gebhart/patrepeval huggingface dataset:
Reducing the energy of speculative instruction schedulers (2006)

Energy dissipation from the issue queue and register file constitutes a large portion of the overall energy budget of an aggressive dynamically scheduled microprocessor. We propose techniques to save energy in these structures by reducing issue queue occupancy and by reducing unnecessary register file accesses that can result from speculative scheduling. Our results show a 44% reduction in issue queue occupancies and an 87% reduction in register file accesses for scheduling replays. Our data show that these savings can translate into a 52% saving in issue queue energy, a 13% savings in register file energy, and a 22% overall energy savings.
Possibility of Cytoplasmic pre-tRNA Splicing: the Yeast tRNA Splicing Endonuclease Mainly Localizes on the Mitochondria (2003)

Pre-tRNA splicing has been believed to occur in the nucleus. In yeast, the tRNA splicing endonuclease that cleaves the exon-intron junctions of pre-tRNAs consists of Sen54p, Sen2p, Sen34p, and Sen15p and was thought to be an integral membrane protein of the inner nuclear envelope. Here we show that the majority of Sen2p, Sen54p, and the endonuclease activity are not localized in the nucleus, but on the mitochondrial surface. The endonuclease is peripherally associated with the cytosolic surface of the outer mitochondrial membrane. A Sen54p derivative artificially fixed on the mitochondria as an integral membrane protein can functionally replace the authentic Sen54p, whereas mutant proteins defective in mitochondrial localization are not fully active. sen2 mutant cells accumulate unspliced pre-tRNAs in the cytosol under the restrictive conditions, and this export of the pre-tRNAs partly depends on Los1p, yeast exportin-t. It is difficult to explain these results from the view of tRNA splicing in the nucleus. We rather propose a new possibility that tRNA splicing occurs on the mitochondrial surface in yeast.
Peptide Aptamers: Development and Applications (2015)

Peptide aptamers are small combinatorial proteins that are selected to bind to specific sites on their target molecules. Peptide aptamers consist of short, 5-20 amino acid residues long sequences, typically embedded as a loop within a stable protein scaffold. Various peptide aptamer scaffolds and in vitro and in vivo selection techniques are reviewed with emphasis on specific biomedical, bioimaging, and bioanalytical applications.
DNA Recognition by Hybrid Oligoether–Oligodeoxynucleotide Macrocycles (1992)

Exceptionally resistant to nucleases, the 1:1 adducts of single-stranded oligonucleotides and cyclic oligoether–oligonucleotide hybrid compounds form triple-helical structures. The picture on the right shows schematically the binding in these systems.
Apoprotein E suppresses phytohemagglutinin-activated phospholipid turnover in peripheral blood mononuclear cells. (1982)

Plasma lipoproteins with hydrated densities less than 1.063 g/ml, very low density, intermediate density, and low density lipoproteins, suppress mitogen-activated inductive biochemical events in lymphocytes. The ability of these lipoproteins to inhibit phytohemagglutinin (PHA)-enhanced incorporation of 32P into lymphocyte phospholipids correlates directly with the amount of associated apoprotein E (apo-E). Apo-E purified from the very low density lipoproteins of subjects with Types III, IV, and V hyperlipoproteinemia also inhibits PHA-induced 32P-phospholipid formation. With all of the apo-E preparations, 50% suppression occurs at approximately 2-4 microgram/ml and 100% suppression at 4-10 microgram/ml. Moreover, delipidated apo-E is an inhibitory as apo-E complexed with dimyristoyl phosphatidylcholine or with sphingomyelin. Other apoproteins, apo-AI, -AII, -CI, and -CIII, do not inhibit PHA-activated phospholipid turnover, indicating that suppression is due to a specific structural feature of apo-E. Suppression by apo-E is not due to a shift in the optimum concentration of PHA, nor is it the result of competition with PHA for mitogen receptors at the cell surface. These data, taken together with the results of previous studies (Hui, D. Y., and Harmony, J. A. K. (1980) Proc. Natl. Acad. Sci. U. S. A. 77, 4764-4768; Hui, D. Y., Harmony, J. A. K. (1980) J. Biol. Chem. 255, 11775-11781), indicate that lipoprotein-associated apo-E serves as a recognition determinant for lymphocyte surface receptors and as a suppressive lipoprotein constituent.
Prokaryotic carbonic anhydrases (2000)

