gebhart/patrepeval huggingface dataset:
Molecular mechanisms of defense by rhizobacteria against root disease. (1995)

Genetic resistance in plants to root diseases is rare, and agriculture depends instead on practices such as crop rotation and soil fumigation to control these diseases. "Induced suppression" is a natural phenomenon whereby a soil due to microbiological changes converts from conducive to suppressive to a soilborne pathogen during prolonged monoculture of the susceptible host. Our studies have focused on the wheat root disease "take-all," caused by the fungus Gaeumannomyces graminis var. tritici, and the role of bacteria in the wheat rhizosphere (rhizobacteria) in a well-documented induced suppression (take-all decline) that occurs in response to the disease and continued monoculture of wheat. The results summarized herein show that antibiotic production plays a significant role in both plant defense by and ecological competence of rhizobacteria. Production of phenazine and phloroglucinol antibiotics, as examples, account for most of the natural defense provided by fluorescent Pseudomonas strains isolated from among the diversity of rhizobacteria associated with take-all decline. There appear to be at least three levels of regulation of genes for antibiotic biosynthesis: environmental sensing, global regulation that ties antibiotic production to cellular metabolism, and regulatory loci linked to genes for pathway enzymes. Plant defense by rhizobacteria producing antibiotics on roots and as cohabitants with pathogens in infected tissues is analogous to defense by the plant's production of phytoalexins, even to the extent that an enzyme of the same chalcone/stilbene synthase family used to produce phytoalexins is used to produce 2,4-diacetylphloroglucinol. The defense strategy favored by selection pressure imposed on plants by soilborne pathogens may well be the ability of plants to support and respond to rhizosphere microorganisms antagonistic to these pathogens.
A Novel Stopped-Flow Assay for Quantitating Carbonic-Anhydrase Activity and Assessing Red-Blood-Cell Hemolysis (2017)

We report a novel carbonic-anhydrase (CA) assay and its use for quantitating red-blood-cell (RBC) lysis during stopped-flow (SF) experiments. We combine two saline solutions, one containing HEPES/pH 7.03 and the other, 1% CO 2 /44 mM HCO - 3 /pH 8.41, to generate an out-of-equilibrium CO 2 /HCO - 3 solution containing 0.5% CO 2 /22 HCO - 3 /pH 7.25 (10 C) in the SF reaction cell. CA catalyzes relaxation of extracellular pH to 7.50:
Scatter-Gather Live Migration of Virtual Machines (2015)

We introduce a new metric for live migration of virtual machines (VM) called eviction time defined as the time to evict the state of one or more VMs from the source host. Eviction time determines how quickly the source can be taken offline or its resources repurposed for other VMs. In traditional live migration, such as pre-copy and post-copy, eviction time equals the total migration time because the source is tied up until the destination receives the entire VM. We present Scatter-Gather live migration which decouples the source and destination during migration to reduce eviction time when the destination is slow. The source scatters the memory of VMs to multiple nodes, including the destination and one or more intermediaries. Concurrently, the destination gathers the VMs' memory from the intermediaries and the source. Thus eviction from the source is no longer bottlenecked by the reception speed of the destination. We support simultaneous live eviction of multiple VMs and exploit deduplication to reduce network overhead. Our Scatter-Gather implementation in the KVM/QEMU platform reduces the eviction time by up to a factor of 6 against traditional pre-copy and post-copy while maintaining comparable total migration time when the destination is slower than the source.
Development of Ultra-Compact Highly Nonlinear Fiber Modules (2007)

Highly nonlinear fiber (HNLF) is a key component holding great promise in applications in the all-optical signal processing devices, broadband light sources, pulse compressors etc., which are essential to high-speed transmission systems. Improvements in HNLF functionality have been realized in recent years, but there is a need for more compact modules when these fibers are to be accommodated. In this paper we provide a theoretical discussion of the limits of reducing cladding diameter using the finite element method (FEM), and have fabricated fiber with a cladding diameter of 51 µm. This fiber shows satisfactory characteristics in tests for mechanical strength and environment performance, and delivers ample reliability while fitting into coin-sized modules. Using prototype ultra-compact modules that we fabricated, we carried out supercontinuum (SC) light generation tests and have confirmed satisfactory characteristics.
Functional Test Generation using Property Decompositions for Validation of Pipelined Processors (2006)

