gebhart/patrepeval huggingface dataset:
Going the distance for TLB prefetching: an application-driven study (2003)

The importance of the translation lookaside buffer (TLB) on system performance is well known. There is a large body of literature on prefetching for caches, and it is not clear how they can be adapted (or if the issues are different) for TLBs, how well suited they are for TLB prefetching, and how they compare with the recency prefetching mechanism. This paper presents the first detailed comparison of different prefetching mechanisms (previously proposed for caches) - arbitrary stride prefetching and Markov prefetching -for TLB entries, and evaluates their pros and cons. In addition, this paper proposes a novel prefetching mechanism, called distance prefetching, that attempts to capture patterns in the reference behavior in a smaller space than earlier proposals. Using detailed simulations of a wide variety of applications (56 in all) from different benchmark suites and all the, SPEC CPU2000 applications, this paper demonstrates the benefits of distance prefetching.
Platelet glycoprotein IIb-IIIa protein antagonists from snake venoms: evidence for a family of platelet-aggregation inhibitors. (1990)

The purification, complete amino acid sequence, and biological activity are described for several homologous snake venom proteins that are platelet glycoprotein (GP) IIb-IIIa antagonists and potent inhibitors of platelet aggregation. The primary structures of kistrin (from Agkistrodon rhodostoma), bitan (from Bitis arietans), three isoforms of trigramin (from Trimeresusus gramineus), and an isoform of echistatin (from Echis carinatus) were determined by automated sequence analysis and fast atom bombardment mass spectrometry analysis. Each of the protein in this family, which range from 47 to 83 residues, contains an Arg-Gly-Asp amino acid sequence found in protein ligands that binds to GPIIb-IIIa, a high (17 +/- 1%) cysteine content conserved in the primary sequence, and a homologous N-terminal region absent only in the echistatin isoforms. Each protein directly inhibits the interaction of purified platelet GPIIb-IIIa to immobilized fibrinogen about 100 times more effectively than does the pentapeptide Gly-Arg-Gly-Asp-Ser; IC50 values range from 1.1 to 3.0 nM. The IC50 value for the inhibition of platelet aggregation, using human platelet-rich plasma stimulated with ADP, ranges from 110 to 550 nM for the various proteins, about 1000-fold more potent than Gly-Arg-Gly-Asp-Ser. Kistrin binds reversibly to both resting and ADP-activated human platelets with high affinity (Kd = 10.8 nM and 1.7 nM, respectively) and to purified GPIIb-IIIa with a lower affinity (Kd = approximately 100 nM). Finally, kistrin injected at 1.0 mg/kg into rabbits reversibly inhibits platelet aggregation ex vivo over 30 min without induction of thrombocytopenia. We propose that these proteins are members of a general class of proteins found in the venom of pit vipers that inhibit platelet aggregation by antagonism of the GPIIb-IIIa-fibrinogen interaction and as such serve as potential antithrombotic agents.
Are 'Pathogenesis-related' Proteins Involved in Acquired Systemic Resistance of Tobacco Plants to Tobacco Mosaic Virus? (1982)

SUMMARY Four host-coded 'pathogenesis-related' proteins accumulate systemically in local-lesion-forming varieties of tobacco after infection with tobacco mosaic virus. It has been suggested that they are involved in the acquired systemic resistance of plants to a second inoculation. Pathogenesis-related protein concentration and amount of resistance (reduction in size and number of lesions formed in the second inoculation) were measured at various times after the first inoculation. The results showed no quantitative or temporal relationship between amounts of resistance and pathogenesis-related proteins. In particular, resistance could be demonstrated in leaves before detectable accumulation of pathogenesis-related protein. Abscisic acid sprayed on plants induced an apparent resistance without inducing pathogenesis-related proteins. Low doses of methyl benzimidazol-2yl-carbamate caused accumulation of pathogenesis-related protein but not resistance. Nicotiana glutinosa plants accumulated large amounts of a similar protein after infection, but became more susceptible to a second inoculation. All these results suggest that the pathogenesis-related proteins do not play a central role in the mechanism of acquired systemic resistance.
Single-Step Covalent Functionalization of Polylactide Surfaces (2005)

