gebhart/patrepeval huggingface dataset:
Multi-Stage Particle Separation based on Microstructure Filtration and Dielectrophoresis (2019)

Particle separation is important in chemical and biomedical analysis. Among all particle separation approaches, microstructure filtration which based particles size difference has turned into one of the most commonly methods. By controlling the movement of particles, dielectrophoresis has also been widely adopted in particle separation. This work presents a microfluidic device which combines the advantages of microfilters and dielectrophoresis to separate micro-particles and cells. A three-dimensional (3D) model was developed to calculate the distributions of the electric field gradient at the two filter stages. Polystyrene particles with three different sizes were separated by micropillar array structure by applying a 35-Vpp AC voltage at 10 KHz. The blocked particles were pushed off the filters under the negative dielectrophoretic force and drag force. A mixture of Haematococcus pluvialis cells and Bracteacoccus engadinensis cells with different sizes were also successfully separated by this device, which proved that the device can separate both biological samples and polystyrene particles.
A Comparison of ABC, Unlabeled Antibody and Conjugated Immunohistochemical Methods with Monoclonal and Polyclonal Antibodies— An Examination of Germinal Center of Tonsils (1983)

Staining of lymphoid tissues with anti-immunoglobulin antibodies often is complicated by heavy interstitial staining and potential unwanted binding through Fc receptors. This problem is aggravated in the germinal center because of an unusually intense extracellular staining. In an attempt to examine a variety of staining methods, we found both poly- or monoclonal antibodies produced satisfactory results only if a suitable method was employed, such as a two-step or three-step avidinbiotin-peroxidase complex (ABC) method. Other staining technics for example, indirect conjugate or four-layer PAP methods, failed to provide a clean background. The use of F(ab')2 fragments did not significantly improve the staining quality, indicating that the role of the Fc receptors in inducing nonspecific staining is not significant in acetone-fixed frozen tissues. Germinal centers also were studied with a panel of monoclonal and polyclonal anti-Ig antibodies, and the results indicated that the number of surface or cytoplasmic Ig-positive cells in the germinal center is variable from one follicle to another. IgG+ cells are generally sparse (less than 10%) and are scattered in the light zone of follicles. IgA+ cells constitute about 0-10% of the total cell population and tend to be distributed randomly either in the dark or light zones. IgM+ and IgD+ cells may be scanty (less than 10%) or abundant (50-70%). The IgM+ and IgD+ cells tend to localize in the dark zone of the follicles. The results indicate that, depending on the stage of differentiation or transformation of the germinal center, s-Ig or c-Ig expression is highly variable.
Fungal Endophytes in Stems and Leaves: From Latent Pathogen to Mutualistic Symbiont (1988)

Endophytes are fungi that form inapparent infections within leaves and stems of healthy plants. Closely related to virulent pathogens but with limited, if any, pathogenic effects themselves, many endophytes protect host plants from natural enemies. Animal herbivores and, in some cases, pathogenic microbes are poisoned by the mycotoxins produced by endophytes. "Constitutive mutualism" is the relatively faithful association, usually with grasses, of endophytes that infect host ovules and are propagated in host seed; substantial fungal biomass with probable high metabolic cost develops throughout the aerial parts of the host plant. "Inducible mutualist" endophytes are not involved with host seed and disseminate independently through air or in water. Infecting only vegetative parts of the host and remaining metabolically inactive for long periods with relatively little fungal biomass, inducible mutualists grow rapidly and produce toxins against herbivores when damaged host tissues provide new sites for infection. I surmise that endophytes may be as common among plants as are mycorrhyzae.
Evidence That the Cannabinoid CB1 Receptor Is a 2-Arachidonoylglycerol Receptor (1999)

