gebhart/patrepeval huggingface dataset:
Functional Characterization of an Aminotransferase Required for Pyoverdine Siderophore Biosynthesis in <i>Pseudomonas aeruginosa</i> PAO1 (2004)

The fluorescent dihydroxyquinoline chromophore of the pyoverdine siderophore in Pseudomonas is a condensation product of D-tyrosine and l-2,4-diaminobutyrate. Both pvdH and asd (encoding aspartate beta-semialdehyde dehydrogenase) knockout mutants of Pseudomonas aeruginosa PAO1 were unable to synthesize pyoverdine under iron-limiting conditions in the absence of l-2,4-diaminobutyrate in the culture media. The pvdH gene was subcloned, and the gene product was hyperexpressed and purified from P. aeruginosa PAO1. PvdH was found to catalyze an aminotransferase reaction, interconverting aspartate beta-semialdehyde and l-2,4-diaminobutyrate. Steady-state kinetic analysis with a novel coupled assay established that the enzyme adopts a ping-pong kinetic mechanism and has the highest specificity for alpha-ketoglutarate. The specificity of the enzyme toward the smaller keto acid pyruvate is 41-fold lower. The enzyme has negligible activity toward other keto acids tested. Homologues of PvdH were present in the genomes of other Pseudomonas spp. These homologues were found in the DNA loci of the corresponding genomes that contain other pyoverdine synthesis genes. This suggests that there is a general mechanism of l-2,4-diaminobutyrate synthesis in Pseudomonas strains that produce the pyoverdine siderophore.
Quantitative Impacts of Project Change: Size Issues (1997)

Change has a tremendous effect on the performance of a construction project. Research that focuses on the quantitative impact is limited, incomplete, and in some cases questionable. The goals of this study were to quantify the nature and impacts of project change and develop recommended practices so that owners and contractors can manage change better. The focus was on project change during detailed design and construction, in particular the size of change and its impact on the project. These results show that the amount of change is negatively correlated with productivity and total installed project cost, whether within the design phase or construction phase, or between them. The greater the amount of change the more productivity and costs are degraded. Recommendations are also offered here on how to mitigate the impact of project change.
Content-Based Tag Generation for the Grouping of Tags (2009)

A tagging system can encounter too few or too many tags. To solve these problems, we propose a content-based automatic generation of tags. Applied to an e-Learning 2.0 application, the proposal creates tags based on lecture slide contents, generating an adequate number of tags so as to allow the tagging system to start up effectively. It also lets student users to group tags. The tag grouping by relations yields more meaningful tag retrieval in the many tags case. This tag-based indexing of lecture slides provides better learning experience to students in studying lecture slides.
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative (2017)

Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.
The equivalent frame method simplified for beam and slab construction (1982)

The three most important steps in the equivalent frame method are the evaluation of the stiffnesses of the equivalent beams, the calculation of the initial joint moments, and the transverse distribution of moments after the frame analysis. The current rules in aci 318 dealing with these items, have been criticized in many quarters for being too complex and ambiguous. The current procedures also include the artificial device of an equivalent column. Given that the mathematical model for the equivalent frame method is far from perfect then there is little justification for a complex and seemingly accurate procedure. This article presents a revised set of rules, for beam and slab construction, that should allay the previous criticisms. The proposed rules, derived from finite element analyses of beam slab floors, involve the direct evaluation of the first two of the dominant items from relatively simple formulae. The transverse distribution of moments, both for interior and edge beams, is obtained from two tables of coefficients. One effect of these rules is the elimination of the need for equivalent columns because the effect of twisting the spandrel beam is included in the second formulae and in the tables of coefficients. A numerical example is used to illustrate the application of both sets of rules to a beam slab structure and the results, together with the design effort, are compared (a).
A unified approach to weak universal source coding (1978)

