gebhart/patrepeval huggingface dataset:
Efficient representations and abstractions for quantifying and exploiting data reference locality (2001)

With the growing processor-memory performance gap, understanding and optimizing a program's reference locality, and consequently, its cache performance, is becoming increasingly important. Unfortunately, current reference locality optimizations rely on heuristics and are fairly ad-hoc. In addition, while optimization technology for improving instruction cache performance is fairly mature (though heuristic-based), data cache optimizations are still at an early stage. We believe the primary reason for this imbalance is the lack of a suitable representation of a program's dynamic data reference behavior and a quantitative basis for understanding this behavior. We address these issues by proposing a quantitative basis for understanding and optimizing reference locality, and by describing efficient data reference representations and an exploitable locality abstraction that support this framework. Our data reference representations (Whole Program Streams and Stream Flow Graphs) are compact—two to four orders of magnitude smaller than the program's data reference trace—and permit efficient analysis—on the order of seconds to a few minutes—even for complex applications. These representations can be used to efficiently compute our exploitable locality abstraction (hot data streams). We demonstrate that these representations and our hot data stream abstraction are useful for quantifying and exploiting data reference locality. We applied our framework to several SPECint 2000 benchmarks, a graphics program, and a commercial Microsoft database application. The results suggest significant opportunity for hot data stream-based locality optimizations.
Superior augmented reality registration by integrating landmark tracking and magnetic tracking (1996)

Accurate registration between real and virtual objects is crucial for augmented reality applications. Existing tracking methods are individually inadequate: magnetic trackers are inaccurate, mechanical trackers are cumbersome, and vision-based trackers are computationally problematic. We present a hybrid tracking method that combines the accuracy of vision-based tracking with the robustness of magnetic tracking without compromising real-time performance or usability.
Time interval measurements using integrated tapped CMOS delay lines (2003)

An integrated seven bit time-to-digital converter (TDC) based on tapped CMOS delay lines was designed and tested. Its single-shot resolution is about 700 ps, and the ultimate resolution of averaged results is 50-100 ps. The linearity and gain of the converter are markedly dependent on the layout and ambient conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evidence for efficient uptake and incorporation of sialic acid by eukaryotic cells (2001)

Sialic acids are the most abundant terminal carbohydrate moiety on cell surface glycoconjugates in eukaryotic cells and are of functional importance for many biological ligand-receptor interactions. It is a widely accepted view that sialic acids cannot be efficiently taken up from the extracellular space by eukaryotic cells. To test this assumption, we cultivated two recently identified human hematopoetic cell lines which are hyposialylated due to a deficiency in de novo sialic acid biosynthesis in the presence of N-acetylneuraminic acid (NeuAc), the most frequently found sialic acid. Surprisingly, NeuAc medium supplementation rapidly and potently compensated for the endogenous hyposialylation in a concentration-dependent manner, resulting in the presentation of cell surface sialoglycans involved in cell adhesion, virus infection and signal transduction. We provide several lines of experimental evidence that all suggest that NeuAc was neither extracellularly incorporated nor degraded to a less complex sugar before uptake. Importantly, NeuAc induced a marked increase in intracellular CMP-NeuAc levels in both human cell lines and in primary cells regardless of the prior sialylation status of the cells. Studies employing 9-[3H]NeuAc revealed an uptake consistent with the observed incorporation of unlabeled NeuAc. We propose the existence of an efficient uptake mechanism for NeuAc in eukaryotic cells.
Aluminium(salen) and Tetrabutylammonium Bromide Catalysed Synthesis of Cyclic Di- and Trithiocarbonates from Epoxides and Carbon Disulfide (2009)

The combination of a bimetallic aluminium(salen) complex and tetrabutylammonium bromide was found to catalyse the synthesis of cyclic di- and trithiocarbonates from epoxides and carbon disulfide. Reactions carried out at 50 ˚C produced 1,3-oxa­thiolane-2-thiones, whilst at 90 ˚C, 1,3-dithiolane-2-thiones were formed.
Morphological enhancement of vascular angiogram with multiscale detected by Gabor filters (2008)

