gebhart/patrepeval huggingface dataset:
A Single Amino Acid Difference Distinguishes Resistant and Susceptible Alleles of the Rice Blast Resistance Gene <i>Pi-ta</i> (2000)

The rice blast resistance (R) gene Pi-ta mediates gene-for-gene resistance against strains of the fungus Magnaporthe grisea that express avirulent alleles of AVR-Pita. Using a map-based cloning strategy, we cloned Pi-ta, which is linked to the centromere of chromosome 12. Pi-ta encodes a predicted 928-amino acid cytoplasmic receptor with a centrally localized nucleotide binding site. A single-copy gene, Pi-ta shows low constitutive expression in both resistant and susceptible rice. Susceptible rice varieties contain pi-ta(-) alleles encoding predicted proteins that share a single amino acid difference relative to the Pi-ta resistance protein: serine instead of alanine at position 918. Transient expression in rice cells of a Pi-ta(+) R gene together with AVR-Pita(+) induces a resistance response. No resistance response is induced in transient assays that use a naturally occurring pi-ta(-) allele differing only by the serine at position 918. Rice varieties reported to have the linked Pi-ta(2) gene contain Pi-ta plus at least one other R gene, potentially explaining the broadened resistance spectrum of Pi-ta(2) relative to Pi-ta. Molecular cloning of the AVR-Pita and Pi-ta genes will aid in deployment of R genes for effective genetic control of rice blast disease.
Coocclusion of Helicoverpa armigera Single Nucleopolyhedrovirus (HearSNPV) and Helicoverpa armigera Multiple Nucleopolyhedrovirus (HearMNPV): Pathogenicity and Stability in Homologous and Heterologous Hosts (2022)

Helicoverpa armigera single nucleopolyhedrovirus (HearSNPV) is a virulent pathogen of lepidopterans in the genera <i>Heliothis</i> and <i>Helicoverpa</i>, whereas Helicoverpa armigera multiple nucleopolyhedrovirus (HearSNPV) is a different virus species with a broader host range. This study aimed to examine the consequences of coocclusion of HearSNPV and HearMNPV on the pathogenicity, stability and host range of mixed-virus occlusion bodies (OBs). HearSNPV OBs were approximately 6-fold more pathogenic than HearMNPV OBs, showed faster killing by approximately 13 h, and were approximately 45% more productive in terms of OB production per larva. For coocclusion, <i>H. armigera</i> larvae were first inoculated with HearMNPV OBs and subsequently inoculated with HearSNPV OBs at intervals of 0-72 h after the initial inoculation. When the interval between inoculations was 12-24 h, OBs collected from virus-killed insects were found to comprise 41-57% of HearSNPV genomes, but the prevalence of HearSNPV genomes was greatly reduced (3-4%) at later time points. Quantitative PCR (qPCR) analysis revealed the presence of HearSNPV genomes in a small fraction of multinucleocapsid ODVs representing 0.47-0.88% of the genomes quantified in ODV samples, indicating that both viruses had replicated in coinfected host cells. End-point dilution assays on ODVs from cooccluded mixed-virus OBs confirmed the presence of both viruses in 41.9-55.6% of wells that were predicted to have been infected by a single ODV. A control experiment indicated that this result was unlikely to be due to the adhesion of HearSNPV ODVs to HearMNPV ODVs or accidental contamination during ODV band extraction. Therefore, the disparity between the qPCR and end-point dilution estimates of the prevalence of mixed-virus ODVs likely reflected virus-specific differences in replication efficiency in cell culture and the higher infectivity of pseudotyped ODVs that were produced in coinfected parental cells. Bioassays on <i>H. armigera</i>, <i>Spodoptera frugiperda</i> and <i>Mamestra brassicae</i> larvae revealed that mixed-virus OBs were capable of infecting heterologous hosts, but relative potency values largely reflected the proportion of HearMNPV present in each mixed-virus preparation. The cooccluded mixtures were unstable in serial passage; HearSNPV rapidly dominated during passage in <i>H. armigera</i> whereas HearMNPV rapidly dominated during passage in the heterologous hosts. We conclude that mixed-virus coocclusion technology may be useful for producing precise mixtures of viruses with host range properties suitable for the control of complexes of lepidopteran pests in particular crops, although this requires validation by field testing.
Suppression of secondary electron blur by using Br-containing resists in x-ray lithography (2002)

