gebhart/patrepeval huggingface dataset:
Potential therapeutic significance of increased expression of aryl hydrocarbon receptor in human gastric cancer (2009)

AhR plays an important role in gastric carcinogenesis. AhR may be a potential therapeutic target for GC treatment.
The signal transduction mechanism responsible for gamma interferon-induced indoleamine 2,3-dioxygenase gene expression (1994)

We examined the signal transduction mechanism responsible for the gamma interferon-induced indoleamine 2,3-dioxygenase (IDO) gene expression in a human monocytic cell line, THP-1. Our results suggest that gamma interferon-induced activation of protein tyrosine kinase is a prerequisite for gene expression and that activation of protein kinase C and another unknown signal(s), both of which are transduced by the protein tyrosine kinase, synergistically induce IDO gene expression. Neither Ca2+ influx nor cyclic nucleotide-dependent kinases were suggested to be involved in the signaling pathway.
Inhibition of Urokinase-Type Plasminogen Activator or Matrix Metalloproteinases Prevents Cardiac Injury and Dysfunction During Viral Myocarditis (2006)

Loss of uPA or MMP activity reduces the cardiac inflammatory response after CVB3 infection, thereby protecting against cardiac injury, dilatation, and failure during CVB3-induced myocarditis.
Fluorescence Rejection in Raman Spectroscopy by Shifted-Spectra, Edge Detection, and FFT Filtering Techniques (1995)

The use of shifted-spectra, first-derivative spectroscopy (or edge detection), and fast Fourier transform filtering techniques for fluorescence rejection in Raman spectra is demonstrated. These techniques take advantage of the fact that Raman signals are very narrow in comparison to fluorescence bands in order to discriminate between the two. None of these techniques require modification of existing instrumentation. Fast Fourier transform filtering and deconvolution techniques also provide a means of improving spectral resolution and the signal-to-noise ratio.
Truncation of the human immunodeficiency virus type 1 envelope glycoprotein allows efficient pseudotyping of Moloney murine leukemia virus particles and gene transfer into CD4+ cells (1997)

Human immunodeficiency virus type 1 (HIV-1) can readily accept envelope (Env) glycoproteins from distantly related retroviruses. However, we previously showed that the HIV-1 Env glycoprotein complex is excluded even from particles formed by the Gag proteins of another lentivirus, visna virus, unless the matrix domain of the visna virus Gag polyprotein is replaced by that of HIV-1. We also showed that the integrity of the HIV-1 matrix domain is critical for the incorporation of wild-type HIV-1 Env protein but not for the incorporation of a truncated form which lacks the 144 C-terminal amino acids of the cytoplasmic domain of the transmembrane glycoprotein. We report here that the C-terminal truncation of the transmembrane glycoprotein also allows the efficient incorporation of HIV-1 Env proteins into viral particles formed by the Gag proteins of the widely divergent Moloney murine leukemia virus (Mo-MLV). Additionally, pseudotyping of a Mo-MLV-based vector with the truncated rather than the full-length HIV-1 Env allowed efficient transduction of human CD4+ cells. These results establish that Mo-MLV-based vectors can be used to target cells susceptible to infection by HIV-1.
Nucleotide sequence analysis of the 5·8S rDNA and adjacent ITS2 region of Candida albicans and related species (1993)

We have determined the nucleotide sequence for the DNA encoding the 5.8S RNAs and downstream internal transcribed spacer (ITS2) regions for Candida albicans and the taxonomically related species C. parapsilosis, C. tropicalis, C. glabrata and C. krusei. Phylogenetic analysis of all known fungal 5.8S RNA sequences revealed a close relationship between C. tropicalis and C. parapsilosis, and to a lesser extent C. albicans within the yeast-like fungi. This group can itself be delineated from predominantly filamentous species. The more distal relationships between Candida (Torulopsis) glabrata and C. krusei support previous findings based on small (18S) ribosomal RNA sequence analysis, suggesting a greater degree of evolutionary divergence of these species from the C. albicans group. Among strains of C. albicans we observed conservation of the ITS2 region at the nucleotide level. Conservation was also observed for a more limited number of C. parapsilosis strains. Although the 3' region of the ITS spacer was species specific, sequence homology was observed in the 5' end within the albicans/parapsilosis/tropicalis group. Our findings suggest a rapid approach to species identification through the use of non-conserved regions flanked by highly conserved, functional domains.
NONLINEAR ANALYSIS OF PHYSIOLOGIC DATA DURING HEMORRHAGIC SHOCK. (2003)

