gebhart/patrepeval huggingface dataset:
Aurora Kinase Inhibitor ZM447439 Blocks Chromosome-induced Spindle Assembly, the Completion of Chromosome Condensation, and the Establishment of the Spindle Integrity Checkpoint in<i>Xenopus</i>Egg Extracts (2004)

The Aurora family kinases contribute to accurate progression through several mitotic events. ZM447439 ("ZM"), the first Aurora family kinase inhibitor to be developed and characterized, was previously found to interfere with the mitotic spindle integrity checkpoint and chromosome segregation. Here, we have used extracts of Xenopus eggs, which normally proceed through the early embryonic cell cycles in the absence of functional checkpoints, to distinguish between ZM's effects on the basic cell cycle machinery and its effects on checkpoints. ZM clearly had no effect on either the kinetics or amplitude in the oscillations of activity of several key cell cycle regulators. It did, however, have striking effects on chromosome morphology. In the presence of ZM, chromosome condensation began on schedule but then failed to progress properly; instead, the chromosomes underwent premature decondensation during mid-mitosis. ZM strongly interfered with mitotic spindle assembly by inhibiting the formation of microtubules that are nucleated/stabilized by chromatin. By contrast, ZM had little effect on the assembly of microtubules by centrosomes at the spindle poles. Finally, under conditions where the spindle integrity checkpoint was experimentally induced, ZM blocked the establishment, but not the maintenance, of the checkpoint, at a point upstream of the checkpoint protein Mad2. These results show that Aurora kinase activity is required to ensure the maintenance of condensed chromosomes, the generation of chromosome-induced spindle microtubules, and activation of the spindle integrity checkpoint.
Salmonella enteritidis FliC (Flagella Filament Protein) Induces Human β-Defensin-2 mRNA Production by Caco-2 Cells (2001)

Antimicrobial peptides are crucial for host defense at mucosal surfaces. Bacterial factors responsible for induction of human beta-defensin-2 (hBD-2) mRNA expression in Caco-2 human carcinoma cells were determined. Salmonella enteritidis, Salmonella typhimurium, Salmonella typhi, Salmonella dublin, and culture supernatants of these strains induced hBD-2 mRNA expression in Caco-2 human carcinoma cells. Using luciferase as a reporter gene for a approximately 2.1-kilobase pair hBD-2 promoter, the hBD-2-inducing factor in culture supernatant of S. enteritidis was isolated. The supernatant factor was heat-stable and proteinase-sensitive. After purification by anion exchange and gel filtration chromatography, the hBD-2-inducing factor was identified as a 53-kDa monomeric protein with the amino-terminal sequence AQVINTNSLSLLTQNNLNK, which is identical to that of the flagella filament structural protein (FliC) of S. enteritidis. Consistent with this finding, the 53-kDa protein reacted with anti-FliC antibody, which prevented its induction of hBD-2 mRNA in Caco-2 cells. In agreement, the hBD-2-inducing activity in culture supernatant was completely neutralized by anti-FliC antibody. In gel retardation analyses, FliC increased binding of NF-kappaB (p65 homodimer) to hBD-2 gene promoter sequences. We conclude that S. enteritidis FliC induces hBD-2 expression in Caco-2 cells via NF-kappaB activation and thus plays an important role in up-regulation of the innate immune response.
EphrinB1 Is Essential in T-cell-T-cell Co-operation during T-cell Activation (2004)

