gebhart/patrepeval huggingface dataset:
A New Set of Monoclonal Antibodies Against Human FcγRII (CD32) and FcγRIII (CD16): Characterization and Use in Various Assays (1997)

Four mouse anti-human Fc gamma RII (CD32) (6C4, 2B2, 3D3, 93.4) (IgG1, kappa) and one anti-human Fc gamma RIII (CD16) (7.5.4) IgG1, kappa) MAbs were raised. An in vitro switch variant, 7.5.4Sw50 (IgG2b, kappa), was also derived from the 7.5.4 MAb. 6C4, 2B2, and 3D3 MAbs bind both Fc gamma RIIa and Fc gamma RIIb isoforms. Two of them (6C4 and 2B2 MAbs) allow a complete blockade of the binding of immune complexes to Fc gamma RII. All three MAbs immunoprecipitate the receptor and bind both its glycosylated and nonglycosylated forms. The fourth anti Fc gamma RII MAb, 93.4, directed against the intracellular region of Fc gamma RIIa1/2, allows its detection by Western blotting only when it is not phosphorylated. The 7.5.4 MAb binds both Fc gamma RIIIa and Fc gamma RIIIb, can be used in Western blotting and does not inhibit aggregated IgG binding. ELISA using IV.3 (anti-Fc gamma RIIa1/2)/6C4 and 3G8 (anti-Fc gamma RIIIa/b)/7.5.4Sw50 MAb pairs make it possible to detect soluble Fc gamma RIIa1/2 and Fc gamma RIII, with a sensitivity of 200 pg/mL and 1 ng/mL, respectively. Surface plasmon resonance analyses indicated that the KD of two of the three anti-Fc gamma RII and of the anti-Fc gamma RIII are in the same order of magnitude (6C4: 0.78 nM, 2B2: 0.28 nM, 7.5.4: 0.47 nM). The anti-Fc gamma RII 3D3 MAb exhibits an off-rate constant higher than the 6C4 and 2B2 MAbs and a KD of 2.19 nM.
Simulation of stent deployment in a realistic human coronary artery (2008)

The method presented in this paper can be used to predict stresses in the stent struts and the vessel wall, and thus evaluate whether a specific stent design is optimal for a specific patient.
Reduced Albumin Binding Promotes the Stability and Activity of Topotecan in Human Blood (1995)

Topotecan, a semisynthetic water-soluble analogue of camptothecin, is the first topoisomerase I targeting anticancer agent to enter comparative phase III clinical trials. Here we elucidate the biophysical factors underlying the markedly improved bloodstream stability and cytotoxic activity of topotecan relative to camptothecin. Each agent contains an alpha-hydroxy-delta-lactone ring that hydrolyzes under physiological pH to yield a biologically-inactive carboxylate form. In human plasma, camptothecin lactone converts rapidly and completely to its carboxylate form due to a 200-fold binding preference by serum albumin (HSA) for the latter [Mi, Z., & Burke, T.G. (1994) Biochemistry 33, 10540-12545]. Time-resolved fluorescence anisotropy measurements reveal that neither topotecan lactone nor carboxylate associates with HSA, thereby resulting in a significantly higher level of lactone stability in plasma for topotecan (t1/2 = 23.1 min, percent lactone at equilibrium of 17.6) relative to camptothecin (t1/2 = 10.6 min, percent lactone at equilibrium of < 0.2). Moreover, studies with HL-60 human promyelocytic leukemia cells reveal that a physiologically-relevant level (40 mg/mL) of HSA dramatically attenuates the cytotoxic activity of camptothecin in excess of 2600-fold (for a 72 h exposure, the IC50 value of 1.5 nM in the absence of HSA increased to 4 microM in the presence of HSA). The activities of other clinically relevant anticancer analogues, 9-aminocamptothecin and SN-38, were also strongly modulated by the presence of 40 mg/mL HSA. In marked contrast, the presence of HSA effected no change on the cytotoxic activity of topotecan (IC50 = 12 nM both in the absence and in presence of HSA).(ABSTRACT TRUNCATED AT 250 WORDS)
Electronic properties of amorphous silicon in solar cell operation (1977)

