gebhart/patrepeval huggingface dataset:
LOX-1 Supports Adhesion of Gram-Positive and Gram-Negative Bacteria (2001)

Adhesion of bacteria to vascular endothelial cells as well as mucosal cells and epithelial cells appears to be one of the initial steps in the process of bacterial infection, including infective endocarditis. We examined whether lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1), a member of scavenger receptor family molecules with C-type lectin-like structure, can support adhesion of Gram-positive and Gram-negative bacteria. Chinese hamster ovary-K1 (CHO-K1) cells stably expressing LOX-1 can support binding of FITC-labeled Staphylococcus aureus and Escherichia coli, which was suppressed by poly(I) and an anti-LOX-1 mAb. Adhesion of these bacteria to LOX-1 does not require divalent cations or serum factors and can be supported under both static and nonstatic conditions. Cultured bovine aortic endothelial cells (BAEC) can also support adhesion of FITC-labeled S. aureus, which was similarly suppressed by poly(I) and an anti-LOX-1 mAb. In contrast, binding of FITC-labeled E. coli to BAEC was partially inhibited by the anti-LOX-1 mAb, and poly(I) did not block FITC-labeled E. coli adhesion to BAEC, but, rather, enhanced it under a static condition. TNF-alpha increased LOX-1-dependent adhesion of E. coli, but not that of S. aureus, suggesting that S. aureus adhesion to BAEC may require additional molecules, which cooperate with LOX-1 and suppressed by TNF-alpha. Taken together, LOX-1 can work as a cell surface receptor for Gram-positive and Gram-negative bacteria, such as S. aureus and E. coli, in a mechanism similar to that of class A scavenger receptors; however, other unknown molecules may also be involved in the adhesion of E. coli to BAEC, which is enhanced by poly(I).
Microinjection of nucleic acids into cultured mammalian cells by electrophoresis. (1981)

Simian virus 40 (SV40) DNA was microinjected into cultured mammalian cells by means of electrophoresis (iontophoresis). Successful transfer of DNA into cells was confirmed by detecting SV40 T antigen using the indirect immunofluorescent technique.
Peptides 1990 : proceedings of the twenty-first European Peptide Symposium, September 2-8, 1990, Platja d'Aro, Spain (1991)

It is our great pleasure to introduce the Proceedings of the Twenty-First European Peptide Symposium, held in Platja d' Aro, Spain, September 2-8, 1990. Over seven hundred scientists from nearly thirty countries, mostly European but also from the Americas, Australia and Japan, assembled at the largest-to-date in a series of European Peptide Symposia to present and discuss their recent findings in the field of peptides. Whenever scientists meet, a good deal of their interaction cannot be appropri ately recorded in book form. Fruitful early morning dialogues go regrettably unrecorded or, at most, precariously scribbled on ephemeral breakfast napkins. Many a brilliant late night debate is bound to fade away through the mists of a noisy discotheque. Alas, this book will unfortunately ignore these potentially splendid contributions to science! No effort has been made either to register the discussions that followed the oral presentations of the Symposium, or the two open sessions on special topics of general interest. Spontaneity, the main appeal of oral discussion, is somewhat lost, we believe, on literal transcription. Once all these non-recordable forms of scientific communication are discounted one is left with the core of the Symposium, i.e., its scientific communications, both in oral and poster form, and it is to these that the book you have in your hands is devoted.
Water-Soluble Polymers. 81. Direct Synthesis of Hydrophilic Styrenic-Based Homopolymers and Block Copolymers in Aqueous Solution via RAFT (2001)

Homopolymers of sodium 4-styrenesulfonate have been synthesized directly in aqueous media by reversible addition−fragmentation chain transfer polymerization (RAFT). The resulting homopolymers have narrow molecular weight distributions, with polydispersity indices in the range 1.12−1.25, as determined by aqueous size exclusion chromatography. Using a dithioester-capped sodium 4-styrenesulfonate homopolymer as a macro chain transfer agent, a block copolymer with sodium 4-vinylbenzoate has been prepared in aqueous media. Additionally, a block copolymer of (ar-vinylbenzyl)trimethylammonium chloride with N,N-dimethylvinylbenzylamine has been synthesized, using the same methodology. We believe these represent the first examples of AB diblock copolymers prepared directly in aqueous media via the RAFT process. Both block copolymers are stimuli-responsive and undergo reversible pH-induced micellization in aqueous solution. Micelles with hydrodynamic diameters in the range 18−38 nm were observed by dynamic light scattering.
Double-Stranded Ribonucleic Acid Decreases C6 Rat Glioma Cell Proliferation in Part by Activating Protein Kinase R and Decreasing Insulin-Like Growth Factor I Levels (2002)

