gebhart/patrepeval huggingface dataset:
Optimizing the production and affinity purification of HIV-1 envelope glycoprotein SOSIP trimers from transiently transfected CHO cells (2019)

We describe methods to improve the efficiency with which HIV-1 Envelope glycoprotein SOSIP trimer immunogens can be produced by transient transfection of ExpiCHO-S cells and then affinity purified using the trimer-specific human monoclonal antibody PGT145. The specificity of PGT145 for properly folded trimers allows for the facile, one-step, isolation of these immunogens in research laboratories. PGT145 columns are also valuable as a component of more complex purification processes in current Good Manufacturing Practice programs. However, we found that PGT145 purification was highly variable and markedly inefficient when used to process supernatants from transiently transfected ExpiCHO-S cells expressing the BG505 SOSIP.664 and other trimeric Env proteins. In contrast, no such problems arose when the same Env proteins derived from a stable CHO cell line were processed on the same PGT145 columns, or with transient transfection supernatants from 293F cells. An investigation of the ExpiCHO-S transfection system identified the presence of polyanions, including but perhaps not limited to dextran sulfate, in the Enhancer component of the transfection system. We hypothesized that these polyanions bound to the cationic PGT145 epitope on the trimers and impeded their ability to bind to the PGT145 affinity column. We found that replacing the Enhancer component with alternative culture medium supplements substantially increased the yield of PGT145-purifiable trimers, and we also confirmed that both dextran sulfate and the Enhancer component were indeed inhibitors of PGT145 binding to BG505 SOSIP.664 trimers in immunoassays. The presence of polyanions, including but not limited to nucleic acids, should be considered in other circumstances where PGT145 columns are less efficient than expected at purifying native-like trimers.
Electronic Measurement of Tree Canopy Volume (1988)

ABSTRACT AN electronic tree canopy volume measurement system was developed. The system was based on commercial ultrasonic range transducers with novel digital interface circuitry. The measurement system and a microcomputer were mounted on an orchard air-blast sprayer for testing. Calibration tests with ideal targets found system error to be < 2% at mid range (2.6 m). Field tests in apple and peach orchards at different stages of leaf development found the system to measure tree width and extension with <10% average error and high precision. Tests at ground speeds of 2, 4 and 6 km/h found no significant effect on system performance due to ground speed.
Simultaneous cell disruption and semi-quantitative activity assays for high-throughput screening of thermostable L-asparaginases (2018)

L-asparaginase, which catalyses the hydrolysis of L-asparagine to L-aspartate, has attracted the attention of researchers due to its expanded applications in medicine and the food industry. In this study, a novel thermostable L-asparaginase from Pyrococcus yayanosii CH1 was cloned and over-expressed in Bacillus subtilis 168. To obtain thermostable L-asparaginase mutants with higher activity, a robust high-throughput screening process was developed specifically for thermophilic enzymes. In this process, cell disruption and enzyme activity assays are simultaneously performed in 96-deep well plates. By combining error-prone PCR and screening, six brilliant positive variants and four key amino acid residue mutations were identified. Combined mutation of the four residues showed relatively high specific activity (3108 U/mg) that was 2.1 times greater than that of the wild-type enzyme. Fermentation with the mutant strain in a 5-L fermenter yielded L-asparaginase activity of 2168 U/mL.
Poster (2019)

The load on wireless cellular networks is not uniformly distributed through the day, and is significantly higher during peak-times. In this context, we present a time-shifted prefetching solution that prefetches content during off-peak periods of network connectivity. We specifically focus on YouTube as it represents a significant portion of overall cellular data-usage. We make the following contributions: first, we establish that a significant portion of a user's YouTube watch behavior is indeed predictable by analyzing a real-life dataset of YouTube watch history spanning a 1-year period, from 206 users comprised of over 1.8 million videos; second, we develop an accurate prediction algorithm using a K-nearest neighbor classifier approach; and finally, we evaluate the prefetching algorithm on two different datasets and show that MANTIS is able to reduce the traffic during peak periods by 34% for a typical user.
Noise Mitigation of Random Data Signals Through Linear Temporal Sampling Based on the Talbot Effect (2019)

