gebhart/patrepeval huggingface dataset:
Antibody affinity maturation using bacterial surface display (1998)

A quantitative system for screening combinatorial single-chain Fv (scFv) antibody libraries was developed utilizing surface display on Escherichia coli and fluorescence-activated cell sorting (FACS). This system was employed to isolate clones with high-affinity to a fluorescently-labeled hapten from libraries constructed by randomizing heavy and light-chain residues in the anti-digoxin 26-10 derived antibody, scFv(dig). The use of flow cytometry enabled the detection of rare library members directly in heterogeneous populations and the optimization of selection conditions prior to sorting. A heavy-chain mutant having wild-type affinity (KD = 0.91+/-0.22 nM) and an expected representation frequency of less than 1 x 10(6), was selected to homogeneity after three rounds utilizing increasingly stringent selection conditions. The isolated clone possessed two distinct point mutations relative to the wild-type DNA sequence, yet still coded for the wild-type amino acid sequence, suggesting that the wild-type residues may be optimal at the randomized positions. An affinity improved clone (KD = 0.30+/-0.05 nM), having a dissociation constant approximately threefold lower than the wild-type antibody, was isolated from a smaller light-chain library in a single sorting step. Flow cytometry was shown to be a simple and rapid method for the determination of the relative hapten dissociation rate constants of selected clones without requiring subcloning. The relative rate constants estimated by FACS were confirmed by producing the scFv antibodies in soluble form and measuring hapten binding kinetics by surface plasmon resonance (SPR). These results demonstrate that E.coli surface display, coupled with quantitative selection and analysis using FACS, has the potential to become a powerful tool for rapid isolation and characterization of desirable mutants from large polypeptide libraries.
Pharmaceutical Application of Biomedical Polymers. Part XXXV. Chitosan and Sodium Alginate Based Bioadhesive Tablets for Intraoral Drug Delivery. (1994)

Bioadhesive tablets for intraoral drug delivery were prepared by directly compressing the drug with a mixture of chitosan and sodium alginate in weight ratios of 4:1, 1:1 and 1:4, and the adhesion and release characteristics of the prepared systems were evaluated in vitro and in vivo. Ketoprofen was used as a model drug. The magnitudes of the adhesion force of chitosan/alginate tablets were observed to be comparable to that of Aftach, which is a typical commercial preparation of an oral mucosal adhesive tablet. Increasing the chitosan content in the tablets resulted in a decrease in the release rate of ketoprofen. When the tablets were administered to the sublingual site of rabbits, ketoprofen from the tablets with chitosan/alginate was rapidly absorbed without an initial sharp peak. Furthermore, the plasma concentration curves for the tablet with a 1:4 chitosan/alginate ratio showed a sustained release 3 h after administration. The data presented suggest that tablets prepared from chitosan and alginate are potential candidates for intraoral drug delivery.
Spinning fibres and fibre blends of an electrically conductive polymer (1983)

Acid solutions of [Si(Pc)O]n(Pc = phthalocyaninato), with or without an added ‘aramid’ polymer can be wet-spun to yield, after halogen doping, air-stable fibres with thermally activated conductivities as high as 2 Ω–1 cm–1.
Hitless Reconfigurable Add/Drop Multiplexers Using Bragg Gratings in Planar Waveguides (1999)

Two reconfigurable add/drop multiplexers that can be switched without degrading the transmission of other channels are reviewed. They are based on UV-induced Bragg gratings and thermo-optic switches in a planar waveguide Mach-Zehnder interferometer. A single-channel and two-channel device are demonstrated. System measurements at 2.5 Gb/s and 10 Gb/s show that hitless switching can be achieved. Reconfiguration times are <500 □s.
In vitro culture of embryonic disc cells from porcine blastocysts (1993)

