gebhart/patrepeval huggingface dataset:
The de novo engineering of pyrrolysyl-tRNA synthetase for genetic incorporation of l -phenylalanine and its derivatives (2011)

Using evolved pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pairs, L-phenylalanine, p-iodo-L-phenylalanine and p-bromo-L-phenylalanine have been genetically incorporated into proteins at amber mutation sites in E. coli.
Task concurrency management experiment for power-efficient speed-up of embedded MPEG4 IM1 player (2002)

Addresses the concurrent task management of complex multimedia systems, like the MPEG4 IM1 (IMplementation 1) player. Starting with a critical part of the code in the IM1 player, we extracted the concurrency hidden by implementation decisions and represented it with our "grey-box" modeling approach. Based on this "grey-box" model, high-level transformations have been made to improve the concurrency. By scheduling the transformed graph, we have improved the performance of an important bottleneck in the system layer of the IM1 player while simultaneously lowering the system energy cost. A two-processor target platform is used in the experiment, combining processors running at a high Vdd (drain supply voltage) and a low Vdd respectively.
Hepatocyte growth factor activator (HGFA): molecular structure and interactions with HGFA inhibitor‐1 (HAI‐1) (2010)

The trypsin-like serine protease hepatocyte growth factor activator (HGFA) undergoes proteolytic activation during blood coagulation, resulting in a 34 kDa 'short form', consisting mainly of the protease domain. The crystal structures of the recombinantly expressed HGFA 'short form' discussed herein have provided molecular insights into its interaction with inhibitors and substrates, as well as the regulation of catalytic activity. The HGFA structures revealed enzymatically competent and noncompetent forms associated with the conformational states of two substrate specificity-determining loops, the 220-loop and 99-loop. The implied dynamic behavior of these loops, which are intimately involved in substrate interaction, has precedents in other members of the S1 family of serine proteases, and may be associated with specific mechanisms of enzyme regulation. Furthermore, HGFA activity is strongly inhibited by HGFA inhibitor-1, a membrane-spanning multidomain inhibitor containing two Kunitz domains, of which only the N-terminal Kunitz domain-1 (KD1) inhibits enzymatic activity. In the structure of the KD1-HGFA complex, the inhibitor interacts with the active site region by making contacts with all substrate specificity-determining loops and by occupying subsites S1, S2 and S4 in a substrate-like manner. In fact, the side chains of KD1 residues occupying these sites are virtually superimposable on the P1, P2 and P4 residues of the pro-hepatocyte growth factor-derived substrate mimic Lys-Gln-Leu-Arg chloromethyl ketone bound to HGFA. These structures also allow us to rationalize the apparently narrow substrate specificity of HGFA, which is limited to the two known macromolecular substrates pro-hepatocyte growth factor and pro-macrophage-stimulating protein.
Rings Plus Double Bonds (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Redirecting adenovirus tropism by genetic, chemical, and mechanical modification of the adenovirus surface for cancer gene therapy (2016)

Surface modification of Ad by genetic, chemical, or mechanical engineering strategies enables Ad to overcome the shortcomings of conventional Ad and enhances delivery efficiency through distinct and unique mechanisms that unmodified Ad cannot mimic. However, although the therapeutic potential of Ad-mediated gene therapy has been enhanced by various surface modification strategies, each strategy still possesses innate limitations that must be addressed, requiring innovative ideas and designs.
Total Hydrogenation of Furfural and 5-Hydroxymethylfurfural over Supported Pd–Ir Alloy Catalyst (2014)

