gebhart/patrepeval huggingface dataset:
In Vitro Resistance to the Human Immunodeficiency Virus Type 1 Maturation Inhibitor PA-457 (Bevirimat) (2006)

3-O-(3',3'-dimethylsuccinyl)betulinic acid (PA-457 or bevirimat) potently inhibits human immunodeficiency virus type 1 (HIV-1) maturation by blocking a late step in the Gag processing pathway, specifically the cleavage of SP1 from the C terminus of capsid (CA). To gain insights into the mechanism(s) by which HIV-1 could evolve resistance to PA-457 and to evaluate the likelihood of such resistance arising in PA-457-treated patients, we sought to identify and characterize a broad spectrum of HIV-1 variants capable of conferring resistance to this compound. Numerous independent rounds of selection repeatedly identified six single-amino-acid substitutions that independently confer PA-457 resistance: three at or near the C terminus of CA (CA-H226Y, -L231F, and -L231M) and three at the first and third residues of SP1 (SP1-A1V, -A3T, and -A3V). We determined that mutations CA-H226Y, CA-L231F, CA-L231M, and SP1-A1V do not impose a significant replication defect on HIV-1 in culture. In contrast, mutations SP1-A3V and -A3T severely impaired virus replication and inhibited virion core condensation. The replication defect imposed by SP1-A3V was reversed by a second-site compensatory mutation in CA (CA-G225S). Intriguingly, high concentrations of PA-457 enhanced the maturation of SP1 residue 3 mutants. The different phenotypes associated with mutations that confer PA-457 resistance suggest the existence of multiple mechanisms by which HIV-1 can evolve resistance to this maturation inhibitor. These findings have implications for the ongoing development of PA-457 to treat HIV-1 infection in vivo.
Pre-equalized Faster-than-Nyquist Transmission (2017)

Faster-than-Nyquist (FTN) transmission applies non-orthogonal linear modulation to increase spectral efficiency compared with the well-known orthogonal transmission at Nyquist rate. This comes at a price of inter-symbol interference (ISI), which usually is equalized through receiver processing. In this paper, we investigate the alternative approach of pre-equalization at the transmitter. First, we consider Tomlinson-Harashima precoding (THP) for FTN and propose two novel soft demapping algorithms to generate the soft-input for the error-correction decoder. The developed demappers effectively compensate the modulo-loss associated with conventional THP transmission. Second, we propose a linear pre-filtering strategy to pre-equalize the ISI induced by FTN. We show that the linear pre-equalization approach is equivalent to an orthogonal transmission with a modified pulse shape. It thus yields the optimal error-rate performance while affording higher spectral efficiency. We validate our proposed precoding algorithms through computer simulations of a coded coherent optical communication system as a practical application example for FTN.
Measurement of a surface heat flux and temperature (1994)

The Heat Flux Microsensor is a new sensor which was recently patented by Virginia Tech and is just starting to be marketed by Vatell Corp. The sensor is made using the thin-film microfabrication techniques directly on the material that is to be measured. It consists of several thin-film layers forming a differential thermopile across a thermal resistance layer. The measured heat flux q is proportional to the temperature difference across the resistance layer q= k(sub g)/delta(sub g) x (t(sub 1) - T(sub 2)), where k(sub g) is the thermal conductivity and delta (sub g) is the thickness of the thermal resistance layer. Because the gages are sputter coated directly onto the surface, their total thickness is less than 2 micrometers, which is two orders of magnitude thinner than previous gages. The resulting temperature difference across the thermal resistance layer (delta is less than 1 micrometer) is very small even at high heat fluxes. To generate a measurable signal many thermocouple pairs are put in series to form a differential thermopile. The combination of series thermocouple junctions and thin-film design creates a gage with very attractive characteristics. It is not only physically non-intrusive to the flow, but also causes minimal disruption of the surface temperature. Because it is so thin, the response time is less than 20 microsec. Consequently, the frequency response is flat from 0 to over 50 kHz. Moreover, the signal of the Heat Flux Microsensor is directly proportional to the heat flux. Therefore, it can easily be used in both steady and transient flows, and it measures both the steady and unsteady components of the surface heat flux. A version of the Heat Flux Microsensor has been developed to meet the harsh demands of combustion environments. These gages use platinum and platinum-10 percent rhodium as the thermoelectric materials. The thermal resistance layer is silicon monoxide and a protective coating of Al2O3 is deposited on top of the sensor. The superimposed thin-film pattern of all six layers is presented. The large pads are for connection with pins used to bring the signal out the back of the ceramic. In addition to the heat flux measurement, the surface temperature is measured with a platinum resistance layer (RTS). The resistance of this layer increases with increasing temperature. Therefore, these gages simultaneously measure the surface temperature and heat flux. The demonstrated applications include rocket nozzles, SCRAM jet engines, gas turbine engines, boiling heat transfer, flame experiments, basic fluid heat transfer, hypersonic flight, and shock tube testing. The laboratory involves using one of these sensors in a small combustion flame. The sensor is made on a 2.5 cm diameter piece of aluminum nitride ceramic.
Velocity Measurements in Metallic Melts (2005)

