gebhart/patrepeval huggingface dataset:
Trapping mammalian protein complexes in viral particles (2016)

Cell lysis is an inevitable step in classical mass spectrometry-based strategies to analyse protein complexes. Complementary lysis conditions, in situ cross-linking strategies and proximal labelling techniques are currently used to reduce lysis effects on the protein complex. We have developed Virotrap, a viral particle sorting approach that obviates the need for cell homogenization and preserves the protein complexes during purification. By fusing a bait protein to the HIV-1 GAG protein, we show that interaction partners become trapped within virus-like particles (VLPs) that bud from mammalian cells. Using an efficient VLP enrichment protocol, Virotrap allows the detection of known binary interactions and MS-based identification of novel protein partners as well. In addition, we show the identification of stimulus-dependent interactions and demonstrate trapping of protein partners for small molecules. Virotrap constitutes an elegant complementary approach to the arsenal of methods to study protein complexes.
Supplementary Figures 1-2, Methods from Antibodies to Merkel Cell Polyomavirus T Antigen Oncoproteins Reflect Tumor Burden in Merkel Cell Carcinoma Patients (2023)

Supplementary Figures 1-2, Methods from Antibodies to Merkel Cell Polyomavirus T Antigen Oncoproteins Reflect Tumor Burden in Merkel Cell Carcinoma Patients
Simplified forced convergence decoding algorithm for low power LDPC decoders (2014)

This paper proposes a simplified forced-convergence (SFC) algorithm to reduce the computational complexity for low-density parity-check (LDPC) decoding. To reduce the computational complexity, the proposed algorithm uses the modified check node (CN) operation that does not use a condition for deactivating CNs. Therefore, the proposed SFC algorithm uses only one threshold value while the existing forced-convergence (FC) algorithm uses two threshold values. The simulation results show that SFC achieves a bit error rate (BER) performance close to min-sum (MS) algorithm. SFC can reduce the computational complexity of check node by approximately 22.21% compared to FC.
Long-Term Transmit Beamforming for Wireless Multicasting (2007)

This paper presents a low-complexity iterative algorithm for long-term transmit beamforming in multicast channels. Since it relies only on antenna correlations at the base station, the algorithm requires only infrequent feedback from the users. Multiantenna receivers are not required, but they are transparently accommodated. Simulation results within the context of the UMTS long-term evolution system indicate that, with half-wavelength antenna spacings and a typical power azimuth spectrum, the performance is close to optimal. The specific gains (in average SINR) then depend on the number of transmit antennas and the number of active users.
A Multiple-Frequency Phase Comparison Technique for the Determination of Remote Layer Thickness (1979)

A continuous-wave phase comparison technique which provides at least an order of magnitude improvement in accuracy over modulated carrier systems which operate in the same spectrum is described in this paper for the remote determination of the thickness of layered targets consisting of a known number of dielectric layers, each of a known maximum thickness. This system uses rationally related frequencies such as the fundamental and its harmonics to establish a multifrequency coherence relationship whereby a phase reference between frequencies can be conserved and information extracted from just the received and not the transmitted signals. Consequently, Doppler effects due to motion between the target layer and the apparatus, as well as local oscillator stability and drift limitations are avoided. Thus this system can measure the parameters of remote layered targets by interferometric techniques without the distance being a constraint.
Call sign specifically optimized for FMCW HF oceanographic radars (2016)

At the end of 2012, the ITU issued Resolution 612, which allotted designated secondary radio spectral slots to coastal oceanographic radars (3 - 50 MHz). Part of the condition for authorized use of these bands is the requirement that each radar transmit a Morse-coded call sign issued by its national authority. The unique call sign identifies the transmitter. The worldwide process of implementing this has begun. In the absence of ITU recommended rules for conformity, we outline and are implementing an optimized procedure that is described herein. It is meant to follow the intended spirit fairly, of allowing identification by AM radio receivers impacted by the radar's signal, when both occupy different spectral bandwidths. Our design also ensures continuous data capture during call-sign broadcast periods, both the radar as well as neighboring radars on the same frequency. We demonstrate this with radar Doppler spectra spanning periods of call-sign transmission. This is based on the FMCW radar waveform, which all commercially available oceanographic radars employ.
Multi-Degree-of-Freedom Stabilization of Large-Scale Photonic-Integrated Circuits (2015)

