gebhart/patrepeval huggingface dataset:
Chemically Sensitive Resistors Based on Monolayer‐Capped Cubic Nanoparticles: Towards Configurable Nanoporous Sensors (2009)

Cube roots: Chemiresistors based on cubic monolayer-capped nanoparticles (MCNPs) produce a higher electrical response upon exposure to volatile organic compounds than those based on spherical MCNPs. These observations are explained in terms of the higher swellability of cubic MCNPs compared to spherical MCNPs (see picture).
α-Ketoacids Are Potent Slow Binding Inhibitors of the Hepatitis C Virus NS3 Protease (2000)

The replication of the hepatitis C virus (HCV), an important human pathogen, crucially depends on the proteolytic maturation of a large viral polyprotein precursor. The viral nonstructural protein 3 (NS3) harbors a serine protease domain that plays a pivotal role in this process, being responsible for four out of the five cleavage events that occur in the nonstructural region of the HCV polyprotein. We here show that hexapeptide, tetrapeptide, and tripeptide alpha-ketoacids are potent, slow binding inhibitors of this enzyme. Their mechanism of inhibition involves the rapid formation of a noncovalent collision complex in a diffusion-limited, electrostatically driven association reaction followed by a slow isomerization step resulting in a very tight complex. pH dependence experiments point to the protonated catalytic His 57 as an important determinant for formation of the collision complex. K(i) values of the collision complexes vary between 3 nM and 18.5 microM and largely depend on contacts made by the peptide moiety of the inhibitors. Site-directed mutagenesis indicates that Lys 136 selectively participates in stabilization of the tight complex but not of the collision complex. A significant solvent isotope effect on the isomerization rate constant is suggestive of a chemical step being rate limiting for tight complex formation. The potency of these compounds is dominated by their slow dissociation rate constants, leading to complex half-lives of 11-48 h and overall K(i) values between 10 pM and 67 nM. The rate constants describing the formation and the dissociation of the tight complex are relatively independent of the peptide moiety and appear to predominantly reflect the intrinsic chemical reactivity of the ketoacid function.
Emergence of human immunodeficiency virus type 1 variants with resistance to multiple dideoxynucleosides in patients receiving therapy with dideoxynucleosides. (1995)

A set of mutations [Ala-62-->Val(A62V), V75I, F77L, F116Y, and Q151M] in the polymerase domain of reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) confers on the virus a reduced sensitivity to multiple antiretroviral dideoxynucleosides and has been seen in HIV-1 variants isolated from patients receiving combination chemotherapy with 3'-azido-3'-deoxythymidine (AZT) plus 2',3'-dideoxycytidine (ddC) or 2',3'-dideoxyinosine (ddI). The IC50 values of AZT, ddC, ddI, 2',3'-dideoxyguanosine, and 2',3'-didehydro-3'-deoxythymidine against an infectious clone constructed to include the five mutations were significantly higher than those of a wild-type infectious clone. The K1 value for AZT 5'-triphosphate determined for the virus-associated RT from a posttherapy strain was 35-fold higher than that of RT from a pretherapy strain. Detailed analysis of HIV-1 strains isolated at various times during therapy showed that the Q151M mutation developed first in vivo, at the time when the viremia level suddenly increased, followed by the F116Y and F77L mutations. All five mutations ultimately developed, and the viremia level rose even further. Analyses based on the three-dimensional structure of HIV-1 RT suggest that the positions where at least several of the five mutations occur are located in close proximity to the proposed dNTP-binding site of RT and the first nucleotide position of the single-stranded template.
A Synthetic Pentasaccharide for the Prevention of Deep-Vein Thrombosis after Total Hip Replacement (2001)