A single-step, nondestructive, and versatile technique for the grafting and chemical surface modification of biodegradable polymers such as polylactide is described. The substrates are subjected to the vapor phase of any of three investigated vinyl monomers: acrylamide, maleic anhydride, and N-vinylpyrrolidone, and grafting is induced by photoinitiation of benzophenone under solvent free conditions. The modified surfaces exhibit higher wettability, and the grafting is verified by X-ray photoelectron spectroscopy, attenuated total reflection Fourier-transform IR, contact-angle measurements, and scanning electron microscopy. The graft-chain pendant groups remain functional and can subsequently be modified so that a tailor-made surface with desired properties may be achieved.
Role of Antibiotic Penetration Limitation in Klebsiella pneumoniae Biofilm Resistance to Ampicillin and Ciprofloxacin (2000)

The penetration of two antibiotics, ampicillin and ciprofloxacin, through biofilms developed in an in vitro model system was investigated. The susceptibilities of biofilms and corresponding freely suspended bacteria to killing by the antibiotics were also measured. Biofilms of Klebsiella pneumoniae were developed on microporous membranes resting on agar nutrient medium. The susceptibilities of planktonic cultures and biofilms to 10 times the MIC were determined. Antibiotic penetration through biofilms was measured by assaying the concentration of antibiotic that diffused through the biofilm to an overlying filter disk. Parallel experiments were performed with a mutant K. pneumoniae strain in which beta-lactamase activity was eliminated. For wild-type K. pneumoniae grown in suspension culture, ampicillin and ciprofloxacin MICs were 500 and 0.18 microgram/ml, respectively. The log reductions in the number of CFU of planktonic wild-type bacteria after 4 h of treatment at 10 times the MIC were 4.43 +/- 0.33 and 4.14 +/- 0.33 for ampicillin and ciprofloxacin, respectively. Biofilms of the same strain were much less susceptible, yielding log reductions in the number of CFU of -0.06 +/- 0.06 and 1.02 +/- 0.04 for ampicillin and ciprofloxacin, respectively, for the same treatment. The number of CFU in the biofilms after 24 h of antibiotic exposure was not statistically different from the number after 4 h of treatment. Ampicillin did not penetrate wild-type K. pneumoniae biofilms, whereas ciprofloxacin and a nonreactive tracer (chloride ion) penetrated the biofilms quickly. The concentration of ciprofloxacin reached the MIC throughout the biofilm within 20 min. Ampicillin penetrated biofilms formed by a beta-lactamase-deficient mutant. However, the biofilms formed by this mutant were resistant to ampicillin treatment, exhibiting a 0.18 +/- 0.07 log reduction in the number of CFU after 4 h of exposure and a 1.64 +/- 0.33 log reduction in the number of CFU after 24 h of exposure. Poor penetration contributed to wild-type biofilm resistance to ampicillin but not to ciprofloxacin. The increased resistance of the wild-type strain to ciprofloxacin and the mutant strain to ampicillin and ciprofloxacin could not be accounted for by antibiotic inactivation or slow diffusion since these antibiotics fully penetrated the biofilms. These results suggest that some other resistance mechanism is involved for both agents.
Insights into corn genes derived from large-scale cDNA sequencing (2008)

