gebhart/patrepeval huggingface dataset:
Activation of methotrexate-.alpha.-alanine by carboxypeptidase A monoclonal antibody conjugate (1992)

Carboxypeptidase A (CP-A) and monoclonal antibody KS1/4 directed against an antigen on human lung adenocarcinoma cells (UCLA-P3) were derivatized by treatment with succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate and N-succinimidyl 3-(2-pyridyldithio)propionate, respectively. The derivatized proteins were reacted to produce thioether-linked enzyme-antibody conjugates. Sequential HPLC size-exclusion and DEAE chromatography separated the conjugate preparation from unreacted enzyme and antibody. On the basis of SDS-PAGE analysis and measurement of catalytic activity, the preparation contained approximately equal amounts of 1:1 and 2:1 (enzyme:antibody) conjugates; binding activity of the conjugate (1.8 x 10(5) molecules/cell) was similar to that of unreacted antibody. In vitro cytotoxicity studies with UCLA-P3 cells demonstrated the ability of cell-bound conjugate to convert the prodrug methotrexate-alpha-alanine (MTX-Ala) to methotrexate (MTX). In the absence of conjugate, ID50 values for MTX-Ala and MTX were 8.9 x 10(-6) and 5.2 x 10(-8) M, respectively. ID50 for the prodrug improved to 1.5 x 10(-6) M with cells containing bound conjugate. This potentiation of MTX-Ala cytotoxicity by conjugate-bound CP-A, which was at least 30-fold greater than that produced by a comparable amount of free enzyme, is attributed to enhanced effectiveness of MTX generated at the cell surface as opposed to the surrounding medium. Examination of the time course of cytotoxicity over a 96-h period showed that the conjugate-prodrug combination (at 2.5 x 10(-6) M) was nearly as effective as MTX in preventing cell replication. These results demonstrate the chemotherapeutic potential of carboxypeptidase-monoclonal antibody conjugates used in conjunction with MTX peptide prodrugs.
Reactive stroma component COL6A1 is upregulated in castration-resistant prostate cancer and promotes tumor growth (2015)

Castration-resistant prostate cancer (CRPC) remains the most critical challenge in the clinical management of prostate cancer (PCa). Reactive stromal changes in PCa are likely involved in the emergence of CRPC. In the present study, we identified a novel oncogene termed COL6A1 which was upregulated in the reactive stroma of CRPC. We established an androgen-independent LNCaP (LNCaP-AI) cell line in steroid-reduced (SR) medium within 2 months. We examined COL6A1 expression with western blot during the LNCaP-AI induction, and studied the function of COL6A1 in vitro and in vivo. Immunohistochemical staining of COL6A1 was performed in ten pairs of androgen-sensitive PCa and CRPC samples. We demonstrated that COL6A1 expression was markedly increased in LNCaP-AI cells and CRPC tissues compared with LNCaP cells and paired androgen-sensitive PCa specimens. In vitro, COL6A1 knockdown resulted in G1-S cell cycle arrest and descended vitality. Overexpression of COL6A1 was associated with accelerated S phase entry and elevated vitality in prostate cancer cells. COL6A1 also promoted tumorigenesis of LNCaP cells in vivo. Taken together, these data suggest an important role of COL6A1 in the molecular etiology of castration-resistant prostate cancer, and support the potential use of COL6A1 in CRPC therapy.
An Arabidopsis mutant deficient in sterol biosynthesis: heterologous complementation by ERG 3 encoding a Δ7‐sterol‐C‐5‐desaturase from yeast (1995)