A synthetic pentasaccharide, Org31540/SR90107A, has the potential to improve significantly the risk-benefit ratio for the prevention of venous thromboembolism, as compared with low-molecular-weight heparin.
Stepwise Regeneration and Recovery of Deoxyribonucleoside Phosphoramidite Monomers During Solid-Phase Oligonucleotide Synthesis (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStepwise Regeneration and Recovery of Deoxyribonucleoside Phosphoramidite Monomers During Solid-Phase Oligonucleotide SynthesisCarlo L. Scremin, Liang Zhou, Kasturi Srinivasachar, and Serge L. BeaucageCite this: J. Org. Chem. 1994, 59, 8, 1963–1966Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://doi.org/10.1021/jo00087a005RIGHTS & PERMISSIONSArticle Views232Altmetric-Citations18LEARN 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 PDF (410 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Molecular Basis for Anaerobic Growth of Saccharomyces cerevisiae on Xylose, Investigated by Global Gene Expression and Metabolic Flux Analysis (2004)

Yeast xylose metabolism is generally considered to be restricted to respirative conditions because the two-step oxidoreductase reactions from xylose to xylulose impose an anaerobic redox imbalance. We have recently developed, however, a Saccharomyces cerevisiae strain that is at present the only known yeast capable of anaerobic growth on xylose alone. Using transcriptome analysis of aerobic chemostat cultures grown on xylose-glucose mixtures and xylose alone, as well as a combination of global gene expression and metabolic flux analysis of anaerobic chemostat cultures grown on xylose-glucose mixtures, we identified the distinguishing characteristics of this unique phenotype. First, the transcript levels and metabolic fluxes throughout central carbon metabolism were significantly higher than those in the parent strain, and they were most pronounced in the xylose-specific, pentose phosphate, and glycerol pathways. Second, differential expression of many genes involved in redox metabolism indicates that increased cytosolic NADPH formation and NADH consumption enable a higher flux through the two-step oxidoreductase reaction of xylose to xylulose in the mutant. Redox balancing is apparently still a problem in this strain, since anaerobic growth on xylose could be improved further by providing acetoin as an external NADH sink. This improved growth was accompanied by an increased ATP production rate and was not accompanied by higher rates of xylose uptake or cytosolic NADPH production. We concluded that anaerobic growth of the yeast on xylose is ultimately limited by the rate of ATP production and not by the redox balance per se, although the redox imbalance, in turn, limits ATP production.
Escherichia coli mutS-encoded protein binds to mismatched DNA base pairs. (1986)

The Escherichia coli mutS gene product is involved in mismatch correction in this organism. We have purified a biologically active form of the 97,000 Mr protein to near homogeneity from an overproducing strain. Enzymatic and chemical protection ("footprinting") experiments have demonstrated that mutS-encoded protein specifically binds to DNA regions containing a single base-pair mismatch. The protein displayed variable affinity for the limited set of mismatches tested (G-T greater than G-A approximately equal to A-C greater than T-C).
Electrokinetic Phenomena and Zeta Potential (2012)

This chapter contains sections titled: Stern–Grahame Model of the Double Layer Calculation of Zeta Potential from Particle Mobility Measurement of Electrophoretic Mobility and Zeta Potential Electroacoustic Methods References
Carbon Monoxide Generated by Heme Oxygenase-1 Suppresses the Rejection of Mouse-to-Rat Cardiac Transplants (2001)

