gebhart/patrepeval huggingface dataset:
Initial Bubble Collapse Plays a Key Role in the Transition to Elongation in T7 RNA Polymerase (2004)

RNA polymerases bind to specific sequences in DNA, melt open duplex DNA around the start site, and start transcription within the initially melted bubble. The initially transcribing complex is relatively unstable, releasing short abortive products. After synthesis of a minimal length of RNA (approximately 10-12 bases in the T7 system), RNA polymerases complete the transition to a processive (highly stable) elongation phase and lose the initial promoter contacts. The current study strongly supports a model for T7 RNA polymerase in which initial bubble collapse from position -4 to position +3 is responsible for initiating RNA displacement in the transition process. More specifically, collapse of the bubble from position -4 to position -1 indirectly and energetically facilitates the direct strand invasion offered by collapse at positions +1 to +3. Parallel work shows that promoter release, another key event occurring during this stage of transcription, begins after translocation to position +8 and is largely complete upon translocation to about position +12. The timing of promoter release agrees with the timing of initial bubble collapse determined by our previous fluorescence studies, suggesting that these two events are closely related.
Interaction of phytate with mustard 12S protein (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteraction of phytate with mustard 12S proteinN. V. Kishore Kumar Murthy and M. S. Narasinga RaoCite this: J. Agric. Food Chem. 1984, 32, 3, 493–498Publication Date (Print):May 1, 1984Publication History Published online1 May 2002Published inissue 1 May 1984https://pubs.acs.org/doi/10.1021/jf00123a019https://doi.org/10.1021/jf00123a019research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations11LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Geology and tectonics of the Archean Superior Province, Canadian Shield (1986)

Superior Province consists mainly of Late Archean rocks with Middle Archean gneisses in the south, and possibly in the north. The Late Archean supracrustal sequences are of island arc and interarc affinity and are cut by abundant plutonic rocks, including early arc-related intrusions, late synorogenic intrusions, and post-orogenic plutons that are possibly the product of crustal melting caused by thermal blanketing of newly-thickened continental crust combined with high mantle heat flux. The contemporaneity of magmatic and deformational events along the lengths of the belts is consistent with a subduction-dominated tectonic regime for assembly of the Kenoran Orogen. Successive addition of volcanic arcs accompanied and followed by voluminous plutonism resulted in crustal thickening and stabilization of the Superior craton prior to uplift of Kapuskasing granulites, emplacement of the Matachewan diabase dykes, and Early Proterozoic marginal rifting.
Suppression of surface segregation and heavy arsenic doping into silicon during selective epitaxial chemical vapor deposition under atmospheric pressure (2007)

The authors investigated the effects of the growth rate and temperature on the surface segregation during in situ As-doped selective epitaxial growth under atmospheric pressure. It was confirmed that high growth rate and high temperature suppress surface segregation. A film with a high As concentration (7.5×1019at.∕cm3) and a smooth surface was obtained by optimizing these conditions.
Water and Ice Dielectric Spectra Scaling at 0°C (2014)

Dielectric spectra (10^4-10^11 Hz) of water and ice at 0 {\deg}C are considered in terms of proton conductivity and compared to each other. In this picture, the Debye relaxations, centered at 1/{\tau}_W ~ 20 GHz (in water) and 1/{\tau}_I ~ 5 kHz (in ice), are seen as manifestations of diffusion of separated charges in the form of H3O+ and OH- ions. The charge separation results from the self-dissociation of H2O molecules, and is accompanied by recombination in order to maintain the equilibrium concentration, N. The charge recombination is a diffusion-controlled process with characteristic lifetimes of {\tau}_W and {\tau}_I, for water and ice respectively. The static permittivity, {\epsilon}(0), is solely determined by N. Both, N and {\epsilon}(0), are roughly constant at the water-ice phase transition, and both increase, due to a slowing down of the diffusion rate, as the temperature is lowered. The transformation of the broadband dielectric spectra at 0 {\deg}C with the drastic change from {\tau}_W to {\tau}_I is mainly due to an abrupt (by 0.4 eV) change of the activation energy of the charge diffusion.
<i>In Vitro</i>Antioxidant and Antiproliferative Activities of 5-Hydroxymethylfurfural (2013)