Amorphous silicon (a-Si) solar cells, which have efficiencies up to 5.5 percent, are unique in several ways, and their cell characteristics no longer depend on the same parameters generally considered in single crystal cells. This paper discusses the operation of such cells, and relates the major new parameters to the electronic properties of a-Si which are highly dependent on the densities of gap centers in this disordered material. The effect of the photoconductivity in intrinsic a-Si on the series resistance of the cell, the quality of a-Si junctions and their ability to transport current densities generated under AM1 illumination are presented. Space-charge densities as low as 5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">15</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> are found in a-Si junctions, which are orders of magnitude lower than previous estimates for glow discharge produced a-Si. The effects of electric field distributions and diffusion lengths of holes on collection efficiencies and cell characteristics are discussed and illustrated. Although significant trapping of photogenerated holes is found in many of the a-Si films, diffusion lengths of few tenths of a micron are also indicated by the results presented.
Bradykinin-Induced Vasodilation of Human Forearm Resistance Vessels Is Primarily Mediated by Endothelium-Dependent Hyperpolarization (2000)

Bradykinin (BK) stimulates endothelial cells to release a number of relaxing factors, such as NO, prostanoids (PGs), and an endothelium-derived hyperpolarizing factor (EDHF). However, the contributions of NO, PG, and EDHF in the vascular relaxation to BK vary with species and anatomic origin of blood vessels used. Therefore, the present study was designed to investigate the contributions of NO, PG, and EDHF in vasodilation caused by BK in human forearm resistance vessels. Forearm blood flow (FBF) was recorded with venous occlusion plethysmography in healthy nonsmoking subjects. At first, studies were performed to validate the NO clamp technique for its ability to inhibit endogenous NO generation. Brachial artery infusion of serotonin (0.6, 1.8, and 6 ng. 100 mL forearm volume [FAV](-1). min(-1)) caused significant forearm vasodilation (2.6 to 4.6 mL. 100 mL FAV(-1). min(-1)), which is known to be NO mediated. Indeed, during the NO clamp, cumulative doses of serotonin caused no vasodilation (2.4 to 2.6 mL. 100 mL FAV(-1). min(-1)), indicating that the generation of endogenous NO was completely blocked. Thereafter, the vasodilative actions of BK were investigated. Brachial artery infusion of BK (50, 100, and 200 ng. 100 mL FAV(-1). min(-1)) caused significant forearm vasodilation in all studies (from 3.1 to 20.4 mL. 100 mL FAV(-1). min(-1)). After the inhibition of cyclooxygenase and NO synthase activity through the use of aspirin and the NO-clamp technique, BK increased FBF in a similar manner (3.9 to 18.9 mL. 100 mL FAV(-1). min(-1)), indicating that the vasodilative actions of BK are independent of NO and PG generation. However, vasodilation caused by the 2 lower doses of BK were significantly attenuated after K(Ca) channel activity was blocked with tetraethylammonium chloride (0.1 mg. 100 mL FAV(-1). min(-1)), suggesting that in the lower dose range, BK mediates vasodilation through the opening of vascular potassium channels. In conclusion, BK is a potent vasodilator peptide in human forearm resistance vessels, causing vasodilation through hyperpolarization of the vascular wall independent of NO and PG production. In addition, the NO-clamp technique is a valid instrument to investigate the contribution of NO in the vasodilative response to different agents.
Glaucoma Detection by Stratus OCT (2007)

The diagnostic accuracy of the full circle RNFLT was as good as any Stratus OCT parameter on the basis of the peripapillary RNFL thickness measurements, including localized measurements. The sensitivity was moderately high in patients with mild glaucomatous VF loss. There seems to be room for further development of OCT interpretation tools for early diagnosis of glaucoma.
Molecular Biology of the Pituitary Gonadotropins (1990)