1U.S. Army Institute of Surgical Research, Fort Sam Houston, TX 78234; 2University of Turku, Turku, Finland.
Purification of melanoma growth stimulatory activity (1986)

The Hs0294 human malignant melanoma cell line produces a monolayer mitogen that stimulates the serum free growth of low-density cultures of Hs0294 cells. This report describes the purification of that mitogen, termed MGSA for melanoma growth stimulatory activity, from serum-free conditioned medium from the Hs0294 cultures. MGSA has been purified from acetic acid extracts of lyophilized conditioned medium by gel filtration, reverse-phase high-pressure liquid chromatography (RP-HPLC), and preparative electrophoresis, resulting in a greater than 400,000-fold purification. MGSA bioactivity resides in acid- and heat-stable polypeptides of high and low molecular weight (24-28 kd and less than 14-16 kd). However, the majority of the activity is reproducibly associated with the approximately 16-kd moiety eluting from RP-HPLC at approximately 35% acetonitrile. Reduction with dithiothreitol or B-mercaptoethanol results in a loss of biological activity but does not convert the 24-28-kd moieties to the less than 14-16-kd forms of MGSA. 125I-MGSA that has been purified by preparative electrophoresis (16 kd) specifically binds to Hs0294 melanoma cells and retains 100% of the growth-stimulatory activity. The 16-kd MGSA stimulates the proliferation of Hs0294 cells at concentrations of 0.3-30 pM. The electrophoretic mobility of MGSA is also unaltered by the preparative electrophoresis procedure, further demonstrating that this procedure does not alter the biochemical integrity of the growth factor. Purified MGSA does not enable anchorage-independent growth of normal rat kidney (NRK) cells and is therefore different from the previously described transforming growth factors. The amino acid composition of MGSA differs from that of other previously described growth factors. These data demonstrate that MGSA represents a separate class of growth factors with biological and biochemical properties different from other growth factors.
A new design of the esophageal Wallstent endoprosthesis resistant to distal migration. (1998)

The frequency of distal migration of cylindrical stents is unacceptably high. Conical stents are resistant to distal migration, although improvements in design are required to deal with the problem of proximal migration.
Purification and Properties of Bacteriophage T4-Induced RNA Ligase (1972)

An enzyme, purified 300-fold from Escherichia coli infected with bacteriophage T4, catalyzes the conversion of 5'-termini of polyribonucleotides to internal phosphodiester bonds. The reaction requires ATP and Mg(++). For every 5'-(32)P terminus rendered resistant to alkaline phosphatase, an equal amount of AMP and PPi are formed. Various polyribonucleotides are substrates in the reaction; to date, the best substrate is [5'-(32)P]polyriboadenylate. With the latter substrate, no evidence of intermolecular reaction was obtained. However, the 5'-(32)P termini of poly(A) rendered resistant to alkaline phosphatase are also resistant to attack by RNase II, polynucleotide phosphorylase, and low concentrations of venom phosphodiesterase. Since the product formed with poly(A) lacks 3'-hydroxyl ends, as measured with these exonucleases, the enzyme appears to convert linear molecules of polyriboadenylate to a circular form by the intramolecular covalent linkage of the 5'-phosphate end to the 3'-hydroxyl terminus.
Concatemers of alternating plus and minus strands are intermediates in adenovirus-associated virus DNA synthesis. (1976)

Replicating DNA molecules of adenovirus-associated virus (AAV) were selectively extracted from KB cells coinfected at 39.5 detrees with a DNA minus, temperature-sensitive mutant of adenovirus 5 (ts125) as helper. Under these conditions AAV DNA replication proceeds normally, but there is little, if any, adenovirus DNA synthesis. An analysis of the replicating molecules in sucrose density gradients reveals that there are AAV DNA intermediates which consist of covalently linked plus and minus DNA strands. Under denaturing conditions, these concatemers are linear single strands whose lengths can reach at least four times the size of the AAV genome. The most abundant concatemeric species is a dimer which presumably exists in vivo as a unit length hairpin. Unit length linear duplexes appear to be immediate precursors of plus and minus progeny strands. These findings are compatible with a self-priming mechanism for the synthesis of AAV DNA.
DARPA Internet gateway (1982)

