gebhart/patrepeval huggingface dataset:
pgaA and pgaB encode two constitutively expressed endopolygalacturonases of Aspergillus niger (2000)

pgaA and pgaB, two genes encoding endopolygalacturonases (PGs, EC 3.2.1.15) A and B, were isolated from a phage genomic library of Aspergillusniger N400. The 1167 bp protein coding region of the pgaA gene is interrupted by one intron, whereas the 1234 bp coding region of the pgaB gene contains two introns. The corresponding proteins, PGA and PGB, consist of 370 and 362 amino acid residues respectively. Northern-blot analysis revealed that pgaA- and pgaB-specific mRNA accumulate in mycelia grown on sucrose. mRNAs are also present upon transfer to media containing D-galacturonic acid and pectin. Recombinant PGA and PGB were characterized with respect to pH optimum, activity on polygalacturonic acid, and mode of action and kinetics on oligogalacturonates of different chain length (n = 3-7). At their pH optimum the specific activities in a standard assay for PGA (pH 4.2) and PGB (pH 5.0) were 16.5 μkat·mg-1 and 8.3 μkat·mg-1 respectively. Product progression analysis, using polygalacturonate as a substrate, revealed a random cleavage pattern for both enzymes and indicated processive behaviour for PGA. This result was confirmed by analysis of the mode of action using oligogalacturonates. Processivity was observed when the degree of polymerization of the substrate exceeded 6. Using pectins of various degrees of methyl esterification, it was shown that PGA and PGB both preferred partially methylated substrates.
Synthesis, Structural Features, and Reactivity of Fe−Mn Mixed Oxides Prepared by Microemulsion (2006)

Iron−manganese mixed oxides have been prepared by the microemulsion (MEM) technique, obtaining solids displaying homogeneously distributed Fe−Mn phases. For the sake of comparison similar samples prepared by different techniques have been studied. Magnetization measurements reveal that the extension of the Fe−Mn interaction was enhanced in the samples prepared by microemulsion and so was the sample homogeneity. The average size of the oxide particles prepared by microemulsion lies in the nanometer range, displaying also a narrow particle size distribution. A certain degree of manganese surface enrichment was observed for all samples and overall in those containing a larger amount of Mn, irrespective of the preparation method as revealed by X-ray photoelectron spectroscopy. Selected solids were used as catalyst precursors for the Fischer−Tropsch reaction. Mn promotion led to an enhancement of the olefin-to-paraffin ratio in the samples over which Fe−Mn interaction developed.
Indoleamine neurons and their processes in the normal rat brain and in chronic diet‐induced thiamine deficiency demonstrated by uptake of <sup>3</sup>H‐Serotonin (1977)

Abstract Indoleamine structures in the brains of normal, pair‐fed control, and thiamine deficient rats are selectively localized by autoradiography following monoamine oxidase inhibition and simultaneous intraventricular infusion of 3 H‐5HT (10 −5 m) and cold d–1 norepinephrine (10 −4 m). The locations of indoleamine neurons and their plexuses are comparable in the normal and control animals and are enumerated and mapped in detail. In addition to numerous labeled neurons in the raphe and reticular formation of pons and medulla, there are indoleamine neurons in several hypothalamic nuclei, in the mammillary, habenular, and interpeduncular nuclei. Labeled axonal plexuses occur in almost all areas of the brain but certain regions in spinal cord, medulla, midbrain, diencephalon, basal ganglia, and hippocampus are particularly rich. Thiamine deficiency causes lack of label in almost all indoleamine neurons and their processes in the midbrain and medulla; only a few dystrophic cells with hypertrophied axons are seen. In the diencephalon more indoleamine neurons and their axonal plexuses are visualized in these uptake studies. The periventricular regions of spinal cord, medulla, midbrain and diencephalon, the mammillary nuclei, habenular nuclei, and cerebellum – areas richly innervated by indoleamine axons in the normal brain – are the most severely affected. The ventricular and leptomeningeal indoleamine structures are preserved, however, and individual axons may hypertrophy. It remains to be resolved whether these changes reflect disturbances in the ability of certain indoleamine neurons to take up and retain 3 H‐5HT or true neuronal degeneration.
Techniques for unit-delay compiled simulation (1990)