The aim of the present study was to define the conditions of preparation and in vitro culture of embryonic discs allowing proliferation of ES-like cells. G5-6 porcine blastocysts (G0 = day of AI) were cultured in toto; in G10-11 blastocysts, trophectoderm and primitive endoderm were microsurgically removed from embryonic discs (ED) which were cultured either on plastic or on a feeder layer. Feeder cells were foetal G30 porcine fibroblasts which had been previously irradiated. Culture medium was DMEM supplemented with 0.1 mM beta-mercaptoethanol, 5% foetal calf serum, 5% Ultroser G and 10(3) IU LIF; cultures were performed at 38 degrees C. Colonies were reseeded weekly. Few embryonic discs from G5-6 and no elongating blastocysts gave rise to ES-like cells. At least 50% G10-11 ED attached and developed multilayered colonies (100 cells) of small ovoid ES-like cells. Colonies from 4 sows were maintained in culture for at least 8 wk. Addition of PDGF, insulin or both, induced a transitory stimulation of growth in G6 or G10-11 ED; TGF beta did not modify growth of G6 ICM. Uterine G10-11 flushing medium or retinol induced differentiation of ES-like cells. These cells introduced in nude mice induced teratoma.
Antioxidant enzyme levels in oral squamous cell carcinoma and normal human oral epithelium (2002)

Detection of antioxidant enzymes may be a useful future marker in the molecular diagnosis of the oral cancer. Moreover, it may be possible to not only monitor the effectiveness of chemopreventive and therapeutic strategies in oral cancer using these enzymes, but to monitor tumor recurrence.
Hydrogen Clusters in Clathrate Hydrate (2002)

High-pressure Raman, infrared, x-ray, and neutron studies show that H2 and H2O mixtures crystallize into the sII clathrate structure with an approximate H2/H2O molar ratio of 1:2. The clathrate cages are multiply occupied, with a cluster of two H2 molecules in the small cage and four in the large cage. Substantial softening and splitting of hydrogen vibrons indicate increased intermolecular interactions. The quenched clathrate is stable up to 145 kelvin at ambient pressure. Retention of hydrogen at such high temperatures could help its condensation in planetary nebulae and may play a key role in the evolution of icy bodies.
Endothelin-1: a multifunctional molecule in cancer (2003)

Endothelin-1 is a small vasoconstrictor peptide that was first identified in 1988. Here we review the evidence implicating ET-1 in tumorigenesis. In particular, we concentrate on the role of ET-1 in mitogenesis, apoptosis, angiogenesis, tumour invasion and metastasis, and discuss the potential for endothelin-system modulation as an adjuvant therapeutic strategy.
Homocysteine Compounds which Influence the Growth of a Malignant Neoplasm (1977)

Since homocysteine metabolism is important in the control of normal and abnormal growth, three homocysteine derivatives were synthesized and tested for effects on the growth of transplanted murine adenocarcinoma. Arachidonoyl homocysteine thiolactone (HCT) amide decreased growth, and oleoyl HCT amide increased growth of the neoplasm. Pyridoxal HCT enamine decreased the growth of the neoplasm when given for 2 weeks prior to transplantation, but the compound had no effect when given after transplantation. The two inhibitory substances were tolerated well by normal mice except in high doses. These findings suggest an approach to prevention and therapy of human malignancy which utilizes homocysteine derivatives of normal biochemical constituents.
Transactivation of pancreas-specific gene sequences in somatic cell hybrids. (1991)

Enhancer/promoter elements from two pancreas-specific genes, those encoding amylase and elastase, were ligated to the bacterial GPT gene. The resulting construct can be used to select for expression of gene products which activate these pancreas-specific promoters in hybrid cells. The selectable GPT construct was stably transferred into several cell lines either directly or by cotransfection with pSV2Neo. GPT was expressed when transferred to pancreatic cell lines but not when transferred to GPT-fibroblast (L) cells or hepatoma cells. When the transformed L cells and hepatoma cells were fused with pancreatic cell lines, GPT was activated in the hybrid cells. Endogenous pancreas-specific genes from the L-cell and hepatoma parents were also activated in the hybrids. In addition, a pancreas-specific nuclear protein, PTF1, was produced in pancreatic and hybrid cells, correlating with GPT expression. The transformed L cells and hepatoma cells thus contained a nonexpressed construct which could be activated in trans by factors present in pancreatic cells. The hepatoma hybrid also continued to produce albumin, demonstrating the coexpression of liver and pancreas-specific genes in the hybrid-cell population. Cell lines carrying the amylase/elastase/GPT construct may be useful as a selection system for cloning of pancreatic transcription activators.
Effects of Combined 405-nm and 880-nm Light on Staphylococcus aureus and Pseudomonas aeruginosa in Vitro (2006)

