gebhart/patrepeval huggingface dataset:
Elements of Light-cured Epoxy-based Dental Polymer Systems (1998)

The greatest problem with current dental composite systems is their polymerization shrinkage. Extensive work is being done by many investigators to alleviate this problem. Our approach has been to examine epoxy- and spiro-orthocarbonate (SOC)-based resins. The hypothesis to be tested in this study was that the cure characteristics of experimental visible-light-cured epoxy resin systems are governed by the types and concentrations of co-reactants and activators. Resin samples containing onium salt initiators and a thiozanthone sensitizer were successfully cured by means of either an experimental visible-light irradiation system or a commercially available dental lamp. Test resins consisted of di-epoxies alone or in combination, epoxy mixtures in combination with an SOC, or an epoxy in combination with a caprolactone-derived polyol. Significant findings were as follows: (a) Resins containing the SOC had longer cure times than their counterparts; (b) the optimum ratios of epoxy to polyol for most rapid cure were 50:50 or 60:40 under conditions tested; (c) resins containing TONE 305 polyol generally were faster to cure than those containing no polyol, or TONES 201 or 310; and (d) a resin mixture was found that had a cure time of 1 to 3 min when irradiated with a commercial dental lamp. Based on this exploratory study, it should be possible for clinically relevant cure times to be achieved for visible-light-cured epoxy-based resins by careful manipulation and optimization of key elements.
Depletion of donor lymphocytes by counterflow centrifugation successfully prevents acute graft-versus-host disease in matched allogeneic marrow transplantation (1986)

Bone marrow from 22 histocompatible siblings was depleted of 98% of the lymphocytes using a combination of density flotation centrifugation followed by counterflow elutriation. Even with the marrow suppressive influence of methotrexate (MTX), the viability of the hematopoietic stem cells was not affected, as indicated by the normal repopulation after grafting in the evaluable patients. One patient (UPN 9) showed a primary graft failure, possibly resulting from persisting septicemia and long-term antibiotic therapy. Two patients have persistent host lymphocytes, one of whom was examined during relapse; the other remains in remission. Two patients did not receive immunosuppression after bone marrow transplantation (BMT), and acute graft-v-host disease (GVHD) developed in both. Nine patients received MTX as immunosuppression following BMT. GVHD did not develop in any of them, but fatal infections in the immediate posttransplant period developed in five patients. Eleven patients received cyclosporine (CsA) after transplantation. Beginning in week 5 after BMT, CsA was gradually replaced by MTX. Acute GVHD, substantial chronic GVHD, or fatal infections did not develop in any of these patients. Removal of 98% of the lymphocytes by counterflow centrifugation prevents development of acute GVHD, provided that immunosuppression is administered after BMT. Graft rejection was not observed, but the number of evaluable patients is limited at present.
The Gene Expression Index c- myc × E2F-1/p21 Is Highly Predictive of Malignant Phenotype in Human Bronchial Epithelial Cells (1998)