A new method of constructing a universal sequence of block codes for coding a class of ergodic sources is given. With this method, a weakly universal sequence of codes is constructed for variable-rate noise. less coding and for fixed- and variable-rate coding with respect to a fidelity criterion. In this way a unified approach to weak universal block source coding is obtained. For the noiseless variable-rate coding and the fixed-rate coding with respect to fidelity criterion, the assumptions made on the alphabets, distortion measures, and class of sources are both necessary and sufficient. For fixed-rate coding with respect to a fidelity criterion, the sample distortion of the universal code sequence converges in <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L^{l}</tex> norm for each source to the optimum distortion for that source. For both variable-rate noiseless coding and variable-rate coding with respect to a fidelity criterion, the sample rate of the universal code sequence converges in <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L^{1}</tex> norm for each source to the optimum rate for that source. Using this fact, a universal sequence of codes for fixed-rate noiseless coding is obtained. Some applications to stationary nonergodic sources are also considered. The results of Davisson, Ziv, Neuhoff, Gray, Pursley, and Mackenthun are extended.
GIDE AND THE CONCEPTION OF THE BASTARD <sup>1</sup> (1963)

GIDE AND THE CONCEPTION OF THE BASTARD1 D. A. STEEL D. A. STEEL PARIS Search for other works by this author on: Oxford Academic Google Scholar French Studies, Volume XVII, Issue 3, July 1963, Pages 238–248, https://doi.org/10.1093/fs/XVII.3.238 Published: 01 July 1963
Electrostrictive Materials for Ultrasonic Probes in the Pb(Mg<sub>1/3</sub>Nb<sub>2/3</sub>)O<sub>3</sub>–PbTiO<sub>3</sub> System (1989)

Electrostrictive ceramics in the Pb(Mg 1/3 Nb 2/3 )O 3 -PbTiO 3 (PMN-PT) solid solution system are investigated as the transducer material for ultrasonic probes whose electro-acoustic conversion efficiency is controlled by an applied DC bias voltage. Considering the electromechanical coupling factors induced under practical DC bias voltage and the normal using temperature, it is concluded that the most promising composition is 0.09 mole fraction of PbTiO 3 . A basic pulse-echo measurement confirmed that electro-acoustic conversion efficiency of an ultrasonic probe made of electrostrictive ceramics is controlled by an applied DC bias field.
Fluorescent Chloride Indicators to Assess the Efficacy of CFTR cDNA Delivery (1999)

Cl(-)-sensitive fluorescent indicators have been used extensively in cell culture systems to measure the Cl(-)-transporting function of the cystic fibrosis transmembrane conductance regulator protein CFTR. These indicators have been used in establishing a surrogate end point to assess the efficacy of CFTR cDNA delivery in human gene therapy trials. The ability to measure Cl- transport with high sensitivity in small and heterogeneous tissue samples makes the use of Cl- indicators potentially attractive in gene delivery studies. In this review article, the important technical aspects of Cl- transport measurements by fluorescent indicators such as SPQ are described, applications of Cl- indicators to assay CFTR function are critically evaluated, and new methodological developments are discussed. The available Cl- indicators have been effective in quantifying Cl- transport rates in cell culture models and in vitro systems such as isolated membrane vesicles and liposomes. However, the imperfect photophysical properties of existing Cl- indicators limit their utility in performing measurements in airway tissues, where gene transfer vectors are delivered in CF gene therapy trials. The low efficiency of gene transfer and the cellular heterogeneity in airway samples pose substantial obstacles to functional measurements of CFTR expression. Significant new developments in generating long-wavelength and dual-wavelength halide indicators are described, and recommendations are proposed for the use of the indicators in gene therapy trials.
Thiol–ene Click Hydrogels for Therapeutic Delivery (2016)

