gebhart/patrepeval huggingface dataset:
Bioinformatic analysis of expressed sequence tags derived from a compatible <i>Alternaria brassicicola</i> – <i>Brassica oleracea</i> interaction (2006)

SUMMARY Alternaria brassicicola is a necrotrophic fungal pathogen that causes black spot disease on members of the Brassicaceae plant family. In order to identify candidate fungal pathogenicity genes and characterize a compatible host response, a suppression subtractive hybridization (SSH) cDNA library enriched for A. brassicicola and Brassica oleracea genes expressed during the interaction was created, along with a fungal cDNA library representing genes expressed during nitrogen starvation (NS). A total of 3749 and 2352 expressed sequence tags (ESTs) were assembled into 2834 and 1264 unisequence sets for the SSH and NS libraries, respectively. We compared two methods to identify the origins (plant vs. fungal) of ESTs in the SSH library using different classification procedures, with and without the availability of a database representing the A. brassicicola whole genome sequence and Brassicaceae-specific genes. BLASTX analyses of the 2834 unisequence set using the GenBank non-redundant database identified 114 fungal genes. Further BLASTN analyses of the genes with unidentifiable origin using a database consisting of the 1264 fungal unisequence set from the nitrogen-starved library identified 94 additional fungal genes. By contrast, BLASTN analyses of the same SSH unisequence set using a partially assembled A. brassicicola whole genome draft sequence identified a total of 310 unisequenes of fungal origin. Our results indicated that even a small number of organism-specific EST sequences can be very helpful to identify pathogen genes in a library derived from infected tissue, partially overcoming the limitation of the public databases for little studied organisms. However, using the whole genome draft sequence of A. brassicicola we were able to identify approximately 30% more fungal genes in the SSH library than without utilizing this resource. The putative role of specific fungal and plant genes identified in this study in a compatible interaction is discussed.
<title>Digital Light Processing and MEMS: reflecting the digital display needs of the networked society</title> (1996)

Digital video technology is becoming increasingly important to the networked society. The natural interface to digital video is a digital display, one that accepts electrical bits at its input and converts them into optical bits at the output. The digital-to-analog processing function is performed in the mind of the observer. Texas Instruments has developed such a display with its recent market introduction of the Digital Light Processing<SUP>TM</SUP> (DLP<SUP>TM</SUP>) projection display. DLP technology is based on the Digital Micromirror Device<SUP>TM</SUP> (DMD<SUP>TM</SUP>), a microelectromechanical systems (MEMS) array of semiconductor-based digital light switches. The DMD switching array precisely controls a light source for projection display and digital printing applications. This paper presents an overview of DLP technology along with the architecture, projection operation, manufacture, and reliability of the DMD. Features of DMD technology that distinguish it from conventional MEMS technology are explored. Finally, the paper provides a view of DLP business opportunities.
RT-level Fault Simulation Techniques based on Simulation Command Scripts (2000)

With the advent of new RT-level design and test flow, new tools are needed to migrate at the RT-level the activities of fault simulation, testability analysis, and test pattern generation. This paper focuses on fault simulation at the RT-level, and aims at exploiting the capabilities of commercial VHDL simulators to compute faulty responses without modifying the VHDL source code. The proposed approach was implemented as a prototypical tool, and experimental results show that simulation of a faulty circuit is no more costly than simulation of the original circuit. For defining RT-level faults, we adopted a refinement of the observabilityenhanced statement coverage metric. While this metric usually handles observability in an approximated way, we were able to efficiently and exactly determine the observability of single-bit stuck-at faults on all assignment statements.
Generation and Characterization of <i>dickkopf3</i> Mutant Mice (2006)

dickkopf (dkk) genes encode a small family of secreted Wnt antagonists, except for dkk3, which is divergent and whose function is poorly understood. Here, we describe the generation and characterization of dkk3 mutant mice. dkk3-deficient mice are viable and fertile. Phenotypic analysis shows no major alterations in organ morphology, physiology, and most clinical chemistry parameters. Since Dkk3 was proposed to function as thyroid hormone binding protein, we have analyzed deiodinase activities, as well as thyroid hormone levels. Mutant mice are euthyroid, and the data do not support a relationship of dkk3 with thyroid hormone metabolism. Altered phenotypes in dkk3 mutant mice were observed in the frequency of NK cells, immunoglobulin M, hemoglobin, and hematocrit levels, as well as lung ventilation. Furthermore, dkk3-deficient mice display hyperactivity.
Predictive Resource Scheduling in Computational Grids (2007)