Carbonic anhydrases catalyze the reversible hydration of CO(2) [CO(2)+H(2)Oright harpoon over left harpoon HCO(3)(-)+H(+)]. Since the discovery of this zinc (Zn) metalloenzyme in erythrocytes over 65 years ago, carbonic anhydrase has not only been found in virtually all mammalian tissues but is also abundant in plants and green unicellular algae. The enzyme is important to many eukaryotic physiological processes such as respiration, CO(2) transport and photosynthesis. Although ubiquitous in highly evolved organisms from the Eukarya domain, the enzyme has received scant attention in prokaryotes from the Bacteria and Archaea domains and has been purified from only five species since it was first identified in Neisseria sicca in 1963. Recent work has shown that carbonic anhydrase is widespread in metabolically diverse species from both the Archaea and Bacteria domains indicating that the enzyme has a more extensive and fundamental role in prokaryotic biology than previously recognized. A remarkable feature of carbonic anhydrase is the existence of three distinct classes (designated alpha, beta and gamma) that have no significant sequence identity and were invented independently. Thus, the carbonic anhydrase classes are excellent examples of convergent evolution of catalytic function. Genes encoding enzymes from all three classes have been identified in the prokaryotes with the beta and gamma classes predominating. All of the mammalian isozymes (including the 10 human isozymes) belong to the alpha class; however, only nine alpha class carbonic anhydrase genes have thus far been found in the Bacteria domain and none in the Archaea domain. The beta class is comprised of enzymes from the chloroplasts of both monocotyledonous and dicotyledonous plants as well as enzymes from phylogenetically diverse species from the Archaea and Bacteria domains. The only gamma class carbonic anhydrase that has thus far been isolated and characterized is from the methanoarchaeon Methanosarcina thermophila. Interestingly, many prokaryotes contain carbonic anhydrase genes from more than one class; some even contain genes from all three known classes. In addition, some prokaryotes contain multiple genes encoding carbonic anhydrases from the same class. The presence of multiple carbonic anhydrase genes within a species underscores the importance of this enzyme in prokaryotic physiology; however, the role(s) of this enzyme is still largely unknown. Even though most of the information known about the function(s) of carbonic anhydrase primarily relates to its role in cyanobacterial CO(2) fixation, the prokaryotic enzyme has also been shown to function in cyanate degradation and the survival of intracellular pathogens within their host. Investigations into prokaryotic carbonic anhydrase have already led to the identification of a new class (gamma) and future research will undoubtedly reveal novel functions for carbonic anhydrase in prokaryotes.
On the Rapid Prototyping and Design of a Wireless Communication System on a Chip (1999)

The evolutionary convergence of computing, integrated circuit technology, and advances in wireless communications has led to an explosive growth of personal communication devices and services (PCS). In fact, the dramatic Moore's Law shrinkage of IC devices, itself, has lead to an unprecedented ability to place increasingly complex systems on a chip (SoC).In a wireless communication environment, the integration task is made more difficult by the need to integrate RF, mixed signal, and digital systems. Furthermore, the digital system design task generally requires a mapping of heterogeneous stacks of software processes onto a similarly diverse collection of digital signal processors, microprocessors and application-specific integrated circuits.In this presentation, we give an overview of a modern wireless communication device and describe advanced system-level design methodologies utilized for rapid prototyping and design of current and next generation systems.
A Genomewide Analysis of the Cinnamyl Alcohol Dehydrogenase Family in Sorghum [Sorghum bicolor(L.) Moench] IdentifiesSbCAD2as theBrown midrib6Gene (2008)

