gebhart/patrepeval huggingface dataset:
Outer acoustic streaming (1990)

There is a general formulation by Nyborg that accounts for the streaming inside the viscous boundary layer on a solid surface in the presence of a sound wave [W. L. Nyborg, J. Acoust. Soc. Am. 30, 329 (1958)]. Using the streaming velocity at the edge of the viscous layer from Nyborg’s theory as a slip boundary condition, the streaming pattern at large outside the layer for various geometries is calculated. Compressibility of the first-order wave motion is retained, such that its effect is reflected in the boundary condition for the secondary flow, although the latter is considered as incompressible. For the case of a cylinder or a sphere situated at a velocity antinode of a plane standing wave, it is found that the streamlines are closed loops as a consequence of compressibility. If the solid body is displaced from the antinode, the vortex pattern becomes asymmetric. A weak viscous drag acts on the object in the direction opposing the displacement. As a reaction, a weak net flow arises in the direction of the displacement. These findings are consistent with observations, and are absent in previous theoretical treatments of the problem, in which the oscillating flow is assumed to be uniform and incompressible.
A human monoclonal antibody, produced following in vitro immunization, recognizing an epitope shared by HLA‐A2 subtypes and HLA‐A28 (1993)

In vitro immunization and subsequent immortalization of peripheral blood cells of a multiparous woman has resulted in the production of a stable human mouse heterohybridoma, 5C2A2, secreting an HLA-A2/A28-specific human monoclonal antibody. Although possibly exposed to HLA-A2 by transfusions, the cell donor showed no HLA-A2-specific serum antibodies. The present protocol for in vitro immunization includes the elimination of suppressor cells from the responder cell population, the presence of irradiated allogeneic lymphocytes as a source of antigen, as well as stimuli--recombinant interleukin-2 and a B-cell specific nucleoside analogue--causing the proliferation of B lymphocytes, prior to immortalization. The ability of the antibody 5C2A2 to detect all known HLA-A2 subtypes, except A2.3, and A28, allows identification of the serological epitope on the HLA-A2 molecule. Application of this in vitro immunization method allows the production of a set of HLA monoclonal antibody-secreting human hybridomas, independent of the existence of serum HLA antibodies in the lymphocyte donors.
Multidimensional Scaling: I. Theory and Method (1952)

Multidimensional scaling can be considered as involving three basic steps. In the first step, a scale of comparative distances between all pairs of stimuli is obtained. This scale is analogous to the scale of stimuli obtained in the traditional paired comparisons methods. In this scale, however, instead of locating each stimulus-object on a given continuum, the distances between each pair of stimuli are located on a distance continuum. As in paired comparisons, the procedures for obtaining a scale of comparative distances leave the true zero point undetermined. Hence, a comparative distance is not a distance in the usual sense of the term, but is a distance minus an unknown constant. The second step involves estimating this unknown constant. When the unknown constant is obtained, the comparative distances can be converted into absolute distances. In the third step, the dimensionality of the psychological space necessary to account for these absolute distances is determined, and the projections of stimuli on axes of this space are obtained. A set of analytical procedures was developed for each of the three steps given above, including a least-squares solution for obtaining comparative distances by the complete method of triads, two practical methods for estimating the additive constant, and an extension of Young and Householder's Euclidean model to include procedures for obtaining the projections of stimuli on axes from fallible absolute distances.
Cyclic GMP-AMP Synthase Is an Innate Immune Sensor of HIV and Other Retroviruses (2013)

Retroviruses, including HIV, can activate innate immune responses, but the host sensors for retroviruses are largely unknown. Here we show that HIV infection activates cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) synthase (cGAS) to produce cGAMP, which binds to and activates the adaptor protein STING to induce type I interferons and other cytokines. Inhibitors of HIV reverse transcriptase, but not integrase, abrogated interferon-β induction by the virus, suggesting that the reverse-transcribed HIV DNA triggers the innate immune response. Knockout or knockdown of cGAS in mouse or human cell lines blocked cytokine induction by HIV, murine leukemia virus, and simian immunodeficiency virus. These results indicate that cGAS is an innate immune sensor of HIV and other retroviruses.
Quantum Superinductor with Tunable Nonlinearity (2012)