Recent methodological developments allow expression measurement of many genes simultaneously, thereby revealing patterns of gene expression that can be related to phenotype. We hypothesized that through the use of such methods we could identify patterns of gene expression associated with the malignant phenotype in human bronchial epithelial cells (BEC). To test this hypothesis, a recently developed quantitative reverse transcriptase polymerase chain reaction method was used to assess simultaneously expression of 15 genes mechanistically associated with cell-cycle control (c-myc, E2F-1, p21, rb, PCNA, cyclin D2, cyclin D3, cyclin E, cdc2, CDK2, CDK4, mad, max p21, max p22, and p53) in normal cell cultures from five individuals and in nine different malignant BEC lines. Relative to the mean expression levels in cultured normal cell populations, expression of c-myc, E2F-1, PCNA, cyclin E, and CDK4 messenger RNA (mRNA) were significantly increased and expression of p21 and p53 mRNA were significantly decreased in one or two, but not all three subtypes (squamous, adenocarcinoma and small cell) of carcinoma cell lines evaluated. No single cell-cycle control gene discriminated all three subtypes from normal cell populations. In contrast, the gene expression index c-myc x E2F-1/p21 separated all carcinoma cell lines from all normal cell populations initially evaluated. This malignancy index was validated in an additional three cultured normal BEC and three carcinoma cell lines, as well as three pairs of matched primary normal bronchial epithelial and primary bronchogenic carcinoma samples, and three pairs of matched primary normal lung parenchyma and primary bronchogenic carcinoma tissue. Again, the c-myc x E2F-1/ p21 index successfully discriminated all cultured and primary normal from malignant samples and thereby had a predictive value of 1 (no false positives and no false negatives). We hypothesize that because of functional mutations in cell-cycle regulatory genes (e.g., p53 and/or rb), cells lose the ability to maintain a pattern of gene expression mechanistically associated with normal, division-limited homeostatic equilibrium. Because the c-myc x E2F-1/p21 gene expression index has high specificity for malignant tissue, it will allow confirmation that there is a significant amount of tumor tissue present in small (e.g., fine-needle) biopsy specimens prior to evaluating them for expression of other genes, such as those involved in chemoresistance or radioresistance. In addition, the goal of most gene therapy efforts is to alter levels of gene expression quantitatively. This index and others derived in a similar manner may better define potential gene therapy targets as well as response of targeted genes to therapy.
Crystal Structures of Prostaglandin D2 11-Ketoreductase (AKR1C3) in Complex with the Nonsteroidal Anti-Inflammatory Drugs Flufenamic Acid and Indomethacin (2004)

It is becoming increasingly well established that nonsteroidal anti-inflammatory drugs (NSAID) protect against tumors of the gastrointestinal tract and that they may also protect against a variety of other tumors. These activities have been widely attributed to the inhibition of cylooxygenases (COX) and, in particular, COX-2. However, several observations have indicated that other targets may be involved. Besides targeting COX, certain NSAID also inhibit enzymes belonging to the aldo-keto reductase (AKR) family, including AKR1C3. We have demonstrated previously that overexpression of AKR1C3 acts to suppress cell differentiation and promote proliferation in myeloid cells. However, this enzyme has a broad tissue distribution and therefore represents a novel candidate for the target of the COX-independent antineoplastic actions of NSAID. Here we report on the X-ray crystal structures of AKR1C3 complexed with the NSAID indomethacin (1.8 A resolution) or flufenamic acid (1.7 A resolution). One molecule of indomethacin is bound in the active site, whereas flufenamic acid binds to both the active site and the beta-hairpin loop, at the opposite end of the central beta-barrel. Two other crystal structures (1.20 and 2.1 A resolution) show acetate bound in the active site occupying the proposed oxyanion hole. The data underline AKR1C3 as a COX-independent target for NSAID and will provide a structural basis for the future development of new cancer therapies with reduced COX-dependent side effects.
Assessment of systemic lupus erythematosus. (2006)

Systemic lupus erythematosus (SLE) is the archetypal autoimmune disease given its complex clinical and molecular manifestations. Like the other rheumatic diseases, appropriate management is critically dependent upon the proper assessment of disease activity, organ damage, and quality of life. Here, we describe the components of the comprehensive assessment of SLE, including accurate physical and laboratory diagnosis, monitoring of disease activity, recording of accumulated organ morbidity, and integration of these with the patient's own perceptions of health status and quality of life. In doing so, we will review the most appropriate laboratory tests and indices currently used in standard clinical care and in clinical research.
Microcontact Printing of Alkanethiols on Silver and Its Application in Microfabrication (1996)