THE pituitary gonadotropins, LH and FSH, play a central role in the mammalian reproductive process. Synthesized in the gonadotropes of the pituitary, the gonadotropins bind to receptors in the gonads leading to effects on steroidogenesis and gametogenesis (Fig. 1). Because these hormones are responsible for sexual maturation and normal reproductive function, the regulation of their synthesis and secretion is essential for the preservation of a species. In recent years, a great deal has been learned about the regulation of synthesis of the gonadotropins using the tools of molecular biology. Before we can fully appreciate these new insights, however, it is important to understand the complex structure of the gonadotropins and to summarize what is known about the regulation of their secretion. In this review, we will discuss the structure of the gonadotropin subunits, the structure of the genes that encode them, and the regulation of their secretion and synthesis.
Adhesion of Mytilus edulis Foot Protein 1 on Silica: Ionic Effects on Biofouling (2002)

To determine the effect of the ionic environment on the marine adhesion molecule Mytilus edulis foot protein 1 (Mefp-1), atomic force microscopy (AFM) was used to measure the adhesion between Mefp-1 and a silica substrate under a range of ionic conditions. Both ion strength and type were varied on the basis of the ions present in natural seawater. Salts containing monovalent ions (NaCl, KCl) increased adhesion only slightly, but salts containing divalent ions (MgCl(2), CaCl(2), Na(2)SO(4)) induced multiple jumpouts in the decompression curve similar to other biological systems and an increase in hydrodynamic radius as observed by light scattering. This behavior may be due to metal complexation between 3,4-dihydroxyphenyl-L-alanine and o-quinone catechol groups on Mefp-1. The addition of a salt containing a trivalent ion (FeCl(3)) resulted in the highest adhesion. The strong effect of salt type and concentration suggests that the ionic composition of the environment within the mussel byssus may be tailored in order to achieve maximum adhesion and minimum curing time.
Selenosemicarbazones as potent cruzipain inhibitors and their antiparasitic properties against Trypanosoma cruzi (2011)

The cysteine protease cruzipain is an essential T. cruzienzyme and one of the few validated drug targets for Chagas disease. Thiosemicarbazones have been described as cruzipain inhibitors. While searching for new antichagasic drugs, we synthesized a series of selenosemicarbazone analogs and demonstrated that the isosteric replacement of the sulfur atom with selenium resulted in an enhancement of the cysteine protease inhibitory effect. Three selenosemicarbazones were characterized enzymatically and proved to be reversible, slow-binding inhibitors for the Z-Phe-Arg-AMC substrate. Their KI values were in the low nM range (3.7 to 29.7 nM), suggesting a strong interaction with the enzyme, approaching a tight binding definition. All selenosemicarbazones tested showed better activities against epimastigotes than Benznidazole, the currently used drug, with IC50 values ranging from 1.2 to 5.9 μM (Bnz IC50 = 12.5 μM). Three of these compounds showed a better Selectivity Index (SI) than Benznidazole. These compounds also displayed activity against the infective intracellular amastigote form at low micromolar range. Overall, our results support the role of these novel organoselenium compounds as promising lead candidates for further drug development studies.
Differential matrix metalloproteinase expression in cases of multiple sclerosis and stroke (1997)

Multiple sclerosis (MS) and stroke pathology are characterized blood-brain barrier breakdown, leucocyte emigration, and tissue destruction. Each process is thought to involve the matrix metalloproteinases (MMP), but little is known of their expression. We undertook to investigate whether MMP expression is dependent on the nature of the CNS lesion and whether expression would coincide with the histopathology. MS or cerebral-infarct tissue was examined for the presence of gelatinase-A, gelatinase-B, matrilysin and stromelysin-1. Gelatinases A and B and matrilysin expression was found to be up-regulated in microglia/macrophages within acute MS lesions. In active-chronic MS lesions, matrilysin and gelatinase-A expression was pronounced in the active borders. In chronic MS lesions, the expression of matrilysin was confined to macrophages within perivascular cuffs. The pattern of MMP expression in infarct lesions differed considerably. Gelatinase-B was strongly expressed by neutrophils in tissue from patients up to 1 week after an infarct, whereas gelatinase-A and matrilysin staining was much less marked. From 1 week to 5 years, neutrophils were absent and the large number of macrophages present were expressing matrilysin and gelatinase A. Only a low level of gelatinase-A and matrilysin expression was observed in normal brain controls. Thus, MMPs are expressed in inflammatory lesions in the CNS, but their individual expression is dependent on the nature and chronicity of the lesion. However, the general pattern of expression, in perivascular cuffs and in active lesions, supports a role for these enzymes as mediators of blood-brain barrier breakdown and tissue destruction, both in MS and in cerebral ischaemia.
Human NK cells of mice with reconstituted human immune system components require preactivation to acquire functional competence (2010)