An endogenous cannabimimetic molecule, 2-arachidonoylglycerol, induces a rapid, transient increase in intracellular free Ca2+ concentrations in NG108-15 cells through a cannabinoid CB1 receptor-dependent mechanism. We examined the activities of 24 relevant compounds (2-arachidonoylglycerol, its structural analogues, and several synthetic cannabinoids). We found that 2-arachidonoylglycerol is the most potent compound examined so far: its activity was detectable from as low as 0.3 nM, and the maximal response induced by 2-arachidonoylglycerol exceeded the responses induced by others. Activities of HU-210 and CP55940, potent cannabinoid receptor agonists, were also detectable from as low as 0.3 nM, whereas the maximal responses induced by these compounds were low compared with 2-arachidonoylglycerol. Anandamide was also found to act as a partial agonist in this assay system. We confirmed that free arachidonic acid failed to elicit a response. Furthermore, we found that a metabolically stable ether-linked analogue of 2-arachidonoylglycerol possesses appreciable agonistic activity, although its activity was apparently lower than that of 2-arachidonoylglycerol. We also confirmed that pretreating cells with various cannabinoid receptor agonists nullified the response induced by 2-arachidonoylglycerol, whereas pretreating cells with other neurotransmitters or neuromodulators did not affect the response. These results strongly suggested that the cannabinoid CB1 receptor is originally a 2-arachidonoylglycerol receptor, and 2-arachidonoylglycerol is the intrinsic physiological ligand for the cannabinoid CB1 receptor.
Oligomerization of G Protein-Coupled Receptors:  Past, Present, and Future (2004)

G protein-coupled receptor (GPCR)-mediated signal transduction has been studied for more than a century. Despite the intense focus on this class of proteins, a molecular understanding of what constitutes the functional form of the receptor is still uncertain. GPCRs have traditionally been conceptualized as monomeric proteins, and this view has changed little over the years until relatively recently. Recent biochemical and biophysical studies have challenged this traditional concept, and point instead to a mechanistic view of signal transduction wherein the receptor functions as an oligomer. Cooperative interactions within such an oligomeric array may be critical for the propagation of an external signal across the cell membrane and to the G protein, and may therefore underlie the mechanistic basis of signaling.
The Mr 193,000 vault protein is up-regulated in multidrug-resistant cancer cell lines. (2000)

Vaults are 13 megadalton ribonucleoprotein particles composed largely of the major vault protein (MVP) and two high molecular weight proteins, p240 and p193, and a small vault RNA (vRNA). Increased levels of MVP expression, vault-associated vRNA, and vaults have been linked directly to multidrug resistance (MDR). To further define the putative role of vaults in MDR, we produced monoclonal antibodies against the Mr 193,000 vault protein and studied its expression levels in various multidrug-resistant cell lines. We find that, like MVP, p193 mRNA and protein levels are increased in various multidrug-resistant cell lines. Subcellular fractionation of vault particles revealed that vault-associated p193 levels are increased in multidrug-resistant cells as compared with the parental, drug-sensitive cells. Furthermore, protein analysis of postnuclear supernatants and co-immunoprecipitation studies show that drug-sensitive MVP-transfected tumor cells lack this up-regulation in vault-associated p193. Our observations indicate that vault formation is limited not only by the expression of the MVP but also by the expression or assembly of at least one of the other vault proteins.
Nonlinear response of silicon photonic crystal micresonators excited via an integrated waveguide and fiber taper (2005)

A technique is demonstrated which efficiently transfers light between a tapered standard single-mode optical fiber and a high-Q, ultra-small mode volume, silicon photonic crystal resonant cavity. Cavity mode quality factors of 4.7x10(4) are measured, and a total fiber-to-cavity coupling efficiency of 44% is demonstrated. Using this efficient cavity input and output channel, the steady-state nonlinear absorption and dispersion of the photonic crystal cavity is studied. Optical bistability is observed for fiber input powers as low as 250 microW, corresponding to a dropped power of 100 microW and 3 fJ of stored cavity energy. A high-density effective free-carrier lifetime for these silicon photonic crystal resonators of ~ 0.5 ns is also estimated from power dependent loss and dispersion measurements.
Binary optics: the optics technology of the 1990s (1990)

Through advances in semiconductor miniaturization technology, microrelief patterns with characteristic dimensions as small as the wavelength of light can now be mass-produced. In a classic example of technology transfer, this capability is allowing optics designers, for the first time/ we believe, to create innovative optical components which promise to rejuvenate a failing U.S. optics industry.
Immunogenicity of WHO-17D and Brazilian 17DD yellow fever vaccines: a randomized trial (2004)

The equivalent immunogenicity of yellow fever vaccines from the 17D and 17DD substrains was demonstrated for the first time in placebo-controlled double-blind randomized trial. The study completed the clinical validation process of a new vaccine seed-lot, provided evidence for use of alternative attenuated virus substrains in vaccine production for a major manufacturer, and for the utilization of the 17DD vaccine in other countries.
Effect of location of the sensor on reflectance pulse oximetry (1997)

