gebhart/patrepeval huggingface dataset:
Sonogashira Coupling with Aqueous Ammonia (2002)

Abstract The coupling reaction of terminal alkynes with organic halides, Sonogashira-(Hagihara) coupling, takes place with only 2 equivalents of dilute aqueous ammonia as an additive. The reaction of phenylacetylene and 4-iodoanisole in the presence of 1 mol% of PdCl2(PPh3)2, 2 mol% of CuI, and 2 equiv of aqueous ammonia in THF proceeds at room temperature for 6 h to afford the coupling product in a quantitative yield.
HumanMetapneumovirusas a Cause of Community-Acquired Respiratory Illness1 (2002)

Human metapneumovirus (HMPV) is a recently identified Paramyxovirus first isolated from hospitalized children with acute respiratory tract infections (ARTI). We sought evidence of HMPV infection in patients who had visited general practitioners, had influenzalike illnesses (ILI), and had negative tests for influenza and Human respiratory syncytial virus (HRSV). As part of national virologic surveillance, sentinel general practices in England and Wales collected samples from patients of all ages with ILI during winter 2000-01. Reverse transcriptase-polymerase chain reaction (PCR) for HMPV, influenza A (H1 and H3), influenza B, and HRSV (A and B) was used to screen combined nose and throat swabs. PCR products from the HMPV-positive samples were sequenced to confirm identity and construct phylogenetic trees. Of 711 swabs submitted, 408 (57.3%) were negative for influenza and HRSV; HMPV was identified in 9 (2.2%) patients. HMPV appears to be associated with community-acquired ARTI. The extent of illness and possible complications related to this new human virus need to be clarified.
A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis (2012)

In this study, a novel universal primer-multiplex-PCR (UP-M-PCR) method adding a universal primer (UP) in the multiplex PCR reaction system was described. A universal adapter was designed in the 5'-end of each specific primer pairs which matched with the specific DNA sequences for each template and also used as the universal primer (UP). PCR products were analyzed on sequencing gel electrophoresis (SGE) which had the advantage of exhibiting extraordinary resolution. This method overcame the disadvantages rooted deeply in conventional multiplex PCR such as complex manipulation, lower sensitivity, self-inhibition and amplification disparity resulting from different primers, and it got a high specificity and had a low detection limit of 0.1 ng for single kind of crops when screening the presence of genetically modified (GM) crops in mixture samples. The novel developed multiplex PCR assay with sequencing gel electrophoresis analysis will be useful in many fields, such as verifying the GM status of a sample irrespective of the crop and GM trait and so on.
The thin-cap fibroatheroma: a type of vulnerable plaque: The major precursor lesion to acute coronary syndromes (2001)

While the concept of plaque 'vulnerability' implies a propensity towards thrombosis, the term vulnerable was originally intended to provide a morphologic description consistent with plaques that are prone to rupture. It is now known that the etiology of coronary thrombi is diverse and can arise from entities of plaque erosion or calcified nodules. These findings have prompted the search for more definitive terminology to describe precursor lesions associated with rupture, now referred to as thin-cap fibroatheromas. This review focuses on the thin-cap fibroatheroma, as a specific cause of acute coronary syndromes. To put these issues into current perspective, we need to revisit some of the older literature describing plaque morphology in stable and unstable angina, acute myocardial infarction, and sudden coronary death. The morphology, frequency, and precise location of these thin-cap fibroatheromas are further discussed in detail. Potential mechanisms of fibrous cap thinning are also addressed, in particular emerging data, which suggests the role of cell death "apoptosis" in cap atrophy.
Polycythemia in transgenic mice expressing the human erythropoietin gene. (1989)

Erythropoietin is a glycoprotein hormone that regulates mammalian erythropoiesis. To study the expression of the human erythropoietin gene, EPO, 4 kilobases of DNA encompassing the gene with 0.4 kilobase of 5' flanking sequence and 0.7 kilobase of 3' flanking sequence was microinjected into fertilized mouse eggs. Transgenic mice were generated that are polycythemic, with increased erythrocytic indices in peripheral blood, increased numbers of erythroid precursors in hematopoietic tissue, and increased serum erythropoietin levels. Transgenic homozygotes show a greater degree of polycythemia than do heterozygotes as well as striking extramedullary erythropoiesis. Human erythropoietin RNA was found not only in fetal liver, adult liver, and kidney but also in all other transgenic tissues analyzed. Anemia induced increased human erythropoietin RNA levels in liver but not kidney. These transgenic mice represent a unique model of polycythemia due to increased erythropoietin levels.
Resistance to the Soybean Aphid in Soybean Germplasm (2004)

