gebhart/patrepeval huggingface dataset:
A Performance Study of NLA 64-State QAM (1983)

The performance of a modulation technique which is both power and bandwidth efficient, termed nonlinearly amplified 64-state quadrature amplitude modulation (NLA 64-state QAM), is studied. To assess the effects of selective fading and/or system filter imperfections, computer simulated results are presented which show the sensitivity of the modulation technique to typical group delay and amplitude distortions. In addition to the above-mentioned results, the effects of modulator imperfections in the power level combining on the P <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</inf> performance are evaluated.
An Execution Infrastructure for TCB Minimization (2018)

We present Flicker, an infrastructure for executing security-sensitive code in complete isolation while trusting as few as 250 lines of additional code. Flicker can also provide meaningful, fine-grained attes-tation of the code executed (as well as its inputs and outputs) to a remote party. Flicker guarantees these properties even if the BIOS, OS and DMA-enabled devices are all malicious. Flicker leverages new commodity processors from AMD and Intel and does not require a new OS or VMM. We demonstrate a full implementation of Flicker on an AMD platform and describe our development environment for simplifying the construction of Flicker-enabled code.
The Principles and Practice of Sleep Medicine, Fourth Edition (2006)

The Principles and Practice of Sleep Medicine, Fourth Edition 

edited by Meir H. Kryger, Thomas Roth, and William C. Dement, 1552 pp., Elsevier, 2005, $195.00

The gold standard of sleep medicine has been The Principles and Practice of Sleep Medicine. Now in its fourth edition with the same editors, it …
Triple-Phase MDCT of Hepatocellular Carcinoma (2004)

The appearances of hepatocellular carcinoma on images obtained using MDCT scanners are similar to those described for images obtained using single-detector helical scanners. However, the prevalence of hypervascular hepatocellular carcinoma on MDCT images is higher than previously described on single-detector helical images and most lesions showed washout on portal venous MDCT images.
Oligodeoxynucleotides containing C-7 propyne analogs of 7-deaza-2'- deoxyguanosine and 7-deaza-2'-deoxyadenosine (1996)

The synthesis, hybridization properties and antisense activities of oligodeoxynucleotides (ODNs) containing 7-(1-propynyl)-7-deaza-2'-deoxyguanosine (pdG) and 7-(1-propynyl)-7-deaza-2'-deoxyadenosine (pdA) are described. The suitably protected nucleosides were synthesized and incorporated into ODNs. Thermal denaturation (Tm) of these ODNs hybridized to RNA demonstrates an increased stability relative to 7-unsubstituted deazapurine and unmodified ODN controls. Antisense inhibition by these ODNs was determined in a controlled microinjection assay and the results demonstrate that an ODN containing pdG is approximately 6 times more active than the unmodified ODN. 7-Propyne-7-deaza-2'-deoxyguanosine is a promising lead analog for the development of antisense ODNs with increased potency.
MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer (2009)

While altered expression of microRNAs (miRs) in tumors has been well documented, it remains unclear how the miR transcriptome intersects neoplastic progression. By profiling the miR transcriptome we identified miR expression signatures associated with steps in tumorigenesis and the acquisition of hallmark capabilities in a prototypical mouse model of cancer. Metastases and a rare subset of primary tumors shared a distinct miR signature, implicating a discrete lineage for metastatic tumors. The miR-200 family is strongly down-regulated in metastases and met-like primary tumors, thereby relieving repression of the mesenchymal transcription factor Zeb1, which in turn suppresses E-cadherin. Treatment with a clinically approved angiogenesis inhibitor normalized angiogenic signature miRs in primary tumors, while altering expression of metastatic signature miRs similarly to liver metastases, suggesting their involvement in adaptive resistance to anti-angiogenic therapy via enhanced metastasis. Many of the miR changes associated with specific stages and hallmark capabilities in the mouse model are similarly altered in human tumors, including cognate pancreatic neuroendocrine tumors, implying a generality.
Effects of CO2 laser pulse duration in ablation and residual thermal damage: Implications for skin resurfacing (1996)

Our results show that although pulse duration is an important determinant in ablation and thermal damage, irradiance is more critical as an independent parameter in predicting the effects of CO2 laser pulses.
Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75 (2005)