Second generation proximity x-ray lithography (PXL-II), which uses shorter incident x-ray wavelengths and resist materials, is expected to be a candidate for next generation lithography. In the PXL-II technique, the x-ray wavelength absorbed in the resist becomes shorter, but degradation of the pattern quality due to secondary electron blur has not been sufficiently evaluated. In this article, we present our investigation of the secondary electron blur’s suppression in Br-containing resist using a lithographic simulator and a Monte Carlo simulator for electron scattering. By introducing the Br element into resist materials, the electron stopping power improves. In addition, secondary electron blur is suppressed in regions with wavelengths shorter than that of the Br absorption edge. In order to evaluate pattern resolution, the image contrast of the lateral absorbed image in the resist is defined. We found that image contrast is improved in Br-containing resist for the wavelength range down to about 4.5 Å, which is suitable for PXL-II. We also show that it should be possible to extend PXL-II for resolutions of less than 40 nm at a narrower gap.
A theoretical investigation of stimulated Brillouin scattering in phase-modulated fiber amplifiers (2010)

We report on theoretical and numerical investigations of stimulated Brillouin scattering (SBS) in optical fibers. A theoretical framework is presented which involves a nonlinear triply-coupled time-dependent system of equations containing the optical, Stokes, and phonon fields. We examine short fibers where previous approximations for long fibers cannot be made. We consider modulation frequencies and linewidths starting at approximately the Brillouin gain bandwidth and all the way up to frequencies of the order of the Brillouin resonance frequency. We provide simulations showing the SBS suppression factor as a function of modulation amplitude and frequency for a single-sinusoidal modulator.
Damaging the Integrated HIV Proviral DNA with TALENs (2015)

HIV-1 integrates its proviral DNA genome into the host genome, presenting barriers for virus eradication. Several new gene-editing technologies have emerged that could potentially be used to damage integrated proviral DNA. In this study, we use transcription activator-like effector nucleases (TALENs) to target a highly conserved sequence in the transactivation response element (TAR) of the HIV-1 proviral DNA. We demonstrated that TALENs cleave a DNA template with the HIV-1 proviral target site in vitro. A GFP reporter, under control of HIV-1 TAR, was efficiently inactivated by mutations introduced by transfection of TALEN plasmids. When infected cells containing the full-length integrated HIV-1 proviral DNA were transfected with TALENs, the TAR region accumulated indels. When one of these mutants was tested, the mutated HIV-1 proviral DNA was incapable of producing detectable Gag expression. TALEN variants engineered for degenerate recognition of select nucleotide positions also cleaved proviral DNA in vitro and the full-length integrated proviral DNA genome in living cells. These results suggest a possible design strategy for the therapeutic considerations of incomplete target sequence conservation and acquired resistance mutations. We have established a new strategy for damaging integrated HIV proviral DNA that may have future potential for HIV-1 proviral DNA eradication.
Quasi-linear depth buffers with variable resolution (2001)

In this paper we present new class of variable-resolution depth buffers, providing a flexible trade-off between depth precision in the distant areas of the view volume and performance. These depth buffers can be implemented using linear or quasi-linear mapping function of the distance to the camera to the depth in the screen space. In particular, the complementary Z buffer algorithm combines simplicity of implementation with significant bandwidth savings.
Raw bit error rate (BER) measurements of a fully populated optical code division multiple access (CDMA) system (2002)

Optical CDMA is one of the few multiple access concepts which permit concurrent, non-blocking virtual channels. However, conventional approaches with linear codes induce stringent device requirements which stem from the bandwidth inefficiency, also denoted as the time penalty, of CDMA. In order to have the advantages of CDMA without its concommitant time penalty, we have been concentrating on multi-attribute CDMA. A previous paper reported on the analysis, design, and analog performance of bandwidth efficient matrix configurations. The research with analog transceivers validated the theory of constructing and implementing matrix codes. In the paper we go a step further and demonstrate the concurrent transmission of digital signals in a fully populated 4/spl times/4 optical matrix (CDMA) system by measuring its raw (no thresholding or processing) bit error rate. The authors measured a raw BER of 2.0*10E-9 at 155 Mb/s.
484. Murine Liver as a Model for AAV Replication, Recombination and Evolution (2006)