Various developments of velocity measuring techniques, their tests in different liquid metals, and applications in hot melts are reported. A Mechano-Optical Probe (MOP) performing local measurements up to temperatures of about 700°C has been developed and successfully tested. The Ultrasound Doppler Velocimetry (UDV) can be considered as another attractive technique to get velocity data from opaque flows. To extend the application range to higher temperatures and to abrasive liquids a new integrated ultrasonic sensor with an acoustic wave guide has been designed. First successful measurements in a CuSn melt of about 620°C and in liquid Al of about 750°C were carried out. A fully contactless investigation of the mean velocity field is possible by magnetic tomography. Local measurements of the induced magnetic field and the application of inverse reconstruction techniques allow an analysis of the flow structure. A first demonstration experiment showing the feasibility of this approach for the reconstruction of the three-dimensional mean velocity structure is presented.
Experiments on a repetitively pulsed electrothermal thruster (1987)

This paper presents experimental results from an investigation of a pulsed electrothermal (PET) thruster using water propellant. The PET thruster is operated on a calibrated thrust stand, and produces a thrust to power ratio of T/P = 0.07 + or - 0.01 N/kW. The discharge conditions are inferred from a numerical model which predicts pressure and temperature levels of 300-500 atm and 20,000 K, respectively. These values in turn correctly predict the measured values of impulse bit and discharge resistance. The inferred ideal exhaust velocity from these conditions is 17 km/sec, but the injection of water propellant produces a test tank background pressure of 10-20 Torr, which reduces the exhaust velocity to 14 km/sec. This value corresponds to a thrust efficiency of 54 + or - 7 percent when all experimental errors are taken into account.
The isolation of a DNA synthesome from human leukemia cells (1997)

In this report we describe, for the first time, the purification and characterization of a replication-competent multiprotein form of DNA polymerase (designated the DNA synthesome) from the human leukemia cell line (HL-60) using a series of centrifugation, ion-exchange chromatography and velocity sedimentation steps. The proteins and enzymatic activities thus far identified to co-purify with the leukemia cell DNA synthesome include the DNA polymerases alpha and delta, DNA primase, proliferating cell nuclear antigen (PCNA), replication factor C (RF-C), replication protein A (RP-A), and DNA topoisomerases I and II. We have demonstrated that the DNA synthesome is fully competent to replicate simian virus 40 (SV40) replication origin containing DNA in vitro in the presence of the viral large T-antigen. This result implies that all of the cellular activities required for large T-antigen-dependent in vitro SV40 DNA synthesis are present in the isolated human leukemia cell DNA synthesome. Since SV40 is extensively dependent on the host cell's DNA synthetic machinery for its own DNA replication, our results indicate that the isolated leukemia cell DNA synthesome may play a role not only in viral DNA synthesis but also in human leukemia cell DNA replication. We recently proposed a model to represent the DNA synthesome that was isolated from HeLa and murine cells. Our data indicate that the organization of the DNA synthesome from HL-60 cells also fits this proposed model. The purified DNA synthesome will not only allow the further study of the molecular mechanisms required to carry out human leukemia cell DNA replication, but may also provide a tool for eventually dissecting some of the regulatory controls of the cell's DNA synthetic machinery.
Succinct Representation Of Static Packet Classifiers (2007)

