gebhart/patrepeval huggingface dataset:
Activation and Evasion of Innate Antiviral Immunity by Herpes Simplex Virus (2009)

Herpes simplex virus (HSV), a human pathogenic virus, has evolved several strategies to evade the production and function of interferons (IFNs) and cytokines generated by the innate immune system to restrict the virus. Equilibrium exists between the virus and the immune response, and a shift in this delicate balance either restricts the virus or enhances virus spread and tissue damage. Therefore, understanding of the cytokine response generated after HSV infection and the underlying virus-cell interactions is essential to improve our understanding of viral pathogenesis. This review summarizes the current knowledge on induction and evasion of the innate immune response by HSV.
The mutational specificity of DNA polymerase-beta during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations. (1985)

The frequency and specificity of mutations produced in vitro by eucaryotic DNA polymerase-beta have been determined in a forward mutation assay using a 250-base target sequence in M13mp2 DNA. Homogeneous DNA polymerase-beta, isolated from four different sources, produces mutations at a frequency of 4-6%/single round of gap-filling DNA synthesis. DNA sequence analyses of 460 independent mutants resulting from this error-prone DNA synthesis demonstrate a wide variety of mutational events. Frameshift and base substitutions are made at approximately equal frequency and together comprise about 90% of all mutations. Two mutational "hot spots" for frameshift and base substitution mutations were observed. The characteristics of the mutations at these sites suggest that certain base substitution errors result from dislocation of template bases rather than from direct mispair formation by DNA polymerase-beta. When considering the entire target sequence, single-base frameshift mutations occur primarily in runs of identical bases, usually pyrimidines. The loss of a single base occurs 20-80 times more frequently than single-base additions and much more frequently than the loss of two or more bases. Base substitutions occur at many sites throughout the target, representing a wide spectrum of mispair formations. Averaged over a large number of phenotypically detectable sites, the base substitution error frequency is greater than one mistake for every 5000 bases polymerized. Large deletion mutations are also observed, at a frequency more than 10-fold over background, indicating that purified DNA polymerases alone are capable of producing such deletions. These data are discussed in relation to the physical and kinetic properties of the purified enzymes and with respect to the proposed role for this DNA polymerase in vivo.
A Study of Point Selection for Loading Cells in Bi-directional Pile Load Test (2013)

Success or failure of the bi-directional pile load test for drilled shaft depends on point selection for loading cells, that is balanced location both uplift force and downward force. Methods to evaluate the ultimate unit side resistance in rockmass layer in both domestic and foreign are based on the uniaxial compression strength of rock core, which can hardly be obtained in domestic rockmass layers which are weathered rockmass layer and soft rockmass layer with very low RQD. Therefore, this study suggested the relation charts between the revised SPT N values and developed unit side resistance of each different layers, which were obtained from bi-directional pile load tests in various domestic sites. To evaluate the appropriateness of the relation charts, the developed unit side resistances from the relation charts were used to select the loading cell position and compared with the measured unit side resistances from field pile load test. Results showed that the developed side resistance from relation charts and the measured side resistance of weathered soil layer and weathered rock layer were very close. Average developed side resistance(), which are average of upper soft rock layer of loading device() and lower(), was similar with the estimated value ().
Recovery of Nucleic Acids from Immobilized Biotin−Streptavidin Complexes Using Ammonium Hydroxide and Applications in MALDI-TOF Mass Spectrometry (1997)

The effects of ammonium hydroxide treatment of complexes consisting of biotinylated nucleic acids and immobilized streptavidin were investigated. It was found that incubation of such complexes with ammonium hydroxide at room temperature leads to denaturation of double-stranded DNA molecules, liberating only the complementary nonbiotinylated strand, whereas incubation at elevated temperatures leads to an efficient dissociation of biotin-streptavidin complexes. The introduced procedure is especially suitable as a purification and conditioning format prior to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric analysis of DNA from complex enzymatic reactions. This is demonstrated by analysis of polymerase chain reaction (PCR) and sequencing products.
Designing an allosterically locked phosphofructokinase (1991)