With an efficient greenhouse screening method, the first resistance to the soybean aphid ( Aphis glycines Matsumura) was found in cultivated soybean [ Glycine max (L.) Merr.] germplasm. No resistance was found in 1425 current North American soybean cultivars, 106 Maturity Group (MG) 000 through VII Asian cultivars, and in a set of 11 ‘Clark’ isolines possessing different pubescence traits. Dense pubescence did not provide protection against the soybean aphid. Resistance was discovered and established in three ancestors of North American genotypes: ‘Dowling’, ‘Jackson’, and PI 71506. Expression of resistance in those genotypes was characterized in choice and nonchoice tests. In choice tests, significantly fewer aphids occurred on Dowling, Jackson, and PI 71506 plants compared with susceptible cultivars ( P = 0.05). Aphid populations did not develop on Dowling and Jackson in nonchoice tests, indicating that there was a negative impact on aphid fecundity on those cultivars. That evidence combined with observations of aphid mortality on those cultivars suggested that antibiosis‐type resistance contributed to the expression of resistance. Possible donors of resistance to Dowling and Jackson were identified. In nonchoice tests, population development on PI 71506 was not significantly different from development on susceptible cultivars, indicating that antixenosis was more important in that genotype. Resistance was expressed in all plant stages. Dowling provided season‐long protection against aphids equal to the use of the systemic insecticide imidacloprid {1‐[(6‐Chloro‐3‐pyridinyl)methyl]‐ N ‐nitro‐2‐imidazolidinimine} in a field test. Four other germplasm accessions, ‘Sugao Zarai’, ‘Sato’, ‘T260H’, and PI 230977, had levels of resistance not significantly different from Dowling, Jackson, and PI 71506 in a choice test ( P = 0.05).
Radially symmetric excitation and collection optics for flow cytometric sorting of aspherical cells (1997)

We report on a new optical configuration for sorting flow cytometers which is optimized for the illumination and collection of light from aspherical cells. This design provides radially symmetric illumination and detection of asymmetric particles while retaining the sort capability of a jet-in-air (or cylindrical cuvette) design. A paraboloidal reflector, symmetrical about the sample stream, both focuses a laser excitation beam and collects cell scatter and fluorescence from the inspection point. The performance of the new optical configuration has been tested and compared to that of a modified commercial flow cytometer, which uses a forward-side fluorescence collection geometry. For fluorescence measurements on calibration microspheres the new system produces histograms with similar coefficients of variation to those obtained with the modified conventional cytometer. Optical artifacts apparent in measurements on flat cells, such as blood cells and mammalian sperm, using conventional optics, are eliminated by the new configuration. Analysis of chinchilla sperm yields a dual-peaked histogram population that has a coefficient of variation and X-Y split which matches that for gated (oriented) fraction of the sample as measured by the conventional system. Bovine sperm, which are larger and flatter than chinchilla sperm, also produce a single population which, when low sample-to-sheath differential pressures are used, has coefficients of variation matching those for an oriented subpopulation as measured by conventional optics. This new optical configuration presents an alternative technique for measuring aspherical cells independent of their orientation, with the potential for higher analysis rates and improved efficiency compared to other optical systems.
Determination of adsorption-induced variation in the spring constant of a microcantilever (2002)

Although resonating microcantilevers are demonstrated to be excellent mass sensors, adsorption-induced changes in the spring constant result in errors in the calculation of adsorbed mass from shifts in resonance frequencies. However, simultaneous measurement of resonance frequency and adsorption-induced cantilever bending can be used to determine the variation in spring constant. Plotting the change in surface stress as a function of analyte concentration, the surface excess of adsorbed molecules and, therefore, the mass adsorbed can be determined. Here, we demonstrate this concept for adsorption of Na+ ions on microcantilevers in NaCl solutions where a change in the spring constant was found to increase from 9.5×10−4 to 7.5×10−3 N/m as the NaCl concentration increased from 0.05 to 0.8 M.
Renewable Long-Chain Fatty Acids for Production of Biodegradable Medium-Chain-Length Polyhydroxyalkanoates (mcl-PHAs) at Laboratory and Pilot Plant Scales (2000)

