gebhart/patrepeval huggingface dataset:
Ability of the Matrix Protein of Vesicular Stomatitis Virus To Suppress Beta Interferon Gene Expression Is Genetically Correlated with the Inhibition of Host RNA and Protein Synthesis (2003)

The vesicular stomatitis virus (VSV) matrix (M) protein plays a major role in the virus-induced inhibition of host gene expression. It has been proposed that the inhibition of host gene expression by M protein is responsible for suppressing activation of host interferon gene expression. Most wild-type (wt) strains of VSV induce little if any interferon gene expression. Interferon-inducing mutants of VSV have been isolated previously, many of which contain mutations in their M proteins. However, it was not known whether these M protein mutations were responsible for the interferon-inducing phenotype of these viruses. Alternatively, mutations in other genes besides the M gene may enhance the ability of VSV to induce interferons. These hypotheses were tested by transfecting cells with mRNA expressing wt and mutant M proteins in the absence of other viral components and determining their ability to inhibit interferon gene expression. The M protein mutations were the M51R mutation originally found in the tsO82 and T1026R1 mutant viruses, the double substitution V221F and S226R found in the TP3 mutant virus, and the triple substitution E213A, V221F, and S226R found in the TP2 mutant virus. wt M proteins suppressed expression of luciferase from the simian virus 40 promoter and from the beta interferon (IFN-beta) promoter, while M proteins of interferon-inducing viruses were unable to inhibit luciferase expression from either promoter. The M genes of the interferon-inducing mutants of VSV were incorporated into the wt background of a recombinant VSV infectious cDNA clone. The resulting recombinant viruses were tested for their ability to activate interferon gene expression and for their ability to inhibit host RNA and protein synthesis. Each of the recombinant viruses containing M protein mutations induced expression of a luciferase reporter gene driven by the IFN-beta promoter and induced production of interferon bioactivity more effectively than viruses containing wt M proteins. Furthermore, the M protein mutant viruses were defective in their ability to inhibit both host RNA synthesis and host protein synthesis. These data support the idea that wt M protein suppresses interferon gene expression through the general inhibition of host RNA and protein synthesis.
Reducing Cache Coherence Traffic with Hierarchical Directory Cache and NUMA-Aware Runtime Scheduling (2016)

Cache Coherent NUMA (ccNUMA) architectures are a widespread paradigm due to the benefits they provide for scaling core count and memory capacity. Also, the flat memory address space they offer considerably improves programmability. However, ccNUMA architectures require sophisticated and expensive cache coherence protocols to enforce correctness during parallel executions, which trigger a significant amount of on- and off-chip traffic in the system.
Calcium channels in higher plant cells: selectivity, regulation and pharmacology (1997)

Rapid influx of Ca(2+) into the cytosol from extracellular pools or intracellular stores via ion channels can have wide-ranging physiological consequences. In addition, influx of Ca(2+) across the plasma membrane is necessary for the large net accumulation of Ca(2+) essential for cellular integrity. In this paper, the properties of Ca(2+) channels in various plant membranes are reviewed, and compared with new results on the Ca(2+) channel from the plasma membrane of wheat roots (rca channel) described originally by Piñeros and Tester (1995). The rca channel has been studied at the single channel level by incorporation of plasma membrane-enriched vesicles into planar lipid bilayers. It has a high affinity for Ca(2+) permeation (K(m) = 99 µM) and a maximal conductance of 30 pS. It is highly selective for Ca(2+) over Cl(-), but allows the movement both of other divalent cations (with a conductivity sequence: Ba(2+) > Sr(2+) > Ca(2+) >Mg(2+) > Mn(2+)) and of monovalent cations. The affinity for K(+) permeation was 6 mM, and the maximal conductance was 164 pS. The permeability ratio, P(Ca(2+))/P(K(+)) ranged from 17 to 41, decreasing with increasing extracellular Ca(2+). With physiologically reasonable membrane potentials and ionic conditions, the channel will catalyse Ca(2+) influx. At normal resting potentials (negative of about -135 mV) the channel remains largely closed, but activates rapidly upon depolarization. It is insensitive to ABA and Ins 1,4,5-P(3), but the voltage-dependence for activation was shifted to more negative potentials upon addition of cytosolic ATP. The channel was inhibited by a range of trivalent cations (La(3+), Al(3+) and Gd(3+)) and by some organic Ca2+ channel effectors (verapamil, diltiazem, ruthenium red), although it was insensitive to bepridil and 1,4 dihydropyridines [nifedipine and (+) and (-) 202-791], at least in the conditions described here. The properties of this channel are compared with those of other plant and animal Ca(2+) channels, and are shown to be consistent with its proposed physiological role of divalent cation uptake into roots.
Crystal structure of an uncleaved <i>α</i><sub>1</sub>‐antitrypsin reveals the conformation of its inhibitory reactive loop (1995)