A multiscale morphology scheme for enhancing local contrast of a coronary angiogram is proposed. The method consists of a combined top-hat operator with structuring elements of different dimensions, which corresponds to the vessel diameter at each pixel point estimated by a group of Gabor wavelets under different orientation and scale. Experiment shows the results on a real angiogram.
Calcium and cell cycle control (1990)

The cell division cycle of the early sea urchin embryo is basic. Nonetheless, it has control points in common with the yeast and mammalian cell cycles, at START, mitosis ENTRY and mitosis EXIT. Progression through each control point in sea urchins is triggered by transient increases in intracellular free calcium. The Cai transients control cell cycle progression by translational and post-translational regulation of the cell cycle control proteins pp34 and cyclin. The START Cai transient leads to phosphorylation of pp34 and cyclin synthesis. The mitosis ENTRY Cai transient triggers cyclin phosphorylation. The motosis EXIT transient causes destruction of phosphorylated cyclin. We compare cell cycle regulation by calcium in sea urchin embryos to cell cycle regulation in other eggs and oocytes and in mammalian cells.
2,5-Diketopiperazines: Synthesis, Reactions, Medicinal Chemistry, and Bioactive Natural Products (2012)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXT2,5-Diketopiperazines: Synthesis, Reactions, Medicinal Chemistry, and Bioactive Natural ProductsAlan D. BorthwickView Author Information DrugMolDesign, 15 Temple Grove, London NW11 7UA, U.K.Tel.: +44 (0)7772112742. E-mail: [email protected]Cite this: Chem. Rev. 2012, 112, 7, 3641–3716Publication Date (Web):May 11, 2012Publication History Received18 October 2011Published online11 May 2012Published inissue 11 July 2012https://pubs.acs.org/doi/10.1021/cr200398yhttps://doi.org/10.1021/cr200398yreview-articleACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views27956Altmetric-Citations676LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Cyclization,Inhibitors,Peptides and proteins,Reaction products,Toxicity Get e-Alerts
New inhibitors of Helicobacter pylori urease holoenzyme selected from phage‐displayed peptide libraries (1999)

Urease is an important virulence factor for Helicobacter pylori and is critical for bacterial colonization of the human gastric mucosa. Specific inhibition of urease activity has been proposed as a possible strategy to fight this bacteria which infects billions of individual throughout the world and can lead to severe pathological conditions in a limited number of cases. We have selected peptides which specifically bind and inhibit H. pylori urease from libraries of random peptides displayed on filamentous phage in the context of pIII coat protein. Screening of a highly diverse 25-mer combinatorial library and two newly constructed random 6-mer peptide libraries on solid phase H. pylori urease holoenzyme allowed the identification of two peptides, 24-mer TFLPQPRCSALLRYLSEDGVIVPS and 6-mer YDFYWW that can bind and inhibit the activity of urease purified from H. pylori. These two peptides were chemically synthesized and their inhibition constants (Ki) were found to be 47 microM for the 24-mer and 30 microM for the 6-mer peptide. Both peptides specifically inhibited the activity of H. pylori urease but not that of Bacillus pasteurii.
The renal urodilatin system: clinical implications (2001)

