gebhart/patrepeval huggingface dataset:
An Autoinducer Analogue Reveals an Alternative Mode of Ligand Binding for the LasR Quorum-Sensing Receptor (2019)

Bacteria use a cell-cell communication process called quorum sensing to coordinate collective behaviors. Quorum sensing relies on production and group-wide detection of extracellular signal molecules called autoinducers. Here, we probe the activity of the Pseudomonas aeruginosa LasR quorum-sensing receptor using synthetic agonists based on the structure of the native homoserine lactone autoinducer. The synthetic compounds range from low to high potency, and agonist activity tracks with the ability of the agonist to stabilize the LasR protein. Structural analyses of the LasR ligand binding domain complexed with representative synthetic agonists reveal two modes of ligand binding, one mimicking the canonical autoinducer binding arrangement, and the other with the lactone head group rotated approximately 150°. Iterative mutagenesis combined with chemical synthesis reveals the amino acid residues and the chemical moieties, respectively, that are key to enabling each mode of binding. Simultaneous alteration of LasR residues Thr75, Tyr93, and Ala127 converts low-potency compounds into high-potency compounds and converts ligands that are nearly inactive into low-potency compounds. These results show that the LasR binding pocket displays significant flexibility in accommodating different ligands. The ability of LasR to bind ligands in different conformations, and in so doing, alter their potency as agonists, could explain the difficulties that have been encountered in the development of competitive LasR inhibitors.
Neutrophils in chronic and aggressive periodontitis in interaction with Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans (2009)

High serum IgG levels against P. gingivalis and A. actinomycetemcomitans promote phagocytosis in periodontitis. The extracellular release of reactive oxygen species and neutrophil elastase by polymorphonuclear neutrophils may also contribute to damage of the surrounding periodontal tissues.
Optical and transport studies of Ni(dmit)2-based organic conductors (1996)

Single-crystal Ni(dmit${)}_{2}$ salts, (${\mathrm{Ph}}_{4}$P)[Ni(dmit${)}_{2}$${]}_{3}$, (${\mathrm{Bu}}_{4}$N${)}_{2}$[Ni(dmit${)}_{2}$${]}_{7}$\ensuremath{\cdot}${2\mathrm{C}\mathrm{H}}_{3}$CN, and (${\mathrm{Me}}_{3}$S)[Ni(dmit${)}_{2}$${]}_{2}$, have been synthesized. All show semiconducting behavior in their temperature-dependent dc conductivities. Room-temperature polarized reflectance measurements have been made over the range between 100 and 32 000 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ (12 meV--4 eV). For light polarized along the Ni(dmit${)}_{2}$ stacking axis, all spectra show an energy gap, with superimposed vibrational fine structure at low frequencies and charge-transfer bands at high frequencies. Band gaps determined from the optical conductivities are consistent with thermal activation energies from dc transport measurements. The stacking-axis conductivity shows the effect of electron-molecular vibration interaction; analysis for (${\mathrm{Me}}_{3}$S)[Ni(dmit${)}_{2}$${]}_{2}$ yields a dimensionless electron-phonon coupling constant \ensuremath{\lambda}\ensuremath{\sim}0.27. For light polarized perpendicular to the stacking axis, only weak vibrational features are observed. \textcopyright{} 1996 The American Physical Society.
The Effect of Fe in Perovskite Catalysts for Steam CO2 Reforming of Methane (2015)

In this work, La0.95Sr0.05Ni(1-x)Fe(x)O3 catalysts were prepared by modified EDTA-cellulose method and the catalysts were characterized by various techniques such as N2 physisorption, TPR, XRD, SEM, TEM-EDS and TG analysis. La00.95Sr0.05Ni0.5Fe0.5O3 catalyst showed better catalytic performance under the reaction conditions of 900 degrees C, 21 bar and feed molar ratio of CH4:CO2:H20 = 1:0.7:1.5. It is considered that the dilution effect on nickel prevented the formation of large monometallic ensembles that favour the carbon deposition in reforming reactions, and the mean metallic particle size of Ni decreased with increasing substitution rate in B site. Therefore, partial substitution of Fe in B site enhances the dilution effect and induces a reaction between CO2 and La2O3, thereby resisting the carbon deposition and increasing CO2 conversion.
Facilitating Medical Care for Latinx Individuals at Risk for CKD: A Pilot Intervention (2023)

