gebhart/patrepeval huggingface dataset:
Activity-dependent changes in MAPK activation in the Angelman Syndrome mouse model (2014)

Angelman Syndrome (AS) is a devastating neurological disorder caused by disruption of the maternal UBE3A gene. Ube3a protein is identified as an E3 ubiquitin ligase that shows neuron-specific imprinting. Despite extensive research evaluating the localization and basal expression profiles of Ube3a in mouse models, the molecular mechanisms whereby Ube3a deficiency results in AS are enigmatic. Using in vitro and in vivo systems we show dramatic changes in the expression of Ube3a following synaptic activation. In primary neuronal culture, neuronal depolarization was found to increase both nuclear and cytoplasmic Ube3a levels. Analogous up-regulation in maternal and paternal Ube3a expression was observed in Ube3a-YFP reporter mice following fear conditioning. Absence of Ube3a led to deficits in the activity-dependent increases in ERK1/2 phosphorylation, which may contribute to reported deficits in synaptic plasticity and cognitive function in AS mice. Taken together, our findings provide novel insight into the regulation of Ube3a by synaptic activity and its potential role in kinase regulation.
Slotless module-based reconfiguration of embedded FPGAs (2009)

The difficult aspect of hardware reconfiguration is not creating the computational blocks, which are generally available from FPGA vendors and third parties, but linking the blocks in a manner that suits each application's unique connectivity, bandwidth, and latency requirements. Our approach uses the standard Xilinx implementation tools to generate dynamic module partial bitstreams, but choosing the module's coordinates and completing connections to other modules are runtime operations. Scripts automatically add interface wrappers to dynamic modules and generate a library of relocatable partial bitstreams. The library is used by an efficient runtime system that completes application requests for instancing and connecting modules, effectively insulating the designer from FPGA reconfiguration complexities. In this way, a large sandbox may be allocated to dynamic modules rather than fixed module slots and interconnect. Application engineers interact with the Wires on Demand (WoD) system through a runtime software API, and do not have to master hardware description languages and implementation tools.
Human Monoclonal Antibodies to a Novel Cluster of Conformational Epitopes on HCV E2 with Resistance to Neutralization Escape in a Genotype 2a Isolate (2012)

The majority of broadly neutralizing antibodies to hepatitis C virus (HCV) are against conformational epitopes on the E2 glycoprotein. Many of them recognize overlapping epitopes in a cluster, designated as antigenic domain B, that contains residues G530 and D535. To gain information on other regions that will be relevant for vaccine design, we employed yeast surface display of antibodies that bound to genotype 1a H77C E2 mutant proteins containing a substitution either at Y632A (to avoid selecting non-neutralizing antibodies) or D535A. A panel of nine human monoclonal antibodies (HMAbs) was isolated and designated as HC-84-related antibodies. Each HMAb neutralized cell culture infectious HCV (HCVcc) with genotypes 1-6 envelope proteins with varying profiles, and each inhibited E2 binding to the viral receptor CD81. Five of these antibodies neutralized representative genotypes 1-6 HCVcc. Epitope mapping identified a cluster of overlapping epitopes that included nine contact residues in two E2 regions encompassing aa418-446 and aa611-616. Effect on virus entry was measured using H77C HCV retroviral pseudoparticles, HCVpp, bearing an alanine substitution at each of the contact residues. Seven of ten mutant HCVpp showed over 90% reduction compared to wild-type HCVpp and two others showed approximately 80% reduction. Interestingly, four of these antibodies bound to a linear E2 synthetic peptide encompassing aa434-446. This region on E2 has been proposed to elicit non-neutralizing antibodies in humans that interfere with neutralizing antibodies directed at an adjacent E2 region from aa410-425. The isolation of four HC-84 HMAbs binding to the peptide, aa434-446, proves that some antibodies to this region are to highly conserved epitopes mediating broad virus neutralization. Indeed, when HCVcc were passaged in the presence of each of these antibodies, virus escape was not observed. Thus, the cluster of HC-84 epitopes, designated as antigenic domain D, is relevant for vaccine design for this highly diverse virus.
Two-antibody pan-ebolavirus cocktail confers broad therapeutic protection in ferrets and nonhuman primates (2018)

