gebhart/patrepeval huggingface dataset:
A Glycine-rich RNA-binding Protein Mediating Cold-inducible Suppression of Mammalian Cell Growth (1997)

In response to low ambient temperature, mammalian cells as well as microorganisms change various physiological functions, but the molecular mechanisms underlying these adaptations are just beginning to be understood. We report here the isolation of a mouse cold-inducible RNA-binding protein (cirp) cDNA and investigation of its role in cold-stress response of mammalian cells. The cirp cDNA encoded an 18-kD protein consisting of an amino-terminal RNAbinding domain and a carboxyl-terminal glycine-rich domain and exhibited structural similarity to a class of stress-induced RNA-binding proteins found in plants. Immunofluorescence microscopy showed that CIRP was localized in the nucleoplasm of BALB/3T3 mouse fibroblasts. When the culture temperature was lowered from 37 to 32 degrees C, expression of CIRP was induced and growth of BALB/3T3 cells was impaired as compared with that at 37 degrees C. By suppressing the induction of CIRP with antisense oligodeoxynucleotides, this impairment was alleviated, while overexpression of CIRP resulted in impaired growth at 37 degrees C with prolongation of G1 phase of the cell cycle. These results indicate that CIRP plays an essential role in cold-induced growth suppression of mouse fibroblasts. Identification of CIRP may provide a clue to the regulatory mechanisms of cold responses in mammalian cells.
Design of Bilateral Teleoperators for Soft Environments with Adaptive Environmental Impedance Estimation (2006)

This paper studies the problem of improving the fidelity of bilateral teleoperators under the stability constraint. First, a new fidelity measure for teleoperators is proposed. Then the teleoperator design problem is formulated as the optimization problem of maximizing the proposed fidelity measure under the stability constraint. The robust stability theory for unstructured uncertainty is applied to analyze the stability of bilateral teleoperators. Third, a new scheme to estimate adaptively the environmental impedance is developed to improve the fidelity of the systems. Finally, a case study is presented to validate the introduced approach.
The Scientific Rediscovery of an Ancient Chinese Herbal Medicine: Cordyceps sinensis Part I (1998)

This review presents Cordyceps sinensis (Berk.) Sacc., a fungus highly valued in China as a tonic food and herbal medicine. The extant records show the continued use of C. sinensis is now centuries old. The major chemical, pharmacological, and toxicological studies on C. sinensis and the various derived, cultured, fermented mycelial products currently in use are reviewed from the English and Chinese literature. Preclinical in vitro and in vivo studies and clinical blinded or open-label trials in to date over 2000 patients are reviewed. These studies show the main activities of the fungus in oxygen-free radical scavenging, antisenescence, endocrine, hypolipidemic, antiatherosclerotic, and sexual function-restorative activities. The safety of the fungus, its effects on the nervous system, glucose metabolism, the respiratory, hepatic, cardiovascular, and immune systems, immunologic disease, inflammatory conditions, cancer, and diseases of the kidney will be reviewed in the second part of this article to be published in the winter issue of this journal.
Lack of correlation of hypoxic cell fraction and angiogenesis with glucose metabolic rate in non-small cell lung cancer assessed by 18F-Fluoromisonidazole and 18F-FDG PET. (2006)

The hypoxic cell fraction of primary NSCLC is consistently low, and there is no significant correlation in NSCLC between hypoxia and glucose metabolism in NSCLC assessed by (18)F-FDG. These findings have direct implications in understanding the role of angiogenesis and hypoxia in NSCLC biology.
Prevalence of mycoplasmal and ureaplasmal recovery from tracheobronchial lavages and of mycoplasmal recovery from pharyngeal swab specimens in cats with or without pulmonary disease. (1993)