Latinx individuals are at a higher risk for kidney failure than non-Latinx White individuals; however, they are less likely to receive pre-kidney failure medical care. We piloted a community health worker intervention that connected people with risk factors or showed evidence of kidney dysfunction at community screening events with medical care. Our findings indicate the acceptability of the intervention. We encountered challenges with feasibility and identified strategies to overcome them.
Phenotypical and Functional Characterization of the CD8+ T Cell Repertoire of HLA-A2.1 Transgenic, H-2K b °D b ° Double Knockout Mice (1999)

Abstract Homozygous HLA-A2.1 transgenic H-2Kb°Db° double knockout (KO) mice were created. Their potential to develop HLA-A2.1-restricted cytolytic responses was compared with that of their classical transgenic counterparts, which still express H-2Kb, Db molecules. On cell surfaces, both strains express similar amounts of chimeric (α1α2 domains of human, α3 cytoplasmic domains of mouse) HLA-A2.1 molecules in noncovalent association with mouse β2-microglobulin. Compared with mice that are totally deprived of histocompatibility class Ia molecules (H-2Kb°Db° double KO), the expression of HLA-A2.1 in transgenic/double KO mice resulted in sizeable increase in the periphery of CD8+ T cells with a normally diversified TCR repertoire. A biased education in favor of HLA-A2.1, ascribable to the absence of H-2 class Ia molecules, was evidenced in these transgenic/double KO mice by their improved capacity to mount HLA-restricted cytolytic responses, regardless of whether they were virally infected or injected with synthetic epitopic peptide. HLA class I transgenic, H-2 class Ia KO mice should represent useful animal models for the preclinical evaluation of vaccine formulations aiming at the induction of HLA class I-restricted CTL responses.
On the Copying of DNA in the RNA Polymerase Reaction (1963)

The reaction by which RNA polymerase catalyzes the synthesis of RNA from a DNA template can be summarized by the equation:
An alpha-1 antitrypsin genetic variant from India. (2007)

The highly polymorphic human alpha-1 antitrypsin (AAT) gene codes for the most abundant circulating plasma serine protease inhibitor. Previously, genetic variants of the AAT gene were reported from different regions of the world. In the present study, the AAT gene was characterized in an Indian sample. The AAT gene was isolated and cloned from a liver biopsy sample through RT-PCR and the full-length gene was sequenced. Nucleotide sequence comparison with the human genome and the AAT sequences available in the GenBank (NCBI) demonstrated four unique variations--(i) an A to G variation at position 286 (Thr96Ala), (ii) an A to G variation at position 839 (Asp280Gly), (iii) a T to C variation at position 1182 that did not result in any change in the protein sequence (TTT to TTC both code for Phe) and (iv) an A to C variation at position 1200 (Glu400Asp) that resulted in replacement by an amino acid of similar nature. Other variations found were T to C at position 710 (Val273Ala) and T to C position 863 (Val288Glu), which were also reported earlier. In conclusion, this study reports the entire 1257 bp nucleotide sequence of protein coding region of the human AAT gene from an Indian sample. This preliminary finding is significant, as it reports for the first time the AAT gene sequence in the Indian sample.
Fabrication of Cr nanostructures with the scanning tunnelling microscope (1997)

In this work, nanometer scale electrically conducting lines and quantum structures on chromium (Cr) films have been fabricated with an ambient scanning tunnelling microscope and a subsequent CR-14 chromium etch. The line width of these structures is approximately 60 nm and the height of the lines is approximately 10 nm. In addition, experiments have been performed to determine the Cr etch rate in CR-14 etchant and the thickness of the Cr layer that could be oxidized through by the STM tunnelling current.
Pyroelectric detection with smectic liquid crystals (1986)

