gebhart/patrepeval huggingface dataset:
Secretion of human hepatitis B virus is inhibited by the imino sugar N-butyldeoxynojirimycin. (1994)

The imino sugar N-butyldeoxynojirimycin (NBDNJ) is a potent inhibitor of the oligosaccharide-trimming enzyme alpha-glucosidase I. Hepatitis B virus (HBV) contains three surface proteins (HBs proteins) of different sizes that are singly or doubly N-glycosylated and are essential for the formation of infectious virus. Therefore, the replication and secretion of HBV in the human hepatoma cell line HepG2 were studied in the presence of NBDNJ. In the stably HBV-transfected HepG 2.2.15 cells and in HBV-infected HepG2 cells, NBDNJ suppressed secretion of HBV particles and caused intracellular retention of HBV DNA. The secretion of subviral particles was less affected. These data suggest that inhibitors of oligosaccharide trimming may be useful for antiviral therapy of hepatitis B and for the study of the intracellular transport of the viral glycoproteins.
Radical versus partial nephrectomy (2009)

Relative to PN, RN predisposes to an increase in overall mortality and non-cancer-related death rate in patients with T1a RCC. In consequence, PN should be attempted whenever technically feasible. Selective referrals should be considered if PN expertise is unavailable.
A methodology and algorithms for post-placement delay optimization (1994)

In this paper we present a placement-intelligent resynthesis methodology and optimization algorithms to meet post-layout timing constraints while at the same time reducing the interconnect congestion. We b egin with the synthesized design netlist after initial placement and make incremental modications { taking placement into account { to generate a nal netlist and placement that meets the delay constraints after place and route. The algorithms described have been implemented a s p art of a tool for placement based r esynthesis. The tool has been used with a number of pre-optimized designs from industry and to obtain improvements in post-placement delays ranging from 13 to 22% with improved r outability.
Cataract- and lens-specific upregulation of ARK receptor tyrosine kinase in Emory mouse cataract. (2002)

The present data confirm that expression of the alphaA-crystallin gene is decreased in cataract in the Emory mouse lens relative to age-matched control lenses and they provide evidence for cataract- and lens-specific upregulation of the ARK receptor tyrosine kinase in the Emory mouse.
Paracetamol (2000)

Paracetamol (acetaminophen) is one of the most widely used of all drugs, with a wealth of experience clearly establishing it as the standard antipyretic and analgesic for mild to moderate pain states. First used clinically by von Mering in 1893, paracetamol did not appear commercially until 1950 in the United States and 1956 in Australia. During the 1960s and 1970s, increasing concern was raised about the toxicity of nonprescription analgesics, but in normal use paracetamol exhibited a consistent safety profile. Its exemplary safety record was marred by the discovery in 1966 that a major overdose could be complicated by severe and sometimes fatal liver damage. Fortunately, early treatment with N-acetylcysteine prevents liver toxicity. A turning point in the choice of pediatric analgesic came in the 1980s when aspirin was linked to Reye's syndrome. As a consequence, paracetamol became the mainstay analgesic and antipyretic for children with a subsequent reduction in the incidence of Reye's syndrome. Currently, paracetamol is a first-line choice for pain management and antipyresis in a variety of patients, including children, pregnant women, the elderly, those with osteoarthritis, simple headaches, and those with noninflammatory musculoskeletal conditions. With proper use, paracetamol seldom causes adverse events and reports of serious side effects are rare. It has a broad tolerability and is of particular value in the treatment of patients in whom nonsteroidal anti-inflammatory drugs are contraindicated such as aspirin-sensitive asthmatics and people at risk of gastrointestinal complications. In the future, a better insight into the mechanism of action of paracetamol may be gained from a fuller understanding of the cyclooxygenase enzymes. In the meantime, paracetamol may find applications in other therapeutic areas, such as the prevention of atherosclerosis via a potential antioxidant activity. In summary, although it is more than a century since the first clinical use of paracetamol, it continues to be a first-line therapy of choice in adults and children with fever and pain. In addition, current research suggests that paracetamol may have a much broader clinical utility in years to come.
Breeding For Resistance To Powdery Mildew Race 2W In Watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] (2008)