The PC-set method and the parallel technique are two methods for performing compiled unit-delay simulation. The PC-set method analyzes the network, determines the set of potential change times for each net, and generates gate simulations for each potential change. The parallel technique, which is based on the concept of parallel fault simulation, is faster and generates less code than the PC-method, but is less flexible. Benchmark comparisons with interpreted event-driven simulation show a factor of four improvement for the PC-set method and a factor of ten improvement for the parallel technique.
Transformation blocks differentiation-induced inhibition of serum response factor interactions with serum response elements. (1999)

The differentiation of nontransformed 3T3T mesenchymal stem cells is a multistep process that is associated with the progressive repression of mitogenic responsiveness to serum growth factors that ultimately results in expression of the terminally differentiated adipocyte phenotype. The repression of serum-induced mitogenesis by differentiation correlates with repression of the serum-inducible transcription of junB and c-fos. In contrast, the differentiation of neoplastically transformed cells does not repress mitogenic responsiveness or junB or c-fos inducibility. Because the junB and c-fos promoters both contain serum response elements (SREs), the current studies tested the possibility that differentiation might repress the ability of serum response factor (SRF) to bind to the SRE in normal cells but not in transformed cells. We now report that differentiation represses SRE serum inducibility using nontransformed cells transiently transfected with pjunB SRE thymidine kinase/chloroamphenicol acetyltransferase (SREtk/CAT) or pc-fos SREtk/CAT containing an intact SRF-binding domain. Adipocyte differentiation of nontransformed cells also markedly represses the ability of SRF to bind to the junB SRE, the c-fos SRE, and other SREs, as determined by mobility shift and gel supershift assays, without affecting the DNA binding characteristics of the nuclear protein SP-1. By comparison, the ability of SRF to bind SRE is not repressed by the differentiation of SV40 large T antigen-transformed 3T3T cells. The results further establish that adipocyte differentiation blocks the nuclear localization of SRF, thus preventing its interaction with SREs in nontransformed cells but not in transformed cells.
Price of Risk Constant (PORC) (1997)

The main idea behind PORC is to adjust the holding period returns and horizon prices of mortgage securities to reflect changing risk levels as interest rates change. OAS models assume constant risk in all interest rate scenarios; PORC allows prepayment risks to change but holds the price of risk constant. The authors illustrate for a regular pass-through security how the PORC-predicted OAS is higher (lower) than constant OAS in down (up) rate scenarios and how constant OAS overestimates (underestimates) rates of return in down (up) rate environments.
Experimental demonstration of postnonlinearity compensation in a multispan DPSK transmission (2006)

We demonstrate significant performance improvement in 10-Gb/s multispan differential phase-shift keying transmissions by employing postnonlinearity compensation (PNC) for both dispersion-managed soliton and quasi-linear transmission. Measurements of timing misalignment tolerance as well as bandwidth requirement of the PNC unit show that the PNC technique is robust and practical, and can be easily extended to higher bit-rate transmissions.
Object migration mechanisms to support updates in object-oriented databases (2002)

Updates in object-oriented database systems are studied. It is pointed out that, owing to the richness of the object-oriented data model, updating an object may affect the object's position in the class lattice. Three types of update operations on objects are considered: adding, dropping, and modifying instance variables. An update may cause object migration, that is, the updated object may change its current class. As the user may not be aware of the side effects of the update, the system has to take some actions to complete the user's update. Classes in a database schema are classified into three types: static, partially dynamic, and dynamic. This classification is based on the way in which an object in a class may migrate. It is shown that the notion of object migration affects answering queries in temporal object-oriented databases. The history of an object will be distributed among several classes in the scheme. Two approaches to determine the class of an object's version are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An Experimental Investigation of the Flow in a Virtual Cyclone (1998)