Appropriate doses of combined 405-nm and 880-nm phototherapy can kill Staphylococcus aureus and Pseudomonas aeruginosa in vitro, suggesting that a similar effect may be produced in clinical cases of bacterial infection.
On the Activity and Regulation of Anaplerotic and Gluconeogenetic Enzymes during the Growth Process of Baker's Yeast (1975)

The anaplerotic and gluconeogenetic metabolism of baker's yeast was studied at the enzymatic level during glucose-ethanol diauxic growth in the presence and absence of aspartate. Of the two possible anaplerotic systems, only the pyruvate carboxylase by-pass was present during the whole growth process. The second system, the glyoxylate by-pass (isocitrate lyase as the indicator), like the specific enzymes of the gluconeogenetic metabolism, phosphoenolpyruvate carboxykinase and hexosediphosphatase began to appear only after the glucose had been consumed. The addition of glucose during the growth phase based on ethanol effected a rapid disappearance of phosphoenolpyruvate carboxykinase and hexosediphosphatase activities. The activity of pyruvate carboxylase decreased when the growth medium was supplied with asparate. The presence of aspartate had no effect on the activities of the other enzymes studied.
Evaluation of segmentation algorithms for vessel wall detection in echo particle image velocimetry (2009)

Recent in-vitro and in-vivo validation studies confirmed the accuracy of echo particle image velocimetry (echo PIV), a simple non-invasive means of measuring multi-component blood velocity vectors. Echo PIV should also be useful for direct measurement of wall shear stress (WSS) in clinical studies. However, calculation of WSS requires accurate delineation of vessel walls in ultrasound images, which may be problematic when conventional segmentation techniques are used. In this paper, we proposed two methods for segmenting contrast enhanced B-mode images. The first is based on the intensity profile of ultrasound images, termed intensity-based edge detection (IBED) and the second based on the movement of microbubbles, termed movement-based quadratic difference (MBQD). The parameters related with the two methods were optimized over large sets of microbubble images acquired from human carotid vessels using an echo PIV system (Illumasonix LLC, Boulder, CO). A validation study on the two algorithms was carried out against manual delineations on both common carotid artery (CCA) and carotid bifurcation images, with 20 frames for each group. The inter-observer variability of three manual delineations, in pixels (about 80 ¿m/pixel), was 0.9±0.4, 1.3±0.6, 1.3±0.6 on CCA images, and 2.5±1.0, 3.9±1.1, 2.3±1.1 on bifurcation images. The absolute difference (mean±SD) between each computer-generated contour and the ground truths, taken as the average of three manual delineations, were 1.3±0.8, 3.8±0.8, 5.3±0.5 on CCA images, and 2.3±0.9, 4.6±1.3, 6.3±0.6 on bifurcation images, for the MBQD, IBED and active contour methods, respectively. The MBQD method shows comparable performance with manual delineations on particle images even with poor intima-media layer quality.
Exploring the Dynamic Range of the Kinetic Exclusion Assay in Characterizing Antigen-Antibody Interactions (2012)

Therapeutic antibodies are often engineered or selected to have high on-target binding affinities that can be challenging to determine precisely by most biophysical methods. Here, we explore the dynamic range of the kinetic exclusion assay (KinExA) by exploiting the interactions of an anti-DKK antibody with a panel of DKK antigens as a model system. By tailoring the KinExA to each studied antigen, we obtained apparent equilibrium dissociation constants (K(D) values) spanning six orders of magnitude, from approximately 100 fM to 100 nM. Using a previously calibrated antibody concentration and working in a suitable concentration range, we show that a single experiment can yield accurate and precise values for both the apparent K(D) and the apparent active concentration of the antigen, thereby increasing the information content of an assay and decreasing sample consumption. Orthogonal measurements obtained on Biacore and Octet label-free biosensor platforms further validated our KinExA-derived affinity and active concentration determinations. We obtained excellent agreement in the apparent affinities obtained across platforms and within the KinExA method irrespective of the assay orientation employed or the purity of the recombinant or native antigens.
Hypotensive Activity of Fibroblast Growth Factor (1991)