Six site-directed mutants of Escherichia coli phosphofructokinase (PFK) were made in an attempt to produce an enzyme "locked" in the inactive or "T"-state. The kinetic properties of the mutants were examined as a function of the substrates fructose 6-phosphate (Fru6P) and ATP, the positive effector GDP, and the negative effector phosphoenolpyruvate (PEP). All mutants exhibited lower activity than wild-type PFK. Three mutants (RS63, LV153, and VT246) had apparent dissociation constants for substrates and effectors similar to those of wild type. One mutant, HN160, had a 10-fold reduced affinity for Fru6P and reduced apparent affinity for the effectors. Two mutants, SN159 and T(GS)156, exhibited hyperbolic kinetics consistent with a "locked" T-state protein. Surprisingly, T(GS)156 showed hyperbolic activation in response to the physiological inhibitor PEP. The mutant PFK properties are discussed in terms of the PFK structure. These results suggest that the kinetic properties of PFK are sensitive to interactions in the homotropic interface; residues 156-160 in particular are critical in mediating the interactions between effector and active sites and in the T to R quaternary transition.
Analyzing Visibility Configurations (2010)

Many algorithms, such as level of detail rendering and occlusion culling methods, make decisions based on the degree of visibility of an object, but do not analyze the distribution, or structure, of the visible and occluded regions across surfaces. We present an efficient method to classify different visibility configurations and show how this can be used on top of existing methods based on visibility determination. We adapt co-occurrence matrices for visibility analysis and generalize them to operate on clusters of triangular surfaces instead of pixels. We employ machine learning techniques to reliably classify the thus extracted feature vectors. Our method allows perceptually motivated level of detail methods for real-time rendering applications by detecting configurations with expected visual masking. We exemplify the versatility of our method with an analysis of area light visibility configurations in ray tracing and an area-to-area visibility analysis suitable for hierarchical radiosity refinement. Initial results demonstrate the robustness, simplicity, and performance of our method in synthetic scenes, as well as real applications.
Phytoremediation of Metals (2001)

The prelims comprise: Introduction Phytoextraction Rhizofiltration
Enhancement of the actions of smg p21 GDP/GTP exchange protein by the protein kinase A-catalyzed phosphorylation of smg p21. (1991)

We have previously shown that cyclic AMP-dependent protein kinase (protein kinase A) phosphorylates smg p21A and -B, ras p21-like small GTP-binding proteins. In the present study, we investigated the function(s) of this phosphorylation by use of the smg p21B purified from human platelets. smg p21B bound to plasma membranes and the protein kinase A-catalyzed phosphorylation of smg p21B reduced this binding. Moreover, the phosphorylation of smg p21B enhanced the two actions of its specific GDP/GTP exchange protein, named GDP dissociation stimulator, when tested in a cell-free system: one is the action to stimulate the GDP/GTP exchange reaction of smg p21B, and the other is the action to inhibit the binding of smg p21B to membranes. Consistently, smg p21B was translocated from the membranes to the cytoplasm when it was phosphorylated by protein kinase A in intact platelets in response to prostaglandin E1 or dibutyryl cyclic AMP. The protein kinase A-catalyzed phosphorylation of smg p21B affected neither its basal GDP/GTP exchange reaction, basal GTPase activity, nor the GTPase activity stimulated by its specific GTPase activating protein. On the other hand, we have recently clarified that the structure of the C-terminal region of the post-translationally processed human platelet smg p21B is Lys-Lys-Ser-Ser-all-trans-geranylgeranyl Cys181 methyl ester, and that this modification of the C-terminal region is essential for smg p21B to bind to membranes. We furthermore determined here that protein kinase A phosphorylated Ser179 in this C-terminal region of smg p21B. These results indicate that protein kinase A-catalyzed phosphorylation of smg p21B makes smg p21B sensitive to the actions of smg p21 GDP dissociation stimulator.
Changes in cell surface antigen expression during hemopoietic differentiation (1982)

