gebhart/patrepeval huggingface dataset:
An investigation of broad coverage automatic pronoun resolution for information retrieval (2003)

Term weighting methods have been shown to give significant increases in information retrieval performance. The presence of pronomial references in documents reduces the term frequencies of associated words with a consequent effect on term weights and information retrieval behaviour. This investigation explores the impact on information retrieval performance of broad coverage automatic pronoun resolution. Results indicate that this approach has potential to improve both precision at fixed cutoff levels and average precision.
Adiponectin Stimulates Angiogenesis by Promoting Cross-talk between AMP-activated Protein Kinase and Akt Signaling in Endothelial Cells (2004)

Adiponectin is an adipocyte-specific adipocytokine with anti-atherogenic and anti-diabetic properties. Here, we investigated whether adiponectin regulates angiogenic processes in vitro and in vivo. Adiponectin stimulated the differentiation of human umbilical vein endothelium cells (HUVECs) into capillary-like structures in vitro and functioned as a chemoattractant in migration assays. Adiponectin promoted the phosphorylation of AMP-activated protein kinase (AMPK), protein kinase Akt/protein kinase B, and endothelial nitric oxide synthesis (eNOS) in HUVECs. Transduction with either dominant-negative AMPK or dominant-negative Akt abolished adiponectin-induced eNOS phosphorylation as well as adiponectin-stimulated HUVEC migration and differentiation. Dominant-negative AMPK also inhibited adiponectin-induced Akt phosphorylation, suggesting that AMPK is upstream of Akt. Dominant-negative Akt or the phosphatidylinositol 3-kinase inhibitor LY294002 blocked adiponectin-stimulated Akt and eNOS phosphorylation, migration, and differentiation without altering AMPK phosphorylation. Finally, adiponectin stimulated blood vessel growth in vivo in mouse Matrigel plug implantation and rabbit corneal models of angiogenesis. These data indicate that adiponectin can function to stimulate the new blood vessel growth by promoting cross-talk between AMP-activated protein kinase and Akt signaling within endothelial cells.
A High‐Throughput Investigation of the Role of pH, Temperature, Concentration, and Time on the Synthesis of Hybrid Inorganic–Organic Materials (2005)

Four reaction parameters and their effects on the formation of cobalt succinate phases were studied by high-throughput methods. In addition to identifying two new phases, we show that higher reaction temperatures lead to products containing less water, more basic conditions favor increasingly condensed M-O-M networks (see phase diagram), and depending on the reaction time the products are formed under either kinetic or thermodynamic control.
Delta Flow: An Accurate, Reliable System for Detecting Kicks and Loss of Circulation During Drilling (1987)

Summary A system to monitor drilling-fluid flow rate has been developed that detects kicks and lost returns in floating, fixed-platform, and land-based drilling operations. The system uses flowmeters that monitor the flow rates of drilling fluids entering the borehole through the standpipe and leaving the well through the return flowline. These readings are processed in a computer-based, data-acquisition system to form a filtered delta-flow signal that identifies the occurrence of downhole fluid gains or losses. The system is designed to trip an alarm when a gain or loss exceeds 25 gal/min [1.6 dm3/s], even in a floating drilling environment. This sensitivity will generally keep gains or losses to less than 5 bbl [0.8 m3].
Microbial transformation of trichothecene mycotoxins (2008)

Trichothecene mycotoxins produced by the Fusarium genus are highly toxic to humans and animals. They are commonly found in cereals worldwide, which is not only a concern for food safety, but also highly relevant to the livestock industry. Controlling trichothecenes in food and feed has been a challenge since the toxins are markedly stable under different environmental conditions. Thermal processing is usually ineffective, and chemical treatments generally are expensive and often result in side effects. Previous studies on innovative biological approaches, such as the use of microorganisms and enzymes, to convert the toxins into non or less toxic compounds have shown promise. This review will briefly describe the chemical structures and toxicity of trichothecenes, and examine the microorganisms, including both bacteria and fungi, from various natural sources that are able to detoxify the toxins as either mixed cultures or a pure culture of single isolates. Finally, challenges and innovative strategies in the development of technology to detoxify trichothecenes by microorganisms are described.
Characterization of pp60c-src Tyrosine Kinase Activities Using a Continuous Assay: Autoactivation of the Enzyme Is an Intermolecular Autophosphorylation Process (1995)