Recent isolation and characterization of a family of novel adeno- associated viruses (AAVs) by our laboratory suggested that AAVs are highly prevalent in primate populations and undergo evolution through mechanisms such as intra-genome recombination. In an attempt to further understand the process of AAV evolution, we evaluated experimental models for AAV recombination. Murine liver is a good target for transduction by AAV and adenovirus vectors and, therefore, could be a potential model for our study. We proposed that the recombination could occur during and after replication of incoming single stranded AAV genomes. The ability of murine liver to support AAV replication becomes a critical qualification for its use as a model to study AAV recombination. Preliminary data generated from immune competent mice indeed suggested that wild type AAV genomes could be sufficiently replicated and possibly packaged in mouse liver (as measured by virus genome and infectivity titration, and DNA hybridization analysis) when co-injected with human adenovirus serotype 5. Experiments to characterize kinetics of AAV replication and dose response to helper adenovirus are under way. Co-administration of either AAV 1 and 8 or AAV1 and AAV2 together with adenovirus helper to the liver of C57BL/6 mice and passage of the resulted liver homogenate onto 293 cells led to recovery of AAV sequences that with either of the two input AAVs (90% of all genomes characterized) indicating that both viruses replicated and were packaged. Importantly, about 10% of the genomes were hybrids between the two AAV serotypes indicating in vivo intertypic recombination. The AAV clones were primarily screened by restriction mapping and representative clones were characterized by sequencing. Our preliminary data suggested that variant clones contained AAV genomic sequences derived from either point mutations or recombination/domain swapping of input parental viral genomes. Our study suggested that murine liver could be a potential model to study AAV biology and evolution.
A Novel Method for Detection of Endo-Xyloglucan Transferase (1992)

A new approach has been developed for quantification of the activity of endo-xyloglucan transferase, a novel enzyme that mediates the transfer of a segment of one xyloglucan molecule to another xyloglucan molecule. Purified xyloglucans with defined molecular-weight distributions and their fluorescent derivatives (pyridylamino xyloglucans) were used as substrates for the enzymatic reaction. The transferase activity was quantified by monitoring changes in molecular-weight distributions of substrates by an alkali compatible gel permeation chromatographic system, equipped with a pulsed amperometric detector and a fluorescence detector. This new method was applied to the rapid detection and characterization of a novel transferase derived from plant tissues.
Detection and tracking of moving objects from a moving platform in presence of strong parallax (2005)

We present a novel approach to detect and track independently moving regions in a 3D scene observed by a moving camera in the presence of strong parallax. Detected moving pixels are classified into independently moving regions or parallax regions by analyzing two geometric constraints: the commonly used epipolar constraint, and the structure consistency constraint. The second constraint is implemented within a "plane+parallax" framework and represented by a bilinear relationship which relates the image points to their relative depths. This newly derived relationship is related to trilinear tensor, but can be enforced into more than three frames. It does not assume a constant reference plane in the scene and therefore eliminates the need for manual selection of reference plane. Then, a robust parallax filtering scheme is proposed to accumulate the geometric constraint errors within a sliding window and estimate a likelihood map for pixel classification. The likelihood map is integrated into our tracking framework based on the spatio-temporal joint probability data association filter (JPDAF). This tracking approach infers the trajectory and bounding box of the moving objects by searching the optimal path with maximum joint probability within a fixed size of buffer. We demonstrate the performance of the proposed approach on real video sequences where parallax effects are significant.
A New High-Sensitivity Subsurface Electromagnetic Sensing System: Part I—System Design (2008)

