gebhart/patrepeval huggingface dataset:
Resistance to Protease Inhibitors (2001)

The availability of protease inhibitors (PIs) and their combination with nucleoside reverse transcriptase inhibitors marked the passage of antiretroviral therapy (ART) from potential for control to effective suppression and thus substantially reduced rates of morbidity and mortality related to HIV. Even so, what was first hoped to be an immutable HIV DNA treatment target has proved to be prone to resistance mutations, with substitutions identified at more than 20 amino acid sites, which reduces PI susceptibility and increases resistance to treatment. The mutation patterns associated with each PI have been defined, and have been observed to occur at one of two locations: at or near the active site, or in the substrate cleavage site. The natural history of PI resistance has been extensively studied, and the genetic and cellular pathways are described in detail in this article. In addition, cross-resistance among PIs is now recognized to be fairly extensive, although the degree of cross-resistance varies with the number of mutations and the variants selected by drug pressure. Thus, it is still possible to salvage a response with another PI after a first regimen with another PI has failed. The extensive basic science and clinical experience with PIs in the fight against HIV are reviewed in this article, which provides data on resistance-mutation profiles, cellular resistance mechanisms, viral fitness studies, and clinical outcome trials with various first-line and subsequent regimens that contain PIs. It is hoped that the information provided will guide physicians in best using PIs as part of a logical and successful ART strategy.
CD63 associates with tyrosine kinase activity and CD11/CD18, and transmits an activation signal in neutrophils (1996)

As a member of the tetraspan family, it has been hypothesized that CD63 may be associated with signal transduction; however, its role in leukocyte function is unknown. To examine the potential ability of CD63 to activate neutrophils, the effects of five CD63 mAbs, AHN-16, -16.1, -16.2, -16.3, and -16.5, were examined for their ability to alter neutrophil adhesion to HUVEC monolayers. These CD63 Abs increased neutrophil adhesion to resting and TNF-stimulated HUVEC monolayers. This increase in neutrophil adhesion caused by CD63 Abs was blocked by a CD18 Ab and was associated with up-regulation of CD11/CD18 and down-regulation of CD62L on the neutrophil surface. CD11/CD18 was also found to be associated with CD63. This increase in neutrophil adhesion required physiologic extracellular calcium concentrations at or near the time of CD63 Ab binding. The incubation of CD63 Abs with cells in the absence of calcium for 10 min before repletion of calcium resulted in no increase in neutrophil adhesion. Protein kinase activity was detected in neutrophils associated with CD63. Most of the protein kinase activity associated with these Ags was tyrosine kinase activity, with a lesser amount of threonine and serine kinase activities. Src family kinases Lyn and Hck accounted for much of the associated tyrosine kinase activity. The data suggest that CD63 Ab binding to the neutrophil surface triggers a transient activation signal that requires extracellular calcium and regulates the adhesive activity of CD11/CD18. Associated protein kinase activity may play a role in signal transduction by CD63 to regulate other cell functions.
Geo-spatial aerial video processing for scene understanding and object tracking (2008)

This paper presents an approach to extracting and using semantic layers from low altitude aerial videos for scene understanding and object tracking. The input video is captured by low flying aerial platforms and typically consists of strong parallax from non-ground-plane structures. A key aspect of our approach is the use of geo-registration of video frames to reference image databases (such as those available from Terraserver and Google satellite imagery) to establish a geo-spatial coordinate system for pixels in the video. Geo-registration enables Euclidean 3D reconstruction with absolute scale unlike traditional monocular structure from motion where continuous scale estimation over long periods of time is an issue. Geo-registration also enables correlation of video data to other stored information sources such as GIS (geo-spatial information system) databases. In addition to the geo-registration and 3D reconstruction aspects, the key contributions of this paper include: (1) exploiting appearance and 3D shape constraints derived from geo-registered videos for labeling of structures such as buildings, foliage, and roads for scene understanding, and (2) elimination of moving object detection and tracking errors using 3D parallax constraints and semantic labels derived from geo-registered videos. Experimental results on extended time aerial video data demonstrates the qualitative and quantitative aspects of our work.
Nitroglycerin: a NO donor inhibits TPA-mediated tumor promotion in murine skin (2001)