This paper describes the use of microcontact printing (μCP) to generate patterned self‐assembled monolayers (SAMs) of alkanethiolates on the surfaces of evaporated films of silver. Using patterned SAMs of alkanethiolates as nanometer‐thick resists, patterned microfeatures of silver with sizes down to ∼200 nm were fabricated on by selective etching in aqueous solutions containing , and . Complete etching of silver can be achieved more rapidly than that of gold: ∼20 s vs. ∼20 min for 50 nm thick metal films when similar ferricyanide etchants were used. Microstructures of silver produced by the present method have higher edge resolution (typically, ∼20 nm vs. ∼100 nm) and far fewer defects (∼10 pits/mm2 vs. ∼103 pits/mm2) than those of gold fabricated by a similar procedure. Silver lines (0.2 μm in thickness, ∼50 μm in width, and ∼5 mm in length) had the expected metallic conductivity (≈5.56 × 105 S/cm); parallel lines of silver (0.2 μm in thickness, ∼10 μm in width, ∼1 mm in length, and separated by ∼10 μm) were electrically isolated from each other. Aqueous solutions containing other coordinating ligands and oxidants, , and , were also selective etchants for use with patterned SAMs of alkanethiolates on silver. Patterned structures of silver (50 nm thick) on could be used as secondary masks for etching of in aqueous solutions of , and of Si(100) in aqueous solutions of KOH and i‐propanol. Patterned films of silver (0.2 μm thick) on silicon wafers could be used as masters to cast elastomeric stamps with surface relief to be used for μCP. By choosing appropriate etching conditions, microparticles of MX (M = Ag; X = Cl, Br, I, OH, and SCN) could be formed in situ on the underivatized regions of the SAM‐patterned surface during etching of silver.
CCR5 Expression Influences the Progression of Human Breast Cancer in a p53-dependent Manner (2003)

Chemokines are implicated in tumor pathogenesis, although it is unclear whether they affect human cancer progression positively or negatively. We found that activation of the chemokine receptor CCR5 regulates p53 transcriptional activity in breast cancer cells through pertussis toxin-, JAK2-, and p38 mitogen-activated protein kinase-dependent mechanisms. CCR5 blockade significantly enhanced proliferation of xenografts from tumor cells bearing wild-type p53, but did not affect proliferation of tumor xenografts bearing a p53 mutation. In parallel, data obtained in a primary breast cancer clinical series showed that disease-free survival was shorter in individuals bearing the CCR5Delta32 allele than in CCR5 wild-type patients, but only for those whose tumors expressed wild-type p53. These findings suggest that CCR5 activity influences human breast cancer progression in a p53-dependent manner.
Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation (1992)

The accuracy of protein biosynthesis rests on the high fidelity with which aminoacyl-tRNA synthetases discriminate between tRNAs. Correct aminoacylation depends not only on identity elements (nucleotides in certain positions) in tRNA (1), but also on competition between different synthetases for a given tRNA (2). Here we describe in vivo and in vitro experiments which demonstrate how variations in the levels of synthetases and tRNA affect the accuracy of aminoacylation. We show in vivo that concurrent overexpression of Escherichia coli tyrosyl-tRNA synthetase abolishes misacylation of supF tRNA(Tyr) with glutamine in vivo by overproduced glutaminyl-tRNA synthetase. In an in vitro competition assay, we have confirmed that the overproduction mischarging phenomenon observed in vivo is due to competition between the synthetases at the level of aminoacylation. Likewise, we have been able to examine the role competition plays in the identity of a non-suppressor tRNA of ambiguous identity, tRNA(Glu). Finally, with this assay, we show that the identity of a tRNA and the accuracy with which it is recognized depend on the relative affinities of the synthetases for the tRNA. The in vitro competition assay represents a general method of obtaining qualitative information on tRNA identity in a competitive environment (usually only found in vivo) during a defined step in protein biosynthesis, aminoacylation. In addition, we show that the discriminator base (position 73) and the first base of the anticodon are important for recognition by E. coli tyrosyl-tRNA synthetase.
Modelling the electrical properties of tissue as a porous medium (2007)