5-HMF is widely presented in foods and produced through the degradation of hexoses and Maillard reaction during heat treatment of foods containing reducing sugars and amino acids in an acid environment. However, controversial conclusions on the biological effects of 5-HMF have been drawn in previous studies. Therefore, the main aim of this study was to investigate the antioxidant and antiproliferative activities of 5-HMF. The 2,2'-azinobis-3-ethylbenzothiazolin-6-sulfonic acid (ABTS) assay, the 1,1-diphenyl-2-picryhydrazyl (DPPH) assay, and the hemolysis assay induced by 2,2'-azobis(2-amidinopropane) dihydrochloride (AAPH) were performed to evaluate the antioxidant capacity of 5-HMF. The results showed that 5-HMF exhibited novel antioxidant activity by scavenging the ABTS and DPPH free radicals and inhibited the AAPH-induced hemolysis in a dose-dependent manner. In the hemolysis assay, the reduction of ROS and MDA contents and the increase in enzyme activities of SOD, CAT, and GPx were found in erythrocytes pretreated with 5-HMF, which demonstrated that 5-HMF could prevent the peroxidation from the source to protect the erythrocytes. The morphological changes of erythrocytes was also verified by observation using atomic force microscopy. The inhibitory effect of 5-HMF on human cancer cell proliferation was investigated by MTT assay, flow cytometric analysis, and the TUNEL and DAPI costaining assay. The results showed that 5-HMF displayed higher antiproliferative activity on human melanoma A375 cells than other cell lines. Further investigation on the action mechanisms revealed that 5-HMF could induce A375 cell apoptosis and G0/G1 cell cycle arrest. The A375 cell apoptosis that 5-HMF induced was characterized by a TUNEL and DAPI costaining assay. These findings suggest that 5-HMF could be developed as a novel natural antioxidant with potential applications in cancer chemoprevention.
Numerical Analysis of Curved Optical Waveguides by the Finite-Element Method (1995)

A numerical approach based on the finite-element method is described for the analysis of curved optical waveguides. Both TE-like and TM-like modes are systematically formulated. Numerical examples of the propagation characteristics of curved rib waveguides are given. Our results for curved rib waveguides with rectangular cross section agree well with the results of the method of lines. We also demonstrate the application of this approach by analyzing curved rib waveguides with trapezoidal cross section.
Synthesis of the Mammalian Telomere Lagging Strand in Vitro (1997)

Using a synthetic telomere DNA template and whole cell extracts, we have identified proteins capable of synthesizing the telomere complementary strand. Synthesis of the complementary strand required a DNA template consisting of 10 repeats of the human telomeric sequence d(TTAGGG) and deoxy- and ribonucleosidetriphosphates and was inhibited by neutralizing antibodies to DNA polymerase alpha. No evidence for RNA-independent synthesis of the lagging strand was observed, suggesting that a stable DNA secondary structure capable of priming the lagging strand is unlikely. Purified DNA polymerase alpha/primase was capable of catalyzing synthesis of the lagging strand with the same requirements as those observed in crude cell extracts. A ladder of products was observed with an interval of six bases, suggesting a unique RNA priming site and site-specific pausing or dissociation of polymerase alpha on the d(TTAGGG)10 template. Removal of the RNA primers was observed upon the addition of purified RNase HI. By varying the input rNTP, the RNA priming site was determined to be opposite the 3' thymidine nucleotide generating a five-base RNA primer with the sequence 5'-AACCC. The addition of UTP did not increase the efficiency of priming and extension, suggesting that the five-base RNA primer is sufficient for extension with dNTPs by DNA polymerase alpha. This represents the first experimental evidence for RNA priming and DNA extension as the mechanism of mammalian telomeric lagging strand replication.
High Field Magnets With HTS Conductors (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Development of high-field magnets using high temperature superconductors (HTS) is a core activity at the NHMFL. Magnet technology based on both YBCO-coated tape conductors and Bi-2212 round wires is being pursued. Two specific projects are underway. The first is a user magnet with a 17 T YBCO coil set which, inside an LTS outsert, will generate a combined field of 32 T. The second is a 7 T Bi2212 demonstration coil set to be operated in a large bore resistive magnet to generate a combined magnetic field of 25 T. Owing to the substantial technological differences of the two conductor types, each project faces different conductor and magnet technology challenges. Two small coils have been tested in a 38-mm cold bore cryostat inserted in a 31 T resistive magnet: a Bi2212 round-wire layer-wound insert coil that generated 1.1 T for a total of 32.1 T and a YBCO double-pancake insert that generated 2.8 T for a total central field of 33.8 T. Four larger layer-wound coils have been manufactured and tested in a 20 T, 186-mm cold bore resistive magnet: a sizeable Bi-2212 coil and three thin large-diameter YBCO coils. The test results are discussed. The current densities and stress levels that these coils tolerate underpin our conviction that <formula formulatype="inline"><tex Notation="TeX">$>$</tex> </formula>30 T all-superconducting magnets are viable. </para>
<i>Oases:</i>robust<i>de novo</i>RNA-seq assembly across the dynamic range of expression levels (2012)

Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/.
Filler‐filler interaction and filler‐polymer interaction in carbon black and silica filled Exxpro<sup>TM</sup> polymer (2003)