Several types of mcl-PHAs were produced by Pseudomonas putida KT2442 at pilot and laboratory scales from renewable long-chain fatty acids (LCFAs) and octanoic acid. These and other mcl-PHAs are now available in sufficient amounts to carry out application and processing studies. We have isolated and purified these polymers in preparative amounts of 10−500 g by solvent recovery and selective enzymolysis. The molecular weights of mcl-PHA copolymers produced from LCFAs were generally similar to those found for octanoic acid based material, but the polydispersity was higher and the degree of polymerization was lower. The polymers showed thermal properties common for amorphous or semicrystalline thermoplastic elastomers above their Tg, which decreased with increasing average pendant chain length. PHAs derived from LCFAs, which contained 3−12 new hydroxyacid comonomers compared to PHA produced from oleic acid, were amorphous, did not crystallize, and showed liquid properties at room temperature. As the number of comonomers and thus the degree of disorder increased in these PHAs, the polymers became more viscous and tacky. PHAs derived from octanoic acid and oleic acid were not affected by the production scale in terms of composition and physical properties. Although different production process control strategies used at lab and pilot scale did influence the process productivity, the substrate yield was not affected by the process control type applied and was always close to the theoretical PHA yield to be expected for fatty acid utilization through the β-oxidation pathway. Isolation and GC−MS analysis of the methanolyzed trimethylsilyl- (TMSI-) derivatives allowed the identification of a large number of previously unknown 3-hydroxy acid PHA components. All purified polymers were subjected to in vitro aerobic biodegradation using a compost isolate. The extent of mineralization varied from 15 to 60% of the theoretical biochemical oxygen demand (ThBOD). The polymer weight loss after 32 days ranged from 40 to 90% for the different mcl-PHAs.
Phosgenations ‐ A Handbook (2003)

Preface. 1. Contradictions. 2. Phosgenation Reagents. 3. Evaluation of Phosgenation Reagents. 4. Phosgenation Reactions. 5. Topics on Specific Synthetic Applications of Phosgenation Reactions. 6. Evaluation of Phosgenation Reactions. 7. Materials and Resources for Phosgenation Reagents. 8. Monitoring Phosgene and Phosgene Substitutes: Analytical Methods. 9. Outlook. Appendix. Index.
Access Ordering Algorithms for a Multicopy Memory (1992)

this document self-contained, the necessary analysis from that report is repeated here. Readers familiar with previous work may skip immediately to the analysis of a multicopy architecture presented in section 5; note: there is an important addition to the MAP access sequence definition presented in 3.1. 1.2 General System Model
Lock Inference for Atomic Sections (2006)

Software transactions allow the programmer to specify sections of code that should be serializable, without the programmer needing to worry about exactly how atomicity is enforced. Recent research proposes using optimistic concurrency to implement transactions. In this short paper, we propose a pessimistic lock-based technique that uses the results of static whole-program analysis to enforce atomicity. The input to our analysis is a program that contains programmer-specified atomic sections and calls to fork. We present a sharing inference algorithm that uses the results of points-to analysis to determine which memory locations are shared. Our analysis uses continuation effects to track the locations accessed after a point in the program. This allows data to be thread-local before a fork and thread-shared afterward. We then present a mutex inference algorithm that determines a sufficient set of locks to guard accesses to shared locations. After mutex inference, a compiler adds the appropriate lock acquires and releases to the beginning and end of atomic sections. Our algorithm is efficient, and provides parallelism according to precision of the alias analysis while minimizing the number of required locks.
Antianginal Effects of Lercanidipine on the Vasopressin or Methacholine Induced Anginal Model in Rats (2005)