An experimental investigation has confirmed the predicted flow pattern in a prototype virtual cyclone, a novel device for nonimpact particle separation proposed by Torcdzynski and Rader (1996, 1997) based solely on computational simulations. The virtual cyclone differs from an ordinary cyclone in that the flow is turned by a virtual wall composed of an eddy rather than by a solid wall. A small-scale version of the computationally simulated geometry has been fabricated out of Lucite. The working fluid is ambient air, which is drawn through the apparatus and flow-metering equipment using a wind-tunnel vacuum source. The flow is seeded with smoke or water droplets produced by a nebulizer so that flow visualization techniques and particle-imaging velocimetry could be applied. Experiments have been performed on this apparatus for flows with Reynolds numbers from 200 up to 40,000 (a Mach number of 0.3). Flow visualization using a laser light sheet passing through the mid-plane of the apparatus verified that the computationally predicted flow is obtained over the entire range of flow rates. The shear layer between the main and recirculating flow is observed to become turbulent around a Reynolds number of 4000. While not changing the flow structure, the turbulent mixing produced by shear-layer roll-up limits particle concentration at the higher flow rates. In order to achieve highly efficient particle separation using a virtual cyclone, turbulence must be suppressed or mitigated. If laminar flow cannot be achieved for macroscopic-scale virtual cyclones, it should be achievable for a small-scale (low Reynolds number) virtual cyclone fabricated using MEMS-related technologies. This approach could lead to a chip-scale particle concentrator.
(o- and p-Nitrobenzyloxycarbonyl)-5-fluorouracil derivatives as potential conjugated bioreductive alkylating agents (1986)

A series of (o- and p-nitrobenzyloxycarbonyl)-5-fluorouracil derivatives were synthesized by reacting o- or p-nitrobenzyl chloroformate with 5-fluorouracil in the presence of triethylamine in DMF or Me2SO. The reductive activation of these agents was hypothesized to generate a reactive methide and 5-fluorouracil, two components that are capable of synergistic interaction through complementary inhibition. Measurement of the surviving fractions of EMT6 tumor cells treated with these agents in culture under conditions of hypoxia and aerobiosis resulted in equal cell kill regardless of the state of oxygenation. One of the synthesized agents, 3-(p-nitrobenzyloxycarbonyl)-5-fluorouracil (4), appeared to be superior to 5-fluorouracil in prolonging the survival time of mice bearing intraperitoneal implants of the P388 leukemia and Sarcoma 180.
MicroRNA Signature in Thyroid Fine Needle Aspiration Cytology Applied to “Atypia of Undetermined Significance” Cases (2011)

We demonstrate that miR amplification from FNA samples is feasible and that the particular four miR profile in this study can identify PTCs. However, further refinement is required for application to FNA cytology of "atypia of undetermined significance" cases due to low accuracy in classifying follicular neoplasias.
Escherichia coli Glycerol Kinase: Role of a Tetramer Interface in Regulation by Fructose 1,6-Bisphosphate and Phosphotransferase System Regulatory Protein IIIglc (1994)

Escherichia coli glycerol kinase (EC 2.7.1.30; ATP:glycerol 3-phosphotransferase) is a key element in a signal transduction pathway that couples expression of genes required for glycerol metabolism to the relative availability of glycerol and glucose. Its catalytic activity is inhibited by protein-protein interactions with IIIglc, a phosphotransferase system protein, and by fructose 1,6-bisphosphate (FBP); each of these allosteric effectors constitutes a positive signal that glucose is available. Loss of glucose inhibition of glycerol metabolism was used to screen for regulatory mutants of glycerol kinase after hydroxylamine mutagenesis of the cloned glpK gene. Two mutant enzymes were identified and shown by DNA sequencing to contain the mutations alanine 65 to threonine (A65T) and aspartate 72 to asparagine (D72N). Initial velocity studies show the mutations do not significantly affect the catalytic properties, hence active-site structures, of the enzymes. Both mutations decrease inhibition by FBP; A65T eliminates the inhibition while D72N appears to decrease the affinity for FBP and the extent of the inhibition. However, neither mutation significantly affects inhibition by IIIglc. Gel-permeation chromatography studies show that both of the mutations alter the dimer-tetramer assembly reaction of the enzyme and the effect of FBP in increasing the molecular weight. The effects of the mutations on the assembly reaction are consistent with the locations of these two amino acid residues in the X-ray structure, which shows them to be associated with an alpha-helix that constitutes one of the two subunit-subunit interfaces within the tetramer.(ABSTRACT TRUNCATED AT 250 WORDS)
Synergy of Penicillin and Gentamicin against Enterococci (1971)