Nitroglycerin (GTN), a nitric oxide (NO) generating vasodilator has been used in the present study to assess the role of NO during tumor promotion in murine skin. Administration of GTN to 12-O tetradecanoyl phorbol 13-acetate (TPA)-treated mice resulted in a dose-dependent inhibition in the level of glutathione and the activity of antioxidant enzymes by approximately 16-40% of acetone-treated control. We also observed that GTN application led to a significant reduction in the ornithine decarboxylase (ODC) activity and decreased the rate of [3H]thymidine incorporation into epidermal DNA when compared with the acetone-treated control (P < 0.001). Treatment of DMBA-initiated TPA-promoted mice with GTN increased the latency period, decreased the tumor incidence by 32% and there was a 2-fold decrease in tumor yield (tumor/mouse) as compared with the TPA (alone)-treated group by 20 weeks. From these data, it can be concluded that NO can abrogate the toxic and tumor promoting effects of TPA and GTN can be used as a chemopreventive agent to inhibit tumorigenesis in murine skin.
Sensitivity of upper atmospheric emissions calculations to solar/stellar UV flux (2014)

The solar UV (UltraViolet) flux, especially the EUV (Extreme UltraViolet) and FUV (Far UltraViolet) components, is one of the main energetic inputs for planetary upper atmospheres. It drives various processes such as ionization, or dissociation which give rise to upper atmospheric emissions, especially in the UV and visible. These emissions are one of the main ways to investigate the upper atmospheres of planets. However, the uncertainties in the flux measurement or modeling can lead to biased estimates of fundamental atmospheric parameters, such as concentrations or temperatures in the atmospheres. We explore the various problems that can be identified regarding the uncertainties in solar/stellar UV flux by considering three examples. The worst case appears when the solar reflection component is dominant in the recorded spectrum as is seen for outer solar system measurements from HST (Hubble Space Telescope). We also show that the estimation of some particular line parameters (intensity and shape), especially Lyman α, is crucial, and that both total intensity and line profile are useful. In the case of exoplanets, the problem is quite critical since the UV flux of their parent stars is often very poorly known.
AN IMPROVED PREPARATION OF 1-METHYL-4-CYANO-4-PHENYLPIPERIDINE (1996)

(1996). AN IMPROVED PREPARATION OF 1-METHYL-4-CYANO-4-PHENYLPIPERIDINE. Organic Preparations and Procedures International: Vol. 28, No. 4, pp. 478-480.
Vision-based detection of dynamic gesture (2009)

The use of gesture as a natural and intuitional interface serves as a motivating force for research in detection and interpretation of gestures. In particular, vision-based gesture detection is the need of human-computer intelligent interaction, which involves many multidisciplinary studies. A review on recent vision-based gesture detection approaches is given in this paper. Firstly, the characteristics and framework of dynamic gesture's detection are introduced. Secondly, many gesture segmentation and tracking methods are summarized and analyzed. In the end, we conclude with some thoughts about future researches.
Multiple Pathways for Triacylglycerol Biosynthesis in Streptomyces coelicolor (2008)

The terminal reaction in triacylglyceride (TAG) biosynthesis is the esterification of diacylglycerol (DAG) with a fatty acid molecule. To study this reaction in Streptomyces coelicolor, we analyzed three candidate genes (sco0958, sco1280, and sco0123) whose products significantly resemble the recently identified wax ester synthase/acyl-coenzyme A (CoA):DAG acyltransferase (DGAT) from Acinetobacter baylyi. The deletion of either sco0123 or sco1280 resulted in no detectable decrease in TAG accumulation. In contrast, the deletion of sco0958 produced a dramatic reduction in neutral lipid production, whereas the overexpression of this gene yielded a significant increase in de novo TAG biosynthesis. In vitro activity assays showed that Sco0958 mediates the esterification of DAG using long-chain acyl-CoAs (C(14) to C(18)) as acyl donors. The K(m) and V(max) values of this enzyme for myristoyl-CoA were 45 muM and 822 nmol mg(-1) min(-1), respectively. Significantly, the triple mutant strain was not completely devoid of storage lipids, indicating the existence of alternative TAG-biosynthetic routes. We present strong evidence demonstrating that the residual production of TAG in this mutant strain is mediated, at least in part, by an acyl-CoA-dependent pathway, since the triple mutant still exhibited DGAT activity. More importantly, there was substantial phospholipid:DGAT (PDAT) activity in the wild type and in the triple mutant. This is the first time that a PDAT activity has been reported for bacteria, highlighting the extreme metabolic diversity of this industrially important soil microorganism.
Enhancement of antigenic potency in vitro and immunogenicity in vivo by coupling the antigen to anti-immunoglobulin. (1986)

