gebhart/patrepeval huggingface dataset:
The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis (2002)

The HNH motif was originally identified in the subfamily of HNH homing endonucleases, which initiate the process of the insertion of mobile genetic elements into specific sites. Several bacteria toxins, including colicin E7 (ColE7), also contain the 30 amino acid HNH motif in their nuclease domains. In this work, we found that the nuclease domain of ColE7 (nuclease-ColE7) purified from Escherichia coli contains a one-to-one stoichiometry of zinc ion and that this zinc-containing enzyme hydrolyzes DNA without externally added divalent metal ions. The apo-enzyme, in which the indigenous zinc ion was removed from nuclease-ColE7, had no DNase activity. Several divalent metal ions, including Ni2+, Mg2+, Co2+, Mn2+, Ca2+, Sr2+, Cu2+ and Zn2+, re-activated the DNase activity of the apo-enzyme to various degrees, however higher concentrations of zinc ion inhibited this DNase activity. Two charged residues located at positions close to the zinc-binding site were mutated to alanine. The single-site mutants, R538A and E542A, showed reduced DNase activity, whereas the double-point mutant, R538A + E542A, had no observable DNase activity. A gel retardation assay further demonstrated that the nuclease-ColE7 hydrolyzed DNA in the presence of zinc ions, but only bound to DNA in the absence of zinc ions. These results demonstrate that the zinc ion in the HNH motif of nuclease-ColE7 is not required for DNA binding, but is essential for DNA hydrolysis, suggesting that the zinc ion not only stabilizes the folding of the enzyme, but is also likely to be involved in DNA hydrolysis.
Modeling of substrate noise injected by digital libraries (2002)

Switching noise is one of the major sources of timing errors and functional hazards in logic circuits. It is caused by the cumulative effect of microscopic spurious currents arising in all devices during logic transitions. These currents are injected into the substrate and in supply lines, resulting in significant ripple noise. Individually, such micro-currents do not usually cause catastrophic failures. However, cumulatively, they can impact power supply and substrate potential across the chip. Thus, the electrical behavior of sensitive digital and analog circuits can be significantly changed, hence limiting circuit performance. The analysis of switching noise at a macroscopic level requires one to accurately compute models for all microscopic spurious currents, known as noise signatures. The challenge is to simultaneously account for a myriad of parameters and their process variations in a compact and accurate model. To address this problem, a new methodology based on response surface methodology and orthogonal polynomial approximation is proposed. Experimental results on a 0.35 /spl mu/m library show that the methodology is capable of accurately approximating noise signatures with a single analytical formula. A library of such formulae has been created and it is being used to accurately characterize switching noise at the macroscopic level.
Chemical and Mutagenic Investigations of Fatty Acid Amide Hydrolase:  Evidence for a Family of Serine Hydrolases with Distinct Catalytic Properties (1999)

Fatty acid amide hydrolase (FAAH) is a membrane-bound enzyme responsible for the catabolism of neuromodulatory fatty acid amides, including anandamide and oleamide. FAAH's primary structure identifies this enzyme as a member of a diverse group of alkyl amidases, known collectively as the "amidase signature family". At present, this enzyme family's catalytic mechanism remains poorly understood. In this study, we investigated the catalytic features of FAAH through mutagenesis, affinity labeling, and steady-state kinetic methods. In particular, we focused on the respective roles of three serine residues that are conserved in all amidase signature enzymes (S217, S218, and S241 in FAAH). Mutation of each of these serines to alanine resulted in a FAAH enzyme bearing significant catalytic defects, with the S217A and S218A mutants showing 2300- and 95-fold reductions in k(cat), respectively, and the S241A mutant exhibiting no detectable catalytic activity. The double S217A:S218A FAAH mutant displayed a 230 000-fold decrease in k(cat), supporting independent catalytic functions for these serine residues. Affinity labeling of FAAH with a specific nucleophile reactive inhibitor, ethoxy oleoyl fluorophosphonate, identified S241 as the enzyme's catalytic nucleophile. The pH dependence of FAAH's k(cat) and k(cat)/K(m) implicated a base involved in catalysis with a pK(a) of 7.9. Interestingly, mutation of each of FAAH's conserved histidines (H184, H358, and H449) generated active enzymes, indicating that FAAH does not contain a Ser-His-Asp catalytic triad commonly found in other mammalian serine hydrolytic enzymes. The unusual properties of FAAH identified here suggest that this enzyme, and possibly the amidase signature family as a whole, may hydrolyze amides by a novel catalytic mechanism.
Purothionin analogues from barley flour (1969)