To investigate human natural killer (NK)-cell reactivity in vivo we have reconstituted human immune system components by transplantation of human hematopoietic progenitor cells into NOD-scid IL2Rγ(null) mice. We demonstrate here that this model allows the development of all NK-cell subsets that are also found in human adult peripheral and cord blood, including NKp46(+)CD56(-) NK cells. Similar to human cord blood, NK cells from these reconstituted mice require preactivation by interleukin-15 to reach the functional competence of human adult NK cells. Mainly the terminally differentiated CD16(+) NK cells demonstrate lower reactivity without this stimulation. After preactivation, both CD16(+) and CD16(-) NK cells efficiently produce interferon-γ and degranulate in response to stimulation with NK cell-susceptible targets, including K562 erythroleukemia cells. NK-cell lines, established from reconstituted mice, demonstrate cytotoxicity against this tumor cell line. Importantly, preactivation can as well be achieved by bystander cell maturation via poly I:C stimulation in vitro and injection of this maturation stimulus in vivo. Preactivation in vivo enhances killing of human leukocyte antigen class I negative tumor cells after their adoptive transfer. These data suggest that a functional, but resting, NK-cell compartment can be established in immune-compromised mice after human hematopoietic progenitor cell transfer.
Prediction of Gene Function by Genome-Scale Expression Analysis: Prostate Cancer-Associated Genes (1999)

We wish to identify genes associated with disease. To do so, we look for novel genes whose expression patterns mimic those of known disease-associated genes, using a method we call Guilt-by-Association (GBA), on the basis of a combinatoric measure of association. Using GBA, we have examined the expression of 40,000 human genes in 522 cDNA libraries, and have discovered several hundred previously unidentified genes associated with cancer, inflammation, steroid-synthesis, insulin-synthesis, neurotransmitter processing, matrix remodeling, and other disease processes. The majority of the genes thus discovered show no sequence similarity to known genes, and thus could not have been identified by homology searches. We present here an example of the discovery of eight genes associated with prostate cancer. Of the 40,000 most-abundant human genes, these 8 are the most closely linked to the known diagnostic genes, and thus are prime targets for pharmaceutical research.
Conformations of Monosubstituted and Disubstituted 3,4′-,3,3′- and 4,4′-Diquinolinyl Sulfides Studied by NMR Spectroscopy (1994)

Abstract 3′,4-Disubstituted 3,4′-diquinolinyl sulfides 1 exibit nontypical and unexpected spectral properties manifested mainly in proton NMR spectroscopy being results of different conformations at a central sulfide bridge1. To complete studies on steric structure-spectral properties relationship in diquinolinyl sulfides several 4,4′-disubstituted-3,3′-diquinolinyl sulfides 2 and 3-mono- and 3,3′-disubstituted 4,4′-diquinolinyl sulfides 3 were synthesized and investigated by proton and carbon NMR spectroscopy.
Comparison of the capacity of different viral internal ribosome entry segments to direct translation initiation in poly(A)-dependent reticulocyte lysates (2003)

