gebhart/patrepeval huggingface dataset:
The Pleiotropic Two-Component Regulatory System PhoP-PhoQ (2001)

PhoP-PhoQ is a two-component system that governs virulence, mediates the adaptation to Mg2+-limiting environments, and regulates numerous cellular activities in several gram-negative species. It consists of the inner membrane sensor PhoQ and the cytoplasmic regulator PhoP. The PhoP-PhoQ system is
Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans (2017)

Nucleotide excision repair is a major DNA repair mechanism in all cellular organisms. In this repair system, the DNA damage is removed by concerted dual incisions bracketing the damage and at a precise distance from the damage. Here, we review the basic mechanisms of excision repair in <i>Escherichia coli</i> and humans and the recent genome-wide mapping of DNA damage and repair in these organisms at single-nucleotide resolution.
Development of ASG-15ME, a Novel Antibody–Drug Conjugate Targeting SLITRK6 , a New Urothelial Cancer Biomarker (2016)

SLITRK6 is a member of the SLITRK family of neuronal transmembrane proteins that was discovered as a bladder tumor antigen using suppressive subtractive hybridization. Extensive immunohistochemistry showed SLITRK6 to be expressed in multiple epithelial tumors, including bladder, lung, and breast cancer as well as in glioblastoma. To explore the possibility of using SLITRK6 as a target for an antibody-drug conjugate (ADC), we generated a panel of fully human mAbs specific for SLITRK6. ADCs showed potent in vitro and in vivo cytotoxic activity after conjugation to Monomethyl Auristatin E or Monomethyl Auristatin F. The most potent ADC, ASG-15ME, was selected as the development candidate and given the product name AGS15E. ASG-15ME is currently in phase I clinical trials for the treatment of metastatic urothelial cancer. This is the first report that SLITRK6 is a novel antigen in bladder cancer and also the first report of the development of ASG-15ME for the treatment of metastatic bladder cancer. Mol Cancer Ther; 15(6); 1301-10. ©2016 AACR.
Cholinesterases from Plant Tissues (1973)

2-Isopropyl-4-dimethylamino-5-methylphenyl-1-piperidine carboxylate methyl chloride (AMO-1618) inhibits the activity of a cholinesterase isolated from mung bean (Phaseolus aureus) roots at concentrations comparable to those which retard growth and inhibit development of secondary roots of bean seedlings. Fifty per cent inhibition of the cholinesterase activity occurred at 0.21 mm. Inhibition of the cholinesterase is non-competitive and irreversible. The growth retardant seems to be a specific cholinesterase inhibitor since it has no effect on non-choline esterases.
Solubilities of the inert gases in water (1954)

T. J. Morrison and N. B. Johnstone, J. Chem. Soc., 1954, 3441 DOI: 10.1039/JR9540003441
Cobalt-catalyzed nucleophilic addition of the allylic C(sp3)–H bond of simple alkenes to ketones (2018)

We herein describe a cobalt/Xantphos-catalyzed regioselective addition of simple alkenes to acetophenone derivatives, affording branched homoallylic alcohols in high yields with perfect branch selectivities. The intermediate of the reaction would be a nucleophilic allylcobalt(I) species generated via cleavage of the low reactive allylic C(sp<sup>3</sup>)-H bond of simple terminal alkenes.
Sulfation of tyrosine residues in coagulation factor V (1990)

Sulfation of human coagulation factor V was investigated by biosynthetically labeling the products of HepG2 cells with [35S]sulfate. There was abundant incorporation of the sulfate label into a product identified as factor V by immunoprecipitation, lability to proteases, affinity for the lectin jacalin, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Two or more sites in factor V incorporated sulfate as indicated by labeling of different peptide chains of factor Va. The 150-Kd activation fragment of factor Va incorporated the greatest amounts of sulfate. This fragment of factor Va was bound selectively by jacalin-agarose, reflecting its content of O-linked oligosaccharides. Analysis of an alkaline hydrolysate of sulfate-labeled factor Va by anion-exchange chromatography showed that the sulfate occurred partly in tyrosine sulfate residues and partly in alkaline-labile linkages. Sulfate groups are potentially important structural and functional elements in factor V, and labeling with [35S]sulfate provides a useful approach for examining the biosynthesis and processing of this protein. The hypothesis is advanced that sites of sulfation in factor V and several other plasma proteins contribute to the affinity and specificity of thrombin for these molecules, just as it does for the interaction of thrombin with the potent inhibitor hirudin from leeches.
Preparation and formation mechanisms of uniform metallic particles in homogeneous solutions (2004)