Abstract Acid treatment of a light‐petroleum extract of barley flour yielded two proteins (termed hordothionins) closely similar in electrophoretic behaviour to the purqthionin doublet obtained from wheat by the same procedure. The major (faster) component, hordothionin a has been obtained apparently pure. Comparison of its amino acid composition, peptide maps, immunological reactions and C‐terminal end group with those of purothionin a has confirmed the relationship between the proteins from the two genera although some differences in amino acid composition and sequence have been found. Extraction of barley flour with buffered saline followed by acid treatment yielded proteins with similar properties to the hordothionins; this supports previous observations on the relationship between the purothionins and their corresponding globulins.
Monoclonal antibodies against core and cellulose‐binding domains of <i>Trichoderma reesei</i> cellobiohydrolases I and II and endoglucanase I (1991)

Cellulases from Trichoderma reesei form an enzyme group with a common structural organization. Each cellulase enzyme is composed of two functional domains, the core region containing the active site and the cellulose-binding domain (CBD). To facilitate the specific detection of each domain, monoclonal antibodies (mAb) against cellobiohydrolase I (CBHI), cellobiohydrolase II (CBHII) and endoglucanase I (EGI) were produced. Five mAb were obtained against CBHI, ten against CBHII and eight against EGI. The location of the antigenic epitope for each antibody was mapped by allowing the antibodies to react with truncated cellulases, synthesized from deleted cDNA in Saccharomyces cerevisiae. Proteolytic fragments of Trichoderma cellulases, obtained by papain digestion, were used to confirm the results. Specific antibodies were detected against the core and the CBD epitopes for all three cellulases. Using the truncated enzymes, it was possible to locate the epitopes to a reasonably short region within the protein. To obtain a quantitative assay for each enzyme, a specific mAb against each antigen was chosen, based on the affinity to the corresponding antigen on Western-blot staining and on filter blots of the cellulolytic yeasts. The mAb were used to quantitative the corresponding enzymes in T. reesei culture medium. Specific quantitation of each cellulase enzyme has not been possible by biochemical assays or using polyclonal antibodies, due to their cross-reactions. Now, these mAb can be specifically used to recognize and quantitate different domains of these three important cellulolytic enzymes.
Cloning of genetic loci involved in endoprotease activity in <i>Streptomyces lividans</i> 66: a novel neutral protease gene with an adjacent divergent putative regulatory gene (1992)

A skimmed-milk clearing assay was used to identify, in a multicopy Streptomyces lividans 66 genomic library, DNA fragments that lead to increased expression of protease activity in S. lividans 66. Three independent loci were identified. The majority class (slpA, which represented 68 of 71 clones) produced large zones of clearing. Two other classes (designated slpB and slpC) showed smaller zones than slpA. Subcloning and deletion analysis of the slpA locus delineated the relevant DNA to within a 2.5 kilobase pair fragment. DNA sequence analysis revealed a structural gene associated with the appearance of an extracellular protein in the culture medium. The derived amino acid sequence indicated the presence of a zinc-binding motif, which was previously noted to be characteristic of metalloprotease enzymes. However, the relatively small size of the protein (apparent molecular weight 20,000-24,000) suggests that it represents a novel class of neutral proteases distinct from the thermolysin-type enzymes. An adjacent divergent open reading frame was identified and shown to cause a significant increase in protease activity when present together with the protease structural gene on a multicopy plasmid in S. lividans 66. The derived amino acid sequence of this open reading frame showed homology with previously characterized regulatory proteins of the LysR family of transcriptional regulator proteins.
Tri(3-pyridyl)phosphine as Amphiphilic Ligand in the Rhodium-catalysed Hydroformylation of 1-Hexene (2007)