The integration of clusters of computers into computational grids has recently gained the attention of many computational scientists. While considerable progress has been made in building middleware and workflow tools that facilitate the sharing of compute resources, little attention has been paid to grid scheduling and load balancing techniques to reduce job waiting time. Based on a detailed analysis of usage characteristics of an existing grid that involves a large CPU cluster, we observe that grid scheduling decisions can be significantly improved if the characteristics of current usage patterns are understood and extrapolated into the future. The paper describes an architecture and an implementation for a predictive grid scheduling framework which relies on Kalman filter theory to predict future CPU resource utilisation. By way of replicated experiments we demonstrate that the prediction achieves a precision within 15-20% of the utilisation later observed and can significantly improve scheduling quality, compared to approaches that only take into account current load indicators.
Laboratory studies evaluating the enhanced biodegradation of weathered crude oil components through the application of nutrients (1990)

Bench-scale biodegradability studies of the Alaskan weathered crude oil were undertaken as part of the bioremediation project for the shorelines of Prince William Sound, Alaska, contaminated by the Exxon oil spill. The purpose of the studies was to evaluate the capability of the indigenous microbial consortium of the sea water and island beach areas, to biodegrade the weathered crude oil alkane hydrocarbon and polynuclear aromatic (PAH) constituents in batch-type respirometric reactors and shaker flask systems. Biodegradation studies incorporated the use of Inipol EAP 22 as the fertilizer nutrient source. In the respirometric studies, the unpolluted beach material in seawater was spiked with 1,000, 300, and 100 mg/L of weathered crude oil and with Inipol at 5% of oil weight was used in shaker flask studies. Temperature of incubation in both studies was 15 C and culture systems were incubated in darkness. Cumulative oxygen uptake data, growth data and GC/MS analysis data demonstrate almost complete utilization of the alkane hydrocarbon constituents in the presence of Inipol fertilizer and significant biodegradation of the PAH constituents after 6 weeks of incubation.
Splice losses in step-index fibers: dependency on fiber-break angle (1977)

Coupling has been measured for dry-spliced fibers as a function of break angle. The angles were measured interferometrically to about 0.1 degrees accuracy. An analysis is performed, and the measurements are found to be within 1.0% RMS of the calculation.
Experimental and Theoretical Studies of Redox Reactions of <i>o</i>-Chloranil in Aqueous Solution (2009)

The electrochemical reduction of o-chloranil (OCA) in aqueous solution has been studied experimentally and theoretically. The effects of temperature and pH on various thermodynamic parameters were studied by means of cyclic voltammetry. The pH dependence of the redox activity of OCA in aqueous solution at temperatures in the range 25-40 degrees C was used for the experimental determination of the standard reduction potentials of both the one-proton-two-electron (0.67 V) and two-proton-two-electron (0.79 V) reduction processes. The temperature dependency of the equilibrium constants of studied reactions has been used in order to determine enthalpy, entropy, and Gibbs energy changes of the reactions. It is found that the two studied redox reactions of OCA are strongly affected by solvation effects and controlled by entropy contributions to the Gibbs free energies. High-level ab initio calculations (G3 and CBS-QB3 using the CPCM solvation model) have been employed to calculate the reduction potentials of OCA in aqueous solution for the one-proton-two-electron (0.65 and 0.69 V at the respective levels of theory) and two-proton-two-electron (0.81 and 0.83 V) reactions, which are in excellent agreement with the corresponding experimental values. The acidic strength of the reduced form of OCA in aqueous solution, pK(a), has been also calculated (5.2) and is also in excellent agreement with the experimental value (5.0). The agreement mutually verifies the accuracy of experimental method and the validity of the mathematical model.
A novel mechanism regulates H<sub>2</sub>S and SO<sub>2</sub> production in <i>Saccharomyces cerevisiae</i> (2010)