A continuous assay for pp60c-src tyrosine kinase (srcTK) was developed. A lag in phosphorylation of the peptide RRLIEDAEYAARG was observed that could be eliminated by preincubation with MgATP. The induction time for this lag was dependent upon MgATP and srcTK concentrations. When autophosphorylation was monitored by 32P incorporation from [gamma-32P]ATP, a lag in the time course was also observed. These results demonstrate that autoactivation is an intermolecular process. The electrospray ionization mass spectrum of the enzyme before and after activation demonstrated an increase in the phosphorylation state of the enzyme after incubation with MgATP. The delta 85-N-terminal mutant protein and a full-length G2A pp60c-src mutant, which removes the myristylation site, used in these studies were partially phosphorylated on Y338 and Y530 as isolated. This is the first report of phosphorylation on Y338, but the significance of this site of phosphorylation is unknown. These phosphorylations were insufficient to active the enzyme for transfer of the gamma-phosphoryl of MgATP to the peptides. The unphosphorylated enzyme initially present was converted to a monophosphorylated species upon treatment with MgATP. Y-419 phosphorylation was evident only after treatment with MgATP. These data are consistent with autophosphorylation on Y-419 as predicted. Intermolecular autophosphorylation is consistent with the ability of srcTK to dimerize, which is analogous to activation of receptor tyrosine kinases such as the EGF receptor kinase in response to growth factors. These results indicate that dimerization leading to activation does not require binding to the membrane or a hydrophobic N-terminus in the case of srcTK.
Computer simulations of Brownian motion of complex systems (1995)

Care is needed with algorithms for computer simulations of the Brownian motion of complex systems, such as colloidal and macromolecular systems which have internal degrees of freedom describing changes in configuration. Problems can arise when the diffusivity or the inertia changes with the configuration of the system. There are some problems in replacing very stiff bonds by rigid constraints. These problems and their resolution are illustrated by some artificial models; firstly in one dimension, then in the neighbourhood of an ellipse in two dimensions and finally for the trimer polymer molecule.
Role of the Cytoplasmic Tail Domains of Bunyamwera Orthobunyavirus Glycoproteins Gn and Gc in Virus Assembly and Morphogenesis (2007)

The M RNA genome segment of Bunyamwera virus (BUNV), the prototype of the Bunyaviridae family, encodes a precursor polyprotein that is proteolytically cleaved to yield two structural proteins, Gn and Gc, and a nonstructural protein called NSm. Gn and Gc are type I integral transmembrane glycoproteins. The Gn protein contains a predicted cytoplasmic tail (CT) of 78 residues, and Gc has a shorter CT of 25 residues. Little is known about the role of the Gn and Gc CT domains in the virus replication cycle. We generated a series of mutant glycoprotein precursor constructs containing either deletions or alanine substitutions in the CT domains of Gn and Gc. We examined the effects of these mutations on glycoprotein maturation, cell surface expression, and low pH-induced syncytium formation. In addition, the effects of these mutations were also assessed using a reverse genetics-based virus assembly assay and a virus rescue system. Our results show that the CT domains of both Gn and Gc play crucial roles in BUNV-mediated membrane fusion, virus assembly, and morphogenesis.
Isolation of a Liver-Specific Promoter for Human Growth Hormone Receptor Gene (1997)

The biological actions of growth hormone (GH) are mediated through the growth hormone receptor (GHR). The GHR gene is expressed in a tissue specific manner and multiple variants (VI to V8) of GHR mRNA have been detected in human tissues. To understand the regulation of GHR gene expression, a human genomic clone containing the 5'-untranslated region (5'UTR) of the V1, V4, V7 and V8 exons of the GHR was isolated. The 2 kilobase (kb) 5' upstream sequence of the V1 specific UTR has promoter activity in transient transfection assays of the human hepatoma cell line, HepG2. The exclusive expression of the V1 variant in adult liver, and the lack of expression of the other variants in this tissue, suggests that the V1 5'UTR represents the liver specific 5' noncoding exon for the human GHR gene. The data are consistent with the first isolation of a liver specific promoter for human GHR.
The redox requirements of proliferating mammalian cells (2018)

Cell growth and division require nutrients, and proliferating cells use a variety of sources to acquire the amino acids, lipids, and nucleotides that support macromolecule synthesis. Lipids are more reduced than other nutrients, whereas nucleotides and amino acids are typically more oxidized. Cells must therefore generate reducing and oxidizing (redox) equivalents to convert consumed nutrients into biosynthetic precursors. To that end, redox cofactor metabolism plays a central role in meeting cellular redox requirements. In this Minireview, we highlight the biosynthetic pathways that involve redox reactions and discuss their integration with metabolism in proliferating mammalian cells.
Product-Related Impurities in Clinical-Grade Recombinant AAV Vectors: Characterization and Risk Assessment (2014)