The mutant STE 1 was isolated by screening an ethylmethane sulfonate (EMS)-mutagenized population of Arabidopsis thaliana which consisted of 22,000 M2 plants divided into 1100 pools of 20 plants by gas chromatography of sterols extracted from small leaf samples. STE 1 was characterized by the accumulation of three delta 7-sterols concomitantly with the decrease of the three corresponding delta 5-sterols which are the end products of the sterol pathway in wild-type leaves. The structure of these delta 7-sterols was determined after two steps of purification on HPLC, by gas chromatography coupled with mass spectrometry (GC-MS) and proton nuclear magnetic resonance spectrometry (1H-NMR). The accumulation of delta 7-sterols suggested that the mutant is deficient in the activity of the delta 7-sterol-C-5-desaturase. Genetic analysis showed that the accumulation of delta 7-sterols was due to a single recessive nuclear mutation. The mutant line STE 1 was backcrossed four times to the wild-type. The resulting STE 1 plants had wild-type morphology and set seeds normally, suggesting that the delta 7-sterols in STE 1 are good surrogates of physiologically active delta 5-sterols to sustain normal development. STE 1 roots were transformed with the Saccharomyces cerevisiae ERG 3 gene encoding the delta 7-sterol-C-5-desaturase under the control of the CaMV 35S promoter. Seven transgenic STE 1 root-derived calli showed an increase in delta 5-sterols and a concomitant decrease in delta 7-sterols in comparison with STE 1 untransformed root-derived calli. Northern blot analysis using the ERG 3 probe showed a strong expression of ERG 3 in three of the seven transgenic calli. These results suggest that the accumulation of delta 7-sterols in the STE 1 mutant is due to a deficiency of the delta 7-sterol-C-5-desaturation step in the plant sterol biosynthesis pathway.
Molecular Identification of a Novel Fibrinogen Binding Site on the First Domain of ICAM-1 Regulating Leukocyte-Endothelium Bridging (1997)

Binding of fibrinogen to intercellular adhesion molecule 1 (ICAM-1) enhances leukocyte adhesion to endothelium by acting as a bridging molecule between the two cell types. Here, a panel of four monoclonal antibodies (mAbs) to ICAM-1 was used to dissect the structure-function requirements of this recognition. All four mAbs bound to ICAM-1 transfectants and immunoprecipitated and immunoblotted ICAM-1 from detergent-solubilized JY lymphocyte extracts. Functionally, mAbs 1G12 and 2D5 inhibited binding of 125I-fibrinogen to ICAM-1-transfectants and abrogated the enhancing effect of fibrinogen on mononuclear cell adhesion to endothelium and transendothelial migration. In contrast, mAbs 3D6 and 6E6 did not affect ICAM-1 recognition of fibrinogen. With respect to other ligands, mAbs 1G12 and 2D5 completely inhibited attachment of Plasmodium falciparum-infected erythrocytes to immobilized recombinant ICAM-1-Fc, whereas they had no effect on LFA-1-dependent T cell binding to ICAM-1-Fc. Conversely, mAbs 3D6 and 6E6 completely abolished LFA-1 binding to ICAM-1-Fc. Epitope assignment using ICAM-1 chimeras and receptor mutants revealed that the fibrinogen-blocking mAbs 1G12 and 2D5 reacted with domain 1 of ICAM-1, and their binding was disrupted by 97 and 70% by mutations of D26 and P70, respectively, whereas mAbs 3D6 and 6E6 bound to domain 2 of ICAM-1. By recognizing a site distinct from that of beta2 integrins Mac-1 or LFA-1, fibrinogen binding to ICAM-1 may provide an alternative pathway of intercellular adhesion and/or modulate integrin-dependent adherence during inflammation and vascular injury.
Synthesis and Characterization of an RNA Dinucleotide Containing a 3‘-S-Phosphorothiolate Linkage (1996)

The synthesis of an RNA dinucleotide (IspU) containing a 3‘-S-phosphorothiolate linkage is described. The compound is prepared from 9-(3-deoxy-3-iodo-β-d-xylofuranosyl)hypoxanthine with installation of the phosphorothiolate group via an Arbusov reaction and protection of the ribose 2‘-hydroxyl as a silyl ether. IspU is found to be a substrate for several enzymes including T4 polynucleotide kinase, snake venom phosphodiesterase, and ribonuclease T2. Base-catalyzed cleavage of the dinucleotide is accelerated (∼2000-fold) relative to that of the phosphate-linked compound IpU. Product characterization and kinetic analysis show that IspU is cleaved through the same mechanism as IpU. The observed rate acceleration is argued to reflect stabilization of the anionic transition state by the polarizable sulfur atom.
Incremental Conversion of Outer-Membrane Permeabilizers into Potent Antibiotics for Gram-Negative Bacteria (1999)

Cholic acid derivatives appended with amine groups have been prepared for use as permeabilizers of the outer membranes of Gram-negative bacteria. These compounds interact synergistically with antibiotics such as erythromycin and novobiocin to inhibit growth of Gram-negative bacteria. When a hydrophobic chain is included on the permeabilizers, they can be converted into potent antibiotics. The role of the hydrophobic chain is to facilitate self-promoted transport of the cholic acid derivatives across the outer membrane of Gram-negative bacteria. These compounds share activities found with polymyxin B and derivatives.
The effects of γ-irradiation on compositional changes in plastic packaging films (1999)