Abstract Due to the presence of reactive benzylic bromide, Exxpro has much better interaction with silica in comparison with polybutadiene as demonstrated by the high bound rubber level. The better silica/Exxpro interaction is further substantiated by the low degree of filler network formation in comparison to that observed for silica filled polybutadiene as demonstrated by the much smaller deviation of low strain shear modulus from the Guth‐Gold relationship for the silica filled Exxpro. Silane treatement of silica reduces filler network formation in polybutadiene but has only slight effect on silica filled Exxpro indicating that even without silane treatment silica already disperse well in Exxpro due to high degree of filler/polymer interaction. This result in silica filled Exxpro compound exhibiting better processability (lower shear viscosity) as well as dynamic performances for tire applications (higher tan δ at −20 and 0°C, lower tan δ at 60°C). We speculate that nucleophilic substitution reaction takes place between benzylic bromide and surface hydroxide group of silica.
Paramagnetic calcium melanins (2013)

Treatment of catechol, pyrogallol, DOPA, dopamine, norepinephrine, and natural polyhydroxy-1,4-naphthoquinone echinochrome by aqueous solution of potassium superoxide (KO2) in the presence of CaCl2 leads to the formation of water-insoluble dark pigments with stable paramagnetic properties ("calcium melanins"). In control experiments in the same procedure without Ca2+, the pigments were not formed. EPR spectra of the calcium melanins had little difference from each other and from known melanins in shape, line width, and the g factor about 2,004. Addition of EDTA water solution to dried paramagnetic pigments leads to their fast dissolving and disappearing of EPR signal. Formation of similar polymers is also observed during autoxidation of o-diphenols in Ca(2+)-containing alkaline buffer solution, however, this process takes a few days instead of few seconds in the presence of KO2. Thus, calcium (and other divalent cation M2+) can consider as a key structural element in formation of M(2+)-catecholate paramagnetic Polymer. We assume the existence of two types of paramagnetic centers in melanin-like polymer: M(2+)-stabilized o-semiquinone radical or bi-radical complex containing o-semiquinone and superoxide anion radicals, stabilized by M2+.
Measuring the latent reservoir in vivo (2016)

Current efforts toward achieving a cure for HIV are focused on developing strategies to eliminate latently infected CD4+ T cells, which represent the major barrier to virus eradication. Sensitive, precise, and practical assays that can reliably characterize and measure this HIV reservoir and can reliably measure the impact of a candidate treatment strategy are essential. PCR-based procedures for detecting integrated HIV DNA will overestimate the size of the reservoir by detecting replication-incompetent proviruses; however, viral outgrowth assays underestimate the size of the reservoir. Here, we describe the attributes and limitations of current procedures for measuring the HIV reservoir. Characterizing their relative merits will require rigorous evaluation of their performance characteristics (sensitivity, specificity, reproducibility, etc.) and their relationship to the results of clinical studies.
Highly Si-doped AlN grown by plasma-assisted molecular-beam epitaxy (2005)

We have studied the influence of the growth conditions on the Si incorporation in AlN films grown by plasma-assisted molecular-beam epitaxy. Nitrogen-rich growth conditions allow controlled incorporation of Si up to a concentration of 5.2×1021cm−3, determined by elastic recoil detection analysis, whereas Si incorporation is supressed under Al-rich growth conditions. The structural and morphological properties determined by x-ray diffraction and atomic force microscopy were not affected up to Si concentrations of 1.2×1021cm−3. The electrical conductivity for the N-rich growth regime first increases with Si concentration followed by a decrease due to an increase of the activation energy up to 570meV for a Si content of 1.2×1021cm−3. For higher silicon concentrations, we have observed a sharp decrease in activation energy and an increase in conductivity by four orders of magnitude, attributed to the onset of impurity band conduction.
Covered stent placement for neurovascular disease. (1997)

We describe an endovascular technique in which covered stents were used to occlude a parent vessel. In one patient, with a giant paraclinoid aneurysm, a Gortex-covered Palmaz stent was used to occlude the cervical internal carotid artery and to create thrombosis in the aneurysm. In the second patient, with a high-flow vertebrojugular fistula, a hooded stent provided definitive treatment after an attempt to close the fistula by detachable balloon therapy failed. Follow-up of these patients revealed stable stent position and no untoward effects of permanent vessel occlusion.
PET detector configuration with thick light guide and GAPD array having large-area microcells (2010)