We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA clones, out of which 31,552 clones are non-redundant. These and other previously sequenced transcripts have been aligned with available genome sequences and have provided new insights into the characteristics of gene structures and promoters within this major crop species. We found that although the average number of introns per gene is about the same in corn and Arabidopsis, corn genes have more alternatively spliced isoforms. Examination of the nucleotide composition of coding regions reveals that corn genes, as well as genes of other Poaceae (Grass family), can be divided into two classes according to the GC content at the third position in the amino acid encoding codons. Many of the transcripts that have lower GC content at the third position have dicot homologs but the high GC content transcripts tend to be more specific to the grasses. The high GC content class is also enriched with intronless genes. Together this suggests that an identifiable class of genes in plants is associated with the Poaceae divergence. Furthermore, because many of these genes appear to be derived from ancestral genes that do not contain introns, this evolutionary divergence may be the result of horizontal gene transfer from species not only with different codon usage but possibly that did not have introns, perhaps outside of the plant kingdom. By comparing the cDNAs described herein with the non-redundant set of corn mRNAs in GenBank, we estimate that there are about 50,000 different protein coding genes in Zea. All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA) and FK944382-FL482108 (EST).
Epstein–Barr Virus Infection (2009)

This chapter contains sections titled: Introduction Aspects of EBV biology and pathogenesis EBV-LPD in HCT Clinical and pathologic aspects Virologic aspects Viral copy number and monitoring Treatment T-cell therapy for EBV-associated tumors Summary References
Photoconductivity and charge transporting properties of metal-containing poly(p-phenylenevinylene)s (1997)

A novel type of poly(p-phenylenevinylene)s which contain (bis(2,2′:6′,2′′-terpyridine) ruthenium (II) complexes has been developed. The absorption of the polymers at 500 nm was strongly enhanced by the metal complexes due to the presence of the metal–ligand charge transfer transition. The charge transportation is dispersive with hole carrier mobilities and activation energy of ∼7×10−5 cm2 V−1 s−1 and 0.20 eV, respectively, depending on the concentration of the metal complex. A log μ vs E1/2 plot shows that hole mobilities decrease with increasing field, which suggests the presence of off-diagonal disorder in the hopping sites.
Transport and receptor proteins of plant membranes : molecular structure and function (1992)

A mixture of reports from researchers who have experienced a breakthrough, and from those who are still beating their heads against a particularly stubborn (cell) wall. The 19 articles represent the major offerings at an international symposium in Bristol, England, September 1991, and discuss primar
Alginate production affects Pseudomonas aeruginosa biofilm development and architecture, but is not essential for biofilm formation (2004)

Extracellular polymers can facilitate the non-specific attachment of bacteria to surfaces and hold together developing biofilms. This study was undertaken to qualitatively and quantitatively compare the architecture of biofilms produced by Pseudomonas aeruginosa strain PAO1 and its alginate-overproducing (mucA22) and alginate-defective (algD) variants in order to discern the role of alginate in biofilm formation. These strains, PAO1, Alg+ PAOmucA22 and Alg- PAOalgD, tagged with green fluorescent protein, were grown in a continuous flow cell system to characterize the developmental cycles of their biofilm formation using confocal laser scanning microscopy. Biofilm Image Processing (BIP) and Community Statistics (COMSTAT) software programs were used to provide quantitative measurements of the two-dimensional biofilm images. All three strains formed distinguishable biofilm architectures, indicating that the production of alginate is not critical for biofilm formation. Observation over a period of 5 days indicated a three-stage development pattern consisting of initiation, establishment and maturation. Furthermore, this study showed that phenotypically distinguishable biofilms can be quantitatively differentiated.
A Controlled Study of Cognitive Behaviour Therapy with Buspirone or Placebo in Panic Disorder with Agoraphobia (1995)

Buspirone enhanced the effects of cognitive behaviour therapy on generalised anxiety and agoraphobia in the short term.
Global Optimization of Dielectric Metasurfaces Using a Physics-Driven Neural Network (2019)

We present a global optimizer, based on a conditional generative neural network, which can output ensembles of highly efficient topology-optimized metasurfaces operating across a range of parameters. A key feature of the network is that it initially generates a distribution of devices that broadly samples the design space and then shifts and refines this distribution toward favorable design space regions over the course of optimization. Training is performed by calculating the forward and adjoint electromagnetic simulations of outputted devices and using the subsequent efficiency gradients for backpropagation. With metagratings operating across a range of wavelengths and angles as a model system, we show that devices produced from the trained generative network have efficiencies comparable to or better than the best devices produced by adjoint-based topology optimization, while requiring less computational cost. Our reframing of adjoint-based optimization to the training of a generative neural network applies generally to physical systems that can utilize gradients to improve performance.
Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. (1984)