Mouse-to-rat cardiac transplants survive long term after transient complement depletion by cobra venom factor and T cell immunosuppression by cyclosporin A. Expression of heme oxygenase-1 (HO-1) by the graft vasculature is critical to achieve graft survival. In the present study, we asked whether this protective effect was attributable to the generation of one of the catabolic products of HO-1, carbon monoxide (CO). Our present data suggests that this is the case. Under the same immunosuppressive regimen that allows mouse-to-rat cardiac transplants to survive long term (i.e., cobra venom factor plus cyclosporin A), inhibition of HO-1 activity by tin protoporphyrin, caused graft rejection in 3--7 days. Rejection was associated with widespread platelet sequestration, thrombosis of coronary arterioles, myocardial infarction, and apoptosis of endothelial cells as well as cardiac myocytes. Under inhibition of HO-1 activity by tin protoporphyrin, exogenous CO suppressed graft rejection and restored long-term graft survival. This effect of CO was associated with inhibition of platelet aggregation, thrombosis, myocardial infarction, and apoptosis. We also found that expression of HO-1 by endothelial cells in vitro inhibits platelet aggregation and protects endothelial cells from apoptosis. Both these actions of HO-1 are mediated through the generation of CO. These data suggests that HO-1 suppresses the rejection of mouse-to-rat cardiac transplants through a mechanism that involves the generation of CO. Presumably CO suppresses graft rejection by inhibiting platelet aggregation that facilitates vascular thrombosis and myocardial infarction. Additional mechanisms by which CO overcomes graft rejection may involve its ability to suppress endothelial cell apoptosis.
Crystal structure of Staphylococcus aureus tyrosyl‐tRNA synthetase in complex with a class of potent and specific inhibitors (2001)

SB-219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl-tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl-tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital-acquired infections. The full-length enzyme yielded crystals that diffracted to 2.8 A resolution, but a truncated version of the enzyme allowed the resolution to be extended to 2.2 A. These inhibitors not only occupy the known substrate binding sites in unique ways, but also reveal a butyl binding pocket. It was reported that the Bacillus stearothermophilus TyrRS T51P mutant has much increased catalytic activity. The S. aureus enzyme happens to have a proline at position 51. Therefore, our structures may contribute to the understanding of the catalytic mechanism and provide the structural basis for designing novel antimicrobial agents.
Avaliação bacteriológica de carne suína (carré = "Longissimus dorsi + base óssea") comercializada em Niterói e São Gonçalo, Estado do Rio de Janeiro, Brasil (1998)

O presente trabalho procurou avaliar as condies higinico-sanitrias de como comercializada a carne suna (carr) em Niteri e So Gonalo, Estado do Rio de Janeiro. Foram adquiridas 30 amostras de carne suna em diversos aougues dos municpios citados e submetidas s seguintes anlises bacteriolgicas: contagem de bactrias heterotrficas aerbias mesfilas viveis; contagem de bactrias heterotrficas psicrotrficas viveis; enumerao de coliformes fecais; isolamento e identificao de Escherichia co/i e contagem, isolamento e identificao de Staphylococcus aureus. Os resultados obtidos foram confrontados com os padres vigentes da legislao nacional e/ou com aqueles sugeridos por autores da bibliografia consultada. Na contagem de bactrias mesfila viveis 1 O amostras (33,3%) apresentaram valores superiores a 1 os UFCs/g; na contagem de bactrias psicrotrficas viveis 8 amostras (26,6%) apresentaram valores superiores a 1 0 6 UFCs/g que, segundo os Padres Bacteriolgicos dos Alimentos Portugueses citados em Ribeiro(1974), teriam extrapolado os limites mximos de 1 os UFCs/g e 10 6 UFCs/g respectivamente. Para a contagem de coliformes fecais e E. co/i 11 amostras (36, 7%) foram classificadas como produto imprprio para consumo segundo a portaria 001 da Diviso Nacional de Alimentos Com relao contagem
Natural and synthetic modulators of SK (Kca2) potassium channels inhibit magnesium‐dependent activity of the kinase‐coupled cation channel TRPM7 (2012)

This study reveals a tight overlap in the pharmacological profiles of TRPM7 and K(Ca)2.1-2.3 channels. NS8593 acts as a negative gating modulator of TRPM7 and is well-suited to study functional features and cellular roles of endogenous TRPM7.
Scalable and Robust Randomized Benchmarking of Quantum Processes (2011)

In this Letter we propose a fully scalable randomized benchmarking protocol for quantum information processors. We prove that the protocol provides an efficient and reliable estimate of the average error-rate for a set operations (gates) under a very general noise model that allows for both time and gate-dependent errors. In particular we obtain a sequence of fitting models for the observable fidelity decay as a function of a (convergent) perturbative expansion of the gate errors about the mean error. We illustrate the protocol through numerical examples.
Generic Routing Encapsulation (GRE) (2000)