We develop algorithms for the compact representation of the 2-dimensional tries that are used for Internet packet classification. Our compact representations are experimentally compared with competing compact representations for multi-dimensional packet classifiers and found to simultaneously reduce the number of memory accesses per lookup as well as the memory required to store the classifier.
Imparting Smolder-Resistance to Cotton Upholstery Fabric (1979)

A number of polymeric materials were examined to evaluate their effectiveness in imparting smolder resistance to cotton upholstery fabrics. Among the factors examined were air permeability, fabric weight, viscosity of the backcoating formulation, positioning of the cigarette, and substrate used in the test panels. Several inorganic and organic compounds were evaluated as possible smolder-resistance agents for incorporation in latex backcoatings.
Hybrid Position/Force Control: A Correct Formulation (1992)

This article will show conclusively that "kinematic instability" is not inherent to the hybrid position/force control scheme of robot manipulators but is a result of an incomplete and inap propriate formulation. The inverse of the manipulator Jacobian matrix is identified as causing the kinematic instability of the hybrid position/force control scheme. Linear algebra is used to explain clearly the implications of mapping between vec tor spaces and to reveal why the inverse of the manipulator Jacobian matrix should not be used in hybrid position/force control. A generalized architecture for hybrid position/force control is presented that can influence both joint positions and torques. This generalized formulation also includes the control of redundant manipulators. Some sufficient conditions for kine matic stability are proposed to determine when a system may become unstable without requiring a complete system analysis. A stable hybrid position/force control scheme is given and is demonstrated using an example that was previously shown to be unstable.
An improved universal CMOS current-mode analogue function synthesiser (2008)

A CMOS integratable current-mode analogue function synthesiser circuit is presented. The proposed circuit is based on approximating the required function using its sixth-order Taylor series expansion. These approximations can be implemented by adding the weighted output currents of a number of basic building blocks, built around a basic current squarer, and a constant current. The proposed circuit can simultaneously realise 32 different mathematical functions and can be easily expanded to accommodate many others. SPICE and Monte Carlo simulation results demonstrating the circuit performance are included.
Dithieno[2,3‐<i>d</i>;2′,3′‐<i>d</i>′]benzo[1,2‐<i>b</i>;4,5‐<i>b</i>′]dithiophene (DTBDT) as Semiconductor for High‐Performance, Solution‐Processed Organic Field‐Effect Transistors (2008)

The facile synthesis of a new five-ring-fused pentacene analog with four symmetrically fused thiophene ring units (Dithieno[2,3-d;2′,3′-d′]benzo[1,2-b;4,5-b′]dithiophene, Cn-DTBDT) is presented. After aligning this material from solution, thin films for organic field-effect transistors were obtained, resulting in excellent hole mobilities of up to 1.7 cm2V−1s−1, and on/off ratio of 107. 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.
SbF<sub>5</sub>/PAF — A Novel Fluorinating Reagent in Preparing Fluorine Compounds. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
[Characterization of the insecticidal crystal protein genes of Bacillus thuringiensis YBT-1520]. (2000)

The insecticidal crystal protein genes of highly toxic Bacillus thuringiensis YBT-1520 were analyzed. Southern hybridization and PCR analysis indicated that this strain bears cry1Aa, cry1Ab, cry1Ac and cry2 genes. The copy number of three cry1A genes is different and cry1Ac gene (here named cry218) is the highest. The restriction location of three genes is different from that in typical strains, such as HD-1 and HD-73 strains. 4190 bp nucleotide sequence of cry218 gene was determined and this gene was named cry1Ac10 in the recently published gene nomenclature.
A robust compliant grasper via shape deposition manufacturing (2006)

Joint compliance can enable successful robot grasping despite uncertainties in target object location. Compliance also enhances manipulator robustness by minimizing contact forces in the event of unintended contacts or impacts. In this paper, we describe the design, fabrication, and evaluation of a novel compliant robotic grasper constructed using polymer-based shape deposition manufacturing. Joints are formed by elastomeric flexures, and actuator and sensor components are embedded in tough rigid polymers. The result is a robot gripper with the functionality of conventional metal prototypes for grasping in unstructured environments but with robustness properties that allow for large forces due to inadvertent contact.
Large scale, templateless, surfactantless route to rapid synthesis of uniform poly(o-phenylenediamine) nanobelts (2004)

