gebhart/patrepeval huggingface dataset:
Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA. (1991)

Growth of human immunodeficiency virus (HIV) after infection requires the integration of a DNA copy of the viral RNA genome into a chromosome of the host. Here we present a simple in vitro system that carries out the integration reaction and the use of this system to probe the mechanism of integration. The only HIV protein necessary is the integration (IN) protein, which has been overexpressed in insect cells and then partially purified. DNA substrates are supplied as oligonucleotides that match the termini of the linear DNA product of reverse transcription. In the presence of HIV IN protein, oligonucleotide substrates are cleaved to generate the recessed 3' ends that are the precursor for integration, and the cleaved molecules are efficiently inserted into a DNA target. Analysis of reaction products reveals that HIV IN protein joins 3' ends of the viral DNA to 5' ends of cuts made by IN protein in the DNA target. We have also used this assay to characterize the sequences at the ends of the viral DNA involved in integration. The assay provides a simple screen for testing candidate inhibitors of HIV IN protein; some such inhibitors might have useful antiviral activity.
Alginate is not a significant component of the extracellular polysaccharide matrix of PA14 and PAO1 Pseudomonas aeruginosa biofilms (2003)

The bacterium Pseudomonas aeruginosa causes chronic respiratory infections in cystic fibrosis (CF) patients. Such infections are extremely difficult to control because the bacteria exhibit a biofilm-mode of growth, rendering P. aeruginosa resistant to antibiotics and phagocytic cells. During the course of infection, P. aeruginosa usually undergoes a phenotypic switch to a mucoid colony, which is characterized by the overproduction of the exopolysaccharide alginate. Alginate overproduction has been implicated in protecting P. aeruginosa from the harsh environment present in the CF lung, as well as facilitating its persistence as a biofilm by providing an extracellular matrix that promotes adherence. Because of its association with biofilms in CF patients, it has been assumed that alginate is also the primary exopolysaccharide expressed in biofilms of environmental nonmucoid P. aeruginosa. In this study, we examined the chemical nature of the biofilm matrix produced by wild-type and isogenic alginate biosynthetic mutants of P. aeruginosa. The results clearly indicate that alginate biosynthetic genes are not expressed and that alginate is not required during the formation of nonmucoid biofilms in two P. aeruginosa strains, PAO1 and PA14, that have traditionally been used to study biofilms. Because nonmucoid P. aeruginosa strains are the predominant environmental phenotype and are also involved in the initial colonization in CF patients, these studies have implications in understanding the early events of the infectious process in the CF airway.
Real-time Visualization of the Cellular Redistribution of G Protein-coupled Receptor Kinase 2 and β-Arrestin 2 during Homologous Desensitization of the Substance P Receptor (1999)

The substance P receptor (SPR) is a G protein-coupled receptor (GPCR) that plays a key role in pain regulation. The SPR desensitizes in the continued presence of agonist, presumably via mechanisms that implicate G protein-coupled receptor kinases (GRKs) and beta-arrestins. The temporal relationship of these proposed biochemical events has never been established for any GPCR other than rhodopsin beyond the resolution provided by biochemical assays. We investigate the real-time activation and desensitization of the human SPR in live HEK293 cells using green fluorescent protein conjugates of protein kinase C, GRK2, and beta-arrestin 2. The translocation of protein kinase C betaII-green fluorescent protein to and from the plasma membrane in response to substance P indicates that the human SPR becomes activated within seconds of agonist exposure, and the response desensitizes within 30 s. This desensitization process coincides with a redistribution of GRK2 from the cytosol to the plasma membrane, followed by a robust redistribution of beta-arrestin 2 and a profound change in cell morphology that occurs after 1 min of SPR stimulation. These data establish a role for GRKs and beta-arrestins in homologous desensitization of the SPR and provide the first visual and temporal resolution of the sequence of events underlying homologous desensitization of a GPCR in living cells.
Synthesis of Some Mannich Bases and Novel Benzofuran Derivatives Containing Imidazo[2,1-b][1,3,4]thiadiazoles as Biological Agents (2010)