We have examined the effect of targeting an antigen to the immune system, by covalently coupling it to anti-immunoglobulin (Ig), on its efficacy for T cell stimulation in vitro and its immunogenicity for antibody production in vivo. In vitro, we compared the potency (for stimulation of a ferritin-specific T cell line) of free ferritin, ferritin coupled to goat antimouse IgM (heavy (H) chain specific), ferritin coupled to anti-IgG (H and light (L) chain specific), or ferritin coupled to anti-IgA (H chain specific), as well as a mixture of free ferritin plus goat anti-IgG. The ferritin coupled to anti-IgM or to anti-IgG (H + L), which could bind to surface Ig of B cells, stimulated T cell proliferation at concentrations of ferritin at least 10-fold lower than those required for the other forms of the antigen over the entire time course of the response, with 1000 rad-irradiated spleen cells as presenting cells. Because the goat antibodies were all of the same IgG isotype and coupling ratio, the failure of goat anti-IgA to enhance potency served as a control to exclude Fc receptor binding as the mechanism. The effect was not due to the nonspecific activation of B cells to become more efficient antigen-presenting cells, because mixtures of ferritin plus anti-IgG (H + L) had no effect, and the anti-IgG coupled to ferritin did not enhance presentation of myoglobin to a myoglobin-specific T cell line. The enhanced presentation of ferritin conjugated to goat anti-IgG (H + L) or to anti-IgM was sensitive to radiation doses greater than 2000 R, and was effective at less than one-tenth the number of spleen cells, consistent with the predominance of B cells as antigen-presenting cells for this form of the antigen rather than macrophages and dendritic cells only. When B cells and accessory cells were purified from T-depleted spleen cells, only the B cell preparation but not the accessory cell population manifested enhanced presentation of ferritin coupled to anti-IgG compared with free ferritin, and it was radiosensitive. Finally, allogeneic B cells could not mediate the enhancement in the presence of syngeneic splenic accessory cells (SAC); therefore, the enhancement was not due to shedding of immune complexes from B cells and subsequent presentation by SAC. We conclude that targeting the antigen to B cells as presenting cells greatly enhances its efficacy in vitro.(ABSTRACT TRUNCATED AT 400 WORDS)
Intelligent Polyelectrolytes and Gels in Oral Drug Delivery (2003)

The present review concerns smart, or intelligent polymers for oral administration that change conformation in aqueous solutions in response to external stimuli such as pH or temperature. We concentrate on charged polymers and gels with polyelectrolyte properties. Because of the ionization at a certain pH or in response to changes in the ionic composition of the solution, a polyelectrolyte has better chances of displaying smart properties than a neutral polymer. When such smart polyelectrolyte is cross-linked by covalent or hydrogen bonding and/or physical aggregation or is entangled, it forms an environmentally sensitive gel capable of swelling and collapse in an aqueous medium. Varying pH, temperature, and microbial flora are found in the gastrointestinal tract, and thus pH- sensitive polymers and gels that can be degraded by specific enzymes and/or inhibit proteolytic enzymes can be tailored for the efficient site-specific therapy. Smart polymers wield a lot of promise in the targeted, site-specific administration where they can provide advantages in loading of sensitive drugs such as proteins and peptides, while releasing the drug at a specific pH or in response to the presence of certain microbial flora.
Constitutive Activation of Peroxisome Proliferator-activated Receptor-γ Suppresses Pro-inflammatory Adhesion Molecules in Human Vascular Endothelial Cells (2002)