The molecular structure of carbonylchlorobis(tri(3-pyridyl)phosphine)rhodium, 1, has been determined by X-ray diffraction methods. The N-protonated trifluoromethanesulfonate (triflate) complex 3 was synthesised as a model compound for the extraction of a rhodium complex bearing amphiphilic ligands which can allow catalyst recycling in the hydroformylation of alkenes by using their distribution behavior in organic and aqueous solvents of different pH. The high water-solubility of the employed ligand renders the recycling method as only partly successful due to insufficient extraction from the water phase into the organic phase. In the hydroformylation of 1-hexene the production of n-heptanal is slightly disfavoured when using the ligand tri(3-pyridyl)phosphine as compared to triphenylphosphine which can be ascribed to a higher amount of ligand-deficient active rhodium complexes of the less basic pyridyl phosphine ligand under CO pressure.
Liberation of Solution Gas During Pressure Depletion of Virgin and Watered-Out Oil Reservoirs (1991)

Summary Multipurpose experimental equipment was constructed to investigate the buildup of gas saturation during depressurization of virgin and watered-out oil reservoirs at representative conditions. The measured dependencies of critical gas saturations on gas/oil interfacial tension (IFT), amount of dissolved gas, pressure-decline rate, and structure of the porous medium are discussed. In addition, experimental results indicating significant reductions of waterflood residual oil saturation (ROS) owing to the presence of a gas saturation are presented.
Photodynamic therapy in the treatment of subfoveal choroidal neovascularisation (2001)

Subfoveal choroidal neovascularisation (CNV) is a major cause of visual disability, with age-related macular degeneration (AMD) the commonest cause. Confluent laser to CNV significantly reduces severe visual loss but the profound visual loss after treatment of subfoveal lesions and the high recurrence rate has meant its restriction to extrafoveal lesions. Developed initially as a treatment for cancers, photodynamic therapy (PDT) has been shown to successfully close CNV in the eye. Large international randomised placebo-controlled studies of the safety and efficacy of PDT with verteporfin are under way. The Treatment of Age-related Macular Degeneration with Photodynamic Therapy (TAP) study has demonstrated a reduction of visual loss in treated patients with any classic CNV. Subgroup analysis showed a greater benefit in predominantly classic lesions (p < 0.001, NNT: 3.6), increasing further for lesions with no occult component, roughly equivalent to pure classic (p < 0.01, NNT: 2.2) A significant benefit at 12 months has been shown in patients with CNV secondary to myopia in the Verteporfin in AMD (VIP) trial, but no benefit in pure occult lesions. Further research is required to establish cost-effectiveness and appropriate referral patterns in the UK and optimise treatment strategies. Further data are awaited from TAP/VIP. At present verteporfin PDT is indicated in eyes with subfoveal predominantly classic CNV secondary to AMD with visual acuity of 6/60 or better and lesions < 5,400 microm in diameter. Juxtafoveal lesions meeting the above criteria and CNV secondary to pathological myopia should also be considered for treatment. The efficacy of treatment of larger lesions, juxtapapillary CNV, occult/no classic with high-risk characteristics (HRC) and CNV from other causes remains unclear. The treatment of minimally classic lesions and those with occult/no classic without HRC is not indicated.
In Vitro Investigation of Enhanced Hemocompatibility and Endothelial Cell Proliferation Associated with Quinone-Rich Polydopamine Coating (2013)

Recent investigations have demonstrated that polydopamine (PDA)-modified surfaces were beneficial to the proliferation of endothelial cells (ECs). In this work, PDA coated 316L stainless steels (316L SS) were thermally treated at 50, 100, and 150 °C respectively (hereafter designated as Th50, Th100, and Th150) and consequently produced diverse surface chemical components. In vitro hemocompatibility and vascular cell-material interactions with ECs and smooth muscle cells (SMCs) affected by surface characteristics have been investigated. The Th150, rich in quinone, showed the best hemocompatibility and could effectively inhibit platelet adhesion, activation, and fibrinogen conformation transition. The polydopamine-modified surfaces were found to induce dramatic cell-material interaction with enhanced ECs proliferation, viability and migration, release of nitric oxide (NO), and reduced SMCs proliferation. The inhibitory effect of SMCs proliferation might be associated with the surface catechol content. The coating on Th150 showed a good resistance to the deformation of compression and expansion of vascular stents. These results effectively suggested that the Th150 coating might be promising when served as a stent coating platform.
<i>In vitro</i> Selection and Characterization of HIV-1 with Reduced Susceptibility to PMPA (1999)