Human bone marrow cells were separated on a fluorescence activated cell sorter (FACS) according to their binding of a series of monoclonal antibodies; the positive and negative fractions were cloned for erythroid burst and colony-forming units (BFU-E and CFU-E) and myeloid colony-forming units (CFU-GM), and cytocentrifuge slides were prepared for microscopy of maturing precursors. The pattern of antigen expression on hemopoietic progenitor and precursor populations has been established using antibodies defining blood group (A, I/i), HLA- associated (*A, B, C, DR, DC1), lineage specific, and transferrin receptor antigens. Like monomorphic HLA-DR, the antigen defined by monoclonal antibody OKT10 is expressed on the earliest progenitors and lost during differentiation, suggesting a role in interactions regulating the differentiation of these cells. The HLA-linked DC1 determinant, in contrast to HLA-DR, is not expressed at a detectable level on progenitor cells. Although a lineage-specific early antigen has not been identified, the transferrin receptor is expressed on the majority of erythroid progenitors, but only weakly on myeloid progenitors, and may provide an approach to isolating erythroid progenitors. These and earlier studies with monoclonal antibodies against HLA-DR and glycophorin now provide a detailed “map” of antigen expression during hemopoietic differentiation.
Impact of channel doping and Ar implant on device characteristics of partially depleted SOI MOSFETs (2002)

It is known that partially depleted (PD) SOI MOSFETs have floating body (FB) effects which degrade device performance. Previously, an argon (Ar) implant technique was proposed to form recombination centers and subsequently suppress FB effects (Ohno et al. 1998). Retrograde channel doping using indium (In) for NMOSFET (NFET) or antimony (Sb) for PMOSFET (PFET) has been widely used for bulk CMOS technologies to achieve reduced short channel effects (Skotnicki et al. 1996). In this work, we present device characteristics of conventional and Ar implanted PD SOI MOSFETs using B or retrograde In as n-channel doping and P or retrograde Sb as p-channel doping. The experiments are based on a CMOS technology which features shallow trench isolation, 0.15/spl plusmn/0.04 /spl mu/m poly gate, surface channel MOSFETs with 35 /spl Aring/ gate oxide, shallow extensions and halo implants, and Co salicidation on a 1500 /spl Aring/ SOI substrate.
Biomarkers That Currently Affect Clinical Practice in Lung Cancer: EGFR, ALK, MET, ROS-1, and KRAS (2014)

Lung cancer remains the most lethal malignancy in the world. Despite improvements in surgical treatment, systemic therapy, and radiotherapy, the 5-year survival rate for all patients diagnosed with lung cancer remains between 15 and 20%. Newer therapeutic strategies rely on specific molecular alterations, or biomarkers, that provide opportunities for a personalized approach to specific patient populations. Classification of lung cancer is becoming increasingly focused on these biomarkers, which renders the term "non-small cell lung" cancer less clinically useful. Non-small cell lung cancer is now recognized as a complex malignancy and its molecular and genomic diversity allows for patient-centered treatment options. Here, we review advances in targeted treatment of lung adenocarcinoma with respect to five clinically relevant biomarkers - EGFR, ALK, MET, ROS-1, and KRAS.
Optical Properties of a Lippmann Lenticulated Sheet (1931)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Herbert E. Ives, "Optical Properties of a Lippmann Lenticulated Sheet," J. Opt. Soc. Am. 21, 171-176 (1931) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Generalized theory of instantaneous active and reactive powers in single-phase circuits based on Hilbert transform (2003)

This paper presents a new theory of instantaneous power in single-phase circuits, which is named "ps-qs theory". The ps-qs theory is formed based on the Hilbert transform and allows us to define the active and reactive powers instantaneously in single-phase circuits that operate in transient state. In addition, a novel control strategy of active and reactive powers in single-phase circuits, which is based on the ps-qs theory, is described. Some significant characteristics of the proposed strategy are shown by experimental results.
Cannabinoids Reduce Markers of Inflammation and Fibrosis in Pancreatic Stellate Cells (2008)

Augmentation of the endocannabinoid system via exogenously administered cannabinoid receptor agonists specifically induces a functionally and metabolically quiescent pancreatic stellate cell phenotype and may thus constitute an option to treat inflammation and fibrosis in chronic pancreatitis.
Colocalization of CGRP with 5‐HT1B/1D receptors and substance P in trigeminal ganglion neurons in rats (2001)