We previously reported that reduction of autocrine IGF-I by polyinosinic-polycytidylic acid [poly(IC)] was permissive for the poly(IC)-mediated decrease in C6 rat glioma cell number. We now report that poly(IC) caused a block in G(1) to S transition in confluent C6 cultures, whereas in subconfluent cultures, poly(IC) decreased the percentage of cells in the G(2)/M phase. Addition of IGF-I to poly(IC)-treated cells decreased the percentage of cells in G(0)/G(1) phase and increased the percentage of cells in G(2)/M phase in confluent and subconfluent C6 cultures, indicating the reversal of cell cycle blocks. Inhibition of protein kinase R (PKR) activation partially prevented the poly(IC)-mediated cytostasis of C6 cells. Poly(IC) induced interferon-alpha in C6 cells. Both IGF-I and a blocking antibody against type I interferon (IFN) prevented the increase in PKR levels and the decrease in cell proliferation caused by poly(IC). We conclude that poly(IC) induces IFN, which mediates the cytostatic effect of poly(IC) on C6 cells at least in part through PKR. IGF-I prevents IFN from inducing PKR, thus explaining the ability of IGF-I to reverse the cell cycle blocks and the decreased C6 proliferation caused by poly(IC).
Dendritic cells sequester antigenic epitopes for prolonged periods in the absence of antigen-encoding genetic information (2012)

Studies with a number of viral systems have shown, on the basis of the ability of a host to prime naïve T cells, that viral antigens persist in the infected host well beyond complete clearance of the infection and even when viral antigen is undetectable by the most sensitive methods. This has led to a reasonable assumption that the antigen persists through persistence of antigen-encoding genetic information (DNA or RNA) that resides in the host at a subdetectable level. Here, we demonstrate that epitopes, or epitope precursors, of a model antigen (ovalbumin) persist in a host for prolonged periods (weeks), well beyond the time at which the intact antigen has disappeared, and in the complete absence of genetic information encoding it. Dendritic cells are shown to be the site of this epitope sequestration in vivo, as well as in cultures in vitro. For sequestration to occur, the uptaken antigen must be significantly large, that is, the epitope and its 18-mer precursor are not sequestered. Dendritic cells are shown to create an hsp90-dependent intracellular pool of epitopes or epitope precursors that continues to release epitopes for presentation on the major histocompatibility complex I molecules for prolonged periods. Demonstration of such long-term sequestration of antigenic epitopes inside dendritic cells presents new opportunities for stimulation of immune response against cancers and viruses.
Prevention of Sudden Cardiac Death by Dietary Pure ω-3 Polyunsaturated Fatty Acids in Dogs (1999)

These results indicate that purified omega-3 fatty acids can prevent ischemia-induced ventricular fibrillation in this dog model of sudden cardiac death.
Dynamic absorption coefficients of chemically amplified resists and nonchemically amplified resists at extreme ultraviolet (2016)

The dynamic absorption coefficients of several chemically amplified resists (CAR) and non-CAR extreme ultraviolet (EUV) photoresists are measured experimentally using a specifically developed setup in transmission mode at the x-ray interference lithography beamline of the Swiss Light Source. The absorption coefficient α and the Dill parameters ABC were measured with unprecedented accuracy. In general, the α of resists match very closely with the theoretical value calculated from elemental densities and absorption coefficients, whereas exceptions are observed. In addition, through the direct measurements of the absorption coefficients and dose-to-clear values, we introduce a new figure of merit called chemical sensitivity to account for all the postabsorption chemical reaction ongoing in the resist, which also predicts a quantitative clearing volume and clearing radius, due to the photon absorption in the resist. These parameters may help provide deeper insight into the underlying mechanisms of the EUV concepts of clearing volume and clearing radius, which are then defined and quantitatively calculated.
Interleukin-18 Promoter Gene Polymorphisms in Chinese Patients With Systemic Lupus Erythematosus: Association With CC Genotype at Position –607 (2007)