The prevalence of mycoplasmal and ureaplasmal recovery from tracheobronchial lavage specimens and prevalence of mycoplasmal recovery from pharyngeal swab specimens from cats with (28) or without (18) pulmonary disease were determined. Mycoplasmas were recovered from tracheobronchial lavage specimens in 21% of cats with pulmonary disease, but in no cats without pulmonary disease; this difference is significant (P = 0.04). Mycoplasmal recovery from tracheobronchial lavage specimens was not significantly associated with concurrent Pasteurella spp isolation, septic inflammation, or bronchitis. Ureaplasmas were only isolated from a tracheobronchial lavage specimen in 1 cat with pulmonary disease and in no cats without pulmonary disease. Similar mycoplasmal recovery rates were found for pharyngeal swab specimens from cats with (39%) or without (35%) pulmonary disease. Seemingly, mycoplasmas are part of the normal pharyngeal flora in approximately a third of the feline population, but mycoplasmas are not normal inhabitants of the lower respiratory tract in cats. It is unknown whether mycoplasmas isolated from tracheobronchial lavage specimens in cats with pulmonary disease are primary pathogens or opportunistic invaders. Seemingly, ureaplasmas are seldom associated with pulmonary disease in cats, and are not normal inhabitants of the trachea and bronchi of cats.
Reining in the outliers in map-reduce clusters using Mantri (2010)

Experience froman operational Map-Reduce cluster reveals that outliers significantly prolong job completion. The causes for outliers include run-time contention for processor, memory and other resources, disk failures, varying bandwidth and congestion along network paths and, imbalance in task workload. We present Mantri, a system that monitors tasks and culls outliers using cause- and resource-aware techniques. Mantri's strategies include restarting outliers, network-aware placement of tasks and protecting outputs of valuable tasks. Using real-time progress reports, Mantri detects and acts on outliers early in their lifetime. Early action frees up resources that can be used by subsequent tasks and expedites the job overall. Acting based on the causes and the resource and opportunity cost of actions lets Mantri improve over prior work that only duplicates the laggards. Deployment in Bing's production clusters and trace-driven simulations show that Mantri improves job completion times by 32%.
Tools for Evaluating Native Grasses as Low Maintenance Turf (2009)

Visual ratings are the standard for evaluating turfgrass quality. However, to provide more objective evaluations and to address statistical concerns, other methods have been developed to measure turfgrass quality, including digital image analysis and measurements of chlorophyll content. These have been largely applied to traditionally used turfgrass species, but here we used these methods to evaluate turfgrass quality of nontraditional species and mixtures that are native or adapted to the intermountain west region of North America. Two fertilizer treatments (1.0 or 2.0 lb/1000 ft 2 nitrogen) were applied to 21 different species and species mixtures in North Logan, UT. These plots were irrigated to replace 60% of the local evapotranspiration rate and were mowed at 4 inches. Turfgrass quality ratings were most effective in measuring quality among the diverse species used in this study. Because of the wider variation in acceptable visual characteristics and lower quality expectations for low-maintenance native turf, the objective evaluation methods proved less useful. Generally, chlorophyll meter data, digital image analysis of cover, and digital image analysis of color data were not well correlated with human visual quality ratings in this study. Measurements were well correlated in some species, but not in others. These methods can supplement, but cannot replace, human visual turfgrass quality ratings for comparison of dissimilar grasses.
REVIEW ■ : Nitric Oxide: Actions and Pathological Roles (1995)

Nitric oxide is a unique biological messenger molecule. It mediates, in part, the immune functions of mac rophages ; it is produced by endothelial cells to mediate blood vessel relaxation; and it also serves as a neurotransmitter in the central and peripheral nervous system. Endothelial nitric oxide synthase and neuronal nitric oxide synthase are thought to be primarily constitutive, with activation induced by calcium entry into cells in the absence of protein synthesis, whereas the macrophage nitric oxide synthase is inducible with large increases in new nitric oxide synthase protein synthesis after immune stimulation. The molecular targets of nitric oxide are expanding, as are its physiological and pathophysiological roles in the nervous system. Nitric oxide may regulate neurotransmitter release, and it may play a key role in nervous system morpho genesis and synaptic plasticity and regulate gene expression. Under conditions of excessive formation, nitric oxide is emerging as an important neurotoxin in a variety of disorders of the nervous system. The Neuro scientist 1:7-18, 1995
The Reconstruction Toolkit (RTK), an open-source cone-beam CT reconstruction toolkit based on the Insight Toolkit (ITK) (2014)