Sterilization of packaging materials for pharmaceutical or food products with ionizing irradiation can cause chemical and physical changes in polymer materials. The effects of γ-irradiation on the formation of solvent extractable radiolysis products of six flexible packaging materials for foodstuffs and/or pharmaceutical applications were studied after treatment in a 60Co-irradiation plant. The polymer materials polyethylene, polypropylene, poly(ethylene terephthalate), polyamide, polystyrene and poly(vinyl chloride) were investigated after treating with an irradiation dose of 44 kGy. The compositional changes in solvent extractable radiolysis products of each packaging material were quantified. In most cases the radiolysis products formed could be identified using GC/MS. The polyolefine materials (PE and PP) showed an increase of low volatile compounds after irradiation due to an oxidative decomposition of the polymer and typical polymer substances like oligomers and additives. Other packaging materials such as PET, PA and PS did not significantly change their amount of solvent extractable compounds after irradiation with 44 kGy. The PVC packaging material used in this study was not resistant to irradiation treatment at all. Because of the release of HCl during irradiation a large amount of volatile substances could be extracted from the PVC sheet. For consumer protection and also to meet general food packaging legislative requirements for irradiated packaging materials, it is necessary to evaluate the compositional changes in the polymers during irradiation, especially for irradiated polyolefines and PVC. Most attention should be paid to low volatile radiolysis products which are the most likely to migrate into a foodstuff or a pharmaceutical product. Copyright © 1999 John Wiley & Sons, Ltd.
Control of Abscisic Acid Catabolism and Abscisic Acid Homeostasis Is Important for Reproductive Stage Stress Tolerance in Cereals1 (2011)

Drought stress at the reproductive stage causes pollen sterility and grain loss in wheat (Triticum aestivum). Drought stress induces abscisic acid (ABA) biosynthesis genes in anthers and ABA accumulation in spikes of drought-sensitive wheat varieties. In contrast, drought-tolerant wheat accumulates lower ABA levels, which correlates with lower ABA biosynthesis and higher ABA catabolic gene expression (ABA 8'-hydroxylase). Wheat TaABA8'OH1 deletion lines accumulate higher spike ABA levels and are more drought sensitive. ABA treatment of the spike mimics the effect of drought, causing high levels of sterility. ABA treatment represses the anther cell wall invertase gene TaIVR1, and drought-tolerant lines appeared to be more sensitive to the effect of ABA. Drought-induced sterility shows similarity to cold-induced sterility in rice (Oryza sativa). In cold-stressed rice, the rate of ABA accumulation was similar in cold-sensitive and cold-tolerant lines during the first 8 h of cold treatment, but in the tolerant line, ABA catabolism reduced ABA levels between 8 and 16 h of cold treatment. The ABA biosynthesis gene encoding 9-cis-epoxycarotenoid dioxygenase in anthers is mainly expressed in parenchyma cells surrounding the vascular bundle of the anther. Transgenic rice lines expressing the wheat TaABA8'OH1 gene under the control of the OsG6B tapetum-specific promoter resulted in reduced anther ABA levels under cold conditions. The transgenic lines showed that anther sink strength (OsINV4) was maintained under cold conditions and that this correlated with improved cold stress tolerance. Our data indicate that ABA and ABA 8'-hydroxylase play an important role in controlling anther ABA homeostasis and reproductive stage abiotic stress tolerance in cereals.
Acidic ethanol extraction of cottonseed (1992)

Ethanol (EtOH) is being evaluated as an alternate solvent to hexane for the extraction of glanded cottonseed. Hot EtOH, needed for efficient oil and aflatoxin extraction, binds gossypol to protein. However, this binding can be minimized by acidifying aqueous EtOH with a tribasic acid, such as phosphoric or citric. While this solvent extracts oil and gossypol, it does not affect EtOH’s ability to extract aflatoxin. The defatted cottonseed meals produced from this process contained 0.03% total gossypol (which is lower than meal prepared by most other processes) and the aflatoxin content was reduced from 69 to 2.9 ppb. These are preliminary results and additional research is needed to determine commercial feasibility. The removal of essentially all gossypol from an extracted meal has the potential to expand the use of cottonseed meal as a feed, increasing its value to both the cotton farmer and the seed processor.
Homocysteine Increases the Expression of Vascular Endothelial Growth Factor by a Mechanism Involving Endoplasmic Reticulum Stress and Transcription Factor ATF4 (2004)