A renal natriuretic peptide and the 'renal urodilatin system' were identified after the observation that immunoassayable ANP in urine may not be identical to the circulating cardiac hormone ANP, which is a peptide of 28 amino acids. Urodilatin (INN: Ularitide) is a natriuretic peptide isolated from human urine and belongs to the family of A-type natriuretic peptides. Urodilatin is differentially processed to a peptide of 32 amino acids from the same precursor as ANP. It is synthesized in kidney tubular cells and secreted luminally. After secretion from epithelial cells of the distal and/or connecting tubules, Urodilatin interacts downstream at distal segments of the nephron with luminally located receptors whereby it regulates Na(+) and water reabsorption. Thus, the physiological function of the renal Urodilatin system can be described as a paracrine intrarenal regulator for Na(+) and water homeostasis, considering Urodilatin as a real diuretic-natriuretic regulatory peptide. However, the regulation upon which the Urodilatin secretion depends is still not clear. Since Urodilatin has been discovered, a great number of pharmacological and clinical investigations have been carried out using Urodilatin as a drug for several indications. So far, clinical phase I and II studies for acute renal failure, congestive heart failure, and bronchial asthma have been performed.
Silicon-on-insulator by wafer bonding and etch-back (2003)

A novel silicon-on-insulator technique utilizing the bonding of oxidized silicon wafers has been investigated. The bonding was achieved by heating in an inert atmosphere a pair of wafers with hydrophilic surfaces, which had been contacted face-to-face. A quantitative method for the evaluation of the surface energy of the bond based on crack propagation theory was developed. The bond strength was found to increase with the bonding temperature from about 60-85 erg/cm/sup 2/ at room temperature to approximately=2200 erg/cm/sup 2/ at 1400 degrees C, which is in the same range as the cohesive energy of bulk quartz. The strength was essentially independent of the bond time. Bonds created during a 10 s annealing at 800 degrees C were strong enough to withstand both the thinning of the top wafer to the desired thickness and the subsequent device processing. Three distinct phases of the bonding process were observed. The electrical properties of the bond between the wafers were tested using MOS capacitors. The results were consistent with a negative charge density at the bond interface of approximately 10/sup 11/ cm/sup -2/. A double etch-back procedure was used to thin the device wafer to the desired thickness. The characteristics of the resulting film are described. CMOS devices made in a 0.3- mu m-thick layer had subthreshold slopes of 68 mV/decade (for both n- and p-channel MOS transistors). The effective carrier lifetime was >30 mu s in 300-nm-thick Si films, and the interface state density at the Si-film/buried oxide interface was <5*10/sup 10/ cm/sup -2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clinical expression correlates with location of rhodopsin mutation in dominant retinitis pigmentosa. (1995)

These data indicate that severity of disease correlates with the location of the amino acid residue altered by a rhodopsin mutation in dominant retinitis pigmentosa.
Palladium hydrides in organic synthesis. Reduction of aryl halides by sodium methoxide catalyzed by tetrakis(triphenylphosphine)palladium (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPalladium hydrides in organic synthesis. Reduction of aryl halides by sodium methoxide catalyzed by tetrakis(triphenylphosphine)palladiumArie Zask and Paul HelquistCite this: J. Org. Chem. 1978, 43, 8, 1619–1620Publication Date (Print):April 1, 1978Publication History Published online1 May 2002Published inissue 1 April 1978https://pubs.acs.org/doi/10.1021/jo00402a042https://doi.org/10.1021/jo00402a042research-articleACS PublicationsRequest reuse permissionsArticle Views1422Altmetric-Citations107LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An obligate cell-intrinsic function for CD28 in Tregs (2013)

Tregs expressing the transcription factor FOXP3 are critical for immune homeostasis. The costimulatory molecule CD28 is required for optimal activation and function of naive T cells; however, its role in Treg function has been difficult to dissect, as CD28 is required for thymic Treg development, and blockade of CD28-ligand interactions has confounding effects in trans on nonregulatory cells. To address this question, we created Treg-specific Cd28 conditional knockout mice. Despite the presence of normal numbers of FOXP3+ cells, these animals accumulated large numbers of activated T cells, developed severe autoimmunity that primarily affected the skin and lungs, and failed to appropriately resolve induced experimental allergic encephalomyelitis. This in vivo functional impairment was accompanied by dampened expression of CTLA-4, PD-1, and CCR6. Disease occurrence was not due to subversion of Cd28-deficient Tregs into pathogenic cells, as complementation with normal Tregs prevented disease occurrence. Interestingly, in these "competitive" environments, Cd28-deficient Tregs exhibited a pronounced proliferative/survival disadvantage. These data demonstrate clear postmaturational roles for CD28 in FOXP3+ Tregs and provide mechanisms which we believe to be novel to explain how interruption of CD28-ligand interactions may enhance immune responses independent of effects on thymic development or on other cell types.
Phase noise considerations in coherent optical FMCW reflectometry (1993)