We report on the realization of a superinductor, a dissipationless element whose microwave impedance greatly exceeds the resistance quantum R(Q). The design of the superinductor, implemented as a ladder of nanoscale Josephson junctions, enables tuning of the inductance and its nonlinearity by a weak magnetic field. The Rabi decay time of the superinductor-based qubit exceeds 1 μs. The high kinetic inductance and strong nonlinearity offer new types of functionality, including the development of qubits protected from both flux and charge noises, fault tolerant quantum computing, and high-impedance isolation for electrical current standards based on Bloch oscillations.
Total Chemical Synthesis of Biologically Active Vascular Endothelial Growth Factor (2011)

Efficient access: the 204-residue covalent-dimer vascular endothelial growth factor with full mitogenic activity was prepared from three unprotected peptide segments by one-pot native chemical ligations. The covalent structure of the synthetic VEGF was confirmed by precise mass measurement, and the three-dimensional structure of the synthetic protein was determined by high-resolution X-ray crystallography.
Imidazopyridine-Based Fatty Acid Synthase Inhibitors That Show Anti-HCV Activity and in Vivo Target Modulation (2012)

Potent imidazopyridine-based inhibitors of fatty acid synthase (FASN) are described. The compounds are shown to have antiviral (HCV replicon) activities that track with their biochemical activities. The most potent analogue (compound 19) also inhibits rat FASN and inhibits de novo palmitate synthesis in vitro (cell-based) as well as in vivo.
Human butyrylcholinesterase produced in insect cells: huprine‐based affinity purification and crystal structure (2012)

Butyrylcholinesterase (BChE) is a serine hydrolase that is present in all mammalian tissues. It can accommodate larger substrates or inhibitors than acetylcholinesterase (AChE), the enzyme responsible for hydrolysis of the neurotransmitter acetylcholine in the central nervous system and neuromuscular junctions. AChE is the specific target of organophosphorous pesticides and warfare nerve agents, and BChE is a stoichiometric bioscavenger. Conversion of BChE into a catalytic bioscavenger by rational design or designing reactivators specific to BChE required structural data obtained using a recombinant low-glycosylated human BChE expressed in Chinese hamster ovary cells. This expression system yields ≈ 1 mg of pure enzyme per litre of cell culture. Here, we report an improved expression system using insect cells with a fourfold higher yield for truncated human BChE with all glycosylation sites present. We developed a fast purification protocol for the recombinant protein using huprine-based affinity chromatography, which is superior to the classical procainamide-based affinity. The purified BChE crystallized under different conditions and space group than the recombinant low-glycosylated protein produced in Chinese hamster ovary cells. The crystals diffracted to 2.5 Å. The overall monomer structure is similar to the low-glycosylated structure except for the presence of the additional glycans. Remarkably, the carboxylic acid molecule systematically bound to the catalytic serine in the low-glycosylated structure is also present in this new structure, despite the different expression system, purification protocol and crystallization conditions.
A Cell-penetrating Peptide Derived from Human Lactoferrin with Conformation-dependent Uptake Efficiency (2009)

The molecular events that contribute to the cellular uptake of cell-penetrating peptides (CPP) are still a matter of intense research. Here, we report on the identification and characterization of a 22-amino acid CPP derived from the human milk protein, lactoferrin. The peptide exhibits a conformation-dependent uptake efficiency that is correlated with efficient binding to heparan sulfate and lipid-induced conformational changes. The peptide contains a disulfide bridge formed by terminal cysteine residues. At concentrations exceeding 10 mum, this peptide undergoes the same rapid entry into the cytoplasm that was described previously for the arginine-rich CPPs nona-arginine and Tat. Cytoplasmic entry strictly depends on the presence of the disulfide bridge. To better understand this conformation dependence, NMR spectroscopy was performed for the free peptide, and CD measurements were performed for free and lipid-bound peptide. In solution, the peptides showed only slight differences in secondary structure, with a predominantly disordered structure both in the presence and absence of the disulfide bridge. In contrast, in complex with large unilamellar vesicles, the conformation of the oxidized and reduced forms of the peptide clearly differed. Moreover, surface plasmon resonance experiments showed that the oxidized form binds to heparan sulfate with a considerably higher affinity than the reduced form. Consistently, membrane binding and cellular uptake of the peptide were reduced when heparan sulfate chains were removed.
Principles and Procedures of Plant Breeding: Biotechnological and Conventional Approaches (2002)