The antianginal effects of lercanidipine, a newly synthesized 1,4-dihydropyridine derivative calcium channel antagonist, were evaluated in experimental angina model rats and the effects were compared with those of nifedipine, benidipine and amlodipine. In the vasopressin-induced angina model, intravenous administration of lercanidipine dose-dependently suppressed vasopressin-induced ST-depression. Amlodipine barely suppressed it, while benidipine, at the same dose, completely suppressed it. Nifedipine had a potency between that of amlodipine and benidipine. Oral administration of lercanidipine showed similar effects to the intravenous administration test on ST change. High doses of amlodipine, benidipine and nifedipine suppressed ST-depression by almost 100%. In the methacholine-induced angina model, lercanidipine suppressed the ST elevation dose dependently. Amlodipine barely suppressed it, while benidipine at 30 μg/kg effected almost total suppression. Nifedipine had a potency between that of amlodipine and benidipine. Intraduodenal administration of lercanidipine also suppressed the ST-elevation dose dependently. Nifedipine, benidipine and amlodipine at 10 mg/kg all markedly suppressed the elevation. Lercanidipine was more potent than the other calcium channel antagonists tested. In conclusion, it was explicitly demonstrated that lercanidipine exerts potent protective effects on the ischemic electrocardiography (ECG) changes in a variety of putative angina pectoris models in rats. An antispasmolytic coronary vasodilating action may be involved in the mechanism. It is expected that lercanidipine will be useful as an antianginal agent.
Design and Synthesis of a Chemically Cleavable Fluorescent Nucleotide, 3‘-O-Allyl-dGTP-allyl-Bodipy-FL-510, as a Reversible Terminator for DNA Sequencing by Synthesis (2006)

We report the construction of a novel chemically cleavable fluorescent labeling system based on an allyl group to modify nucleotide for DNA sequencing by synthesis (SBS). We have found that an allyl moiety can be used successfully as a linker to tether a fluorophore to a 3'-O-allyl-modified nucleotide, forming a chemically cleavable reversible terminator, 3'-O-allyl-dGTP-allyl-Bodipy-FL-510, for application in SBS. The fluorophore and the 3'-allyl group on a DNA extension product, which is generated by incorporating 3'-O-allyl-dGTP-allyl-Bodipy-FL-510, are removed simultaneously in 30 s by Pd-catalyzed deallylation in aqueous buffer solution. The resulting DNA product is successfully used as a primer for further extension in polymerase reaction. This one-pot dual-deallylation reaction thus allows the reinitiation of the polymerase reaction and increases the SBS efficiency.
Multiclass Multimodal Detection and Tracking in Urban Environments (2010)

This paper presents a novel approach to detect and track people and cars based on the combined information retrieved from a camera and a laser range scanner. Laser data points are classified by using boosted Conditional Random Fields, while the image based detector uses an extension of the Implicit Shape Model (ISM), which learns a codebook of local descriptors from a set of hand-labeled images and uses them to vote for centers of detected objects. Our extensions to ISM include the learning of object parts and template masks to obtain more distinctive votes for the particular object classes. The detections from both sensors are then fused and the objects are tracked using a Kalman Filter with multiple motion models. Experiments conducted in real-world urban scenarios demonstrate the effectiveness of our approach.
Proteasome inhibitors: fromin vitro uses to clinical trials (2000)

Proteasomes are multicatalytic proteinase complexes which play a central role in intracellular protein degradation. They catalyse key events in cell cycle regulation and in the activation of the transcription factor NFkappaB. Proteasome inhibitors have been useful for the characterization of proteasome catalytic components and in the elucidation of proteasome functions in animal cells. Potent small peptide inhibitors of proteasomes also represent a novel approach to the treatment of inflammatory diseases (which involve activation of NFkappaB) and cancer. Such compounds have recently been shown to be effective in a variety of animal models, and at least one is currently in use in clinical trials.
Dopamine-induced Exocytosis of Na,K-ATPase Is Dependent on Activation of Protein Kinase C-ε and -δ (2002)