Because combinations of penicillin plus streptomycin and penicillin plus kanamycin do not produce synergism against all strains of enterococci, the effect of penicillin plus gentamicin against enterococci was examined. A very high level of resistance to gentamicin was absent in 172 strains of enterococci isolated from clinical specimens. Penicillin plus gentamicin was synergistic against all of 30 strains tested. The size of the inoculum had a significant effect when low concentrations of gentamicin were tested against certain of the strains. Nonetheless, the combination of penicillin plus gentamicin produced enhanced killing of all enterococci tested when used in clinically achievable concentrations.
Automated Workflows to Monitor, Diagnose, Optimize, and Perform Multi-Scenario Forecasts of Waterflooding in Low-Permeability Carbonate Reservoirs (a KwIDF Project) (2013)

Abstract Surveillance and optimization of waterfloods in low-permeability carbonate reservoirs pose many challenges. Updating reservoir models is tedious and time-consuming, involving multiple data sources, model updates, and simulations. Technological challenges include large simulation models, waterflood complexities, and limited real-time data. Human challenges must be addressed as well, since waterflooding decisions affect multiple disciplines: reservoir engineers, production engineers, facilities engineers, IT, Operations, and asset managers. The ‘languages’ and interests of these disciplines are quite different; necessitating a workflow that satisfies the needs of all disciplines and integrates people, processes, and technology. This paper presents an innovative automated workflow to enable monitoring, diagnostics, forecasting, and optimization of waterflooding processes in days instead of weeks. This workflow seamlessly captures historical and monthly real-time data, updates simulation history, creates simulation restart prediction points, runs numerical simulations with optimization scenarios, selects the global optimum solution by scenario, and compares results so that multi-disciplinary teams can make reactive or proactive decisions to maximize short-term oil rates and long-term oil recovery, while honoring constraints on voidage replacement ratios, reservoir pressure, sweep efficiencies, production, and injection. The workflow automatically updates real-time production data in the simulator each month. A base case is run to recalculate waterflooding indicators. The process then starts a 24-month production forecast, running hundreds of scenarios under constrained optimization to achieve global optimization points. The optimizer changes control variables such as injection volumes, tubing head pressure, bottomhole pressure, and production allowable. The workflow ranks potential well decisions with important impacts on oil rate and water cut. The workflow uses an intuitive user interface incorporating the needs of multiple engineering and operations disciplines, and facilitates one common language while evaluating and optimizing waterfloods. This workflow has been implemented for a waterflood in a Middle East carbonate reservoir to help engineers evaluate the waterflood and make better, faster decisions.
ISEE: An Intuitive Sound Editing Environment (1994)

This article presents ISEE, an intuitive sound editing environment, as a general sound synthesis model based on expert auditory perception and cognition of musical instruments.It discusses the backgrounds of current synthesizer user interface design and related timbre space research.Of the three principal parameters of sound-pitch, loudness and timbre-ISEE focuses on control of timbre, and affects only the range of pitch and loudness.Timbre is manipulated using four abstract timbre parameters: overtones, brightness, articulation and envelope.These abstract timbre parameters are implemented in different ways for different instruments.They define instrument spaces of which a hierarchy can be built to structure refinement of timbre parameter behavior.An Apple Macintosh implementation of ISEE is described.ISEE has four main advantages over traditional sound synthesis editors.Firstly, it allows musicians to control sound synthesis as they control their musical instrument: by continuous movement, reducing cognitive control load.Secondly, it uses timbre parameters identified by human experience instead of indirect and intricate synthesis model parameters.Thirdly, it integrates a librarian system in the sound synthesis model.Finally, it enables transparent use of several synthesis models at a time.
[Ocular complications of atopic dermatitis]. (1997)