The content and composition of the plant cell wall polymer lignin affect plant fitness, carbon sequestration potential, and agro-industrial processing. These characteristics, are heavily influenced by the supply of hydroxycinnamyl alcohol precursors synthesized by the enzyme cinnamyl alcohol dehydrogenase (CAD). In angiosperms, CAD is encoded by a multigene family consisting of members thought to have distinct roles in different stages of plant development. Due to the high sequence similarity among CAD genes, it has been challenging to identify and study the role of the individual genes without a genome sequence. Analysis of the recently released sorghum genome revealed the existence of 14 CAD-like genes at seven genomic locations. Comparisons with maize and rice revealed subtle differences in gene number, arrangement, and expression patterns. Sorghum CAD2 is the predominant CAD involved in lignification based on the phylogenetic relationship with CADs from other species and genetic evidence showing that a set of three allelic brown midrib (bmr) lignin mutants contained mutations in this gene. The impact of the mutations on the structure of the protein was assessed using molecular modeling based on X-ray crystallography data of the closely related Arabidopsis CAD5. The modeling revealed unique changes in structure consistent with the observed phenotypes of the mutants.
Emulsion copolymerization of methyl methacrylate with ethyl acrylate, 1. Effect of the initiator concentration on the polymerization behaviour (1986)

Abstract The emulsion copolymerization of methyl methacrylate with ethyl acrylate, initiated by ammonium persulfate in the presence of both anionic and nonionic emulsifiers, was kinetically investigated at 60°C by the conventional gravimetric method. In the range of low conversions the rate of polymerization was found to be proportional to the 0,5 power of the initiator concentration. Over the range of medium conversions the rate of polymerization is approximately proportional to the 0,35 power of the initiator concentration and the number‐average molecular weight is inversely proportional to the 0,4 power of the initiator concentration. The molecular weight increases up to 30% conversion and then it remains constant up to the total monomer consumption. It was found that the mean particle diameter decreases while the number of particles per volume unit, the conductivity of final latices, the coagulate yield and the number of radicals per particle increase with increasing concentration of the initiator.
Differences in stride between healthy ostriches (Struthio camelus) and those affected by tibiotarsal rotation : research note (2007)

Twenty healthy ostriches (ten cocks and ten hens), and twenty birds with tibiotarsal rotation (nine cocks and 11 hens) (14 months old) were isolated, hooded and weighed. A run (50 m x 2.5 m) was divided into sections marked 5 m, 10 m, 15 m and 20 m. Time taken for each bird to pass these points was recorded and speed computed. The degree of tibiotarsal rotation in the right foot was mean +/- SEM, 156 +/- 2.69 degrees. Comparisons between left and right foot length in healthy birds showed no significant differences. Foot length was significantly lower in tibiotarsal rotation (P = 0.03). The right foot in tibiotarsal rotation was significantly shorter than the left foot. The number of strides per each 5 m division were significantly (P < 0.05) greater in tibiotarsal rotation by comparison with healthy birds. At 20 m, healthy cocks had more strides than hens. The stride length in hens was significantly (P < 0.05) greater than cocks at 5, 10 and 15 m, respectively, but lower throughout in tibiotarsal rotation (P = 0.001). The speed of hens was significantly (P < 0.05) greater than cocks. Tibiotarsal rotation resulted in significantly (P < 0.05) reduced speeds. Hens may be able to escape danger faster than cocks. The occurrence of tibiotarsal rotation necessitates consideration of genetics, management, sex, nutrition and growth rates.
On partial transmit sequences for PAR reduction in OFDM systems (2008)

Partial transmit sequences (PTS) is a popular technique to reduce the peak-to-average power ratio (PAR) in orthogonal frequency division multiplexing (OFDM) systems. PTS is highly successful in PAR reduction and efficient redundancy utilization, but the considerable computational complexity for the required search through a high-dimensional vector space and the necessary transmission of side information (SI) to the receiver are potential problems for a practical implementation. In this paper, we revisit PTS for PAR reduction and tackle these two problems. To address the complexity issue, we formulate the search problem of PTS as a combinatorial optimization (CO) problem. This enables us to (i) unify various search strategies proposed earlier in the PTS literature and (ii) adapt efficient search algorithms known from the CO literature to PTS. We also propose a modified PTS objective function, which reduces the number of multiplications required for PTS. Numerical results show that, perhaps surprisingly, simple random search yields the best performance-complexity tradeoff for moderate PAR reduction, whereas two novel CO-based methods excel if close-to-optimum PAR reduction is desired. The SI transmission problem is solved by a simple preprocessing of the data stream before PAR reduction. This preprocessing introduces the minimal possible redundancy and allows SI embedding without affecting the PAR reduction capability of PTS or causing peak regrowth.
Expression profiling of genes involved in starch synthesis in sink and source organs of rice (2005)