Preface / Introduction / Reproduction in Crop Plants / Plant Genetic Resources-Origin, Conservation and Utilization / Genetic Basis and Application of Selection in Self-pollinated Crops / Mendelian Consequences of Planned Hybridization in Self-pollinated Crops / Quantitative Inheritance / The Analysis of Genotype-Environment Interactions / Application of Biometrical Genetics in Plant Breeding / Pedigree Method / Bulk Population Breeding Method / The Single Seed Descent Method / Backcross Method / Fertility Regulating Mechanisms / Genetic Basis of Hetrosis / Breeding for Hetrosis / Genetic Structure of Cross-pollinated Crops / Population Improvement in Cross Pollinated Crops / Population Improvement Methods / Synthetic and Composite Varieties / Breeding for Asexually Propagated Crops / Breeding for Resistance to Diseases and Insect Pests / Mutation Breeding / Polyploidy in Plant Breeding / Tissue Culture in Crop Improvement / Molecular Approaches to Crop Improvement / Genetic Transformation and Production of Transgenic Plants / Biometry in Relation to Molecular Biology in Plant Breeding/ Field Plot Techniques in Plant Breeding / Plant Breeder's Rights, Release and Multiplication of Varieties/ Glossary / Index
Bioavailability of Quercetin in Humans with a Focus on Interindividual Variation (2018)

After consumption of plant-derived foods or beverages, dietary polyphenols such as quercetin are absorbed in the small intestine and metabolized by the body, or they are subject to catabolism by the gut microbiota followed by absorption of the resulting products by the colon. The resulting compounds are bioavailable, circulate in the blood as conjugates with glucuronide, methyl, or sulfate groups attached, and they are eventually excreted in the urine. In this review, the various conjugates from different intervention studies are summarized and discussed. In addition, the substantial variation between different individuals in the measured quercetin bioavailability parameters is assessed in detail by examining published human intervention studies where sources of quercetin have been consumed in the form of food, beverages, or supplements. It is apparent that most reported studies have examined quercetin and/or metabolites in urine and plasma from a relatively small number of volunteers. Despite this limitation, it is evident that there is less interindividual variation in metabolites which are derived from absorption in the small intestine compared to catabolites derived from the action of microbiota in the colon. There is also some evidence that a high absorber of intact quercetin conjugates could be a low absorber of microbiota-catalyzed phenolics, and vice versa. From the studies reported so far, the reasons or causes of the interindividual differences are not clear, but, based on the known metabolic pathways, it is predicted that dietary history, genetic polymorphisms, and variations in gut microbiota metabolism would play significant roles. In conclusion, quercetin bioavailability is subject to substantial variation between individuals, and further work is required to establish if this contributes to interindividual differences in biological responses.
Mild Regioselective Halogenation of Activated Pyridines with N-Bromosuccinimide (2001)

Regioselective mono and dihalogenations of amino, hydroxy and methoxy pyridines (2-, 3-, and 4-substituted) as well as 2,6-dimethoxy pyridine with N-bromosuccinimide in different solvents have been studied. Reactivity of the substrates decreases in the order amino>hydroxy>methoxy and regioselectivity depends on the position of the substituent (2-substituted > 3-substituted). In most of the cases we obtained monobrominated derivatives regioselectively and in high yields. Hydroxy and amino pyridines can also be dibrominated in almost quantitative yield with 2 equivalents of NBS.
Finding a minimum equivalent graph of a digraph (1982)

Abstract The problem considered is that of removing the maximum number of edges from a digraph without affecting its reachability properties. The worst‐case performance of algorithms from the related literature is analyzed; it is found that Hsu's method contains some mistakes. A new algorithm is presented, based on a reduction procedure and on a branch and bound search; its efficiency is studied both theoretically and through computational experiments.
Electrowetting-controlled droplet generation in a microfluidic flow-focusing device (2007)