Models of the electrical properties of biological tissue have been the subject of many studies. These models have sought to explain aspects of the dielectric dispersion of tissue. This paper develops a mathematical model of the complex permittivity of tissue as a function of frequency f, in the range 10(4) < f < 10(7) Hz, which is derived from a formulation used to describe the complex permittivity of porous media. The model introduces two parameters, porosity and percolation probability, to the description of the electrical properties of any tissue which comprises a random arrangement of cells. The complex permittivity for a plausible porosity and percolation probability distribution is calculated and compared with the published measured electrical properties of liver tissue. Broad agreement with the experimental data is noted. It is suggested that future detailed experimental measurements should be undertaken to validate the model. The model may be a more convenient method of parameterizing the electrical properties of biological tissue and subsequent measurement of these parameters in a range of tissues may yield information of biological and clinical significance.
Identification of Human T Cell Antigens for the Development of Vaccines against Mycobacterium tuberculosis (2008)

Development of a subunit vaccine for Mycobacterium tuberculosis (Mtb) depends on the identification of Ags that induce appropriate T cell responses. Using bioinformatics, we selected a panel of 94 Mtb genes based on criteria that included growth in macrophages, up- or down-regulation under hypoxic conditions, secretion, membrane association, or because they were members of the PE/PPE or EsX families. Recombinant proteins encoded by these genes were evaluated for IFN-gamma recall responses using PBMCs from healthy subjects previously exposed to Mtb. From this screen, dominant human T cell Ags were identified and 49 of these proteins, formulated in CpG, were evaluated as vaccine candidates in a mouse model of tuberculosis. Eighteen of the individual Ags conferred partial protection against challenge with virulent Mtb. A combination of three of these Ags further increased protection against Mtb to levels comparable to those achieved with bacillus Calmette-Guérin vaccination. Vaccine candidates that led to reduction in lung bacterial burden following challenge-induced pluripotent CD4 and CD8 T cells, including Th1 cell responses characterized by elevated levels of Ag-specific IgG2c, IFN-gamma, and TNF. Priority vaccine Ags elicited pluripotent CD4 and CD8 T responses in purified protein derivative-positive donor PBMCs. This study identified numerous novel human T cell Ags suitable to be included in subunit vaccines against tuberculosis.
Inducible Interaction of Integrin α2β1 with Calreticulin (1995)

We have previously demonstrated an interaction between the highly conserved KXGFFKR sequence of the integrin alpha-subunit cytoplasmic domains and calreticulin. Since this highly conserved sequence motif has been implicated in the regulation of the integrin affinity state, we wanted to determine whether the calreticulin-integrin interaction also depended on the integrin affinity state, and whether calreticulin occupation of integrin via the KXGFFKR motif was involved in the regulation of the ligand affinity state. We now demonstrate that anti-integrin antibody- or phorbol 12-myristate 13-acetate (PMA)-induced activation of the alpha 2 beta 1 integrin on Jurkat cells, as determined by stimulation of adhesion to collagen type I, resulted in an increased amount of calreticulin bound to this integrin. alpha 2 beta 1 activation with either anti-beta 1 or anti-alpha 2 monoclonal antibodies resulted in a greater amount of calreticulin coimmunoprecipitating with this integrin. Inactivation by neutralizing anti-integrin antibodies abrogated the calreticulin-integrin interaction. A correlation was also found between PMA-induced alpha 2 beta 1 activation and the amount of calreticulin bound to this integrin. Furthermore, pretreatment of streptolysin O-permeablized Jurkat cells with an anti-calreticulin antibody resulted in a significant and specific inhibition of the adhesion to collagen type I that could be induced by antibodies to alpha 2 beta 1 or by PMA. These data suggest that the active, high affinity form of alpha 2 beta 1 binds calreticulin and that calreticulin binding to the alpha 2 cytoplasmic domain may be required for stabilizing the high affinity state of this integrin. The data presented here also demonstrate, for the first time, an inducible interaction of an integrin with an intracellular protein that occurs via the alpha subunit of the integrin.
Cellular and molecular mechanisms of HGF/Met in the cardiovascular system (2015)