An efficient route for the synthesis of 6-(1-benzofuran-2-yl)-2-phenyl imidazo[2,1-b] [1,3,4] thiadiazole(4a-e), was achieved by the reaction of 1-(1-benzofuran-2-yl)-2-bromoethanone (2) with 5-aryl-1,3,4-thiadiazol-2-amine(3-ae). The reaction mixture containing compound 4d with secondary amines and formaldehyde with catalytic amount of acetic acid, furnished corresponding Mannich bases (5-7). All newly synthesized compounds were screened for analgesic and antimicrobial activity. Among all the compounds tested for antibacterial activity, compound 7 showed significant activity against S. aureus when compared to other compounds, compound 4a, 4d and 5 exhibited highest activity against B. subtilis, compound 4b, 4d and 7 exhibited equipotent activity against K. pneumoniae and compound 6 exhibited promising activity against E. coli comparable with the standard drug Tetracycline. Among all the compounds tested for antifungal activity, the compound 4b and 4c exhibited significant activity against A. niger, compound 4c and 4e showed highest activity against C. albicans, compound 7 exhibited promising activity against P. chrysozenous and compound 4a and 4b exhibited highest activity against T. vridar as compared with standard drug Flucanozole. Compound 4b and 4d proved to be potent analgesic agents, as they exhibited significant analgesic activity comparable to standard drug and the remaining compounds showed moderate activity as compared to standard drug. Keywords: 2-Acetylbenzofuran, Mannich bases, imidazo[2,1-b][1,3,4]thiadiazole, analgesic and antimicrobial activity
Dynamic class loading in the Java virtual machine (1998)

Class loaders are a powerful mechanism for dynamically loading software components on the Java platform. They are unusual in supporting all of the following features: laziness, type-safe linkage, user-defined extensibility, and multiple communicating namespaces.We present the notion of class loaders and demonstrate some of their interesting uses. In addition, we discuss how to maintain type safety in the presence of user-defined dynamic class loading.
On-Chip Infrared Spectroscopic Sensing: Redefining the Benefits of Scaling (2016)

Infrared (IR) spectroscopy is widely recognized as a gold standard technique for chemical analysis. Recent strides in photonic integration technologies offer a promising route towards enabling miniaturized, rugged platforms for IR spectroscopic analysis. Here we show that simple size scaling by replacing bulky discrete optical elements used in conventional IR spectroscopy with their on-chip counterparts is not a viable route for on-chip infrared spectroscopic sensing, as it cripples the system performance due to the limited optical path length accessible on a chip. In this context, we discuss two novel photonic sensor designs uniquely suited for microphotonic integration. We leverage strong optical and thermal confinement in judiciously designed microcavities to circumvent the thermal diffusion and optical diffraction limits in conventional photothermal sensors and achieve parts-per-billion level gas molecule limit of detection. In the second example, an on-chip spectrometer design with Fellgett's advantage is proposed for the first time. The design enables sub-nm spectral resolution on a millimeter-sized, fully packaged chip without mechanical moving parts.
Catalyzed Addition of Aldehydes to Activated Double Bonds—A New Synthetic Approach (1976)

Abstract In the presence of cyanide ions as catalyst, aromatic and heterocyclic aldehydes can be smoothly added to α,β‐unsaturated ketones, esters, and nitriles in aprotic solvents to form γ‐diketones, 4‐oxo carboxylic esters, and 4‐oxo nitriles. Thiazolium salts in the presence of bases are also suitable catalysts; they permit not only addition of aromatic and heterocyclic aldehydes but also the addition of aliphatic aldehydes.
A Survey of Multicast Security Issues and Architectures (1998)

This paper addresses issues relevant to implementing security for IP multicast networks.These issues are of importance to application developers wishing to implement security services for their multicast applications.The paper investigates the steps required to create a secure multicast session including issues of group membership and key distribution.A common simple criteria is established that can be used to evaluate multicast keying architectures.The criteria focuses on the efficiency and scalability of the keying solution.Using this criteria, several keying architectures are evaluated and compared to determine their strengths and weaknesses.
[Vacuum sealing as treatment of soft tissue damage in open fractures]. (1993)