Eph kinases are the largest family of receptor tyrosine kinases, and their ligands are ephrins (EFNs), which are also cell surface molecules. We have very limited knowledge about the expression and function of these kinases and their ligands in the immune system. In this study we investigated the effect of EFNB1 on mouse T-cells. EFNB1 and the Eph kinases it interacts with (collectively called EFNB1 receptors (EFNB1R)) were expressed on T-cells, B cells, and monocytes/macrophages. Some T-cells were double positive for EFNB1 and EFBB1R. Solid phase EFNB1 in the presence of suboptimal TCR ligation augmented T-cell responses in terms interferon-gamma secretion, proliferation, and cytotoxic T lymphocyte activity but not interleukin-2 production. After T-cell receptor (TCR) ligation, EFNB1R congregated to TCR caps, and then both of them translocated to raft caps. This provides a morphological basis for EFNB1R to enhance TCR signaling. Further downstream of the signaling pathway, EFNB1R stimulation led to increased LAT (linker for activation of T-cells) phosphorylation and p44/42 and p38 MAPK activation. Similar to CD28 costimulation, EFNB1R costimulation was insensitive to cyclosporin A inhibition. On the other hand, unlike the former, EFNB1R costimulation failed to activate Akt, which is essential in triggering interleukin-2 production. Our study suggests that EFNB1 is pivotal in T-cell-T-cell costimulation and in reducing T-cell response threshold to antigen stimulation.
Pattern formation during the evaporation of a colloidal nanoliter drop: a numerical and experimental study (2009)

An efficient way to precisely pattern particles on solid surfaces is to dispense and evaporate colloidal drops, as for bioassays. The dried deposits often exhibit complex structures exemplified by the coffee ring pattern, where most particles have accumulated at the periphery of the deposit. In this work, the formation of deposits during the drying of nanoliter colloidal drops on a flat substrate is investigated numerically and experimentally. A finite-element numerical model is developed that solves the Navier-Stokes, heat and mass transport equations in a Lagrangian framework. The diffusion of vapor in the atmosphere is solved numerically, providing an exact boundary condition for the evaporative flux at the droplet-air interface. Laplace stresses and thermal Marangoni stresses are accounted for. The particle concentration is tracked by solving a continuum advection-diffusion equation. Wetting line motion and the interaction of the free surface of the drop with the growing deposit are modeled based on criteria on wetting angles. Numerical results for evaporation times and flow field are in very good agreement with published experimental and theoretical results. We also performed transient visualization experiments of water and isopropanol drops loaded with polystyrene microsphere evaporating on respectively glass and polydimethylsiloxane substrates. Measured evaporation times, deposit shape and sizes, and flow fields are in very good agreement with the numerical results. Different flow patterns caused by the competition of Marangoni loops and radial flow are shown to determine the deposit shape to be either a ring-like pattern or a homogeneous bump.
Proteomic analysis of albumin and globulin fractions of pea (Pisum sativum L.) seeds (2014)

Two-dimensional gel electrophoresis proved to be a useful tool for identifying pea proteins. Patterns of spots with similar isoelectric points and different molecular weights or spots with different isoelectric points and similar molecular weights play an important role in proteome analysis. The regions characteristic of albumin, globulin and legumin and vicilin fractions of globulin with typical MW and pi values were identified as the results of performed 2D electrophoretic separations of pea proteins. 2D gel electrophoresis of albumins and the vicilin fraction of globulins revealed the presence of 4 and 2 spots, respectively, representing potentially allergenic proteins. They probably corresponded to vicilin fragments synthesized during post-translational modification of the analysed protein.
Leukotriene production by fresh human bone marrow cells: evidence of altered lipoxygenase activity in chronic myelocytic leukemia. (1987)

The metabolism of arachidonic acid through the lipoxygenase pathway was studied in suspensions of fresh human bone marrow cells from eight patients with chronic myelocytic leukemia (CML) and 10 normal controls. After the cells were incubated with the calcium ionophore A23187 and arachidonic acid, a technique including reverse- and straight-phase high-pressure liquid chromatography (HPLC) was employed to isolate and detect different lipoxygenase-mediated compounds. The detected compounds included leukotriene B4 (LTB4), with its two major nonenzymatic isomers 6-trans-LTB4 and 12-epi-6-trans-LTB4 5S,12S-DHETE, and the monohydroxy eicosatetraenoic acids 5-HETE, 12-HETE, and 15-HETE. The pattern of lipoxygenase-mediated products from the bone marrows was similar to that previously described from human peripheral blood. Of eight bone marrow samples from CML patients, five expressed values above 600 ng LTB4/10(8) nucleated cells, as compared to only one out of 10 controls. In contrast, the CML patients produced significantly lower amounts of both the double-dioxygenation product 5S,12S-DHETE (56.8 +/- 16.0 ng [mean +/- SE] versus 146.1 +/- 31.3 ng; p less than 0.05) and the monohydroxy acid 12-HETE (965 +/- 351 ng versus 4390 +/- 1801 ng; p less than 0.05), indicating a 12-lipoxygenase deficiency. The present results show that leukotrienes are formed by human bone marrow cells and further suggest the existence of altered lipoxygenase activity in CML.
Construction of a<i>tetR</i>-Integrated<i>Salmonella enterica</i>Serovar Typhi CVD908 Strain That Tightly Controls Expression of the Major Merozoite Surface Protein of<i>Plasmodium falciparum</i>for Applications in Human Vaccine Production (2002)

