gebhart/patrepeval huggingface dataset:
Potent human monoclonal antibodies against SARS CoV, Nipah and Hendra viruses (2009)

Structural, functional and biochemical analyses [corrected] have provided insights into the molecular mechanisms of receptor recognition and antibody neutralization, and suggested that these antibodies alone or in combination could fight the viruses' heterogeneity and mutability, which is a major problem in the development of effective therapeutic agents against viruses, including therapeutic antibodies.
Controlling Factors in the Synthesis of Cucurbituril and Its Homologues (2001)

The acid-catalyzed synthesis of cucurbit[n]urils from formaldehyde and glycoluril is poorly understood. In this paper, we examine a wide range of reaction conditions that include the effects of acid type, acid concentration, reactant concentrations, and temperature to both probe the mechanism and optimize the yields of isolated cucurbit[n]urils, where n = 5-10. A mechanism for the formation of these cucurbit[n]urils is presented. Individual cucurbit[n]urils were unambiguously identified in reaction mixtures using ESMS and (13)C NMR.
All-optical remote location of high polarization mode dispersion fiber spans using stimulated Brillouin scattering (2002)

We report an all-optical remote locator of high PMD fiber spans using stimulated Brillouin scattering (SBS). Both the length of the high PMD fiber span and the magnitude of PMD itself can be inferred from the slope change of the reflected SBS pulse.
New writing strategy in electron beam direct write lithography to improve critical dense lines patterning for sub-45nm nodes (2009)

Electron beam direct write lithography is known for its high resolution capabilities, which enables studies ahead of the technology in production. That is why this technique is used for many years in laboratories for R&D. Recently it was shown that electron beam lithography can be integrated within the flows of the microelectronics industry for prototyping applications, low volume production and to support optical lithography for ASIC manufacturing. Moreover recent lithography workshops highlighted that the multi beam solution is identified as one potential technique for next generation lithography techniques to meet the requirements of sub-32nm technological nodes. The present proximity correction methods for electron beam lithography are based on the standard dose modulation principle. However these methods cannot properly ensure a sufficient control of the patterning of the most critical designs. To push the resolution capability of electron beam lithography, a new correction method is proposed. It consists in a multiple pass exposure strategy. For example instead of patterning a line in one pass (standard exposure), the pattern is split in several basic blocks with potential overlaps exposed in several passes and with an adapted dose. Compared to standard exposure, this solution provides an improved process window and a better control of the critical dimensions. We could achieve energy latitude of 22.2% and we improved the line edge roughness by 27% on 45nm dense lines (line width equal to space) with this method.
Water‐Gas‐Shift over Metal‐Free Nanocrystalline Ceria: An Experimental and Theoretical Study (2017)

Abstract A tandem experimental and theoretical investigation of a mesoporous ceria catalyst reveals the properties of the metal oxide are conducive for activity typically ascribed to metals, suggesting reduced Ce 3+ and oxygen vacancies are responsible for the inherent bi‐functionality of CO oxidation and dissociation of water required for facilitating the production of H 2 . The degree of reduction of the ceria, specifically the (1 0 0) face, is found to significantly influence the binding of reagents, suggesting reduced surfaces harbor the necessary reactive sites. The metal‐free catalysis of the reaction is significant for catalyst design considerations, and the suite of in situ analyses provides a comprehensive study of the dynamic nature of the high surface area catalyst system. This study postulates feasible improvements in catalytic activity may redirect the purpose of the water‐gas shift reaction from CO purification to primary hydrogen production.
Synthesis of 2‐Arylbenzo[b]furans via Copper(I)‐Catalyzed Coupling of o‐Iodophenols and Aryl Acetylenes. (2003)

We report a copper(I)-catalyzed procedure for the synthesis of 2-arylbenzo[<i>b</i>]furans. This protocol can be used to synthesize a variety of\n2-arylbenzo[<i>b</i>]furans in good to excellent yields. This method can tolerate a variety of functional groups, does not require the use of expensive\nadditives, and is palladium-free.
Transposon Mutagenesis of <i>Xylella fastidiosa</i> by Electroporation of Tn<i>5</i> Synaptic Complexes (2001)