Hydrogels are of growing interest for the delivery of therapeutics to specific sites in the body. For use as a delivery vehicle, hydrophilic precursors are usually laden with bioactive moieties and then directly injected to the site of interest for <i>in situ</i> gel formation and controlled release dictated by precursor design. Hydrogels formed by thiol-ene click reactions are attractive for local controlled release of therapeutics owing to their rapid reaction rate and efficiency under mild aqueous conditions, enabling <i>in situ</i> formation of gels with tunable properties often responsive to environmental cues. Herein, we will review the wide range of applications for thiol-ene hydrogels, from the prolonged release of anti-inflammatory drugs in the spine to the release of protein-based therapeutics in response to cell-secreted enzymes, with a focus on their clinical relevance. We will also provide a brief overview of thiol-ene click chemistry and discuss the available alkene chemistries pertinent to macromolecule functionalization and hydrogel formation. These chemistries include functional groups susceptible to Michael type reactions relevant for injection and radically-mediated reactions for greater temporal control of formation at sites of interest using light. Additionally, mechanisms for the encapsulation and controlled release of therapeutic cargoes are reviewed, including <i>i)</i> tuning the mesh size of the hydrogel initially and temporally for cargo entrapment and release and <i>ii)</i> covalent tethering of the cargo with degradable linkers or affinity binding sequences to mediate release. Finally, myriad thiol-ene hydrogels and their specific applications also are discussed to give a sampling of the current and future utilization of this chemistry for delivery of therapeutics, such as small molecule drugs, peptides, and biologics.
Biases and complex patterns in the residues flanking protein N-glycosylation sites (2003)

N-Glycosylation, the most common and most versatile protein modification reaction, occurs at the beta-amide of the aspargine of the Asn-Xaa-Ser/Thr sequon. For reasons that are unclear, not all such sequons are glycosylated. To find patterns that affect glycosylation, we examined the amino acid residues from the 20th preceding the sequon to the 20th residue following it, using bioinformatics tools. A clean data set of annotated, experimentally verified, glycosylated and nonglycosylated sequons derived from 617 well-defined nonredundant N- and N-,O-glycoproteins listed in SWISS-PROT (June 2002) was used. NXS and NXT sequons were analyzed separately. Although no overt patterns were found to explain sequon occupancy or nonoccupancy, trends for over- or underrepresentation of certain amino acids at particular positions were statistically significant and different in NXS and NXT sequons. In extension of earlier reports, none of the 80 Asn-Pro-Ser/Thr found were glycosylated, and a markedly low level of glycosylation was seen in sequons with Pro at the position following the Ser/Thr. In addition, a general observation was made that the considerable number of glycosylated sequons in the C-terminal 10 residues of glycoproteins suggests that N-glycosylation in these cases may be posttranslational and not cotranslational, as widely accepted.
Short circuit and overcurrent protection of IGCT-based three-level NPC inverters (2004)

In this paper, a new method for protection of IGCT based three-level NPC inverters is introduced and compared with other protection methods already presented in the technical literature. A system for fast overcurrent detection and inverter tripping is also presented as well as a complete discussion of the inverter design issues involved in the proposed protection scheme. Simulation results are included to support a comparative analysis of the considered inverter protection schemes. Experimental results from a lab scale prototype illustrate the performance of the proposed short-circuit and overcurrent detection circuitry. Although the discussion in this paper is aimed at three-level NPC inverters, it can be extended to two level inverters.
Design of the linear array CCD acquisition system that line frequency and integration time adjustable (2011)

Linear array CCD acquisition system is generally used for high precision measurement and control field. In this paper, firstly introduce a design of linear array CCD acquisition system that provide two features of adjustable line frequency and integration time, and secondly present linear array CCD acquisition system components, linear array CCD device principles, timing-driven design, signal processing circuit and data acquisition circuit, then highlights the linear array CCD timing-driven design, the design of line frequency and integration time adjustable, and illustrate the advantages of the system such as the convenience, the agility and the reliability, etc.
The translocation, folding, assembly and redox-dependent degradation of secretory and membrane proteins in semi-permeabilized mammalian cells (1995)