Sulfite (SO(2) ) plays an important role in flavour stability in alcoholic beverages, whereas hydrogen sulfide (H(2) S) has an undesirable aroma. To discover the cellular processes that control SO(2) and H(2) S production, we screened a library of Saccharomyces cerevisiae deletion mutants. Deletion of 12 genes led to increased H(2) S productivity. Ten of these genes are known to be involved in sulfur-containing amino acid metabolism, whereas UBI4 functions in the ubiquitin-proteasome system and SKP2 encodes an F-box-containing protein whose function is unknown. We found that the skp2 mutant accumulated H(2) S and SO(2) , because the adenosylphophosulfate kinase Met14p is a substrate of SCF(Skp2) and more stable in the skp2 mutant than in the wild-type strain. Furthermore, the skp2 mutant grew more slowly than the wild-type strain under nutrient-limited conditions. Metabolome analysis showed that the concentration of intracellular cysteine is lower in the skp2 mutant than in the wild-type strain. The slow growth of the skp2 mutant was due to a lower concentration of intracellular cysteine, because the addition of cysteine suppressed the slow growth. In the skp2 mutant, the cysteine biosynthesis proteins Str2p, Str3p and Str4p are more stable than in the wild-type strain. Moreover, supplementation with methionine, S-adenosylmethionine, S-adenosylhomocysteine and homocysteine also suppressed the slow growth. Overexpression of STR1 or STR4 caused a more severe defect in the skp2 mutant. These results suggest that the balance of methionine and cysteine biosynthesis is important for yeast cell growth. Thus, Skp2p is one of the key components regulating this balance and H(2) S/SO(2) production.
Katalytische Hydrierung von Imidazolen (1968)

Abstract Bei der Pd‐katalysierten Hydrierung von Carbonsäure‐imidazoliden wird in Essigester die Carbonyl‐Gruppe reduziert (1 → 2) , in Eisessig (auch mit Pt) dagegen der Imidazol‐Kern hydriert und teilweise acetyliert (4 → 5 → 6) .
Cu metallization using a permanent magnet electron cyclotron resonance microwave plasma/sputtering hybrid system (1996)

A permanent magnet electron cyclotron resonance microwave plasma source has been coupled to a copper sputter target to produce ionized copper fluxes for submicron integrated circuit metallization. A custom launcher assembly allows the use of microwave powers up to 5 kW in a metal deposition environment to produce plasma densities ≳1012 cm−3, well above the cutoff density at 2.45 GHz of ∼1×1011 cm−3. Six hundred nm, 1.1:1 aspect ratio features have been filled with copper, and 250 nm, 6:1 aspect ratio features have been successfully lined. Copper ionization fractions for the conditions used for lining and filling, determined by a combination of Langmuir probe measurements and optical emission spectroscopy, are between 10% and 35%.
Fibronectin adsorption or/and covalent grafting on chemically modified PEEK film surfaces (1999)

Poly(ether ether ketone) (PEEK) films were chemically modified, by surface wet chemistry, into PEEK-OH, PEEK-NH2, and PEEK-NCO. Fibronectin (FN) adsorption, in the presence or absence of two non-ionic surfactants, was compared onto PEEK, PEEK-OH, and PEEK-NH2 on which the protein can only be adsorbed, and onto PEEK-NCO on which FN could be covalently grafted. The amounts of FN present on the various supports were assayed by ELISA and LSC (with 125I-labeled FN). The remarkable effect of Pluronic F68 in preventing non-specific protein adhesion on the less hydrophilic surfaces was pointed out. Accordingly, a procedure could be proposed that allows minimal FN adhesion vs FN fixation on PEEK-NCO. The resulting PEEK-FN film, which immobilized 120-150 ng FN cm(-2), constitutes a new substratum for cell cultivation.
EyeTap technology for wireless electronic news gathering (1999)