Pierce's disease, a lethal disease of grapevine, is caused by Xylella fastidiosa, a gram-negative, xylem-limited bacterium that is transmitted from plant to plant by xylem-feeding insects. Strains of X. fastidiosa also have been associated with diseases that cause tremendous losses in many other economically important plants, including citrus. Although the complete genome sequence of X. fastidiosa has recently been determined, the inability to transform or produce transposon mutants of X. fastidiosa has been a major impediment to understanding pathogen-, plant-, and insect-vector interactions. We evaluated the ability of four different suicide vectors carrying either Tn5 or Tn10 transposons as well as a preformed Tn5 transposase-transposon synaptic complex (transposome) to transpose X. fastidiosa. The four suicide vectors failed to produce any detectable transposition events. Electroporation of transposomes, however, yielded 6 x 10(3) and 4 x 10(3) Tn5 mutants per microg of DNA in two different grapevine strains of X. fastidiosa. Molecular analysis showed that the transposition insertions were single, independent, stable events. Sequence analysis of the Tn5 insertion sites indicated that the transpositions occur randomly in the X. fastidiosa genome. Transposome-mediated mutagenesis should facilitate the identification of X. fastidiosa genes that mediate plant pathogenicity and insect transmission.
The <i>MKK7</i> Gene Encodes a Group of c-Jun NH <sub>2</sub> -Terminal Kinase Kinases (1999)

The c-Jun NH2-terminal protein kinase (JNK) is a member of the mitogen-activated protein kinase (MAPK) group and is an essential component of a signaling cascade that is activated by exposure of cells to environmental stress. JNK activation is regulated by phosphorylation on both Thr and Tyr residues by a dual-specificity MAPK kinase (MAPKK). Two MAPKKs, MKK4 and MKK7, have been identified as JNK activators. Genetic studies demonstrate that MKK4 and MKK7 serve nonredundant functions as activators of JNK in vivo. We report here the molecular cloning of the gene that encodes MKK7 and demonstrate that six isoforms are created by alternative splicing to generate a group of protein kinases with three different NH2 termini (alpha, beta, and gamma isoforms) and two different COOH termini (1 and 2 isoforms). The MKK7alpha isoforms lack an NH2-terminal extension that is present in the other MKK7 isoforms. This NH2-terminal extension binds directly to the MKK7 substrate JNK. Comparison of the activities of the MKK7 isoforms demonstrates that the MKK7alpha isoforms exhibit lower activity, but a higher level of inducible fold activation, than the corresponding MKK7beta and MKK7gamma isoforms. Immunofluorescence analysis demonstrates that these MKK7 isoforms are detected in both cytoplasmic and nuclear compartments of cultured cells. The presence of MKK7 in the nucleus was not, however, required for JNK activation in vivo. These data establish that the MKK4 and MKK7 genes encode a group of protein kinases with different biochemical properties that mediate activation of JNK in response to extracellular stimuli.
Large-scale neural networks implemented with Non-Volatile Memory as the synaptic weight element: Impact of conductance response (2016)

We assess the impact of the conductance response of Non-Volatile Memory (NVM) devices employed as the synaptic weight element for on-chip acceleration of the training of large-scale artificial neural networks (ANN). We briefly review our previous work towards achieving competitive performance (classification accuracies) for such ANN with both Phase-Change Memory (PCM) [1], [2] and non-filamentary ReRAM based on PrCaMnO (PCMO) [3], and towards assessing the potential advantages for ML training over GPU-based hardware in terms of speed (up to 25× faster) and power (from 120-2850× lower power) [4]. We then discuss the “jump-table” concept, previously introduced to model real-world NVM such as PCM [1] or PCMO, to describe the full cumulative distribution function (CDF) of conductance-change at each device conductance value, for both potentiation (SET) and depression (RESET). Using several types of artificially-constructed jump-tables, we assess the relative importance of deviations from an ideal NVM with perfectly linear conductance response.
Real-Time Ablation Recession Rate Sensor System for Advanced Reentry Vehicles (2012)

The development of a new sensor system for in-situ, real-time measurements of recession rate of heat shield ablative materials is described. The sensor utilizes a focused ultrasound approach to non-intrusively detect the ablative material's surface loss while simultaneously correcting for acoustic velocity dependencies on temperature. The latter correction is done via a closed loop feedback approach. The multi-source focusing approach is atypical of current ultrasound based sensors used for ablation recession rate measurement, which require a-priori knowledge of temperature distribution within the ablative to yield accurate data on recession rate. The paper describes the operating principles of the sensor and reports on results obtained in testing the breadboard sensor system in a relevant environment at ATK GASL’s POET facility.
OFDM peak power reduction using metric-based amplitude predistortion (2005)

In this paper, we propose a new peak-to-average power ratio (PAPR) reduction technique for OFDM systems. It consists of predistorting the amplitude of a set of symbols per block using a simple metric-based algorithm, and it does not require transmitting any side information to the receiver. The metrics measure how much each symbol contributes to the output signal samples of large magnitude, and the predistorted symbols are selected as those with the largest metrics. The proposed technique can be implemented as a one-shot procedure or as an iterative algorithm. Its performance is investigated using the QPSK signal constellation.
Root biomass response to foliar application of imazapyr for two imidazolinone tolerant alleles of sunflower (<i>Helianthus annuus</i> L.) (2012)

Imisun and CLPlus are two imidazolinone tolerance traits in sunflower (Helianthus annuus L.) determined by the expression of two alleles at the locus Ahasl1. Both traits differed in their tolerance level to imazapyr -a type of imidazolinone herbicide- when aboveground biomass is considered, but the concomitant herbicide effect over the root system has not been reported. The objective of this work was to quantify the root biomass response to increased doses of imazapyr in susceptible (ahasl1/ahasl1), Imisun (Ahasl1-1/Ahasl1-1) and CLPlus (Ahasl1-3/Ahasl1-3) homozygous sunflower genotypes. These materials were sprayed at the V2-V4 stage with increased doses of imazapyr (from 0 to 480 g active ingredient ha(-1)) and 14 days after treatment root biomass of each plant was assessed. Genotype at the Ahasl1 locus, dose of imazapyr and their interaction significantly contributed (P < 0.001) to explain the reduction in root biomass accumulation after herbicide application. Estimated dose of imazapyr required to reduce root biomass accumulation by fifty percent (GR(50)) differed statistically for the three genotypes under study (P < 0.001). CLPlus genotypes showed the highest values of GR(50), 300 times higher on average than the susceptible genotypes, and almost 8 times higher than Imisun materials, demonstrating that both alleles differ in their root biomass response to foliar application of increased doses of imazapyr.
Detection of Mutations in RNA Polymerase Beta Subunit Gene Encoding Resistance to Rifampin in<i>Mycobacterium tuberculosis</i>by DNA Microarray (2005)

Abstract Rapid and efficient diagnosis is essential in the management of drug‐resistant tuberculosis. A DNA microarray technique based on differential hybridization method was described in the present study for detecting mutations in the RNA polymerase beta subunit (rpoB) gene of Mycobacterium tuberculosis (M. tuberculosis) cultures and in clinical specimens. The mutations in rpoB confer resistance to rifampin, an important first‐line antituberculosis drug. The differential hybridization approach was mainly based on the effect of a single base mismatch on the melting temperature of the hybridized DNA; therefore, any point mutation of rpoB gene resulting in the rifampin resistance can be detected efficiently. The development of the DNA microarray involves the design of dozens of oligonucleotide probes for identifying rifampin‐resistant and ‐sensitive strains. The method comprises isolating genomic DNA from the samples containing M. tuberculosis cells, amplifying rpoB gene coding sequence to produce fluorescently labelled product, and hybridization with the oligonucleotide arrays. The results demonstrated the capability of DNA microarray to provide important clinically relevant information about the rpoB gene of mycobacterial organisms. The DNA microarray offers a reliable diagnostic test for rapidly detecting multidrug resistance caused by gene mutations of mycobacteria.
Oxygen saturation changes in the optic nerve head during acute intraocular pressure elevation in monkeys (2009)

Background and Objective: To evaluate the effect of an acute elevated intraocular pressure (IOP) on oxygen saturation of structures of the optic nerve head. Study Design/Materials and Methods: In the cynomolgus monkey eye, IOP was set to 10 mm Hg, and then raised to 30, 45, and 55 mm Hg. The ONH and overlying vessels were imaged using a fundus camera attached to a hyperspectral imaging system (HSI) at 10 and 30 minutes after IOP elevation. Results: Raising IOP from 10 to 30 mm Hg did not significantly (P < 0.0001) change saturation in vessels or ONH tissue structures but at 55 mm Hg, all structures showed significant reduction. Conclusions: Quantitative assay of the blood oxygen saturation in structures on the surface and overlying the optic nerve head is possible using hyperspectral imaging techniques.
Some new methods for preparing 2,3‐ and 3,4‐diaminopyridines (1986)

Abstract New methods of preparing 2,3‐diaminopyridine ( 13 ) from 2‐chloro‐3‐nitropyridine ( 11 ) and 3,4‐diaminopy‐ridine ( 8 ) from 4‐ethoxy‐3‐nitropyridine hydrochloride ( 5 ) have been explored and evaluated.
Developing highly-responsive user interfaces with DHTML and servlets (2002)

Due to communication overhead and latency, Web-based user interfaces that rely exclusively on the server to refresh client screens suffer from poor performance. In this paper we show that implementation of the classic model-view-controller architecture on the client enables the client to refresh the screen in certain cases, and thus improves performance. This "dual-MVC" approach is discussed in the context of a sample Web-based application.
“Black holes” and bacterial pathogenicity: A large genomic deletion that enhances the virulence of <i>Shigella</i> spp. and enteroinvasive <i>Escherichia coli</i> (1998)

Plasmids, bacteriophages, and pathogenicity islands are genomic additions that contribute to the evolution of bacterial pathogens. For example, Shigella spp., the causative agents of bacillary dysentery, differ from the closely related commensal Escherichia coli in the presence of a plasmid in Shigella that encodes virulence functions. However, pathogenic bacteria also may lack properties that are characteristic of nonpathogens. Lysine decarboxylase (LDC) activity is present in approximately 90% of E. coli strains but is uniformly absent in Shigella strains. When the gene for LDC, cadA, was introduced into Shigella flexneri 2a, virulence became attenuated, and enterotoxin activity was inhibited greatly. The enterotoxin inhibitor was identified as cadaverine, a product of the reaction catalyzed by LDC. Comparison of the S. flexneri 2a and laboratory E. coli K-12 genomes in the region of cadA revealed a large deletion in Shigella. Representative strains of Shigella spp. and enteroinvasive E. coli displayed similar deletions of cadA. Our results suggest that, as Shigella spp. evolved from E. coli to become pathogens, they not only acquired virulence genes on a plasmid but also shed genes via deletions. The formation of these "black holes," deletions of genes that are detrimental to a pathogenic lifestyle, provides an evolutionary pathway that enables a pathogen to enhance virulence. Furthermore, the demonstration that cadaverine can inhibit enterotoxin activity may lead to more general models about toxin activity or entry into cells and suggests an avenue for antitoxin therapy. Thus, understanding the role of black holes in pathogen evolution may yield clues to new treatments of infectious diseases.
Targeted Inhibition of Replication Protein A Reveals Cytotoxic Activity, Synergy with Chemotherapeutic DNA-Damaging Agents, and Insight into Cellular Function (2010)

Targeting uncontrolled cell proliferation and resistance to DNA-damaging chemotherapeutics with a single agent has significant potential in cancer treatment. Replication protein A (RPA), the eukaryotic ssDNA-binding protein, is essential for genomic maintenance and stability via roles in both DNA replication and repair. We have identified a novel small molecule that inhibits the in vitro and cellular ssDNA-binding activity of RPA, prevents cell cycle progression, induces cytotoxicity, and increases the efficacy of chemotherapeutic DNA-damaging agents. These results provide new insight into the mechanism of RPA-ssDNA interactions in chromosome maintenance and stability. This represents the first molecularly targeted eukaryotic DNA-binding inhibitor and reveals the utility of targeting a protein-DNA interaction as a therapeutic strategy for cancer treatment.
Lithium Incorporation by  V 6 O 13 and Related Vanadium (+4, +5) Oxide Cathode Materials (1981)

The known vanadium oxides have been examined as cathode materials in ambient temperature nonaqueous secondary lithium cells. The discharge products have also been chemically prepared and characterized by x‐ray diffraction, thermal analysis, and magnetic susceptibility. The best cathode materials are and a slightly oxygen‐rich . Electrochemical and chemical preparations afford . The is described as an insertion compound of .
Embedded Ultrasonics With Piezoelectric Wafer Active Sensors for Structural Health Monitoring of Thin-Wall Structures (2003)

The capability of embedded piezoelectric water active sensors (PWAS) to perform in-situ ultrasonic nondestructive evaluation (NDE) is explored. Laboratory tests are used to prove that PWAS can satisfactorily perform Lamb wave transmission and reception. Subsequently, pulse-echo method for crack detection in an aircraft panel is illustrated. For large area scanning, a PWAS phased array is used to create the embedded ultrasonics structural radar (EUSR). In conclusion, opportunities for implementation into structural health monitoring applications and further research needs are discussed.
RAPID PROTOCOL (5.25 H) FOR THE DETECTION OF <i>ESCHERICHIA COLI</i> O157:H7 IN RAW GROUND BEEF BY AN IMMUNO‐CAPTURE SYSTEM (PATHATRIX) IN COMBINATION WITH COLORTRIX AND CT‐SMAC <sup>1</sup> (2004)

ABSTRACT A same day protocol for the detection of Escherichia coli O157:H7 by Pathatrix (a novel immuno‐capture method) and Colortrix (a rapid ELISA test) was developed. This study indicated that Pathatrix system, which circulated the pre‐enriched (4.5 h) samples over paramagnet beads with antibodies (0.5 h), increased the concentration of E. coli O157:H7 by 1.2–2.6 log CFU/25 g in 0.5 h from enrichment broth (modified EC broth with novobiocin or buffered peptone water). Colortrix, a rapid ELISA system, was used to detect the pathogens in another 0.25 h. Excellent correlation (100%) between positive Pathatrix/Colortrix (5.25 h system) results and positive Pathatrix/plating method with cefixime tellurite sorbitol‐MacConkey agar, with initial concentration of 0.7 to 2.1 log CFU/25 g was obtained. This new protocol offers a significant benefit to the meat industry allowing compliance with a “test” and “hold” program for E. coli O157: H7 in ground beef.
System identification of anti-vibration units in semiconductor exposure apparatus (2003)

System identification of semiconductor exposure apparatus is discussed. It has a multi-degrees-of-freedom mechanism which includes anti-vibration units for microvibration control. A dynamical model of the mechanism is necessary in order to design the microvibration controller. The model is practically constructed in a short time using a subspace method. Identification results are evaluated through experimental data in comparison with a conventional frequency response method.
Role of Tunneling Matrix Elements in Determining the Magnitude of the Tunneling Spin Polarization of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mn>3</mml:mn><mml:mi>d</mml:mi></mml:math>Transition Metal Ferromagnetic Alloys (2005)

We have measured the tunneling spin polarization and associated tunneling magnetoresistance for Co-Pt and Co-V alloys using ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ and AlN barriers. These properties are insensitive to the Pt content of Co-Pt alloys for up to $40\text{ }\mathrm{at}.\text{ }%$ Pt, whereas the spin polarization of Co-V alloys decreases significantly with the addition of small amounts of V. We attribute these different behaviors to the relative strengths of bonds formed between the alloy constituents and oxygen in the ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ tunnel barrier, which thereby influence the corresponding tunneling rates. The results for AlN barriers are consistent with this argument.