Abstract We have developed a prototype frequency-domain electromagnetic geophysical system that currently has a usable dynamic range of 134 dB. In order to achieve this large dynamic range, we substantially reduced the measurement errors that are common limiting factors in achieving high measurement sensitivity. First, we reduced the measurement error caused by mechanical deformations of the measurement apparatus from 70 ppm to the order of 0.1 ppm. Second, as a result of developing a novel Alternating Target Antenna Coupling (ATAC) measurement method, we reduced the temporal drift from 400 ppm to the order of 0.1 ppm over a 50 min time period. Finally, as a result of using transmitter and receiver monitoring and dynamic calibration, we reduced the percentage error in the Real and Imaginary components of the target response, measured over a 105-minute period of time, from 5% and 80% to 0.5% and 2%, respectively. By increasing the TX moment, further increasing the TX/RX stability, and reducing the RX noise level, we estimate that the full potential of the ATAC system can achieve a usable dynamic range of the order of 200 dB.
Controlling plasma stimulated media in cancer treatment application (2014)

Cold atmospheric plasma (CAP) constitutes a “cocktail” of various reactive species. Accumulating evidence shows the effectiveness of CAP in killing cancer cells and decreasing the tumor size, which provides a solid basis for its potential use in cancer treatment. Currently, CAP is mainly used to directly treat cancer cells and trigger the death of cancer cells via apoptosis or necrosis. By altering the concentration of fetal bovine serum in Dulbecco's modified Eagle's medium and the temperature to store CAP stimulated media, we demonstrated controllable strategies to harness the stimulated media to kill glioblastoma cells in vitro. This study demonstrated the significant role of media in killing cancer cells via the CAP treatment.
Luminescent probes for optical in vivo imaging (2005)

Going along with instrumental development for small animal fluorescence in vivo imaging, we are developing molecular fluorescent probes, especially for tumor targeting. Several criteria have to be taken into account for the optimization of the luminescent label. It should be adapted to the in vivo imaging optical conditions : red-shifted absorption and emission, limited overlap between absorption and emission for a good signal filtering, optimized luminescence quantum yield, limited photo-bleaching. Moreover, the whole probe should fulfill the biological requirements for in vivo labeling : adapted blood-time circulation, biological conditions compatibility, low toxicity. We here demonstrate the ability of the imaging fluorescence set-up developed in LETI to image the bio-distribution of molecular probes on short times after injection. Targeting with Cy5 labeled holo-transferrin of subcutaneous TS/Apc (angiogenic murine breast carcinoma model) or IGROV1 (human ovarian cancer) tumors was achieved. Differences in the kinetics of the protein uptake by the tumors were evidenced. IGROV1 internal metastatic nodes implanted in the peritoneal cavity could be detected in nude mice. However, targeted metastatic nodes in lung cancer could only be imaged after dissection of the mouse. These results validate our fluorescence imaging set-up and the use of Cy5 as a luminescent label. New fluorescent probes based on this dye and a molecular delivery template (the RAFT molecule) can thus be envisioned.
Lignin alkaline oxidation using reversibly-soluble bases (2022)

When excess base is required to drive desired reactions, such as in lignin alkaline oxidation, Sr(OH) 2 can offer a reversibly-soluble alternative to NaOH that allows simple recycle of the excess base with concomitant cost and environmental benefits.
Simultaneous High Data Rate Communication and Highly Efficient Wireless Power Transfer Through a Coplanar Link (2019)

A coplanar link consisting of a Conformal Strongly Coupled Magnetic Resonant (CSCMR) system for a unified wireless power transfer (WPT) and high data rate communication is proposed in this paper. The proposed system has the ability to simultaneously transmit power with high efficiency (i.e., 75% efficiency) and high data rate (i.e., 3 Mbps). Different parameters that affect the resonant frequency of CSCMR are investigated and reported. The proposed topology is designed to operate at 120 MHz, with an achieved bandwidth of 7 MHz.
Interconnecting Microfluidic Package and Hybrid Interface for Chip-Based Sensor (2005)

