gebhart/patrepeval huggingface dataset:
Macrophage tropism of human immunodeficiency virus type 1 and utilization of the CC-CKR5 coreceptor (1997)

The recent identification of the CC-CKR5 beta chemokine receptor as a major cofactor for entry of macrophage-tropic isolates of human immunodeficiency virus type 1 (HIV-1) raises the question of whether macrophage tropism is determined by utilization of this chemokine receptor. We observe that in addition to macrophage-tropic isolates of clades A, B, and E, macrophage-tropic isolates of clade F also utilize the CC-CKR5 molecule for entry. However, using single-round replication-competent reporter viruses carrying the envelope genes of T-cell line-tropic or macrophage-tropic phenotypic recombinant and mutant HIV-1 strains in infection of stable cell lines that coexpress the CD4 and chemokine receptors, we were unable to establish a strict correlation between macrophage tropism and utilization of the CC-CKR5 chemokine receptor. This latter finding suggests that a cofactor other than CC-CKR5 serves to determine entry into primary macrophages.
<i>Chlamydomonas IFT</i>88 and Its Mouse Homologue, Polycystic Kidney Disease Gene <i>Tg</i>737, Are Required for Assembly of Cilia and Flagella (2000)

Intraflagellar transport (IFT) is a rapid movement of multi-subunit protein particles along flagellar microtubules and is required for assembly and maintenance of eukaryotic flagella. We cloned and sequenced a Chlamydomonas cDNA encoding the IFT88 subunit of the IFT particle and identified a Chlamydomonas insertional mutant that is missing this gene. The phenotype of this mutant is normal except for the complete absence of flagella. IFT88 is homologous to mouse and human genes called Tg737. Mice with defects in Tg737 die shortly after birth from polycystic kidney disease. We show that the primary cilia in the kidney of Tg737 mutant mice are shorter than normal. This indicates that IFT is important for primary cilia assembly in mammals. It is likely that primary cilia have an important function in the kidney and that defects in their assembly can lead to polycystic kidney disease.
<title>Shape memory alloy actuation for a variable area fan nozzle</title> (2001)

The ability to control fan nozzle exit area is an enabling technology for next generation high-bypass-ratio turbofan engines. Performance benefits for such designs are estimated at up to 9% in thrust specific fuel consumption (TSFC) relative to current fixed-geometry engines. Conventionally actuated variable area fan nozzle (VAN) concepts tend to be heavy and complicated, with significant aircraft integration, reliability and packaging issues. The goal of this effort was to eliminate these undesirable features and formulate a design that meets or exceeds leakage, durability, reliability, maintenance and manufacturing cost goals. A Shape Memory Alloy (SMA) bundled cable actuator acting to move an array of flaps around the fan nozzle annulus is a concept that meets these requirements. The SMA bundled cable actuator developed by the United Technologies Corporation (Patents Pending) provides significant work output (greater than 2200 in-lb per flap, through the range of motion) in a compact package and minimizes system complexity. Results of a detailed design study indicate substantial engine performance, weight, and range benefits. The SMA- based actuation system is roughly two times lighter than a conventional mechanical system, with significant aircraft direct operating cost savings (2-3%) and range improvements (5-6%) relative to a fixed-geometry nozzle geared turbofan. A full-scale sector model of this VAN system was built and then tested at the Jet Exit Test Facility at NASA Langley to demonstrate the system's ability to achieve 20% area variation of the nozzle under full scale aerodynamic loads. The actuator exceeded requirements, achieving repeated actuation against full-scale loads representative of typical cruise as well as greater than worst-case (ultimate) aerodynamic conditions. Based on these encouraging results, work is continuing with the goal of a flight test on a C-17 transport aircraft.
NUMA Aware I/O in Virtualized Systems (2015)

In a Non Uniform Memory Access (NUMA) system, I/O to a local device is more efficient than I/O to a remote device. A device connected to the same socket having the CPU and memory offers a closer proximity for I/O operations. Modern microprocessors also support on-chip I/O interconnects with which the processor may drive I/O to a local device from the processor cache, without the need to interact with main memory. Modern systems are also highly virtualized. In NUMA systems, scheduling of Virtual Machines (VMs) is very complex because multiple VMs are competing for CPU, memory and devices spread across NUMA nodes. In this paper, we study how to schedule VMs for better I/O on a NUMA system. We propose the design of a NUMA aware I/O hypervisor scheduler, which aligns VMs, hypervisor threads on NUMA boundaries, while extracting the most benefit from local device I/O. Wedemonstrate a benefit of more than 25% in throughput and packet rate, a benefit of more than 10% in CPU utilization, and a benefit of higher than 5% in VM consolidation ratio.
Anticariogenic Activity of Agarobiose and Agarooligosaccharides Derived from Red Macroalgae (2019)