This document specifies a protocol for encapsulation of an arbitrary network layer protocol over another arbitrary network layer protocol.
Equilibrium of a liquid in a spherical shell caused by gravity, surface tension, and van der Waals forces (1985)

A rigorous proof is presented which shows that the classical Young–Laplace equation cannot predict a continuous liquid layer inside a spherical-shell container. An augmented Young–Laplace equation is in turn derived to describe the equilibrium profiles of a continuous liquid hydrogen layer inside a spherical-shell inertial fusion target. The augmentation is achieved by adding to the total free energy a term originating from the attractive intermolecular forces of the van der Waals type.
Targeted developmental overexpression of calmodulin induces proliferative and hypertrophic growth of cardiomyocytes in transgenic mice. (1993)

Calmodulin (CaM) levels are developmentally regulated in the mouse heart. During late gestational and early postnatal stages, CaM levels decline several-fold in close temporal association with the declining population of proliferating cardiomyocytes. This correlation suggests that CaM may influence cardiomyocyte cell cycle activity, particularly since CaM is implicated in cell cycle control in several eukaryotic nonmuscle cells. To test this possibility, nucleotides -500 to 77 of the human atrial natriuretic factor gene were linked to a chicken CaM minigene to establish two pedigrees of transgenic mice that express 3- to 5-fold increased levels of CaM in cardiomyocytes. Developmental overexpression of CaM in mouse cardiomyocytes produced a markedly exaggerated cardiac growth response, characterized by the presence of cardiomyocyte hypertrophy in regions demonstrated to overexpress CaM and by cardiomyocyte hyperplasia, apparent at early developmental stages. Early postnatal suppression of fusion gene expression in the cardiac ventricles correlated with regression of the ventricular growth response in transgenic relative to nontransgenic mice between 3 days and 6-10 weeks of age, but was not apparent in the cardiac atria, where levels of CaM remained constitutively elevated until advanced stages. To test the possibility that increased cytosolic Ca2+ buffering contributes to the growth response induced by CaM over-expression, two additional lines of transgenic mice were generated using the same human atrial natriuretic factor promoter to target expression of a CaM mutant (amino acids 75-82 deleted) in cardiomyocytes. This mutant has previously been shown to bind Ca2+ with kinetic properties similar to those of wild-type CaM, but was unable to activate several CaM-dependent target enzymes in vitro. Despite high level expression of the CaM mutant, no growth response was apparent in the hearts of transgenic relative to those of nontransgenic mice, suggesting that increased Ca2+ buffering is unlikely to contribute to the growth response induced by CaM overexpression. Taken together, these findings reveal that cardiomyocyte growth regulation is specifically influenced by CaM concentrations in transgenic mice.
Fluorometric Detection of Ca2+ Based on an Induced Change in the Conformation of Sol−Gel Entrapped Parvalbumin (1998)

We report the development of a fluorometric detection strategy for Ca(2+) based on induced changes in the conformation of cod III parvalbumin entrapped within a sol-gel processed glass. The detection scheme utilizes a fluorescent allosteric signal transduction (FAST) strategy wherein conformational changes induced by Ca(2+) binding result in alterations in the intrinsic fluorescence from the single tryptophan residue at position 102. Intrinsic fluorescence was also used to examine chemically induced changes in protein structure to ascertain the effects of entrapment on the conformational motions and stability of the protein. Fluorescence analysis indicated that the behavior of the protein depended on the entrapment protocols used. The entrapped protein retained conformational flexibility similar to that observed in solution and remained accessible to analytes such as Ca(2+). Entrapment also caused improvements in protein stability against chemical denaturants. However, entrapment caused the apparent affinity constant for binding of Ca(2+) to decrease substantially with aging time. Even so, in optimum cases, fluorometric detection of Ca(2+) could be done over a 600 μM range with a limit of detection of 3 μM and with no interference from divalent ions such as Mg(2+), Sr(2+), or Cd(2+), indicating the viability of using sol-gel entrapped FAST proteins for the detection of Ca(2+).
Modification of Seed Oil Composition in Arabidopsis by Artificial microRNA-Mediated Gene Silencing (2012)