We present and elaborate the principles of a novel <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">control and calibration</i> (C&C) systematic approach, aiming at feedback stabilization of large scale <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">photonic-integrated circuits</i> (PIC) to their nominal operating points in <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> -dimensional spaces of tuning parameters, based on refinement of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> extremum-seeking</i> (ES) real-time optimization techniques. The novel methodology enables, in principle, stabilizing a large number <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> of tuning <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">degrees of freedom</i> (DOF) of PICs, with just one optical power monitoring (probe) point. The proposed C&C digital controller ports multidimensional ES stabilization concepts to photonics for the first time and further introduces novel improvements to known ES techniques, proposing a new frame-based <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">discrete-multitone</i> method of actuation signals generation and probe signals detection, akin to an <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">orthogonal-frequency-division multiplexing</i> modulation format. Another novel element is that the iterative digital algorithm adaptively selects between gradient- versus Newton-based descent and between various methods of line search. This approach enables real-time application of unconstrained optimization techniques for C&C of photonic circuits with multiple tuning DOFs. The new technique is exemplified by numeric simulations of the stabilization of a Silicon photonic microring modulator with <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> = 2 tuning DOFs, concurrently tuning both resonant phase and a second coupling phase parameter, optimizing critical coupling into the microring based on observing the optical power at single low-frequency monitoring point.
Time-Multiplexed Integral Imaging For 3D Sensing and Display (2004)

We perceive the world in depth as well as in color, but the generation of high-quality three-dimensional (3D) images is still an area that is fraught with challenges for researchers. Now a ray-optics-based technique - integral imaging - shows promise for 3D TV and visualization.
Monitoring expression profiles of <i>Arabidopsis</i> gene expression during rehydration process after dehydration using <i>ca</i>. 7000 full‐length cDNA microarray (2003)

Plants respond and adapt to drought stress in order to survive under stress conditions. Several genes that respond to drought at the transcriptional level have been described, but there are few reports on genes involved in the recovery from dehydration. Analysis of rehydration-inducible genes should help not only to understand the molecular mechanisms of stress responses in higher plants, but also to improve the stress tolerance of crops by gene manipulation. We used a full-length cDNA microarray containing ca. 7000 Arabidopsis full-length cDNAs and identified 152 rehydration-inducible genes. Venn diagram analysis showed relationship of the rehydration-inducible genes to proline-inducible and water-treatment-inducible genes. Among the 152 rehydration-inducible genes, 58 genes contained the ACTCAT sequence involved in proline- and hypoosmolarity-inducible gene expression in their promoter regions, suggesting that ACTCAT sequence is a major cis-acting element involved in rehydration-inducible gene expression, and that some novel cis-acting elements are involved in rehydration-inducible gene expression. Functional analysis of rehydration-inducible and rehydration-repressed genes revealed their functions not only in the release from a stressed status but also in the recovery of growth in plants.
3-[(2-Methyl-1,3-thiazol-4-yl)ethynyl]- pyridine:  A Potent and Highly Selective Metabotropic Glutamate Subtype 5 Receptor Antagonist with Anxiolytic Activity (2002)

2-Methyl-6-(phenylethynyl)pyridine (3), a potent noncompetitive mGlu5 receptor antagonist widely used to characterize the pharmacology of mGlu5 receptors, suffers from a number of shortcomings as a therapeutic agent, including off-target activity and poor aqueous solubility. Seeking to improve the properties of 3 led to the synthesis of compound 9, a highly selective mGlu5 receptor antagonist that is 5-fold more potent than 3 in the rat fear-potentiated startle model of anxiety.
Distributed sensing of signals linked by sparse filtering (2009)