The crystal structure of a recombinant human alpha 1-antitrypsin, in the uncleaved and uncomplexed state, has been determined by X-ray crystallographic methods and refined to an R-factor of 18.4% for 8.0-3.46 A data with good stereochemistry. This structure provides the first view at the inhibitory loop and the central beta-sheet A of the uncleaved alpha 1-antitrypsin. The reactive loop takes a distorted helical conformation and no pre-insertion of two residues in the reactive loop into the beta-sheet A is observed. The present structure is largely in agreement with the model predicted by Engh, Wright, and Huber [Prot. Eng. 3 (1990) 469-477].
Optical Forces Arising from Phase Gradients (2008)

We demonstrate both theoretically and experimentally that phase gradients in a light field can be used to create a new category of optical traps complementary to the more familiar intensity-gradient traps known as optical tweezers. We further show that the work done by phase-gradient forces is path dependent and briefly discuss some ramifications of this nonconservativity.
Interactions between endothelin-1 and the renin–angiotensin–aldosterone system (1999)

The renin-angiotensin-aldosterone (RAA) system and the endothelin (ET) system entail the most potent vasopressor mechanisms identified to date. Although they were studied in depth in relation to arterial hypertension and cardiovascular diseases, limited information on their interrelationships in causing hypertension and related target organ damage exists. The identification of consensus sequences for jun in the regulatory region of the preproendothelin-1 (ppET-1) gene raised the possibility of its transcriptional regulation by angiotensin II (Ang II). This was confirmed by the finding that stimulation with Ang II of cultured vascular smooth muscle cells (VSMCs) and endothelial cells (ECs) induced expression of the ppET-1 gene and synthesis of ET-1. Endogenously produced ET-1 was found to contribute to the hypertrophic response of cardiomyocytes to Ang II and thereby to cardiac hypertrophy. Furthermore, ET-1 exerts multifaceted effects on the RAA system, such as dose-dependent inhibition of renin synthesis, and stimulation of aldosterone secretion. The finding of abundant specific ET-1 receptors in the adrenocortical zona glomerulosa (ZG) suggested a direct secretagogue effect of ET-1. In rats, ETB receptors mediate such an effect, whilst in humans, both ETA and ETB receptor subtypes intervene in regulating the transcription of the aldosterone synthase gene. In addition, ET-1 stimulates DNA synthesis and proliferation of ZG cells via ETA receptors and, therefore, might play a role in cell turnover of the normal adrenal cortex and in the onset of adrenal tumours. Studies on the in vivo interactions between ETs and the RAA system have given conflicting results, insofar as some suggested a participation of ET-1 in the pressor and cellular effects of exogenously administered Ang II, whereas others did not in the transgenic TGR(Ren 2m)27 rats and in the two-kidney, one clip.
Transesterification of Various Methyl Esters Under Mild Conditions Catalyzed by Tetranuclear Zinc Cluster (2008)

A new catalytic transesterification promoted by a tetranuclear zinc cluster was developed. The mild reaction conditions enabled the reactions of various functionalized substrates to proceed in good to high yield. A large-scale reaction under solvent-free conditions proceeded with a low E-factor value (0.66), indicating the high environmental and economical advantage of the present catalysis.
Variables affecting the accuracy of stereotactic localization using computerized tomography (1993)