Noiseless passive amplification of non-repetitive waveforms, e.g., non-return-to-zero data signals, is achieved up to a factor of 28.5 through a linear Talbot-based lossless temporal sampling process, enabling recovery of signals entirely buried under noise.
On the Completeness of Attack Mutation Algorithms (2006)

An attack mutation algorithm takes a known instance of an attack and transforms it into many distinct instances by repeatedly applying attack transformations. Such algorithms are widely used for testing intrusion detection systems. We investigate the notion of completeness of a mutation algorithm: its capability to generate all possible attack instances from a given set of attack transformations. We define the notion of a Phi-complete mutation algorithm. Given a set of transformations Phi, an algorithm is complete with respect to Phi, if it can generate every instance that the transformations in Phi derive. We show that if the rules in Phi are uniform and reversible then a Phi-complete algorithm exists. Intuitively speaking, uniform and reversible transformations mean that we can first exclusively apply transformations that simplify the attack, then exclusively apply transformations that complicate it, and still get all possible instances that are derived by the rules in Phi. Although uniformity and reversibility may appear severe restrictions, we show that common attack transformations are indeed uniform and reversible. Therefore, our Phi-complete algorithm can be incorporated into existing testing tools for intrusion detection systems. Furthermore, we show that a Phi-complete algorithm is useful, not only for testing purposes, but also for determining whether two packet traces are two different mutations of the same attack
Tumor-Infiltrating Merkel Cell Polyomavirus-Specific T Cells Are Diverse and Associated with Improved Patient Survival (2017)

Tumor-infiltrating CD8<sup>+</sup> T cells are associated with improved survival of patients with Merkel cell carcinoma (MCC), an aggressive skin cancer causally linked to Merkel cell polyomavirus (MCPyV). However, CD8<sup>+</sup> T-cell infiltration is robust in only 4% to 18% of MCC tumors. We characterized the T-cell receptor (TCR) repertoire restricted to one prominent epitope of MCPyV (KLLEIAPNC, "KLL") and assessed whether TCR diversity, tumor infiltration, or T-cell avidity correlated with clinical outcome. HLA-A*02:01/KLL tetramer<sup>+</sup> CD8<sup>+</sup> T cells from MCC patient peripheral blood mononuclear cells (PBMC) and tumor-infiltrating lymphocytes (TIL) were isolated via flow cytometry. TCRβ (TRB) sequencing was performed on tetramer<sup>+</sup> cells from PBMCs or TILs (n = 14) and matched tumors (n = 12). Functional avidity of T-cell clones was determined by IFNγ production. We identified KLL tetramer<sup>+</sup> T cells in 14% of PBMC and 21% of TIL from MCC patients. TRB repertoires were strikingly diverse (397 unique TRBs were identified from 12 patients) and mostly private (only one TCRb clonotype shared between two patients). An increased fraction of KLL-specific TIL (>1.9%) was associated with significantly increased MCC-specific survival P = 0.0009). T-cell cloning from four patients identified 42 distinct KLL-specific TCRa/b pairs. T-cell clones from patients with improved MCC-specific outcomes were more avid (P < 0.05) and recognized an HLA-appropriate MCC cell line. T cells specific for a single MCPyV epitope display marked TCR diversity within and between patients. Intratumoral infiltration by MCPyV-specific T cells was associated with significantly improved MCC-specific survival, suggesting that augmenting the number or avidity of virus-specific T cells may have therapeutic benefit. Cancer Immunol Res; 5(2); 137-47. ©2017 AACR.
Ultra-refractive and extended range one-dimensionsal photonic crystal superprisms (2003)