Functional validation is a major bottleneck in pipelined processor design. Simulation using functional test vectors is the most widely used form of processor validation. While existing model checking based approaches have proposed several promising ideas for efficient test generation, many challenges remain in applying them to realistic pipelined processors. The time and resources required for test generation using existing model checking based techniques can be extremely large. This paper presents an efficient test generation technique using decompositional model checking. The contribution of the paper is the development of both property and design decomposition procedures for efficient test generation of pipelined processors. Our experimental results using a multi-issue MIPS processor demonstrate several orders-of-magnitude reduction in memory requirement and test generation time
Designing Neat and Composite Carbon Nanotube Materials by Porosimetric Characterization (2017)

We propose a porosimetry-based method to characterize pores formed by carbon nanotubes (CNTs) in the CNT agglomerates for designing neat CNT-based materials and composites. CNT agglomerates contain pores between individual CNTs and/or CNT bundles (micropore < 2 nm, mesopores 2-50 nm, and macropores > 50 nm). We investigated these pores structured by CNTs with different diameters and number of walls, clarifying the broader size distribution and the larger volume with increased diameters and number of walls. Further, we demonstrated that CNT agglomerate structures with different bulk density were distinguished depending on the pore sizes. Our method also revealed that CNT dispersibility in solvent correlated with the pore sizes of CNT agglomerates. By making use of these knowledge on tailorable pores for CNT agglomerates, we successfully found the correlation between electrical conductivity for CNT rubber composites and pore sizes of CNT agglomerates. Therefore, our method can distinguish diverse CNT agglomerate structures and guide pore sizes of CNT agglomerates to give high electrical conductivity of CNT rubber composites.
Waveform design for electroseismic exploration (2007)

Abstract In earlier work, we described field tests that successfully detected electromagnetic-to-seismic (ES) conversions from gas sands and carbonate reservoirs. ES conversion amplitudes measure the electric properties of permeable rock with near-seismic resolution. This information is a new indicator of hydrocarbons. ES conversions produce small seismic responses. Detecting these signals requires high-power electromagnetic sources and high-sensitivity detectors. Extraction of signal from noise also requires sophisticated signal processing. Here, we describe coded waveforms of binary sequences optimized for the expected signals. These coded waveforms distinguish between linear and nonlinear conversions. We detected both linear and nonlinear conversions in field studies. Novel, high-power signal generators synthesize the required sequences from three-phase power lines. The electroseismic exploration system includes optimized source electrodes and digital accelerometers that are free of electromagnetic interference.
Isolated Boost Converters (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Two implementations of the isolated boost converter that exhibit no parasitic voltage ringing across all semiconductor devices on the primary and secondary sides of the transformer are introduced. Ringing-free operation is achieved by clamping the voltages of the primary switches and rectifiers to the voltage of the primary-side energy-storage capacitor and clamping the voltage across the secondary-side rectifiers to the output filter capacitor. The performance of the proposed topology was verified on a dual ac-input, 900-W experimental prototype operating at 67 kHz. </para>
Design of Scalable Hardware-Efficient Compressive Sensing Image Sensors (2017)

This paper presents a new compressive sensing (CS) measurement method for image sensors, which limits pixel summation within neighbor pixels and follows regular summation patterns. Simulations with a large set of benchmark images show that the proposed method leads to improved image quality. Circuit implementation for the proposed CS measurement method is presented with the use of current mode pixel cells; and the resultant CS image sensor circuit is significantly simpler than existing designs. With compression rates of 4 and 8, the developed CS image sensors can achieve 34.2- and 29.6-dB PSNR values with energy consumption of 1.4 and 0.73 μJ per frame, respectively.
Cell surface antigens of human renal cancer defined by mouse monoclonal antibodies: identification of tissue-specific kidney glycoproteins. (1981)