Polyadenylation stimulates translation of capped eukaryotic mRNAs and those carrying picornaviral internal ribosome entry segments (IRESes) in vivo. Rabbit reticulocyte lysates (RRL) reproduce poly(A)-mediated translation stimulation in vitro after partial depletion of ribosomes and ribosome-associated factors. Here, we have evaluated the effects of varying different parameters (extent of extract depletion, cleavage of eIF4G, concentrations of KCl, MgCl(2) and programming mRNA) on IRES-driven translation efficiency and poly(A)-dependency in ribosome-depleted RRL. For comparison, the study included a standard capped, polyadenylated mRNA. Dramatic differences were observed in the abilities of the different IRESes to direct translation in ribosome-depleted extracts. While the hepatitis A virus IRES was incapable of driving translation in physiological conditions in depleted RRL, mRNAs carrying the foot-and-mouth disease virus and hepatitis C virus IRESes were translated significantly better than a standard cellular mRNA in the same conditions. Indeed, the capacities of these IRESes to direct translation in ribosome-depleted RRL were similar to those reported previously in certain cell lines. Both the abilities of the IRESes to drive translation and their individual salt optima in ribosome-depleted extracts suggest that these elements have dramatically different affinities for some component(s) of the canonical translation machinery. Finally, using poliovirus as an example, we show that the ribosome-depleted system is well suited to the study of the translational capacity of naturally occurring IRES variants.
Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains (2008)

In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes -- the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells.
Proteolytic activation of receptor-bound anthrax protective antigen on macrophages promotes its internalization (2000)

Immunofluorescence and other methods have been used to probe the self-assembly and internalization of the binary toxin, anthrax lethal toxin (LeTx), in primary murine macrophages. Proteolytic activation of protective antigen (PA; 83 kDa, the B moiety of the toxin) by furin was the rate-limiting step in internalization of LeTx and promoted clearance of PA from the cell surface. A furin-resistant form of PA remained at the cell surface for at least 90 min. Oligomerization of receptor-bound PA63, the 63 kDa active fragment of PA, was manifested by its conversion to a pronase-resistant state, characteristic of the heptameric prepore form in solution. That oligomerization of PA63 triggers toxin internalization is supported by the observation that PA20, the complementary 20 kDa fragment of PA, inhibited clearance of nicked PA. The PA63 prepore, with or without lethal factor (LF), cleared slowly from the cell surface. These studies show that proteolytic cleavage of PA, in addition to permitting oligomerization and LF binding, also promotes internalization of the protein. The relatively long period of activation and internalization of PA at the cell surface may reflect adaptation of this binary toxin that maximizes self-assembly.
Nucleotide Sequence and Temporal Expression of a Baculovirus Regulatory Gene (1987)

The nucleotide sequence of a trans-activating regulatory gene (IE-1) of the baculovirus Autographa californica nuclear polyhedrosis virus has been determined. This gene encodes a protein of 581 amino acids with a predicted molecular weight of 66,856. A DNA fragment containing the entire coding sequence of IE-1 was inserted downstream of an RNA promoter. Subsequent cell-free transcription and translation directed the synthesis of a single peptide with an apparent molecular weight of 70,000. Quantitative S1 nuclease analysis indicated that IE-1 was maximally synthesized during a 1-h virus adsorption period and that steady-state levels of IE-1 message were maintained during the first 24 h of infection. Northern blot hybridization indicated that several late transcripts which overlap the IE-1 gene were transcribed from both strands. The precise locations of the 5' and 3' ends of these overlapping transcripts were mapped using S1 nuclease. The overlapping transcripts were grouped in two transcriptional units. One unit was composed of IE-1 and overlapping gamma transcripts which initiated upstream of IE-1 and terminated downstream of IE-1. The other unit, transcribed from the opposite strand, consisted of gamma transcripts with coterminal 5' ends and extended 3' ends. The shorter, more abundant transcripts in this unit overlapped 30 to 40 bases of IE-1 at the 3' end, while the longer transcripts overlapped the entire IE-1 gene. Transcription of several early A. californica nuclear polyhedrosis virus genes, in addition to 39K, was shown to be trans-activated by IE-1, indicating that IE-1 may have a central role in the regulation of beta-gene expression.
Experimental Realization of an Order-Finding Algorithm with an NMR Quantum Computer (2000)

We report the realization of a nuclear magnetic resonance quantum computer which combines the quantum Fourier transform with exponentiated permutations, demonstrating a quantum algorithm for order finding. This algorithm has the same structure as Shor's algorithm and its speedup over classical algorithms scales exponentially. The implementation uses a particularly well-suited five quantum bit molecule and was made possible by a new state initialization procedure and several quantum control techniques.