We describe theoretical analysis and design of one-dimensional photonic crystal prisms. We find that inside the photonic crystal, for frequencies near the band edges, light propagation direction is extremely sensitive to the variations in wavelength and incident angle. Outside the photonic crystal, propagation direction of transmitted light is highly sensitive to changes in wavelength, but less so to incident angle. For transmitted light outside the photonic crystal, the superprism effect can be used for wavelength dispersion over entire photonic bands, rather than just near the band edges only. This extended-range superprism effect broadens the useful wavelength rage, admits better optical transmission, and exhibits angular dependence on wavelength with greatly reduced non-linearity.
Pseudomorphic bipolar quantum resonant-tunneling transistor (1989)

A bipolar tunneling transistor in which ohmic contact is made to the strained p/sup +/ InGaAs quantum well of a double-barrier resonant-tunneling structure is discussed. The heterojunction transistor consists of an n-GaAs emitter and collector, undoped AlGaAs tunnel barriers, and a pseudomorphic p/sup +/ InGaAs quantum-well base. By making ohmic contact to the p-type quantum well, the hole density in the quantum-well base is used to modulate the base potential relative to the emitter and collector terminals. With control of the quantum-well potential, the tunneling current can be modulated by application of a base-to-emitter potential. The authors detail the physical and electrical characteristics of the device. It is found that the base-emitter voltages required to bias the transistor into resonance are well predicted by a self-consistent calculation of the electrostatic potential.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Acoustic lens characterization for ultrasound and photoacoustic C-scan imaging modalities (2008)

From a fundamental perspective, image reconstruction tasks in both ultrasound pulse echo and photoacoustic imaging are identical. We propose a C-scan imaging scheme that is applicable to both modalities where the image reconstruction is achieved through focusing action of an acoustic lens. The theory to characterize the imaging system is presented. Experimental methodology to determine the system point-spread-function is outlined and demonstrated with preliminary results.
Automobile Crash Modeling and the Monte Carlo Method (1992)

<div class="htmlview paragraph">The lack of a large number of crash data waveforms can limit the reliability of electronic Crash Detection Algorithms (CDAs). This paper discusses how statistics and the Monte Carlo (MC) method can be used to generate a large number of crash waveforms, and therefore increase CDA reliability. The MC method is used to model a crash waveform into two parts: 1) an underlying crash waveform, and 2) noise superimposed on the crash. The noise statistics are then varied and recombined with the underlying crash waveform to generate a large number of new crash waveforms. In addition Rough Road models were developed and concatenated with crash waveforms to better simulate real life. Finally a comparison between two CDAs was performed. The results show that one CDA is more robust than the other.</div>
Design of miniaturized slot antennas (2002)

A procedure for the design of a novel small slot antenna is presented. Using this method enables us to achieve a perfectly matched antenna with a fairly high efficiency for a given arbitrary small size. The miniaturization is achieved by terminating the short slot by an inductor. Inductive loading is realized by coiling the shortened slot line with a length of less than a quarter wavelength. Although the choice of antenna size is optional, it is subject to limitations such as antenna bandwidth and gain/efficiency. However, the directivity of this small dipole-slot antenna, in the limit, is equal to that of the infinitesimal Hertzian dipole, and its gain depends on the substrate material specifications and antenna size. Microstrip line is used to feed the antenna, which provides more stable feeding compared to coaxial feed. Then simulation results for a prototype antenna at 300 MHz as well as the input impedance and radiation pattern of the antenna are presented and compared with measurements.
Binding of fibronectin to Staphylococcus strains (1983)

Fibronectin, a major protein component of plasma and loose connective tissue has previously been shown to bind to several strains of Staphylococcus aureus. We examined a large number of strains of different species of Staphylococcus with respect to their ability to bind fibronectin. The relative numbers of strains defined as fibronectin-binders among the different species were as follows: S. aureus (22 of 23), S. haemolyticus (5 of 5), S. warneri (8 of 11), S. hyicus (5 of 6), S. hominis (13 of 17), S. saprophyticus (11 of 20), S. epidermidis (4 of 7), and S. simulans (8 of 10). Only three species showed a predominance of nonbinders over binders: S. capitis (4 of 14), S. xylosus (0 of 4), and S. cohnii (3 of 11). These data indicate that staphylococcal species isolated from soft tissue infections frequently have the ability to bind fibronectin and suggest that the ability to bind to this protein may contribute to the virulence of coagulase-positive and coagulase-negative staphylococci.
Four-Dimensional Breast Imaging, Part I: Introduction of a Technology-Driven, Evidence-Based Approach to Breast Augmentation Planning (2011)