Attenuated Salmonella strains are an attractive live vector for delivery of a foreign antigen to the human immune system. However, the problem with this vector lies with plasmid segregation and the low level of expression of the foreign gene in vivo when constitutive expression is employed, leading to a diminished immune response. We have established inducible expressions of foreign genes in the Salmonella enterica serovar Typhi CVD908 vaccine strain using the tetracycline response regulatory promoter. To set up this system, a tetracycline repressor (tetR) was integrated into a defined Delta aroC locus of the chromosome via suicide plasmid pJG12/tetR-neo. To remove the neo gene conferring kanamycin resistance from the locus, a cre expression vector under the control of the tetracycline response promoter was transformed into the clone; expression of the Cre recombinase excised the neo gene and generated the end strain CVD908-tetR. Expression of the luciferase reporter gene in this strain is dependent on the presence of tetracycline in the medium and can be regulated up to 4,773-fold. Moreover, the tightly controlled expression of major merozoite surface protein 1 (MSP1) and parts of Plasmodium falciparum was achieved, and the product yield was increased when the inducible expression system was employed. Inoculation of bacteria harboring plasmid pZE11/MSP1(42) in mice produced the protein in liver and spleen controlled by the inducer. The persistence of the plasmid-carrying bacteria in mice was determined. Peak colonization of both liver and spleen was detected on the third day postinoculation and was followed by a decline in growth curves. After 14 days postinfection, the majority of the bacteria (>90%) recovered from the liver and spleen of the mice retained the plasmid when expression was induced; this clearly indicated that stability of the expression vector in vivo was improved by inducible expression. Establishment of the regulatory system in the vaccine strain may broaden the range of its use by enhancing plasmid stability and expression levels in vivo. Moreover, the availability of the vaccine strain inducibly expressing the entire MSP1 provides possibilities for examining its immunogenicity, particularly the cellular response in animal models.
Zinc Borosilicate Thick Films as a Ag-Protective Layer for Dye-Sensitized Solar Cells (2009)

A zinc borosilicate glass having a low softening temperature of 490 o C has been investigated as a protective layer for Ag patterns against chemical reactions with a I -/I 3 -electrolyte in dye-sensitized solar cells (DSSCs). A thick glass layer was prepared by the typical screen printing and firing processes to obtain a final thickness of ~5 m. The chemical leaching performance of the glass layer in the electrolyte revealed that the reactive Ag pattern can be significantly protected by utilizing the low softening protective layer. The electrical resistance of the FTO-coated glass substrate was effectively maintained at a low value of ~27 as long as the glass layer was well densified at a sufficiently high temperature of ~520 o C. The transmittance of the layer was near 60%, depending on the firing temperature of the glass layer.
Probability of Collision Between Space Objects (2000)