Vasodilatation in the dura mater has been implicated in migraine pathogenesis. Anti-migraine triptan drugs block vasodilatation by binding to 5-HT1B/1D receptors localized on the peripheral sensory terminals and dural blood vessel smooth muscles. Previous studies suggest that calcitonin gene-related peptide (CGRP) released from Adelta-fibres plays a more important role than substance P (SP) released from C-fibres in inducing dural vasodilatation and that one of the antimigraine mechanisms of triptan drugs is inhibiting CGRP release. In the present study, the relationship between CGRP and 5-HT1B/1D receptors, and between CGRP and SP in the trigeminal ganglion neurons in rats was examined by double immunohistochemical staining. CGRP, 5-HT1B, 5-HT1D and SP-positive trigeminal ganglion neurons were all predominantly small and medium-sized. In the trigeminal ganglia, approximately 50% of CGRP-positive neurons were 5-HT1B positive. Similarly, approximately 55% of CGRP-positive neurons were 5-HT1D immunoreactive. Approximately 50% of CGRP-positive neurons were SP-positive, while 93% of SP-positive neurons were CGRP-positive, suggesting that nearly all SP-positive neurons also contain CGRP. The fibre types of the 5-HT1B- and 5-HT1D-positive neurons were further investigated with an antibody against the A-fibre marker 200-kDa neurofilaments (NF200). Approximately 46% of the 5-HT1B-positive and 43% of the 5-HT1D-positive trigeminal ganglion neurons were also NF200 positive, indicating that many A-fibre trigeminal neurons express 5-HT1B or 5-HT1D receptors. These results support the hypothesis that one important action of antimigraine drugs is the inhibition of CGRP release and that Adelta-fibres may play an important role in migraine pathogenesis.
Targeted deletions of sequences from closed circular DNA. (1980)

Closed circular DNA interacts with complementary sequences of single-stranded DNA to form displacement loop (D loop) structures in vitro. The site of D-loop formation can be directed by using single-stranded DNA derived from a selected restriction fragment. Circular DNA containing a D loop can then be linearized by cleavage with endonuclease S1. This cleavage appears to remove a limited number of nucleotides from each strand of the circular DNA substrate. Incubation with polynucleotide ligase followed by propagation in vivo leads to circular DNA molecules that bear small, single deletions in the region of the single-stranded DNA sequence chosen for the formation of the D loops. We have utilized these manipulations of DNA to construct tetracycline-sensitive deletion mutants of plasmid pBR322. The level of mutagenesis obtained by the procedure is sufficiently high that selective growth and screening procedures are not necessary for the isolation or identification of mutants. The frequency, variety, and small size of the deletions obtained within the selected target regions present considerable advantage for genetic and biochemical analysis. The method is quite general in rationale and should be immediately applicable to phage and viruses having infectious circular DNA genomes or recombinant DNA species propagated in circular plasmid vectors.
Visio-Acoustic screen for contactless touch interface with tactile sensation (2013)

This paper proposes a contactless touch screen that produces tactile sensation just 1-3cm before the actual touch on the screen. The system has a screen, visual projectors, and sensors for finger motion detection, which composes a non-contact touch screen by gesture sensing. In this paper we add a non-contact tactile display using an airborne ultrasound phased array. The key device of the system is a screen that is a scattering plane for visual projectors and transparent for ultrasound. We show the design of the screen and examine the effectiveness through numerical simulations and experiments. The screen has an additional property that stops the air flow going through the screen maintaining the transparency for the ultrasound. We constructed the contactless touch screen system and examined the position sensing accuracy under the tactile support.
Synthesis and anti-HIV-1 activity of 4,5,6,7-tetrahydro-5-methylimidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-one (TIBO) derivatives (1991)

A series of 6-substituted 4,5,6,7-tetrahydro-5-methylimidazo[4,5,1-jk][1,4]benzodiazepin- 2(1H)-ones (9) have been synthesized and tested for their ability to inhibit the replication of the HIV-1 virus in MT-4 cells. Two synthetic methods are described, one of which allows the synthesis of single enantiomers of the final products. A structure-activity study was done within the series of compounds to determine the optimum group for the 6-position substitution and to determine whether the activity was enantiospecific at the 5-position, which was substituted with a methyl group. The best analogue, 9jj, inhibited HIV-1 with an IC50 of 4 microM, which is comparable to the activity level of DDI, a 2',3'-dideoxynucleoside-type structure undergoing clinical trials as an anti-AIDS therapy.
Prevention of Induced Lactic Acidosis in Cattle by Thiopeptin (1981)