Hydrogenation of aqueous furfural was conducted with SiO2-suported palladium-based bimetallic catalysts. The combination of palladium and iridium gave the best performance for the total hydrogenation to tetrahydrofurfuryl alcohol. Higher H2 pressure and lower reaction temperature were advantageous to suppress side reactions. The synergy between Pd and Ir in the hydrogenation catalysis is most remarkable for substituted furans as substrates. Furfural was first converted into furfuryl alcohol, which was further converted to tetrahydrofurfuryl alcohol. A small amount of tetrahydrofurfural was formed in the first step (∼20% selectivity), and the subsequent hydrogenation of tetrahydrofurfural was much slower. The combined yield of tetrahydrofurfuryl alcohol and tetrahydrofurfural reached 98%. The yield of tetrahydrofurfuryl alcohol reached 94% with larger amount of catalyst. Total hydrogenation of 5-hydroxymethylfurfural was also possible using Pd–Ir/SiO2 catalyst. The performance of Pd–Ir/SiO2 catalyst was slightly changed by repeated uses, and the used catalyst can be regenerated by calcination and reduction at 573 K. Characterization results showed that Pd–Ir alloy particles with size of ≤4 nm were formed on the catalyst. Addition of Ir much increased the TOF values as compared with Pd/SiO2 with similar particle size, especially for C═O hydrogenation. One factor of higher activity of Pd–Ir/SiO2 than Pd/SiO2 can be the change of adsorption mode: Ir atom on the surface promotes the adsorption at C═O site, whereas the Pd surface strongly interacts with furan ring.
Effects of aging on glucose-mediated glucose disposal and glucose transport. (1986)

To assess the effects of aging on glucose-mediated glucose disposal and glucose transport, glucose disposal rates were measured in 10 nonelderly (32 +/- 4 yr) and 11 elderly (64 +/- 4 yr) subjects at five different plasma glucose concentrations. Glucose disposal was decreased by 30-35% in the elderly at each level of glycemia (100-350 mg/dl) in the presence of similar levels of hyperinsulinemia (approximately 100 microU/ml), and the 50% effective concentration (EC50) was similar in both the nonelderly (100 +/- 9) and elderly (103 +/- 5 mg/dl). The Michaelis constant (Km) of 3-O-methyl glucose transport in adipocytes was unchanged with aging (3.8 +/- 0.5 vs. 3.2 +/- 0.2 mM) while the maximum velocity of insulin stimulated transport was reduced by 34% in the elderly (8.3 +/- 1.3 vs. 12.6 +/- 1.5 pmol/5 X 10(4) cells per s, P less than 0.05). The insulin resistance of aging is therefore due to a reduction in the capacity of the glucose uptake system, while the affinity of glucose utilization (EC50 and Km) is unchanged. This supports the hypothesis that a reduction in the number of glucose transport and metabolic units occurs with aging, but that each unit functions normally.
GaAs whiskers grown by metal-organic vapor-phase epitaxy using Fe nanoparticles (2007)

GaAs nanowhiskers were grown by metal-organic vapor-phase epitaxy on (111)B GaAs substrates. The diameter of the nanowhiskers was defined by monodisperse Fe nanoparticles deposited on the GaAs substrate from the vapor phase. The growth temperature of the whiskers was investigated from 480to520°C. The whiskers are preferentially directed along the crystal orientations of ⟨001⟩, ⟨111⟩, and their equivalents. High-resolution transmission electron microscopy characterization including energy disperse x-ray spectroscopy measurements revealed not only iron oxide but also arsenic inside the seed particle at the top of the GaAs whiskers. This indicates that the particle stays at the top during the whisker growth.
[Direct cell reprogramming to chondrogenic cells from dermal fibroblast culture]. (2012)

In regenerative medicine, converting one cell type to another type associates with altering epigenome of cells without changing their genome sequences. Since development of iPS cells, it has become possible to convert cell types through altering epigenome by transducing plural kye transcription factors into cells. We found that transduction of two reprogramming factors (c-Myc and Klf4) and one chondrogenic factor (SOX9) into mouse dermal fibroblasts results in direct induction of chondrogeni cells. Directly induced chondrogenic cells showed highly methylated promoter sequences of fibroblastic markers, type I collagen genes. These induced cells, when transplanted into nude mice, produced hyaline cartilage without expressing type I collagen, suggesting that type I collagen genes were silenced in these induced chondrogenic cells in vivo . It is also expected to apply cell reprogramming technique to treatment of osteoarthritis in some aspects including reversion of degenerated fibrocartilage into hyalinecartilage.
Effect of a Monoclonal Anti-sperm Antibody (A-1) on in Vitro Fertilization in the Mouse. (1993)