A comprehensive analysis of the transcript levels of genes which encode starch-synthesis enzymes is fundamental for the assessment of the function of each enzyme and the regulatory mechanism for starch biosynthesis in source and sink organs. Using quantitative real-time RT-PCR, an examination was made of the expression profiles of 27 rice genes encoding six classes of enzymes, i.e. ADPglucose pyrophosphorylase (AGPase), starch synthase, starch branching enzyme, starch debranching enzyme, starch phosphorylase, and disproportionating enzyme in developing seeds and leaves. The modes of gene expression were tissue- and developmental stage-specific. Four patterns of expression in the seed were identified: group 1 genes, which are expressed very early in grain formation and are presumed to be involved in the construction of fundamental cell machineries, de novo synthesis of glucan primers, and initiation of starch granules; group 2 genes, which are highly expressed throughout endosperm development; group 3 genes, which have transcripts that are low at the onset but which rise steeply at the start of starch synthesis in the endosperm and are thought to play essential roles in endosperm starch synthesis; and group 4 genes, which are expressed scantly, mainly at the onset of grain development, and might be involved in synthesis of starch in the pericarp. The methodology also revealed that the defect in the cytosolic AGPase small subunit2b (AGPS2b) transcription from the AGPS2 gene in endosperm sharply enhanced the expressions of endosperm and leaf plastidial AGPS1, the endosperm cytosolic AGPase large subunit2 (AGPL2), and the leaf plastidial AGPL1.
Activation and Active Site Occupation Alter Conformation in the Region of the First Epidermal Growth Factor-like Domain of Human Factor VII (2000)

The first epidermal growth factor-like domain (EGF-1) of factor VII (FVII) provides the region of greatest contact during the interaction of FVIIa with tissue factor. To understand this interaction better, the conformation-sensitive FVII EGF-1-specific monoclonal antibody (mAb) 231-7 was used to investigate the conformational effects occurring in this region upon both FVII activation and active site occupation. The binding affinity of mAb 231-7 was approximately 3-fold greater for the zymogen state than for the active state; a result affected by the presence of both calcium and the adjacent Gla domain. Once activated, active site inhibition of FVIIa with a variety of chloromethyl ketone inhibitors resulted in a 10-fold range of affinities of FVIIai molecules to mAb 231-7. Gla domain removal eliminated this variation in affinity, suggesting the involvement of a Gla/EGF-1 interaction in this conformational effect. In addition, the binding of mAb 231-7 to FVIIa EGF-1 stimulated the amidolytic activity of free FVIIa. Taken together, these results imply an allosteric interaction between the FVIIa active site and the EGF-1 domain that is sensitive to variation in active site occupant structure. Thus, these present studies indicate that the conformational change associated with FVII activation and active site occupation involves the EGF-1 domain and suggest potential functional consequences of these changes.
Matrix metalloproteinases and diseases of the central nervous system with a special emphasis on ischemic brain (2006)

Matrix metalloproteinases (MMPs) are involved in the pathogenesis of several diseases of the CNS, that share common pathophysiological processes, such as blood-brain barrier (BBB) disruption, oxidative stress, remodeling of the extracellular matrix (ECM) and inflammation. In ischemic brain injury, MMPs are implicated in various stages of the disease. Early after the onset of ischemia, MMPs contribute to the disruption of the BBB leading to vasogenic edema and to the influx of leucocytes into the CNS. The ability of MMPs to digest the basal lamina of capillaries increases the risk of hemorrhagic transformation of the ischemic tissue. During the acute ischemic phase, maintenance of the ECM is essential for neuronal survival. However, ECM degradation and its reconstitution are critical to tissue recovery. MMPs as a key modulator of ECM homeostasis play a role in the cascades leading to neuronal cell death and tissue regeneration. This pleiotropic implication of MMPs in brain injury has open new areas of investigation, which should lead to innovative therapeutic strategies. Yet MMPs may have a detrimental or beneficial role depending on the stage of brain injury. Simple therapeutic strategies based on MMP inhibition have thus little chance to favorably alter prognosis.
<title>Quantitative DIC microscopy using a geometric phase shifter</title> (1997)

