gebhart/patrepeval huggingface dataset:
The catalytic subunit of the DNA polymerase of herpes simplex virus type 1 interacts specifically with the C terminus of the UL8 component of the viral helicase-primase complex (1997)

The herpes simplex virus type 1 (HSV-1) UL8 DNA replication protein is a component of a trimeric helicase-primase complex. Sixteen UL8-specific monoclonal antibodies (MAbs) were isolated and characterized. In initial immunoprecipitation experiments, one of these, MAb 804, was shown to coprecipitate POL, the catalytic subunit of the HSV-1 DNA polymerase, from extracts of insect cells infected with recombinant baculoviruses expressing the POL and UL8 proteins. Coprecipitation of POL was dependent on the presence of UL8 protein. Rapid enzyme-linked immunosorbent assays (ELISAs), in which one protein was bound to microtiter wells and binding of the other protein was detected with a UL8- or POL-specific MAb, were developed to investigate further the interaction between the two proteins. When tested in the ELISAs, five of the UL8-specific MAbs consistently inhibited the interaction, raising the possibility that these antibodies act by binding to epitopes at or near a site(s) on UL8 involved in its interaction with POL. The epitopes recognized by four of the inhibitory MAbs were approximately located by using a series of truncated UL8 proteins expressed in mammalian cells. Three of these MAbs recognized an epitope near the C terminus of UL8, which was subjected to fine mapping with a series of overlapping peptides. The C-terminal peptides were then tested in the ELISA for their ability to inhibit the POL-UL8 interaction: the most potent exhibited a 50% inhibitory concentration of approximately 5 microM. Our findings suggest that the UL8 protein may be involved in recruiting HSV-1 DNA polymerase into the viral DNA replication complex and also identify a potential new target for antiviral therapy.
Differential mechanisms of morphine antinociceptive tolerance revealed in (beta)arrestin-2 knock-out mice. (2002)

Morphine induces antinociception by activating mu opioid receptors (muORs) in spinal and supraspinal regions of the CNS. (Beta)arrestin-2 (beta)arr2), a G-protein-coupled receptor-regulating protein, regulates the muOR in vivo. We have shown previously that mice lacking (beta)arr2 experience enhanced morphine-induced analgesia and do not become tolerant to morphine as determined in the hot-plate test, a paradigm that primarily assesses supraspinal pain responsiveness. To determine the general applicability of the (beta)arr2-muOR interaction in other neuronal systems, we have, in the present study, tested (beta)arr2 knock-out ((beta)arr2-KO) mice using the warm water tail-immersion paradigm, which primarily assesses spinal reflexes to painful thermal stimuli. In this test, the (beta)arr2-KO mice have greater basal nociceptive thresholds and markedly enhanced sensitivity to morphine. Interestingly, however, after a delayed onset, they do ultimately develop morphine tolerance, although to a lesser degree than the wild-type (WT) controls. In the (beta)arr2-KO but not WT mice, morphine tolerance can be completely reversed with a low dose of the classical protein kinase C (PKC) inhibitor chelerythrine. These findings provide in vivo evidence that the muOR is differentially regulated in diverse regions of the CNS. Furthermore, although (beta)arr2 appears to be the most prominent and proximal determinant of muOR desensitization and morphine tolerance, in the absence of this mechanism, the contributions of a PKC-dependent regulatory system become readily apparent.
DNA Unwinding Functions of Minute Virus of Mice NS1 Protein Are Modulated Specifically by the Lambda Isoform of Protein Kinase C (1999)