We studied the generation of aqueous microdrops in an oil–water flow-focusing device with integrated insulator-covered electrodes that allow for continuous tuning of the water wettability by means of electrowetting. Depending on the oil and water inlet pressures three different operating conditions were identified that shift upon applying a voltage: stable oil–water interface, drop generation, and laminar water jet formation. Full control over the drop generation is achieved within a well-defined range of inlet pressures, in quantitative agreement with a model based on the additive contributions from electrowetting and the local hydrostatic pressure at the junction. The tuning power of electrowetting is shown to increase upon device miniaturization, which makes this approach particularly attractive for flow control on the sub-micrometer scale.
Optimised room temperature, water-based synthesis of CPO-27-M metal–organic frameworks with high space-time yields (2015)

The exceptional porosity of Metal-Organic Frameworks (MOFs) could be harnessed for countless practical applications. However, one of the challenges currently precluding the industrial exploitation of these materials is a lack of green methods for their synthesis. Since green synthetic methods obviate the use of organic solvents, they are expected to reduce the production costs, safety hazards and environmental impact typically associated with MOF fabrication. Herein we describe the stepwise optimisation of reaction parameters (pH, reagent concentrations and reaction time) for the room temperature, water-based synthesis of several members of the CPO-27/MOF-74-M series of MOFs, including ones made from Mg(II), Ni(II), Co(II) and Zn(II) ions. Using this method, we built MOFs with excellent BET surface areas and unprecedented Space-Time Yields (STYs). Employing this approach, we have synthesised CPO-27-M MOFs with record BET surface areas, including 1279 m<sup>2</sup> g<sup>-1</sup> (CPO-27-Zn), 1351 m<sup>2</sup> g<sup>-1</sup> (CPO-27-Ni), 1572 m<sup>2</sup> g<sup>-1</sup> (CPO-27-Co), and 1603 m<sup>2</sup> g<sup>-1</sup> (CPO-27-Mg). We anticipate that our method could be applied to produce CPO-27-Ni, -Mg, -Co and -Zn with STYs of 44 Kg m<sup>-3</sup> day<sup>-1</sup>, 191 Kg m<sup>-3</sup> day<sup>-1</sup>, 1462 Kg m<sup>-3</sup> day<sup>-1</sup> and a record 18720 Kg m<sup>-3</sup> day<sup>-1</sup>, respectively.
The human MDM-2 oncogene is overexpressed in leukemias (1993)

The human homologue of the mouse double minute 2 (MDM-2) gene codes for a cellular protein that forms a complex with the mutant and wild-type p53 protein and modulates its trans-activation activity. Overexpression of the MDM-2 gene in cells increases their tumorigenic potential and overcomes the growth-suppressive activity of p53. Previous reports have shown that the MDM-2 gene is amplified in approximately one third of human sarcomas. To examine the role of MDM-2 in leukemia, we analyzed MDM-2 gene amplification and mRNA expression in various types of leukemias. We did not detect gene amplification in any of the 48 cases of leukemia that we examined. In contrast, we observed significant MDM-2 mRNA overexpression in 34 of 64 cases (53%). The level of mRNA overexpression in some cases of leukemias was comparable to that observed in some cases of sarcomas, which demonstrate more than 50-fold MDM-2 gene amplification. Furthermore, we divided these cases into different prognostic groups according to their karyotypic abnormalities. MDM-2 overexpression seemed to be associated with unfavorable chromosomal abnormalities. These findings suggest that the expression of the MDM-2 gene is altered in a significant fraction of human leukemias and MDM-2 may play a significant role in leukemogenesis. In addition, these results suggest that mechanisms other than gene amplification may play a significant role in deregulating the MDM-2 expression.
Progresses in Fetal Monitoring by Improved Data Acquisition (1984)

The results of the studies discussed here show that the processing and interpreting of routinely acquired fetal and maternal data has, so far, not been fully utilized. It would thus appear to make good sense, not only to continue the search for new measuring methods for determining additional physiological parameters, but also to pursue attempts to improve the evaluation of presently obtainable data. All in all, the procedures described have proved valuable in clinical trials. The simplicity of simultaneous recording of fetal and maternal heart activity in addition to uterine contraction is highly suitable for routine clinical work. The proposed extension of CTG interpretation by including the maternal cardiovascular condition will provide improved surveillance of both mother and fetus during pregnancy and parturition.
Current measurement of nonaqueous solvents: Applicatons to capillry electrophoresis and electrochromatography (1997)