In 1992, 15 of 152 patients with open fractures were treated with vacuum sealing. Drainage tubes are inserted into polyvinyl foam, which is used to fill in the wound or tissue defect. Polyvinyl foam and adjacent skin are covered with a transparent polyurethane dressing which is impermeable to bacteria. The connection of the drainage tubes to a suction device, such as vacuum bottles, produces negative pressure in the polyvinyl foam, which means a high-contact zone of the foam-wound interface. This results in efficient cleaning and conditioning of the wound, with marked proliferation of granulation tissue. Bone infection did not occur in any of our 15 patients; 1 patient sustained a soft tissue infection due to an insufficient sealing technique. When the correct technique was applied the infection cleared up.
Interaction between the Water Soluble Poly{1,4-phenylene-[9,9-bis(4-phenoxy butylsulfonate)]fluorene-2,7-diyl} Copolymer and Ionic Surfactants Followed by Spectroscopic and Conductivity Measurements (2005)

The interaction has been studied in aqueous solutions between a negatively charged conjugated polyelectrolyte poly{1,4-phenylene-[9,9-bis(4-phenoxybutylsulfonate)]fluorene-2,7-diyl} copolymer (PBS-PFP) and several cationic tetraalkylammonium surfactants with different structures (alkyl chain length, counterion, or double alkyl chain), with tetramethylammonium cations and with the anionic surfactant sodium dodecyl sulfate (SDS) by electronic absorption and emission spectroscopy and by conductivity measurements. The results are compared with those previously obtained on the interaction of the same polymer with the nonionic surfactant C12E5. The nature of the electrostatic or hydrophobic polymer-surfactant interactions leads to very different behavior. The polymer induces the aggregation with the cationic surfactants at concentrations well below the critical micelle concentration, while this is inhibited with the anionic SDS, as demonstrated from conductivity measurements. The interaction with cationic surfactants only shows a small dependence on alkyl chain length or counterion and is suggested to be dominated by electrostatic interactions. In contrast to previous studies with the nonionic C12E5, both the cationic and the anionic surfactants quench the PBS-PFP emission intensity, leading also to a decrease in the polymer emission lifetime. However, the interaction with these cationic surfactants leads to the appearance of a new emission band (approximately 525 nm), which may be due to energy hopping to defect sites due to the increase of PBS-PFP interchain interaction favored by charge neutralization of the anionic polymer by cationic surfactant and by hydrophobic interactions involving the surfactant alkyl chains, since the same green band is not observed by adding either tetramethylammonium hydroxide or chloride. This effect suggests that the cationic surfactants are changing the nature of PBS-PFP aggregates. The nature of the polymer and surfactant interactions can, thus, be used to control the spectroscopic and conductivity properties of the polymer, which may have implications in its applications.
Identification and nucleotide sequence of the thymidine kinase gene of Shope fibroma virus (1986)

The thymidine kinase (TK) gene of Shope fibroma virus (SFV), a tumorigenic leporipoxvirus, was localized within the viral genome with degenerate oligonucleotide probes. These probes were constructed to two regions of high sequence conservation between the vaccinia virus TK gene and those of several known eucaryotic cellular TK genes, including human, mouse, hamster, and chicken TK genes. The oligonucleotide probes initially localized the SFV TK gene 50 kilobases (kb) from the right terminus of the 160-kb SFV genome within the 9.5-kb BamHI-HindIII fragment E. Fine-mapping analysis indicated that the TK gene was within a 1.2-kb AvaI-HaeIII fragment, and DNA sequencing of this region revealed an open reading frame capable of encoding a polypeptide of 176 amino acids possessing considerable homology to the TK genes of the vaccinia, variola, and monkeypox orthopoxviruses and also to a variety of cellular TK genes. Homology matrix analysis and homology scores suggest that the SFV TK gene has diverged significantly from its counterpart members in the orthopoxvirus genus. Nevertheless, the presence of conserved upstream open reading frames on the 5' side of all of the poxvirus TK genes indicates a similarity of functional organization between the orthopoxviruses and leporipoxviruses. These data suggest a common ancestral origin for at least some of the unique internal regions of the leporipoxviruses and orthopoxviruses as exemplified by SFV and vaccinia virus, respectively.
Structure and Synthesis of a New Monoterpenoidal Carboxamide from the Seeds of the Thai Medicinal Plant Acacia concinna. (1997)