We describe here a semi-permeabilized cell-system which reconstitutes the efficient synthesis, translocation, folding, assembly and degradation of membrane and secretory proteins. Cells grown in culture were treated with the detergent digitonin which selectively permeabilized the plasma membrane leaving the cellular organelles, such as the endoplasmic reticulum (ER) and trans-Golgi network intact. These permeabilized cells were added to an in vitro translation system, either wheatgerm or reticulocyte lysate, supplemented with RNA coding for either membrane or secretory proteins. Efficient translocation and modification of proteins by these cells was demonstrated by protease protection, photocross-linking of nascent chains to components of the translocation apparatus and by post-translational modifications such as glycosylation or hydroxylation. A comparison was made between the ability of semi-permeabilized cells and microsomal vesicles to fold and assemble proteins. The results show that the intact ER within these cells can assemble proteins much more efficiently than vesicularized ER. Furthermore, the semi-permeabilized cells carried out the redox-dependent degradation of tissue-type plasminogen activator. This system has all the advantages of conventional cell-free systems, including speed and, importantly, the ability to manipulate the components of the assay, while retaining intracellular organelles and, therefore, allowing cellular processes to occur as they would in the intact cell.
Cross-presentation: how to get there – or how to get the ER (2012)

Antigen cross-presentation enables dendritic cells (DCs) to present extracellular antigens on major histocompatibility complex (MHC) I molecules, a process that plays an important role in the induction of immune responses against viruses and tumors and in the induction of peripheral tolerance. In order to allow intracellular processing for cross-presentation, internalized antigens are targeted by distinct endocytic receptors toward specific endosomal compartments, where they are protected from rapid lysosomal degradation. From these compartments, antigens are processed for loading onto MHC I molecules. Such processing generally includes antigen transport into the cytoplasm, a process that is regulated by members of the ER-associated degradation (ERAD) machinery. After proteasomal degradation in the cytoplasm, antigen-derived peptides have been shown to be re-imported into the same endosomal compartment by endosomal transporter associated with antigen processing, another ER protein, which is recruited toward the endosomes after DC maturation. In our review, we highlight the recent advances on the molecular mechanisms of cross-presentation. We focus on the necessity of such antigen storage compartments and point out important parallels to MHC I-restricted presentation of endogenous antigens. We discuss the composition of such endosomes and the targeting of extracellular antigens into this compartment by specific endocytic receptors. Finally, we highlight recent advances on the recruitment of the cross-presentation machinery, like the members of the MHC I loading complex and the ERAD machinery, from the ER toward these storage compartments, a process that can be induced by antigen encounter or by activation of the dendritic cell after contact with endotoxins.
Loading and release of a model protein from porous silicon powders (2007)

Abstract Porous silicon (p‐Si) has been investigated as a novel delivery system for protein therapeutics. The loading of a model hydrophilic protein, Papain into anodised and stain etched p‐Si powders has been investigated using X‐ray photoelectron spectroscopy (XPS) and infrared spectroscopy (FTIR) and correlations made with the release kinetics. Variation in specific Papain (Amide I/II) and p‐Si (Si–H x ) functional group absorbances with Papain loading level was characterised using FTIR, while the surface chemical distribution was assessed using XPS. A combination of burst release and sustained release of Papain was observed from p‐Si powders; this was dependent on p‐Si type and the Papain loading level. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characteristics of Fluidized-Bed Membrane Reactors:  Scale-up and Practical Issues (1997)