We reported the interesting finding that large scale uniform poly(o-phenylenediamine) nanobelts with several hundred micrometers in length, several hundred nanometers in width, and several ten nanometers in height can be rapidly yielded from an o-phenylenediamine–HAuCl4 aqueous solution without the additional introduction of other templates or surfactants at room temperature.
Run-Length Base-Delta Encoding for High-Speed Compression (2018)

In modern supercomputers, nodes are connected by networking hardware capable of up to 40 Gb/s. Data compression could allow for even higher effective bandwidth. However, data compression for such systems requires a unique tradeoff between the compression rate delivered by the compressing scheme and the speed of compression/decompression. While traditional software compression techniques may deliver high compression rates, they cannot maintain the high compression/decompression throughput that is needed. We present Run-Length Base-Delta (RLBD) encoding, a software compression format and algorithm that delivers a highspeed compression/decompression that is suitable for data transfers at up to 40GbE. RLBD can be implemented in CPUs or in parallel accelerator devices to improve network throughput by up to 57% while transmitting data from real datasets.
A CVaR Scenario-Based Framework for Minimizing Downside Risk in Multi-Asset Class Portfolios (2017)

Multi-asset class (MAC) portfolios can be composed of investments in equities, fixed income, commodities, foreign exchange, credit, derivatives, and alternatives such as real estate and private equity. The return for such <i>nonlinear</i> portfolios is <i>asymmetric</i> with significant tail risk. The traditional Markowitz mean–variance optimization (MVO) framework, which linearizes all the assets in the portfolio and uses the standard deviation of return as a measure of risk, does not always accurately measure the risk for such portfolios. The authors consider a scenario-based conditional value at risk (CVaR) approach for minimizing the downside risk of an existing portfolio with MAC overlays. The approach consists of two phases: Phase 1 uses Monte-Carlo simulations to generate the asset return scenarios, and Phase 2 incorporates the return scenarios in a scenario-based convex optimization model to generate the overlay holdings. The authors illustrate the methodology in two examples involving the hedging of an equity portfolio with index puts and the hedging of a callable bond portfolio with interest rate caps. They compare the CVaR approach with parametric MVO approaches that linearize all the instruments in the MAC portfolio and show that the CVaR approach generates portfolios with better downside risk statistics; and further, it selects hedges that produce more attractive risk decompositions and stress test numbers—tools commonly used by risk managers to evaluate the quality of hedges. <b>TOPICS:</b>Portfolio management/multi-asset allocation, tail risks, VAR and use of alternative risk measures of trading risk
Quantum dot multiwavelength comb lasers with Si ring resonator (2010)

The gain media of the quantum dot lasers consist of InAs QDs in an InGaAsP matrix on an InP substrate. The quantum dot lasers have different free spacing ranges (FSRs) corresponding to Fabry-Pérot (F-P) cavity lengths. A silicon ring resonator and a QD laser have been combined to form comb laser. The output characteristics of the combined comb laser were investigated. The measured FSR was about 2.8nm and the extinction ratio was about 10(dB) when the FSR of the QD laser was about 0.4nm and the FSR of the ring resonator was about 0.47nm. The experimental results show that the ring resonator had a strong control on the FSR and extinction ratio of the comb laser.
The Bacterial Biofilm Matrix as a Platform for Protein Delivery (2012)

Surface-associated bacterial structures known as biofilms are the target of intense antimicrobial research efforts. We recently identified several secreted proteins that are retained in the bacterial biofilm matrix by their association with the biofilm exopolysaccharide scaffold. Based on our findings, we hypothesized that these problematic bacterial structures might be reengineered to serve as reservoirs for surface-active secreted proteins of biomedical, bioengineering, or biotechnological importance. By piggybacking onto one of these scaffold-associated proteins, we were able to sequester a functional enzyme to the biofilm matrix. We hypothesize that this technology may have diverse applications in vaccine design, digestive disease, and bioremediation.
A CONFIGURABLE BOSE–CHAUDHURI–HOCQUENGHEM CODEC ARCHITECTURE FOR FLASH CONTROLLER APPLICATIONS (2013)