This RFC is a status report on the Internet Gateway developed by BBN.
It describes the Internet Gateway as of September 1982. This memo
presents detailed descriptions of message formats and gateway
procedures, however, this is not an implementation specification, and
such details are subject to change.
Total synthesis of a tyrosine suppressor transfer RNA gene. XIV. Chemical synthesis of oligonucleotide segments corresponding to the terminal regions. (1979)

Chemical syntheses of the two dodecanucleotides d(T-C-A-A-C-G-T-A-A-C-A-C) and d(A-C-G-T-T-G-A-G-A-A-A-G), the two undecanucleotides d(T-T-T-A-C-A-G-C-G-G-C) and d(T-G-T-A-A-A-G-T-G-T-T), the decanucleotide d(A-G-T-C-C-G-A-A-A-G), and the nonanucleotide d(A-A-T-T-C-T-T-T-C) are described. These deoxyribo-oligonucleotide segments, excluding the decanucleotide, represent the DNA duplex corresponding to the previously determined nucleotide sequence -30 to -51 of the promoter region of the gene for the tyrosine suppressor tRNA (Sekiya, T., Gait, M.J., Norris, K., Ramamoorthy, B., and Khorana, H.G. (1976) J. Biol. Chem. 251, 4481-4489) and include the EcoRI restriction endonuclease sequence at the appropriate 5'-end. The nona- and decanucleotide along with the previously synthesized deoxyribo-oligonucleotide segments 25 to 27 (Ramamoorthy, B., Lees, R.G., Kleid, D., and Khorana, H.G. (1976) J. Biol. Chem. 251, 676-694) together represent the DNA duplex corresponding to the natural nucleotide sequence 121 to 142 of the region adjoining the C-C-A end of the tyrosine tRNA gene and, in addition, a run of nine nucleotides which include the EcoRI restriction enzyme sequence at the 5'-end. The syntheses used protected mono- and oligonucleotides and stepwise condensation methods. A noteworthy feature of the present syntheses was the use of reverse phase high pressure liquid chromatography for the rapid and efficient separation of synthetic reaction mixtures.
TLR4 Mediates Vaccine-Induced Protective Cellular Immunity to Bordetella pertussis : Role of IL-17-Producing T Cells (2006)

Whole cell pertussis vaccines (Pw) induce Th1 responses and protect against Bordetella pertussis infection, whereas pertussis acellular vaccines (Pa) induce Ab and Th2-biased responses and also protect against severe disease. In this study, we show that Pw failed to generate protective immunity in TLR4-defective C3H/HeJ mice. In contrast, protection induced with Pa was compromised, but not completely abrogated, in C3H/HeJ mice. Immunization with Pw, but not Pa, induced a population of IL-17-producing T cells (Th-17), as well as Th1 cells. Ag-specific IL-17 and IFN-gamma production was significantly lower in Pw-immunized TLR4-defective mice. Furthermore, treatment with neutralizing anti-IL-17 Ab immediately before and after B. pertussis challenge significantly reduced the protective efficacy of Pw. Stimulation of dendritic cells (DC) with Pw promoted IL-23, IL-12, IL-1beta, and TNF-alpha production, which was impaired in DC from TLR4-defective mice. B. pertussis LPS, which is present in high concentrations in Pw, induced IL-23 production by DC, which enhanced IL-17 secretion by T cells, but the induction of Th-17 cells was also dependent on IL-1. In addition, we identified a new effector function for IL-17, activating macrophage killing of B. pertussis, and this bactericidal activity was less efficient in macrophages from TLR4-defective mice. These data provide the first definitive evidence of a role for TLRs in protective immunity induced by a human vaccine. Our findings also demonstrate that activation of innate immune cells through TLR4 helps to direct the induction of Th1 and Th-17 cells, which mediate protective cellular immunity to B. pertussis.
Reactive Oxygen Species and the Central Nervous System (1992)