Integrase (IN) is an essential retroviral enzyme, and human transcriptional coactivator p75, which is also referred to as lens epithelium-derived growth factor (LEDGF), is the dominant cellular binding partner of HIV-1 IN. Here, we report the crystal structure of the dimeric catalytic core domain of HIV-1 IN complexed to the IN-binding domain of LEDGF. Previously identified LEDGF hotspot residues anchor the protein to both monomers at the IN dimer interface. The principal structural features of IN that are recognized by the host factor are the backbone conformation of residues 168-171 from one monomer and a hydrophobic patch that is primarily comprised of alpha-helices 1 and 3 of the second IN monomer. Inspection of diverse retroviral primary and secondary sequence elements helps to explain the apparent lentiviral tropism of the LEDGF-IN interaction. Because the lethal phenotypes of HIV-1 mutant viruses unable to interact with LEDGF indicate that IN function is highly sensitive to perturbations of the structure around the LEDGF-binding site, we propose that small molecule inhibitors of the protein-protein interaction might similarly disrupt HIV-1 replication.
Influenza C virus uses 9-O-acetyl-N-acetylneuraminic acid as a high affinity receptor determinant for attachment to cells. (1986)

Identification of the receptor-destroying enzyme of influenza C virus as a specific neuraminate O-acetylesterase has suggested that 9-O-acetyl-N-acetylneuraminic acid is an essential component of the cell surface receptor of influenza C virus (Herrler, G., Rott, R., Klenk, H.-D., Muller, H.-P., Shukla, A. K., and Schauer, R. (1985) EMBO (Eur. Mol. Biol. Organ.) J. 4, 1503-1506). In this report, three common sialic acids, N-acetylneuraminic acid (NeuAc), N-glycollylneuraminic acid (NeuGc), and 9-O-acetyl-N-acetylneuraminic acid (9-O-Ac-NeuAc) were compared for their ability to mediate attachment of influenza A, B, and C viruses to cells. Human asialoerythrocytes were resialylated to contain the three sialic acids in defined sequence on glycoprotein carbohydrate groups using purified sialyltransferases and corresponding CMP-sialic acid donor substrates. While influenza C virus failed to agglutinate native cells or resialylated cells containing NeuAc and NeuGc, resialylated cells containing 9-O-Ac-NeuAc in three different sialyloligosaccharide sequences were agglutinated in high titer. In contrast, most representative influenza A and B viruses examined preferentially agglutinated cells containing NeuAc and NeuGc and failed to agglutinate cells containing 9-O-Ac-NeuAc. Cells containing 9-O-Ac-NeuAc were sensitive to the action of influenza C virus neuraminate O-acetylesterase which converts 9-O-Ac-NeuAc to NeuAc. This treatment abolished agglutination by influenza C while making the cells agglutinable by several influenza A and B viruses. Finally, the ability of influenza C virus to agglutinate the erythrocytes of various species correlated with the presence of 9-O-Ac-NeuAc. The results provide direct evidence that influenza C virus utilizes 9-O-acetyl-N-acetylneuraminic acid as the primary receptor determinant for attachment to cell surface receptors.
Demonstration of the Immature Glycosaminoglycan Tetrasaccharide Sequence GlcAβ1–3Galβ1–3Galβ1–4Xyl on Recombinant Soluble Human α-Thrombomodulin (1998)