Fistulated bull calves that were given ground wheat intraruminally at 40 g/kg body weight developed both ruminal and systemic lactic acidosis. Rumen lactate increased from less than 1 to over 100 μmoles/ml by 6 hr after wheat administration. Plasma lactate increased and blood base excess decreased after elevation of rumen lactate, with calves dying when plasma lactate and blood base excess reached 36 μmoles/ml and -22 meq/liter, respectively. Steers, which were abruptly shifted to a micronized milo diet, developed ruminal, but not systemic, lactic acidosis. Rumen lactate increased from less than 1 to over 150 μmoles/ml by 16 hr after milo feeding. However, plasma lactate and blood base excess remained in the normal range. Thiopeptin, a sulfur-containing peptide antibiotic, prevented lactic acidosis in both cases by reducing the production of ruminal lactic acid. Fistulated calves given a single dose of thiopeptin at .75 or 1.50 mg/kg body weight and steers given thiopeptin at 11 or 22 ppm in the feed had 80 and 70% less rumen lactate, respectively, than controls. In addition, in both studies thiopeptin allowed “normal” rumen fermentation to proceed, as indicated by dramatic increases in total volatile fatty acids. Forty Angus steers were tested for the effect of thiopeptin on performance following a lactic acidosis challenge. Steers that were abruptly shifted to micronized milo developed ruminal lactic acidosis. Thiopeptin at 11 ppm in the feed prevented lactic acidosis and improved (P<.10) weight gain, feed intake and efficiency of feed utilization at 2 weeks. At 4 weeks, steers fed thiopeptin were still performing better than controls, but the differences were not statistically significant.
TRAFFIC CONFLICT TECHNIQUE IN TAINAN, TAIWAN (1980)

A traffic conflict is any potential traffic accident situation. A traffic control technique (TCT) was developed by General Motors Research Laboratories. As a result of this study, TCT was identified as a useful technique for measuring traffic safety and improvement.
Pyramid vector coding for high quality audio compression (2002)

The target of this work is the high quality audio coding at low bit rate. It is shown how pyramid vector coding (PVC) can conveniently replace the classical Huffman coding technique in audio compression systems, providing also an advantage in the bit allocation procedure. The compression performances can be further improved by fixing an upper limit value to the vector components.
[Analysis and regulation of interferon-gamma production by peripheral blood lymphocytes from patients with bronchial asthma]. (1994)

As with normal lymphocytes, small amounts of interferon-gamma (IFN-gamma) were spontaneously produced by lymphocytes from patients with bronchial asthma, and this bronchial asthma, and this production was markedly enhanced by concanavalin A (Con A) stimulation. Distinct from normal lymphocytes, however, IFN-gamma synthesis from patients' lymphocytes decreased in a dose dependent manner on stimulation with Dermatophagoides farinae (Df) antigen. IFN-gamma-producing cells are defined as being of the CD4+ 45RO+ T cell subset, which failed to produce IFN-gamma in Df-stimulated patients' lymphocytes. As the decreased production of IFN-gamma by antigenic stimulation was exclusively induced by Df antigen, but not by ovalbumin (OVA) or Japanese cedar (JC) antigen, it is concluded that Df antigen specifically suppressed IFN-gamma production in patients' lymphocytes. The IFN-gamma synthesis from normal lymphocytes was suppressed by the addition of IL-4 in a dose dependent manner. Moreover, anti-IL-4 antibody dose dependently enhanced IFN-gamma production from Df-stimulated patients' lymphocytes but not from unstimulated lymphocytes. These results indicate that IFN-gamma production by patients' lymphocytes is suppressed by the endogenous IL-4. Reduced IFN-gamma production in patients' lymphocytes on stimulation with Df antigen may lead to the overproduction of IgE in vivo.