As a result of its versatility and simplicity, the chemical precipitation technique remains one of the most widely used methods for the preparation of finely dispersed matter with well-controlled properties. This review deals with the synthesis of highly uniform metallic particles of simple and complex natures by precipitation in homogeneous solutions. The mechanisms of the formation of such particles and the ability to tailor their size, size distribution, morphology, internal composition, and surface properties to the requirements of specific applications are discussed.
Activities of the enzymes of the Ehrlich pathway and formation of branched-chain alcohols in Saccharomyces cerevisiae and Candida utilis grown in continuous culture on valine or ammonium as sole nitrogen source (1993)

Valine aminotransferase, a key enzyme in both biosynthesis and breakdown of branched-chain amino acids, showed consistently higher activity in Candida utilis grown in continuous culture than in Saccharomyces cerevisiae, while pyruvate decarboxylase and alcohol dehydrogenase, the other two enzymes of the Ehrlich pathway of branched-chain alcohol formation, were lower in activity. By spheroplast lysis, it was shown that valine aminotransferase followed the distribution of pyruvate decarboxylase in being located in the cytosol. Replacement of ammonium as nitrogen source by valine during conditions of carbon or nitrogen limitation caused increased specific activities of these three enzymes in S. cerevisiae, but (with one exception) decreased those of C. utilis. Of the metabolites accumulating in the culture medium, little or no ethanol or branched-chain alcohols were present during carbon-limited growth of either organism, but the change to nitrogen limitation resulted in increases in concentration of 20- to 100-fold in pyruvate, acetate and non-pyruvate keto acids as well as the accumulation of branched-chain alcohols in both organisms, and of ethanol, ethyl acetate and glycerol in S. cerevisiae. When valine was the limiting nitrogen source, there was an increase in non-pyruvate keto acids and a 10- to 16-fold increase in 2-methylpropanol. Total branched-chain alcohols formed under nitrogen limitation were 2-fold higher in S. cerevisiae than in C. utilis, irrespective of nitrogen source. Accumulation of branched-chain alcohols, ethanol, acetate and glycerol was also observed during carbon-limited growth of S. cerevisiae with valine as nitrogen source at dilution rates above the critical rate for transition to respirofermentative growth. Less than 70% of the valine carbon metabolized during growth of S. cerevisiae and only 15% of that used during growth of C. utilis was recovered in identified metabolic products. Even allowing for losses by volatilization during aeration, this suggests that a significant amount of the valine is being metabolized by a route or routes other than the Ehrlich pathway, possibly via the action of branched-chain 2-keto acid dehydrogenase. The molar growth yield for the nitrogen source under either carbon or nitrogen limitation was significantly lower for growth on valine than for growth on ammonium, suggesting that breakdown of valine requires more energy. It is evident that not all the enzymes involved in branched-chain amino acid metabolism in yeasts have yet been identified, nor are their interactions properly understood.
Homologous recombination of exogenous DNA fragments with genomic DNA in somatic cells of mice. (1991)

We compared liposomes and empty viral capsids for their use as vehicles for DNA transfer into cells and animals. DNA binding capacity was high for liposomes, but DNase I protection of DNA bound to liposomes was only moderate in comparison to DNA incorporated into viral capsids. Cellular uptake of radiolabeled and physiologically active DNA was also compared. For animal studies we chose an endogenous retroposon as target gene. To identify recombinational events we replaced a part of this gene with an artificial sequence not present in the mouse genome. The recombination rate for DNA fragments transfected in Polyoma capsids in live mice was higher than for liposome mediated transfection. Homologous recombination could be observed for both DNA transfer methods, mediated by positively charged liposomes (DOTMA) and by empty Polyoma viral capsids.
Regulation of Macrophage Chemokine Expression by Lipopolysaccharide In Vitro and In Vivo (1999)