The parvovirus minute virus of mice NS1 protein is a multifunctional protein involved in a variety of processes during virus propagation, ranging from viral DNA replication to promoter regulation and cytotoxic action to the host cell. Since NS1 becomes phosphorylated during infection, it was proposed that the different tasks of this protein might be regulated in a coordinated manner by phosphorylation. Indeed, comparing biochemical functions of native NS1 with its dephosphorylated counterpart showed that site-specific nicking of the origin and the helicase and ATPase activities are remarkably reduced upon NS1 dephosphorylation while site-specific affinity of the protein to the origin became enhanced. As a consequence, the dephosphorylated polypeptide is deficient for initiation of DNA replication. By adding fractionated cell extracts to a kinase-free in vitro replication system, the combination of two protein components containing members of the protein kinase C (PKC) family was found to rescue the replication activity of the dephosphorylated NS1 protein upon addition of PKC cofactors. One of these components, termed HA-1, also stimulated NS1 helicase function in response to acidic lipids but not phorbol esters, indicating the involvement of atypical PKC isoforms in the modulation of this NS1 function (J. P. F. Nüesch, S. Dettwiler, R. Corbau, and J. Rommelaere, J. Virol. 72:9966-9977, 1998). The present study led to the identification of atypical PKClambda/iota as the active component of HA-1 responsible for the regulation of NS1 DNA unwinding and replicative functions. Moreover, a target PKClambda phosphorylation site was localized at S473 of NS1. By site-directed mutagenesis, we showed that this residue is essential for NS1 helicase activity but not promoter regulation, suggesting a possible modulation of NS1 functions by PKClambda phosphorylation at residue S473.
Staded preformed-surfactant-optimized aqueous alkine flood (1985)

Oil is recovered from an acidic oil reservoir by injecting an alkaline, saline, aqueous solution containing proportions of preformed cosurfactant which are decreased as increasing amounts of the solution are injected.
Inverted Brayton Cycle With Exhaust Gas Condensation (2018)

Approximately 30% of the energy from an internal combustion engine is rejected as heat in the exhaust gases. An inverted Brayton cycle (IBC) is one potential means of recovering some of this energy. When a fuel is burnt, water and CO2 are produced and expelled as part of the exhaust gases. In an IBC, in order to reduce compression work, the exhaust gases are cooled before compression up to ambient pressure. If coolant with a low enough temperature is available, it is possible to condense some of the water out of the exhaust gases, further reducing compressor work. In this study, the condensation of exhaust gas water is studied. The results show that the IBC installed in series on a turbocharged engine can produce an improvement of approximately 5% in brake-specific fuel consumption at the baseline conditions chosen and for a compressor inlet temperature of 310 K. The main factors that influence the work output are heat exchanger pressure drop, turbine expansion ratio, coolant temperature, and turbine inlet temperature. For conditions when condensation is possible, the water content of the exhaust gas has a significant influence on work output. The hydrogen to carbon ratio of the fuel has the most potential to vary the water content and hence the work generated by the system. Finally, a number of uses for the water generated have been presented such as to reduce the additional heat rejection required by the cycle. It can also potentially be used for engine water injection to reduce emissions.
Rapid and Highly Informative Diagnostic Assay for H5N1 Influenza Viruses (2006)

A highly discriminative and information-rich diagnostic assay for H5N1 avian influenza would meet immediate patient care needs and provide valuable information for public health interventions, e.g., tracking of new and more dangerous variants by geographic area as well as avian-to-human or human-to-human transmission. In the present study, we have designed a rapid assay based on multilocus nucleic acid sequencing that focuses on the biologically significant regions of the H5N1 hemagglutinin gene. This allows the prediction of viral strain, clade, receptor binding properties, low- or high-pathogenicity cleavage site and glycosylation status. H5 HA genes were selected from nine known high-pathogenicity avian influenza subtype H5N1 viruses, based on their diversity in biologically significant regions of hemagglutinin and/or their ability to cause infection in humans. We devised a consensus pre-programmed pyrosequencing strategy, which may be used as a faster, more accurate alternative to de novo sequencing. The available data suggest that the assay described here is a reliable, rapid, information-rich and cost-effective approach for definitive diagnosis of H5N1 avian influenza. Knowledge of the predicted functional sequences of the HA will enhance H5N1 avian influenza surveillance efforts.
Threshold Tracking for Assessment of Long-Term Adaptation and Sensitization in Pain Perception (1989)