Various post transcriptional gene silencing strategies have been developed and exploited to study gene function or engineer disease resistance. The recently developed artificial microRNA strategy is an alternative method of effectively silencing target genes. The Δ12-desaturase (FAD2), Fatty acid elongase (FAE1), and Fatty acyl-ACP thioesterase B (FATB) were targeted with amiR159b-based constructs in Arabidopsisthaliana to evaluate changes in oil composition when expressed with the seed-specific Brassica napus truncated napin (FP1) promoter. Fatty acid profiles from transgenic homozygous seeds reveal that the targeted genes were silenced. The down-regulation of the AtFAD-2 gene substantially increased oleic acid from the normal levels of ∼15% to as high as 63.3 and reduced total PUFA content (18:2(Δ9,12) + 18:3(Δ9,12,15) + 20:2(Δ11,14) + 20:3(Δ11,14,17)) from 46.8 to 4.8%. Δ12-desaturase activity was reduced to levels as low as those in the null fad-2-1 and fad-2-2 mutants. Silencing of the FAE1 gene resulted in the reduction of eicosenoic acid (20:1(Δ11)) to 1.9 from 15.4% and silencing of FATB resulted in the reduction of palmitic acid (16:0) to 4.4% from 8.0%. Reduction in FATB activity is comparable with a FATB knock-out mutant. These results demonstrate for the first time amiR159b constructs targeted against three endogenous seed-expressed genes are clearly able to down-regulate and generate genotypic changes that are inherited stably over three generations.
Electroluminescence of a cubic GaN/GaAs (001) p–n junction (2000)

A cubic GaN p–n diode has been grown on n-type GaAs (001) substrates by plasma assisted molecular epitaxy. For p- and n-type doping, elemental Mg and Si beams have been used, respectively. The optical properties are characterized by photoluminescence at room temperature and 2 K. Current–voltage and capacitance–voltage measurements of the cubic GaN n+–p junction are performed at room temperature. The electroluminescence at 300 K is measured through a semitransparent Au contact. A peak emission at 3.2 eV with a full width at half maximum as narrow as 150 meV is observed, indicating that near-band edge transitions are the dominating recombination processes in our device. A linear increase of the electroluminescence intensity with increasing current density is measured.
Iterative Optimization and Simplification of Hierarchical Clusterings (1996)

Clustering is often used for discovering structure in data. Clustering systems differ in the objective function used to evaluate clustering quality and the control strategy used to search the space of clusterings. Ideally, the search strategy should consistently construct clusterings of high quality, but be computationally inexpensive as well. In general, we cannot have it both ways, but we can partition the search so that a system inexpensively constructs a `tentative' clustering for initial examination, followed by iterative optimization, which continues to search in background for improved clusterings. Given this motivation, we evaluate an inexpensive strategy for creating initial clusterings, coupled with several control strategies for iterative optimization, each of which repeatedly modifies an initial clustering in search of a better one. One of these methods appears novel as an iterative optimization strategy in clustering contexts. Once a clustering has been constructed it is judged by analysts -- often according to task-specific criteria. Several authors have abstracted these criteria and posited a generic performance task akin to pattern completion, where the error rate over completed patterns is used to `externally' judge clustering utility. Given this performance task, we adapt resampling-based pruning strategies used by supervised learning systems to the task of simplifying hierarchical clusterings, thus promising to ease post-clustering analysis. Finally, we propose a number of objective functions, based on attribute-selection measures for decision-tree induction, that might perform well on the error rate and simplicity dimensions.