We propose the Reconstruction Toolkit (RTK, http://www.openrtk.org), an open-source toolkit for fast cone-beam CT reconstruction, based on the Insight Toolkit (ITK) and using GPU code extracted from Plastimatch. RTK is developed by an open consortium (see affiliations) under the non-contaminating Apache 2.0 license. The quality of the platform is daily checked with regression tests in partnership with Kitware, the company supporting ITK. Several features are already available: Elekta, Varian and IBA inputs, multi-threaded Feldkamp-David-Kress reconstruction on CPU and GPU, Parker short scan weighting, multi-threaded CPU and GPU forward projectors, etc. Each feature is either accessible through command line tools or C++ classes that can be included in independent software. A MIDAS community has been opened to share CatPhan datasets of several vendors (Elekta, Varian and IBA). RTK will be used in the upcoming cone-beam CT scanner developed by IBA for proton therapy rooms. Many features are under development: new input format support, iterative reconstruction, hybrid Monte Carlo / deterministic CBCT simulation, etc. RTK has been built to freely share tomographic reconstruction developments between researchers and is open for new contributions.
Drug‐conjugated antibodies for the treatment of cancer (2012)

Despite considerable effort, application of monoclonal antibody technology has had only modest success in improving treatment outcomes in patients with solid tumours. Enhancing the cancer cell-killing activity of antibodies through conjugation to highly potent cytotoxic 'payloads' to create antibody-drug conjuates (ADCs) offers a strategy for developing anti-cancer drugs of great promise. Early ADCs exhibited side-effect profiles similar to those of 'classical' chemotherapeutic agents and their performance in clinical trials in cancer patients was generally poor. However, the recent clinical development of ADCs that have highly potent tubulin-acting agents as their payloads have profoundly changed the outlook for ADC technology. Twenty-five such ADCs are in clinical development and one, brentuximab vedotin, was approved by the FDA in August, 2011, for the treatment of patients with Hodgkin's lymphoma and patients with anaplastic large cell lymphoma, based on a high rate of durable responses in single arm phase II clinical trials. More recently, a second ADC, trastuzumab emtansine, has shown excellent anti-tumour activity with the presentation of results of a 991-patient randomized phase III trial in patients with HER2-positive metastatic breast cancer. Treatment with this ADC (single agent) resulted in a significantly improved progression-free survival of 9.6 months compared with 6.4 months for lapatinib plus capecitabine in the comparator arm and significantly prolonged overall survival. Besides demonstrating excellent efficacy, these ADCs were remarkably well tolerated. Thus these, and other ADCs in development, promise to achieve the long sought goal of ADC technology, that is, of having compounds with high anti-tumour activity at doses where adverse effects are generally mild.
Metabolic Engineering of Glycerol Production inSaccharomyces cerevisiae (2002)

Inactivation of TPI1, the Saccharomyces cerevisiae structural gene encoding triose phosphate isomerase, completely eliminates growth on glucose as the sole carbon source. In tpi1-null mutants, intracellular accumulation of dihydroxyacetone phosphate might be prevented if the cytosolic NADH generated in glycolysis by glyceraldehyde-3-phosphate dehydrogenase were quantitatively used to reduce dihydroxyacetone phosphate to glycerol. We hypothesize that the growth defect of tpi1-null mutants is caused by mitochondrial reoxidation of cytosolic NADH, thus rendering it unavailable for dihydroxyacetone-phosphate reduction. To test this hypothesis, a tpi1delta nde1delta nde2delta gut2delta quadruple mutant was constructed. NDE1 and NDE2 encode isoenzymes of mitochondrial external NADH dehydrogenase; GUT2 encodes a key enzyme of the glycerol-3-phosphate shuttle. It has recently been demonstrated that these two systems are primarily responsible for mitochondrial oxidation of cytosolic NADH in S. cerevisiae. Consistent with the hypothesis, the quadruple mutant grew on glucose as the sole carbon source. The growth on glucose, which was accompanied by glycerol production, was inhibited at high-glucose concentrations. This inhibition was attributed to glucose repression of respiratory enzymes as, in the quadruple mutant, respiratory pyruvate dissimilation is essential for ATP synthesis and growth. Serial transfer of the quadruple mutant on high-glucose media yielded a spontaneous mutant with much higher specific growth rates in high-glucose media (up to 0.10 h(-1) at 100 g of glucose. liter(-1)). In aerated batch cultures grown on 400 g of glucose. liter(-1), this engineered S. cerevisiae strain produced over 200 g of glycerol. liter(-1), corresponding to a molar yield of glycerol on glucose close to unity.
Inhibitory Specificity of the Anti-inflammatory Myxoma Virus Serpin, SERP-1 (1998)