To assess temporal variations in the perception of "phasic" heat pain stimuli a psychophysical tracking procedure was developed that enables repeated assessment of the pain threshold at short intervals. This "double-tracking" procedure produces two tracking curves simultaneously, one that approaches the pain threshold gradually from above, the other from below. The threshold for phasic heat pain was measured in 80 tracking trials with stimuli at temperatures near the pain threshold. Concurrently, the threshold for "tonic" heat pain was determined after every 20 tracking trials with a stimulus adjustment procedure. Eleven healthy subjects (age: 26.4 yr. +/- 6.0) participated in 2 sessions each. Phasic stimulation near the pain threshold did not produce any trends in either of the two threshold measures. Hence there was no long-term adaptation or sensitization. However, there were random variations (random walks) in the tracking curves, which we interpret as resulting from a stochastic relationship between stimulus and sensation. In agreement with other reports, discrimination seemed to be better at painful than at nonpainful temperatures.
Toward a Union-Find Decoder for Quantum LDPC Codes (2022)

Quantum LDPC codes are a promising direction for low overhead quantum computing. In this paper, we propose a generalization of the Union-Find decoder as a decoder for quantum LDPC codes. We prove that this decoder corrects all errors with weight up to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$An^\alpha $ </tex-math></inline-formula> for some <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$A, \alpha > 0$ </tex-math></inline-formula> , where <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$n$ </tex-math></inline-formula> is the code length, for different classes of quantum LDPC codes such as toric codes and hyperbolic codes in any dimension <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$D \geq 3$ </tex-math></inline-formula> and quantum expander codes. To prove this result, we introduce a notion of covering radius which measures the spread of an error from its syndrome. We believe this notion could find application beyond the decoding problem. We also perform numerical simulations, which show that our Union-Find decoder outperforms the belief propagation decoder in the low error rate regime in the case of a quantum LDPC code with length 3600.
Multi Topology Routing Based Failure Protection for Software Defined Networks (2018)

The fast recovery from network failures in the data plane of Software Defined Networks (SDN) is a stringent requirement to seamlessly support the real-time communications. IETF standardized Multi Topology Routing (MTR) which provides a redundancy in routing tables by computing virtual topologies (VTs) which differ in their link weights. MTR based failure recovery techniques use VTs each of which assigns a very high weight to certain links in the physical topology so that these links are not traversed by the shortest paths. When a network component actually fails, the routing tables corresponding to the VT isolating the component are activated for traffic forwarding. In this paper, the architecture for MTR based failure protection (MTR-P) in SDN is defined and implemented, and its performance is analyzed using different network topologies. The experimental results expose important properties of MTR-P for fast failure recovery in SDN.
[New biologically active theophylline derivatives. Synthesis and pharmacologic properties of flufylline and fluprofylline]. (1984)

Within the course of the research project for finding new cardiovascular drugs we have synthetized since 1976 piperazine- and piperidine derivatives of theophylline. The screening shows for the substances Sgd 19578 (flufylline) and Sgd 14480 (fluprofylline) a long-lasting blood pressure lowering activity as well as a remarkable serotonin- and histamine antagonism and broncholytic activity. On the basis of these results these compounds were selected for further investigation.
Asthma–COPD Overlap. Clinical Relevance of Genomic Signatures of Type 2 Inflammation in Chronic Obstructive Pulmonary Disease (2015)

These data identify airway gene expression alterations that can co-occur in asthma and COPD. The association of the T2S score with increased severity and "asthma-like" features (including a favorable corticosteroid response) in COPD suggests that Th2 inflammation is important in a COPD subset that cannot be identified by clinical history of asthma.
Immunodiagnostics: Evaluation of Functional T-Cell Immunocompetence in Whole Blood Independent of Circulating Cell Numbers (2007)