Stereotactic localization using computerized tomography (CT) is increasingly employed to guide neurosurgical procedures in crucial areas of the brain such as the brain stem. This technique allows the surgeon to resect a lesion in its entirety while sparing critical areas of the brain. Thus, the parameters used for scanning should be selected for maximum accuracy. While the small pixel size of CT scanners suggests a high degree of precision in localization, there have been few systematic studies of this accuracy. The authors have studied the amount of error in localization created by variables such as CT scan thickness, interscan spacing, size of lesion, and method of computation when using the Brown-Roberts-Wells (BRW) stereotactic system. Over 1000 CT scans were made of a phantom composed of spheres of differing diameter and location. The CT slice thickness was varied from 1.5 to 5.0 mm, and interscan spacing was varied from 0.5 to 3.0 mm. The coordinates of the center of the spheres were calculated independently using the laptop computer supplied with the unit and also by a stereotactic computer which automatically calculates the center of the fiducials. The actual BRW coordinates of the sphere center were obtained using the phantom base and were then compared to the computer-calculated coordinates to determine error in localization. Variables with a significant effect on error included the scan thickness, interscan spacing, and sphere size. The mean error decreased 23% as the scan thickness decreased from 5.0 to 1.5 mm and 45% as the interscan spacing decreased from 3.0 to 0.5 mm. Mean error was greatest for the smallest sphere sizes. The two computational methods did not differ in error. This study suggests that, for critical areas of the brain or for small lesions, a scan thickness of 1.5 mm and interscan spacing of 0.5 mm should be employed.
Disruption of the mouse <i>RBP-J</i>к gene results in early embryonic death (1995)

The RBP-J kappa protein is a transcription factor that recognizes the sequence C(T)GTGGGGA. The RBP-J kappa gene is highly conserved in a wide variety of species and the Drosophila homologue has been shown to be identical to Suppressor of Hairless [Su(H)] which plays important roles in the development of the peripheral nervous system. To explore the function of the RBP-J kappa gene in mouse embryogenesis, a mutation was introduced into the functional RBP-J kappa gene in embryonic stem (ES) cells by homologous recombination. Null mutant ES cells survived but null mutant mice showed embryonic lethality before 10.5 days of gestation. The mutant mice showed severe growth retardation as early as 8.5 days of gestation. Developmental abnormalities, including incomplete turning of the body axis, microencephaly, abnormal placental development, anterior neuropore opening and defective somitogenesis, were observed in the mutant mice at 9.5 days of gestation. RBP-J kappa mutant embryos expressed a posterior mesodermal marker FGFR1. Their irregularly shaped somites expressed a somite marker gene Mox 1 but failed to express myogenin. The RBP-J kappa gene was revealed to be essential for postimplantation development of mice.
Application Requested IP over ATM (Arequipa) and its use in the Web (1996)

: When using the Web over the TCP/IP protocol suite of the Internet, there is (yet) no possibility to guarantee bandwidth or delay for the transmission of a document. For the multimedia documents of the Web, transmission with guaranteed quality of service (QoS) is however very desirable. ATM networks which are being deployed now are one means of solving this problem. They offer high bandwidths and QoS negotiation at connection establishment. Current implementations of IP over ATM do not pass these advantages of the underlying network to the application level. Assuming that standard solutions involving RSVP [5] and NHRP [8] will not soon be available, we present a service built on a dual stack (IP &amp;amp; ATM) approach which allows to transport IP streams over application requested ATM connections. We show how this service can be used to offer guaranteed QoS to Web users on ATM while preserving compatibility with users which can not benefit of ATM connections. Finally we show how this solutio...
Versatile Pd(II)-Catalyzed C−H Activation/Aryl−Aryl Coupling of Benzoic and Phenyl Acetic Acids (2008)