All available experimental vaccines and immunotherapeutics 1,2 against Ebola virus (EBOV), including rVSV-ZEBOV 3 and ZMapp TM4 , lack activity against other ebolaviruses associated with human disease outbreaks. This year, two separate outbreaks of EBOV in the Democratic Republic of Congo underscored the unpredictable nature of ebolavirus reemergence in a region that has historically experienced outbreaks of the divergent ebolaviruses Sudan virus (SUDV) and Bundibugyo virus (BDBV) 5 . Here we show that MBP134 AF , a pan-ebolavirus therapeutic comprising two broadly neutralizing human antibodies (bNAbs) 6,7 (see companion manuscript, Wec et al .) could protect against lethal EBOV, SUDV, and BDBV infection in ferrets and nonhuman primates (NHPs). MBP134 AF not only not only establishes a viable therapeutic countermeasure to outbreaks caused by antigenically diverse ebolaviruses but also affords unprecedented effectiveness and potency—a single 25-mg/kg dose was fully protective in NHPs. This best-in-class antibody cocktail is the culmination of an intensive collaboration spanning academia, industry and government in response to the 2013-2016 EBOV epidemic 6,7 and provides a translational research model for the rapid development of immunotherapeutics targeting emerging infectious diseases.
Accelerating Large-Scale Inference with Anisotropic Vector Quantization (2019)

Given a training set P ⊂ ℝ^d, the nearest-neighbor classifier assigns any query point q ∈ ℝ^d to the class of its closest point in P. To answer these classification queries, some training points are more relevant than others. We say a training point is relevant if its omission from the training set could induce the misclassification of some query point in ℝ^d. These relevant points are commonly known as border points, as they define the boundaries of the Voronoi diagram of P that separate points of different classes. Being able to compute this set of points efficiently is crucial to reduce the size of the training set without affecting the accuracy of the nearest-neighbor classifier. Improving over a decades-long result by Clarkson (FOCS'94), Eppstein (SOSA’22) recently proposed an output-sensitive algorithm to find the set of border points of P in 𝒪(n² + nk²) time, where k is the size of such set. In this paper, we improve this algorithm to have time complexity equal to 𝒪(nk²) by proving that the first phase of their algorithm, which requires 𝒪(n²) time, are unnecessary.
A novel synthesis of N-fluoroperfluoroalkanimines. Reaction of perfluorinated secondary amines with antimony pentafluoride (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA novel synthesis of N-fluoroperfluoroalkanimines. Reaction of perfluorinated secondary amines with antimony pentafluorideV. A. Petrov and D. D. DesMarteauCite this: Inorg. Chem. 1992, 31, 18, 3776–3778Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/ic00044a020https://doi.org/10.1021/ic00044a020research-articleACS PublicationsRequest reuse permissionsArticle Views222Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
THz Frequency Selective Surface Filters for Earth Observation Remote Sensing Instruments (2011)

The purpose of this paper is to review recent developments in the design and fabrication of Frequency Selective Surfaces (FSS) which operate above 300 GHz. These structures act as free space electromagnetic filters and as such provide passive remote sensing instruments with multispectral capability by separating the scene radiation into separate frequency channels. Significant advances in computational electromagnetics, precision micromachining technology and metrology have been employed to create state of the art FSS which enable high sensitivity receivers to detect weak molecular emissions at THz wavelengths. This new class of quasi-optical filter exhibits an insertion loss <;0.3 dB at 700 GHz and can be designed to operate independently of the polarization of the incident signals at oblique incidence. The paper concludes with a brief overview of two major technical advances which will greatly extend the potential applications of THz FSS.
Magnetic properties of carbon-coated, ferromagnetic nanoparticles produced by a carbon-arc method (1994)