Seventeen monoclonal antibodies derived from fusions with spleen cells of mice immunized with established culture lines of renal cancers identified nine cell-surface antigenic systems. Six of the systems (gp160, S25, gp120r, gp120nr, gp115, and V1) represent antigens not previously described. The other three systems are related to HLA-A, -B, and -C heavy chain and A and B blood group antigens. The most restricted of the newly described antigens are gp160, S25, and gp120r. These determinants are found only on cells of renal origin, both normal and malignant, and represent differentiation antigens of human kidney. In addition to the difference in the molecular weight of two of these antigens, gp160, S25, and gp120r can be distinguished on the basis of differential expression on a panel of cultured renal cancers and normal kidney epithelium and fetal kidney cells. Glycoproteins bearing gp120r share a determinant with renal gp120nr (as indicated by sequential precipitations with monoclonal antibodies that detect gp120r and gp120nr), but gp120nr is found on a broader range of cell types, including fibroblasts and cell lines derived from lung, bladder, and colon cancers. The two other new systems, gp115 and V1, have characteristics of broadly occurring differentiation antigens but can be distinguished from each other and from gp120nr by differences in molecular weight, heat stability (V1 is a heat-stable determinant), and differential expression on cell types of diverse origin.
AN IMPROVED SYNTHESIS OF<i>bis</i>(<i>p</i>-PHENYLENE)-32-CROWN-4 (1997)

(1997). AN IMPROVED SYNTHESIS OF bis(p-PHENYLENE)-32-CROWN-4. Organic Preparations and Procedures International: Vol. 29, No. 2, pp. 234-236.
Conclusions of a seven-year translational research initiative: Defining and validating a molecular signature of high-risk multiple myeloma (2007)

PR-2 Introduction: Survival of patients diagnosed with multiple myeloma (MM) can vary considerably. While most disease is initially responsive to intervention, a small subset is primary refractory and acquisition of drug resistance represents a difficult barrier to long-term disease control. Aim: We used genome-wide mRNA expression profiling to identify molecular signatures to improve risk stratification. Methods: We performed expression analyses, using Affymetrix U133Plus2.0 microarrays, on mRNA from CD138-enriched bone marrow plasma cells from 532 consecutive newly diagnosed patients treated with tandem stem ell transplants on two separate protocols at our center. We segregated gene expression levels into quartiles and performed log rank tests to identify genes whose expression extremes were linked to disease related death. Results: We identified 70 genes, 30% mapping to chromosome 1 (P
Portable tritium processing using a drum bubbler (1998)

Abstract The removal of free tritium (primarily in the oxide form) is required for personnel and environmental protection prior to maintenance inslde the Tokamak Fusion Test Reactor (TFTR) vacuum vessel. The conventional methods for reducing the tritium hazard involve removing gas from TFTR and processing it through catalyst and molecular sieve beds using the Tritium Processing Systems. Among these methods, the most effective is the introduction of ambient air into the vacuum vessel which improves the removal of tritium oxide. Princeton Plasma Physics Laboratory (“PPPL”) refers to this activity as pump-purges. Pump-purges are very effective, but significantly increase tiie amount of radioactive waste because of the number of Disposable Molecular Sieve Beds (“DMSB”) required.
Design of Access-Tube TDR Sensor for Soil Water Content: Theory (2011)

Soil water measurement is important in water management for irrigation and hydrologic sciences. The purpose of this paper is to describe the design of a cylindrical access-tube mounted waveguide for use in time-domain reflectometry (TDR) for in-situ soil water content sensing. In order to optimize the design with respect to sampling volume and losses, we derived the electromagnetic fields produced by a TDR sensor with this geometry. Using this analytical derivation, the effects on sampling area, waveform shape, and losses while varying design and soil water content were examined. It was found that when the soil and tube substrate have identical dielectrics, then sampling area has a local extremum. Tube radius has the largest impact of any geometrical parameter on sampling area with increases in radius causing increases in sampling area. Increasing electrode separation angle increases the sampling area slightly. The effects on TDR waveform are greatest for soil water content, tube dielectric, and tube radius: where increasing any of these increase delay and dispersion.
Discovery of a Series of Thiazole Derivatives as Novel Inhibitors of Metastatic Cancer Cell Migration and Invasion (2013)