Objective The influence of the location of the sensor on reflectance pulse oximetry during fetal monitoring in labour was investigated using the newborn infant as a model. Methods Seven healthy infants were studied between 19 and 48 hours after term delivery. Recordings of reflectance pulse oximetry were obtained from eight different sites on the infant's head. The relative changes in red to infrared light (R/IR) were determined. In pulse oximetry R/IR values are converted to arterial oxygen values by means of an empirically derived calibration curve. Results Significantly lower R/IR values were found at the forehead compared with the fontanelle, the parietal and occipital position, and the temporal area. Conversion to oxygen saturation values revealed a difference of up to 13.4% in oxygen saturation between the forehead and the occipital area. Conclusion Assuming that the arterial blood oxygen saturation did not change substantially, our findings indicate that in reflectance pulse oximetry there is no unique relation between R/IR and arterial oxygen saturation. The differences in reflectance pulse oximetry at the various sites are explained by differences in optical properties (scattering and absorption) of the tissue underneath the sensor. These will affect the red and infrared light reaching the detectors in a different way, and consequently R/IR changes. Because during intrapartum monitoring exact positioning of the sensor on the fetal head is usually impossible, the accuracy of fetal reflectance pulse oximetry is impaired.
Inhibition of Membrane-Type 1 Matrix Metalloproteinase by Hydroxamate Inhibitors:  An Examination of the Subsite Pocket (1998)

The membrane-type 1 matrix metalloproteinase (MT1-MMP) has been reported to mediate the activation of pro-gelatinase A (proMMP-2), which is associated with tumor proliferation and metastasis. MT1-MMP can also digest extracellular matrix (ECM) such as interstitial collagens, gelatin, and proteoglycan and thus may play an important role in pathophysiological digestion of ECM. We studied the inhibitory effect of various hydroxamate MMP inhibitors, including known inhibitors such as BB-94, BB-2516, GM6001, and Ro31-9790, on a deletion mutant of MT1-MMP lacking the transmembrane domain (DeltaMT1) to further characterize the enzyme and develop a selective inhibitor for MT1-MMP. The evaluation of the inhibitory activities of various hydroxamates reveals general structural profiles affecting selectivities toward MMPs. In particular, a longer side chain at the P1' position is preferable for the binding to MMP-2, -3, and -9 and MT1-MMP. For the P2' position, an alpha-branched alkyl group is critical for the binding toward DeltaMT1, while the introduction of a bulky group at the alpha-position of hydroxamic acid seems to diminish the activity against DeltaMT1. Summation of the data on the sensitivity of DeltaMT1 to various hydroxamate inhibitors indicates that (1) the volume of the S1' subsite of DeltaMT1 is similar to that of MMP-2, -3, and -9, which is bigger than that of MMP-1, and (2) the S1 and S2' subsites are narrower than those in other MMPs. On the basis of these results, the hydroxamates with a P1' phenylpropyl and P2' alpha-branched alkyl group were synthesized and evaluated for inhibitory activity. These inhibitors (1h,i) showed strong activity against DeltaMT1 over MMP-1, but no selectivity between DeltaMT1 and MMP-9. These results are explained using molecular modeling studies conducted on MT1-MMP.
Specificity of Bactericidal Antibody Response to Serogroup B Meningococcal Strains in Brazilian Children after Immunization with an Outer Membrane Vaccine (1998)

Pre- and postvaccination serum samples from 77 children aged 2 to 6 years, who received the Cuban BC vaccine (B:4:P1.15), were analyzed for bactericidal antibodies against a local B:4:P1.15 strain (N44/89). Sera from 16 individuals with bactericidal antibodies against the B:4:P1.15 strain were tested against 23 Brazilian isolates. These include B:4 strains of distinct serosubtypes: P1.15, P1.7,1, P1.3, P1.9, P1.nt, and a B:8,19,23:P1.16 strain. A Cuban B:4:P1.15 strain (Cu385/83) was also included in the study. The specificities of bactericidal antibodies were analyzed by using mutant strains lacking a class 1 protein (PorA protein) or a class 5 protein or both. The results indicated that PorA and class 5 proteins are the main targets recognized by the bactericidal antibodies of vaccinees. Nonetheless, a complex pattern of recognition by bactericidal antibodies was found, and vaccinees were grouped according to antibody specificity. Antibodies from some individuals recognized PorA of serosubtype P1.15. However, antibodies from these individuals could not kill all P1.15 strains tested. Antibodies from a second group recognized both PorA and class 5 proteins, and antibodies from a third group recognized an as yet unidentified target antigen. The results demonstrate the importance of determining the fine epitope specificity of bactericidal antibodies to improve the existing vaccines against B meningococci.
Enhanced Boiling Heat Transfer (1990)