We consider the task of recovering correlated vectors at a central decoder based on fixed linear measurements obtained by distributed sensors. A general formulation of the problem is proposed, under both a universal and an almost sure reconstruction requirement. We then study a specific correlation model which involves a filter that is sparse in the time domain. While this sparsity assumption does not allow reducing the description cost in the universal case, we show that large gains can be achieved in the almost sure scenario by means of a novel distributed scheme based on annihilating filters. The robustness of the proposed method is also investigated.
Principles of a resonant cavity optical modulator (1986)

We describe the principles of a resonant cavity optical modulator capable of modulation frequencies in the 10-GHz range. The dispersive properties of waveguides are used to achieve phase matching of the optical and rf waves, which differ in velocity by a factor of 3 in bulk electrooptic materials. The difference in propagation velocities also allows us to form a rectangular cavity with two opposite sides open through which the optical beam may be easily passed. A modulator employing this design is thus both efficient in its use of rf power and is easily optically aligned.
Autonomous Inspection of Electrical Transmission Structures with Airborne UV Sensors and Automated Air Traffic Management (2018)

This report details test and measurement flights to demonstrate autonomous UAV (Unmanned Aerial Vehicle) inspection of high-voltage electrical transmission structures. A UAV built with commercial, off-the-shelf hardware and software, supplemented with custom sensors and logging software, measured ultraviolet (UV) emissions from a test generator placed on a low-altitude substation and a medium-altitude switching tower. Since corona discharge precedes catastrophic electrical faults on high-voltage structures, detection and geolocation of ultraviolet emissions is needed to develop a UAV-based self-diagnosing power grid. Signal readings from an onboard ultraviolet sensor were validated during flight with a commercial corona camera. Geolocation was accomplished with onboard GPS; the UAV position was logged to a local ground station and transmitted in real time to a NASA server for tracking in the national airspace. The method has practicality and relevance but not adequacy; either improved UAV position determination technology or increased sensor range is needed to enable broad deployment of this method.
Protecting and evaluating genomic privacy in medical tests and personalized medicine (2013)

In this paper, we propose privacy-enhancing technologies for medical tests and personalized medicine methods that use patients' genomic data. Focusing on genetic disease-susceptibility tests, we develop a new architecture (between the patient and the medical unit) and propose a "privacy-preserving disease susceptibility test" (PDS) by using homomorphic encryption and proxy re-encryption. Assuming the whole genome sequencing to be done by a certified institution, we propose to store patients' genomic data encrypted by their public keys at a "storage and processing unit" (SPU). Our proposed solution lets the medical unit retrieve the encrypted genomic data from the SPU and process it for medical tests and personalized medicine methods, while preserving the privacy of patients' genomic data. We also quantify the genomic privacy of a patient (from the medical unit's point of view) and show how a patient's genomic privacy decreases with the genetic tests he undergoes due to (i) the nature of the genetic test, and (ii) the characteristics of the genomic data. Furthermore, we show how basic policies and obfuscation methods help to keep the genomic privacy of a patient at a high level. We also implement and show, via a complexity analysis, the practicality of PDS.
Path Criticality Computation in Parameterized Statistical Timing Analysis Using a Novel Operator (2012)

This paper presents a method to compute criticality probabilities of paths in parameterized statistical static timing analysis. We partition the set of all the paths into several groups and formulate the path criticality into a joint probability of inequalities. Before evaluating the joint probability directly, we simplify the inequalities through algebraic elimination, handling topological correlation. Our proposed method uses conditional probabilities to obtain the joint probability, and statistics of random variables representing process parameters are changed to take into account the conditions. To calculate the conditional statistics of the random variables, we derive analytic formulas by extending Clark's work. This allows us to obtain the conditional probability density function of a path delay, given the path is critical, as well as to compute criticality probabilities of paths. Our experimental results show that the proposed method provides 4.2X better accuracy on average in comparison to the state-of-art method.
Optimizing Pyrazolopyrimidine Inhibitors of Calcium Dependent Protein Kinase 1 for Treatment of Acute and Chronic Toxoplasmosis (2020)