The Krätschmer–Huffman carbon-arc method of preparing fullerenes has been used to generate carbon-coated transition metal (TM) and TM-carbide nanocrystallites. The magnetic nanocrystallites were extracted from the soot with a magnetic gradient field technique. For TM=Co the majority of nanocrystals exist as nominally spherical particles, 0.5–5 nm in radius. Hysteretic and temperature-dependent magnetic response, in randomly and magnetically aligned powder samples frozen in epoxy, correspond to fine particle magnetism associated with monodomain TM particles. The magnetization exhibits a unique functional dependence on H/T, and hysteresis below a blocking temperature TB. Below TB, the temperature dependence of the coercivity can be expressed as Hc=Hc0[1−(T/TB)1/2], where Hc0 is the 0 K coercivity.
Forced Air Cooling With Synthetic Jet Ejectors (2005)

This paper discusses the concept of synthetic jet ejectors for forced air cooling and some practical implementations of the same. Synthetic or “zero-mass-flux” jets, unlike conventional jets, require no mass addition to the system, and thus provide means of efficiently directing airflow across a heated surface. Because these jets are zero net mass flux in nature and are comprised entirely of the ambient fluid, they can be conveniently integrated with the surfaces that require cooling without the need for complex plumbing. A synthetic jet ejector mechanism for obtaining high heat transfer rates at low flow rates is discussed. Synthetic jet ejectors consist of a primary “zero-mass-flux” unsteady jet driving a secondary airflow through a channel. Several practical implementations of synthetic jets are introduced from low form factor, low power spot cooling applications to high heat dissipation applications and flow bypass control where synthetic jets are used to enhance fan performance.
Real-time recognition of large-scale driving patterns (2002)

This work has explored the possibilities of real-time, automatic, recognition of large-scale driving situations. Employing a statistical pattern recognition framework, implemented by means of feedforward neural networks, models were developed for recognising, from vehicle control data, four classes of driving situations: highway, main road, suburban traffic and city traffic.
Brain Factor Control of Sex Pheromone Production in the Female Corn Earworm Moth (1984)

Sex pheromone production in the female corn earworm moth Heliothis zea is controlled by a hormonal substance produced in the female's brain. It is present in the brain in scotophase as well as photophase, but it is released into the hemolymph to stimulate pheromone production only in the scotophase. The stimulatory activity was also detected in the brains of male corn earworm moths and of other moths.
Insights Into the Oxygen Reduction Reaction Activity of Pt/C and PtCu/C Catalysts (2015)

A mechanistic electrochemical study of the oxygen reduction reaction (ORR) on a carbon-supported PtCu catalyst is presented. The catalyst was prepared by galvanic displacement of nanoporous copper with Pt. The electrochemistry of the catalyst was explored at pH 1 and pH 13. Hydrogen peroxide reduction and rotating ring–disk electrode (RRDE) studies showed that the PtCu/C catalyst facilitates a 4e– direct or series reduction to water in alkaline electrolyte. A Tafel study suggests that the ORR rate-limiting step for PtCu/C does not change when the catalyst is subject to pH extremes. The ORR activity of the PtCu/C catalyst was found to be 2–3 times higher than the ORR activity of commercially available Pt/C (Johnson Matthey). Adsorption of OH– was quantified for PtCu/C and Pt/C, and PtCu/C was observed to have a reduced affinity toward OHads in both acid and alkaline electrolyte, which was found to promote the rate of the ORR relative to Pt/C. On the basis of this study, we propose that (1) each Pt-based catalyst has a unique rate of change of OHads coverage which is correlated to its ORR activity and (2) all Pt-based catalysts have the same rate of change of OHads coverage during irreversible oxide formation.
Sulfonated polystyrene as a new gradient-index medium for light-focusing elements (1995)