In realizing a portable chemical analysis system, adequate partitioning of a reusable component and a disposable is required. For successful implementation of micromachined sensors in an instrument, reliable methods for interconnection and interface are in great demand between these two major parts. In this work we investigated interconnection methods of micromachined chip devices and hybrid fluidic interface system. The interconnection method based on micromachining and injection molding techniques was developed and an interconnecting microfluidic package was designed, fabricated and tested. For the hybrid interface, sequencing of the chemical analysis was examined and accordingly, syringe containers, a peristaltic pump and pinch valves were assembled to compose a reliable meso-scale fluidic control unit. The system using the interconnecting package and the hybrid interface was tested for a chip-based sensor.
Photocatalytic Color Switching of Transition Metal Hexacyanometalate Nanoparticles for High-Performance Light-Printable Rewritable Paper (2016)

Developing efficient photoreversible color switching systems for constructing rewritable paper is of significant practical interest owing to the potential environmental benefits including forest conservation, pollution reduction, and resource sustainability. Here we report that the color change associated with the redox chemistry of nanoparticles of Prussian blue and its analogues could be integrated with the photocatalytic activity of TiO<sub>2</sub> nanoparticles to construct a class of new photoreversible color switching systems, which can be conveniently utilized for fabricating ink-free, light printable rewritable paper with various working colors. The current system also addresses the phase separation issue of the previous organic dye-based color switching system so that it can be conveniently applied to the surface of conventional paper to produce an ink-free light printable rewritable paper that has the same feel and appearance as the conventional paper. With its additional advantages such as excellent scalability and outstanding rewriting performance (reversibility >80 times, legible time >5 days, and resolution >5 μm), this novel system can serve as an eco-friendly alternative to regular paper in meeting the increasing global needs for environment protection and resource sustainability.
Synthesis of hexagonal phases of <scp>WN</scp> and W <sub>2.25</sub> N <sub>3</sub> by high‐pressure metathesis reaction (2017)

Abstract Hexagonal tungsten nitrides were synthesized by the metathesis reaction between WC l 6 and NaN 3 under high pressure and temperature. As well as tungsten mononitride ( WN ), which is isostructural with hexagonal tungsten carbide ( WC ), a nitrogen‐rich hexagonal compound was also confirmed in the product. The ratio of nitrogen to tungsten was determined to be 1.34 by the quantitative combustion method. The composition was estimated to be W 2.25 N 3 by considering the crystal structure that is best explained by the X‐ray diffraction profile. Volume compression measurements under hydrostatic pressure revealed that the WC ‐type WN has a higher bulk modulus ( K 0 = 342 ± 1 GP a) than that of hexagonal W 2.25 N 3 ( K 0 = 291 ± 2 GP a).
The green vessel scheduling problem with transit time requirements in a liner shipping route with Emission Control Areas (2017)

Increasing volumes of the international seaborne trade and new regulations on vessel emissions require liner shipping companies to enhance efficiency of their operations to remain competitive and in the meantime comply with the established restrictions on emissions that are produced by vessels. This paper presents a novel mixed integer nonlinear mathematical programming model for the green vessel scheduling problem with transit time requirements in a liner shipping route with “Emission Control Areas”, which not only enforces constraints on the quantity of emissions that are produced by vessels within “Emission Control Areas”, but also captures the cargo transit time requirements. The model’s objective aims to minimize the overall route service cost. A number of linearization techniques are proposed for linearizing the original nonlinear problem. The dynamic secant approximation procedure is used to solve the linearized problem. A set of numerical experiments are performed to evaluate the efficiency of the proposed solution approach and assess the effect of introducing both emission constraints and cargo transit time requirements on design of vessel schedules.
Analysis of multi-phase LLC resonant converters (2009)

In this paper a topology for multi-phase interleaved LLC resonant converter is presented. The proposed solution, based on three LLC modules with transformer primary windings star connection allows to drastically reduce the output current ripple and consequently to minimize the output filter capacitor size. Differently from other multi-phase solutions, that are greatly susceptible to resonant component mismatch and consequently can be affected by a considerable current imbalance among modules, the proposed topology exhibits an inherent balancing capability. Small-signal analysis is presented and the possibility to turn-off one or two modules (phase shedding) at reduced output current levels is discussed, highlighting the trade-off between converter efficiency and output capacitor current ripple reduction. Measurements on a prototype will be included in the paper as validation of assertions and proposals.