Genes that regulate the development of the fruit fly Drosophila melanogaster exist as tightly linked clusters in at least two cases. These clusters, the bithorax complex (BX-C) and the Antennapedia complex (ANT-C), both contain multiple homoeotic loci: mutations in each locus cause a transformation of one part of the fly into another. Several repetitive DNA sequences, including at least one transposon, were mapped in the ANT-C. DNA from the 3' exon of Antennapedia (Antp), a homoeotic locus in the ANT-C, hybridized weakly to DNA from the 3' exon of Ultrabithorax (Ubx), a homoeotic locus in the BX-C. DNA from each of these 3' exons also hybridized weakly to DNA from the fushi tarazu locus of the ANT-C. The fushi tarazu (ftz) locus controls the number and differentiation of segments in the developing embryo. Sequence analysis of the cross-hybridizing DNA from the three loci revealed the conservation of predicted amino acid sequences derived from coding parts of the genes. This suggests that two homoeotic loci and a "segment-deficient" locus encode protein products with partially shared structures and that the three loci may be evolutionarily and functionally related.
Mobile diagnosis [of vehicle mechatronic systems] (2003)

The increasing utilization of mechatronic systems in vehicles requires the integration of diagnosis functions which will be widely implemented as onboard software in the vehicle. These diagnosis functionalities will be based in the future on functional and mathematical models and will enable the depth of diagnosis to be improved. The ascertained data from the diagnosis functions describe the overall condition of the vehicle and are stored in nonvolatile memories. The development of mobile telephones capable of handling data and the increased availability of wireless networks build up the second basis of mobile diagnosis. Using a suitable IT infrastructure, data can be obtained from the vehicle by every PC. In addition to the data channel, which allows precise vehicle identification and describes the condition of the vehicle, customer complaints can be dealt with over the voice channel and serve as a fundamental source of information. Vehicle data as well as the information from the driver are compared with previously occurred faults in other vehicles. Case based reasoning (CBR) systems applications are identified. The result is a precise ascertainment of the fault cause, from which the defective vehicle components can be determined. Thus, service vehicles can carry with them correct replacement parts which can be inserted directly at the customers location in order to remove the fault. Mobile diagnosis allows an optimized diagnosis and repair process particularly if vehicles breakdown far away from a workshop.
Anatomic-Electrophysiological Correlations Concerning the Pathways for Atrioventricular Conduction (2001)

The remarkable success of radiofrequency ablation in recent decades in curing atrioventricular nodal reentrant tachycardias has intensified efforts to provide a solid theoretical basis for understanding the mechanisms of atrioventricular transmission. These efforts, which were made by both anatomists and electrophysiologists, frequently resulted in seemingly controversial observations. Quantitatively and qualitatively, our understanding of the mysteries of propagation through the inhomogeneous and extremely complex atrioventricular conduction axis is much deeper than it was at the beginning of the past century. We must go back to the initial sources, nonetheless, in an attempt to provide a common ground for evaluating the morphological and electrophysiological principles of junctional arrhythmias. In this review, we provide an account of the initial descriptions, which still provide an appropriate foundation for interpreting recent electrophysiological findings.
Neutrophil Secretion During Blood Coagulation: Evidence for a Prekallikrein Independent Pathway (1988)