We prepared four monoclonal antibodies raised against mouse spermatozoa. The ability of the hybridoma culture supernatants to inhibit in vitro mouse fertilization was determined. One of these monoclonal antibodies, termed A-1, strongly inhibits sperm penetration into zona pellucida of egg in a concentration-dependent fashion. On the other hand, even in the presence of the same concentration of A-1 antibody, sperm binding to comulus-free eggs was slightly inhibited and sperm-egg fusion was not inhibited at all. Immuno-fluorescence studies with A-1 showed that it recognizes an antigen(s) localized in the acrosome of mouse spermatozoa. In the case of unfixed sperm, the acrosome-intact sperm (i.e., sperm bound to egg zona pellucida) and unbound sperm were slightly immunostained with A-1 antibody (1.6% and 9.0%, respectively). All the full acrosome reacted sperm (i.e., sperm penetrating into the perivitelline space) were not immunoreacted. On the other hand, when sperm were fixed with methanol, approximately 80% of unbound sperm were immunoreacted with this antibody. Furthermore, almost all of zona-binding sperm were immunostained, whereas acrosome reacted, penetrating sperm were not. These data suggested that the antigen recognized by A-1 was located inside the plasma membrane of spermatozoa, and appeared on the surface of the spermatozoa during the period of penetration into egg zona pellucida. After sperm penetration into the perivitelline space this antigen must be released from the sperm.
Erratum: “Stress determination in nickel monosilicide films using x-ray diffraction” [J. Appl. Phys. 106, 073521 (2009)] (2011)

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Cloning and expression of the murine homologue of a putative human X-linked nuclear protein gene closely linked to PGK1 in Xq13.3 (1994)

Several human inherited diseases have been localized to the Xq13.3 region of the human X chromosome (X-linked dystonia with Parkinsonism, sideroblastic anemia, SCID, Menkes disease and X-linked mental retardation loci). Genes involved in the phenotypes have been isolated for only two of them (Menkes and SCIDX). It was therefore interesting to isolate and characterize new genes from the region. In a previous work (12 and Consalez et al, in preparation) we isolated a gene (XNP), located 350 Kb proximal to PGK1, potentially coding for a nuclear protein. We describe here the cloning and characterization of the murine homologue. The pattern of expression of the gene in the newborn mouse (especially the expression in particular regions of the brain: optical lobe, frontal cortex, hippocampus and cerebellum), as well as the expression in human tissues, suggests that this gene might be involved in neuronal differentiation. Among the different morbid phenotypes assigned to the region, X-linked mental retardation would be the best candidate to be associated with this gene.
Pupil Replication (2006)

Pupil Replication is a technique which could be added to many existing high contrast imaging systems to improve the inner working angle or the contrast when using Pupil Replication. The output pupil of the telescope is replicated and mapped onto the input pupil of the high contrast imaging system. This decreases the size of the image of the star on axis and thereby increases the performance of the high contrast imaging system. In this paper the viability of such a system is assessed through mathematical analysis and simulations.
Rice‐Endosperm and Rice‐Bran Proteins: A Review (2018)