The IL-18 promoter gene polymorphism SNP-607 C allele is associated with SLE and may result in the enhanced production of IL-18 protein in SLE and normal individuals.
ENHANCED IMAGEMAP 2.0: WEB DESIGN ADVANTAGES CONFERED BY PARAMETERIZATION (1995)

This paper discusses the shortcomings of unparameterizable image maps and presents a solution to the problem through the use of PATH_INFO and textual substitution in the mapping configuration file. After some discussion on why this scheme was chosen instead of the alternatives, two example of actual use are given: passing parameters to the mapping file (1) as a path and (2) as arguments to a CGI script. Both techniques offer convenience and ease of design to the website administrator and we explore these advantages.
Objective analysis of temperature and salinity historical data set over the Mediterranean basin (2002)

The hydrological data set of the MEDATLAS project, is used to compute temperature (T) and salinity (S) climatological fields over the Mediterranean sea. The method used to perform objective analysis of the historical data set is optimal interpolation by kriging. Its implementation to compute basinscale climatology led the authors to address specific issues on data preparation, neighborhood search procedure and optimization of estimation points location. Consequently, estimation is achieved suboptimaly, due to large amount of data, and with a local computation of the spatial variogram to account for the changes in spatial scales over the domain. No temporal variogram is adopted but estimation is performed with observations each acquired by a different year to avoid bias by synoptic data subset, to retrieve long term component and to reach requested temporal representativeness. Results show that the MEDATLAS project succeeded in building up a comprehensive, quite homogeneous and very clean data set (0.65% rejection rate during the cross validation). With this data set a monthly, 40-km resolution climatology with 10-year representativeness could be computed. A first validation, by comparing with other recent climatology, shows that a precision within 0.2/spl deg/C rms is achieved.
Transformation, Ranking, and Clustering for Face Recognition Algorithm Comparison (2002)

The performance of face recognition algorithms is recently of increased interest. Empirical analyses of algorithms have traditionally been limited to rank-based scores such as cumulative match and receiver operating characteristics. This restriction to performance measures based on rank-based statistics arises because it is not possible to directly compare similarities output by algorithms. This paper presents the Phi-PIT transformation that makes it possible to compare such heterogeneous outputs, and allows a large body of classical statistical methods to be used to measure and analyze performance. These statistical techniques inclucde multiple comparison techniques, analysis of variance (ANOVA), and regression techniques. This paper presents ANOVA, graphical ANOVA, and Student-Newman-Keuls clustering analyses of the transformed outputs of fifteen face recognition algorithms. 1
Accomplices of the Hypoxic Tumor Microenvironment Compromising Antitumor Immunity: Adenosine, Lactate, Acidosis, Vascular Endothelial Growth Factor, Potassium Ions, and Phosphatidylserine (2017)

In this minireview, we aim to highlight key factors of the tumor microenvironment, including adenosine, lactate, acidosis, vascular endothelial growth factor, phosphatidylserine, high extracellular K<sup>+</sup> levels, and tumor hypoxia with respect to antitumor immune functions. Most solid tumors have an immature chaotic microvasculature that results in tumor hypoxia. Hypoxia is a key determinant of tumor aggressiveness and therapy resistance and hypoxia-related gene products can thwart antitumor immune responses.
Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations (1990)

The growth characteristics and acetate production of several Escherichia coli strains were compared by using shake flasks, batch fermentations, and glucose-feedback-controlled fed-batch fermentations to assess the potential of each strain to grow at high cell densities. Of the E. coli strains tested, including JM105, B, W3110, W3100, HB101, DH1, CSH50, MC1060, JRG1046, and JRG1061, strains JM105 and B were found to have the greatest relative biomass accumulation, strain MC1060 accumulated the highest concentrations of acetic acid, and strain B had the highest growth rates under the conditions tested. In glucose-feedback-controlled fed-batch fermentations, strains B and JM105 produced only 2 g of acetate.liter-1 while accumulating up to 30 g of biomass.liter-1. Under identical conditions, strains HB101 and MC1060 accumulated less than 10 g of biomass.liter-1 and strain MC1060 produced 8 g of acetate.liter-1. The addition of various concentrations of sodium acetate to the growth medium resulted in a logarithmic decrease, with respect to acetate concentration, in the growth rates of E. coli JM105, JM105(pOS4201), and JRG1061. These data indicated that the growth of the E. coli strains was likely to be inhibited by the acetate they produced when grown on media containing glucose. A model for the inhibition of growth of E. coli by acetate was derived from these experiments to explain the inhibition of acetate on E. coli strains at neutral pH.
A Grid Algorithm for High Throughput Fitting of Dose-Response Curve Data (2010)