In this paper we investigate the use of a geometric phase- shifting (GPS) technique which allows us to convert conventional transmission or reflection differential interference contrast (DIC) microscopy into a quantitative mode. A phase-shifting algorithm is employed to extract the specimen phase gradient from the mixture of phase and amplitude information which is common in DIC. Fourier techniques are then used to recover the exact phase (i.e. optical path length variations) throughout the biological specimen viewed. In addition to this quantitative 'phase map,' we demonstrate that the GPS process simultaneously yields an 'amplitude-only' representation in which various absorption and transmission properties of the specimen are displayed as intensity variations in the image, similar to brightfield microscopy. These two resulting images can then be analyzed or further processed in a number of ways that are not possible with conventional DIC and which improve the microscopist's ability to correctly identify, interpret and measure features in the specimen.
The 3′-to-5′ Exonuclease Activity of Vaccinia Virus DNA Polymerase Is Essential and Plays a Role in Promoting Virus Genetic Recombination (2009)

Poxviruses are subjected to extraordinarily high levels of genetic recombination during infection, although the enzymes catalyzing these reactions have never been identified. However, it is clear that virus-encoded DNA polymerases play some unknown yet critical role in virus recombination. Using a novel, antiviral-drug-based strategy to dissect recombination and replication reactions, we now show that the 3'-to-5' proofreading exonuclease activity of the viral DNA polymerase plays a key role in promoting recombination reactions. Linear DNA substrates were prepared containing the dCMP analog cidofovir (CDV) incorporated into the 3' ends of the molecules. The drug blocked the formation of concatemeric recombinant molecules in vitro in a process that was catalyzed by the proofreading activity of vaccinia virus DNA polymerase. Recombinant formation was also blocked when CDV-containing recombination substrates were transfected into cells infected with wild-type vaccinia virus. These inhibitory effects could be overcome if CDV-containing substrates were transfected into cells infected with CDV-resistant (CDV(r)) viruses, but only when resistance was linked to an A314T substitution mutation mapping within the 3'-to-5' exonuclease domain of the viral polymerase. Viruses encoding a CDV(r) mutation in the polymerase domain still exhibited a CDV-induced recombination deficiency. The A314T substitution also enhanced the enzyme's capacity to excise CDV molecules from the 3' ends of duplex DNA and to recombine these DNAs in vitro, as judged from experiments using purified mutant DNA polymerase. The 3'-to-5' exonuclease activity appears to be an essential virus function, and our results suggest that this might be because poxviruses use it to promote genetic exchange.
Long-Distance Electron Transfer Across Molecule−Nanocrystalline Semiconductor Interfaces (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTLong-Distance Electron Transfer Across Molecule−Nanocrystalline Semiconductor InterfacesElena Galoppini, Wenzhuo Guo, Ping Qu, and Gerald J. MeyerView Author Information Chemistry Department, Rutgers University 73 Warren Street, Newark, New Jersey 07102 Chemistry Department and the Department of Materials Science and Engineering, Johns Hopkins University Baltimore, Maryland 21218 Cite this: J. Am. Chem. Soc. 2001, 123, 18, 4342–4343Publication Date (Web):April 11, 2001Publication History Received29 December 2000Published online11 April 2001Published inissue 1 May 2001https://doi.org/10.1021/ja005932hCopyright © 2001 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views785Altmetric-Citations74LEARN 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 InReddit Read OnlinePDF (50 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Charge transfer,Molecules,Nanoparticles,Oxides,Semiconductors Get e-Alerts