A new monoterpenoidal carboxamide, concinnamide (1), has been isolated from the seeds of a Thai medicinal plant, Acacia concinna DC. (Leguminosae). Its structure has been revised to (E)-2, 6-dimethyl-6-hydroxy-2, 7-octadienamide by detailed spectroscopic and synthetic studies, though it had been preliminarily assigned as a seven-membered lactam derivative by our previous work. (-)-Concinnamide, (-)-1, was synthesized from (-)-linalool (2) by stepwise oxidation, followed by amidation to confirm the structure. The inhibitory effects of 1 and related compounds on the arachidonate 5-lipoxygenase of RBL-1 cells are also described.
Dielectric surface-relief gratings with high diffraction efficiency (1984)

Diffraction properties of dielectric surface-relief gratings were investigated by solving Maxwell’s equations numerically using the differential method. The diffraction efficiency of a grating with a groove depth about twice as deep as the grating period is comparable with the efficiency of a volume phase grating. Dielectric surface-relief gratings interferometrically recorded in photoresist can possess a high diffraction efficiency of up to 94% (throughput efficiency 85%). Calculated results were also found in good agreement with the experimental data.
Correcting Sample Selection Bias by Unlabeled Data (2007)

We consider the scenario where training and test data are drawn from different distributions, commonly referred to as sample selection bias.Most algorithms for this setting try to first recover sampling distributions and then make appropriate corrections based on the distribution estimate.We present a nonparametric method which directly produces resampling weights without distribution estimation.Our method works by matching distributions between training and testing sets in feature space.Experimental results demonstrate that our method works well in practice.
Quantifying flexibility in EV charging as DR potential: Analysis of two real-world data sets (2016)

The increasing adoption of electric vehicles (EVs) presents both challenges and opportunities for the power grid, especially for distribution system operators (DSOs). The demand represented by EVs can be significant, but on the other hand, sojourn times of EVs could be longer than the time required to charge their batteries to the desired level (e.g., to cover the next trip). The latter observation means that the electrical load from EVs is characterized by a certain level of flexibility, which could be exploited for example in demand response (DR) approaches (e.g., to balance generation from renewable energy sources). This paper analyzes two data sets, one from a charging-at-home field trial in Flanders (about 8.5k charging sessions) and another from a large-scale EV public charging pole deployment in The Netherlands (more than 1M sessions). We rigorously analyze the collected data and quantify aforementioned flexibility: (1) we characterize the EV charging behavior by clustering the arrival and departure time combinations, identifying three behaviors (charging near home, charging near work, and park to charge), (2) we fit statistical models for the sojourn time, and flexibility (i.e., non-charging idle time) for each type of observed behavior, and (3) quantify the the potential of DR exploitation as the maximal load that could be achieved by coordinating EV charging for a given time of day t, continuously until t + Δ.
A double-level-V/sub th/ select gate array architecture for multilevel NAND flash memories (1996)

In multilevel flash memories, the threshold voltages of the memory cells should be controlled precisely. This paper describes how in a conventional NAND flash memory, the threshold voltages of the memory cells fluctuate due to array noise during the bit-by-bit program verify operation, and as a result, the threshold voltage distribution becomes wider. This paper describes a new array architecture, "A double-level-V/sub th/ select gate array architecture" to eliminate the array noise, together with a reduction of the cell area. The array noise is mainly caused by interbitline capacitive coupling noise and by the high resistance of the diffused source-line. The threshold voltage fluctuation can be as much as 0.7 V in a conventional array. In the proposed array, bitlines are alternately selected, and the unselected bitlines are used as low resistance source-lines. Moreover, the unselected bitlines form a shield between the neighboring selected bitlines. As a result, the array noise is strongly suppressed. The threshold voltage fluctuation is estimated to be as small as 0.03 V in the proposed array and a reliable operation of a multilevel NAND flash memory can be realized.
Oral Salmonella typhimurium (AroA-) vaccine expressing a major leishmanial surface protein (gp63) preferentially induces T helper 1 cells and protective immunity against leishmaniasis. (1990)