Vascular endothelial growth factor (VEGF) plays a key role in the development and progression of diabetic retinopathy. We previously demonstrated that amino acid deprivation and other inducers of endoplasmic reticulum-stress (ER stress) up-regulate the expression of VEGF in the retinal-pigmented epithelial cell line ARPE-19. Because homocysteine causes ER stress, we hypothesized that VEGF expression is increased by ambient homocysteine. dl-Homocysteine-induced VEGF expression was investigated in confluent ARPE-19 cultures. Northern analysis showed that homocysteine increased steady state VEGF mRNA levels 4.4-fold. Other thiol-containing compounds, including l-homocysteine thiolactone and DTT, induced VEGF expression 7.9- and 8.8-fold. Transcriptional run-on assays and mRNA decay studies demonstrated that the increase in VEGF mRNA levels was caused by increased transcription rather than mRNA stabilization. VEGF mRNA induction paralleled that of the ER-stress gene GRP78. Homocysteine treatment caused transient phosphorylation of eIF2alpha and an increase in ATF4 protein level. Overexpression of a dominant-negative ATF4 abolished the VEGF response to homocysteine treatment and to amino acid deprivation. VEGF mRNA expression by ATF4-/- MEF did not respond to homocysteine treatment and the response was restored with expression of wild-type ATF4. These studies indicate that expression of the pro-angiogenic factor VEGF is increased by homocysteine and other thiol-containing reductive compounds via ATF4-dependent activation of VEGF transcription.
Analysis of the ERK-Stimulated ETS Transcription Factor ER81 (1996)

A plethora of extracellular signals leads to the stimulation of Ras, which triggers intracellular protein kinase cascades, resulting in activation of transcription factors and thus in enhanced gene activity. In this report, it is demonstrated that the ETS transcription factor ER81, which appears to be localized within the cell nucleus by virtue of its DNA binding domain, is transcriptionally activated by oncogenic Ras. Since this activation was dependent on the presence of Raf-1 and ERK-1, ER81 is a target of the Ras/Raf/MEK/ERK signaling cascade. Consistently, activated ERK-1 is capable to phosphorylate ER81. However, the carboxy-terminal region of ER81, which contains no potential ERK phosphorylation sites, is also transcriptionally activated by ERK-1, suggesting that an ERK-stimulated protein kinase phosphorylates and thus stimulates ER81 activity. Two acidic stretches of amino acids, which are conserved in the related PEA3 and ERM proteins, are localized within the amino-and carboxy-terminal transactivation domains of ER81. In addition, an inhibitory domain may dampen the activation function of these two domains. In conclusion, ER81 is a target of Ras-dependent signaling cascades and may thus contribute to the nuclear response upon stimulation of cells and also to cellular transformation due to oncogenic Ras.
Interferometric lithography of sub-micrometer sparse hole arrays for field-emission display applications (1996)

Interferometric lithography, the use of interactions between coherent laser beams to define sub- wavelength patterns, is well adapted to the periodic nature of field-emitter structures. Techniques to fabricate sparse (hole diameter to pitch ratio of 1:3 or larger) emitter arrays to improve reliability and lifetime are presented. These include: multiple exposures at two different pitches; integration of interferometric and optical imaging lithography; and various multiple beam techniques that both provide a sparse array and result in a two dimensional pattern in a single exposure. Moiré alignment techniques are demonstrated to provide a simple process for aligning multiple levels. Manufacturing related issues such as process latitude and photoresist profiles and their suitability for subsequent processing are also discussed. Exposure-dose process control using latent image monitoring is demonstrated.
A structural mechanism of flavonoids in inhibiting serine proteases (2017)