An analysis of coherent optical FMCW is presented. It shows the limitations imposed on measurements of discrete reflections and of Rayleigh backscattering due to phase noise originating in the finite coherence length of the optical source. The dependence of the range for accurate measurements on particular parameters of the optical system is discussed in the general case and for three specific laser sources.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Deoxyguanosine enhances the cytotoxicity of the topoisomerase i inhibitor camptothecin by reducing the repair of double-strand breaks induced in replicating dna (1991)

Deoxyguanosine (dG) enhances the S phase cytotoxicity of camptothecin (CPT), a topoisomerase I (topo I) inhibitor, but by contrast does not affect the toxicity of VM26, a topoisomerase II inhibitor. The 80% survival of S phase human fibroblasts after a 60 min exposure to 0.2 microM CPT is reduced by half in the presence of 25 microM dG. G1 cells are resistant to CPT toxicity, though the levels of the single-strand DNA breaks induced by the drug are similar in G1 and S phase cells. Higher concentrations of dG retard the recovery of RNA and DNA synthesis and inhibit recovery from the S-G2 cycle block after CPT removal. At 100 microM dG the number of CPT-induced protein-linked single-strand DNA breaks is almost doubled, suggestive of a direct effect of dG on the cellular activity of topo I. In the presence or absence of dG, single-strand breaks disappear within minutes of the removal of CPT. We found that the inhibition of topo I by CPT induces the formation of double as well as single-strand breaks in the chromosomal DNA. Previously we have shown, using a pulse-field gel electrophoresis technique, that the double-strand breaks (DSBs) are generated predominantly at sites of replication and not in the bulk DNA. A number of these DSBs are long-lived. The present study shows that dG affects the repair of these DSBs in a dose-dependent manner, and that a higher proportion of the initial lesions induced in nascent DNA remain 24 h after removal of CPT. We suggest that the long-lived double-strand breaks, formed in replicating DNA at the time of CPT exposure, are the lethal drug-induced lesions, which explains both the selective cytotoxicity of CPT towards S phase cells and the enhancement of CPT cytotoxicity by dG.
Immune Response in Infants to the Heptavalent Pneumococcal Conjugate Vaccine against Vaccine-Related Serotypes 6A and 19A (2009)

ABSTRACT The currently available 7-valent pneumococcal conjugate vaccine (PCV7) elicits good immune response to and is effective against vaccine serotypes. However, its effectiveness against vaccine-related serotypes is variable. Serum samples were obtained 1 month after the last vaccination from 31 infants immunized with PCV7 at 2, 4, and 6 months of age. The sera were used to determine immunoglobulin G antibody levels to eight serotypes (seven vaccine serotypes and serotype 19A) with enzyme-linked immunosorbent assay (ELISA) and opsonic capacity against 11 serotypes (seven vaccine serotypes, serotypes 19A and 6A, and nonvaccine serotypes 5 and 7F) using a multiplexed opsonization assay. ELISA results showed antibody concentrations varied between 1.84 and 10.49 μg/ml, and all subjects had antibody concentrations of ≥0.35 μg/ml for all serotypes, including serotype 19A. In contrast, the opsonic index was detectable (i.e., opsonic index ≥ 8) in all children for the seven vaccine serotypes, 81% for serotype 6A, and merely 19% for serotype 19A. PCV7 shows good immunogenicity for vaccine serotypes in infants after a primary series. PCV7 does not elicit opsonic antibodies to serotype 19A. ELISA may thus be an inadequate surrogate assay for evaluating the response for cross-reactive serotypes in infants.
Nicotine absorption from electronic cigarette use: comparison between first and new-generation devices (2014)