Met tyrosine kinase receptor, also known as c-Met, is the HGF (hepatocyte growth factor) receptor. The HGF/Met pathway has a prominent role in cardiovascular remodelling after tissue injury. The present review provides a synopsis of the cellular and molecular mechanisms underlying the effects of HGF/Met in the heart and blood vessels. In vivo, HGF/Met function is particularly important for the protection of the heart in response to both acute and chronic insults, including ischaemic injury and doxorubicin-induced cardiotoxicity. Accordingly, conditional deletion of Met in cardiomyocytes results in impaired organ defence against oxidative stress. After ischaemic injury, activation of Met provides strong anti-apoptotic stimuli for cardiomyocytes through PI3K (phosphoinositide 3-kinase)/Akt and MAPK (mitogen-activated protein kinase) cascades. Recently, we found that HGF/Met is also important for autophagy regulation in cardiomyocytes via the mTOR (mammalian target of rapamycin) pathway. HGF/Met induces proliferation and migration of endothelial cells through Rac1 (Ras-related C3 botulinum toxin substrate 1) activation. In fibroblasts, HGF/Met antagonizes the actions of TGFβ1 (transforming growth factor β1) and AngII (angiotensin II), thus preventing fibrosis. Moreover, HGF/Met influences the inflammatory response of macrophages and the immune response of dendritic cells, indicating its protective function against atherosclerotic and autoimmune diseases. The HGF/Met axis also plays an important role in regulating self-renewal and myocardial regeneration through the enhancement of cardiac progenitor cells. HGF/Met has beneficial effects against myocardial infarction and endothelial dysfunction: the cellular and molecular mechanisms underlying repair function in the heart and blood vessels are common and include pro-angiogenic, anti-inflammatory and anti-fibrotic actions. Thus administration of HGF or HGF mimetics may represent a promising therapeutic agent for the treatment of both coronary and peripheral artery disease.
Radioimmunometric assay for a monoclonal antibody-defined tumor marker, CA 19-9. (1983)

We describe a solid-phase radioimmunometric sandwich assay for a new tumor marker defined by a monoclonal antibody (19-9). This antibody reacts with a carbohydrate antigenic determinant (CA 19-9) found at low concentrations in sera from healthy individuals but frequently increased in sera from patients with adenocarcinomas. The assay is sensitive and simple to perform. It requires duplicate 100-microL samples and may be performed in 6 h. The concentration of CA 19-9 in samples is determined by reference to a standard curve, which is essentially linear from 0 to 120 arbitrary units/mL. The average CV is approximately 10% in the range of 5.8 to 120 units/mL. The minimum detectable dose is 1.4 units/mL and analytical recovery of CA 19-9 is 97.6 to 100.6%. The average concentration of CA 19-9 in sera from 1020 healthy individuals was 8.4 (SD 7.4) units/mL; only 0.6% of such sera had concentrations greater than 37 units/mL. The assay has high specificity (98.5%), even among patients with benign diseases, and has high sensitivity (up to 79%) for patients with gastrointestinal adenocarcinomas, especially those of the pancreas.
Field Evaluation of a Novel Inhibitive Water-Based Drilling Fluid for Tertiary Shales (1992)

ABSTRACT Laboratory tests showed that tetra-potassium pyrophosphate (TKPP or K4P207) gave levels of shale inhibition well beyond that obtained with equivalent concentrations of potassium chloride. A detailed evaluation indicated that stable mud formulations could be prepared which were considerably more inhibitive than other mud systems currently available. Inhibition even approached the level of that observed with oil based mud with some shale types. Two North Sea field trials were selected to evaluate the field performance of these phosphate muds. In both cases there were extensive formations of very reactive Tertiary shale which were known to be unstable when drilled using conventional water based muds. Each location also provided good offset data from similar wells drilled with both oil based and conventional water based fluids. This allowed the performance and economics of the phosphate muds to be thoroughly assessed. In both field trials the highly inhibitive nature of the new systems was confirmed when the shale sections remained open and stable for extended periods. However, in both wells the overall performance of the system was disappointing because of severe problems caused by very firm cuttings adhering to the stabilisers. This "accretion" resulted in slow, tight trips to surface, gave problems with blocked flowlines and a rapid buildup of drill solids, which consequentially required higher than planned mud dilution. The cause of the accretion problem has been investigated and explained. Work is now underway to find a practical solution.