The host response to Gram-negative LPS is characterized by an influx of inflammatory cells into host tissues, which is mediated, in part, by localized production of chemokines. The expression and function of chemokines in vivo appears to be highly selective, though the molecular mechanisms responsible are not well understood. All CXC (IFN-gamma-inducible protein (IP-10), macrophage inflammatory protein (MIP)-2, and KC) and CC (JE/monocyte chemoattractant protein (MCP)-1, MCP-5, MIP-1alpha, MIP-1beta, and RANTES) chemokine genes evaluated were sensitive to stimulation by LPS in vitro and in vivo. While IL-10 suppressed the expression of all LPS-induced chemokine genes evaluated in vitro, treatment with IFN-gamma selectively induced IP-10 and MCP-5 mRNAs, but inhibited LPS-induced MIP-2, KC, JE/MCP-1, MIP-1alpha, and MIP-1beta mRNA and/or protein. Like the response to IFN-gamma, LPS-mediated induction of IP-10 and MCP-5 was Stat1 dependent. Interestingly, only the IFN-gamma-mediated suppression of LPS-induced KC gene expression was IFN regulatory factor-2 dependent. Treatment of mice with LPS in vivo also induced high levels of chemokine mRNA in the liver and lung, with a concomitant increase in circulating protein. Hepatic expression of MIP-1alpha, MIP-1beta, RANTES, and MCP-5 mRNAs were dramatically reduced in Kupffer cell-depleted mice, while IP-10, KC, MIP-2, and MCP-1 were unaffected or enhanced. These findings indicate that selective regulation of chemokine expression in vivo may result from differential response of macrophages to pro- and antiinflammatory stimuli and to cell type-specific patterns of stimulus sensitivity. Moreover, the data suggest that individual chemokine genes are differentially regulated in response to LPS, suggesting unique roles during the sepsis cascade.
Electrocardiograms During Atrial Fibrillation: A Biophysical Model (2005)

Keywords: LTS1 Reference LTS-CONF-2005-043 Record created on 2006-06-14, modified on 2016-08-08
Object-based transparent video watermarking (2002)

We present a watermarking procedure to embed copyright protection into video sequences. To address issues associated with video motion and redundancy, individual watermarks are created for objects within the video. Each watermark is created by shaping an author and video dependent pseudo-random sequence according to the perceptual masking characteristics of the video. As a result, the watermark adapts to each video to ensure invisibility and robustness. Furthermore, the noise-like watermark is statistically undetectable. The watermark also resolves multiple ownership claims. We demonstrate the robustness of the watermarking procedure to video degradations, e.g., those that result from noise, MPEG compression, cropping, and printing and scanning.
Adhesion of Thermally Reversible Gels to Solid Surfaces (1997)

We have developed methods for quantifying very weak adhesive interactions between two bodies in contact. Our approach is based on the use of a low-modulus material in conjunction with a linear elastic fracture mechanics analysis based on the treatment of Johnson, Kendall, and Roberts (JKR.) The JKR theory can be used to describe the effects of adhesive interactions between a soft, elastomeric lens and a solid, rigid surface, under the assumption that the contact area is small relative to the size of the lens. When the ratio of the contact radius to the height of the lens becomes large, it is necessary to account for finite size corrections to the compliance and displacement of the lens. This situation has been addressed by using results from finite element analyses to modify the JKR equations so that an appropriate expression for G, the energy release rate, can be obtained. Adhesion experiments have been performed on low-modulus lenses formed by diluting a triblock copolymer, consisting of poly(methyl methacrylate) end blocks and a poly(n-butyl acrylate) midblock, with 2 ethylhexanol. Rheological studies on this swollen copolymer indicate that the material is completely elastic at room temperature and undergoes a rapid, thermally reversible gelation, thus making it an excellent model system. For this low-modulus material, the applied loads are too low to measure directly. Instead, we obtain expressions for G/E, the energy release rate normalized by Young's modulus. Comparisons to rheological data show that this analysis provides an accurate yet simple method for obtaining this information. Our approach has great potential for quantifying the adhesion of a variety of materials without the need to directly measure the applied load.
Real-Time Classification of Bladder Events for Effective Diagnosis and Treatment of Urinary Incontinence (2015)