Quercetin is a member of the flavonoids and was previously demonstrated to inhibit trypsin-like serine proteases at micromolar potencies. Different molecular models were proposed to explain such inhibition. However, controversies remain on the molecular details of inhibition. Here, we report the X-ray crystal structure of quercetin in a complex with the urokinase-type plasminogen activator (uPA), an archetypical serine protease. The structure showed that quercetin binds to the specific substrate binding pocket (S1 pocket) of uPA mainly through its two neighboring phenolic hydroxyl groups. Our study thus provides unambiguous evidence to support quercetin binding to serine proteases and defines the molecular basis of the interaction. Our results further establish that natural products with two adjacent phenolic hydroxyl groups (or catechol) are likely to inhibit other trypsin-like serine proteases, a new mechanism formerly under-recognized.
Digital Signal Processing Applications Using the ADSP-2100 Family and Digital Signal Processing Applications with the TMS320 Family, Volumes 2 and 3 (1991)

First Page
La soledad del conservador del museo universitario (2000)

Doublement isoles � a la fois de leurs collegues au sein de l�universite et de leurs confreres du monde des musees �, les conservateurs des musees universitaires s�emploient a concevoir pour l�institution ou ils travaillent de nouvelles methodes et des missions inedites. Jane Weeks, museologue specialisee dans le fonctionnement des musees des organisations non museales, decrit les activites de ceux-ci au Royaume-Uni. Pour avoir dirige la realisation d�un grand projet de gestion des collections de l�University College de Londres, elle a une riche experience des musees universitaires et a entrepris deux enquetes regionales sur les collections et les musees universitaires du sud-ouest de l�Angleterre et des Midlands, conjointement avec Kate Arnold-Forster.
Antigenic analysis of hematopoiesis. VI. Flow cytometric characterization of My-10-positive progenitor cells in normal human bone marrow. (1987)

We have previously shown [1] that the anti-My-10 murine monoclonal antibody detected an epitope of a 115-kDa glycoprotein expressed specifically on KG-1a leukemia cells and a small subset of normal human bone marrow cells. This My-10+ marrow cell subset was shown to contain a highly enriched population of morphologic blast cells and hematopoietic colony-forming cells [1]. In this report, My-10+ cells were characterized, by flow cytometry, as an approximately 1% subpopulation of normal human bone marrow cells. My-10+ cells were slightly larger than lymphocytes and agranular, as determined by their fluorescence-activating cell sorting (-er) (FACS) light-scattering properties. In two-color immunofluorescence experiments, My-10+ cells coexpressed the HLA-DR antigen. However, there was no detectable cellular coexpression of My-10 with either the Leu 1-5, 7, 9, 11, 15, M3, or My-18 antigens. There was an average of approximately 50,000 My-10 molecules per My-10+ marrow cell. This provides further evidence that the My-10 molecule is expressed, at relatively low levels, selectively on early human marrow cells but not on mature lymphohematopoietic cells.
3-dimensional control over lamella orientation and order in thick block copolymer films (2008)

The general strategies for achieving macroscopic order in thin block copolymer films typically utilize external stimuli and activation energies, which become less effective with increasing the film thickness to ∼0.5–1 µm. Here we show a facile and effective approach towards multi-level control over lamella orientation and order in thick diblock copolymer films. The novel finding concerns the reorientation of lamella domains relative to the substrate upon annealing under a selective solvent, and is combined with alignment of the lamellar director along a preferred direction by simultaneous application of an electric field. The multiple approach yields a method for the single step fabrication of a striped nanostructure with a controlled orientation and long-range order of the microdomains.
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations (2003)

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here we report that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n2) clustering algorithm that computes time averages over a continuously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 105-fold for short, multistable molecules (<or=150 bases). We performed extensive folding statistics on random and natural RNA sequences and found that pseudoknots are distributed unevenly among RNA structures and account for up to 30% of base pairs in G+C-rich RNA sequences (online RNA-folding kinetics server including pseudoknots: http://kinefold.u-strasbg.fr).
Isolation and Characterization of Human Blood Platelet mRNA and Construction of a cDNA Library in λgt11 (1989)

Summary We have developed a purification method for the isolation of platelet-specific poly (A+) RNA and demonstrated that human blood platelets, despite the absence of a nucleus, contain stable mRNA. The poly (A+) RNA was used to construct a platelet- specific cDNA expression library in λgtll. The platelet derivation of the purified mRNA was confirmed by identification of membrane glycoprotein Ib (GPIb) message by immunoprecipitation of rabbit reticulocyte lysate translation products with poly- and monoclonal antibodies against GPIbα and by sequencing of a GPIbα cDNA clone