Abstract The solvents acetonitrile, methanol, N, N‐dimethylformamide, dimethyl sulfoxide, formamide, and deionized water were investigated for their ability to support current flow without added electrolyte. Using open tubular capillary electrophoresis, currents were measured to be in the nanoampere (10 −9 A) range for all solvents but formamide (10 −6 A). Comparisons with flow data showed no clear relationship between current and electroosmotic flow. Packed capillary columns (3‐μm ODS) were used for separations using both pure solvent and hydrophobic dyes showed mild retention in pure ACN. A 16 polynuclear aromatic hydrocarbon (PAH) standard soluton was separated in 80/20 ACN/H 2 O with reduced plate heights (h) between 2.8 and 3.1 for retained species. A separation of nine androstenediones was achieved using a 70/30 MeOH/H 2 O mobile phase.
New algorithm for polynomial spectral factorization with quadratic convergence. II (1976)

In this paper new efficient algorithm for the numerical spectral factorization of polynomials arising continuous optfmality problem is derived.
RAPAMYCIN, A POTENT IMMUNOSUPPRESSIVE DRUG FOR VASCULARIZED HEART, KIDNEY, AND SMALL BOWEL TRANSPLANTATION IN THE RAT (1991)

The effectiveness of rapamycin (RAPA) was examined for heart, kidney, and small bowel allografts in rats. Untreated or vehicle only-infused Wistar Furth (RT1u) recipients rejected Buffalo (RT1b) heart allografts within a mean survival time (MST) of 6.5 +/- 0.5 and 6.3 +/- 0.5 days, respectively. In contrast, a 14-day continuous intravenous (i.v.) infusion by an osmotic pump of 0.08 mg/kg/day RAPA to WFu recipients prolonged BUF heart allograft survival to an MST of 34.4 +/- 12.1 days (P = 0.0001). There was a graded dose-response to 0.16 mg/kg (39.0 +/- 8.7 days; P = 0.0001), 0.32 mg/kg (55.7 +/- 3.3 days; P = 0.0001) and 0.8 mg/kg (48.0 +/- 3.6; P = 0.0001). Furthermore, intraarterial/intragraft but not i.v. infusion of 0.02 mg/kg/day prolonged BUF heart allografts--namely, an MST of 14.6 +/- 1.4 days versus 8.6 +/- 2.6 days (P = 0.0001), respectively. Local delivery doses of RAPA were about as effective as the same dose delivered i.v.: 0.08 mg/kg MST 37.0 +/- 18.3 days (P = 0.0001); 0.32 mg/kg, 40.0 +/- 3.9 days (P = 0.0001); and 0.8 mg/kg, 54.8 +/- 8.2 days (P = 0.0001). Systemic i.v. RAPA therapy with 0.08 or 0.8 mg/kg/day prolonged the survival of BUF kidney grafts in WFu recipients--namely, an MST of 52.7 +/- 42.7 (NS) and 90.2 +/- 62.4 (P = 0.001) days, respectively, versus an MST of 11.6 +/- 1.5 days in control WFu recipients only infused with vehicle. While normal WFu rats reject heterotopic BUF small bowel allografts within an MST of 10.0 days, a 14-day course of i.v. RAPA treatment significantly (P = 0.0001) prolonged small bowel allograft survival to an MST of 26.8 +/- 3.7 days.
Intraframe image decoding based on a nonlinear variational approach (1998)

Despite advances in the domain of source coding, little recent work has been devoted to the problem of joint coding and decoding. In particular, to our knowledge, the design of decoders has been little investigated. In this article, we focus on decoding for intraframe images of video data. In our approach, we propose a new method for decoding by nonlinear filtering. Here, we break with the usual approach of perfect reconstruction filters at the decoder, and instead pose the reconstruction model as a minimization problem. The solution can be viewed as an inverse problem with the optimization of the transform/quantization/decoding structure formulated using a variational approach. We introduce sufficient conditions on the design of the decoder involving a priori assumptions on the solution and knowledge of the coder (transformation and quantization). We develop an optimization method for the reconstruction filters at the decoder to account for effects due to quantization noise. Experiments using this nonlinear inverse dynamic filtering demonstrate peak signal-to-noise ratio gains over standard linear inverse filtering as well as appreciable visual improvements. © 1998 John Wiley & Sons, Inc. Int J Imaging Syst Technol, 9, 369–380, 1998