Peroxisome proliferator-activated receptor-gamma (PPAR-gamma) is a ligand-activated nuclear receptor that has an essential role in adipogenesis and glucose homeostasis. PPAR-gamma is expressed in vascular tissues including endothelial cells (ECs). PPAR-gamma activity can be regulated by many pathophysiological and pharmacological agonists. However, the role of PPAR-gamma activation in ECs remains unclear. In this study, we examined the effect of the constitutive activation of PPAR-gamma on the phenotypic modulation of ECs. Adenovirus-mediated expression of a constitutively active mutant of PPAR-gamma resulted in significant ligand-independent activation of PPAR-gamma and specific induction of the PPAR-gamma target genes. However, PPAR-gamma activation significantly suppressed the expression of vascular adhesion molecules in ECs and the ensuing leukocyte recruitment. Furthermore, constitutive activation of PPAR-gamma resulted in simultaneous repression of AP-1 and NF-kappaB activity, which suggests that PPAR-gamma may reduce pro-inflammatory phenotypes via, at least in part, suppression of the AP-1 and NF-kappaB pathways. Therefore, using a gain-of-function approach, our study provides novel evidence showing that constitutive activation of PPAR-gamma is sufficient to prevent ECs from converting into a pro-inflammatory phenotype. These results also suggest that, in addition to pharmacological agonists, the genetic modification of the PPAR-gamma activity in ECs may be a potential approach for therapeutic intervention in various inflammatory disorders.
Initiation of Retarded Styrene Anionic Polymerization Using Complexes of Lithium Hydride with Organometallic Compounds (2003)

The hydrogenolysis of poly(styryllithium) species leads to the in situ formation of lithium hydride, which is able to reinitiate styrene anionic polymerization at 100 °C. However, the slow addition rate of LiH to styrene with respect to propagation yields incomplete initiation. The presence of an organometallic derivative such as dibutylmagnesium or triisobutylaluminum was found to improve both the solubility and the reinitiation efficiency of lithium hydride. This behavior is explained by the formation of bimetallic complexes which slow down the propagation and favor the initiation. Following these findings, the use of hydrogen as chain transfer agent in the anionic retarded polymerization of styrene was investigated.
Differential Expression of Brain-Derived Neurotrophic Factor, Neurotrophin-3, and Neurotrophin-4/5 in the Adult Rat Spinal Cord: Regulation by the Glutamate Receptor Agonist Kainic Acid (1999)

Previous in vitro studies indicate that select members of the neurotrophin gene family, namely brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), and neurotrophin-4/5 (NT-4/5), contribute to survival and differentiation of spinal cord motoneurons. To investigate the potential roles of these factors in the adult spinal cord, we examined their cellular localization and regulation after systemic exposure to an excitotoxic stimulus, kainic acid (KA). Of the neurotrophins examined, NT-4/5 mRNA was most robustly expressed in the lumbosacral spinal cord of the normal adult rat, including expression by neurons throughout the gray matter, and in a subpopulation of white and gray matter glia. Both BDNF and NT-3 mRNAs were also densely expressed by alpha motoneurons of lamina IX, but were detected at lower levels elsewhere in the gray matter. NT-3 mRNA was additionally expressed by spinal cord glia, but was less widespread compared to NT-4/5. In response to systemic administration of KA, NT-4/5 and BDNF mRNAs were dramatically upregulated in a spatially and temporally restricted fashion, whereas levels of NT-3 mRNA were unchanged. These results provide strong in vivo evidence to support the idea that BDNF, NT-3, and in particular, NT-4/5, play a role in the normal function of the adult spinal cord. Furthermore, our results indicate that the actions of BDNF and NT-4/5 participate in the response of the cord to excitotoxic stimuli, and that those of NT-4/5 and NT-3 include both neurons and glia.
Verification of secure distributed systems in higher order logic: A modular approach using generic components (2002)

A generalization of D. McCullough's (1987; 1988) restrictiveness model is given as the basis for providing security properties for distributed system designs. This generalization is mechanized for an event-based model of computer systems in the HOL (higher order logic) system to prove the composability of the model and several other properties about the model. A set of generalized classes of system components is developed and it is shown for which families of user views they satisfy the model. Using these classes, a collection of general system components that are specializations of one of these classes is delineated and it is shown that the specializations also satisfy the security property. A sample distributed secure system is presented along with an example of how the proposed mechanized verification system can be used to verify such designs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Human Betacoronavirus 2c EMC/2012–related Viruses in Bats, Ghana and Europe (2013)