The potential of ferroelectric liquid crystals for application as pyroelectric infrared detectors is examined. The liquid crystals studied belong to a family of biphenyl and phenylbenzoate esters. It is found that even within this first liquid-crystal family examined, the materials figure of merit compares well with ferroelectric solid materials commonly used for infrared detection and imaging. Because they permit very simple and flexible device design, liquid crystals are attractive candidates for these applications. However, for low-frequency applications, attention must be paid to the reduction of thermal loading by the cell walls.
An extensible environment discovery and negotiation method for self-configuring networks (2009)

Recently, we have been faced the rise of several technologies that aim to communicate easier with the users. Solutions to support specific requirements, such as mobility and security, were designed. However, few works can be found regarding to automate the discovery of environment features, as well as to automate the network configuration to allow a better utilization of the network resources. This also includes the adaptation to changes in the network environment and adapting to new requirements from the users. In this paper, we propose XDNM, a method to discover network elements' capabilities in a network and negotiate configurations to be used by them and also the optimization of these configuration according to changes mentioned above. Some questions related with the implementation of this kind of solution are also discussed in the paper in order to give a more practical view of this method in current technologies.
Generalized Policy Elimination: an efficient algorithm for Nonparametric Contextual Bandits (2020)

We propose the Generalized Policy Elimination (GPE) algorithm, an oracle-efficient contextual bandit (CB) algorithm inspired by the Policy Elimination algorithm of \cite{dudik2011}. We prove the first regret optimality guarantee theorem for an oracle-efficient CB algorithm competing against a nonparametric class with infinite VC-dimension. Specifically, we show that GPE is regret-optimal (up to logarithmic factors) for policy classes with integrable entropy. For classes with larger entropy, we show that the core techniques used to analyze GPE can be used to design an $\varepsilon$-greedy algorithm with regret bound matching that of the best algorithms to date. We illustrate the applicability of our algorithms and theorems with examples of large nonparametric policy classes, for which the relevant optimization oracles can be efficiently implemented.
A 200Mbps+ 2.14nJ/b digital baseband multi processor system-on-chip for SDRs (2009)

International audience
A comparative study of oxidized spacer trench and micro-pattern trench concepts for 1200 V IGBTs (2020)

The micro-pattern trench (MPT) cell topology is a common front-side concept for current IGBT technologies, used in voltage classes ranging from 650 V to 1200 V and higher. In contrast, the side-gate concept is mostly applied to higher voltage classes above 1200 V showing a gain in performance. A comparison of these concepts was made based on an adapted new structure labeled oxidized spacer trench (OST). It maintains the cell dimensions and parameters as gate charge, trench depth and shape from the MPT-IGBT, while oxidizing the areas between the gate trenches, to focus purely on the physical effects of the remaining structural change.
Small fitness effect of mutations in highly conserved non-coding regions (2005)

Comparison of human and mouse genomes has revealed that many non-coding regions have levels of sequence conservation similar to protein-coding genes. These regions have attracted a lot of attention as potentially functional genomic sequences. However, little is known about the effect mutations in these conserved non-coding regions have on fitness and how many of them are present in the human genome as deleterious polymorphisms. To gain insight into the selective constraints imposed on conserved non-coding and protein-coding regions, we compared substitution rates in primate and rodent lineages and analyzed the density and allele frequencies of human polymorphism. Genomic regions conserved between primate and rodent groups show higher relative conservation within rodents than within primates. Thus, our analysis indicates a genome-wide relaxation of selective constraint in the primate lineage, which most likely resulted from a smaller effective population size. We found that this relaxation is much more profound in conserved non-coding regions than in protein-coding regions, and that mutations at a large proportion of sites in conserved non-coding regions are associated with very small fitness effect. Data on human polymorphism are also consistent with very weak selection in conserved non-coding regions. This staggering enrichment in sites at the borderline of neutrality can be explained by assuming an important role for synergistic epistasis in the evolution of non-coding regions. Our results suggest that most individual mutations in conserved non-coding regions are only slightly deleterious but are numerous and may have a significant cumulative impact on fitness.
Analysis of mathematical modeling of PV module with MPPT algorithm (2015)