Acidic and basic fibroblast growth factors (FGFs) are members of a family of proteins that are broad-spectrum mitogens, have diverse hormone-like activities, and function in tumorigenesis. FGF's ability to raise the concentration of intracellular calcium ion suggests that FGF could induce the synthesis of endothelium-derived relaxing factor (EDRF) and consequently vasodilation. Systemic administration of FGF decreased arterial blood pressure. This effect was mediated by EDRF and by adenosine triphosphate-sensitive potassium ion channels. The hypotensive effect of FGF was segregated from its mitogenic activity by protein engineering. These results extend the range of FGF autocrine activities and potential therapeutic applications, emphasize the role of endothelium as an arterial blood pressure--regulating organ, and provide insight on the structural basis of FGF functions.
High level methods for scene exploration (2024)

Virtual worlds exploration techniques are used in a wide variety of domains — from graph drawing to robot motion. This paper is dedicated to virtual world exploration techniques which have to help a human being to understand a 3D scene. An improved method of viewpoint quality estimation is presented in the paper, together with a new off-line method for automatic 3D scene exploration, based on a virtual camera. The automatic exploration method is working in two steps. In the first step, a set of “good” viewpoints is computed. The second step uses this set of points of view to compute a camera path around the scene. Finally, we define a notion of semantic distance between objects of the scene to improve the approach.
Identification of DNA Elements Cooperatively Activating Proopiomelanocortin Gene Expression in the Pituitary Glands of Transgenic Mice (1992)

The proopiomelanocortin (POMC) gene is highly expressed in adult mouse pituitary anterior lobe corticotrophs and intermediate lobe melanotrophs. To identify the DNA elements important for this tissue-specific expression, we analyzed a series of POMC reporter genes in transgenic mice. A DNA fragment containing rat POMC 5'-flanking sequences from -323 to -34 recapitulated both basal pituitary cell-specific and hormonally stimulated expression in adult mice when fused to a heterologous thymidine kinase promoter. Developmental onset of the reporter gene expression lagged by 1 day but otherwise closely paralleled the normal ontogeny of murine POMC gene expression, including corticotroph activation at embryonic day 14.5 (E14.5) followed by melanotroph activation at E15.5 to E16.5. AtT20 corticotroph nuclear protein extracts interacted with three specific regions of the functional POMC promoter in DNase I protection assays. The positions of these protected sites were -107 to -160 (site 1), -182 to -218 (site 2), and -249 to -281 (site 3). Individual deletions of these footprinted sites did not alter transgene expression; however, the simultaneous deletion of sites 2 and 3 prevented transgene expression in both corticotrophs and melanotrophs. Electrophoretic mobility shift and Southwestern (DNA-protein) assays demonstrated that multiple AtT20 nuclear proteins bound to these footprinted sites. We conclude that the sequences between -323 and -34 of the rat POMC gene promoter are both necessary and sufficient for correct spatial, temporal, and hormonally regulated expression in the pituitary gland. Our data suggest that the three footprinted sites within the promoter are functionally interchangeable and act in combination with promoter elements between -114 and -34. The inability of any reporter gene construction to dissociate basal and hormonally stimulated expression suggests that these DNA elements are involved in both of these two characteristics of POMC gene expression in vivo.
Ectopic bone formation after implantation of a slow release system of polylactid acid and rhBMP‐2 (2008)

The results suggest that release rates of rhBMP-2 for ectopic bone induction have to be >100 ng/72 h to maintain the osteoinductive activity of the tested porous PLA implants. This slow release system may have impact on alveolar bone augmentation procedures when used as individually preformed osteoinductive implants.
Increasing the amylose content of durum wheat through silencing of the SBEIIagenes (2010)

We have found that the silencing of SBEIIa genes in durum wheat causes obvious alterations in granule morphology and starch composition, leading to high amylose wheat. Results obtained with two different methods of transformation and in two durum wheat cultivars were comparable.
Cookson-type reagents: highly sensitive derivatization reagents for conjugated dienes in high-performance liquid chromatography (1991)