Calcium dependent protein kinase 1 (CDPK1) is an essential Ser/Thr kinase that controls invasion and egress by the protozoan parasite <i>Toxoplasma gondii</i>. The Gly gatekeeper of CDPK1 makes it exquisitely sensitive to inhibition by small molecule 1<i>H</i>-pyrazolo[3,4-<i>d</i>]pyrimidine-4-amine (PP) compounds that are bulky ATP mimetics. Here we rationally designed, synthesized, and tested a series of novel PP analogs that were evaluated for inhibition of CDPK1 enzyme activity <i>in vitro</i> and parasite growth in cell culture. Optimal substitution on the PP scaffold included 2-pyridyl ethers directed into the hydrophobic pocket and small carbocyclic rings accessing the ribose-binding pocket. Further optimization of the series led to identification of the lead compound <b>3a</b> that displayed excellent potency, selectivity, safety profile, and efficacy <i>in vivo</i>. The results of these studies provide a foundation for further work to optimize CDPK1 inhibitors for the treatment of acute and chronic toxoplasmosis.
Topographic mapping using polarimetric SAR data (1998)

A new remote sensing technique using polarimetric synthetic aperture radar (SAR) data has been developed which can measure terrain slopes in the azimuthal, or along-track, direction. Terrain elevation maps can then be generated by integrating these slopes. The processing of both single-pass, and orthogonal two-pass, datasets is investigated. When single-pass SAR data is used elevation groundtruth must be available for at least one point of each profile formed in the azimuthal direction. When orthogonal two-pass slope data is employed, the elevation surface may be generated as an iterative solution of the Poisson equation and only a single elevation tie-point is required. The results of two studies are presented. In the first study slopes have been measured using single-pass P-band data for a forested area in northern California. The elevation surface generated with this data has been compared with a Digital Elevation Model (DEM) produced by a C-band interferometric SAR. The second study uses orthogonal two- pass P-band data as a test of the Poisson equation approach for an area in Death Valley National Park, California. The orthogonal two-pass results have been compared with a co-registered, conventional, U.S. Geological Survey (USGS) product. Technique accuracy and potential applications are discussed.
An achromatic refractive laser beam reshaper (2003)

Methods will be described for achromatizing a previously described highly efficient refractive laser beam reshaper which allow a propagating, collimated, diffraction limited flat-top laser beam to be generated over a 200 nm spectral interval. Although the beam reshaper utilizes two aspheric lenses, the achromatizers detailed in this paper use only conventional spherical refracting elements. This allows a practical and cost effective path to upgrade such a beam reshaper to broad wavelength operation.
Vacuum Arc Evolution Characteristics in Low-Voltage DC Current Interruption Under Composite Transverse Magnetic Fields (2021)

Based on our novel dc vacuum interruption technology under composite transverse magnetic fields (TMFs), the arc voltage of dc vacuum arc can be effectively improved to interrupt the dc current. The objective of this work is to experimentally investigate the vacuum arc characteristics and their evolution in dc current interruption under composite TMFs. The composite TMFs were generated by both multipole permanent magnets and cup-type TMF contacts. The vacuum arc photos were recorded by a high-speed camera. The experimental results indicate that under these composite TMFs, the dc current could be successfully interrupted, which was closely related to the dc vacuum arc characteristics and their evolution. The experimental dc current and voltage were less than 500 A and 500 V. First, the evolution of the dc vacuum arc could be divided into Stable and Unstable stages, according to the characteristics of the arc voltage waveform. In the Stable stage, the dc vacuum arc might be stagnated, constricted, and rotated with a stable arc voltage of 20 V. In the Unstable stage, the dc vacuum arc was transferred to the outer periphery of the contact in the form of a “C”-shape, and the arc voltage significantly increased higher than the supply dc voltage. Second, there was an Extinction Area in the middle of Area 4 under the composite TMFs, which made the dc vacuum arc always extinguish at this position. Third, repeated fluctuations of the arc voltage are caused by the formation and extinction of the “C”-shaped arc. Finally, when the distance between the igniting area and Extinction Area increased, the duration of the Stable stage increased, while the duration of the Unstable stage decreased.
Sensing grain moisture content through dielectric properties (2003)