The need for a systematic approach for immune function monitoring has becoming increasingly apparent in the past decade due to the rapid expansion of the development and use of immunomodulatory drug therapies and vaccines. While there has been a great deal of progress in the development of methodologies for evaluating and enumerating T-lymphocyte responses to infection and cancer, the translation of these assays into the clinical setting has remained seemingly elusive. This is likely due to inherent difficulties in the standardization and validation of cell-based assays. Here, we describe a novel assay that measures ATP production in CD4(+) T-lymphocytes in response to stimulation. Results from the test, unlike absolute cell counts, assess the functional response of lymphocytes. Clinical utility of the assay has been demonstrated in managing immunosuppression in solid organ transplant recipients such that adverse events such as infection and rejection can be avoided. The need for a global immune response test in the clinical setting of transplantation and the value of such a test in post-transplant management is discussed. Furthermore, additional applications of this assay for monitoring diseases that impact immune function including autoimmunity and infection are considered.
Minimum-latency dual-leaky-bucket shapers for packet multiplexers: theory and implementation (2002)

The need for integrating per-flow dual leaky-bucket regulators with a scheduler that enforces strict bandwidth guarantees is becoming a crucial issue in networks that provide differentiated services. Despite the increasing relevance of the topic, existing solutions either lack accuracy in their shaping action, or compromise the provision of strict bandwidth guarantees to the shaped flows, or suboptimally utilize the output link. In this paper, we present the monolithic shaper-scheduler (MSS), which integrates the shaping and scheduling functions while preserving the bandwidth guarantees of the shaped flows. The MSS handles shaped and unshaped flows simultaneously. It allows us to provision per flow shaping parameters that are independent of the corresponding bandwidth requirements; thus, the available link bandwidth can be fully utilized. The latency and worst case fairness properties of the new scheduler are optimal among GPS-related schedulers. We describe how the MSS can be easily implemented in practice, with minimal overhead with respect to a conventional GPS-related scheduler.
Stable Levitation of a Passive Magnetic Bearing (2012)

A design for a passive magnetic bearing system that can stably levitate a rotor in all directions is described. The bearing system consists of levitation magnets coupled with a Halbach array stabilizer, which induces currents in stabilization coils, in order to overcome the inherent instability of a system composed only of permanent magnets. The levitation magnet system consists of two pairs of annular ring magnets which provide an upward magnetic levitation force to counteract the downward gravitational force of the rotor. The Halbach array stabilizer consists of two stabilization coils shifted in angular position with respect to one another and centered in the vertical direction between two rotating Halbach arrays. Magnetic fields from permanent magnets are calculated using superposition of fields due to patches of magnetization charge at surfaces where the magnetization is discontinuous. Induced currents in the stabilization coils are calculated by computing the time derivative of the magnetic flux through those coils. Magnetic forces on the rotor are computed using a superposition of forces on each patch of magnetization charge. The entire magnetic bearing system, consisting of both the levitation magnets and the Halbach array stabilizer, is stable to both vertical and lateral displacements. Results are compared with a simpler straightened approximation of the Halbach array stabilizer.
Learning Differentially Private Recurrent Language Models (2017)

We demonstrate that it is possible to train recurrent language models with user-level differential privacy guarantees with only a negligible cost in predictive accuracy. Our work builds on recent advances in the training of deep networks on user-partitioned data and privacy accounting for stochastic gradient descent. In particular, we add user-level privacy protection to the federated averaging algorithm, which makes large step updates from user-level data. Our work demonstrates that given a dataset with a sufficiently number of users (a requirement easily met by even small internet-scale datasets), achieving differential privacy comes at the cost of increased computation, rather than in decreased utility as in most prior work. We find that our private LSTM language models are quantitatively and qualitatively similar to un-noised models when trained on a dataset.
Broadband achromatic optical metasurface devices (2017)