The results of actual field tests of a new class of Personal Imaging systems, the Electronic News Gathering WearComp (ENGwear), are presented. These incorporate EyeTap Technology to cause the eye itself to function as if it were a camera, and to allow the eye to be wirelessly tapped out of and tapped into, capturing exactly what the user is viewing. This brings the point of view of the camera to the same point as the user's eye, and also allows the user to allow others to wirelessly modify his/her perception of visual reality. Images thus captured are simultaneously sent and received live to and from the internet using IP-over-wireless technology. This novel application of wireless technology empowers reporters: ENGwear systems allow for a great degree of mobility, and are constantly operational and recording to a circular buffer allowing the reporter to never 'miss a shot'.
Comparative gene expression profile analysis of GLI and c-MYC in an epithelial model of malignant transformation. (2002)

Transcription factor oncogenes such as GLI and c-MYC are central to the pathogenesis of human tumors. GLI encodes a zinc finger protein that is activated by Sonic Hedgehog signaling. Mutations in this pathway induce GLI expression in basal cell carcinoma, and expression of GLI in mice is sufficient to induce these skin tumors. We used microarrays to identify transcripts regulated by GLI or c-MYC after retroviral transduction and short-term culture of epithelial RK3E cells. Although each of these oncogenes induces malignant transformation of RK3E, two distinct sets of genes were identified. Of approximately 17,500 transcripts represented on the microarrays, GLI up-regulated the expression of 158 and repressed the expression of 52. In contrast, transcripts regulated by c-MYC were mainly repressed (424 of 682 regulated transcripts). Transcripts induced by the GLI transgene are likewise expressed in association with endogenous GLI in Ptch-deficient murine fibroblasts or in human skin tumors, but are not up-regulated in RK3E cells transformed by c-MYC, KLF4, or HRAS1. Unlike these other oncogenes, GLI induced the expression of mesenchymal cell markers including Snail, a zinc finger protein implicated in epithelial-mesenchymal transition in development and during tumor progression. A novel GLI-estrogen receptor fusion protein rapidly induced Snail mRNA expression in a manner like Ptch, a known direct transcriptional target gene. Induction of Snail expression and epithelial-mesenchymal transition by GLI may account for certain histopathological features of basal cell carcinoma, such as the absence of a well-defined, intraepithelial precursor lesion. In addition, consistent expression of the newly identified GLI-induced transcripts within GLI-expressing tumors in vivo indicates that oncogene-specific transcriptional profiles may be useful diagnostic tools for analysis of human tumors.
Manipulation of Coupled Osmotic Flows for Stabilisation of Shales Exposed to Water-Based Drilling Fluids (1995)

Abstract Coupled osmotic flows have been studied as a means of stabilising shales exposed to water-based muds. The prime factor that governs the magnitude of chemical osmotic flow, i.e. the shale-fluid membrane efficiency, was investigated in detail. Its dependence on shale parameters, fluid parameters and external conditions was quantified. Membrane efficiency was found to increase with an increase in (hydrated) solute-to-pore-size ratio, with an increase in the shale’s high-surface area clay content and with a decrease shale permeability when increasing effective confining stress. Moreover, new drilling fluid chemistries for improving the efficiencies of low- and non-selective shale-fluid systems were identified. Induced osmotic flow with optimised shale-fluid membrane efficiencies in water-based environments is presented as a new strategy for improving wellbore stability in shales.
A MEMS-based ionization gas sensor using carbon nanotubes and dielectric barrier (2008)

We have demonstrated here the successful operation of an ionization gas sensor with gap spacing 2~10 mum and using CNTs (carbon nanotubes) as the electrode material. By set up an appropriate threshold current, the application of less than 20 V DC bias could generate electric field enough to effectively ionize various gases in atmospheric pressure. Working by the fingerprinting ionization characteristics of distinct gases, the sensor can effectively distinguish several gases by their various breakdown voltages and serves as an effective human breath monitor. TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> dielectric barrier is introduced to the discharging system to improve the performance of the device. Experimental tests prove that with the dielectric barrier discharge mechanism has improved both the stability and ionization capability of the device.
Hydrothermal synthesis of the novel rutile-mixed anatase TiO<sub>2</sub> nanosheets with dominant {001} facets for high photocatalytic activity (2016)