Diagnosis of lower urinary tract dysfunction with urodynamics has historically relied on data acquired from multiple sensors using nonphysiologically fast cystometric filling. In addition, state-of-the-art neuromodulation approaches to restore bladder function could benefit from a bladder sensor for closed-loop control, but a practical sensor and automated data analysis are not available. We have developed an algorithm for real-time bladder event detection based on a single in situ sensor, making it attractive for both extended ambulatory bladder monitoring and closed-loop control of stimulation systems for diagnosis and treatment of bladder overactivity. Using bladder pressure data acquired from 14 human subjects with neurogenic bladder, we developed context-aware thresholding, a novel, parameterized, user-tunable algorithmic framework capable of real-time classification of bladder events, such as detrusor contractions, from single-sensor bladder pressure data. We compare six event detection algorithms with both single-sensor and two-sensor systems using a metric termed Conditional Stimulation Score, which ranks algorithms based on projected stimulation efficacy and efficiency. We demonstrate that adaptive methods are more robust against day-to-day variations than static thresholding, improving sensitivity and specificity without parameter modifications. Relative to other methods, context-aware thresholding is fast, robust, highly accurate, noise-tolerant, and amenable to energy-efficient hardware implementation, which is important for mapping to an implant device.
Características hidroquímicas de un acuífero kárstico sobreexplotado: el caso del Cabeçó d' Or (SE de España) (2004)

El sistema karstico del Cabeco d'Or es un pequeno acuifero sobreexplotado donde los niveles han descendido mas de 200 m entre los anos 60 y 1987. Despues de ese ano los niveles han recuperado 20 m y se han estabilizado. Las aguas de este acuifero son sulfatadas calcicas y presentan un claro caracter termal. Su mineralizacion ha sido relacionada con la presencia de rocas evaporiticas (facies Keuper rica en yesos) en profundidad. Algunos de los procesos que tienen lugar en el seno del acuifero son la disolucion de yeso, calcita, dolomita y precipitacion de calcita. Las menores concentraciones de sodio que de cloruro apuntan a procesos de intercambio ionico entre el agua con minerales de la arcilla. Estos procesos podrian estar favorecidos por la entrada de CO2. Los contenidos de carbono-13 parecen estar relacionados con la existencia de aportes de CO2 de origen profundo. Las fracturas de gran envergadura existentes en el area de estudio parecen ser las responsables del ascenso calorifico, del CO2, asi como de las elevadas concentraciones de radon y radio encontradas en estas aguas. Los contenidos de oxigeno-18 y carbono-13 han permanecido relativamente constantes, lo que manifiesta unas condiciones hidrogeologicas e hidrogeoquimicas bastante estables. La relativa estabilidad hidrogeoquimica a lo largo del tiempo se manifiesta como un indicador de que la sobreexplotacion del acuifero no ha originado cambios significativos en el deterioro de la calidad del agua. La anomalia termal del agua subterranea de este acuifero puede ser responsable de los procesos de mezcla, lo que dificulta la existencia de una zonacion hidrogeoquimica en la vertical.
Fibronectin Type III Domain Based Monobody with High Avidity (2007)

Significant efforts have been made to improve the target-binding strength of numerous affinity molecules that are widely used in biomedical research and clinical applications. While many antibody-like fragments have been successfully optimized through affinity maturation, the process is time-consuming and restricted by the stability, solubility, and expression level of the protein sequences. To generate a fibronectin type III domain (FN3) based monobody that binds to the tumor-related biomarkers with exceptional high strength and stability, we developed a multivalent strategy by fusing an alphavbeta3-binding FN3 monobody with a short COMP pentamerization domain through a linker that facilitates appropriate display of multivalent FN3 domains. The fusion protein was highly expressed in the soluble fraction of Escherichia coli and efficiently self-assembled into a pentameric molecule that could be readily purified. Compared to the monomeric form, the pentameric monobody bound to alphavbeta3 integrin much more tightly with significantly slower off-rate, while still maintaining its excellent specificity toward alphavbeta3 when tested by using purified integrins and integrin-expressing cell lines. The multivalent strategy we describe here could be applied to engineer other FN3 monobodies to acquire significantly improved targeting-binding strengths.
The endothelium in clinical practice : source and target of novel therapies (1997)