SERP-1 is a myxoma virus-encoded serpin, secreted from infected cells, that is required for virulence and has anti-inflammatory activity. We report that purified recombinant SERP-1 forms SDS-stable complexes with urokinase-type plasminogen activator (uPA), tissue-type plasminogen activator (tPA), plasmin, thrombin, and factor Xa. N-terminal sequencing confirmed Arg319-Asn320 as the site of reaction. Mutation of these residues to Ala-Ala abolished inhibitory activity but had no effect on the specific cleavage at Thr315-Leu316 seen with elastase and with cathepsin G. Kinetic analysis of the reactions with uPA, tPA, plasmin, thrombin, Xa, and C1s showed second-order rate constants to vary over 3 logs, from kinh = 3 x 10(5) M-1 s-1 with thrombin to approximately 600 M-1 s-1 with C1s, while steady-state inhibition constants ranged from KI = 10 pM with thrombin to approximately 100 nM with C1s. Stoichiometries of inhibition varied between SI = 1.4 +/- 0.1 for uPA to SI = 13 +/- 3 for thrombin. Analysis of the variations in inhibition kinetics shows that when serpins act at low concentrations, comparable with the target protease or with KI (as appears likely for SERP-1 in vivo), inhibitory specificity becomes less dominated by kinh and is increasingly dependent on partitioning within the branched reaction mechanism and on the lifetime of the inhibited complex.
Molecular cloning ofPhaseolus vulgarislectin mRNA and use of cDNA as a probe to estimate lectin transcript levels in various tissues (1982)

The complete amino acid sequence of a Phaseolus vulgaris cv. Tendergreen lectin was deduced from the nucleotide sequence of a cDNA plasmid. The lectin appears to be synthesized as a prepeptide consisting of a signal sequence of at least 20 residues and a mature protein of 223 amino acids. The 5' region of the lectin cDNA contains four AUG codons, one of which may initiate a 58 amino acid peptide out of phase with lectin translation. Lectin transcripts 1.1 kb long begin accumulating in cotyledons by the 9 mm stage, increasing in amount until about the 16 mm stage, after which their levels dramatically decrease. In addition, larger lectin-specific transcripts are detected in mid-maturation phase cotyledons. A 1.1 kb RNA species in leaves from plants filling their pods hybridizes with lectin cDNA, but no hybridizing RNA is found in primary leaves or roots.
High-performance heat sinking for VLSI (1981)

The problem of achieving compact, high-performance forced liquid cooling of planar integrated circuits has been investigated. The convective heat-transfer coefficient h between the substrate and the coolant was found to be the primary impediment to achieving low thermal resistance. For laminar flow in confined channels, h scales inversely with channel width, making microscopic channels desirable. The coolant viscosity determines the minimum practical channel width. The use of high-aspect ratio channels to increase surface area will, to an extent, further reduce thermal resistance. Based on these considerations, a new, very compact, water-cooled integral heat sink for silicon integrated circuits has been designed and tested. At a power density of 790 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , a maximum substrate temperature rise of 71°C above the input water temperature was measured, in good agreement with theory. By allowing such high power densities, the heat sink may greatly enhance the feasibility of ultrahigh-speed VLSI circuits.
Identification of a granulocytotropic Ehrlichia species as the etiologic agent of human disease (1994)

Six patients from northern Minnesota and Wisconsin with a febrile illness accompanied by granulocytic cytoplasmic morulae suggestive of ehrlichial infection were identified. Two patients died, and splenic granulocytes of one patient contained cytoplasmic vacuoles with organisms ultrastructurally characteristic of ehrlichiae. From one patient, a 1.5-kb DNA product was amplified by PCR with universal eubacterial primers of 16S rDNA. Analysis of the nucleotide sequence of the amplified product revealed 99.9 and 99.8% similarities with E. phagocytophila and E. equi, respectively, neither of which has previously been known to infect humans. From the variable regions of the determined sequence, a forward primer specific for three organisms (human granulocytic ehrlichia, E. phagocytophila, and E. equi) and a reverse primer for these ehrlichiae and E. platys were designed. By nested PCR with amplification by the universal primers and then reamplification with the specific primers described above, the expected 919-bp product was generated from the blood of the index patient and three additional patients. Blood from these four patients and two more patients with granulocytic morulae contained DNA which was amplified by nested PCR involving a combination of a universal primer and the human granulocytic ehrlichia-E. phagocytophila-E. equi-E. platys group-specific primer. This apparently vector-borne human granulocytic ehrlichia has only 92.5% 16S rDNA homology with E. chaffeensis. Nested PCR with group-specific primers did not amplify E. chaffeensis DNA, and E. chaffeensis-specific primers did not amplify DNAs of the human granulocytic ehrlichia. Thus, six patients were shown to be infected by an Ehrlichia species never previously reported to infect humans.
The Effect of Recombinant Stem Cell Factor (SCF) on Purified CD34-Positive Human Umbilical Cord Blood Progenitor Cells (1992)