Radicals are species containing one or more unpaired electrons, such as nitric oxide (NO.). The oxygen radical superoxide (O2.-) and the nonradical hydrogen peroxide (H2O2) are produced during normal metabolism and perform several useful functions. Excessive production of O2.- and H2O2 can result in tissue damage, which often involves generation of highly reactive hydroxyl radical (.OH) and other oxidants in the presence of "catalytic" iron or copper ions. An important form of antioxidant defense is the storage and transport of iron and copper ions in forms that will not catalyze formation of reactive radicals. Tissue injury, e.g., by ischemia or trauma, can cause increased metal ion availability and accelerate free radical reactions. This may be especially important in the brain because areas of this organ are rich in iron and CSF cannot bind released iron ions. Oxidative stress on nervous tissue can produce damage by several interacting mechanisms, including increases in intracellular free Ca2+ and, possibly, release of excitatory amino acids. Recent suggestions that free radical reactions are involved in the neurotoxicity of aluminum and in damage to the substantia nigra in patients with Parkinson's disease are reviewed. Finally, the nature of antioxidants is discussed, it being suggested that antioxidant enzymes and chelators of transition metal ions may be more generally useful protective agents than chain-breaking antioxidants. Careful precautions must be used in the design of antioxidants for therapeutic use.
[Differences in the localization of Alu-repeats in various chromosomes of peripheral blood cells from normal donors and bone marrow cells from patients with acute leukemia]. (1988)

The dispersion of the Alu-family DNA repeats in phytohemagglutinin-stimulated lymphocytes from peripheral blood of normal donors as well as in nonstimulated bone marrow cells of four patients suffering from acute leukemia was studied by hybridization on metaphase chromosomes in situ. DNA of bacteriophage lambda CAR42 clone containing the insertion of at least 8 copies of Alu-family DNA-repeats and labelled with tritium was used as a probe in hybridization. All patients with acute leukemia had the same pattern of changes in hybridization of the bone marrow cells. It consists of silver grains clustering over 3q26, 8p12, 14q24. The pattern may reflect amplification transposition of Alu-family DNA repeats in the human genome connected with cellular differentiation or malignant transformation of blood cells.
Correlated mass spectrometry imaging and confocal Raman microscopy for studies of three-dimensional cell culture sections (2014)

A novel method of correlated imaging, combining confocal Raman microscopy (CRM) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) was developed in order to investigate the structural and chemical diversity inherent in three-dimensional (3D) cell cultures. These 3D spheroidal cell cultures are high throughput in vitro model systems that recapitulate some of the chemical and physiological gradients characteristic of tissues. As a result, they are ideal for testing new imaging approaches due to the native diversity of cellular phenotypes found within a single culture. Individually, confocal Raman microscopy (CRM) and mass spectrometry imaging (MSI) produce different kinds of chemical information. CRM imaging reveals differences in cellular integrity and protein secretion across a typical near-equatorial transverse slice, while MSI shows localization of small molecules to discrete regions of the spheroid section. Correlating information obtained from these disparate imaging methods begins with an external fiducial mask, added to the spheroidal samples to orient image acquisition on the two orthogonal platforms. Rather than combine the images directly, principal component analysis is used to reveal the most chemically-informative elements, which are then combined using digital image correlation. Using this approach, relationships between the principal components of each method are visualized so that they may be compared on commensurate spatial length scales.
A New Generation of Gypsum Dispersing Agents (2003)

As global energy costs continue to increase there is an ever growing need to reduce energy consumption in the production of wallboard and other gypsum-based products. A new generation of commercially available colorless dispersants based on polycarboxylate comb copolymers has been developed that produces flows at lower water use levels than obtainable with conventional dispersants. At conventional water use levels, dispersant dosage is reduced by up to 80%, while maintaining flow. This paper compares the performance of this new generation of dispersants to the conventional dispersants. A focus is placed on the performance in synthetic gypsum. Dispersant dosage versus performance, set times and hydration rates, are discussed. A discussion on how changes to the structure of this new generation of dispersa nts affect performance is also discussed.
Semiconductor Devices: Pioneering Papers (1991)

Semiconductor Devices: Pioneering Papers makes available an important collection of 141 pioneering papers on semiconductor devices covering a period of 100 years, from the earliest systematic investigation of metal-semiconductor contacts in 1874 to the first observation of the resonant tunneling in 1974. The first papers on all of the major semiconductor devices including the p - n junction, the heterojunction, the bipolar transistor, hot electron transistors, thyristors, the Schottky barrier, the Mott barrier, the JFET, the MESFET, the MOS diode, the charge-coupled device, the MOSFET, the CMOS, the nonvolatile memory, the tunnel diode, the quantum well, superlattice structures, the IMPATT diode, the BARITT diode, the transferred-electron device, the LED, the laser diode, the photodetector and the solar cell are included. Also presented are the classic papers on device physics and characterization such as the generation-recombination theory, the high injection theory, the avalanche breakdown theory, the Fowler-Nordheim tunneling theory, the noise theory, the Debye length concept, the Hall effect, the Early voltage, the Ebers-Moll model, the differential capacitance method, and the lifetime measurement technique.The papers are divided into four parts: bipolar, unipolar, special microwave, and photonic devices, with a commentary for each part to highlight the importance of each of the collected papers. This book serves as a useful reference for a first-hand look at the operational principles of devices as conceived by their inventors and to understand the basic device physics as documented by their discoverers.
Pretargeted Versus Directly Targeted Radioimmunotherapy Combined with Anti-CD20 Antibody Consolidation Therapy of Non-Hodgkin Lymphoma (2009)

These studies suggest that administering unlabeled anti-CD20 IgG therapy after the radioactivity dose provides the best efficacy and that the amount of unlabeled anti-CD20 IgG administered as a predose to anti-CD20-targeted radionuclide therapy should be minimized.
Molecular cloning of cDNA encoding a second cellular retinoic acid-binding protein. (1990)

The vitamin A derivative retinoic acid is known to be a potent agent for control of differentiation and proliferation of epithelial cells and to exert profound effects on pattern formation during embryogenesis. Its action at the molecular level appears to be mediated by two distinct classes of proteins: a family of nuclear receptors that regulates gene transcription in a ligand-dependent fashion and a small cellular retinoic acid-binding protein (CRABP) for which a precise function remains to be elucidated. In this report, we describe the identification (by molecular cloning of its cDNA) of an isoform of CRABP, referred to as CRABP-II, expressed at high levels during mouse embryogenesis and in adult skin. We also show that CRABP-II mRNA levels are induced by at least 50-fold upon treatment of F9 teratocarcinoma cells with retinoic acid. The up-regulation of the gene encoding CRABP-II by its ligand suggests that CRABP-II might be involved in a feedback regulatory role in the mechanism of action of retinoic acid on cellular differentiation.
Phosphorylation of Ser-20 mediates stabilization of human p53 in response to DNA damage (1999)

Stabilization of p53 in response to DNA damage is caused by its dissociation from Mdm2, a protein that targets p53 for degradation in the proteasome. Dissociation of p53 from Mdm2 could be caused by DNA damage-induced p53 posttranslational modifications. The ATM and ATR kinases, whose activation in response to ionizing radiation (IR) and UV light, respectively, is required for p53 stabilization, directly phosphorylate p53 on Ser-15. However, phosphorylation of Ser-15 is critical for the apoptotic activity of p53 and not for p53 stabilization. Thus, whether any p53 modifications, and which, underlie disruption of the p53-Mdm2 complex after DNA damage remains to be determined. We analyzed the IR- and UV light-induced stabilization of p53 proteins with substitutions of Ser known to be posttranslationally modified after DNA damage. Substitution of Ser-20 was sufficient to abrogate p53 stabilization in response to both IR and UV light. Furthermore, both IR and UV light induced phosphorylation of p53 on Ser-20, which involved the majority of nuclear p53 protein and weakened the interaction of p53 with Mdm2 in vitro. ATM and ATR cannot phosphorylate p53 on Ser-20. We therefore propose that ATM and ATR activate an, as yet unidentified, kinase that stabilizes p53 by phosphorylating it on Ser-20.
Methylated DNA in Borrelia species (1990)

The DNA of Borrelia species was examined for the presence of methylated GATC sequences. The relapsing-fever Borrelia sp., B. coriaceae, and only 3 of 22 strains of B. burgdorferi contained adenine methylation systems. B. anserina lacked an adenine methylation system. Fundamental differences in DNA methylation exist among members of the genus Borrelia.