The Endothelium as the Source of Novel Therapies Prostacyclin (Prostaglandin I2) and Atherosclerosis, Karsten Schror Prostacyclin and Thromboxane: Role in Ischemic Heart Disease, Jawahar L. Mehta and Baichun C. Yang Clinical Use of Prostacyclins, John A. Dormandy and Glyn Belcher Nitric Oxide Synthases: Enzymology and Mechanism-Based Inhibitors, John F. Parkinson and Gary Phillips Endothelin: From Basic to Pathophysiological Research, Katsutoshi Goto Transmigration of Leukocytes, B. Stein, Y. Khew-Goodall, J. Gamble, and M. A. Vadas Transforming Growth Factor-b and Cardiovascular Protection, David J. Grainger and James C. Metcalfe Coagulation Factors, Michael Kalafatis, Jack O. Egan, and Kenneth G. Mann The Endothelium as a Target for Novel Therapies Endothelial Dysfunction and Vascular Disease, Paul M. Vanhoutte, Louis Perrault, and Jean Paul Vilaine Complement and Endothelium: Novel Complement-Inhibitory Therapeutics, Una S. Ryan The Receptor for Advanced Gycation Endproducts: Implications for the, Development of Diabetic Vascular Disease, Osamu Hori, Shi Du Yan, and Ann Marie Schmidt Hypertension, Pierre Moreau and Thomas F. Luscher Arterial Restenosis, Michael A. Reidy and Stephen M. Schwartz Pathobiology and Clinical Consequences of Plaque Rupture, Richard Gallo, Juan J. Badimon, James H. Chesebro, Valentin Fuster, and Lina Badimon Isoprostanes and Antioxidant Therapy in Human Diseases, Emma A. Meagher and Garrett A. FitzGerald Vasculoprotection by Estrogen Contributes to Gender Difference in Cardiovascular Diseases: Potential Mechanism and Role of Endothelium, Katalin Kauser and Gabor M. Rubanyi Lipoprotein(a): Insights from Transgenic Mice, Steven D. Hughes and Edward M. Rubin Gene Therapy Gene Therapy with Vascular Endothelial Growth Factor, Jeffrey M. Isner Vascular Disease and the Prospect of Gene Therapy, Heiko E. von der Leyen and Victor J. Dzau
Methotrexate-resistant Variants of Human Dihydrofolate Reductase with Substitutions of Leucine 22 (1995)

Although substitution of tyrosine, phenylalanine, tryptophan, or arginine for leucine 22 in human dihydrofolate reductase greatly slows hydride transfer, there is little loss in overall activity (kcat) at pH 7.65 (except for the arginine 22 variant), but Km for dihydrofolate and NADPH are increased significantly. The greatest effect, decreased binding of methotrexate to the enzyme-NADPH complex by 740- to 28,000-fold due to a large increase in the rate of methotrexate dissociation, makes these variants suitable to act as selectable markers. Affinities for four other inhibitors are also greatly decreased. Binding of methotrexate to apoenzyme is decreased much less (decreases as much as 120-fold), binding of tetrahydrofolate is decreased as much as 23-fold, and binding of dihydrofolate is decreased little or increased. Crystal structures of ternary complexes of three of the variants show that the mutations cause little perturbation of the protein backbone, of side chains of other active site residues, or of bound inhibitor. The largest structural deviations occur in the ternary complex of the arginine variant at residues 21-27 and in the orientation of the methotrexate. Tyrosine 22 and arginine 22 relieve short contacts to methotrexate and NADPH by occupying low probability conformations, but this is unnecessary for phenylalanine 22 in the piritrexim complex.
SentiMerge: Combining Sentiment Lexicons in a Bayesian Framework (2014)

Many approaches to sentiment analysis rely on a lexicon that labels words with a prior polarity. This is particularly true for languages other than English, where labelled training data is not easily available. Existing efforts to produce such lexicons exist, and to avoid duplicated effort, a principled way to combine multiple resources is required. In this paper, we introduce a Bayesian probabilistic model, which can simultaneously combine polarity scores from several data sources and estimate the quality of each source. We apply this algorithm to a set of four German sentiment lexicons, to produce the SentiMerge lexicon, which we make publically available. In a simple classification task, we show that this lexicon outperforms each of the underlying resources, as well as a majority vote model.
Uncovering the Interplay Between CD8, CD4 and Antibody Responses to Complex Pathogens (2010)

Vaccinia virus (VACV) was used as the vaccine strain to eradicate smallpox. VACV is still administered to healthcare workers or researchers who are at risk of contracting the virus, and to military personnel. Thus, VACV represents a weapon against outbreaks, both natural (e.g., monkeypox) or man-made (bioterror). This virus is also used as a vector for experimental vaccine development (cancer/infectious disease). As a prototypic poxvirus, VACV is a model system for studying host-pathogen interactions. Until recently, little was known about the targets of host immune responses, which was likely owing to VACVs large genome (>200 open reading frames). However, the last few years have witnessed an explosion of data, and VACV has quickly become a useful model to study adaptive immune responses. This review summarizes and highlights key findings based on identification of VACV antigens targeted by the immune system (CD4, CD8 and antibodies) and the complex interplay between responses.