TETTEH, ANTONIA YARBEH.Breeding for Resistance
CELLULOSIC NANOCOMPOSITES: A REVIEW (2008)

Because of their wide abundance, their renewable and environmentally benign nature, and their outstanding mechanical properties, a great deal of attention has been paid recently to cellulosic nanofibrillar structures as components in nanocomposites. A first major challenge has been to find efficient ways to liberate cellulosic fibrils from different source materials, including wood, agricultural residues, or bacterial cellulose. A second major challenge has involved the lack of compatibility of cellulosic surfaces with a variety of plastic materials. The water-swellable nature of cellulose, especially in its non-crystalline regions, also can be a concern in various composite materials. This review of recent work shows that considerable progress has been achieved in addressing these issues and that there is potential to use cellulosic nano-components in a wide range of high-tech applications.
Metabolism of threo-beta-fluoroaspartate by H4 cells. Inhibition of adenylosuccinate lyase by fluoro analogs of its substrates. (1986)

DL-threo-beta-Fluoroaspartate is a substrate for the two enzymes in de novo purine biosynthesis that use aspartate, namely 4-(N-succino)-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR) synthetase and adenylosuccinate synthetase. With both enzymes, Vmax with threo-beta-fluoroaspartate is about 50% of that observed with aspartate. The products of the two enzyme reactions, threo-beta-fluoro-SAICAR and threo-beta-fluoroadenylosuccinate, are inhibitors of adenylosuccinate lyase purified from rat skeletal muscle. In 20 mM phosphate buffer, pH 7.4, the KI values for threo-beta-fluoro-SAICAR are 5 and 3 microM and for threo-beta-fluoroadenylosuccinate are 3 and 1 microM, in the SAICAR and adenylosuccinate cleavage reactions, respectively. In 20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer, pH 7.4, the KI values for threo-beta-fluoro-SAICAR are approximately 0.14 and 0.03 microM and for threo-beta-fluoroadenylosuccinate are approximately 0.05 and 0.015 microM, in the same two reactions, respectively. These KI values are one-half to one-hundredth of the Km values for SAICAR and adenylosuccinate, the two substrates of adenylosuccinate lyase. After an 8-h incubation with 45 microM threo-beta-fluoroaspartate, H4 cells contain 200-300 microM threo-beta-fluoro-SAICAR and 60-90 microM threo-beta-fluoroadenylosuccinate. These concentrations of fluoro analogs are sufficient to substantially inhibit adenylosuccinate lyase and hence the de novo synthesis of purines in H4 cells.
Synthesis and characterization of thermoplastic copolyesters containing copolymerized azoic dyes (1995)

Abstract Poly(ethylene terephthalate) and a series of other amorphous copolyesters based on ethylene glycol and terephthalic/isophthalic or 2,6‐naphthalenedicarboxylic/isophthalic acid mixtures were prepared by melt polycondensation. Comonomers consisting of azoic dyes having two polymerizable functions on the aromatic rings (either one alcoholic and one carbomethoxyl, two alcoholic or two carbomethoxyl groups) were also added, in amounts lower than 1% mol with respect to the sum of diesters used as starting monomers. In these conditions (P&lt;0.1 torr and T=280°C), only few azoic dyes were found to be stable. Among the prepared polymers, those based on dyes having sufficient thermal stability were characterized by differential scanning calorimetry and solution properties. Inherent viscosities suggest that molecular weights are high. Glass transition and melting temperatures as well as mechanical properties of colored polyesters are not affected by the presence of the azoic comonomers. UV–visible spectra of copolyester solutions were registered, and absorption coefficients were correlated with the amount of dye.
Differential Requirements for VirB1 and VirB2 during Brucella abortus Infection (2004)