The gp63 gene of Leishmania major was transformed into the AroA- vaccine strain of Salmonella typhimurium (SL3261). The construct (SL3261-gp63), which stably expresses the gp63 Ag in vitro, was used to immunize CBA mice by the oral route. Spleen cells from mice inoculated with SL3261-gp63 developed antibody and proliferative T cell response to L. major. They did not express detectable delayed-type hypersensitivity reactivity. The activated T cells are mainly CD4+ and secrete IL-2 and IFN-gamma but no IL-4. The orally immunized mice developed significant resistance against a challenge L. major infection. We have, therefore, demonstrated the feasibility of oral vaccination against leishmaniasis and that the oral route of antigen delivery via the heterologous carrier may preferentially induce Th1 subsets of CD4+ cells.
Regulation of Concentrated Animal Feeding Operations: The Legal Context (2000)

Abstract Tasty or not, the human health and legal ramifications of literally “bringing home the bacon” have intensified. The recent declining number of family pig farms has been paralleled with a rise in corporate-run hog complexes.1 These complexes, commonly referred to as Concentrated Animal Feeding Operations or “CAFOs,” often manage tens of thousands of animals at a single site. See U.S. Environmental Protection Agency, Guide Manual on NPDES Regulations for Concentrated Animal Feeding Operations, at 4 (December 1995). Such large numbers of animals “concentrated” in a relatively small area produce enormous amounts of fecal waste. This waste is laced with a variety of compounds that may adversely affect human health. See health and environmental impacts of CAFOs, infra, at 10, 11. Effects range from water pollution due to excess nitrogen and phosphorus, to breathing difficulties from ammonia and hydrogen sulfide gases. See J. Schwab, Planning and Zoning for Concentrated Animal Feeding Operations, Planning Advisory Service Report No. 482 at 12 (December 1998). Numerous nuisance lawsuits have arisen as citizens fight to prevent or abate these adverse health affects resulting from CAFOs.
Polymeric arrayed-waveguide grating multiplexeroperating around 1.3 µm (1994)

An arrayed-waveguide grating multiplexer is demonstrated, which is fabricated using deuterated fluoro-methacrylate polymers. A channel spacing of 0.65 nm, a crosstalk of less than –20dB, and a loss of 7.8–11 dB are obtained around 1.3 µm. The multiplexer exhibits small polarisation shift of 0.03 nm without special compensation methods.
Serum-free production of recombinant proteins and adenoviral vectors by 293SF-3F6 cells (1998)

This article describes the step-wise approach undertaken to select a serum-free medium (SFM) for the efficient production of a recombinant adenoviral vectors expressing beta-galactosidase (Ad5 CMV-LacZ), in the complementing human embryonic kidney 293S cells. In the first step, a 293S-derived transfectoma, secreting a soluble epidermal growth factor receptor sEGFr (D2-22), was used to estimate the potential of selected serum-free formulations to support the production of a recombinant protein as compared to serum-containing medium. Assays showed that only one among six commercial serum-free formulations could support both sEGFr production and cell growth in static or suspension culture. In commercially available calcium-containing serum-free formulations, the cell aggregates reached up to 3 mm in diameter. In the second step, 293S cells were gradually adapted to a low-calcium version of the selected medium (LC-SFM). Cells were cloned, then screened according to their ability to grow at a rate and an extent comparable to parental cells in serum-containing medium (standard) as single cells or small aggregates. The 293SF-3F6 clone, first adapted to and then cloned in the selected serum-free medium, was selected for further experiments. Bioreactor run performed with the 293SF-3F6 clone showed similar growth curve as in the shake-flask controls. In the final step, the recombinant viral vector productivity of the 293S cells and the 293SF-3F6 clone was tested. The 293SF-3F6 cells infected by Ad5 CMV-LacZ in 3 L-scale bioreactor maintained the specific productivities of both beta-galactosidase and adenoviral vector equivalent to the shake-flask controls in suspension culture. Results from this study clearly demonstrate that the 293SF-3F6 cell line thus selected may be used either for establishing stable transfected cell line or for the production of adenoviral vectors required for gene therapy studies.