Effective inhibitors of cancer cell migration and invasion can potentially lead to clinical applications as therapy to block tumor metastasis, the primary cause of death in cancer patients. To this end we have designed and synthesized a series of thiazole derivatives that showed potent efficacy against cell migration and invasion in metastatic cancer cells. The most effective compound, <b>5k</b>, was found to have an IC<sub>50</sub> value of 176 nM in the dose-dependent transwell migration assays in MDA-MB-231cells. At the dose of 10 μM, <b>5k</b> also blocked about 80% of migration in HeLa and A549 cells and 60% of invasion of MDA-MB-231 cells. Importantly, the majority of the derivatives exhibited no apparent cytotoxicity in the clonogenic assays. The low to negligible inhibition of cell proliferation is a desirable property of these anti-migration derivatives because they hold promise of low toxicity to healthy cells as potential therapeutic agents. Mechanistic studies analyzing the actin cytoskeleton by microscopy demonstrate that compound <b>5k</b> substantially reduced cellular f-actin, and prevented localization of fascin to actin-rich membrane protrusions. These results suggest that the anti-migration activity may result from impaired actin structures in protrusions that are necessary to drive migration.
Secure optical communication using antisqueezing (2006)

When considering an application of quantum-information technology, we should consider realistic conditions first. From this point of view, we propose using antisqueezed light as a resource for optical communication because antisqueezing maintains its nature even after loss and amplification. Applying antisqueezed light to cipher communication using randomized sender bases, we can increase, by high order of magnitude, the bit-error rate of eavesdroppers who do not have the basis information. Even at macroscopic optical intensity, an ordinary level of optical communication, we can cause the bit-error rate of eavesdroppers to be as high as it would be at low intensity, through increased antisqueezing depending on optical intensity, leading to more secure optical communication.
Nonhazardous Solvent Systems for Processing Perovskite Photovoltaics (2016)

Replacing toxic solvents with nonhazardous solvents is one of the key challenges for industrial scale commercialization of thin film perovskite photovoltaics. Here, nonhazardous solvent/alcohol/acid systems are presented for the single‐step deposition of pinhole‐free perovskite layers with combined lead halide precursors of Pb(CH 3 CO 2 ) 2 ·3H 2 O, PbCl 2 , and CH 3 NH 3 I. Comparable performance to standard hazardous inks is achieved: devices with 15.1% power conversion efficiency are demonstrated and maintain 13.5% tracked for 5 min at maximum power point. Blade coated 4 cm 2 solar modules fabricated with highest performing device ink attain 11.9% in power conversion efficiency.
PC-based system for 3D registration of ultrasound and magnetic resonance images based on a magetic position sensor (1999)

Stereotactic systems are based on preoperative tomographic images for assisting neurosurgeons to accurately guide the surgical tool into the brain. In addition, intraoperative ultrasound (US) images are used to monitor the brain in real time during the surgical procedure. The main disadvantage of stereotactic system is that preoperative images can become outdated during the course of the surgery. The main disadvantage of intraoperative US is the low signal-to-noise ratio that prevents the surgeon from appreciating the contents and orientation of the US images. A system that combines preoperative tomographic with intraoperative US imags could overcome the above-mentioned disadvantages. We have successfully developed and implemented a new PC-based system for interactive 3D registration of US and magnetic resonance images. Our software is written in Microsoft Visual C++ and it runs on a Pentium II 450-MHz PC. We have performed an extensive analysis of the errors of our system with a custom-built phantom. The registration error between US and MR space was dependent on the depth of the target within the US image. For a 3.5-MHz phased 1D array transducer and a depth of 6 cm, the mean value of the registration error was 2.00 mm and the standard deviation was 0.75 mm. The registered MR images were reconstructed using either zero-order or first-order interpolation. The interactive nature of our system demonstrates its potential to be used in the operating room.
The isolation and characterisation of astroviruses from chickens (2004)