The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface, where they could potentially interact with host cells. Studies to date have focused on characterization of transposon mutations in these genes, which are expected to exert polar effects on downstream genes in the operon. In order to determine whether VirB1 and VirB2 are required for the function of the T4SS apparatus, we constructed and characterized nonpolar deletion mutations of virB1 and virB2. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB2 mutant was unable to cause persistent infection in the mouse model, demonstrating the essential role of VirB2 in the function of the T4SS apparatus during infection. In contrast, the nonpolar virB1 mutant persisted at wild-type levels, showing that the function of VirB1 is dispensable in the mouse model of persistent infection.
Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes (2004)

We describe here a new method for highly efficient detection of microRNAs by northern blot analysis using LNA (locked nucleic acid)-modified oligonucleotides. In order to exploit the improved hybridization properties of LNA with their target RNA molecules, we designed several LNA-modified oligonucleotide probes for detection of different microRNAs in animals and plants. By modifying DNA oligonucleotides with LNAs using a design, in which every third nucleotide position was substituted by LNA, we could use the probes in northern blot analysis employing standard end-labelling techniques and hybridization conditions. The sensitivity in detecting mature microRNAs by northern blots was increased by at least 10-fold compared to DNA probes, while simultaneously being highly specific, as demonstrated by the use of different single and double mismatched LNA probes. Besides being highly efficient as northern probes, the same LNA-modified oligonucleotide probes would also be useful for miRNA in situ hybridization and miRNA expression profiling by LNA oligonucleotide microarrays.
PRODUCTION OF HYDROGEN FROM POST-CONSUMER WASTES (2002)

At present, the commercial production of hydrogen is essentially carried out by catalytic steam reforming of hydrocarbons: natural gas and naphtha. However, the instability of the prices of natural gas makes the use of other raw materials increasingly attractive. This research focuses on the development of a technology for producing hydrogen from alternative resources, specifically from two types of waste post-consumer materials: plastics and “trap grease”. The concept proposed for plastics is a two-stage process: fast pyrolysis to convert polymers to a gas/vapor stream of monomers and other low-molecular weight compounds followed by catalytic steam reforming of this gas to yield hydrogen and carbon oxides. “Trap grease”, a waste material recovered from traps on sewer lines, does not require a depolymerization step and can be directly steam reformed to produce hydrogen. To prove the process concept, we employed a two-stage micro-scale reactor interfaced with a molecular-beam massspectrometer. Samples of plastics were pyrolyzed in the bottom part of the reactor then the created gases and vapors were steam reformed in a fixed bed of a commercial catalyst located in the upper part of the reactor. The product gas was analyzed by mass spectroscopy. Preliminary tests showed that at process conditions similar to those used for reforming natural gas, polymers were almost completely converted to hydrogen and carbon oxides. “Trap grease”, after washing and filtering, was catalytically steam reformed in a 2”-diameter fluidized bed reactor using the same commercial nickel catalyst. At 850°C, using steam-to-carbon ratio 5, and with a space velocity of 1000 h-1, hydrogen was produced with a yield of 25 g per 100 g of grease during 135 hours of continuous testing. This yield could be increased to over 28 g H2/100 g grease (85 % of the stoichiometric potential) if CO were further converted by water-gas shift.
Cloning of human and bovine homologs of SNF2/SWI2: a global activator of transcription in yeastS.cerevisiae (1992)

We performed positional cloning of genes carried on yeast artificial chromosomes that span a human translocation breakpoint associated with a human disease and isolated by chance human and bovine genes with strong homology to the S. cerevisiae genes, SNF2/SWI2 and STH1, and the D. melanogaster gene brahma. We report here sequence analysis, expression data, and functional studies for this human SNF2-like gene (hSNF2L) and its bovine homolog (bovSNF2L). Despite strong homology at the amino acid level, hSNF2L is not capable of complementing the yeast mutations snf2 or sth1 in S. cerevisiae. Furthermore, in contrast to SNF2 itself, a fusion protein consisting of the DNA binding domain of LexA and hSNF2L did not transactivate a reporter gene downstream of LexA binding sites in a yeast expression system. The strong similarity between hSNF2L and these yeast and drosophila genes suggest that the mammalian genes are part of an evolutionarily conserved family that has been implicated as global activators of transcription in yeast and fruitflies but whose function in mammals remains unknown.
The Effects of Exogenous Crosslinking on Hydration and Fluid Flow in the Intervertebral Disc Subjected to Compressive Creep Loading and Unloading (2010)