Adeno-associated virus (AAV)-based vectors expressing therapeutic genes continue to demonstrate great promise for the treatment of a wide variety of diseases and together with other gene transfer vectors represent an emerging new therapeutic paradigm comparable in potential impact on human health to that achieved by recombinant proteins and vaccines. A challenge for the current pipeline of AAV-based investigational products as they advance through clinical development is the identification, characterization and lot-to-lot control of the process- and product-related impurities present in even highly purified preparations. Especially challenging are AAV vector product-related impurities that closely resemble the vector itself and are, in some cases, without clear precedent in established biotherapeutic products. The determination of acceptable levels of these impurities in vectors prepared for human clinical product development, with the goal of new product licensure, requires careful risk and feasibility assessment. This review focuses primarily on the AAV product-related impurities that have been described in vectors prepared for clinical development.
Neuronal nitric oxide synthase and dystrophin-deficient muscular dystrophy. (1996)

Neuronal nitric oxide synthase (nNOS) in fast-twitch skeletal muscle fibers is primarily particulate in contrast to its greater solubility in brain. Immunohistochemistry shows nNOS localized to the sarcolemma, with enrichment at force transmitting sites, the myotendinous junctions, and costameres. Because this distribution is similar to dystrophin, we determined if nNOS expression was affected by the loss of dystrophin. Significant nNOS immunoreactivity and enzyme activity was absent in skeletal muscle tissues from patients with Duchenne muscular dystrophy. Similarly, in dystrophin-deficient skeletal muscles from mdx mice both soluble and particulate nNOS was greatly reduced compared with C57 control mice. nNOS mRNA was also reduced in mdx muscle in contrast to mRNA levels for a dystrophin binding protein, alpha 1-syntrophin. nNOS levels increased dramatically from 2 to 52 weeks of age in C57 skeletal muscle, which may indicate a physiological role for NO in aging-related processes. Biochemical purification readily dissociates nNOS from the dystrophin-glycoprotein complex. Thus, nNOS is not an integral component of the dystrophin-glycoprotein complex and is not simply another dystrophin-associated protein since the expression of both nNOS mRNA and protein is affected by dystrophin expression.
PATRIC: The VBI PathoSystems Resource Integration Center (2006)

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: 'breadth first' beginning with whole-genome and proteome curation using standardized protocols, a 'targeted' approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website (https://patric.vbi.vt.edu) will continually grow with the addition of data, analysis and functionality over the course of the project.
Optimization of Escherichia coli growth by controlled addition of glucose (1989)

During aerobic growth of Escherichia coli (recombinant K-12 and strain B) on protein hydrolysate (L-broth) and a carbon source (glucose), acetic acid is produced via glucose metabolism until the late log phase. At this point, the culture pH starts to increase and the growth rate decreases. In cultures without further glucose supplementation, these changes are associated with the accumulation of ammonia, the utilization of acetic acid, the depletion of amino acids, and the complete depletion of glucose. We hypothesize that, after depletion of the glucose, the bacteria catabolize amino acids for energy and carbon and give off the nitrogen as ammonia. Also contributing to the overall increase in pH is the depletion of the acetic acid produced earlier as it is metabolized upon exhaustion of glucose. However, there is a lag time of about 1 hour after the initial pH increase before the sustained accumulation of ammonia begins. This lag indicates that an unidentified factor, in addition to the increase in ammonia, contributes to the increase in pH. Advantage was taken of the turnaround from acid production to base production as reflected in the culture pH to implement the addition of glucose. In growth experiments during which the pH was controlled in the basic direction by glucose addition, the observed decrease in growth rate was significantly postponed and the pH change in the basic direction was reversed as a result of acid production by the cells from the newly added glucose. Furthermore, coll densities of twice that obtained without glucose feeding were demonstrated. Based on the media cost per unit cell density, the data indicate a 31% cost savings.
Variable-rate trellis source encoding (1999)

The fixed slope lossy algorithm derived from the kth-order adaptive arithmetic codeword length function is extended to finite-state decoders or trellis-structured decoders. When this algorithm is used to encode a stationary, ergodic source with a continuous alphabet, the Lagrangian performance converges with probability one to a quantity computable as the infimum of an information-theoretic functional over a set of auxiliary random variables and reproduction levels, where /spl lambda/>0 and -/spl lambda/ are designated to be the slope of the rate distortion function R(D) of the source at some D; the quantity is close to R(D)+/spl lambda/D when the order k used in the arithmetic coding or the number of states in the decoders is large enough, An alternating minimization algorithm for computing the quantity is presented; this algorithm is based on a training sequence and in turn gives rise to a design algorithm for variable-rate trellis source codes. The resulting variable-rate trellis source codes are very efficient in low-rate regions. With k=8, the mean-squared error encoding performance at the rate 1/2 bits/sample for memoryless Gaussian sources is comparable to that afforded by trellis-coded quantizers; with k=8 and the number of states in the decoder=32, the mean-squared error encoding performance at the rate 1/2 bits/sample for memoryless Laplacian sources is about 1 dB better than that afforded by the trellis-coded quantizers with 256 states, with k=8 and the number of states in the decoder=256, the mean-squared error encoding performance at the rates of a fraction of 1 bit/sample for highly dependent Gauss-Markov sources with correlation coefficient 0.9 is within about 0.6 dB of the distortion rate function.
Immunocytochemical localization of urokinase-type plasminogen activator in Lewis lung carcinoma. (1984)