We describe the effect of soluble c-kit ligand (stem cell factor, SCF) on highly purified CD34-positive hemopoietic progenitors from human umbilical cord blood. Progenitor cells were purified from cord blood mononuclear cells by immune rosetting with lineage specific antibodies and subsequent sorting of the rosette-negative population for CD34(BI3C5)-positive cells. This procedure enriched greater than 100-fold for colony forming cells (CFC). Using optimal concentrations of colony-stimulating factors (CSF) without added SCF approximately 2.5% of cells formed colonies. SCF also had CSF activity on this population, up to 0.5% of cells forming small colonies in response to SCF alone. In contrast, the addition of SCF to optimal concentrations of the other growth factors produced a greater than 10-fold increase in colony number. However, the most notable effect was an approximately 100-fold increase in the number of cells in each colony. Equally striking was the very high proportion (50-80%) of mixed colonies (CFU-MIX). These findings suggest the progenitor cell pool in cord blood is skewed towards very early cells. However, when day 14 colonies formed in response to SCF and other factors were assessed for their re-cloning potential they did not contain significant numbers of CFC, implying that SCF did not support the self-renewal of these CD34 positive cord blood progenitor cells. These findings support a role for SCF as an enhancing factor for hemopoietic progenitor cells but it does not promote self-renewal in these populations.
Cloning and expression of human erythropoietin cDNA in Escherichia coli. (1984)

Human erythropoietin (Ep) cDNA has been cloned in Escherichia coli by using pBR322 as a vector. Polyadenylylated RNA was isolated from selected human renal carcinomas with elevated Ep titers. The presence of Ep mRNA was detected by immunoprecipitation of in vitro translation products with monoclonal antibody to human Ep. Double-stranded cDNA was synthesized and inserted into the Pst I site of pBR322 by homopolymeric dG . dC tailing. The cDNA library was initially screened by colony hybridization with 32P-labeled cDNA synthesized from size-fractionated mRNA enriched in Ep message. Positive colonies were further screened immunologically by in situ radioimmunoassay with monoclonal antibody to human Ep. Three positive clones were identified that express the Ep gene sequences as a beta-lactamase fusion protein. These clones contain inserts of approximately 1400, 600, and 200 base pairs. Human renal Ep mRNA, of which the translation products immunoreact with anti-Ep on immunoblots, was hybrid-selected by plasmid DNA from these recombinants. Purified human Ep competes with 35S-labeled hybrid-selected translation products for antibody binding.
Urokinase Regulates Vitronectin Binding by Controlling Urokinase Receptor Oligomerization (2002)

Adhesion of monocytes to the extracellular matrix is mediated by a direct high affinity interaction between cell-surface urokinase-type plasminogen activator (uPA) receptor (uPAR) and the extracellular matrix protein vitronectin. We demonstrate a tight connection between uPA-regulated uPAR oligomerization and high affinity binding to immobilized vitronectin. We find that binding of soluble uPAR (suPAR) to immobilized vitronectin is strictly ligand-dependent with a linear relationship between the observed binding and the concentration of ligand added. Nevertheless, a comparison of experimentally obtained binding curves to those generated using a simple equilibrium model suggests that the high affinity vitronectin-binding pro-uPA.suPAR complex contains two molecules of suPAR. In co-immunoprecipitation experiments, using different epitope-tagged suPAR molecules, suPAR/suPAR co-immunoprecipitation displayed a similar uPA dose dependence as that observed for vitronectin binding, demonstrating that the high affinity vitronectin-binding complex indeed contains oligomeric suPAR. Structurally, the kringle domain of uPA was found to be critical for the formation of the vitronectin-binding competent complex because the amino-terminal fragment, but not the growth factor-like domain, behaved as a full-length uPA. Our data represent the first demonstration of functional, ligand-induced uPAR oligomerization having extensive implications for glycosylphosphatidylinositol-anchored receptors in general, and for the biology of the uPA/uPAR system in particular.