK EVALUATION WITH CASMO5 AND SIMULATE5

The MIT BEAVRS benchmark problem, which was primarily setup for the verification and validation of high-fidelity tools that have coupled neutron transport, thermal-hydraulics, and fuel isotopic depletion models, has also found extensive usage in the reactor physics community for validating core analysis tools. The primary purpose of this paper is to provide an accurate, comprehensive evaluation of the BEAVRS benchmark with CASMO5 and SIMULATE5 codes. The CMS5 calculated results for low-power physics tests (hot zero power critical boron, control rod worth and isothermal temperature coefficients) and full power operation (boron let-down and flux map reaction rate distributions) are compared to plant measured data provided in the benchmark specification. The CMS5 model, using ENDF/BVII.1 nuclear data library, predicts HZP critical boron concentration for all-rods-out conditions within 10 ppm for Cycle-1, and 25 ppm in Cycle-2; the control rod worth is predicted with a difference of 0.7% ± 3.8%, where the maximum difference is less than 10%. For the core follow calculations at the hot full power condition, the average difference in predicting the critical boron concentration is less than 20 ppm. In addition, the radial and nodal reaction rate distributions are predicted with a mean difference of about 1.6% and 3.8%, respectively. The CMS5 calculations are repeated using the most recent ENDF/B-VIII.0 library. No significant difference is observed in predicting measured plant parameters with different nuclear data libraries. Additionally, the impact of various modeling options, which are typically employed with nodal diffusion codes, on the predictions of important core parameters are presented as part of the benchmark evaluation.

Plasmonic evolution maps for planar metamaterials

Understanding the mode’s origin in planar metamaterials is fundamental for related applications in nanophotonics and plasmonics. For complex planar metamaterials, conventional analysis that directly obtains the final charge/current distribution of a mode is usually difficult in helping to understand the mode’s origin. In this paper, we propose a mode evolution method (MEM) with a core analysis tool, i.e., plasmonic evolution maps (PEMs), to describe the mode evolution in several complementary planar metamaterials with designed plasmonic atoms/molecules. The PEMs could not only clearly explain a mode’s origin, but also reveal the role of a structure’s symmetry in the mode formation process. The MEM with PEMs can work as a simple, efficient, and universal approach for the mode analysis in different kinds of planar metamaterials.

Rat astrocytes during anoxia: Secretome profile of cytokines and chemokines.

IntroductionThe precise mechanisms of the inflammatory responses after cerebral ischemia in vivo are difficult to elucidate because of the complex nature of multiple series of interactions between cells and molecules. This study explored temporal patterns of secretion of 30 cytokines and chemokines from Sprague Dawley rat astrocytes in primary culture in order to elucidate signaling pathways that are triggered by astrocytes during anoxia.MethodsPrimary cultures of rat brain astrocytes were incubated for periods of 2–24 hr in the absence of oxygen (anoxia) or under normal partial pressure of oxygen (controls). Simultaneous detection of 29 cytokines and chemokines in the samples was performed using a rat cytokine array panel, while the temporal pattern of angiopoietin‐1 (Ang‐1) secretion was determined separately using ELISA. Wilcoxon–Mann–Whitney test was used to compare normoxic and anoxic samples and the Hodge–Lehman estimator with exact 95% confidence intervals was computed to assess the size of differences in cytokine secretion. The obtained data were imported into the Core Analysis tool of Ingenuity Pathways Analysis software in order to relate changes in secretion of cytokines and chemokines from astrocytes during anoxia to potential molecular signal networks.ResultsWith the exception of Ang‐1, concentrations of all cytokines/chemokines in samples collected after anoxia exposure were either the same, or higher, than in control groups. No clear pattern of changes could be established for groups of cytokines with similar effects (i.e., pro‐ or anti‐inflammatory cytokines). The pattern of changes in cytokine secretion during anoxia was associated with the HIF‐1α‐mediated response, as well as cytokines IL‐1β and cathepsin S pathways, which are related to initiation of inflammation and antigen presentation, respectively, and to ciliary neurotrophic factor.ConclusionsThese in vitro findings suggest that astrocytes may play a role in triggering inflammation during anoxia/ischemia of the brain.

The State of Software for Evolutionary Biology.

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development.

Mechanical behavior of hydrate-bearing pressure-core sediments visualized under triaxial compression

Geomechanical and geotechnical properties are essential for evaluating the stability of deep seabed and subsea production systems for gas hydrate extraction from marine sediments. In this study, natural gas hydrate-bearing sediment was subjected to triaxial compression tests (shearing) using a newly developed triaxial testing system (TACTT) to investigate the geomechanical behavior of sediments recovered from below the seafloor in the eastern Nankai Trough, where the first Japanese offshore production test was conducted in 2013. The sediments were recovered using a hybrid pressure coring system, with pressure cores cut using onboard pressure core analysis tools. The pressure cores were subsequently transferred to our shore-based laboratory and subsampled using pressure core non-destructive analysis tools (PNATS) for the TACTT system. Pressure and temperature conditions were maintained within the hydrate stability boundary during coring and laboratory testing. An image processing technique was used to capture deformation of the sediment sample within the transparent acrylic test cell, and digital photographs were obtained for each 0.1% strain level experienced by the sample during the triaxial compression test. Analysis of the digitized images showed that sediments with 63% hydrate saturation exhibited brittle failure, whereas hydrate-free sediments exhibited ductile failure. The increase in shear strength with increasing hydrate saturation in natural gas hydrates is in agreement with previous data from sediments containing synthetic gas hydrates.