This paper presents the mathematical modeling of photovoltaic (PV) module with the effective comparison of two popular maximum power point tracking (MPPT) techniques namely. Generally, Maximum Power Point Tracking (MPPT) techniques are used in PV System to extract maximum possible power which in turn depends on solar irradiance and temperature of PV module. Two most widely used MPPT techniques namely incremental conductance (INC), and perturb & observe (P&O) method are analyzed in this paper. The PV models compared are simplified single diode model, improved two diode model and simplified two-diode model. The effectiveness of the comparison has been done through MATLAB/Simulink Environment and the results are analyzed.
Pediatric brain arteriovenous malformation recurrence: a cohort study, systematic review and meta-analysis (2021)

Location of infratentorial AVMs and younger age at presentation may be associated with earlier and more frequent recurrences. The higher rates of recurrence in patients with AVMs obliterated with EVT questions its role in an intent-to-cure approach and reinforces its position as an adjunct to surgery and/or radiosurgery.
Methods for performance evaluation of VBR video traffic models (1994)

Models for predicting the performance of multiplexed variable bit rate video sources are important for engineering a network. However, models of a single source are also important for parameter negotiations and call admittance algorithms. In this paper we propose to model a single video source as a Markov renewal process whose states represent different bit rates. We also propose two novel goodness-of-fit metrics which are directly related to the specific performance aspects that we want to predict from the model. The first is a leaky bucket contour plot which can be used to quantify the burstiness of any traffic type. The second measure applies only to video traffic and measures how well the model can predict the compressed video quality.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
CRISPR‐Cas‐Assisted Multiplexing (CAM): Simple Same‐Day Multi‐Locus Engineering in Yeast (2016)

Demands on the industrial and academic yeast strain engineer have increased significantly in the era of synthetic biology. Installing complex biosynthetic pathways and combining point mutations are tedious and time-consuming using traditional methods. With multiplex engineering tools, these tasks can be completed in a single step, typically achieving up to sixfold compression in strain engineering timelines. To capitalize on this potential, a variety of yeast CRISPR-Cas methods have been developed, differing largely in how the guide RNA (gRNA) reagents that direct the Cas9 nuclease are delivered. However, in nearly all reported protocols, the time savings of multiplexing is offset by multiple days of cloning to prepare the required reagents. Here, we discuss the advantages and opportunities of CRISPR-Cas-assisted multiplexing (CAM), a same-day, cloning-free method for multi-locus engineering in yeast. J. Cell. Physiol. 231: 2563-2569, 2016. © 2016 Wiley Periodicals, Inc.
Diffractive moire features for optically variable devices (2006)

We present diffractive second-line security features based on the moiré phenomenon, that are designed for use in Optically Variable Devices (OVDs). After a short introduction of our 2D and 1D moire methods, we first present the integration of line-based, 1D animated moire patterns into OVDs. These covert features are verified using a printed, high-resolution screen, which causes the covert information to become visible. When the screen is moved back and forth, the covert information, for example a text, appears to move dynamically in a well defined way. We then present diffractive OVDs where specially designed 2D moire features have been integrated into graytone images. Such an integration has the advantage that the area in which the second-line security feature appears can be used simultaneously for a visually attractive first-line effect rather than just having a homogeneous background. The integrated diffractive moire features are verified with a 2D microlens array through which the OVD is viewed; as the verifier or the OVD together with the verifier is moved, one observes dynamic visual effects. A special form of integrating a diffractive moire-feature into an OVD is shown in the last part of the paper, where the 2D microlens verifier is used in a fixed combination together with the information layer that consists of diffractive microstructures. Such a diffractive moire magnifier feature is characterized by the unique visual impression that it creates where projected images appear to move as the sample is tilted.
Multitrack power factor correction architecture (2019)