The use of aryltrifluoroborates as coupling partners and O(2) as the oxidant substantially improves the scope and practicality of the Pd-catalyzed C-H activation/C-C coupling reaction. The newly discovered protocol made possible, for the first time, the ortho-coupling of electron-deficient arenes and phenyl acetic acids with organometallic reagents.
Perfectly Alternating Copolymerization of CO<sub>2</sub> and Epichlorohydrin Using Cobalt(III)-Based Catalyst Systems (2011)

Selective transformations of carbon dioxide and epoxides into biodegradable polycarbonates by the alternating copolymerization of the two monomers represent some of the most well-studied and innovative technologies for potential large-scale utilization of carbon dioxide in chemical synthesis. For the most part, previous studies of these processes have focused on the use of aliphatic terminal epoxides or cyclohexene oxide derivatives, with only rare reports concerning the synthesis of CO(2) copolymers from epoxides containing electron-withdrawing groups such as styrene oxide. Herein we report the production of the CO(2) copolymer with more than 99% carbonate linkages from the coupling of CO(2) with epichlorohydrin, employing binary and bifunctional (salen)cobalt(III)-based catalyst systems. Comparative kinetic studies were performed via in situ infrared measurements as a function of temperature to assess the activation barriers for the production of cyclic carbonate versus copolymer involving two electronically different epoxides: epichlorohydrin and propylene oxide. The relative small activation energy difference between copolymer versus cyclic carbonate formation for the epichlorohydrin/CO(2) process (45.4 kJ/mol) accounts in part for the selective synthesis of copolymer to be more difficult in comparison with the propylene oxide/CO(2) case (53.5 kJ/mol). Direct observation of the propagating polymer-chain species from the binary (salen)CoX/MTBD (X = 2,4-dinitrophenoxide and MTBD = 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene) catalyst system by means of electrospray ionization mass spectrometry confirmed the perfectly alternating nature of the copolymerization process. This observation in combination with control experiments suggests possible intermediates involving MTBD in the CO(2)/epichlorohydrin copolymerization process.
Les chaînes de référence dans les portraits journalistiques : éléments de description (2006)

Résumé À partir d’un corpus constitué d’une quarantaine de portraits extraits du quotidien Le Monde , cet article montre que l’expression de la référence ne s’y conforme pas aux prédictions de la théorie de l’accessibilité ou la théorie du centrage. À la suite de certains auteurs, on suggère que le genre textuel conditionne fortement les modalités de la cohésion référentielle. L’inventaire et le dénombrement des SN référentiels permet en effet de distinguer, selon leur matériau grammatical et lexical, deux types de chaînes, dont les unités répondent à des principes d’alternance particuliers. Il s’agit notamment de dégager les contraintes lexicales et discursives qui pèsent sur l’emploi des SN définis, très nombreux, en tenant compte du contexte « droit » de leur occurrence.
Indoor scene reconstruction from sets of noisy range images (2003)

The paper describes a system for indoor scene modeling from sets of noisy laser range images. We address several important aspects thereof: preprocessing, which includes image segmentation and planar model fitting; view registration, which is the method of determining the rigid transformation that describes the relative pose of the camera platform between views; and reconstruction, which is the subsequent integration or fusion of separate range images into a single 3D model. We give an empirical analysis, which demonstrates the efficacy of our plane-based registration strategy and results in real data that show the performance of the reconstruction system in its entirety.
Soluble recombinant influenza vaccines (2001)

Soluble, recombinant forms of influenza A virus haemagglutinin and neuraminidase have been produced in cells of lower eukaryotes, and shown in a mouse model to induce complete protective immunity against a lethal virus challenge. Soluble neuraminidase, produced in a baculovirus system, consisted of tetramers, dimers and monomers. Only the tetramers were enzymatically active. The immunogenicity decreased very considerably in the order tetra > di > mono. Therefore, we fused the head part of the neuraminidase gene to a tetramerizing leucine zipper sequence; the resulting product was enzymatically active, tetrameric neuraminidase. The protective immunity induced by this engineered neuraminidase, however, remained fairly strain-specific. A third influenza A virus protein, the M2 protein, has only 23 amino acids exposed on the outer membrane surface. This extracellular part, M2e, has been remarkably conserved in all human influenza A strains since 1933. By fusing the M2e sequence to hepatitis B virus core protein, we could obtain highly immunogenic particles that induced complete, strain-independent, long-lasting protection in mice against a lethal viral challenge. Native M2 is a tetrameric protein and this conformation of the M2e part can also be mimicked by fusing this sequence to a tetramerizing leucine zipper. The potential of the resulting protein as a vaccine candidate remains to be evaluated.
Quantitation of residual WBCs in filtered blood components by high‐throughput, real‐time kinetic PCR (2002)