We screened fecal specimens of 4,758 bats from Ghana and 272 bats from 4 European countries for betacoronaviruses. Viruses related to the novel human betacoronavirus EMC/2012 were detected in 46 (24.9%) of 185 Nycteris bats and 40 (14.7%) of 272 Pipistrellus bats. Their genetic relatedness indicated EMC/2012 originated from bats.
PA7200: a PA-RISC processor with integrated high performance MP bus interface (2002)

A new processor implementing Hewlett-Packard's PA-RISC 1.1 (Precision Architecture) has been designed. This latest design incorporates many improvements over the HP PA7100 CPU, including increased frequency, instruction and data cache prefetching, enhanced superscalar execution, and enhanced multiprocessor support. The PA7200 connects directly to a new split transaction, 120 MHz, 64-bit bus capable of supporting multiple processors and multiple outstanding memory reads per processor. A novel fully associative on-chip data cache, which is accessed in parallel with an external data cache, is used to reduce the miss rate and facilitate hardware and software directed prefetching to reduce average memory access time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Cobalt Porphyrin−Lewis Base System:  A Highly Selective Catalyst for Alternating Copolymerization of CO2 and Epoxide under Mild Conditions (2007)

The use of a cobalt porphyrin ((TPP)CoCl, 1) in combination with dimethylaminopyridine (DMAP) for the alternating copolymerization of CO2 and epoxide is described. The (TPP)CoCl (1)−DMAP system quantitatively produced the alternating copolymer from CO2 and cyclohexene oxide (CHO) under optimized conditions (50 atm, 80 °C). This calatyst system also worked satisfactorily for the alternating copolymerization of CO2 and a terminal epoxide, e.g., propylene oxide (PO), without formation of cyclic carbonate to give the polycarbonate. The alternating copolymerization of CO2 and epoxide (CHO, PO) was achieved under very mild conditions, such as at ambient temperature and under CO2 at 1 atm, by using the 1−DMAP catalyst system.
Effect of the Layer-by-Layer (LbL) Deposition Method on the Surface Morphology and Wetting Behavior of Hydrophobically Modified PEO and PAA LbL Films (2008)

We demonstrate that the surface morphology and surface-wetting behavior of layer-by-layer (LbL) films can be controlled using different deposition methods. Multilayer films based upon hydrogen-bonding interactions between hydrophobically modified poly(ethylene oxide) (HM-PEO) and poly(acrylic acid) (PAA) have been prepared using the dip- and spin-assisted LbL methods. A three-dimensional surface structure in the dip-assisted multilayer films appeared above a critical number of layer pairs owing to the formation of micelles of HM-PEO in its aqueous dipping solution. In the case of spin-assisted HM-PEO/PAA multilayer films, no such surface morphology development was observed, regardless of the layer pair number, owing to the limited rearrangement and aggregation of HM-PEO micelles during spin deposition. The contrasting surface morphologies of the dip- and spin-assisted LbL films have a remarkable effect on the wetting behavior of water droplets. The water contact angle of the dip-assisted HM-PEO/PAA LbL films reaches a maximum at an intermediate layer pair number, coinciding with the critical number of layer pairs for surface morphology development, and then decreases rapidly as the surface structure is evolved and amplified. In contrast, spin-assisted HM-PEO/PAA LbL films yield a nearly constant water contact angle due to the surface chemical composition and roughness that is uniform independent of layer pair number. We also demonstrate that the multilayer samples prepared using both the dip- and spin-assisted LbL methods were easily peeled away from any type of substrate to yield free-standing films; spin-assisted LbL films appeared transparent, while dip-assisted LbL films were translucent.
Uniform GaAs quantum dots in a polymer matrix (1994)

A novel technique suitable for the preparation of uniformly sized nano- and microparticles of a wide range of compound semiconductors embedded in different polymers is described. Optical absorption spectra and high resolution electron micrographs of a new composite material—GaAs quantum dots in a polymer matrix—are presented and are discussed.