The rapid, nondestructive, reliable sensing of moisture content in cereal grains and other agricultural crops is essential in modem agriculture for prevention of losses and improvements in efficiency of production of these sources of food. Measurement, or sensing, of the relative complex permittivity, or dielectric properties, at microwave frequencies offers advantages that include density-independent sensing of moisture content. Recent research findings support the idea of a universal calibration, which would provide a significant advantage and should encourage the development of microwave moisture sensors for on-line applications for grain and other granular or particulate materials in agriculture and other industries.
Exocellular esterase and emulsan release from the cell surface of Acinetobacter calcoaceticus (1985)

An esterase activity has been found, both in the cell-free growth medium and on the cell surface of the hydrocarbon-degrading Acinetobacter calcoaceticus RAG-1. The enzyme catalyzed the hydrolysis of acetyl and other acyl groups from triglycerides and aryl and alkyl esters. Emulsan, the extracellular heteropolysaccharide bioemulsifier produced by strain RAG-1, was also a substrate for the enzyme. Gel filtration showed that the cell-free enzyme was released from the cell surface either emulsan free or associated with the bioemulsifier. The partially purified enzyme was found to interact specifically with the esterified fully active emulsan, but not with the deesterified polymer. A role for esterase in emulsan release from the cell surface was indicated when the enzyme was preferentially depleted from the cell surface under conditions in which emulsan was not released. Such cells lost the capacity to release the biopolymer.
Synthesis of 2-phenylthiazolidine derivatives as cardiotonic agents. V. Modification of the thiazolidine moiety of 2-(phenylpiperazinylalkoxyphenyl)thiazolidine-3-thiocarboxamides and the corresponding carboxamides. (1987)

The carba (2) and oxa analogues (3) of 2- (phenylpiperazinylalkoxyphenyl) thiazolidine-3-carboxamide (1, Y=O) and-thiocarboxamide (1, Y=S) were synthesized and tested for cardiotonic activity. These analogues (2 and 3) were prepared from the aldehydes (4) through several intermediates (7, 10, and 13). In a series of the N-methylcarboxamides, positive inotropic activity in anesthetized dogs decreased in the following order : the thiazolidine (1a) >>oxazolidine (3a) >pyrrolidine (2a). In the corresponding thiocarboxamide series, however, the oxazolidine (3b) was the most potent, followed by the thiazolidine (1b) and the pyrrolidine (2c).
Nuclear Resonance Fluorescence of /sup 235/U (2006)

Nuclear resonance fluorescence is a physical process that provides an isotopic-specific signature that can be used for the identification and characterization of materials. The technique involves the detection of prompt discrete-energy photons emitted from a sample which is exposed to photons in the MeV energy range. Potential applications of the technique range from detection of high explosives to characterization of special nuclear materials. One isotope of significant interest is <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">235</sup> U. Pacific Northwest National Laboratory and Passport Systems have collaborated to conduct measurements searching for nuclear resonance fluorescence signatures of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">235</sup> U below 3 MeV using a 220 g sample of highly enriched uranium. Nine <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">235</sup> U resonances between 1650 and 2010 keV were identified in the preliminary analysis. Analysis of the measurement data to determine the integrated cross sections of the resonances is in progress.