We introduce a hydrothermal route to synthesize rutile-mixed anatase nanosheets with dominant {001} facets for high photocatalytic activity.
Statistical Modeling of Simulation Errors and Their Reduction via Response Surface Techniques (2001)

Errors of computational simulations in design of a high-speed civil transport (HSCT) are investigated. First, discretization error from a supersonic panel code, WINGDES, is considered. Second, convergence error from a structural optimization procedure using GENESIS is considered along with the Rosenbrock test problem. A grid converge study is performed to estimate the order of the discretization error in the lift coefficient (CL) of the HSCT calculated from WINGDES. A response surface (RS) model using several mesh sizes is applied to reduce the noise magnification problem associated with the Richardson extrapolation. The RS model is shown to be more efficient than Richardson extrapolation via careful use of design of experiments. A programming error caused inaccurate optimization results for the Rosenbrock test function, while inadequate convergence criteria of the structural optimization produced error in wing structural weight of the HSCT. The Weibull distribution is successfully fit to the optimization errors of both problems. The probabilistic model enables us to estimate average errors without performing very accurate optimization runs that can be expensive, by using differences between two sets of results with different optimization control parameters such as initial design points or convergence criteria. Optimization results with large errors, outliers, produced inaccurate RS approximations. A robust regression technique, M-estimation implemented by iteratively reweighted least squares (IRLS), is used to identify the outliers, which are then repaired by higher fidelity optimizations. The IRLS procedure is applied to the results of the Rosenbrock test problem, and wing structural weight from the structural optimization of the HSCT. A nonsymmetric IRLS (NIRLS), utilizing one-sidedness of optimization errors, is more effective than IRLS in identifying outliers. Detection and repair of the outliers improve accuracy of the RS approximations. Finally, configuration optimizations of the HSCT are performed using the improved wing bending material weight RS models.
<i>Digital Data System</i>: System Overview (1975)

This paper presents an overview of the Digital Data System. The services to be provided are described and the premises for establishing both service and system objectives are discussed. The network concept, planning for its growth and administration, and a description of the network elements are presented as an introduction to the detailed papers which follow.
Ultrastructure, Morphology and Organization of Biogenic Magnetite from Sockeye Salmon, <i>Oncorhynchus Nerka</i>: Implications for Magnetoreception (1988)

Although ferromagnetic material has been detected in the tissues of a variety of animals that are known or suspected to respond to magnetic fields, in only a few cases has the material been identified and its suitability for use in magnetoreception been determined. Using high-resolution transmission electron microscopy (HRTEM), we have studied magnetic particles isolated from ethmoid tissue of the sockeye salmon, Oncorhynchus nerka. Low-magnification electron micrographs showed chains containing up to 58 (median = 21-25) electron-dense particles that were held together by intimately attached organic material. The particle size range was 25-60 nm with a mean of 48 nm and a standard deviation of 8.5 nm. Elemental analysis, by energy-dispersive X-ray analysis (EDXA), electron diffraction patterns and HRTEM lattice images, showed that many of the particles were structurally well-ordered and crystallographically single-domain magnetite. These results imply that the production of the biomineral is under precise biological control. The crystal morphology was cubo-octahedral with the (111) faces of adjacent crystals lying perpendicular to the chain axis. The magnetic moments of the particles will therefore be aligned along the chain axis and will sum to produce a total moment dependent on the number of particles present in each chain. In the presence of the geomagnetic field, the mean moment for the particles will give a magnetic to thermal energy ratio of about 0.2. The corresponding calculations for individual chains gave two clusters of ratios ranging between 2.7 and 5.3 and between 6.6 and 9.5. The implications of these results in the possible use of the particles in magnetoreception are discussed.