Single-phase universal-input ac-dc converters are needed in a wide range of applications. This paper presents a novel power factor correction (PFC) architecture that can achieve high-power density and high efficiency for grid-interface power electronics. The multitrack PFC architecture reduces the internal device voltage stress of the power converter subsystems, allowing PFC circuits to maintain zero-voltage-switching at high frequency (1 MHz-4 MHz) across universal input voltage range (85 V ac-265 V ac). The high performance of the power converter is enabled by delivering power in multiple stacked voltage domains and reconfiguring the power processing paths depending on the input voltage. This multitrack concept can be used together with many other design techniques for PFC systems to create mutual advantages in many function blocks. A prototype 150 W, universal ac input, 12 V dc output, isolated multitrack PFC system with a power density of 50 W/in3, and a peak end-to-end efficiency of 92% has been built and tested to verify the effectiveness of the multitrack PFC architecture.
Determination of phonon deformation potentials and strain-shift coefficients in Ge-rich Si1− x Ge x using bulk Ge-rich Si1− x Ge x crystals and oil-immersion Raman spectroscopy (2018)

The strain-free Raman shift of the Ge–Ge mode, , of Ge-rich Si1−xGex (x: Ge fraction) was determined accurately from the bulk Ge-rich Si1−xGex samples fabricated by the Czochralski (Cz) method. Using the obtained , the phonon deformation potentials (PDPs), p and q, and the strain-shift coefficient bLO of isotropic biaxial strained Ge-rich Si1−xGex thin films were extracted by oil-immersion Raman spectroscopy using Raman peak shifts of longitudinal and transverse optical (LO and TO) phonon modes. As a result, it was confirmed that these parameters are almost constant with small variations and that the strain-shift coefficient bLO is in good agreement with ab initio calculations. The parameters determined in this work are essential to realize accurate strain measurements using Raman spectroscopy for Ge-rich Si1−xGex devices.
Amino‐acid‐functionalized solvatochromic probes (2008)

Abstract N ‐(4‐nitrophenyl)‐L‐proline ( 2 ) has been obtained by a nucleophilic aromatic substitution reaction of 4‐fluoronitrobenzene with L‐proline. The corresponding amide derivatives 3 – 5 have been synthesized by peptide coupling of 2 with different amino acid derivatives and chiral amines. Solvatochromism of the long‐wavelength UV/Vis band in the electronic absorption spectra of the compounds 2 – 5 has been studied and analyzed using the empirical Kamlet–Taft solvent polarity parameters π* (dipolarity/polarizability), α (hydrogen bond donating ability), and β (hydrogen bond accepting ability). Reasonable Kamlet–Taft solvatochromic correlations ( r &gt; 0.95) were established for the three amide derivatives 3 – 5 in a range of common solvents and three room temperature ionic liquids (RTILs). The UV/Vis absorption of the 4‐nitroaniline derivative 2 showed a hypsochromic shift with increasing concentration due to intermolecular hydrogen bonded aggregate formation in protic solvents, which is not observed for compounds 3 – 5 . Copyright © 2008 John Wiley &amp; Sons, Ltd.
Longitudinal Functional Principal Component Analysis (2011)

We introduce models for the analysis of functional data observed at multiple time points. The model can be viewed as the functional analog of the classical mixed effects model where random effects are replaced by random processes. Computational feasibility is assured by using principal component bases. The methodology is motivated by and applied to a diffusion tensor imaging (DTI) study on multiple sclerosis.
Planar "20-electron" osmium imido complexes. A linear imido ligand does not necessarily donate its lone pair of electrons to the metal (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPlanar "20-electron" osmium imido complexes. A linear imido ligand does not necessarily donate its lone pair of electrons to the metalJ. T. Anhaus, T. P. Kee, M. H. Schofield, and R. R. SchrockCite this: J. Am. Chem. Soc. 1990, 112, 4, 1642–1643Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/ja00160a061https://doi.org/10.1021/ja00160a061research-articleACS PublicationsRequest reuse permissionsArticle Views967Altmetric-Citations103LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts