gebhart/patrepeval huggingface dataset:
DHCR24 gene expression is upregulated in melanoma metastases and associated to resistance to oxidative stress‐induced apoptosis (2005)

The DHCR24 gene encoding for the 3beta-hydroxysterol delta24-reductase, an oxidoreductase involved in cholesterol biosynthesis, was isolated by subtractive hybridization as highly expressed in a short-term melanoma cell line derived from a cutaneous metastases (S/M2) compared to that obtained from the autologous primary tumor (S/P). DHCR24 (alias seladin-1, diminuto/dwarf1 homolog) has been reported to act as an antiapoptotic factor in neurons. Gene expression analysis by Northern blot confirmed that DHCR24 was 5-fold upregulated in S/M2 compared to S/P cells. High levels of DHCR24 gene expression were detected in 13/25 melanoma metastases and in 1/7 primary melanomas by real-time PCR, indicating that upregulation of this gene may occur in melanoma progression. In S/M2 cells, high DHCR24 gene expression associated with resistance to apoptosis triggered by oxidative stress induced by exposure to hydrogen peroxide. DHCR24 gene transfer was shown to protect melanoma cells from H2O2-induced cytotoxicity. Although higher cholesterol levels were shown in S/M2 cells compared to S/P cells, DHCR24 gene transfer did not increase cholesterol content. To evaluate whether DHCR24 acts as an antiapoptotic factor in melanoma metastases, the cytotoxic effect of chemotherapeutic agents was tested in DHCR24 transfectants and in the presence of a DHCR24 inhibitor, U18666A. High DHCR24 gene expression in transfectants did not result in a higher resistance to cytotoxic agents; treatment with U18666A was cytotoxic in S/P cells with a lower DHCR24 content and showed additive cytotoxic effect only when associated with H2O2 and not with cysplatin or etoposide, indicating that the DHCR24 protective effect is exerted through an oxidative stress-specific mechanism.
Fluorescence studies of the secondary structure and orientation of a model ion channel peptide in phospholipid vesicles (1992)

A 21-residue peptide of the sequence (LSSLLSL)3 forms ion channels when incorporated into planar lipid bilayer membranes of diphytanoylphosphatidylcholine (diPhy-PC). The frequency of channel openings increases with the applied voltage gradient. We investigated the molecular and structural mechanisms underlying this voltage dependence. A series of seven peptides, each containing a tryptophan substituted for a single residue in the middle heptad, was synthesized, purified, and incorporated into small, unilamellar, diPhy-PC vesicles. We measured circular dichroism, maximum fluorescence emission wave-lengths, and fluorescence quenching by both aqueous and lipid hydrocarbon-associated quenchers. Circular dichroism spectra and the observed sequence periodicity of all fluorescence and fluorescence quenching data are consistent with an alpha-helical peptide secondary structure. Energy transfer quenching measurements using N-terminally labeled (LSSLLSL)3 co-incorporated at lipid/peptide ratios greater than 100 into vesicles with one of the Trp-substituted peptides showed that the vesicle-associated peptide, in the absence of a voltage gradient across the bilayer, exists as an equilibrium mixture of monomers and dimers. Static fluorescence quenching measurements using different lipid-bound quenchers indicate that the helical axis of a representative lipid-associated peptide is, on average, oriented parallel to the surface of the membrane and located a few angstroms below the polar head group/hydrocarbon boundary. This surface orientation for the peptide is confirmed by the complementary sequence periodicity observed for Trp fluorescence emission wavelength shifts and collisional quenching by aqueous CsCl.(ABSTRACT TRUNCATED AT 250 WORDS)
IMGT/LIGM-DB, the IMGT(R) comprehensive database of immunoglobulin and T cell receptor nucleotide sequences (2005)

IMGT/LIGM-DB is the IMGT comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species. It was created in 1989 by LIGM, Montpellier, France and is the oldest and the largest database of IMGT. IMGT/LIGM-DB includes all germline (non-rearranged) and rearranged IG and TR genomic DNA (gDNA) and complementary DNA (cDNA) sequences published in generalist databases. IMGT/LIGM-DB allows searches from the Web interface according to biological and immunogenetic criteria through five distinct modules depending on the user interest. For a given entry, nine types of display are available including the IMGT flat file, the translation of the coding regions and the analysis by the IMGT/V-QUEST tool. IMGT/LIGM-DB distributes expertly annotated sequences. The annotations hugely enhance the quality and the accuracy of the distributed detailed information. They include the sequence identification, the gene and allele classification, the constitutive and specific motif description, the codon and amino acid numbering, and the sequence obtaining information, according to the main concepts of IMGT-ONTOLOGY. They represent the main source of IG and TR gene and allele knowledge stored in IMGT/GENE-DB and in the IMGT reference directory. IMGT/LIGM-DB is freely available at http://imgt.cines.fr.
The Role of Cyclic Adenosine Monophosphate, Cyclic Guanosine Monophosphate, Endothelium and Nonadrenergic, Noncholinergic Neurotransmission in Canine Penile Erection (1993)

To elucidate the neuropharmacology of erection, we undertook an in vivo canine study to examine the role of cholinergic and nonadrenergic, noncholinergic (NANC) neuroeffectors and the sinusoidal endothelium in erection induced by electrostimulation. We also examined the effect of adenylate cyclase and guanylate cyclase blockers by intravenous injection of N-ethylmaleimide and methylene blue, respectively. In addition, the effects of intracavernous injection of the nitric oxide-releasing substance, nitroprusside, and bromocyclic adenosine monophosphate (AMP) and bromocyclic guanosine monophosphate (GMP) were also studied. In contrast to in vitro results, atropine reduced the increase of intracavernous pressure after neurostimulation (p = 0.029). Intracavernous injection of CHAPS to destroy the sinusoidal endothelium abolished the response to acetylcholine (p = 0.001), but only partially inhibited the response to electrostimulation (mean = 75% pressure increase, p = 0.022), indicating that neuronal nitric oxide plays a major role in penile erection. Methylene blue, a guanylate cyclase inhibitor, significantly inhibited the erectile response to both neurostimulation and sodium nitroprusside (p = 0.000 and 0.017, respectively). However, N-ethylmaleimide, an adenylate cyclase inhibitor, could not reduce the response to neurostimulation (p = 0.078). The erectile response to intracavernous injection of cGMP was significantly better than that induced by cAMP (p = 0.025). Our results suggest that both the cholinergic and NANC neuroeffectors and the sinusoidal endothelium are involved in erection. In addition, our data imply that the neuronal nitric oxide/cyclic GMP system is the most likely pathway for penile smooth muscle relaxation and erection.
Christliches Amulett (1982)

Der uns erhaltene Teil des Blattes trägt die letzten Zeilen des auf Amuletten beliebten „Vater Unser“ (Matthäus 6, 12–13). Daran schließt sich eine doxologische Formel an, die uns aus dem Euchologium des Serapion von Thmuis bekannt ist. Den magischen Charakter des Stückes sichern das folgende dreimal wiederholte ἀμήν und das dreifache ἅγιος, die jeweils durch drei Waagerechte voneinander getrennt sind.
Detection of Babesia microti by polymerase chain reaction (1992)

Human babesiosis, which is caused by infection with the intraerythrocytic malarialike protozoan Babesia microti, has recently been diagnosed with increasing frequency in residents of New England. Diagnosis is difficult because of the small size of the parasite and the sparse parasitemia that is characteristic of most infections with this pathogen. We generated B. microti-specific DNA sequence information by universal primer amplification of a portion of the eukaryotic 16S-like gene; this was followed by direct DNA sequence analysis. Specific primers were synthesized on the basis of this sequence information for use in the polymerase chain reaction (PCR). The PCR-based system demonstrates a strong bias for detection of B. microti as opposed to Babesia gibsoni and does not amplify vertebrate DNA. The analytical sensitivity of the system is approximately three merozoites. Blood specimens from 12 patients with clinically diagnosed and parasitologically confirmed babesiosis from Nantucket Island, Mass., were PCR positive in a blinded test of this procedure. Thus, DNA amplification may provide an adjunct to conventional methods for the diagnosis of human babesiosis and may provide a new means of monitoring therapy or enhancing epidemiological surveillance for this emerging pathogen.
Using Fourier Series Methods to Reduce Correlation of Nuclear Power Reactor Data (1992)

Sequential probability ratio tests (SPRTs) are applied to the monitoring of nuclear power reactor signals. The theory of SPRTs applied to correlated data that have an unknown distribution is very incomplete. Unfortunately, a common problem regrading the application of sequential methods to reactor variables is that the variables are often contaminated with noise that is either non-Gaussian or serially correlated (or both). A Fourier series approximation can be used to remove much of the correlation in the data. This method is relatively simple to implement but has the desirable property of reducing correlation, thereby allowing the assumption of Gaussian, independent data to hold more readily. Delayed neutron signal data and reactor coolant pump data are analyzed. The theory has been validated by extensive testing with data from the Experimental Breeder Reactor II. The use of SPRT techniques as decision aids in two artificial intelligence-based expert systems for surveillance and diagnosis applications in nuclear reactors is also discussed.
Transparent Dynamic Optimization (1999)

Dynamic optimization refers to the runtime optimization of a native program binary. This paper describes the design and implementation of Dynamo, a prototype dynamic optimizer that is capable of optimizing a native program binary at runtime. Dynamo is a realistic implementation, not a simulation, that is written entirely in user-level software, and runs on a PA-RISC machine under the HPUX operating system. Dynamo does not depend on any special programming language, compiler, operating system or hardware support. The program binary is not instrumented and is left untouched during Dynamo&amp;apos;s operation. Dynamo observes the program&amp;apos;s behavior through interpretation to dynamically select hot instruction traces from the running program. The hot traces are optimized using low-overhead optimization techniques and emitted into a software code cache. Subsequent instances of these traces cause the cached version to be executed, resulting in a performance boost. Contrary to intuition, we ...
A simple and efficient method for making site-directed mutants, deletions, and fusions of large DNA such as P1 and BAC clones. (1996)

This study addresses two important technical problems: how to perform targeted alterations such as site-directed mutagenesis and deletions in large fragments of DNA and how to construct full-length genes from two partly overlapping bacterial artificial chromosome (BAC) plasmids. Given the size and the lack of convenient unique restriction sites in these large-insert bacterial clones, these are nontrivial tasks. Here we describe a simple and efficient protocol based on RecA-assisted restriction endonuclease (RARE) cleavage, a method that enables sequence-specific cleavage of genomic DNA. The same protocol has been used with minor modifications to introduce site-specific mutations into an apolipoprotein-B 90-kb P1 clone, to generate deletions in a 160-kb BAC, and to generate a 160-kb BAC containing the complete 92-kb gene for low-density lipoprotein-related protein-1 (LRP-1) from two smaller overlapping BACs ("BAC marriage").
Signal Transduction Due to HIV-1 Envelope Interactions with Chemokine Receptors CXCR4 or CCR5 (1997)

Infection with HIV-1 requires expression of CD4 and the chemokine receptors CXCR4 or CCR5 at the target cell surface. Engagement of these receptors by the HIV-1 envelope glycoprotein is essential for membrane fusion, but may additionally activate intracellular signaling pathways. In this study, we demonstrate that chemokines and HIV-1 envelope glycoproteins from both T-tropic and macrophage-tropic strains rapidly induce tyrosine phosphorylation of the protein tyrosine kinase Pyk2. The response requires CXCR4 and CCR5 to be accessible on the cell surface. The results presented here provide the first evidence for activation of an intracellular signaling event that can initiate multiple signaling pathways as a consequence of contact between HIV-1 and chemokine receptors.
Requirement for CD44 in Activated T Cell Extravasation into an Inflammatory Site (1997)

Leukocytes extravasate from the blood into inflammatory sites through complementary ligand interactions between leukocytes and endothelial cells. Activation of T cells increases their binding to hyaluronate (HA) and enables CD44-mediated primary adhesion (rolling). This rolling could be induced in vivo in murine Vbeta8(+) T cells in response to specific superantigen stimulation; it was initially found in lymph nodes, then in peripheral blood, and finally within the peritoneum, the original inflamed site. The migration of Vbeta8(+) cells into the peritoneal cavity was dependent on CD44 and HA, as shown by inhibition studies. Thus, CD44-HA interactions can target lymphocytes to specific extralymphoid effector sites.
Augmented mobilization and collection of CD34+ hematopoietic cells from normal human volunteers stimulated with granulocyte–colony‐stimulating factor by single‐dose administration of AMD3100, a CXCR4 antagonist (2005)

These findings indicate that AMD3100 can be used alone or as an adjunct to G-CSF to mobilize cells for HPC transplantation.
Phenomenological model for gate length bias dependent inverter delay change with emphasis on library characterization (2009)

A novel phenomenological inverter delay model is presented. The model focuses on capturing the percentage delay change as a function of gate length change (i.e., bias) over a wide, practical range of input slews and output capacitances that are typically used in library characterization. The model is derived based on physical device equations with empirical fitting parameters for improved accuracy. In the model, a physically based parameter, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sc</sub> , is introduced that represents the output voltage value at the end of the short circuit region. Fitting results for inverters of five different drive strengths show an average accuracy of 0.24% and 0.37% with respect to HSPICE simulations for cell rise and fall delays, respectively. Applications of this delay model include library characterization and optimal gate length biasing during physical design implementation and circuit optimization.
HLA CLASS II NUCLEOTIDE SEQUENCES, 1991 (1991)

The HLA Class II sequences included in this compilation are taken from publications listed in the papers: Nomenclature for factors of the HLA system, 1990 (1) and Nomenclature for factors of the HLA system, 1989 (2). Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identity between residues is indicated by a hyphen (-). An unavailable sequence is indicated by an asterisk (*). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.
Polyester Composite Thermal Neutron Scintillation Films (2012)

Novel <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{6}{\rm Li}$</tex> </formula> -loaded polyester scintillation films have been designed and fabricated to detect thermal neutrons. Lithium fluoride crystals containing enriched <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{6}{\rm Li}$</tex></formula> were synthesized and integrated into polyethylene naphthalate polyester matrix containing appropriate luminescent molecules. Thermal neutron capture by <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{6}{\rm Li}$</tex></formula> ions produces charged particles with kinetic energy sufficient to ionize and subsequently excite the components of the polymeric matrix. This energy is transferred to secondary luminescent molecules, which produce net radioluminescence responses detectable by a photomultiplier tube. Design, production and characterization of these scintillation films are discussed herein. The films due to their thinness <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$(&lt;220\ \mu{\rm m})$</tex></formula> and low atomic number components have low susceptibility to gamma induced scintillation and thus are effective discriminators for thermal neutrons.
Optically detected magnetic resonance (ODMR) studies of π-conjugated polymer films and light-emitting diodes (LEDs) (1995)

The photoluminescence (PL)-, electroluminescence (EL)- and conductivity ((sigma) )-detected magnetic resonance of poly(p-phenylene vinylene) (PPV), poly(p-phenylene ethynylene) (PPE), and PPV/CN-PPV LEDs is reviewed and discussed. In the PPV- and PPE-based LEDs the polaron resonance is EL-quenching, but in the PPV/CN-PPV bilayer diodes it contains both EL-quenching and enhancing components. While the (sigma) -detecting polaron resonance is invariably quenching in the PPV devices, in some of the PPE-based LEDs it is (sigma) -enhancing. The PL-enhancing resonance is attributed to nonradiative recombination of trapped polaron pairs, which reduces their population and consequently the rate at which they nonradiatively quench singlet excitons; the EL-enhancing resonance is tentatively assigned to the same mechanism in the CN-PPV layer, but other mechanisms are not ruled out. Interchain coupling, some defects induced by structural disorder, and sites adjacent to dopant molecules (e.g., C<SUB>60</SUB>) apparently enhance the generation of these trapped polarons as well as intersystem crossing from the singlet to the triplet manifold. The EL- and (sigma) - quenching resonances are attributed to the fusion of like-charged free polarons to bipolarons, which is also suspected to be induced by disorder and/or impurities. The LEDs also exhibit half-field EL- and (sigma) -detected triplet exciton resonances. Triplet-triplet fusion to singlets and the role of triplets as quenching sites for singlet excitons are discussed as possible mechanisms leading to the triplet resonances.
Portrait of transcriptional responses to ultraviolet and ionizing radiation in human cells (2004)

To understand the human response to DNA damage, we used microarrays to measure transcriptional responses of 10 000 genes to ionizing radiation (IR) and ultraviolet radiation (UV). To identify bona fide responses, we used cell lines from 15 individuals and a rigorous statistical method, Significance Analysis of Microarrays (SAM). By exploring how sample number affects SAM, we rendered a portrait of the human damage response with a degree of accuracy unmatched by previous studies. By showing how SAM can be used to estimate the total number of responsive genes, we discovered that 24% of all genes respond to IR and 32% respond to UV, although most responses were less than 2-fold. Many genes were involved in known damage-response pathways for cell cycling and proliferation, apoptosis, DNA repair or the stress response. However, the majority of genes were involved in unexpected pathways, with functions in signal transduction, RNA binding and editing, protein synthesis and degradation, energy metabolism, metabolism of macromolecular precursors, cell structure and adhesion, vesicle transport, or lysosomal metabolism. Although these functions were not previously associated with the damage response in mammals, many were conserved in yeast. These insights reveal new directions for studying the human response to DNA damage.
Chronic Staphylococcal Osteomyelitis: Treatment with Regimens Containing Rifampin (1983)

Experience with rifampin as a component of combination antibiotic therapy for chronic staphylococcal osteomyelitis was reviewed. These data included the preliminary results of a randomized, prospective trial of parenteral nafcillin alone vs. parenteral nafcillin plus oral rifampin; the results of use of rifampin in combination with other oral antibiotics for the treatment of chronic staphylococcal osteomyelitis; and experience with rifampin regimens at the Oregon Health Sciences University. A total of 28 patients are described in this report; 70% of those who received regimens including rifampin experienced an apparent cure of infection. Most patients whose infections were not cured had inadequate surgical therapy or were also infected with other bacteria. Staphylococcus aureus was eradicated from the sinus drainage of all but one patient. Although these results are encouraging, a larger number of patients and a longer follow-up period are required for an adequate evaluation of the place of rifampin in therapy for chronic staphylococcal osteomyelitis.
The platelet glycoprotein thrombospondin binds specifically to sulfated glycolipids. (1985)

The human platelet glycoprotein thrombospondin (TSP) binds specifically and with high affinity to sulfatides (galactosylceramide-I3-sulfate). Binding of 125I-TSP to lipids from sheep and human erythrocytes and human platelets resolved on thin layer chromatograms indicates that sulfatides are the only lipids in the membrane which bind TSP. Binding to less than 2 ng of sulfatide could be detected. TSP failed to bind to other purified lipids including cholesterol 3-sulfate, phospholipids, neutral glycolipids, and gangliosides. Binding of 125I-TSP was inhibited by unlabeled TSP, by low pH, and by reduction of intersubunit disulfide bonds with dithiothreitol. A monoclonal antibody against TSP (A2.5), which inhibits hemagglutination and agglutination of fixed activated platelets by TSP, strongly inhibited TSP binding to sulfatides. A second monoclonal antibody (C6.7), which inhibits hemagglutination and aggregation of thrombin-activated live platelets, weakly inhibited sulfatide binding. Binding was inhibited by high ionic strength and by some monosaccharide sulfates including methyl-alpha-D-GlcNAc-3-sulfate. Neutral sugars did not inhibit. Fucoidan, a sulfated fucan, strongly inhibited binding with 50% inhibition at 0.3 micrograms/ml fucoidan. Other sulfated polysaccharides including heparin and dextran sulfates were good inhibitors, whereas hyaluronic acid and keratan sulfate were very weak.