Methodology to Evaluate Active Transportation and Demand Management Strategies

This paper describes a methodology for predicting the impacts of active transportation and demand management (ATDM) measures on highway performance that can be applied using either microsimulation or Highway Capacity Manual (HCM) analysis techniques.Active transportation and demand management (ATDM) is a comprehensive approach to facility management and operation that seeks to increase facility productivity by proactively balancing supply and demand to avoid or delay facility breakdown. Examples of ATDM measures include: adaptive ramp metering, congestion pricing, speed harmonization, traveler information systems, and adaptive traffic signal control systems. Incident management and work zone management programs may employ one or more of these ATDM measures.The proposed ATDM analysis methodology is employed as a “wrapper” to a “core” analysis tool, such as the HCM or microsimulation. The core analysis tool is applied several times to a set of demand/capacity scenarios. The demand/capacity scenarios are developed based on observations of annual fluctuations in weekday peak period demands and capacities for the facility. The scenario results are then combined according to their probability of occurrence in order to predict the full-year peak period performance of the street, highway, or freeway facility.The application of the methodology is illustrated on a real-world freeway facility. The Highway Capacity Manual FREEVAL procedure, the selected “core” analysis tool, was adapted to test ramp metering, HOV (High Occupancy Vehicle) lanes, and HOT (High Occupancy Toll) lanes within the ATDM evaluation methodology. FREEVAL was applied to each of several demand/capacity scenarios and the results combined into an estimate of average performance improvements for each ATDM measure. The predicted facility performance improvements were compared to a before/after field studies reported in the literature. © 2011 Published by Elsevier Ltd.

Within-Pin Reaction Rate Distributions: CASMO-4 and HELIOS Compared Against Tomographic Measurements at the PROTEUS Reactor

In the framework of the LWR-PROTEUS project—an extended validation program for advanced light water reactor core analysis tools conducted at the Paul Scherrer Institute—the radial, internal variations of the total fission rate (Ftot) and the capture rate in 238U (C8) have been calculated for zero-burnup pins of a Westinghouse SVEA-96+ boiling water reactor fuel assembly using two codes, namely, CASMO-4 and HELIOS. While Ftot distributions predicted by CASMO-4 and HELIOS are in good agreement, C8 distributions show significant inconsistencies (20 to 30%). The calculations are compared with experimental results obtained using single photon emission computerized tomography for several SVEA-96+ pins irradiated in the zero-power reactor PROTEUS. The comparisons confirm the predicted shape of the Ftot distributions within UO2 pins and clearly indicate that HELIOS within-pin predictions for C8 are more reliable than CASMO-4 results. This is important for the derivation of gamma-ray self-absorption corrections when pin-integrated reaction rates are to be determined using the gamma-scanning technique. Thus, the use of CASMO-4-type within-pin distributions would lead to 3 to 4% discrepancies in the absolute, self-absorption-corrected pin-integrated values deduced for C8 and hence for C8/Ftot. For relative C8 distributions, the discrepancy would be much smaller, namely, up to ~1% if pins containing a burnable absorber are involved.

Strategy as simplicity—rediscovering the essence of strategic management

Strategic management (and especially strategic planning) has come under increasing challenge in recent times. From a manager (and thus a customer) perspective, strategic management may seem to be unduly complex, hard to understand, and sometimes remote from everyday management realities. These impressions may or may not be justified. Nevertheless strategic management might benefit considerably through rediscovering its essence—and simplifying its core analysis tools might provide a fruitful first step. In this article, a single analysis tool (derived from force field analysis) is applied to a dozen key management issues. The result is a more manager-friendly framework for analysing strategy, implementation and performance. It also gives academic researchers a means of exploring managers' cognitive maps. Copyright © 1998 John Wiley & Sons, Ltd.

X-ray Computed Tomography (CT) Applied in Routine Core Analysis: Examples from New Guinea and the North West Shelf, Australia: ABSTRACT

X-ray Computed Tomography (CT) is a powerful technique for nondestructive 3-D analyses of cores. It provides sedimentological and structural information that is difficult or impossible to obtain by other means. Nevertheless, x-ray CT has until recently lacked acceptance by the petroleum industry as a routine core analysis tool. The reasons for this stem mainly from resolution limitations of second generation CT scanners used to carry out early research on cores, a lack of image analysis software specific to core analysis, and the relatively high cost of scanning. Increased emphasis is now being placed on detailed reservoir characterization and the need to better define heterogeneity on the core scale. Core analysis has become more sophisticated and expensive. These factors, combined with more advanced CT scanner hardware and image analysis software, have resulted in a resurgence of company interest in x-ray CT. Indeed, the technique has now evolved to where it plays an increasingly important part in the process of routine core analysis. The authors present examples from New Guinea and the North West Shelf, Australia, where x-ray CT is being successfully used to scan sealed core for selection of core plug sites, determination of plug integrity prior to special core analysis,more » and assessment of formation damage through testing of various mud systems flushed through core plugs. Drilling-induced damage is also being quickly assessed through the scanning of sealed core. In addition, minipermeameter results have been related to CT images as a means by which core-scale permeability pathways can be mapped in 3-D.« less

Computerised tomography as a core analysis tool: application, instrument evaluation, and image improvement techniques

Computerised tomography as a core analysis tool: application, instrument evaluation, and image improvement techniques

Computed Tomography as a Core Analysis Tool: Applications, Instrument Evaluation, and Image Improvement Techniques

In recent years, the use of computerized tomography (CT) to characterize two-phase fluid flow through porous media has become increasingly popular. This paper describes a different application of CT: it use as a core analysis tool. The advantages and disadvantages of the different technological generations of commercial medical CT scanners available as core analysis instruments are also discussed. Additionally, methods are presented for improving images and reducing CT-number errors inherent in the scanning of high-density rock samples on instruments whose software was designed for the scanning of the low-density human patients.