Error correction coding (ECC) has become one of the most important tasks of flash memory controllers. The gate count of the ECC unit is taking up a significant share of the overall logic. Scaling the ECC strength to the growing error correction requirements has become increasingly difficult when considering cost and area limitations. This work presents a configurable encoding and decoding architecture for binary Bose–Chaudhuri–Hocquenghem (BCH) codes. The proposed concept supports a wide range of code rates and facilitates a trade-off between throughput and space complexity. Commonly, hardware implementations for BCH decoding perform many Galois field multiplications in parallel. We propose a new decoding technique that uses different parallelization degrees depending on the actual number of errors. This approach significantly reduces the number of required multipliers, where the average number of decoding cycles is even smaller than with a fully parallel implementation.
UFP‐101, a Peptide Antagonist Selective for the Nociceptin/Orphanin FQ Receptor (2005)

Nociceptin/orphanin FQ modulates various biological functions at central and peripheral levels by selectively activating a G-protein coupled receptor named N/OFQ peptide (NOP) receptor. For extending our knowledge on the biological roles of the N/OFQ-NOP receptor system the identification of selective NOP ligands, especially antagonists, is mandatory. [Nphe1, Arg14, Lys15] N/OFQ-NH2 (UFP-101) is a novel NOP ligand that was designed by combining, in the same molecule, the [Nphe1] chemical modification which eliminates efficacy and the [Arg14, Lys15] substitution which increases ligand potency and duration of action in vivo. In the present article, we summarize the pharmacological features of UFP-101 as determined in a series of in vitro and in vivo assays. Moreover, some biological actions and possible therapeutic indications of NOP ligands are discussed on the basis of results obtained with UFP-101. Data obtained with this compound were compared with those generated using other NOP antagonists, especially J-113397 and [Nphe1]N/OFQ(1-13)-NH2, receptor or peptide knockout mice and other pharmacological tools useful for blocking N/OFQ - NOP receptor signaling. The analysis of the available data demonstrates that UFP-101 is a useful pharmacological tool for the investigation of the central and peripheral biological functions regulated by the N/OFQ-NOP receptor system and for defining the therapeutic potential of NOP receptor ligands.
Engineering enhanced cellobiohydrolase activity (2018)

Glycoside Hydrolase Family 7 cellobiohydrolases (GH7 CBHs) catalyze cellulose depolymerization in cellulolytic eukaryotes, making them key discovery and engineering targets. However, there remains a lack of robust structure-activity relationships for these industrially important cellulases. Here, we compare CBHs from Trichoderma reesei (TrCel7A) and Penicillium funiculosum (PfCel7A), which exhibit a multi-modular architecture consisting of catalytic domain (CD), carbohydrate-binding module, and linker. We show that PfCel7A exhibits 60% greater performance on biomass than TrCel7A. To understand the contribution of each domain to this improvement, we measure enzymatic activity for a library of CBH chimeras with swapped subdomains, demonstrating that the enhancement is mainly caused by PfCel7A CD. We solve the crystal structure of PfCel7A CD and use this information to create a second library of TrCel7A CD mutants, identifying a TrCel7A double mutant with near-equivalent activity to wild-type PfCel7A. Overall, these results reveal CBH regions that enable targeted activity improvements.
GaInAsP/AlGaInP-based near-IR (780 nm)vertical-cavity surface-emitting lasers (1995)

Near-infra-red (760–780 nm) vertical-cavity surface-emitting laser (VCSEL) diodes with GaInAsP-based active-region heterostructures are demonstrated for the first time. The devices consist of GaInAsP/GaInP/AlGaInP-based quantum-well active regions and AlAs/Al0.25Ga0.75As distributed Bragg reflectors. Different-sized devices emitting in the 760–780 nm-wavelength range exhibit threshold currents in the 3–10 mA range, threshold voltages of 2.1 V and peak power output > 4 mW.