Among various flat optical devices, metasurfaces have presented their great ability in efficient manipulation of light fields and have been proposed for variety of devices with specific functionalities. However, due to the high phase dispersion of their building blocks, metasurfaces significantly suffer from large chromatic aberration. Here we propose a design principle to realize achromatic metasurface devices which successfully eliminate the chromatic aberration over a continuous wavelength region from 1200 to 1680 nm for circularly-polarized incidences in a reflection scheme. For this proof-of-concept, we demonstrate broadband achromatic metalenses (with the efficiency on the order of ∼12%) which are capable of focusing light with arbitrary wavelength at the same focal plane. A broadband achromatic gradient metasurface is also implemented, which is able to deflect wide-band light by the same angle. Through this approach, various flat achromatic devices that were previously impossible can be realized, which will allow innovation in full-color detection and imaging.Metasurfaces suffer from large chromatic aberration due to the high phase dispersion of their building blocks, limiting their applications. Here, Wang et al. design achromatic metasurface devices which eliminate the chromatic aberration over a continuous region from 1200 to 1680 nm in a reflection schleme.
Using Personal Electronic Device for Authentication-Based Service Access (2008)

A person usually carries multiple authentication tokens in the form of various cards to access services electronically. Often the service outlets are equipped with a strong infrastructure to permit the user interactions. The network connectivity is usually a must for the service outlet to authenticate the user with the server. In this paper, we propose a solution which uses the personal mobile devices held by the user to interact with the service outlets. Such a system can then alleviate the needs for interaction console and communication infrastructure at service outlets.
A Markov Model for Driver Turn Prediction (2008)

<div class="htmlview paragraph">This paper describes an algorithm for making short-term route predictions for vehicle drivers. It uses a simple Markov model to make probabilistic predictions by looking at a driver's just-driven path. The model is trained from the driver's long term trip history from GPS data. We envision applications including driver warnings, anticipatory information delivery, and various automatic vehicle behaviors. The algorithm is based on discrete road segments, whose average length is 237.5 meters. In one instantiation, the algorithm can predict the next road segment with 90% accuracy. We explore variations of the algorithm and find one that is both simple and accurate.</div>
Perceptual Temporal Quality Metric for Compressed Video (2007)

This paper presents a metric to quantify frame loss according to the impact on perceived temporal quality. This metric particularly aims at measuring the temporal quality degradation caused by both regular and irregular frame loss. Experimental results with subjective viewing demonstrate high performance on prediction of perceptual temporal quality.
Measuring liquid properties with smooth- and textured-surface resonators (1993)

The sensitivity of quartz resonators to surface mass accumulation enables their use in a number of sensing applications. The linear change in resonant frequency that occurs with mass accumulation allows the device to function as a general-purpose gravimetric detector or ``microbalance.`` The device is easily instrumented as a sensor by incorporating it as the frequency-control element of an oscillator circuit. The response of thickness shear mode (TSM) resonators in liquids is examined. Smooth-surface devices, which viscously entrain a layer of contacting liquid, respond to the product of liquid density and viscosity. Textured-surface devices, which also trap liquid in surface features, exhibit an additional response that depends on liquid density alone. Combining smooth and textured resonators in a monolithic sensor allows simultaneous measurement of liquid density and viscosity.
A role for CYR61 in ovarian cancer progression (2006)

1858 CYR61 is a secreted, heparin-binding, extracellular matrix-associated angiogenic inducer. We have previously shown that CYR61 is involved in ovarian angiogenesis and that its expression is also detected in ovarian cancer cells. The goal of the present study was to determine the function(s) of CYR61 in ovarian tumor angiogenesis and progression. To accomplish this, we established stable CYR61 overexpressing OVCAR-5 clones along with appropriate pCDNA3.1 vector controls. Compared to parental OVCAR-5 and vector control cells, CYR61 stable clones exhibited a loss of cell-cell contact and an irregular cell morphology. These morphological changes were accompanied by increased mRNA expression of the epithelial-mesenchymal transition (EMT)-related transcription factors, Snail, Twist, and SIP1, but not of Slug. Western blotting of cell lysates demonstrated that CYR61 stable clones have significantly decreased (p
Treatment of Irritable Bowel Syndrome With Chinese Herbal Medicine (1998)

Chinese herbal formulations appear to offer improvement in symptoms for some patients with IBS.