3,6-Anhydro-l-galactose (AHG) produced from agarose in red macroalgae was recently suggested as an anticariogenic sugar to replace widely used xylitol. However, the multi-step process for obtaining monomeric sugar AHG from agarose may be expensive. Generally, it is easier to obtain oligosaccharides than monosaccharides from polysaccharides. Therefore, a one-step process to obtain agarobiose (AB) from agarose was recently developed, and here, we suggest AB as a new anticariogenic agent, owing to its anticariogenic activity against Streptococcus mutans. Among AHG-containing oligosaccharides, AB, neoagarobiose (NAB), agarooligosaccharides (AOSs), and neoagarooligosaccharides (NAOSs), AB showed higher inhibitory activity than AOSs against the growth and lactic acid production of S. mutans; no such inhibitory activity was observed for NAB and NAOSs. This inhibitory effect of AB was comparable to the previously reported inhibitory activity of AHG against S. mutans. These results suggest that AB, which can be more economically and simply produced than AHG, may serve as an anticariogenic sugar.
Regularity driven logic synthesis (2000)

We present a new and innovative logic synthesis approach using regularity information of a design to selectively apply transformations and globally guide the synthesis process. Since traditional logic synthesis applies transformations without consideration of global design characteristics such as regularity and dataflow, it destroys a substantial amount of regular structures. In addition, due to the non-incremental nature of most logic transformations, synthesis relies vastly on the computationally expensive concept of trial and error application of transformations, a time-consuming process in the synthesis of large designs. The proposed approach addresses both shortcomings of traditional logic synthesis and describes a mechanism to speed up logic synthesis and preserve regularity. It selectively applies transformations to places with similar characteristics and to the same stage of a regular structure, introducing a notion of dataflow-aware synthesis. Preservation of regular structures has tremendous advantages to the following physical design stages. It yields high-density layouts, shorter wiring length and improved delay. In addition, the layout becomes more predictable at an earlier design stage.
Resonant optical interactions in active dielectric films (1989)

An investigation of oblique plane-wave electromagnetic scattering in active dielectric films reveals the existence of anomalously large resonances that occur at discrete plane-wave angles of incidence. These resonances may be understood from a ‘‘leaky wave’’ phase matching condition whose predictions for the first three modes agree to within a few percent of those obtained from a rigorous treatment using Maxwell’s equations. Experiments using finite-diameter pump and probe laser beams verify the existence of these scattering resonances with enhancements of the scattered field intensities on the order of 100 observed in active dielectric films as thin as 6 μm. Saturation effects are discussed in the context of a very simple model whose predictions agree qualitatively with experimental measurements. Two novel laser oscillator configurations based upon resonant leaky waveguide interactions were tested and found to have very high-energy extraction efficiency (≥18%) with oscillation being easily achieved using active dielectric films as thin as 6 μm.
Isolation of novel antibiotics x-14667A and x-14667B from Streptomyces cinnamonensis subsp. urethanofaciens and their characterization as 2-phenethylurethanes of monensins B and A. (1981)

Antibiotics X-14667A (1) and X-14667B (2) are novel monovalent polyether antibiotics of the spiroketal type isolated from fermented cultures of Streptomyces cinnamonensis subsp. urethanofaciens together with monensin (3), its lower homolog, factor B (4) and 1,3-diphenethylurea (6). By a combination of microanalysis, mass spectrometry and 13C nmr, antibiotics X-14667A and B have been shown to be natural 2-phenethylurethanes of monensin B and A respectively. Both structures have been confirmed by reacting the appropriate monensin with 2-phenethylisocyanate to yield semi-synthetic compounds that are identical to the natural products.
Properties of Fe-B-Ga and Fe-B-Si-C-Al amorphous alloys (1981)