The International Space Station is being designed to perform debris avoidance maneuvers based on certain criteria developed from the probability of collision Pc. Existing methods to determine the Pc are based on the dee nitionofacollision/conjunctionplanethatcontainsallofthepositionuncertaintyassociatedwiththeproblem.In thispaperwedevelopa directand more naturalway of obtaining probability ofcollision and presentanalternative but equivalent dee nition for Pc that leads to the same results obtained earlier. Because debris avoidance is crucial for every orbiting asset in low Earth orbit, a study of this nature helps to establish the equivalence of different methods for risk assessment and evaluation. HE International Space Station (ISS) shall continuously face the threat of collision with orbiting debris. Hence, there needs to be a comprehensive methodology that can assess the risks posed byindividualdebrisencountersand suggestmaneuverswhenneces- sary. Such a study shall not only benee t the ISS, but also any future orbital asset placed in low Earth orbits. Thus, although we refer to the ISS in the rest of our paper, the analysis presented here holds true for any other orbiting asset of size and orbit comparable with that of the upcoming ISS. Space shuttle (SS) maneuvers are commanded to avoid poten- tial collisions with cataloged space objects (maintained by the U.S. Space Command ) whenever the estimated conjunction with an ob- jectfalls within a box centered on the estimated SSposition. The di- mensionsofthisconjunctionboxare §5 kmin thein-track direction and §2kmintheradialandout-of-planedirections.Thedimensions of such a conjunction box are probably based on prior estimates of position error covariances. The determination was made that this simple criterion, or any other known deterministic criterion 1,2 when applied to the ISS, would result in too many maneuvers. 3 In addi- tion, unnecessary maneuvers waste fuel and hamper the micrograv- ity experiments onboard the ISS. Although the size of the conjunc- tion box could be decreased to decrease the manuever rate, such a step clearly increases the risk to unacceptable levels. Therefore, the ISS needs a more rigorous probability-based approach for collision avoidance. 4
Expression and processing of mouse proopiomelanocortin in bovine adrenal chromaffin cells. A model system to study tissue-specific prohormone processing (1991)

Many neuroendocrine precursor proteins, such as proopiomelanocortin (POMC), are cleaved in a tissue specific manner at distinct pairs of basic amino acids. Elucidating the specificity of the prohormone endoprotease(s) is essential to understanding cleavage specificity. However, isolation of these enzymes has been difficult, due to the inability to distinguish authentic maturation enzyme from the many other trypsin-like activities present in tissue homogenates. Recently, a "signature" of the insulin cell endoprotease(s) was defined in vivo by assessing the processing of a series of mutant cleavage sites in a model prohormone, mouse POMC (mPOMC) (Thorne, B. A., and Thomas, G. (1990) J. Biol. Chem. 265, 8436-8443. To investigate mechanisms of tissue-specific processing, we sought to identify the endoprotease signature of a cell having a processing phenotype distinct from insulinoma cells. In this report, the cleavage site specificity of the endoprotease(s) expressed in bovine adrenal chromaffin cells is examined. High levels of mPOMC (1.6 pmol/10(6) cells) were expressed in these cells using a vaccinia virus vector, and the precursor was targeted to the regulated secretory pathway. Analysis of POMC-derived peptides revealed that chromaffin cells processed the prohormone to a set of peptides highly similar to anterior pituitary corticotrophs, including adrenocorticotropin hormone (ACTH) and beta-lipotropin, gamma-lipotropin, and beta-endorphin. This processing contrasted with the pattern of cleavage site utilization in Rin m5F insulinoma cells, which more closely resembled that of the intermediate pituitary melanotrophs. However, the processing preference for the sequences of pairs of basic amino acids (as tested using the entire series of mutant cleavage sites; -LysArg- (native), -ArgArg-, -ArgLys-, -LysLys-, -HisArg-, -MetArg- at the ACTH/beta-lipotropin junction and -LysLys- (native), -LysArg-, -ArgArg-, -ArgLys- in beta-endorphin) was the same in both insulinoma and adrenal chromaffin cells, suggesting recognition and cleavage by similar enzymes in both cell types. The cell-specific processing of mPOMC may thus result from expression of a common core set of processing enzymes and factors unique to each cell type affecting the enzyme accessibility to precursor cleavage sites.
Adaptive noise cancelling applied to image restoration (2005)

The one-dimensional adaptive noise cancelling principle is applied to two-dimensional imagery to remove line-interferences and random noise. For destriping LANDSAT or TM images, the preliminary results indicate that application of the adaptive cancelling principle is a promising and effective approach. Two different implementations are discussed. One models the stripings as periodic interferences and includes such a model in the adaptive cancelling scheme. The other one adaptively 'zero-means' the striped image on a line-by-line basis. For 'cancelling' wide-band noise, a novel bootstrap scheme is used to overcome the unavailability of the secondary noise source required by the adaptive cancelling scheme. The result is satisfactory and this novel scheme is applicable to time-signals as well.
Chemical Oxidation Technologies: Ultraviolet Light/Hydrogen Peroxide, Fenton's Reagent, and Titanium Dioxide-Assisted Photocatalysis (1993)