A wide range of electronic cigarette (EC) devices, from small cigarette-like (first-generation) to new-generation high-capacity batteries with electronic circuits that provide high energy to a refillable atomizer, are available for smokers to substitute smoking. Nicotine delivery to the bloodstream is important in determining the addictiveness of ECs, but also their efficacy as smoking substitutes. In this study, plasma nicotine levels were measured in experienced users using a first- vs. new-generation EC device for 1 hour with an 18 mg/ml nicotine-containing liquid. Plasma nicotine levels were higher by 35-72% when using the new- compared to the first-generation device. Compared to smoking one tobacco cigarette, the EC devices and liquid used in this study delivered one-third to one-fourth the amount of nicotine after 5 minutes of use. New-generation EC devices were more efficient in nicotine delivery, but still delivered nicotine much slower compared to tobacco cigarettes. The use of 18 mg/ml nicotine-concentration liquid probably compromises ECs' effectiveness as smoking substitutes; this study supports the need for higher levels of nicotine-containing liquids (approximately 50 mg/ml) in order to deliver nicotine more effectively and approach the nicotine-delivery profile of tobacco cigarettes.
Viral-Induced Enhanced Disease Illness (2018)

Understanding immune responses to viral infections is crucial to progress in the quest for effective infection prevention and control. The host immunity involves various mechanisms to combat viral infections. Under certain circumstances, a viral infection or vaccination may result in a subverted immune system, which may lead to an exacerbated illness. Clinical evidence of enhanced illness by preexisting antibodies from vaccination, infection or maternal passive immunity is available for several viruses and is presumptively proposed for other viruses. Multiple mechanisms have been proposed to explain this phenomenon. It has been confirmed that certain infection- and/or vaccine-induced immunity could exacerbate viral infectivity in Fc receptor- or complement bearing cells- mediated mechanisms. Considering that antibody dependent enhancement (ADE) is a major obstacle in vaccine development, there are continues efforts to understand the underlying mechanisms through identification of the epitopes and antibodies responsible for disease enhancement or protection. This review discusses the recent findings on virally induced ADE, and highlights the potential mechanisms leading to this condition.
The cyclosome, a large complex containing cyclin-selective ubiquitin ligase activity, targets cyclins for destruction at the end of mitosis. (1995)

The ubiquitin-mediated degradation of mitotic cyclins is required for cells to exit from mitosis. Previous work with cell-free systems has revealed four components required for cyclin-ubiquitin ligation and proteolysis: a nonspecific ubiquitin-activating enzyme E1, a soluble fraction containing a ubiquitin carrier protein activity called E2-C, a crude particulate fraction containing a ubiquitin ligase (E3) activity that is activated during M-phase, and a constitutively active 26S proteasome that degrades ubiquitinated proteins. Here, we identify a novel approximately 1500-kDa complex, termed the cyclosome, which contains a cyclin-selective ubiquitin ligase activity, E3-C. E3-C is present but inactive during interphase; it can be activated in vitro by the addition of cdc2, enabling the transfer of ubiquitin from E2-C to cyclin. The kinetics of E3-C activation suggest the existence of one or more intermediates between cdc2 and E3-C. Cyclosome-associated E3-C acts on both cyclin A and B, and requires the presence of wild-type N-terminal destruction box motifs in each cyclin. Ubiquitinated cyclins are then rapidly recognized and degraded by the proteasome. These results identify the cyclosome-associated E3-C as the component of the cyclin destruction machinery whose activity is ultimately regulated by cdc2 and, as such, the element directly responsible for setting mitotic cyclin levels during early embryonic cell cycles.