We describe a novel algorithm, Grid algorithm, and the corresponding computer program for high throughput fitting of dose-response curves that are described by the four-parameter symmetric logistic dose-response model. The Grid algorithm searches through all points in a grid of four dimensions (parameters) and finds the optimum one that corresponds to the best fit. Using simulated dose-response curves, we examined the Grid program's performance in reproducing the actual values that were used to generate the simulated data and compared it with the DRC package for the language and environment R and the XLfit add-in for Microsoft Excel. The Grid program was robust and consistently recovered the actual values for both complete and partial curves with or without noise. Both DRC and XLfit performed well on data without noise, but they were sensitive to and their performance degraded rapidly with increasing noise. The Grid program is automated and scalable to millions of dose-response curves, and it is able to process 100,000 dose-response curves from high throughput screening experiment per CPU hour. The Grid program has the potential of greatly increasing the productivity of large-scale dose-response data analysis and early drug discovery processes, and it is also applicable to many other curve fitting problems in chemical, biological, and medical sciences.
ACID HYDROLYSIS OF HEMICELLULOSE FROM SUGARCANE BAGASSE (1997)

Hydrolysis of the hemicellulosic fraction of sugarcane bagasse by sulphuric acid was performed in laboratory (25 mL) and semi-pilot (25 L) reactors under different conditions of temperature, time and acid concentration. On the laboratory scale, the three highest recovery yields were obtained at: 140ºC for 10 min with 100 mg acid/g dm (yield=73.4%); 140ºC for 20 min with 100 mg acid/g dm (yield=73.9%) and 150ºC for 20 min with 70 mg acid/g dm (yield=71.8%). These conditions were also used for hydrolysis in a semi-pilot reactor, and the highest xylose recovery yield (83.3%) was obtained at 140ºC for 20 min with 100 mg acid/g dm
An Adenosine 3′,5′-Monophosphate-dependant Protein Kinase from Rabbit Skeletal Muscle (1968)

Abstract A protein kinase that catalyzes an adenosine 3',5'-monophosphate (cyclic AMP)-dependent phosphorylation of casein and protamine has been purified from rabbit skeletal muscle. The Km values of cyclic AMP for these reactions are 1 x 10-7 and 6 x 10-8 m, respectively. The protein kinase markedly increases the rate of the cyclic AMP-dependent activation and phosphorylation of phosphorylase kinase by ATP.
Noninvasive simultaneous determination of conductivity and permeability (1999)

Simultaneous measurements of both the conductivity and permeability are presented using noninvasive methods based on inductive coupling. Explicit expressions for cylindrical and spherical geometries are derived. The technique, especially relevant to liquids and solids in extreme environments, will also be valuable for nanomaterials and other systems where external contacts are difficult to establish.
The GLI-Kruppel family of human genes. (1988)

Previous characterization of GLI, a gene found to be amplified and expressed in a subset of human brain tumors, revealed the presence of five tandem zinc fingers related to those of Krüppel (Kr), a Drosophila segmentation gene of the gap class. We have used the GLI cDNA as a molecular probe to isolate related sequences from the human genome. Partial characterization of six related loci, including sequence determination, expression studies, and chromosome localization, revealed that each locus could encode a separate finger protein. The predicted proteins all had similar H-C links, i.e., a conserved stretch of 9 amino acids connecting the C-terminal histidine of one finger to the N-terminal cysteine of the next. On the basis of amino acid sequence and intron-exon organization, the genes could be placed into one of two subgroups: the GLI subgroup (with the consensus finger amino acid sequence [Y/F]XCX3GCX3[F/Y]X5LX2HX3-4H[T/S]GEKP) or the Kr subgroup (with the consensus finger amino acid sequence [Y/F]XCX2CX3FX5LX2HXRXHTGEKP). Unlike GLI or Kr, most of the newly isolated genes were expressed in many adult tissues. The predicted proteins probably control the expression of other genes and, by analogy with Kr and GLI, may be important in human development, tissue-specific differentiation, or neoplasia.
Dianilinophthalimides: Potent and Selective, ATP-Competitive Inhibitors of the EGF-Receptor Protein Tyrosine Kinase (1994)