Fluidized-bed membrane reactors (FBMR) are examined from a scale-up and practical point of view. Mathematical modeling is utilized to explore potential configurations for commercial FBMR steam methane reforming (SMR) as well as to quantify the effects of key design parameters such as membrane capacity, distribution of membrane surface between the dense bed and dilute phase, permeate side pressure, and sweep gas flow. Key factors affecting the performance of a commercial FBMR are analyzed and qualitatively compared with corresponding factors in packed-bed membrane reactors. Issues which pose challenges to the commercial viability of this technology are identified. These include maintenance of bed mobility in the presence of gas withdrawal, providing sufficient membrane capacity, wear, and mechanical forces on vertical surfaces.
Hybrid Beamforming With Selection for Multiuser Massive MIMO Systems (2018)

This paper studies a variant of hybrid beamforming, namely, hybrid beamforming with selection (HBwS), as an attractive solution to reduce the hardware cost of multiuser Massive Multiple-Input-Multiple-Output systems, while retaining good performance. Unlike conventional hybrid beamforming, in a transceiver with HBwS, the antenna array is fed by an analog beamforming matrix with L̅ input ports, where L̅ is larger than the number of up/down-conversion chains K̅. A bank of switches connects the instantaneously best K̅ out of the L̅ input ports to the up/down-conversion chains. The analog beamformer is designed based on average channel statistics and therefore needs to be updated only infrequently, while the switches operate based on instantaneous channel knowledge. HBwS allows use of simpler hardware in the beamformer that only need to adjust to the statistics, while also enabling the effective analog beams to adapt to the instantaneous channel variations via switching. This provides better user separability, beamforming gain, and/or simpler hardware than some conventional hybrid schemes. In this paper, a novel design for the analog beamformer is derived and approaches to reduce the hardware and computational cost of a multiuser HBwS system are explored. In addition, we study how L̅, the switch bank architecture, the number of users and the channel estimation overhead impact system performance.
Printed antenna arrays: examples of commercial applications (2002)

The flexibility of printed technology offers the possibility of innovative radiating structures well suited to various system requirements. Different systems often need specific radiation patterns such as shaped, directive mono or multibeam with prescribed relative level and positions of lobes, or on the contrary omnidirectional radiation in azimuth; both a large bandwidth and directive patterns are more common requirements for communication systems. Research in the University of Rennes I Laboratory has focused on the corner fed square patch and the array design of such elements. Both planar and cylindrical structures have been investigated and some results are reported here. The properties of the corner fed patch are first given and four examples of arrays and applications are presented: dual beam Doppler radar for accurate measurements of speed and shaped beam for radio distribution (Bognais, 1986) (with sector and cosecant square patterns), omnidirectional cylindrical array for search and rescue maritime systems, and large bandwidth planar directive array.
A Common Complement C3 Variant Is Associated with Protection against Wet Age-Related Macular Degeneration in a Japanese Population (2011)

Our study provides evidence that C3 is a common AMD-associated locus that transcends racial boundaries and provides an impetus for more detailed genetic characterization of the C3 locus in Asian populations.
Vector tracking loops in GNSS receivers for dynamic weak signals (2013)

Vehicle positioning with the global navigation satellite system(GNSS) in urban environments faces two problems which are attenuation and dynamic.For traditional GNSS receivers hardly able to track dynamic weak signals,the coupling between all visible satellite signals is ignored in the absence of navigation state feedback,and thermal noise error and dynamic stress threshold are contradictory due to non-coherent discriminators.The vector delay/frequency locked loop(VDFLL) with navigation state feedback and the joint vector tracking loop(JVTL) with coherent discriminator which is a synchronization parameter tracking loop based on maximum likelihood estimation(MLE) are proposed to improve the tracking sensitivity of GNSS receiver in dynamic weak signal environments.A joint vector position tracking loop(JVPTL) directly tracking user position and velocity is proposed to further improve tracking sensitivity.The coherent navigation parameter discriminator of JVPTL,being able to ease the contradiction between thermal noise error and dynamic stress threshold,is based on MLE according to the navigation parameter based linear model of received baseband signals.Simulation results show that JVPTL,which combines the advantages of both VDFLL and JVTL,performs better than both VDFLL and JVTL in dynamic weak signal environments.