Abstract Rice protein is the most preferred protein among all other cereal proteins in terms of its amino acid structure, and it contains the second highest content of lysine, the limiting amino acid in cereals. Processing rough rice into edible rice yields different by‐products including rice bran. Rice‐endosperm and rice‐bran proteins are known to be hypoallergenic, nutritious, and healthful, which gives them high potential in the food‐ingredient industry, especially in gluten‐free preparations and in infant formulas. Multiple methods can be used for the extraction of rice‐endosperm and rice‐bran proteins, including chemical and enzymatic extraction methods. The functional properties, including emulsification, foaming, gelation, and water and oil absorption, of rice‐endosperm and rice‐bran proteins require enhancement before utilizing them in food applications because of their low solubilities, which affects the other functionalities. Enhancement methods include manipulating pH and salt concentration of extracting solvents and selecting specific extraction procedures. Rice‐endosperm and rice‐bran peptides are known to exhibit different bioactivities. These peptides can be generated by different hydrolysis approaches, including the enzymatic, chemical, or microbial assays. Some of the confirmed bioactivities of rice‐endosperm and rice‐bran peptides are the antioxidant, antihypertensive, anticancer, anti‐inflammatory, and antimicrobial activities. These bioactivities increase the potential of rice‐endosperm and rice‐bran proteins to be utilized in food applications, as natural preservatives, or in pharmaceutical applications.
Bleeding complications in oral anticoagulant therapy. An analysis of risk factors (1993)

The risk of anticoagulant therapy in a routine, real-life situation is similar as in the setting of several well-organized clinical trials. The risk of bleeding complications rises significantly with age and with the achieved intensity of anticoagulation, and is dependent on the type of coumarin derivative that is used.
Initial Results on a New Light-Duty 2.7-L Opposed-Piston Gasoline Compression Ignition Multi-Cylinder Engine (2022)

Abstract Gasoline compression ignition (GCI) is a cost-effective approach to achieving diesel-like efficiencies with low emissions. The fundamental architecture of the two-stroke Achates Power Opposed-Piston (OP) Engine enables GCI by decoupling piston motion from cylinder scavenging, allowing for flexible and independent control of cylinder residual fraction and temperature leading to improved low-load combustion. In addition, the high peak cylinder pressure and noise challenges at high-load operation are mitigated by the lower brake mean effective pressure (BMEP) operation and faster heat release for the same pressure rise rate of the OP Engine. These advantages further solidify the performance benefits of the OP Engine and demonstrate the near-term feasibility of advanced combustion technologies, enabled by the opposed-piston architecture. This paper presents initial results from steady-state testing on a brand new 2.7-L OP GCI multi-cylinder engine (MCE) designed for light-duty truck applications. Successful GCI operation calls for a high compression ratio (CR), leading to higher combustion stability at low loads, higher efficiencies, and lower cycle HC + NOX emissions. Initial results show a cycle average brake thermal efficiency (BTE) of 31.7%, which is already greater than 11% conventional engines, after only ten weeks of testing. Emissions results suggest that Tier 3 Bin 160 levels can be achieved using a traditional diesel after-treatment system. Combustion noise was well controlled at or below the United States Council for Automotive Research limits. In addition, initial results on catalyst light-off mode with GCI are also presented.
A Title IX Challenge (2000)

RETURN TO ISSUEPREVEditorialNEXTA Title IX ChallengeThis guest editorial marking Women's History Month is by Debra R. Rolison, who heads Advanced Electrochemical Materials at the Naval Research Laboratory. She received a B.S. in chemistry from Florida Atlantic University in 1975 and a Ph.D. in chemistry from the University of North Carolina, Chapel Hill, in 1980DEBRA R. ROLISONView Author Information Naval Research LaboratoryCite this: Chem. Eng. News 2000, 78, 11, 5Publication Date (Print):March 13, 2000Publication History Published online12 November 2010Published inissue 13 March 2000https://pubs.acs.org/doi/10.1021/cen-v078n011.p005https://doi.org/10.1021/cen-v078n011.p005editorialACS PublicationsCopyright © 2000 American Chemical Society. This publication is available under these Terms of Use. This publication is free to access through this site. Learn MoreArticle Views103Altmetric-Citations-LEARN 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 PDF (659 KB) Get e-Alerts
Study of mutual and self-thermal resistance in 90nm SiGe HBTs (2013)