The crystallization temperature, Curie temperature, saturation magnetization, and coercivity of amorphous alloys in the ternary Fe-B-Ga system are reported. The range of compositions containing Ga for which these alloys can be made amorphous by casting onto a rapidly rotating drum is much more restricted than for Fe-B-C, Fe-B-Si, or Fe-B-Ge alloys; only up to 5 a/o Ga could be substituted for B. On replacing B by Ga the crystallization temperature typically decreases, the Curie temperature increases, the saturation magnetization at low temperatures and at room temperature decreases, and the coercivity increases. Some alloys in the series Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">84</inf> -(B, Al) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">16</inf> , Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">84</inf> Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -(B, Al) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</inf> , Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">80</inf> Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> -(B, Al) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">16</inf> , and Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">82</inf> B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</inf> C <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> -(Si, Al) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</inf> were also prepared. Aluminum contents of only up to 3 a/o could be used to make amorphous ribbons. In all of these alloys, with increasing Al, the crystallization temperature decreased, the Curie temperature decreased, and the room temperature saturation magnetization decreased.
Phase II Study of Celecoxib and Trastuzumab in Metastatic Breast Cancer Patients Who Have Progressed after Prior Trastuzumab-Based Treatments (2004)

Celecoxib combined with trastuzumab is well tolerated. However, this combination in patients with HER2/neu-overexpressing, trastuzumab-refractory disease, was not active.
Lattice-Based Search for Spoken Utterance Retrieval (2004)

Recent work on spoken document retrieval has suggested that it is adequate to take the singlebest output of ASR, and perform text retrieval on this output. This is reasonable enough for the task of retrieving broadcast news stories, where word error rates are relatively low, and the stories are long enough to contain much redundancy. But it is patently not reasonable if one’s task is to retrieve a short snippet of speech in a domain where WER’s can be as high as 50%; such would be the situation with teleconference speech, where one’s task is to find if and when a participant uttered a certain phrase. In this paper we propose an indexing procedure for spoken utterance retrieval that works on lattices rather than just single-best text. We demonstrate that this procedure can improve F scores by over five points compared to singlebest retrieval on tasks with poor WER and low redundancy. The representation is flexible so that we can represent both word lattices, as well as phone lattices, the latter being important for improving performance when searching for phrases containing OOV words. 1
Photonics and Plasmonics in 4D Ultrafast Electron Microscopy (2015)

Light–matter interactions at the nanoscale are fundamental to the rapidly developing fields of plasmonics and nanophotonics. These fields hold the promise of advancing both the speed of computers along with communications and may also provide methods to create a new generation of ultrasensitive molecular biosensors. While there are a variety of techniques that can provide static images of these devices with suboptical wavelength precision there are only a few that are capable of capturing the ultrafast dynamics of electromagnetic fields interacting with or produced by nanomaterials. In this Perspective, we aim to introduce the reader to the newly developed field of 4D ultrafast electron microscopy (4D UEM), which provides a unique window into ultrafast dynamics at the nanoscale. We will describe the basic technique and how internal structural, bulk electronic, and surface near-field dynamics can all be obtained with nanometer and femtosecond resolutions. In addition, we will discuss how a variety of different ultrafast electron microscopes have been used to map the evolution of photonics-related phenomena. Throughout, we discuss the direction of research that will help advance the understanding of light–matter interactions near the atomic scale in both space and time.
Terahertz-wave generation in quasi-phase-matched GaAs (2006)

The authors demonstrate an efficient room temperature source of terahertz radiation using femtosecond laser pulses as a pump and GaAs structures with periodically inverted crystalline orientation, such as diffusion-bonded stacked GaAs and epitaxially grown orientation-patterned GaAs, as a nonlinear optical medium. By changing the GaAs orientation-reversal period (504–1277μm), or the pump wavelength (2–4.4μm), we were able to generate narrow-bandwidth (∼100GHz) terahertz wave packets, tunable between 0.9 and 3THz, with the optical-to-terahertz photon conversion efficiency of 3.3%.
An Extended-Speed Low-Ripple Torque Control of Switched Reluctance Motor Drives (2014)

In this paper, an extended-speed low-ripple torque control of switched reluctance motor (SRM) drives using torque sharing function (TSF) is proposed. Two operational modes are defined for the online TSF during commutation: In Mode I, absolute value of rate of change of flux linkage (ARCFL) of incoming phase is higher than outgoing phase; in Mode II, ARCFL of outgoing phase is higher than incoming phase. In order to compensate the torque error produced by imperfect tracking of phase current, a proportional and integral compensator with torque error is added to the torque reference of outgoing phase in Mode I and incoming phase in Mode II. Therefore, the total torque is determined by the phase with lower ARCFL rather than the phase with higher ARCFL as in conventional TSFs. The maximum torque-ripple-free speed of the proposed TSF is increased to more than ten times as the best case in conventional TSFs. Finally, the proposed TSF is verified by both simulations and experiments with a 2.3 kW, 6000 rpm, three-phase 12/8 SRM operating in both linear magnetic and saturated magnetic regions. Results show that the proposed TSF has higher average torque, and much lower torque ripples compared to conventional TSFs.
Carbon nanotube vacuum gauges utilizing long, dissipative tubes (2008)