The application status and potential of three chemical oxidation treatment methods which generate powerful oxidants (hydroxyl radicals): ultraviolet light (UV)/hydrogen peroxide (H2O2) process, Fenton's reagent treatment, and titanium dioxide (TiO2)-assisted photocatalytic degradation, are described and discussed. These oxidation methods are known to effectively degrade and, in several cases, mineralize contaminants ranging from inorganic compounds (such as cyanides) to chlorinated aliphatic compounds and complex aromatic compounds in reaction times on the order of a few minutes to a few hours. Of the three oxidation systems discussed, the technology for the UV/H2O2 process is the most advanced, with numerous successful full-scale treatment units already in existence. Applications of both the Fenton's reagent and TiO2-assisted photodegradation processes are currently being developed, with the concepts proven in numerous laboratory-scale studies for a wide range of contaminants. However, both of these processes have only been studied at the pilot/field scale to a limited extent. The application of Fenton's reagent as a pretreatment step prior to biological treatment for industrial wastes and contaminated soils appears promising. Improved system configuration and quantum efficiency of photoreactors are likely to improve the economics of TiO2-assisted photodegradation for groundwater treatment, especially with the use of solar illumination.
Preparation and application of ion exchangers with azacrown‐ether and cryptands to alkali and alkaline‐earth cation separation (1982)

Abstract Three macrocyclic exchangers are prepared and characterized by grafting on chloromethylated styrene‐divinylbenzene resin, one diazacrown‐ether (7,16‐bis(2‐hydroxyethyl)‐1,4,10,13‐tetraoxa‐7,16‐diazacyclooctadecane ( 1 )), one cryptand (21‐(2‐aminoethyl)‐4,7,13,16‐tetraoxa‐1,10,21‐triazabicyclo[8.8.5]tricosane ( 2b )), and one polymeric cryptand (poly(4,7,13,16‐tetraoxa‐1,10,21,24‐tetraazabicyclo[8.8.8]hexacos‐21,24‐ylene‐2,7‐dihydroxyoctamethylene ( 3 )). Separation of alkali and alkaline‐earth cations is studied by liquid column chromatography with these exchangers in water. The separations occur according to the binding properties of the ligands in solution with an increase of the binding constants in the resin. The resolutions obtained are limited by relatively low capacities of the resins (0,4–0,9 mmol M n+ /g) and mainly by slow diffusion of the cations inside the resins.
Malware classification based on extracted API sequences using static analysis (2012)

In this paper, we propose a highly accurate, automatic malware-classification method, which extracts features by conducting static analysis of malware samples and the structure of malware source code. In the proposed extraction method, the presence and absence of particular pairs of consecutive Application Program Interface function calls (APIs) in the API-sequence graph are compared with those in the executable code for a sample within which malware features have been identified. To determine the degree of similarity between samples, Dice's coefficient is applied. To visualize the grouping of samples with similar features, we use hierarchical cluster analysis based on the extracted features. The results of the analysis are presented as a dendrogram with colored nodes for each family name. To evaluate the proposed method, we set up a malware-analysis system comprising a combination of disassembler, control-flow analyzer, API-sequence extractor, similarity calculator and hierarchical cluster analyzer. We acquired 4,684 malware samples, from 1,821 of which we successfully extracted API sequences to which we applied our proposed classification method. We found that the automatic hierarchical cluster analysis was processed rapidly, with significant clusters of variant groups obtained.
HTS Electrical System for a Distributed Propulsion Aircraft (2015)

As the commercial aircraft industry aims to meet the challenge of 2050 emissions targets, it becomes apparent that unconventional aircraft configurations may be necessary to achieve them. Distributed electrical propulsion offers opportunities for improving aircraft efficiency. However, the conversion and transfer of power could prove prohibitive when using conventional machines and conductors due to weight and inefficiency. An aircraft with distributed propulsion and boundary layer ingestion is considered in this paper, and the current view of the future of high-temperature superconductor technology as applied to aircraft is explained.