In association with blood coagulation, neutrophils undergo a secretory response (Plow, J Clin Invest 69: 564, 1982) and it has been suggested that plasma kallikrein is responsible for inducing this reaction (Wachtfogel et al., J Clin Invest 72: 1672, 1983). To assess the contribution of kallikrein to this response, the capacity of normal and prekallikrein-deficient blood and plasma to support secretion has been compared utilizing elastase as a marker of secretion. Serial dilutions of prekallikrein-deficient plasma were as effective as normal plasma in supporting neutrophil release of elastase. The extent of elastase release in spontaneously clotting normal and prekallikrein-deficient blood was similar. At 37 degrees C in whole blood or at 22 degrees C in plasma, prekallikrein activators had the same effect in neutrophil secretion in normal and prekallikrein-deficient blood and plasma samples. Taken together, these results provide evidence for the existence of a prekallikrein independent pathway that can function as a predominant mechanism for induction of neutrophil secretion during blood coagulation.
5 Gbit/s optical transmission terminal equipmentusing forwarderror correcting code and optical amplifier (1994)

Using forward error correction (FEC) technology and erbium-doped fibre amplifiers (EDFAs), 5 Gbit/s optical transmission terminal equipment provides better than −40dBm receiver sensitivity at a BER of 10-11. The experiments focused on the FEC feature of the removal of the BER floor together with long-distance repeaterless transmission.
Experimental rabbit models of Chlamydia pneumoniae infection. (1996)

Chlamydia pneumoniae (TWAR), a common cause of acute respiratory disease in humans, has recently been associated with coronary and aortic atherosclerosis. In this study, we evaluated rabbit models of chlamydial infection to investigate the pathogenesis of C. pneumoniae infection. New Zealand White rabbits were inoculated intranasally and intratracheally with C. pneumoniae, strain AR-39, and primary and repeated infection were assessed. After a single inoculation, lung pathology was characterized by a moderate self-resolving interstitial pneumonia with bronchiolitis of 21 days in duration. Chlamydial DNA was detected by polymerase chain reaction (PCR) intermittently in the upper respiratory tract and lung tissue through day 21 postinoculation, spleen tissue at day 14, and peripheral blood mononuclear cells at days 3 and 21. After repeated inoculations, chlamydial DNA was detected by PCR in the upper respiratory tract and lung tissue through day 42. Lung lesions consisted of multifocal interstitial mononuclear cell aggregates that persisted up to day 42. Watanabe heritable hyperlipidemic rabbits were less susceptible to C. pneumoniae infection. After multiple inoculations of Watanabe rabbits, C. pneumoniae was detected by PCR and/or immunocytochemistry until day 21. In conclusion, C. pneumoniae induced a moderate respiratory infection in these rabbit models.
Guanidinium-cholesterol cationic lipids: efficient vectors for the transfection of eukaryotic cells. (1996)

Two cationic lipids, bis-guanidinium-spermidine-cholesterol (BGSC) and bis-guanidinium-trencholesterol (BGTC)-cholesterol derivatives bearing two guanidinium groups-have been synthesized and tested as artificial vectors for gene transfer. They combine the membrane compatible features of the cholesterol subunit and the favorable structural and high pKa features of the guanidinium functions for binding DNA via its phosphate groups. Reagent BGTC is very efficient for transfection into a variety of mammalian cell lines when used as a micellar solution. In addition, both BGTC and BGSC present also a high transfection activity when formulated as liposomes with the neutral phospholipid dioleoylphosphatidyl ethanolamine. These results reveal the usefulness of cholesterol derivatives bearing guanidinium groups for gene transfer.
Tetranucleotide repeat polymorphism at the human aromatase cytochrome P-450 gene (CYP19) (1991)

Journal Article Tetranucleotide repeat polymorphism at the human aromatase cytochrome P-450 gene (CYP19) Get access M.H. Polymeropoulos, M.H. Polymeropoulos * National Institute of Mental Health Neuroscience CenterSt Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar H. Xiao, H. Xiao National Institute of Mental Health Neuroscience CenterSt Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar D.S. Rath, D.S. Rath National Institute of Mental Health Neuroscience CenterSt Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar C.R. Merril C.R. Merril National Institute of Mental Health Neuroscience CenterSt Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 1, 11 January 1991, Page 195, https://doi.org/10.1093/nar/19.1.195 Published: 11 January 1991