Cookson-type reagents, 4-substituted 1,2,4-triazoline-3,5-diones, having a chromophore, fluorophore or electrophore at the 4-position, have been synthesized for high-performance liquid chromatographic measurements of conjugated dienes. The reactivity of these reagents and the properties of their adducts were examined by using 7-dehydrocholesterol (7-DHC) as a model compound. 4-(1-Anthryl)- and 4-(1-pyrenyl)-1,2,4-triazoline-3,5-dione quantitatively produced adducts, in 5 min under ice-cooling, that could be detected using an ultraviolet detector but not a fluorescence detector. The adducts with 4-[2-(1-pyrenyl)ethyl]- and 4-amino-1,2,4-triazoline-3,5-dione were also easily formed and could be easily detected using fluorescence [detection limit: signal-to-noise ratio (S/N)= 5, 0.025 pmol] and electrochemical (S/N = 5, 0.029 pmol) detectors, respectively. The chromatographic behaviour of the adducts with 7-DHC and vitamin D3, and the application of the method to the detection of 7-DHC in human skin, are also reported.
A low-voltage, low-capacitance, vertical multi-layer thin-film-edge dispenser field emitter array electron source (2002)

A new low-voltage low-capacitance field emitter array (FEA) electron source has been developed for field emitter displays (FEDs) and high frequency power amplifiers. The new FEA cell has a horizontal gate and a vertical multi-layer thin-film low work function dispenser edge emitter made by sandwiching a lithium thin-film between two noble metal thin-films.
Imbalance between interstitial collagenase and tissue inhibitor of metalloproteinases 1 in synoviocytes and fibroblasts upon direct contact with stimulated T lymphocytes: Involvement of membrane-associated cytokines (1998)

Synovial tissue TCCs and PBTL stimulated for long periods of time trigger the production of PGE2 and MMP-1, but not TIMP-1, in synoviocytes and dermal fibroblasts, thus inducing an imbalance between the metalloenzyme and its inhibitor. These results demonstrate that T cells may affect fibroblast and synoviocyte functions directly (i.e., by contact activation) and indirectly (i.e., by activation of cytokine production in monocyte/macrophages, which in turn, trigger stromal cell functions). Since the production of MMPs in monocyte/macrophages is also induced upon contact with stimulated T cells, our results strongly suggest that contact of synovial cells with chronically stimulated T lymphocytes favors matrix catabolism. By analogy, this mechanism may trigger tissue destruction in vivo and, thus, may potentiate tissue destruction in chronic inflammatory diseases such as RA.
Small repeating units within the Ureaplasma urealyticum MB antigen gene encode serovar specificity and are associated with antigen size variation (1995)

Ureaplasma urealyticum is a common commensal of the female lower urogenital tract, yet it has been shown to be an important cause of chorioamnion infection, respiratory and central nervous system disease, and death in premature infants. It has been suggested that only certain serovars are capable of producing invasive disease. However, we previously showed that many serotypes are invasive and that perhaps antigen variability and host factors are more important determinants of ureaplasma infections than are different serotypes per se. The molecular characterization in this report describes a mechanism available to ureaplasmas for producing antigen variation. That antigen, designated MB and previously identified on U. urealyticum, contains serovar-specific and cross-reactive epitopes, is produced both in vitro and in vivo, is a predominant antigen recognized during ureaplasma infections of humans, undergoes a high rate of size variation in vitro, and is size variable on invasive ureaplasma isolates. In the present study, we cloned and sequenced the gene of the MB antigen from serovar 3, the serovar most commonly isolated from humans. The 3' two-thirds of the gene was shown to contain identical 18-nucleotide tandem repeats. PCR analysis and direct sequencing of two variants indicated that alterations within this repeat region are responsible for the size variation of the MB antigen. Intact recombinant serovar 3 MB antigen and truncated products, expressed by coupled in vitro transcription and translation of the cloned gene, were immunoprecipitated by both a serovar-specific monoclonal antibody and the serum of a U. urealyticum-infected patient, and these results identified the repeat region of the MB antigen as serovar defining. Resolution of the precise amino acids responsible for specific epitopes and characterization of similar genes in the other serovars should yield reagents useful in elucidating the role of antigen size variants in disease production and the role of specific antibody in protection from ureaplasma disease.