Keywords: chaleur: transfert de: : : ; ebullition: : : ; evaporation: : : ; tubes: : : ; surface d': evaporation: : : ; melanges: : : ; chimie: : : ; nucleation: : : Reference Record created on 2004-09-07, modified on 2016-08-08
Isolated Cu2+ions: active sites for selective catalytic reduction of NO (2010)

Cu chabazite catalysts show remarkable low temperature activity in selective catalytic reduction (SCR) of NO. This high activity is due to the unique character of the zeolite framework that allows only the presence of one type of isolated mononuclear Cu(2+) species. These Cu(2+) species are the active sites for SCR.
Fast-Response Proteomics by Accelerated In-Gel Digestion of Proteins (2003)

Kinetics of in-gel digestion of proteins by modified and native trypsins was studied by MALDI TOF mass spectrometry using 18O-labeled peptides as internal standards. The effect of the temperature, enzyme concentration, digestion time, and surface area of gel pieces on the yield of digestion products was characterized. Based on the kinetic data, we developed a protocol that enabled the identification of gel-separated proteins with 30-min digestion time without compromising the peptide yield and the sensitivity compared to conventional protocols that typically rely upon overnight enzymatic cleavage. The accelerated digestion protocol was tested in identification of more than 120 proteins from budding and fission yeasts at the subpicomole level.
Removal of Heterologous Sequences from Plasmodium falciparum Mutants Using FLPe-Recombinase (2010)

Genetically-modified mutants are now indispensable Plasmodium gene-function reagents, which are also being pursued as genetically attenuated parasite vaccines. Currently, the generation of transgenic malaria-parasites requires the use of drug-resistance markers. Here we present the development of an FRT/FLP-recombinase system that enables the generation of transgenic parasites free of resistance genes. We demonstrate in the human malaria parasite, P. falciparum, the complete and efficient removal of the introduced resistance gene. We targeted two neighbouring genes, p52 and p36, using a construct that has a selectable marker cassette flanked by FRT-sequences. This permitted the subsequent removal of the selectable marker cassette by transient transfection of a plasmid that expressed a 37°C thermostable and enhanced FLP-recombinase. This method of removing heterologous DNA sequences from the genome opens up new possibilities in Plasmodium research to sequentially target multiple genes and for using genetically-modified parasites as live, attenuated malaria vaccines.
Time-resolved reflectance spectroscopy in turbid tissues (1989)

Monte Carlo simulations illustrate how various absorption mu a and scattering mu s coefficients influence time-dependent reflectance R (t) from a semi-infinite homogeneous turbid tissue following an impulse of narrow-beam irradiation. The tissue absorption coefficient mu a in cm -1 can be obtained from measurements of R (t) after the first 20-200 ps (depends on mu s) following an impulse by the expression: mu a = -(n/c) d In [R(t)]/dt - 3n/2ct where n is the tissue-refractive index and c is the in vacuo speed of light. Early data in the first 20-200 ps do not conform to this expression or to diffusion theory. Monte Carlo simulations allow study of the early R(t) behavior. The volume of tissue involved in a measurement is specified by a volume radius r that approximately equals (6Dtc/n)1/2 where t is the time of measurement and D is the optical diffusion constant D = (3 mu s (1 - g]-1. At 50 ps and typical values of mu s = 100 cm-1 and anisotropy equal to 0.9, r equals 5 mm. The upper limit for measurable mu a values is limited by how quickly the reflectance signal is attenuated, and is estimated for current streak camera technology to be mu a less than or equal to 21 cm-1, assuming several measurements are taken over a dynamic range of two orders of magnitude within a 10 ps period.
Well-Defined Poly(2-hydroxyl-3-(2-hydroxyethylamino)propyl methacrylate) Vectors with Low Toxicity and High Gene Transfection Efficiency (2010)