The invasively growing and metastasizing Lewis lung carcinoma consistently contained urokinase-type plasminogen activator (u-PA) enzyme activity. When investigated immunocytochemically with antibodies against u-PA, different parts of individual tumors showed a pronounced heterogeneity in staining intensity. Strong staining was found in areas with invasive growth and degradation of surrounding normal tissue, while other areas were completely devoid of staining. Immunoreactivity occurred both with a perinuclear cytoplasmic localization in tumor cells and associated with apparently extracellular material. SDS PAGE of tumor extracts, under both reducing and nonreducing conditions, followed by immunoblotting, showed only one immunocytochemically stainable band with an electrophoretic mobility corresponding to that of purified proenzyme to u-PA, while no two-chain u-PA was detected. This indicates that the major part of the activator in Lewis lung carcinoma is present as one-chain pro-u-PA.
Beiträge zur Kenntnis der amerikanischen Passifloraceen. I (1923)

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Identification of the Region within the Neuroendocrine Polypeptide 7B2 Responsible for the Inhibition of Prohormone Convertase PC2 (1995)

The highly conserved polypeptide 7B2 and the subtilisin-related prohormone convertases PC1/PC3 and PC2 are broadly distributed in neurons and endocrine cells and are localized to secretory granules. We recently showed that recombinant 7B2 is in vitro a potent inhibitor of PC2 activity, but not of PC1/PC3, and that newly synthesized 7B2 is transiently associated with proPC2 in vivo. In the present study, in vitro mutagenesis was used to identify the region within the 7B2 sequence responsible for the inhibition of PC2. Mutant proteins were produced in a prokaryotic expression system and their effects on PC1/PC3 and PC2 activities were studied by two different in vitro enzyme assays. None of the 7B2 mutant proteins inhibited PC1/PC3 activity. Truncation studies revealed that a short segment within the COOH-terminal portion of 7B2 is critical for its inhibitory effect on PC2. This segment contains a pair of basic amino acid residues which may represent a recognition motif for PC2. Single amino acid substitutions within this Lys171-Lys172 site strongly diminished and a double mutation abolished the inhibitory potency of 7B2. Our results indicate that, although amino acid residues directly surrounding this dibasic pair also contribute to PC2 inhibition, the Lys171-Lys172 site is particularly important for the ability of 7B2 to inhibit PC2.
HIGHWAY MAINTENANCE AND INTEGRATED MANAGEMENT SYSTEMS (1993)

Maintenance management systems were among the first applications of rational management principles and the then-new technology of computers to highway operations. Recent changes in the composition and funding of highway programs, the organizational structures and missions of highway agencies, and federal legislation governing the development and use of management systems have focused increased attention on the design and use of such systems, as well as how to integrate maintenance management with other departmental management functions. The conceptual design of an idealized maintenance management system, the integration of this system with other management systems, and potential applications of new management capabilities and technology within these next-generation systems are described.
Histamine H2-receptor agonists. Synthesis, in vitro pharmacology, and qualitative structure-activity relationships of substituted 4- and 5-(2-aminoethyl)thiazoles (1992)

It is well known that both histamine and dimaprit show moderate histamine H2-receptor agonistic activities on the guinea pig right atrium. Quantum chemical calculations on these two compounds showed similarities in electron distributions and molecular electrostatic potentials (MEP's), which could be extended to rigid analogues [2-amino-5-(2-aminoethyl)thiazoles] of the latter structure. On the base of these results a series of substituted 4- and 5-(2-aminoethyl)thiazoles was synthesized applying small alkyl substitution variations as reported for histamine. 2-Amino-5-(2-aminoethyl)-4-methylthiazole (Amthamine) proved to be the most potent full histamine H2-receptor agonist on the guinea pig right atrium, being with a pD2 value of 6.21 slightly more potent than histamine. This compound shows no affinity for H1-receptors and is a full but weak agonist on the histamine H3-receptor with a pD2 value of 4.70, thus showing a marked specificity for histamine H2-receptors. In the 5-(2-aminoethyl)thiazole series the presence of a 2-amino substituent proved to be not essential for stimulation of the histamine H2-receptor, leading to the important conclusion that in contrast to histamine, for this series, acceptance of a proton by the thiazole nucleus of the agonist from the active site of the receptor is sufficient for the stimulation of the histamine H2-receptor.