9-(2-phosphonomethoxypropyl)adenine (PMPA) has demonstrated remarkable anti-simian immunodeficiency virus (SIV) activity in macaque models of SIV infection and transmission prevention. Recently, PMPA and its oral prodrug, bis-POC PMPA, have also shown potent anti-human immunodeficiency virus type 1 (HIV-1) activity in Phase I clinical studies. In vitro experiments were performed to address the resistance properties of PMPA. After eight passages in increasing concentrations of PMPA, HIV-1IIIB was able to grow in the presence of 2 microM PMPA, fivefold above the IC50 of PMPA for wild-type parental virus. Sequence analysis of the reverse transcriptase (RT) genes from four of 15 RT clones demonstrated the presence of a K65R substitution in RT and recombinant HIV expressing the K65R RT mutation showed a threefold to fourfold increase in IC50 value for PMPA as compared to wild-type. Additional experiments demonstrated that viruses expressing other nucleoside-associated RT resistance mutations all showed wild-type or < threefold reduced susceptibility to PMPA in vitro. Interestingly, lamivudine-resistant viruses expressing the M184V RT mutation showed wild-type to slightly increased susceptibility to PMPA in vitro and addition of the M184V mutation to HIV with the K65R mutation resulted in reversion to wild-type susceptibility for PMPA. In agreement with the cell culture findings, Escherichia coli-expressed K65R RT showed fivefold reduced susceptibility to PMPA diphosphate, the active moiety of PMPA. Furthermore, in combination experiments, PMPA with hydroxyurea showed synergistic inhibition of HIV replication in vitro. The potent antiretroviral activity and favourable resistance profile of PMPA and bis-POC PMPA are being further investigated in ongoing clinical trials.
Plasma-surface kinetics and feature profile evolution in chlorine etching of polysilicon (1998)

Chlorine-based plasma etching of polysilicon was characterized as a function of the impinging Cl+, Cl–to–Cl+ flux ratio, ion bombardment energy, ion bombardment angle, and the flux of etching by-products (SiCl2) using a multiple beam scattering apparatus. The ion-enhanced etching yield was a strong function of the neutral-to-ion flux ratio, and scaled linearly with the square root of the ion energy. The ion-enhanced etching yield was independent of the ion bombardment angle at near normal ion incidence angles, but decreased almost linearly above 40° off-normal angles. The presence of SiCl2 greatly suppressed the etching of polysilicon by either Cl+ or Cl+ with Cl. A Monte Carlo based profile simulator was constructed which incorporated the dominant reaction mechanisms of surface chlorination under ion bombardment, surface re-emission, and ion reflection. The profile evolution of patterned samples etched by Cl and Cl+ beams were simulated. Quantitatively good agreement was found between the simulated profiles and the measured profiles. A sensitivity analysis of the recombination probability of Cl on photoresist suggested that the recombination of atomic chlorine on the photoresist had a significant impact on the profile evolution.
Point mutations within the betaG-betaH loop of foot-and-mouth disease virus O1K affect virus attachment to target cells (1997)