Successful gene delivery vectors for clinical translation should have high transfection efficiency and minimal toxicity. In this work, well-defined poly(2-hydroxyl-3-(2-hydroxyethylamino)propyl methacrylate) (PGEA) vectors with flanking cationic secondary amine and nonionic hydroxyl units were prepared via the ring-opening reaction of the pendant epoxide groups of poly(glycidyl methacrylate) with the amine moieties of ethanolamine. It was found that PGEA carriers possess very low toxicity (<10% of the toxicity of branched polyethylenimine (PEI, 25 kDa), while exhibiting surprisingly excellent transfection efficiency (higher than or comparable to that of PEI (25 kDa)) in different cell lines. A series of transfection and cytotoxicity assays revealed that PGEAs are highly promising as a new class of safe and efficient gene delivery vectors for future clinical gene therapies.
Naturally Occurring Mutations in the Largest Extracellular Loops of ABCA1 Can Disrupt Its Direct Interaction with Apolipoprotein A-I (2002)

The ABCA1 transporter contains two large domains into which many of the genetic mutations in individuals with Tangier disease fall. To investigate the structural requirements for the cellular cholesterol efflux mediated by ABCA1, we have determined the topology of these two domains and generated transporters harboring five naturally occurring missense mutations in them. These mutants, unlike wild type ABCA1, produced little or no apoA-I-stimulated cholesterol efflux when transfected into 293 cells, establishing their causality in Tangier disease. Because all five mutant proteins were well expressed and detectable on the plasma membrane, their interaction with the ABCA1 ligand, apolipoprotein (apo) A-I, was measured using bifunctional cross-linking agents. Four of five mutants had a marked decline in cross-linking to apoA-I, whereas one (W590S) retained full cross-linking activity. Cross-linking of apoA-I was temperature-dependent, rapid in onset, and detectable with both lipid- and water-soluble cross-linking agents. These results suggest that apoA-I-stimulated cholesterol efflux cannot occur without a direct interaction between the apoprotein and critical residues in two extracellular loops of ABCA1. The behavior of the W590S mutant indicates that although binding of apoA-I by ABCA1 may be necessary, it is not sufficient for stimulation of cholesterol efflux.
Ex Vivo Large‐Scale Generation of Human Platelets from Cord Blood CD34 + Cells (2006)

In the present investigation, we generated platelets (PLTs) from cord blood (CB) CD34(+) cells using a three-phase culture system. We first cultured 500 CB CD34(+) cells on telomerase gene-transduced human stromal cells (hTERT stroma) in serum-free medium supplemented with stem cell factor (SCF), Flt-3/Flk-2 ligand (FL), and thrombopoietin (TPO) for 14 days. We then transferred the cells to hTERT stroma and cultured for another 14 days with fresh medium containing interleukin-11 (IL-11) in addition to the original cytokine cocktail. Subsequently, we cultured the cells in a liquid culture medium containing SCF, FL, TPO, and IL-11 for another 5 days to recover PLT fractions from the supernatant, which were then gel-filtered to purify the PLTs. The calculated yield of PLTs from 1.0 unit of CB (5 x 10(6) CD34(+) cells) was 1.26 x 10(11) - 1.68 x 10(11) PLTs. These numbers of PLTs are equivalent to 2.5-3.4 units of random donor-derived PLTs or 2/5-6/10 of single-apheresis PLTs. The CB-derived PLTs exhibited features quite similar to those from peripheral blood in morphology, as revealed by electron micrographs, and in function, as revealed by fibrinogen/ADP aggregation, with the appearance of P-selectin and activated glycoprotein IIb-IIIa antigens. Thus, this culture system may be applicable for large-scale generation of PLTs for future clinical use.
Population dynamics of flaviviruses revealed by molecular phylogenies. (1996)

The phylogeny of 123 complete envelope gene sequences was reconstructed in order to understand the evolution of tick- and mosquito-borne flaviviruses. An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. The distinction between these two viral groups probably reflects differences in modes of dispersal, propagation, and changes in the size of host populations. The most serious implication of this work is that growing human populations are being exposed to an expanding range of increasingly diverse viral strains.