Although there are many three-dimensional imaging systems currently available on the market, all of them require a high degree of interaction on the part of the user, making them clinically impractical. Moreover, though claims have been made regarding the validity of these systems for imaging the breast form, there have been no previous reports validating any commercially-available implant simulation models in the plastic surgery literature. In this article, the authors describe the development and evaluate the efficacy of a novel four-dimensional (automated three-dimensional) breast imaging system, validating it as an evidence-based simulation tool for patient consultation, surgical planning, and outcomes analysis in cosmetic breast augmentation. This report, based on a series of longitudinal correlation studies with several patient cohorts, found a highly statistically significant degree of correlation and reliability between the automated measurements obtained with the four-dimensional system and manual measurements.
Magnetic nanoparticle temperature estimation using AC magnetic filed (2013)

This paper aims to discuss a temperature measurement method based on the harmonic response of the magnetic nanoparticles by using AC magnetization. The simulation indicates that the harmonic response of magnetic nanoparticles in AC applied magnetic field has the potential of temperature probing. From the methods, we can find that the measurement accuracy of harmonics amplitude plays a critical role in the temperature estimation using magnetic nanoparticles.
Polymer‐Protected Sub‐2‐nm‐Nanogap Fabrication for Biological Sensing in Near‐Physiological Conditions (2009)

Polymer-protected sub-2-nm nanogaps that are fabricated via a novel electrical stressing approach exhibit substantial ionic-current reduction in near-physiological conditions. These devices enable direct DNA detection in aqueous solution by utilizing assembly of oligonucleotide-modified gold nanoparticles to the nanogap (see image). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Reconstitution of EPA and DHA biosynthesis in Arabidopsis: Iterative metabolic engineering for the synthesis of n−3 LC-PUFAs in transgenic plants (2013)

An iterative approach to optimising the accumulation of non-native long chain polyunsaturated fatty acids in transgenic plants was undertaken in Arabidopsis thaliana. The contribution of a number of different transgene enzyme activities was systematically determined, as was the contribution of endogenous fatty acid metabolism. Successive iterations were informed by lipidomic analysis of neutral, polar and acyl-CoA pools. This approach allowed for a four-fold improvement on levels previously reported for the accumulation of eicosapentaenoic acid in Arabidopsis seeds and also facilitated the successful engineering of the high value polyunsaturated fatty acid docosahexaenoic acid to 10-fold higher levels. Our studies identify the minimal gene set required to direct the efficient synthesis of these fatty acids in transgenic seed oil.
Deep-Ultraviolet Light-Emitting Diodes (2009)

Compact solid-state deep-ultraviolet (DUV) light-emitting diodes (LEDs) go far beyond replacing conventional DUV sources such as mercury lamps. DUV LEDs enable new applications for air, water, and surface sterilization and decontamination, bioagent detection and identification, UV curing, and biomedical and analytical instrumentation. We review materials growth, device physics, design, fabrication, and performance of DUV LEDs with wavelength ranging from 210 to 365 nm, describe prototype systems for water purification and sterilization, and discuss other emerging applications and systems using DUV LEDs.
Improved Communication and Autonomy with Downhole Memory Logging Tools (2019)