The amino acid sequence Arg-Gly-Asp (RGD) is a highly conserved region located on the P1D protein of most sero- and subtypes of foot-and-mouth disease virus (FMDV)and participates in binding of FMDV to their target cells. In order to analyze the role of the RGD sequence in FMDV infection of cells in more detail, 13 mutations within or near the RGD sequence of virus type O1Kaufbeuren were designed by using a full-length cDNA plasmid. Transfection of baby hamster kidney cells (BHK-21) with in vitro-transcribed cRNAs containing mutations bordering the RGD sequence led to the production of infectious virus in most cases. In contrast, almost all of the mutants containing changes within the RGD sequence produced noninfectious viral particles indistinguishable from wild-type virus by electron microscopy. In order to demonstrate that these noninfectious progeny from the RGD mutants were defective only in their cell adsorption, the respective cRNAs were cotransfected together with a cRNA expressing the wild-type P1 protein. The resulting virus particles were able to infect BHK-21 cells. These results demonstrate the important role of the RGD sequence in FMDV binding to cells but also emphasize the influence of other amino acids in the bordering region.
A Half Adder Based on a Photochemically Driven [2]Rotaxane (2005)

A molecular abacus: In a [2]rotaxane that mimicks a half adder with distinct AND and XOR logic gates, all the inputs (I) and outputs (O) are photochemical (see scheme; F=fluorescence, A=absorbance). Reversible E→Z photoisomerization about two double bonds (shown in red and dark blue) in the thread molecule leads to four conformers that have different spectral properties. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501215_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Principal component transforms of triaxial recordings by singular value decomposition (1991)

Abstract Polarization analysis can be achieved efficiently by treating a time window of a single-station triaxial recording as a matrix and doing a singular value decomposition (SVD) of this seismic data matrix. SVD of the triaxial data matrix produces an eigenanalysis of the data covariance (cross-energy) matrix and a rotation of the data onto the directions given by the eigenanalysis (Karhunen-Loeve transform), all in one step.SVD provides a complete principal components analysis of the data in the analysis time window. Selection of this time window is crucial to the success of the analysis and is governed by three considerations: the window should contain only one arrival; the window should be such that the signal-to-noise ratio is maximized; and the window should be long enough to be able to discriminate random noise from signal. The SVD analysis provides estimates of signal, signal polarization directions, and noise. An F-test is proposed which gives the confidence level for the hypothesis of rectilinear polarization.This paper illustrates the analysis and interpretation of synthetic rectilinearly and elliptically polarized arrivals at a single triaxial station by SVD.
Single-particle tunneling in semiconductor quantum dots (2001)

We present a calculation of single-charge tunneling in a semiconductor quantum dot based on a full self-consistent tight-binding calculation of the charging energies, applicable to quantum dots of realistic size (up to 8 nm diameter). Comparison with recent tunneling spectroscopy experiments on InAs nanocrystals shows excellent agreement and allows an unambiguous assignation of the conductance peaks. For bias voltages V larger that the band gap of the quantum dot we show that both electrons and holes can tunnel into the quantum dot, leading to specific features in the $I(V)$ curves.
Purines Are Required at the 5′ Ends of Newly Initiated RNAs for Optimal RNA Polymerase III Gene Expression (1996)

We have made specific alterations in the CAACAA element at the transcription start site of a Saccharomyces cerevisiae suppressor tRNA gene. The mutant genes were tested for their ability to suppress the ochre nonsense alleles ade2-1, lys4-1, and met4-1. Many of the mutants showed either no phenotypic change or a weak loss of suppression relative to that of SUP4-o. A 2-bp change, CTCCAA, which alters bases encoding the +1 and +2 nucleotides of pre-tRNA Tyr, had a strong deleterious effect in vivo, as did the more extensive change CTCCTC. In contrast, mutant genes bearing each of the possible single changes at nucleotide +1 retained normal suppression levels. The transcription start point could be shifted in a limited fashion in response to the specific sequences encountered by RNA polymerase III at the start site. ATP was preferentially utilized as the 5' nucleotide in the growing RNA chain, while with start site sequences that precluded utilization of a purine, CTP was greatly preferred to UTP as the +1 nucleotide. Short oligopyrimidine RNAs formed on the CTCCTC allele could be repositioned in the active center of the newly formed ternary complex. Early postinitiation complexes containing short nascent RNAs formed on the CTCCTC mutant were more sensitive to the effects of heparin and produced more abortive transcripts than similar complexes formed on SUP4-o. Our results suggest that the purine-rich sequences at the 5' ends of the nascent transcripts of many genes act to stabilize the early ternary complex.