Light sharing PET detector configuration coupled with thick light guide and Geiger-mode avalanche photodiode (GAPD) with large-area microcells was proposed to overcome the energy non-linearity problem and to obtain high light collection efficiency (LCE). Theoretical evaluations were performed for 90 types of PET detector modules. A Monte Carlo simulation was conducted for the three types of LSO block, 4×4 array of 3×3×20 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , 6×6 array of 2×2×20 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , and 12×12 array of 1×1×20 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> discrete crystals, to investigate the scintillation light distribution after conversion of the γ-rays in LSO. The incident photons were read out by three types of 4×4 array photo-sensors, which were PSPMT of 25% quantum efficiency (QE), GAPD1 with 50×50 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> microcells of 30% photon detection efficiency (PDE) and GAPD2 with 100×100 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of 45% PDE. The number of counted photons in each photo-sensor was analytically calculated. The LCE, linearity and flood histogram were examined for each PET detector module as a function of light guide thickness ranging from 1 to 10 mm. The performance of PET detector modules based on GAPDs was significantly improved by using the thick light guide. The LCE was increased from 24 to 30% and from 14 to 41%, and the linearity was also improved from 0.96 to 0.99, from 0.78 to 0.99, for GAPD1 and GAPD2, respectively. In the contrary, the performance was not changed for PSPMT based detector. The flood histogram of 12×12 array PET detector modules using 3 mm light guide coupled with GAPDs was obtained by simulation, and all crystals of 1×1×20 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> size was clearly identified. PET detector module coupled with thick light guide and GAPD array with large-area microcells was proposed to obtain high QE and high spatial resolution, and its feasibility was verified. It demonstrates GAPDs could be a competitive and cost-effective photo-sensor respect to the high QE (~40%) PMT.
Anisotropic point set surfaces (2006)

Point Set Surfaces define smooth surfaces from regular samples based on weighted averaging of the points. Because weighting is done based on a spatial scale parameter, point set surfaces apply basically only to regular samples. We suggest to attach individual weight functions to each sample rather than to the location in space. This extends Point Set Surfaces to irregular settings, including anisotropic sampling adjusting to the principal curvatures of the surface. In particular, we describe how to represent surfaces with ellipsoidal weight functions per sample. Details of deriving such a representation from typical inputs and computing points on the surface are discussed.
Marine ecosystem baseline study (2004)

This environmental assessment for the Philippines Ilocos Norte Wind Farm Project, which harnesses wind energy for power generation, is comprised of a marine ecosystem baseline study that examines the 9-kilometer stretch of Bangui Bay within the project site covering 5 communities of Bangui. Additional study sites including 2 barangays in Burgos Ilocos Norte were included in the study as reference sites. The report identifies possible impacts and proposes measures to mitigate them. They include: Leveling of construction sites, vehicular traffic, and increased activity in the area may cause dust generation that may smother corals and algae. Offsetting measure should include putting up dust barriers on construction sites, and scheduling construction during the dry season. Increased activity during construction may also disorient turtle hatchings, affecting the nesting of turtles. Since the green turtle nesting period is from March to May, construction activities should be limited during that period. Use of the perimeter lights at the site and increased public access to the beach area may also disorient turtle hatchlings. Thus both lights and the public should be limited/controlled, especially during the nighttime.
Health Care Chaplaincy Research: A Need Within Aged Care Facilities (1999)

Health care chaplaincy has become an important field of research since 1995, particularly in several western countries. Health Care Chaplaincies are only one of many pastoral care chaplaincy ministries encouraged by government, church, and community resources.
Integrated system architecture and technology roadmap toward WAMPAC (2011)

With the advancement of sensor, communication and information technologies, Wide Area Monitoring, Protection and Control (WAMPAC) systems have been identified as the new generation of solutions to improve power system planning, operation and protection. There are a number of Southern California Edison (SCE) advanced initiatives that are related to the WAMPAC systems. Despite differences among various WAM/WAC/WAP systems and capabilities, their similarities favor an integrated WAMPAC system architecture design. This paper reviews existing relevant smart grid initiatives at SCE and proposes an integrated WAMPAC system architecture designed to support SCE's future smart grid and WAMPAC vision. It recommends a technology migration roadmap that considers technology maturity, practical deployment constraints, standardization, and a phased approach to ensure an effective and feasible WAMPAC system under the overall smart grid framework.
Controllable Surface Expression of Bioactive Peptides Incorporated into a Silica Thin Film Matrix (2009)

Mammalian cell culture platforms often require biomolecular modification to enhance cell adhesion and proliferation. Often, these modifications are performed using self-assembled monolayers or whole protein coatings, such as collagen. These protocols are inherently useful but generally suffer from repeatability. Undesirable conditions during self-assembly can lead to complications in the surface presentation of the biological ligands. Whole proteins are often unstable and derived from animal sources, making them less attractive for tissue engineering applications. As the biological effect of the material often depends strongly on the concentration of the integrated ligand(s), any complication due to synthesis or stability can lead to unexpected biological results. In this research, we expand upon previous work in peptide−silane modifications to sol−gel derived silica matrixes, demonstrating that the surface density of the peptide can be calibrated by simply modifying the starting liquid precursor concentration. The potential for calibration of peptide surface presentation allows for well-defined cell culture platforms that have the potential to mimic natural proteins in a stable, repeatable manner.