Thrombomodulin (TM), a cell surface glycoprotein, is a critical mediator of endothelial anticoagulant defenses occurring both as a chondroitin sulfate proteoglycan (beta-TM) and a protein (alpha-TM) unsubstituted by chondroitin sulfate (CS), hence its description as a "part-time" proteoglycan (PG) (Fransson, L. A. (1987) Trends Biochem. Sci. 12, 406-411). Sugar analysis was performed on alpha-TM to investigate a possible biosynthetic mechanism for part-time PGs. Recombinant human alpha-TM, which was expressed in CHO-K1 cells, separated by anion-exchange chromatography from beta-TM, and purified by immunoaffinity chromatography (Nawa, K., Sakano, K., Fujiwara, H., Sato, Y., Sugiyama, N., Teruuchi, T., Iwamoto, M., and Marumoto, Y. (1990) Biochem. Biophys. Res. Commun. 171, 729-737), was used for analysis. Preliminary sugar composition analysis after acid hydrolysis showed Xyl in addition to Gal, GalNAc, GlcNAc, Man, Fuc, and Glc. O-Glycosidically-linked oligosaccharides were liberated by mild alkaline treatment and purified. The isolated oligosaccharide fraction was derivatized with a fluorophore 2-aminobenzamide (2AB), resulting in two fluorescent components, a 2AB-oligosaccharide and a putative 2AB-Glc. Based on structural analysis by a combination of sequential exoglycosidase digestion and 500-MHz 1H NMR spectroscopy of the 2AB-oligosaccharide, the structure of the oligosaccharide was elucidated as GlcAbeta1-3Galbeta1-3Galbeta1-4Xyl, which turned out to represent a glycosaminoglycan (GAG)-protein linkage region tetrasaccharide common to various PGs and was considered to be a biosynthetic intermediate of an immature GAG chain. The results may indicate that at least one class of the so-called part-time PGs bear the linkage tetrasaccharide at the GAG attachment sites and that the critical determining step or the rate-limiting step for PG biosynthesis is the transfer of the fifth sugar residue, the first hexosamine, rather than xylose.
Selective binding and cytotoxicity of rat basophilic leukemia cells (RBL-1) with immunoglobulin E-biotin and avidin-glucose oxidase conjugates. (1980)

Abstract One approach to the selective destruction of tumor cells in heterogeneous cell populations is to use specific receptors to localize cytotoxic or potentially cytotoxic molecules. Since basophilic leukemia cells, as well as mast cells and basophils, frequently or invariably contain IgE receptors, it should be possible to use IgE immunoglobulin as a cytotoxic carrier for the ablation of these cells. With rat basophilic leukemia (RBL-1) cells as the target, selective cytotoxicity was accomplished by the use of rat IgE conjugated to biotin followed by avidin (which has affinity for biotin) coupled to a cytotoxic enzyme system composed of an avidin-glucose oxidase conjugate (Av-GO) and the cofactors lactoperoxidase and iodide. Greater than 90% cell killing was obtained by using as little as 0.2 µg/ml Av-GO. The addition of free biotin or the exclusion of IgE-biotin, Av-GO, or cofactors from the complete system reduced cytotoxicity to 7 to 40% of control values and the substitution of unconjugated Av and GO for Av-GO caused no killing, demonstrating the requirement for each component of the specific cytotoxic system. In addition to its potential as a model and possibly practical system for the induction of enzyme amplified affinity cytotoxicity in neoplastic cells, this cytotoxic system may be of value in the selection of variant cell lines with mutant or absent IgE receptors in the study of IgE-cell receptor interactions.
Observation of Critical Coupling in a Fiber Taper to a Silica-Microsphere Whispering-Gallery Mode System (2000)

We present the observation of critical coupling in a high- Q fused-silica microsphere whispering-gallery mode resonator coupled to a fiber taper. Extremely efficient and controlled power transfer to high- Q ( approximately 10(7)) resonators has been demonstrated. Off-resonance scattering loss was measured to be less than 0.3%. On-resonance extinction in transmitted optical power through the fiber coupler was measured as high as 26 dB at the critical coupling point. This result opens up a range of new applications in fields as diverse as near-field sensing and quantum optics.
Safety and efficacy of high dose etanercept in treatment of juvenile rheumatoid arthritis. (2001)

High dose etanercept is safe and well tolerated in children, but efficacy seems limited. In children with unsatisfactory response to standard dose etanercept, an increased dose or treatment prolongation may not offer any additional benefit.
Return of the Trojan horse: intracellular phenotype switching and immune evasion by Staphylococcus aureus (2011)

Abstract Staphylococcus aureus small colony variants (SCVs), which are characterized by slow growth and a range of morphological and metabolic changes including altered antibiotic resistance profiles, have been studied for several decades. This Closeup highlights findings described in this issue of EMBO Molecular Medicine by Tuchscherr et al ( 2011 ), who present strong evidence that SCVs can arise in chronic infection models when S. aureus is internalized in non‐professional phagocytes and survives intracellularly. As the intracellular residency time increases, the proportion of SCVs grows and the host cell inflammatory response diminishes. The study suggests that this mode of phenotype switching is an essential feature of the S. aureus infection process and can explain an underlying cause of chronic and relapsing infections. See related article in EMBO Mol Med (Tuchscherr et al (2011) EMBO Mol Med 3: 129‐141 )
Protocol for predictable restoration of anterior teeth with composite resins. (1998)