The purpose of this study was to define mechanisms by which dopamine (DA) regulates the Na,K-ATPase in alveolar epithelial type 2 (AT2) cells. The Na,K-ATPase activity increased by twofold in cells incubated with either 1 microM DA or a dopaminergic D(1) agonist, fenoldopam, but not with the dopaminergic D(2) agonist quinpirole. The increase in activity paralleled an increase in Na,K-ATPase alpha1 and beta1 protein abundance in the basolateral membrane (BLM) of AT2 cells. This increase in protein abundance was mediated by the exocytosis of Na,K-pumps from late endosomal compartments into the BLM. Down-regulation of diacylglycerol-sensitive types of protein kinase C (PKC) by pretreatment with phorbol 12-myristate 13-acetate or inhibition with bisindolylmaleimide prevented the DA-mediated increase in Na,K-ATPase activity and exocytosis of Na,K-pumps to the BLM. Preincubation of AT2 cells with either 2-[1-(3-dimethylaminopropyl)-5-methoxyindol-3-yl]-3-(1H-indol-3-yl)maleimide (Gö6983), a selective inhibitor of PKC-delta, or isozyme-specific inhibitor peptides for PKC-delta or PKC-epsilon inhibited the DA-mediated increase in Na,K-ATPase. PKC-delta and PKC-epsilon, but not PKC-alpha or -beta, translocated from the cytosol to the membrane fraction after exposure to DA. PKC-delta- and PKC-epsilon-specific peptide agonists increased Na,K-ATPase protein abundance in the BLM. Accordingly, dopamine increased Na,K-ATPase activity in alveolar epithelial cells through the exocytosis of Na,K-pumps from late endosomes into the basolateral membrane in a mechanism-dependent activation of the novel protein kinase C isozymes PKC-delta and PKC-epsilon.
Probing the surface-enhanced Raman scattering properties of Au–Ag nanocages at two different excitation wavelengths (2009)

The surface-enhanced Raman scattering (SERS) properties of bimetallic Au-Ag nanocages has been thoroughly investigated by changing the nanocage composition, localized surface plasmon resonance (LSPR) peak position and excitation wavelength. We found a significant dependency on excitation wavelength for the Au-Ag nanocages, independent of the underlying LSPR, which can be extended to other bimetallic SERS substrates. While it is well-understood that plasmon damping can occur for Au nanoparticles when their LSPR peaks are close to interband transition frequencies and thereby attenuate SERS intensities, this study probes an additional aspect and shows that SERS intensities are reduced when the excitation light source is near interband transition frequencies regardless of the LSPR location.
ASCORBATE AND GLUTATHIONE: Keeping Active Oxygen Under Control (1998)

To cope with environmental fluctuations and to prevent invasion by pathogens, plant metabolism must be flexible and dynamic. Active oxygen species, whose formation is accelerated under stress conditions, must be rapidly processed if oxidative damage is to be averted. The lifetime of active oxygen species within the cellular environment is determined by the antioxidative system, which provides crucial protection against oxidative damage. The antioxidative system comprises numerous enzymes and compounds of low molecular weight. While research into the former has benefited greatly from advances in molecular technology, the pathways by which the latter are synthesized have received comparatively little attention. The present review emphasizes the roles of ascorbate and glutathione in plant metabolism and stress tolerance. We provide a detailed account of current knowledge of the biosynthesis, compartmentation, and transport of these two important antioxidants, with emphasis on the unique insights and advances gained by molecular exploration.
Identification and Characteristics of a Novel Burkholderia Strain with Broad-Spectrum Antimicrobial Activity (2000)

A Burkholderia strain isolated from soil is capable of inhibiting the growth of bacteria, plant-pathogenic fungi, pathogenic yeasts, and protozoa. Inhibition does not involve cell contact or the presence of living cells, suggesting that at least a substantial portion of the antimicrobial activity is due to the excretion of extracellular compounds.
Novel selection for tetracycline- or chloramphenicol-sensitive Escherichia coli (1982)

A method for selecting tetracycline- or chloramphenicol-sensitive Escherichia coli cells from a population of predominantly resistant cells is described. This method depends on the inability of drug-sensitive cells to induce lambda receptors in the presence of chloramphenicol or tetracycline, protein synthesis-inhibiting drugs. The addition of bacteriophage lambda vir to a mixture of drug-sensitive and drug-resistant cells, induced for lambda receptors in the presence of tetracycline or chloramphenicol, preferentially kills the drug-resistant cells (which are capable of inducing lambda receptors). The result is a culture enriched for the sensitive cells. Several common strains used for transformation were compared for their ability to be selected. E. coli 294 was found to be superior.
Coupling vocabularies and data structures: lessons from LOINC. (1996)

Using LOINC's data model for laboratory test result names as a starting point, an extended model is presented, coupled to a more complete vocabulary model. Justifications for this approach are obtained from a matching experiment that attempts to identify SNOMED terms that correspond to the various components of the LOINC names. Some limitations of LOINC's current vocabulary model, exposed during the matching process, are discussed.