Impact of mutual thermal coupling on the performance of a single 90nm SiGe heterojunction bipolar transistor (HBT) due to the presence of power dissipating elements like other HBTs in near vicinity is presented in this paper. Mutual thermal resistance (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th,mutual</sub> ) has been computed as a function of spacing between the single HBT and a ring of HBTs surrounding the device. HBT structural design variations including device layout schemes, metal wire stack connected to the emitter, deep trench (DT) depth and emitter to DT spacing, for reduced self thermal resistance (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ), have been explored in this paper. An updated thermal resistance model accounting for the heat flow through the metal wiring stack connected to the emitter is also reported.
Depth-dependent porous silicon photoluminescence (1993)

Porous silicon showing a two-layer structure is studied by stepwise peeling the surface layer to clarify the nonuniformity in photoluminescence (PL) emission as a function of depth. The upper layer is amorphous and luminesces at higher energy and efficiency. The deeper the depth or the lower the excitation energy Eex, the lower the PL peak Ep; but, at a low Eex, Ep is not sensitive to the depth. Both intrinsic PL emission and the variation of penetration depth with Eex contribute to the linear dependence of Ep on Eex, which is in contrast to the cases of a-Si:H and siloxene exhibiting thermalization gaps. The total PL excitation spectrum, the integrated PL intensities versus Eex, saturates rather than exhibiting a peak. Its leading edge profile is similar to that for the absorption spectrum, unchanged by the depth, and described by an Urbach tail with energy of 0.26 eV, which is 4–5 times larger than that of a-Si:H. The results can be understood based on silicon clusters embedded in amorphous silicon incorporating oxygen and/or hydrogen.
Loss-based estimation with cross-validation (2003)

Current statistical inference problems in genomic data analysis involve parameter estimation for high-dimensional multivariate distributions, with typically unknown and intricate correlation patterns among variables. Addressing these inference questions satisfactorily requires: (i) an intensive and thorough search of the parameter space to generate good candidate estimators; (ii) an approach for selecting an optimal estimator among these candidates; and (iii) a method for reliably assessing the performance of the resulting estimator. We propose a unified loss-based methodology for estimator construction, selection, and performance assessment with cross-validation. In this approach, the parameter of interest is defined as the risk minimizer for a suitable loss function and candidate estimators are generated using this (or possibly another) loss function. Cross-validation is applied to select an optimal estimator among the candidates and to assess the overall performance of the resulting estimator. This general estimation framework encompasses a number of problems which have traditionally been treated separately in the statistical literature, including multivariate outcome prediction and density estimation based on either uncensored or censored data. This article provides an overview of the methodology and describes its application to the prediction of biological and clinical outcomes (possibly censored) using microarray gene expression measures.
Oxidation study of Ge Condensation on SGOI Nanowire Biosensor Fabrication (2013)

The Ge condensation method is effective in increasing the Ge fraction of Ge in SGOI. Previous studies by the authors confirmed a correlation between the Ge fraction and the sensitivity of the SiGe nano-wire sensor. To understand how Ge condensation on an SGOI nano-wire sensor helps to optimize oxidation conditions and sensitivity, the effect of oxidizing gas and the SiGe/α-Si stacked structure on the movement of Ge is investigated. The analytical results reveal that the sensitivity of SiGe nano-wires can be optimized by stacking an Si1-xGex layer that contains 14% Ge on a 200 Å-thick α-Si layer and treating the stack with O2 gas diluted by 13% N2 for 3 min.
The impact of optional type information on jit compilation of dynamically typed languages (2011)

Optionally typed languages enable direct performance comparisons between untyped and type annotated source code. We present a comprehensive performance evaluation of two different JIT compilers in the context of ActionScript, a production-quality optionally typed language. One JIT compiler is optimized for quick compilation rather than JIT compiled code performance. The second JIT compiler is a more aggressively optimizing compiler, performing both high-level and low-level optimizations.