The composite resins have reached a high degree of excellence and are now used with predictable results in restoring the anterior dentition. This article discusses the development of these resins and the histologic and optical considerations (polychromatic characteristics, hue translucency and opacity, chroma, value, strength and polishability). In restorative materials, the use of universal or all-purpose restorative resins is considered: i.e. materials that combine the junctional strength necessary for the posterior regions and the high gloss polishability necessary to emulate enamel in the anterior. The restorative sequence of cervical, middle, and incisal thirds describes the materials best suited for each third, along with aids to create the intricate refinement of hue, chroma, and value. The learning objective of this article is to review the principles involved in these restorations and to provide a protocol for their clinical implementation.
Chimerism in monochorionic dizygotic twins: Case study and review (2013)

Chimerism occurs when an organism contains cells derived from more than one distinct zygote. We focus on monochorionic dizygotic twin blood chimerism, and particularly twin-twin transfusion syndrome in such pregnancies. For years, researchers have understood chimerism to be a common phenomenon in cattle. Although, this review will not delve deeply into animal chimerism, an understanding of chimerism in the animal world can provide clues regarding health implications for human chimeras. This report serves two purposes: an update and assessment of the twins we reported previously in 2010 [Assaf et al., 2010] and a review on dizygotic monochorionic chimeric twins. First, our updated assessment of the twins shows no identifiable regression of Müllerian sex derivatives in the female, and normal neurodevelopment was documented in both. Our research has suggested several key points; one that blood chimerism persists from fetal life to at least age two years. Second, chimerism in humans is not as rare as previously thought, although it has been studied only recently. Third, assisted reproductive technologies appear to increase the risk of monochorionic dizygotic twin pregnancies.
Phagocytosis: Flow Cytometric Quantitation with Fluorescent Microspheres (1982)

The phagocytosis of uniform fluorescent latex particles by pulmonary macrophages in the rat was analyzed by flow cytometric methods. The percentage of phagocytic macrophages and the number of particles per cell were determined from cell-size and fluorescence histograms. A comparison of in vivo and in vitro phagocytosis data showed that the percentage of phagocytic lavaged macrophages reflected the availability of instilled particles. With sodium azide used to model phagocytosis inhibition, it was shown that the percentage of phagocytic cells and the number of particles per cell can be determined simultaneously.
Identification of activated cytokine pathways in the blood of systemic lupus erythematosus, myositis, rheumatoid arthritis, and scleroderma patients (2011)

A novel gene expression measurement of activated cytokines in five different rheumatic diseases is presented. Characterizing the cytokine pathways most activated in specific patient subpopulations has the potential to help target the appropriate patient populations for corresponding anti-cytokine therapies.
Evolution of CD33-related siglecs: regulating host immune functions and escaping pathogen exploitation? (2010)

Sialic-acid-binding immunoglobulin-like lectins, siglecs, are important immune receptors expressed widely in mammals. A unique feature of siglecs is their ability to bind sialylated glycans and transmit signals to immune cells. The CD33-related siglecs (CD33rSiglecs) form a major subfamily of the siglecs, containing a large, rapidly evolving group of genes that expanded in mammals through an inverse duplication event involving a primordial cluster of siglec genes over 180 million years ago. Humans express a much larger set of CD33rSiglecs than mice and rats, a feature that can be explained by a dramatic loss of CD33rSiglec genes in rodents. Most CD33rSiglecs have immune receptor tyrosine-based inhibitory motifs and signal negatively. Interestingly, novel DAP-12-coupled 'activating' CD33rSiglecs have been identified, such as siglec-14 and siglec-16, which are paired with the inhibitory receptors, siglec-5 and siglec-11, respectively. The evolution of these activating receptors may have been driven in part by pathogen exploitation of inhibitory siglecs, thereby providing the host with additional pathways by which to combat these pathogens. Inhibitory siglecs seem to play important and varied roles in the regulation of host immune responses. For example, several CD33rSiglecs have been implicated in the negative regulation of Toll-like receptor signalling during innate responses; siglec-G functions as a negative regulator of B1-cell expansion and appears to suppress inflammatory responses to host-derived 'danger-associated molecular patterns'. Recent work has also shown that engagement of neutrophil-expressed siglec-9 by certain strains of sialylated Group B streptococci can suppress killing responses, thereby providing experimental support for pathogen exploitation of host CD33rSiglecs.
Efficient Asymmetric Synthesis of Biologically Important Tryptophan Analogues via a Palladium-Mediated Heteroannulation Reaction (2001)