The isolation, cultivation and characterization of three chicken astroviruses (CAstV) isolates are described. They are antigenically related to each other but unrelated to avian nephritis virus (ANV) and duck hepatitis virus type 2 (DVH2) in neutralization, immunofluorescence and gel diffusion tests. CAstV, ANV and DVH2 all grew well in the LMH cell line, which was used for assay and serological tests. Serological surveys in 1982 and 2001 showed that antibody to CAstV virus was widespread in broiler and broiler breeder flocks and present in some turkey flocks. Infection of 1-day-old specific pathogen free chicks with one isolate in the laboratory resulted in mild diarrhoea and some distention of the small intestine. The virus could be isolated in high titres from all parts of the small intestine but rarely from other organs. Electron microscopic examination of purified particles of this agent revealed the presence of clusters of small round viruses with a diameter ranging from 25 to 30 nm. The amino acid sequence derived from the relatively conserved non-structural polyprotein region of this virus shows 62% identity with the corresponding region of turkey astrovirus 2, 58% identity with turkey astrovirus 1, 55% identity with avian nephritis virus and 33% identity with sheep astroviruses. Taken together, the results indicate that the agent is a new chicken astrovirus belonging to the family Astroviridae.
Identification of a novel inhibitor of breast cell growth that is down-regulated by estrogens and decreased in breast tumors. (2003)

Lifetime exposure to estrogens is a major risk factor in breast cancer, but the mechanism for this action is not fully defined. To better determine this mechanism, the activation domain of estrogen receptor (ER) alpha was used in yeast two-hybrid screenings. These screenings resulted in the identification of a novel antiproliferative protein, estrogen down-regulated gene 1 (EDG1), of which the mRNA and protein were shown to be down-regulated directly by estrogens. Our studies additionally suggested an important role for EDG1 in ER alpha-mediated breast cancer development. Analysis of 43 invasive breast cancer samples and 40 adjacent normal breast samples demonstrated EDG1 protein levels to be significantly higher in normal breast epithelial tissue as compared with breast epithelial tumor tissue. EDG1 expression levels were also correlated with the proliferation activity and ER alpha status of the tumors to examine the prognostic value of EDG1 in invasive breast tumors. EDG1 expression was more disassociated from proliferative activity as compared with ER alpha expression in tumor cells. A growth regulatory function for EDG1 is additionally indicated by studies wherein overexpression of EDG1 protein in breast cells resulted in decreased cell proliferation and decreased anchorage-independent growth. Conversely, inhibiting EDG1 expression in breast cells resulted in increased breast cell growth. Thus, we have identified a novel growth inhibitor that is down-regulated by estrogens and colocalizes with ER alpha in breast tissue. These studies support a role for EDG1 in breast cancer.
Geometry‐Induced Mechanical Properties of Carbon Nanotube Foams (2014)

Carbon nanotube (CNT) foams have unmatched energy absorption properties derived from their complex hierarchical structure. The control of the micro‐scale geometry of these foams allows tuning their behavior to specific application‐driven needs. Geometrical structures in CNT foams are obtained by synthesizing CNTs on substrates patterned with different growth templates: circles, lines and concentric rings. To study the effects of the microstructural geometry on the bulk mechanical response of the foams, the samples are tested under cyclic quasi‐static compressive deformation (up to 50% strain). The geometry of the patterns plays a fundamental role on the samples' macroscopic energy absorption capability, maximum stress, and strain recovery. Patterned CNT structures demonstrated mechanical properties comparable or improved over non‐patterned, bulk CNT foams, but with much lower density. Quasi‐static compressive tests performed on different patterned structures with the same effective density (ρ = 0.02 g cm −3 ) exhibit considerably different responses. For example, the stress reached by foams patterned in concentric rings is ≈15 times higher than that observed for pillars and lines. The results show how the mechanical response of CNT foams can be tailored by varying the CNT microstructural architecture.
A Convenient High Yield Synthesis of N<sup>4</sup>-Isobutyryl-2′-O-Methylcytidine and Its Monomer Units For Incorporation into Oligonucleotides (1993)

Abstract We designed an efficient three step procedure for the synthesis of N4-isobutyryl-2′-O-methylcytidine. This protected nucleoside was then used to prepare a methylphosphonamidite monomer for incorporation into oligonucleotides. Transamination at the C4 position of cytidine using ethylenediamine, which has been reported for the N4-benzoyl cytidine, was not observed with N4-isobutyryl protected 2′-O-methylcytidine.