We examined the frequency and types of ocular complications that developed in 560 eyes of 280 patients with atopic dermatitis at the Department of Dermatology, Tokyo Medical College Hospital. Mild ocular involvement included blepharitis in 294 eyes (52.5%), conjunctivitis in 221 eyes (39.5%), and superficial punctate keratopathy in 65 eyes (11.6%). More serious ocular complications leading to decreased visual function occurred in 133 eyes (23.8%) that developed lens opacities, and 34 eyes (6.0%) that developed retinal break or retinal detachment. Because of the presence of abnormalities in the peripheral retina, we believe that a pathogenic factor may have been present in the vitreous of these atopic dermatitis patients. Many of our patients with atopic dermatitis had serious ocular complications in the absence of ocular symptoms. Thus it is important to conduct a thorough ophthalmological examination in the early period of disease in atopic dermatitis patients, both for the management of early but serious ocular complications, as well as for the preservation of visual function.
Comparison of bee products based on assays of antioxidant capacities (2009)

On the basis of the present assays, propolis is the most powerful antioxidant of all the bee product examined, and its effect may be partly due to the various caffeic acids it contains. Pollen, too, exhibited strong antioxidant effects.
Spacecraft Adaptive Attitude and Power Tracking with Variable Speed Control Moment Gyroscopes (2002)

Control laws for an integrated powerlattitude control system (IPACS) for a satellite using variable-speed single-gimbal control moment gyroscopes (VSCMGs) are introduced. Whereas the wheel spin rates of the conventional CMGs are constant, the VSCMGs are allowed to have variable speeds. Therefore, VSCMGs have extra degrees of freedom and can be used to achieve additional objectives, such as energy storage, as well as attitude control. We use VSCMGs in conjunction with an IPACS system. The gimbal rates of the VSCMGs are used to provide the reference-tracking torques, whereas the wheel accelerations are used for both attitude and power reference tracking. The latter objective is achieved by storing or releasing the kinetic energy in the wheels. The control algorithms perform both the attitude and power tracking goals simultaneously. A model-based control and an indirect adaptive control for a spacecraft with uncertain inertia properties are developed. Moreover, control laws for equalization of the wheel speeds are also proposed. Wheel speed equalization distributes evenly the kinetic energy among the wheels, minimizing the possibility of wheel speed saturation and the occurrence of zero-speed singularities. Finally, a numerical example for a satellite in a low Earth, near-polar orbit is provided to test the proposed IPACS algorithm.
Cell-Free Replication of the Hepatitis C Virus Subgenomic Replicon (2002)

The hepatitis C virus (HCV) contains a plus-strand RNA genome. The 5' noncoding region (NCR) of the viral genome functions as an internal ribosome entry site, and its unique 3' NCR is required for the assembly of the replication complex during initiation of HCV RNA replication. Lohmann et al. (V. Lohmann, F. Korner, J.-O. Koch, U. Herian, L. Theilman, and R. Batenschlager, Science 285:110-113, 1999) developed a subgenomic HCV replicon system, which represents an important tool in studying HCV replication in cultured cells. In this study, we describe a cell-free replication system that utilizes cytoplasmic lysates prepared from Huh-7 cells harboring the HCV subgenomic replicons. These lysates, which contain ribonucleoprotein complexes associated with cellular membranes, were capable of incorporating [alpha(32)P]CTP into newly synthesized RNA from subgenomic replicons in vitro. Replicative forms (RFs) and replicative intermediates (RIs) were synthesized from the endogenous HCV RNA templates. Consistent with previous observations, RFs were found to be resistant to RNase A digestion, whereas RIs were sensitive to RNase treatment. The radiolabeled HCV RF-RI complexes contained both minus and plus strands and were specific to the lysates derived from replicon-expressing cells. The availability of a cell-free replication system offers opportunities to probe the mechanism(s) of HCV replication. It also provides a novel assay for potential therapeutic agents.