The effects of genipin crosslinking on matrix permeability and proteoglycan retention can alter hydration levels and fluid flow in the intervertebral disc. Resulting increases in fluid flow, including a doubling of flow to and from the nucleus, could lead to enhanced nutritional inflow and waste product outflow for the disc, and may have implications for emerging cell-based therapies.
Sensitive enzyme‐linked immunosorbent assay for antibody to varicella‐zoster virus using purified VZV glycoprotein antigen (1990)

The development of an ELISA of increased sensitivity has permitted a more critical evaluation of human humoral immune responses to the live attenuated varicella (Oka/Merck) vaccine. For use as a solid-phase antigen, the glycoprotein (gp) antigens are prepared by lectin-affinity chromatography from lysates of VZV-infected MRC-5 cells. The lot-to-lot variation in VZV gp content is controlled by standardization of antigen against a panel of human serum providing antigen-coated plates of consistent quality. The increased sensitivity of the gpELISA over the VAR ELISA is reflected in the greater seroconversion rate and prepositive rate specificity. These determinations have been shown to be specific for anti-VZV by absorption experiments using purified VZV gp antigens.
Subfemtosecond compression of periodic laser pulses (1999)

It is shown that a recently proposed technique of molecular modulation can be used to compress mode-locked laser pulses into the subfemtosecond domain. The method relies on driving a molecular oscillation with a periodic pulse train. The coherent molecular motion, in turn, modulates the laser frequency and allows pulse compression by group-velocity dispersion of the same molecular medium.
Structural characterization of the circulating soluble FGF receptors reveals multiple isoforms generated by secretion and ectodomain shedding (2001)

Soluble fibroblast growth factor receptors (FGFRs) have been identified in multiple biological fluids, including blood. Efforts to examine the biological properties of these proteins have been hampered by the incomplete chemical characterization of the receptors within the second half of the third immunoglobulin (Ig)-like domain, where alternative splicing leads to receptor variants with different ligand binding properties. Using mass spectrometry techniques, we have mapped the soluble FGFRs to the secreted receptor, FGFR1(IIIa), the two and three Ig-like domain isoforms of FGFR1(IIIc) and a carboxyl-terminal cleavage peptide from the two and three Ig-like domain isoforms of FGFR1(IIIb). The secreted FGFR is produced by the translation of an alternatively spliced transcript and the cleaved receptors are released by ectodomain shedding of the transmembrane receptors.
Mutations within the NH2-terminal transmembrane domain of membrane immunoglobulin (Ig) M alters Ig alpha and Ig beta association and signal transduction. (1994)

Potentiation of initial signal transduction events through the cross-linking of the B cell antigen receptor complex appears to be dependent upon the association of membrane immunoglobulin (mIg) with Ig alpha and Ig beta. We made two groups of mutations within the COOH terminus of mIgM substituting: 1) the spacer, transmembrane, and cytoplasmic domains and 2) the NH2-terminal 2-8 amino acids within the transmembrane domain (NLWTTAST). We then evaluated the ability of the mutated receptors to associate with Ig alpha and Ig beta and to initiate signal transduction events (Ca2+ mobilization and phosphorylation by tyrosine protein kinases) after cross-linking mIgM receptors. Mutant mIgM receptors containing substitutions of gamma 2b (spacer, transmembrane, and cytoplasmic domains), AA for TT, and AAAAA for TTAST bound Ig alpha and Ig beta and initiated signal transduction events after mIgM receptor cross-linking. However, substitutions of I-A alpha (spacer, transmembrane, and cytoplasmic domains) or TTVVCALGL for NLWTTAST blocked association of Ig alpha and Ig beta and initiation of signal transduction events. Results indicate that residues within the first 8 amino acids of the transmembrane domain other than TTAST are necessary for receptor function and association with Ig alpha and Ig beta.
Advanced glycosylation products quench nitric oxide and mediate defective endothelium-dependent vasodilatation in experimental diabetes. (1991)