Abstract Openhole logging tools have been used without wireline in memory logging for 20 years, in an important and growing market. A new system in field trials in Canada and Russia in 2019 further expands the operating envelope overlap between wireline and logging-while-drilling by making step changes in communications, autonomy, performance, and reliability. The new approach advances the logging of horizontal and challenging wells, and permits operations in managed pressure drilling and foam drilled wells. The vast majority of openhole memory work is achieved with a hydro-mechanical system that indicates successful deployment but lacks two-way communication between the engineer at surface and the tools downhole. Pressure-pulse communications have been used for 10 years with a wide range of measurements including memory logging with wireline formation testers. The experience gained from operating these systems informed the development of a new system that uses drillpipe rotation to communicate to the tools, pressure pulses to reply for the uplink, and a more powerful downhole processor. These enhancements in autonomy and communication improve the outcome of logging jobs. The system incorporates a new rotation downlink method which employs data from an angular rate sensor to identify a series of commands sent by rotating the drillstring. Control software in the downhole tools executes the commands, and replies are transmitted uphole by pressure pulses. The toolstring is released from a safe ‘garage’ position inside the drillpipe and deployed into openhole, with the top of the toolstring retained by a no-go. The engineer is supplied with far more diagnostic information than previously, including the axial position of the tools, with context sensitive encoding to provide maximum troubleshooting information to the surface over a limited bandwidth channel. The pressure-pulse downlink remains in place as a secondary method. Other material improvements include high data sampling rate, debris tolerance and downhole recovery strategies. All of these advances improve the autonomy of the downhole memory equipment as well as the real-time communication and control from the surface. Autonomous memory logging toolstrings, with powerful downhole software and rotation downlink communications, are important components in improving the performance and reliability of these successful and innovative formation evaluation systems.
Separation of hydrogen isotopes. [Patent application] (1981)

An object of the present invention is to separate hydrogen isotopes using an inexpensive and readily available feedstock by a highly energy efficient, pressure-scalable process having a high enrichment factor. A further object of this invention is to excite, at moderate laser fluxes and in reasonable path lengths, isotopic forms of reagent molecules which could not be excited directly by a laser. A still further object of the present invention is to produce isotopical selective excitation by energy not coming from lasers. These and other objects are achieved by imparting vibrational excitation to sensitizer molecules, transferring the vibrational excitation to a mixture of normal and deuterated alkanes, whereby the deuterated alkane is preferentially excited, reacting the alkane mixture with bromine atoms, and separating the deuterated end products.
A New Sensor for On-Line Monitoring the Temperature and Velocity of Thermal Spray Particles (2000)

Abstract In this paper, we describe a new sensor for monitoring inflight particles in thermal spray processes. The sensor can measure simultaneously and in real-time, the mean velocity and mean temperature of the particle jet for a very broad range of powder feed rates. The thermal radiation emitted by the hot particles is collected by a lens and focused on two optical fibers. Knowing the distance between the optical fibers and the magnification of the optics, the mean particle velocity is computed by measuring the time delay between the signals collected in the two fibers by cross-correlation. The signals are band-pass filtered to prevent spurious reflection, equipment movement and noise from disturbing the measurement. Using the same signals filtered at two specific wavelengths, the mean temperature of the particle jet is obtained by the two-color pyrometry technique. In this technique, the temperature is computed from the ratio of the light intensity detected at two different wavelengths.
Novel Liquid Chromatography–Tandem Mass Spectrometry Method for Analysis of 102 Pesticides and Five Mycotoxins Regulated by the State of Colorado in Dried Hemp (2023)

A novel liquid chromatography–tandem mass spectrometry (LC–MS/MS) method with a dual electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) source was developed for analyzing 102 pesticides and five mycotoxins that are regulated by the state of Colorado in hemp. The limit of quantitation (LOQ) of the 102 pesticides and five mycotoxins met Colorado state action limit requirements for these analytes in a hemp matrix. For this study, 88 out of 102 pesticides and all five mycotoxins were analyzed using LC–MS/MS with an ESI source, whereas the remaining 14 pesticides were determined using LC–MS/MS with an APCI source. A simple, fast, green, and cheap acetonitrile solvent extraction method was used to extract the pesticides and mycotoxins from the hemp matrix with good extraction efficiency in the range of 80–120%. A hemp matrix is challenging and causes matrix effects such as ion suppression or enhancement. We optimized the LC method and added 30 internal standards to reduce and compensate for these matrix effects to obtain method accuracy in the range of 70–120%. The ionization mechanism of nonpolar pesticides (normally analyzed by gas chromatography–tandem mass spectrometry [GC–MS/MS]) with an APCI ion source was elucidated.