A novel and concise synthesis of optically active tryptophan derivatives was developed via a palladium-catalyzed heteroannulation reaction of substituted o-iodoanilines with an internal alkyne. The required internal alkyne 14a or 25 was prepared in greater than 96% de via alkylation of the Schöllkopf chiral auxiliary 19 employing diphenyl phosphate as the leaving group. The Schöllkopf chiral auxiliary was chosen here for the preparation of L-tryptophans would be available from D-valine while the D-isomers required for natural product total synthesis would originate from the inexpensive L-valine (300-g scale). Applications of the palladium-catalyzed heteroannulation reaction were extended to the first asymmetric synthesis of L-isotryptophan 38 and L-benz[f]tryptophan 39. More importantly, the optically pure 6-methoxy-D-tryptophan 62 was prepared by this protocol on a large scale (>300 g). This should permit entry into many ring-A oxygenated indole alkaloids when coupled with the asymmetric Pictet-Spengler reaction. In addition, an improved total synthesis of tryprostatin A (9a) was accomplished in 43% overall yield employing this palladium-mediated process.
Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver (2007)

MicroRNA-122 (miR-122) is an abundant liver-specific miRNA, implicated in fatty acid and cholesterol metabolism as well as hepatitis C viral replication. Here, we report that a systemically administered 16-nt, unconjugated LNA (locked nucleic acid)-antimiR oligonucleotide complementary to the 5' end of miR-122 leads to specific, dose-dependent silencing of miR-122 and shows no hepatotoxicity in mice. Antagonism of miR-122 is due to formation of stable heteroduplexes between the LNA-antimiR and miR-122 as detected by northern analysis. Fluorescence in situ hybridization demonstrated uptake of the LNA-antimiR in mouse liver cells, which was accompanied by markedly reduced hybridization signals for mature miR-122 in treated mice. Functional antagonism of miR-122 was inferred from a low cholesterol phenotype and de-repression within 24 h of 199 liver mRNAs showing significant enrichment for miR-122 seed matches in their 3' UTRs. Expression profiling extended to 3 weeks after the last LNA-antimiR dose revealed that most of the changes in liver gene expression were normalized to saline control levels coinciding with normalized miR-122 and plasma cholesterol levels. Combined, these data suggest that miRNA antagonists comprised of LNA are valuable tools for identifying miRNA targets in vivo and for studying the biological role of miRNAs and miRNA-associated gene-regulatory networks in a physiological context.
Detection and analysis of diverse herpesviral species by consensus primer PCR (1996)

A consensus primer PCR method which amplifies a region of herpesviral DNA-directed DNA polymerase (EC 2.7.7.7) and which uses degenerate primers in a nested format was developed. Primers were designed to target sequences coding for highly conserved amino acid motifs covering a region of approximately 800 bp. The assay was applied to 22 species of herpesviruses (8 human and 14 animal viruses), with PCR products obtained for 21 of 22 viruses. In the process, 14 previously unreported amino acid-coding sequences from herpesviral DNA polymerases were obtained, including regions of human herpesviruses 7 and 8. The 50 to 60 amino acid-coding sequences recovered in the present study were determined to be unique to each viral species studied, with very little sequence variation between strains of a single species when studied. Template dilution studies in the presence of human carrier DNA demonstrated that six human herpesviruses (herpesviruses 1, 2, 3, 4, 5, and 6B) could be detected at levels at or below 100 genome equivalents per 100 ng of carrier DNA. These data suggest that consensus primer PCR targeted to herpesviral DNA polymerase may prove to be useful in the detection and identification of known herpesviruses in clinical samples and the initial characterization of new herpesviral genomes.