We have discovered that the sulfonation of polystyrene can form a gradient-index medium useful for lightfocusing purposes. We found that the refractive index of sulfonated polystyrene varies with the degree of sulfonation and that the refractive index of the fully sulfonated polystyrene decreased by approximately 0.06 at 0.633 microm from that of pure polystyrene.
Immunogenicity of a low-virulence vaccinal strain against Salmonella abortus-ovis infection in mice (1983)

Strain Rv6, a streptomycin-independent reverse mutant of Salmonella abortus-ovis, multiplied and disseminated in vivo to a lesser extent than the virulent parental strain 15/5, as determined by subcutaneous inoculation of two outbred strains of mice with different susceptibilities to salmonella infection. This lower virulence of strain Rv6 was not modified by 10 passages in susceptible mice. Vaccination with strain Rv6 induced a dose-dependent capacity of mice to control subsequent infection with the virulent parental strain. Induced resistance began as early as 3 days after vaccination and lasted at least 11 months. Its efficiency was controlled by different routes and doses of challenge. Strain Rv6 induced a greater protection than that conferred by heat-killed bacteria or by tested commercial killed vaccines.
The Plasminogen Receptor, , and Macrophage Function (2012)

When plasminogen binds to cells its activation to plasmin is markedly enhanced compared to the reaction in solution. Thus, cells become armed with the broad spectrum proteolytic activity of plasmin. Cell-surface plasmin plays a key role in macrophage recruitment during the inflammatory response. Proteins exposing basic residues on the cell surface promote plasminogen activation on eukaryotic cells. We have used a proteomics approach combining targeted proteolysis with carboxypeptidase B and multidimensional protein identification technology, MudPIT, and a monocyte progenitor cell line to identify a novel transmembrane protein, the plasminogen receptor, Plg-R(KT). Plg-R(KT) exposes a C-terminal lysine on the cell surface in an orientation to bind plasminogen and promote plasminogen activation. Here we review the characteristics of this new protein, with regard to membrane topology, conservation of sequence across species, the role of its C-terminus in plasminogen binding, its function in plasminogen activation, cell migration, and its role in macrophage recruitment in the inflammatory response.
<i>Classical swine fever virus</i> detection (2011)

The current study reports on a real-time reverse transcription polymerase chain reaction (real-time RT-PCR) ring trial for the detection of Classical swine fever virus (CSFV) genomic RNA undertaken by 10 European laboratories. All laboratories were asked to use their routine in-house real-time RT-PCR protocols and a standardized protocol commonly used by the Friedrich-Loeffler-Institute (FLI) on a panel of well-characterized samples. In general, all participants produced results within the acceptable range. The FLI assay, several in-house assays, and the commercial kits had high analytical sensitivity and specificity values. Nevertheless, some in-house systems had unspecific reactions or suboptimal sensitivity with only a single CSFV genotype. Follow-up actions involved either improvement of suboptimal assays or replacement of specific laboratory assays with the FLI protocol, with or without modifications. In conclusion, the ring trial showed reliability of classical swine fever diagnosis on an international level and helped to optimize CSFV-specific RT-PCR diagnostics.
Centrifuge Permeameter for Unsaturated Soils. I: Theoretical Basis and Experimental Developments (2010)

A new centrifuge permeameter was developed with the specific objective of expediting the measurement of the hydraulic characteristics of unsaturated soils. The development, theoretical basis, and typical results associated with using the centrifuge permeameter for concurrent determination of the soil-water retention curve (SWRC) and hydraulic conductivity function (K function) of unsaturated soils are presented in this paper. Components developed for the centrifuge permeameter are described, including the centrifuge, permeameter, water flow control system, and instrumentation used to concurrently and nondestructively measure the infiltration rate (flow pump and outflow transducer), volumetric water content (time domain reflectometry), and matric suction (tensiometers) in flight during steady-state infiltration. A companion paper focuses on definition of the SWRC and K function for a clay soil using the procedures described in this paper. While conventional geotechnical centrifuges are used to reproduce the response of earth structure prototypes, the centrifuge developed in this study is used to accelerate flow processes. Accordingly, it required a comparatively small radius (0.7 m) but high angular velocity (up to 875 rpm or 600 g’s) to impart a wide range of hydraulic gradients to an unsaturated soil specimen. Analytical solutions to Richards’ equation in the centrifuge indicate that steady-state infiltration allows direct determination of the relationships between suction, volumetric water content, and hydraulic conductivity from the instrumentation results. Typical instrumentation results during a drying stage are presented to illustrate determination of data points on the SWRC and K function at steady state. These results were found to be consistent with analytical flow solutions.
Exact Force Vector Regulation of the Three-Pole Magnetic Bearing (2021)

The three-pole magnetic bearing is an attractive alternative to the conventional four- and eight-pole magnetic bearings because of its simple structure and ability to be operated with three-phase power electronics. However, accurately controlling the three-pole bearing is significantly more complicated. The conventional control implementations are prone to large force vector errors that can lead to instability in the magnetic suspension system. This article proposes a new control implementation for externally biased three-pole bearings that eliminates force vector error. This control implementation is based on solving a fourth-order polynomial in the form of a depressed quartic to determine coil current commands. An analytic framework and graphic techniques are developed to study the solution space for the bearing's coil currents and explain discontinuities that can arise in certain bearing designs. It is shown that bearings with either no bias or a normalized bias field in excess of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\frac{1}{3}$</tex-math></inline-formula> are preferred for suspension stability. The exact force vector regulator is experimentally demonstrated in a bearing prototype and shown to be advantageous over the conventional regulation approach.
Production of Thermostable α-Amylase, Pullulanase, and α-Glucosidase in Continuous Culture by a New <i>Clostridium</i> Isolate (1987)

The production of alpha-amylase, pullulanase, and alpha-glucosidase and the formation of fermentation products by the newly isolated thermophilic Clostridium sp. strain EM1 were investigated in continuous culture with a defined medium and an incubation temperature of 60 degrees C. Enzyme production and excretion were greatly influenced by the dilution rate and the pH of the medium. The optimal values for the formation of starch-hydrolyzing enzymes were a pH of 5.9 and a dilution rate of 0.075 to 0.10 per h. Increase of the dilution rate from 0.1 to 0.3 per h caused a drastic drop in enzyme production. The ethanol concentration and optical density of the culture, however, remained almost constant. Growth limitation in the chemostat with 1% (wt/vol) starch was found optimal for enzyme production. Under these conditions 2,800 U of pullulanase per liter and 1,450 U of alpha-amylase per liter were produced; the amounts excreted were 70 and 55%, respectively.
A bio-driven lime and pickle free tanning paves way for greener garment leather production (2004)

Conventional methods employed in leather processing subject the skin or hide to a wide variety of chemicals. This contributes to an increase in COD, TDS, chlorides, sulfates and other mineral salts in tannery effluent. A process sequence has now been explored viz., enzymatic dehairing, enzymatic fiber opening, and pickle-free chrome tanning for tanning red hair sheepskins, which limits the use of unsafe chemicals. A process for dehairing at pH 8.0 has been achieved by employing a commercial enzyme. A novel opening up system has been established again using enzymes. A pickle-basification free chrome tanning has been adopted to tan the enzyme treated matrices. Using the above said strategy, garment leathers have been made from wet-salted sheepskins. This leads to substantial decrease in chemical consumption from 442 to 38 kg for tanning one metric ton raw skins. Performances of leathers are on a par with conventionally opened up leathers, which is substantiated through physical and hand evaluation. This has also been verified through scanning electron microscopic analysis and softness measurements. The process also enjoys reduction in COD and TS loads on the environment by 84%. This process has also been proved to be economically viable, when compared with conventional process. Thus, the bio-driven pickle-free chrome tanning process leads to the manufacture of garment leathers with a cleaner environment.