Dianilinophthalimides represent a novel class of inhibitors of the EGF-receptor protein tyrosine kinase with a high degree of selectivity versus other tyrosine and serine/threonine kinases. Steady-state kinetic analysis of compound 3, which showed potent inhibitory activity, revealed competitive type kinetics relative to ATP. Despite a highly symmetrical structure of compound 3, X-ray studies revealed an unsymmetrical propeller-shaped conformation of the molecule which differs clearly from that of the constitutionally related staurosporine aglycons. These conformational differences may explain the reversal of the selectivity profile of compound 3 relative to the staurosporine aglycons. In cellular assays compounds 3 and 4 have been shown to inhibit EGF-induced receptor autophosphorylation, c-fos induction and EGF-dependent proliferation of Balb/c MK cells. This inhibition was selective as compounds had no effect on PDGF-induced receptor autophosphorylation and c-fos induction. Furthermore, compound 3 showed potent antitumor activity in vivo at well-tolerated doses.
Secretion of basement membrane collagen degrading enzyme and plasminogen activator by transformed cells – role in metastasis (1982)

The relationship of a basement membrane collagen degrading enzyme (BM collagenase) and plasminogen activator (PA) was studied in a number of non-malignant and malignant human and murine cell lines. Several non-malignant cell lines secreted significant amounts of PA but not detectable BM collagenase activity whereas the malignant cell lines, with one exception, secreted both enzymes. Therefore, the secretion of BM collagenase appears to be a characteristic of many malignant cells whereas PA is synthesized also by normal cells. The BM collagenase needed proteolytic activation for maximal activity indicating that it is secreted in a latent form. The addition of plasminogen to the culture medium of human fibrosarcoma cells (HT-1080) resulted in maximal activation of the enzyme. Plasmin, but not plasminogen, increased the activity of partially purified enzyme protein. Accordingly, the activation of latent BM collagenase in vivo may be facilitated by PA through the conversion of plasminogen to plasmin. It is suggested that the secretion of BM collagenase concomitantly with PA is a prerequisite for metastasis.
Methods of Blood Collection in the Mouse (2000)

for a wide variety of scientific studies, and there are a number of efficient methods available. It is important to remember that blood collection, because it can stress the animals, may have an impact on the outcome of research data. In addition, it is extremely important that those who collect blood become skilled in the techniques they employ, and seek to stress the mice as little as possible. Drawing from experience, personal communication, and published resources1-4, the following techniques are described: • Blood collection not requiring anesthesia: –Saphenous vein –Dorsal pedal vein • Blood collection requiring anesthesia: –Tail vein –Orbital sinus –Jugular vein • Terminal procedures: –Cardiac puncture –Posterior vena cava –Axillary vessels –Orbital sinus
Comparison of iron chelator efficacy in iron-overloaded beagle dogs and monkeys (Cebus apella). (2004)

Rodents and dogs are frequently used for preclinical toxicologic assessment of candidate iron chelators. Although the iron-clearing profile of a ligand often is known in rodents, and sometimes in primates, such information in dogs is rarely, if ever, available. Because of this, toxicity studies in dogs could be misleading; chelators that may otherwise be suitable for human clinical studies may be abandoned as being unacceptably toxic, simply because, unknown to the investigator, these drugs remove more iron in this species than would have been expected on the basis of iron clearance results in other species. This is a scenario that we encountered during toxicity trials of (S)-beta,beta-dimethyl-4'-hydroxydesazadesmethyldesferrithiocin in dogs. Thus, we developed an iron-overloaded dog model in which it is possible to evaluate iron-clearing efficiencies of potential therapeutic ligands. Seven deferration agents have been screened in this model, and the results were compared with the iron-clearing efficiency of the same ligands in an iron-loaded Cebus apella monkey model. The data suggest that while the iron-clearing efficiencies of most of the drugs were similar between the two species, there can be profound differences. This is consistent with the idea that caution needs to be exercised when carrying out preclinical toxicity evaluations of a chelator in dogs without first measuring the drug's iron-clearing efficiency in this species.