Nitric oxide (an endothelium-derived relaxing factor) induces smooth muscle relaxation and is an important mediator in the regulation of vascular tone. Advanced glycosylation end products, the glucose-derived moieties that form nonenzymatically and accumulate on long-lived tissue proteins, have been implicated in many of the complications of diabetes and normal aging. We demonstrate that advanced glycosylation products quench nitric oxide activity in vitro and in vivo. Acceleration of the advanced glycosylation process in vivo results in a time-dependent impairment in endothelium-dependent relaxation. Inhibition of advanced glycosylation with aminoguanidine prevents nitric oxide quenching, and ameliorates the vasodilatory impairment. These results implicate advanced glycosylation products as important modulators of nitric oxide activity and endothelium-dependent relaxation.
Analysis of RNA-binding proteins by in vitro genetic selection: identification of an amino acid residue important for locking U1A onto its RNA target. (1995)

An in vitro genetic system was developed as a rapid means for studying the specificity determinants of RNA-binding proteins. This system was used to investigate the origin of the RNA-binding specificity of the mammalian spliceosomal protein U1A. The U1A domain responsible for binding to U1 small nuclear RNA was locally mutagenized and displayed as a combinatorial library on filamentous bacteriophage. Affinity selection identified four U1A residues in the mutagenized region that are important for specific binding to U1 hairpin II. One of these residues (Leu-49) disproportionately affects the rates of binding and release and appears to play a critical role in locking the protein onto the RNA. Interestingly, a protein variant that binds more tightly than U1A emerged during the selection, showing that the affinity of U1A for U1 RNA has not been optimized during evolution.
ANARCI: antigen receptor numbering and receptor classification (2015)

deane@stats.ox.ac.uk.
Quantitative shear wave imaging of cell culture gels (2009)

An ultrasonic shear wave imaging technique is being developed for estimating viscoelastic properties of hydrogels. A needle placed in the medium is vibrated along its axis to generate harmonic shear waves. Doppler pulses synchronously track shear wave propagation to estimate the local speed. Fitting shear-wave speed estimates to the dispersion relation obtained from two rheological models, we estimate the complex shear modulus, viz., elastic and viscous components. The dispersion equation estimated using the standard solid-body (Zener) model is compared to that from the Kelvin-Voigt model to explore the frequency landscape of hydrogel viscoelasticity within the 50-450 Hz shear wave bandwidth. We found both models give comparable estimates that each agree with independent rheometer measurements obtained at lower strain rates, as might be expected form these highly elastic gels.
Localizing and Tracking Single Nanoscale Emitters in Three Dimensions with High Spatiotemporal Resolution Using a Double-Helix Point Spread Function (2009)

Three-dimensional nanoscale localization and tracking of dim single emitters can be obtained with a widefield fluorescence microscope exhibiting a double-helix point spread function (DH-PSF). We describe in detail how the localization precision quantitatively depends upon the number of photons detected and the z position of the nanoscale emitter, thereby showing a approximately 10 nm localization capability along x, y, and z in the limit of weak emitters. Experimental measurements are compared to Fisher information calculations of the ultimate localization precision inherent in the DH-PSF. The DH-PSF, for the first time, is used to track single quantum dots in aqueous solution and a quantum dot-labeled structure inside a living cell in three dimensions.
Differential privacy under continual observation (2010)

Differential privacy is a recent notion of privacy tailored to privacy-preserving data analysis [11]. Up to this point, research on differentially private data analysis has focused on the setting of a trusted curator holding a large, static, data set; thus every computation is a "one-shot" object: there is no point in computing something twice, since the result will be unchanged, up to any randomness introduced for privacy. However, many applications of data analysis involve repeated computations, either because the entire goal is one of monitoring, e.g., of traffic conditions, search trends, or incidence of influenza, or because the goal is some kind of adaptive optimization, e.g., placement of data to minimize access costs. In these cases, the algorithm must permit continual observation of the system's state. We therefore initiate a study of differential privacy under continual observation. We identify the problem of maintaining a counter in a privacy preserving manner and show its wide applicability to many different problems.