A carbon nanotube-based thermal conductivity vacuum gauge is described which utilizes 5-10 μm long diffusively contacted SWNTs for vacuum sensing. By etching the thermal SiO<sub>2</sub> beneath the tubes and minimizing heat conduction through the substrate, pressure sensitivity was extended toward higher vacuums. The pressure response of unannealed and annealed devices was compared to that of released devices. The released devices showed sensitivity to pressure as low as 1 x 10<sup>-6</sup> Torr. The sensitivity increased more dramatically with power for the released device compared to that of the unreleased device. Low temperature electronic transport measurements of the tubes were suggestive of a thermally activated hopping mechanism where the activation energy for hopping was calculated to be ~ 39 meV.
pH sensing properties of flexible, bias-free graphene microelectrodes in complex fluids: from phosphate buffer solution to human serum (2017)

Advances in techniques for monitoring pH in complex fluids could have significant impact on analytical and biomedical applications ranging from water quality assessment to in vivo diagnostics. We developed flexible graphene microelectrodes (GEs) for rapid (< 5 seconds), very low power (femtowatt) detection of the pH of complex biofluids. The method is based on real-time measurement of Faradaic charge transfer between the GE and a solution at zero electrical bias. For an idealized sample of phosphate buffer solution (PBS), the Faradaic current varied monotonically and systematically with the pH with resolution of ~0.2 pH unit. The current-pH dependence was well described by a hybrid analytical-computational model where the electric double layer derives from an intrinsic, pH-independent (positive) charge associated with the graphene-water interface and ionizable (negative) charged groups described by the Langmuir-Freundlich adsorption isotherm. We also tested the GEs in more complex bio-solutions. In the case of a ferritin solution, the relative Faradaic current, defined as the difference between the measured current response and a baseline response due to PBS, showed a strong signal associated with the disassembly of the ferritin and the release of ferric ions at pH ~ 2.0. For samples of human serum, the Faradaic current showed a reproducible rapid (<20s) response to pH. By combining the Faradaic current and real time current variation, the methodology is potentially suitable for use to detect tumor-induced changes in extracellular pH.
Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of<i>Saccharomyces cerevisiae</i>Used in Biofuels Research (2016)

The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.
A New Reverse Base Current (RBC) of the Bipolar Transistor Induced by Impact Ionization (1989)

We report the observation of base current characteristics of bipolar transistors at a certain collector voltage. The reverse base current (RBC) effect is a newly found phenomenon. The mechanism of the RBC effect can be explained by the impact ionization between the base and the collector. We can successfully analyze the RBC effect. The agreement between simulation and measurement is shown to be very good.
Very high efficiency spectral inverter for fiber dispersion compensation (1996)

Summary form only given. Mid-span spectral inversion can overcome the limitations set by chromatic dispersion on high-bit-rate transmission based on conventional fibers (i.e., fibers dispersion-optimized at 1300 nm) and combat fiber nonlinearities. Here we demonstrate a high efficiency and cost saving optical spectral inverter (SI) exploiting the modulation instability (MI) effect. Theoretical considerations show that the parametric gain of MI can lead to a substantial improvement of the conversion efficiency when a strong pump signal (about 17 dBm) is injected into a dispersion-shifted fiber in the anomalous dispersion regime. Such a SI is a completely transparent device, which contains just one booster optical fiber amplifier (OFA).
Multiplier architectures for GF(p) and GF(2n) (2004)

Two new hardware architectures are proposed for performing multiplication in GF(p) and GF (2n), which are the most time-consuming operations in many cryptographic applications. The architectures provide very fast and efficient execution of multiplication in both GF(p) and GF(2n), and can be mainly used in elliptic curve cryptography. Both architectures are scalable and therefore can handle operands of any size. They can be configured to the available area and/or desired performance. The algorithm implemented in the architectures is the Montgomery multiplication algorithm which proved to be very efficient in both fields. The first architecture utilises a precomputation technique that reduces the critical path delay at the expense of using extra logic, which has a limited negative impact on the silicon area for operand precisions of cryptographic interest. The second architecture computes multiplication faster in GF(2n) than GF(p), which conforms with the premise of GF(2n) for hardware realisations. Both architectures provide new alternatives that offer faster computation of multiplication and useful features.