kPCR is a high-throughput, sensitive assay that could prove useful in routine quality assurance of the WBC reduction process.
Eosinophil-Granule Major Basic Protein, a C-Type Lectin, Binds Heparin<sup>,</sup> (2005)

The eosinophil major basic protein (EMBP), a constituent of the eosinophil secondary granule, is implicated in cytotoxicity and mediation of allergic disorders such as asthma. It is a member of the C-type lectin family, but lacks a Ca(2+)- and carbohydrate-binding site as seen in other members of this family. Here, we report the crystal structure of EMBP in complex with a heparin disaccharide and in the absence of Ca(2+), the first such report of any C-lectin with this sugar. We also provide direct evidence of binding of EMBP to heparin and heparin disaccharide by surface plasmon resonance. We propose that the sugars recognized by EMBP are likely to be proteoglycans such as heparin, leading to new interpretations for EMBP function.
Immunogenicity of Murine Solid Tumor Models as a Defining Feature of In Vivo Behavior and Response to Immunotherapy (2013)

Immune profiling has been widely used to probe mechanisms of immune escape in cancer and identify novel targets for therapy. Two emerging uses of immune signatures are to identify likely responders to immunotherapy regimens among individuals with cancer and to understand the variable responses seen among subjects with cancer in immunotherapy trials. Here, the immune profiles of 6 murine solid tumor models (CT26, 4T1, MAD109, RENCA, LLC, and B16) were correlated to tumor regression and survival in response to 2 immunotherapy regimens. Comprehensive profiles for each model were generated using quantitative reverse transcriptase polymerase chain reaction, immunohistochemistry, and flow cytometry techniques, as well as functional studies of suppressor cell populations (regulatory T cells and myeloid-derived suppressor cells), to analyze intratumoral and draining lymphoid tissues. Tumors were stratified as highly or poorly immunogenic, with highly immunogenic tumors showing a significantly greater presence of T-cell costimulatory molecules and immune suppression in the tumor microenvironment. An absence of tumor-infiltrating cytotoxic T lymphocytes and mature dendritic cells was seen across all models. Delayed tumor growth and increased survival with suppressor cell inhibition and tumor-targeted chemokine+/-dendritic cells vaccine immunotherapy were associated with high tumor immunogenicity in these models. Tumor MHC class I expression correlated with the overall tumor immunogenicity level and was a singular marker to predict immunotherapy response with these regimens. By using experimental tumor models as surrogates for human cancers, these studies demonstrate how select features of an immune profile may be utilized to identify patients most likely to respond to immunotherapy regimens.
MEMS devices for high isolation switching and tunable filtering (2002)

This paper presents resonant capacitive microelectromechanical switches and their possible applications in tunable filtering. Single switches with a down capacitance of 2.9 pF and inductive sections of 3 to 50 pH are demonstrated, resulting in resonant frequencies from 13 to 54 GHz. Designs of resonant switches connected in parallel are also implemented with major advantages in isolation and bandwidth. Finally, tunable filters using these switches are discussed.
Lack of an Effect of Body Mass on the Hemodynamic Response to Arginine Vasopressin During Septic Shock (2008)

Body mass index did not alter the effects of arginine vasopressin on hemodynamic stability or changes in MAP when the drug was administered as a fixed-dose infusion of 0.04 U/minute. Our results do not support weight-based dosing of vasopressin, unlike the dosing for catecholamine vasopressors.